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Conserved domains on  [gi|6680718|ref|NP_031504|]
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ADP-ribosylation factor 3 [Mus musculus]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
5-179 3.60e-133

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member smart00177:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 175  Bit Score: 369.64  E-value: 3.60e-133
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718       5 FGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQN 84
Cdd:smart00177   1 MGKLFSKLFGNKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718      85 TQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGD 164
Cdd:smart00177  81 TQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGD 160
                          170
                   ....*....|....*
gi 6680718     165 GLYEGLDWLANQLKN 179
Cdd:smart00177 161 GLYEGLTWLSNNLKN 175
 
Name Accession Description Interval E-value
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
5-179 3.60e-133

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 369.64  E-value: 3.60e-133
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718       5 FGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQN 84
Cdd:smart00177   1 MGKLFSKLFGNKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718      85 TQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGD 164
Cdd:smart00177  81 TQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGD 160
                          170
                   ....*....|....*
gi 6680718     165 GLYEGLDWLANQLKN 179
Cdd:smart00177 161 GLYEGLTWLSNNLKN 175
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
1-180 3.36e-132

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 367.37  E-value: 3.36e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     1 MGNIFGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH 80
Cdd:PLN00223   1 MGLSFTKLFSRLFAKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    81 YFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCA 160
Cdd:PLN00223  81 YFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQSTCA 160
                        170       180
                 ....*....|....*....|
gi 6680718   161 TSGDGLYEGLDWLANQLKNK 180
Cdd:PLN00223 161 TSGEGLYEGLDWLSNNIANK 180
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
18-176 5.13e-125

ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 348.24  E-value: 5.13e-125
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:cd04150   1 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6680718   98 ERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQ 176
Cdd:cd04150  81 ERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSNN 159
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
18-177 9.52e-106

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 299.52  E-value: 9.52e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     98 ERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQL 177
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 160
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
17-133 7.45e-20

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 81.26  E-value: 7.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     17 EMRILMVGLDAAGKTTILYKLKLGE--IVTTIPTIGFNVET--VEYKNIS--FTVWDVGGQDKIRPLWRHYFQNTQGLIF 90
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKgsITEYYPGTTRNYVTtvIEEDGKTykFNLLDTAGQEDYDAIRRLYYPQVERSLR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 6680718     91 VVDSNdrERVNEAREELM--RMLAEDELR-DAVLLVFANKQDLPNA 133
Cdd:TIGR00231  81 VFDIV--ILVLDVEEILEkqTKEIIHHADsGVPIILVGNKIDLKDA 124
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
15-166 1.16e-15

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 70.78  E-value: 1.16e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   15 KKEMRILMVGLDAAGKTTILYKLkLGEIVTT---IPTIGFNVETVEYK----NISFTVWDVGGQD---KIRPLWRHYFQN 84
Cdd:COG1100   1 MGEKKIVVVGTGGVGKTSLVNRL-VGDIFSLekyLSTNGVTIDKKELKldglDVDLVIWDTPGQDefrETRQFYARQLTG 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   85 TQGLIFVVDSnDRERVNEAREELMRMLAEDELRDAVLLVFaNKQDLpnaMNAAEITDKLGLHSLR--HRNWYIQATCATS 162
Cdd:COG1100  80 ASLYLFVVDG-TREETLQSLYELLESLRRLGKKSPIILVL-NKIDL---YDEEEIEDEERLKEALseDNIVEVVATSAKT 154

                ....
gi 6680718  163 GDGL 166
Cdd:COG1100 155 GEGV 158
 
Name Accession Description Interval E-value
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
5-179 3.60e-133

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 369.64  E-value: 3.60e-133
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718       5 FGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQN 84
Cdd:smart00177   1 MGKLFSKLFGNKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718      85 TQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGD 164
Cdd:smart00177  81 TQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGD 160
                          170
                   ....*....|....*
gi 6680718     165 GLYEGLDWLANQLKN 179
Cdd:smart00177 161 GLYEGLTWLSNNLKN 175
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
1-180 3.36e-132

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 367.37  E-value: 3.36e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     1 MGNIFGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH 80
Cdd:PLN00223   1 MGLSFTKLFSRLFAKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    81 YFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCA 160
Cdd:PLN00223  81 YFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQSTCA 160
                        170       180
                 ....*....|....*....|
gi 6680718   161 TSGDGLYEGLDWLANQLKNK 180
Cdd:PLN00223 161 TSGEGLYEGLDWLSNNIANK 180
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
1-181 1.87e-127

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 355.31  E-value: 1.87e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     1 MGNIFGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH 80
Cdd:PTZ00133   1 MGLWLSSAFKSLFGKKEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRH 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    81 YFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCA 160
Cdd:PTZ00133  81 YYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRNWYIQGCCA 160
                        170       180
                 ....*....|....*....|.
gi 6680718   161 TSGDGLYEGLDWLANQLKNKK 181
Cdd:PTZ00133 161 TTAQGLYEGLDWLSANIKKSM 181
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
18-176 5.13e-125

ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 348.24  E-value: 5.13e-125
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:cd04150   1 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6680718   98 ERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQ 176
Cdd:cd04150  81 ERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSNN 159
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
19-176 3.99e-107

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 302.96  E-value: 3.99e-107
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRE 98
Cdd:cd00878   1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRE 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6680718   99 RVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQ 176
Cdd:cd00878  81 RIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIEQ 158
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
18-177 9.52e-106

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 299.52  E-value: 9.52e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     98 ERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQL 177
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 160
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
9-175 5.87e-104

ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection.


Pssm-ID: 206716  Cd Length: 168  Bit Score: 295.53  E-value: 5.87e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    9 LKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGL 88
Cdd:cd04149   1 LSKLFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   89 IFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYE 168
Cdd:cd04149  81 IFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYE 160

                ....*..
gi 6680718  169 GLDWLAN 175
Cdd:cd04149 161 GLTWLSS 167
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
19-176 1.66e-96

ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 276.21  E-value: 1.66e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRE 98
Cdd:cd04151   1 RILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRD 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6680718   99 RVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQ 176
Cdd:cd04151  81 RLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKDRTWQIFKTSATKGEGLDEGMDWLVNT 158
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
3-176 1.79e-89

Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 259.20  E-value: 1.79e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    3 NIFGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYF 82
Cdd:cd04153   1 LLFSSLWSLFFPRKEYKVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYY 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   83 QNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATS 162
Cdd:cd04153  81 TNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSIRDHTWHIQGCCALT 160
                       170
                ....*....|....
gi 6680718  163 GDGLYEGLDWLANQ 176
Cdd:cd04153 161 GEGLPEGLDWIASR 174
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
15-176 2.34e-70

Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 210.72  E-value: 2.34e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   15 KKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS 94
Cdd:cd04155  13 RQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDS 92
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   95 NDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLA 174
Cdd:cd04155  93 ADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDRSWHIQACSAKTGEGLQEGMNWVC 172

                ..
gi 6680718  175 NQ 176
Cdd:cd04155 173 KN 174
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
16-175 5.76e-70

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 209.49  E-value: 5.76e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   16 KEMRILMVGLDAAGKTTILYKLkLGEIVTTI-PTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS 94
Cdd:cd04154  13 REMRILMLGLDNAGKTTILKKF-NGEDISTIsPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDS 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   95 NDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLA 174
Cdd:cd04154  92 SDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTGENLLDGIDWLV 171

                .
gi 6680718  175 N 175
Cdd:cd04154 172 D 172
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
19-174 7.09e-69

Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer.


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 206.50  E-value: 7.09e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEY-KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:cd04156   1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLeKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDE 80
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6680718   98 ERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL-RHRNWYIQATCATSGDGLYEGLDWLA 174
Cdd:cd04156  81 ARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYcSDRDWYVQPCSAVTGEGLAEAFRKLA 158
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
19-177 2.03e-67

(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization.


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 203.34  E-value: 2.03e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRE 98
Cdd:cd04158   1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   99 RVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL-RHRNWYIQATCATSGDGLYEGLDWLANQL 177
Cdd:cd04158  81 RVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLcCGRSWYIQGCDARSGMGLYEGLDWLSRQL 160
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
18-181 1.55e-62

Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206719 [Multi-domain]  Cd Length: 183  Bit Score: 191.17  E-value: 1.55e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEY-----KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd04152   4 LHIVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVslgnaKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVV 83
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   93 DSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL-RHRNWYIQATCATSGDGLYEGLD 171
Cdd:cd04152  84 DSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVEKLLALHELsSSTPWHVQPACAIIGEGLQEGLE 163
                       170
                ....*....|.
gi 6680718  172 WLANQ-LKNKK 181
Cdd:cd04152 164 KLYEMiLKRRK 174
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
20-176 8.04e-58

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 178.39  E-value: 8.04e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   20 ILMVGLDAAGKTTILYKLKLGEIVTTI--PTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:cd04157   2 ILVLGLDNSGKTTIINQLKPSNAQSQNivPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDR 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   98 ERVNEAREELMRMLAEDEL--RDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLAN 175
Cdd:cd04157  82 LRMVVAKDELELLLNHPDIkhRRIPILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWLQA 161

                .
gi 6680718  176 Q 176
Cdd:cd04157 162 Q 162
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
1-145 4.26e-46

Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.


Pssm-ID: 206645 [Multi-domain]  Cd Length: 191  Bit Score: 149.74  E-value: 4.26e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    1 MGNIFGNLLKSL-IGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWR 79
Cdd:cd00879   2 IFDWFYNVLSSLgLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWK 81
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6680718   80 HYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL 145
Cdd:cd00879  82 DYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGL 147
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
20-173 1.92e-43

Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 142.10  E-value: 1.92e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   20 ILMVGLDAAGKTTILYKLK-----------LGEIVttiPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGL 88
Cdd:cd04160   2 VLILGLDNAGKTTFLEQTKtkfsknykglnPSKIT---PTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGV 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   89 IFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITD--KLGLHSLRHRNWYIQATCATSGDGL 166
Cdd:cd04160  79 IYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEvfDDCIALIGRRDCLVQPVSALEGEGV 158

                ....*..
gi 6680718  167 YEGLDWL 173
Cdd:cd04160 159 EEGIEWL 165
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
20-162 1.08e-38

Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.


Pssm-ID: 133362 [Multi-domain]  Cd Length: 164  Bit Score: 129.88  E-value: 1.08e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   20 ILMVGLDAAGKTTILYKLKlGEIV--TTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:cd04162   2 ILVLGLDGAGKTSLLHSLS-SERSleSVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADS 80
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6680718   98 ERVNEAREELMRMLAEDElrDAVLLVFANKQDLPNAMNAAEITDKLGLHSL-RHRNWYIQATCATS 162
Cdd:cd04162  81 ERLPLARQELHQLLQHPP--DLPLVVLANKQDLPAARSVQEIHKELELEPIaRGRRWILQGTSLDD 144
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
20-173 1.36e-37

Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.


Pssm-ID: 206724 [Multi-domain]  Cd Length: 159  Bit Score: 127.05  E-value: 1.36e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   20 ILMVGLDAAGKTTILYKLKLGE-IVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRE 98
Cdd:cd04159   2 ITLVGLQNSGKTTLVNVIASGQfSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADRE 81
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6680718   99 RVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWL 173
Cdd:cd04159  82 KLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWL 156
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
20-173 6.41e-34

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 117.88  E-value: 6.41e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   20 ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRER 99
Cdd:cd04161   2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDR 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718  100 VNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL--RHRNWYIQATCATSGDG-------LYEGL 170
Cdd:cd04161  82 VQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLvnENKSLCHIEPCSAIEGLgkkidpsIVEGL 161

                ...
gi 6680718  171 DWL 173
Cdd:cd04161 162 RWL 164
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
3-145 7.08e-33

Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 197556 [Multi-domain]  Cd Length: 184  Bit Score: 115.80  E-value: 7.08e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718       3 NIFGNLLKSL-IGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHY 81
Cdd:smart00178   2 DWFYDILASLgLWNKHAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDY 81
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6680718      82 FQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL 145
Cdd:smart00178  82 FPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGL 145
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
17-133 7.45e-20

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 81.26  E-value: 7.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     17 EMRILMVGLDAAGKTTILYKLKLGE--IVTTIPTIGFNVET--VEYKNIS--FTVWDVGGQDKIRPLWRHYFQNTQGLIF 90
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKgsITEYYPGTTRNYVTtvIEEDGKTykFNLLDTAGQEDYDAIRRLYYPQVERSLR 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 6680718     91 VVDSNdrERVNEAREELM--RMLAEDELR-DAVLLVFANKQDLPNA 133
Cdd:TIGR00231  81 VFDIV--ILVLDVEEILEkqTKEIIHHADsGVPIILVGNKIDLKDA 124
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
23-175 1.04e-19

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 80.96  E-value: 1.04e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   23 VGLDAAGKTTILYKLKLGEIV----TTIPTIGFNVETVEY--KNISFTVWDVGGQDKIRPLW-----RHYFQNTQGLIFV 91
Cdd:cd00882   3 VGRGGVGKSSLLNALLGGEVGevsdVPGTTRDPDVYVKELdkGKVKLVLVDTPGLDEFGGLGreelaRLLLRGADLILLV 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   92 VDSNDRERVNEAREELMRMLAEDELRdavLLVFANKQDLPNAMNAAEItdKLGLHSLRHRNWYIQATCATSGDGLYEGLD 171
Cdd:cd00882  83 VDSTDRESEEDAKLLILRRLRKEGIP---IILVGNKIDLLEEREVEEL--LRLEELAKILGVPVFEVSAKTGEGVDELFE 157

                ....
gi 6680718  172 WLAN 175
Cdd:cd00882 158 KLIE 161
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
15-166 1.16e-15

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 70.78  E-value: 1.16e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   15 KKEMRILMVGLDAAGKTTILYKLkLGEIVTT---IPTIGFNVETVEYK----NISFTVWDVGGQD---KIRPLWRHYFQN 84
Cdd:COG1100   1 MGEKKIVVVGTGGVGKTSLVNRL-VGDIFSLekyLSTNGVTIDKKELKldglDVDLVIWDTPGQDefrETRQFYARQLTG 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   85 TQGLIFVVDSnDRERVNEAREELMRMLAEDELRDAVLLVFaNKQDLpnaMNAAEITDKLGLHSLR--HRNWYIQATCATS 162
Cdd:COG1100  80 ASLYLFVVDG-TREETLQSLYELLESLRRLGKKSPIILVL-NKIDL---YDEEEIEDEERLKEALseDNIVEVVATSAKT 154

                ....
gi 6680718  163 GDGL 166
Cdd:COG1100 155 GEGV 158
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
20-143 2.95e-15

Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.


Pssm-ID: 206691 [Multi-domain]  Cd Length: 202  Bit Score: 70.04  E-value: 2.95e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   20 ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETV---EYKNISFTVWDVGGQDKIRP-LWRHYFQNTQGLIFVVDSN 95
Cdd:cd04105   3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFysnSSKGKKLTLVDVPGHEKLRDkLLEYLKASLKAIVFVVDSA 82
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 6680718   96 DRER-VNEAREELMRMLAEDELRDAV--LLVFANKQDLPNAMNAAEITDKL 143
Cdd:cd04105  83 TFQKnIRDVAEFLYDILTDLEKIKNKipILIACNKQDLFTAKPAKKIKELL 133
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
18-132 6.28e-13

Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.


Pssm-ID: 206640 [Multi-domain]  Cd Length: 159  Bit Score: 63.24  E-value: 6.28e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGlDAA-GKTTILYKLKLGE-IVTTIPTIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFV 91
Cdd:cd00154   1 FKIVLIG-DSGvGKTSLLLRFVDNKfSENYKSTIGvdFKSKTIEVdgKKVKLQIWDTAGQERFRSITSSYYRGAHGAILV 79
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 6680718   92 VDSNDRERVNEArEELMRMLAEDELRDAVLLVFANKQDLPN 132
Cdd:cd00154  80 YDVTNRESFENL-DKWLNELKEYAPPNIPIILVGNKSDLED 119
PLN03118 PLN03118
Rab family protein; Provisional
19-98 2.04e-12

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 62.77  E-value: 2.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    19 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVE----TVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS 94
Cdd:PLN03118  16 KILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKikqlTVGGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDV 95

                 ....
gi 6680718    95 NDRE 98
Cdd:PLN03118  96 TRRE 99
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
19-129 5.50e-12

Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.


Pssm-ID: 462490 [Multi-domain]  Cd Length: 114  Bit Score: 59.44  E-value: 5.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     19 RILMVGLDAAGKTTILYKLKLGE-IVTTIPTIGFNVETVEY-------KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIF 90
Cdd:pfam08477   1 KVVLLGDSGVGKTSLLKRFVDDTfDPKYKSTIGVDFKTKTVlenddngKKIKLNIWDTAGQERFRSLHPFYYRGAAAALL 80
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 6680718     91 VVDSNDRERVnearEELMRMLaEDELRDAVLLVFANKQD 129
Cdd:pfam08477  81 VYDSRTFSNL----KYWLREL-KKYAGNSPVILVGNKID 114
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
19-177 1.55e-11

Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206656 [Multi-domain]  Cd Length: 161  Bit Score: 59.63  E-value: 1.55e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTI-PTIG--FNVE--TVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:cd01863   2 KILLIGDSGVGKSSLLLRFTDDTFDEDLsSTIGvdFKVKtvTVDGKKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYD 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   94 SNDRERVnearEELMRMLAEDEL----RDAVLLVFANKQDLPNamnaAEITDKLGLHSLRHRNWYIQATCATSGDGLYEG 169
Cdd:cd01863  82 VTRRDTF----DNLDTWLNELDTystnPDAVKMLVGNKIDKEN----REVTREEGQKFARKHNMLFIETSAKTRIGVQQA 153

                ....*...
gi 6680718  170 LDWLANQL 177
Cdd:cd01863 154 FEELVEKI 161
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
19-143 3.19e-11

Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.


Pssm-ID: 462797 [Multi-domain]  Cd Length: 181  Bit Score: 58.99  E-value: 3.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     19 RILMVGLDAAGKTTILYKLKLGEIVTTIPTI--GFNVETVEYKNISFTVWDVGGQDKIRP--LWRHYFQ-NTQGLIFVVD 93
Cdd:pfam09439   5 AVIIAGLCDSGKTSLFTLLTTDSVRPTVTSQepSAAYRYMLNKGNSFTLIDFPGHVKLRYklLETLKDSsSLKGIVFVVD 84
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 6680718     94 SN-DRERVNEAREELMRMLAEDEL-RDAV-LLVFANKQDLPNAMNAAEITDKL 143
Cdd:pfam09439  85 STiFPKEVTDTAEFLYDILSITELlKNGIdILIACNKQESFTARPPKKIKQAL 137
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
19-130 6.45e-11

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 57.91  E-value: 6.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     19 RILMVGLDAAGKTTILYKLKLGEIVTT-IPTIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKFPEEyIPTIGvdFYTKTIEVdgKTVKLQIWDTAGQERFRALRPLYYRGADGFLLVYD 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 6680718     94 SNDRERVNEAR---EELMRMLAEdelrDAVLLVFANKQDL 130
Cdd:pfam00071  81 ITSRDSFENVKkwvEEILRHADE----NVPIVLVGNKCDL 116
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
18-132 5.57e-10

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 55.21  E-value: 5.57e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718      18 MRILMVGLDAAGKTTILYKLKLGE-IVTTIPTIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:smart00175   1 FKIILIGDSGVGKSSLLSRFTDGKfSEQYKSTIGvdFKTKTIEVdgKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVY 80
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 6680718      93 DSNDR---ERVNEAREELmRMLAEDelrDAVLLVFANKQDLPN 132
Cdd:smart00175  81 DITNResfENLENWLKEL-REYASP---NVVIMLVGNKSDLEE 119
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
18-132 6.90e-10

Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206659 [Multi-domain]  Cd Length: 167  Bit Score: 54.97  E-value: 6.90e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTT-IPTIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd01867   4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSfISTIGidFKIRTIELdgKKIKLQIWDTAGQERFRTITTSYYRGAMGIILVY 83
                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 6680718   93 DSNDRERVNEAReELMRMLAEDELRDAVLLVFANKQDLPN 132
Cdd:cd01867  84 DITDEKSFENIK-NWMRNIDEHASEDVERMLVGNKCDMEE 122
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
46-161 6.87e-09

G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 53.75  E-value: 6.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     46 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV-----DSNDRE--RVNEARE--ELMRMLAEDE- 115
Cdd:pfam00503 152 VKTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVslseyDQVLYEddSTNRMEEslKLFEEICNSPw 231
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6680718    116 LRDAVLLVFANKQDL---------------------PNAMNAAE-ITDK-LGLHSLRHRNWYIQATCAT 161
Cdd:pfam00503 232 FKNTPIILFLNKKDLfeeklkksplsdyfpdytgnpNDYEEALKyIRNKfLDLNKNPNRKIYTHFTCAT 300
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
19-145 1.40e-08

Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206661 [Multi-domain]  Cd Length: 166  Bit Score: 51.56  E-value: 1.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTT-IPTIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:cd01869   4 KLLLIGDSGVGKSCLLLRFADDTYTESyISTIGvdFKIRTIELdgKTVKLQIWDTAGQERFRTITSSYYRGAHGIIIVYD 83
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   94 SNDRERVNEARE---ELMRMLAEDELRdavLLVfANKQDLPNA-----MNAAEITDKLGL 145
Cdd:cd01869  84 VTDQESFNNVKQwlqEIDRYASENVNK---LLV-GNKCDLTDKkvvdyTEAKEFADELGI 139
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
49-129 6.37e-08

Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 50.40  E-value: 6.37e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   49 IGFNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEArEELMRMLAEDELRDAVLLVFAN 126
Cdd:cd04120  35 VDFKIKTVELrgKKIRLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDL-PKWMKMIDKYASEDAELLLVGN 113

                ...
gi 6680718  127 KQD 129
Cdd:cd04120 114 KLD 116
PLN03110 PLN03110
Rab GTPase; Provisional
19-138 1.80e-07

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 49.16  E-value: 1.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    19 RILMVGLDAAGKTTILYKLKLGEI-VTTIPTIGFNVET----VEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:PLN03110  14 KIVLIGDSGVGKSNILSRFTRNEFcLESKSTIGVEFATrtlqVEGKTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYD 93
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 6680718    94 SNDRERVnearEELMRMLAedELRD-----AVLLVFANKQDLPNAMNAAE 138
Cdd:PLN03110  94 ITKRQTF----DNVQRWLR--ELRDhadsnIVIMMAGNKSDLNHLRSVAE 137
Rab15 cd04117
Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early ...
19-97 3.26e-07

Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206698 [Multi-domain]  Cd Length: 164  Bit Score: 47.66  E-value: 3.26e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTT-IPTIG--FNVETVEYKNIS--FTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:cd04117   2 RLLLIGDSGVGKTCLLCRFTDNEFHSShISTIGvdFKMKTIEVDGIKvrIQIWDTAGQERYQTITKQYYRRAQGIFLVYD 81

                ....*
gi 6680718   94 -SNDR 97
Cdd:cd04117  82 iSSER 86
Rab21 cd04123
Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, ...
18-132 4.88e-07

Rab GTPase family 21 (Rab21); The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133323 [Multi-domain]  Cd Length: 162  Bit Score: 47.22  E-value: 4.88e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLG-----EIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd04123   1 FKVVLLGEGRVGKTSLVLRYVENkfnekHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPIYYRDADGAILVY 80
                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 6680718   93 DSNDR---ERVNEAREELMRMLAEdelrDAVLLVFANKQDLPN 132
Cdd:cd04123  81 DITDAdsfQKVKKWIKELKQMRGN----NISLVIVGNKIDLER 119
Rab27A cd04127
Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly ...
18-164 5.07e-07

Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206700 [Multi-domain]  Cd Length: 180  Bit Score: 47.49  E-value: 5.07e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTT-IPTIG--FNVETVEYKN------------ISFTVWDVGGQDKIRPLWRHYF 82
Cdd:cd04127   5 IKLLALGDSGVGKTTFLYRYTDNKFNPKfITTVGidFREKRVVYNSqgpdgtsgkafrVHLQLWDTAGQERFRSLTTAFF 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   83 QNTQGLIFVVDSNDRERVNEARE--ELMRMLAEDELRDAVLLvfANKQDLP-----NAMNAAEITDKLGLHslrhrnwYI 155
Cdd:cd04127  85 RDAMGFLLMFDLTSEQSFLNVRNwmSQLQAHAYCENPDIVLI--GNKADLPdqrevSERQARELADKYGIP-------YF 155

                ....*....
gi 6680718  156 QATCATSGD 164
Cdd:cd04127 156 ETSAATGQN 164
Srp102 COG2229
Signal recognition particle receptor subunit beta, a GTPase [Intracellular trafficking, ...
70-177 5.74e-07

Signal recognition particle receptor subunit beta, a GTPase [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441830 [Multi-domain]  Cd Length: 189  Bit Score: 47.51  E-value: 5.74e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   70 GQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAR--EELmrmlaEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLhs 147
Cdd:COG2229  79 GQVRFDFMWDILLRGADGVVFLADSRRLEDSFNAEslDFF-----EERLEKLPFVVAVNKRDLPDALSLEELREALDL-- 151
                        90       100       110
                ....*....|....*....|....*....|
gi 6680718  148 lrHRNWYIQATCATSGDGLYEGLDWLANQL 177
Cdd:COG2229 152 --GPDVPVVEADARDGESVKETLIALLELV 179
Rab26 cd04112
Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, ...
19-130 6.79e-07

Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206695 [Multi-domain]  Cd Length: 191  Bit Score: 47.17  E-value: 6.79e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIV--TTIPTIGFN----VETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd04112   2 KVMLVGDSGVGKTCLLVRFKDGAFLagSFIATVGIQftnkVVTVDGVKVKLQIWDTAGQERFRSVTHAYYRDAHALLLLY 81
                        90       100       110
                ....*....|....*....|....*....|....*...
gi 6680718   93 DSNDRERVNEAREELMRMLaEDELRDAVLLVFANKQDL 130
Cdd:cd04112  82 DVTNKSSFDNIRAWLTEIL-EYAQSDVVIMLLGNKADM 118
RJL cd04119
Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with ...
19-177 1.16e-06

Rab GTPase family J-like (RabJ-like); RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.


Pssm-ID: 133319 [Multi-domain]  Cd Length: 168  Bit Score: 46.19  E-value: 1.16e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTT-IPTIG--FNVETVEYKNISFTV--WDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:cd04119   2 KVISMGNSGVGKSCIIKRYCEGRFVSKyLPTIGidYGVKKVSVRNKEVRVnfFDLSGHPEYLEVRNEFYKDTQGVLLVYD 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   94 SNDRERVnEAREELMRML-----AEDELRDAVLLVFANKQDLPNAMNAAEITDKlgLHSLRHRNWYIQaTCATSGDGLYE 168
Cdd:cd04119  82 VTDRQSF-EALDSWLKEMkqeggPHGNMENIVVVVCANKIDLTKHRAVSEDEGR--LWAESKGFKYFE-TSACTGEGVNE 157

                ....*....
gi 6680718  169 GLDWLANQL 177
Cdd:cd04119 158 MFQTLFSSI 166
Rab36_Rab34 cd04108
Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily ...
48-168 1.46e-06

Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206693 [Multi-domain]  Cd Length: 170  Bit Score: 46.02  E-value: 1.46e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   48 TIG--FNVETVEYKNISFTV--WDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLV 123
Cdd:cd04108  32 TIGvdFEMERFEVLGVPFSLqlWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFL 111
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 6680718  124 FANKQDLPNAmNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYE 168
Cdd:cd04108 112 VGTKKDLSSP-AQYALMEQDAIKLAREMKAEYWAVSALTGENVRD 155
RocCOR cd09914
Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein ...
17-176 1.51e-06

Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; in Dictyostelium discoideum, which encodes 11 Roco proteins, they are involved in cell division, chemotaxis and development, while in human, where 4 Roco proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded, these proteins are involved in epilepsy and cancer. Mutations in LRRK2 (leucine-rich repeat kinase 2) are known to cause familial Parkinson's disease.


Pssm-ID: 206741 [Multi-domain]  Cd Length: 161  Bit Score: 45.79  E-value: 1.51e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   17 EMRILMVGLDAAGKTTILYKLkLGEIV--TTIPTIGFNVET-----VEYKNISFTVWDVGGQDKIRPLWRHyFQNTQGLI 89
Cdd:cd09914   1 EAKLMLVGQGGVGKTSLCKQL-IGEKFdgDESSTHGINVQDwkipaPERKKIRLNVWDFGGQEIYHATHQF-FLTSRSLY 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   90 FVVDSNDRERVNEAREELMRMLAEDELRDAVLLVfANKQDlpnAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEG 169
Cdd:cd09914  79 LLVFDLRTGDEVSRVPYWLRQIKAFGGVSPVILV-GTHID---ESCDEDILKKALNKKFPAIINDIHFVSCKNGKGIAEL 154

                ....*..
gi 6680718  170 LDWLANQ 176
Cdd:cd09914 155 KKAIAKE 161
Rab39 cd04111
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ...
19-132 1.64e-06

Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133311 [Multi-domain]  Cd Length: 211  Bit Score: 46.29  E-value: 1.64e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIV-TTIPTIGFN-----VETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd04111   4 RLIVIGDSTVGKSSLLKRFTEGRFAeVSDPTVGVDffsrlIEIEPGVRIKLQLWDTAGQERFRSITRSYYRNSVGVLLVF 83
                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 6680718   93 DSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPN 132
Cdd:cd04111  84 DITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLES 123
Rab33B_Rab33A cd04115
Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ...
19-93 1.70e-06

Rab GTPase family 33 includes Rab33A and Rab33B; Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133315 [Multi-domain]  Cd Length: 170  Bit Score: 45.89  E-value: 1.70e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIV-TTIPTIG--FNVETVEY--KNISFTVWDVGGQDKIR-PLWRHYFQNTQGLIFVV 92
Cdd:cd04115   4 KIIVIGDSNVGKTCLTYRFCAGRFPeRTEATIGvdFRERTVEIdgERIKVQLWDTAGQERFRkSMVQHYYRNVHAVVFVY 83

                .
gi 6680718   93 D 93
Cdd:cd04115  84 D 84
Rab3 cd01865
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ...
19-145 2.17e-06

Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206657 [Multi-domain]  Cd Length: 165  Bit Score: 45.67  E-value: 2.17e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLK----LGEIVTTIpTIGFNVETV--EYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd01865   3 KLLIIGNSSVGKTSFLFRYAddsfTSAFVSTV-GIDFKVKTVyrNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMY 81
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 6680718   93 DSNDRERVNEAREELMRMLAEDELRDAVLLVfANKQDLPN-----AMNAAEITDKLGL 145
Cdd:cd01865  82 DITNEESFNAVQDWSTQIKTYSWDNAQVILV-GNKCDMEDervvsAERGRQLADQLGF 138
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
46-130 4.55e-06

G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding site


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 45.65  E-value: 4.55e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718      46 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV-----DSNDRERVNEAR-EELMRMLAE----DE 115
Cdd:smart00275 169 VPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCValseyDQVLEEDESTNRmQESLNLFESicnsRW 248
                           90
                   ....*....|....*
gi 6680718     116 LRDAVLLVFANKQDL 130
Cdd:smart00275 249 FANTSIILFLNKIDL 263
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
19-130 7.05e-06

Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet characterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133267 [Multi-domain]  Cd Length: 165  Bit Score: 43.96  E-value: 7.05e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTI-PTIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:cd01864   5 KIILIGDSNVGKTCVVQRFKSGTFSERQgNTIGvdFTMKTLEIqgKRVKLQIWDTAGQERFRTITQSYYRSANGAIIAYD 84
                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 6680718   94 SNDR---ERVNEAREELMRMLAEdelrDAVLLVFANKQDL 130
Cdd:cd01864  85 ITRRssfESVPHWIEEVEKYGAS----NVVLLLIGNKCDL 120
G-alpha cd00066
Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins ...
46-130 1.27e-05

Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.


Pssm-ID: 206639 [Multi-domain]  Cd Length: 315  Bit Score: 44.44  E-value: 1.27e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   46 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRD------- 118
Cdd:cd00066 146 VKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDsicnsrw 225
                        90
                ....*....|....*.
gi 6680718  119 ----AVLLvFANKQDL 130
Cdd:cd00066 226 fantSIIL-FLNKKDL 240
Rho2 cd04129
Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal ...
19-96 1.34e-05

Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).


Pssm-ID: 206702 [Multi-domain]  Cd Length: 190  Bit Score: 43.67  E-value: 1.34e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVET---VEYKNISFTVWDVGGQ---DKIRPLwrHYFQNTQGLI-F 90
Cdd:cd04129   3 KLVIVGDGACGKTSLLYVFTLGEFPEEyHPTVFENYVTdcrVDGKPVQLALWDTAGQeeyERLRPL--SYSKAHVILIgF 80

                ....*.
gi 6680718   91 VVDSND 96
Cdd:cd04129  81 AIDTPD 86
Rab35 cd04110
Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate ...
19-131 1.69e-05

Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133310 [Multi-domain]  Cd Length: 199  Bit Score: 43.30  E-value: 1.69e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLK----LGEIVTTIpTIGFNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd04110   8 KLLIIGDSGVGKSSLLLRFAdntfSGSYITTI-GVDFKIRTVEIngERVKLQIWDTAGQERFRTITSTYYRGTHGVIVVY 86
                        90       100       110
                ....*....|....*....|....*....|....*....
gi 6680718   93 DSNDRERVNEAREELMRMLAEDELRDAVLLvfANKQDLP 131
Cdd:cd04110  87 DVTNGESFVNVKRWLQEIEQNCDDVCKVLV--GNKNDDP 123
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
19-132 1.79e-05

Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206653 [Multi-domain]  Cd Length: 163  Bit Score: 42.92  E-value: 1.79e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTI-PTIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:cd01860   3 KLVLLGDSSVGKSSIVLRFVKNEFSENQeSTIGaaFLTQTVNLddTTVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYD 82
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 6680718   94 SNDRERVNEAREELmrmlaeDELR-----DAVLLVFANKQDLPN 132
Cdd:cd01860  83 ITSEESFEKAKSWV------KELQehgppNIVIALAGNKADLES 120
PLN03071 PLN03071
GTP-binding nuclear protein Ran; Provisional
19-97 2.96e-05

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 178620 [Multi-domain]  Cd Length: 219  Bit Score: 42.82  E-value: 2.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    19 RILMVGLDAAGKTTILYKLKLGEI-VTTIPTIGFNVETVEYKN----ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD 93
Cdd:PLN03071  15 KLVIVGDGGTGKTTFVKRHLTGEFeKKYEPTIGVEVHPLDFFTncgkIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFD 94

                 ....
gi 6680718    94 SNDR 97
Cdd:PLN03071  95 VTAR 98
Rab30 cd04114
Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi ...
19-130 3.29e-05

Rab GTPase family 30 (Rab30); Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133314 [Multi-domain]  Cd Length: 169  Bit Score: 42.19  E-value: 3.29e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGeivtTIP-----TIG--FNVETVEYKN--ISFTVWDVGGQDKIRPLWRHYFQNTQGLI 89
Cdd:cd04114   9 KIVLIGNAGVGKTCLVRRFTQG----LFPpgqgaTIGvdFMIKTVEIKGekIKLQIWDTAGQERFRSITQSYYRSANALI 84
                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 6680718   90 FVVDSNDRERVnEAREELMRMLAEDELRDAVLLVFANKQDL 130
Cdd:cd04114  85 LTYDITCEESF-RCLPEWLREIEQYANNKVITILVGNKIDL 124
Gtr1_RagA pfam04670
Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a ...
19-130 8.05e-05

Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologs of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B.


Pssm-ID: 398377 [Multi-domain]  Cd Length: 231  Bit Score: 41.80  E-value: 8.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718     19 RILMVGLDAAGKTT----ILYKLKLGEIVTTIPTIGFNVETVE-YKNISFTVWDVGGQDKIRPLWRHY-----FQNTQGL 88
Cdd:pfam04670   1 KVLLMGLSGSGKSSmrsvIFSNYSPRDTLRLGATIDVEHSHVRfLGNLVLNLWDCGGQDDFFDNYLTFqkehiFSNVGVL 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 6680718     89 IFVVDSNDRErVNEAREELMRML--AEDELRDAVLLVFANKQDL 130
Cdd:pfam04670  81 IYVFDVQSRE-YEEDLARLKETIeaLYQYSPDAKVFVLIHKMDL 123
Rab28 cd04109
Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown ...
18-131 1.30e-04

Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206694 [Multi-domain]  Cd Length: 213  Bit Score: 40.94  E-value: 1.30e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTIL-----------YKLKLGeivttiptIGFNVETVEY---KNISFTVWDVGGQDKIRPLWRHYFQ 83
Cdd:cd04109   1 IKIVVLGDGASGKTSLIrrfaqegfgksYKQTIG--------LDFFSRRITLpgsLNVTLQVWDIGGQQIGGKMLDKYIY 72
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 6680718   84 NTQGLIFVVD---SNDRERVNEAREELMRMLAEDELRDAVLLVfANKQDLP 131
Cdd:cd04109  73 GAQAVCLVYDitnSQSFENLEDWLSVVKKVNEESETKPKMVLV-GNKTDLE 122
PLN03108 PLN03108
Rab family protein; Provisional
55-130 1.36e-04

Rab family protein; Provisional


Pssm-ID: 178655 [Multi-domain]  Cd Length: 210  Bit Score: 41.08  E-value: 1.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    55 TVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELmrmlaEDELRDA----VLLVFANKQDL 130
Cdd:PLN03108  49 TIDNKPIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWL-----EDARQHAnanmTIMLIGNKCDL 123
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
21-130 1.82e-04

Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133322 [Multi-domain]  Cd Length: 166  Bit Score: 40.20  E-value: 1.82e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   21 LMVGLDAAGKTTILYKLKLGEIVTTIP-TIG--FNVETVEY--KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSN 95
Cdd:cd04122   6 IIIGDMGVGKSCLLHQFTEKKFMADCPhTIGveFGTRIIEVngQKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDIT 85
                        90       100       110
                ....*....|....*....|....*....|....*..
gi 6680718   96 DRERVNEAREELM--RMLAEDelrDAVLLVFANKQDL 130
Cdd:cd04122  86 RRSTYNHLSSWLTdaRNLTNP---NTVIFLIGNKADL 119
Rho cd00157
Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho ...
20-77 1.95e-04

Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy.


Pssm-ID: 206641 [Multi-domain]  Cd Length: 171  Bit Score: 40.22  E-value: 1.95e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6680718   20 ILMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVET-VEYKNISFTV--WDVGGQ---DKIRPL 77
Cdd:cd00157   3 IVVVGDGAVGKTCLLISYTTNKFPTEyVPTVFDNYSAnVTVDGKQVNLglWDTAGQeeyDRLRPL 67
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
23-177 2.48e-04

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 39.99  E-value: 2.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718      23 VGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVETVEYKN----ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDR 97
Cdd:smart00176   1 VGDGGTGKTTFVKRHLTGEFEKKyVATLGVEVHPLVFHTnrgpIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTAR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718      98 ---ERVNEAREELMRMlaedeLRDAVLLVFANKQDLPN-AMNAAEITdklgLHslRHRNWYIQATCATSGDGLYEGLDWL 173
Cdd:smart00176  81 vtyKNVPNWHRDLVRV-----CENIPIVLCGNKVDVKDrKVKAKSIT----FH--RKKNLQYYDISAKSNYNFEKPFLWL 149

                   ....
gi 6680718     174 ANQL 177
Cdd:smart00176 150 ARKL 153
PTZ00132 PTZ00132
GTP-binding nuclear protein Ran; Provisional
17-97 3.32e-04

GTP-binding nuclear protein Ran; Provisional


Pssm-ID: 240284 [Multi-domain]  Cd Length: 215  Bit Score: 39.68  E-value: 3.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    17 EMRILMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVETVE-YKN---ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFV 91
Cdd:PTZ00132   9 EFKLILVGDGGVGKTTFVKRHLTGEFEKKyIPTLGVEVHPLKfYTNcgpICFNVWDTAGQEKFGGLRDGYYIKGQCAIIM 88

                 ....*.
gi 6680718    92 VDSNDR 97
Cdd:PTZ00132  89 FDVTSR 94
PTZ00099 PTZ00099
rab6; Provisional
61-179 3.36e-04

rab6; Provisional


Pssm-ID: 185444 [Multi-domain]  Cd Length: 176  Bit Score: 39.34  E-value: 3.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718    61 ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDElRDAVLLVFANKQDLPNAMnaaEIT 140
Cdd:PTZ00099  29 VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERG-KDVIIALVGNKTDLGDLR---KVT 104
                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 6680718   141 DKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN 179
Cdd:PTZ00099 105 YEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKIAAKLPN 143
Rab20 cd04126
Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be ...
18-130 3.57e-04

Rab GTPase family 20 (Rab20); Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133326 [Multi-domain]  Cd Length: 220  Bit Score: 39.89  E-value: 3.57e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIG--FNVETVEYKNISftVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSN 95
Cdd:cd04126   1 LKVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGgaFYLKQWGPYNIS--IWDTAGREQFHGLGSMYCRGAAAVILTYDVS 78
                        90       100       110
                ....*....|....*....|....*....|....*
gi 6680718   96 DRERVNEAREELMRmLAEDELRDAVLLVFANKQDL 130
Cdd:cd04126  79 NVQSLEELEDRFLG-LTDTANEDCLFAVVGNKLDL 112
Rab40 cd04121
Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains ...
18-97 1.08e-03

Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133321 [Multi-domain]  Cd Length: 189  Bit Score: 37.99  E-value: 1.08e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTTIPT---IGFNVETV--EYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV 92
Cdd:cd04121   7 LKFLLVGDSDVGKGEILASLQDGSTESPYGYnmgIDYKTTTIllDGRRVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVY 86

                ....*
gi 6680718   93 DSNDR 97
Cdd:cd04121  87 DITNR 91
RalA_RalB cd04139
Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily ...
19-130 2.21e-03

Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206710 [Multi-domain]  Cd Length: 163  Bit Score: 37.02  E-value: 2.21e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   19 RILMVGLDAAGKTTILYKLKLGEIVTTI-PTIG---FNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS 94
Cdd:cd04139   2 KVIMVGSGGVGKSALTLQFMYDEFVEDYePTKAdsyRKKVVLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSI 81
                        90       100       110
                ....*....|....*....|....*....|....*....
gi 6680718   95 NDRERVN---EAREELMRMLAEDELRdavLLVFANKQDL 130
Cdd:cd04139  82 TDMESFTalaEFREQILRVKEDDNVP---LLLVGNKCDL 117
Rab2 cd01866
Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi ...
50-131 3.59e-03

Rab GTPase family 2 (Rab2); Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206658 [Multi-domain]  Cd Length: 168  Bit Score: 36.25  E-value: 3.59e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   50 GFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNeareELMRMLaeDELRD-----AVLLVF 124
Cdd:cd01866  42 GARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFN----HLTSWL--EDARQhsnsnMTIMLI 115

                ....*..
gi 6680718  125 ANKQDLP 131
Cdd:cd01866 116 GNKCDLE 122
RHO smart00174
Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like ...
23-77 6.17e-03

Rho (Ras homology) subfamily of Ras-like small GTPases; Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.


Pssm-ID: 197554 [Multi-domain]  Cd Length: 174  Bit Score: 35.67  E-value: 6.17e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6680718      23 VGLDAAGKTTILYKLKLGEI-VTTIPTIGFN-VETVEYKN--ISFTVWDVGGQ---DKIRPL 77
Cdd:smart00174   4 VGDGAVGKTCLLIVYTTNAFpEDYVPTVFENySADVEVDGkpVELGLWDTAGQedyDRLRPL 65
Rab23_like cd04106
Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family ...
18-130 8.66e-03

Rab GTPase family 23 (Rab23)-like; Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133306 [Multi-domain]  Cd Length: 162  Bit Score: 35.11  E-value: 8.66e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6680718   18 MRILMVGLDAAGKTTILYKLKLGEIVTTI-PTIGfnVETVEYK--------NISFTVWDVGGQDKIRPLWRHYFQNTQGL 88
Cdd:cd04106   1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYkKTIG--VDFLEKQiflrqsdeDVRLMLWDTAGQEEFDAITKAYYRGAQAC 78
                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 6680718   89 IFVVDSNDRERVNeaREELMRMLAEDELRDAVLLVFANKQDL 130
Cdd:cd04106  79 ILVFSTTDRESFE--AIESWKEKVEAECGDIPMVLVQTKIDL 118
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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