NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1039728086|ref|XP_017174969|]
View 

histone deacetylase 4 isoform X1 [Mus musculus]

Protein Classification

histone deacetylase 4( domain architecture ID 10178366)

histone deacetylase 4 (HD4) is a class IIa histone deacetylase that is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4)

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HDAC4 cd10006
Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes ...
 651-1059 0e+00

Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis. However, biological substrates for HDAC4 have not been identified; only low lysine deacetylation activity has been demonstrated and active site mutant has enhanced activity toward acetylated lysines. HDAC4 does not bind DNA directly, but through transcription factors MEF2C (myocyte enhancer factor-2C) and MEF2D. Other known interaction partners of the protein are 14-3-3 proteins, SMRT and N-CoR co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein, and ANKRA2. It appears to interact in a multiprotein complex with RbAp48 and HDAC3. Furthermore, HDAC4 is required for TGFbeta1-induced myofibroblastic differentiation.


:

Pssm-ID: 212530 [Multi-domain]  Cd Length: 409  Bit Score: 927.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  651 KPRFTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 730
Cdd:cd10006      1 KPRFTTGLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  731 NRQKLDSKKLLGSLTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 810
Cdd:cd10006     81 NRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  811 PMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 890
Cdd:cd10006    161 PMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  891 NVNMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRL 970
Cdd:cd10006    241 NVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRI 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  971 VLALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKC 1050
Cdd:cd10006    321 VLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQTC 400


                   ....*....
gi 1039728086 1051 EKEEAETVT 1059
Cdd:cd10006    401 ENEEAETVT 409
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
 90-151 7.06e-33

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


:

Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 122.23  E-value: 7.06e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10162     29 AEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQELLEHQRKLERHRQEQEMEKQQREQKL 90
 
Name Accession Description Interval E-value
HDAC4 cd10006
Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes ...
 651-1059 0e+00

Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis. However, biological substrates for HDAC4 have not been identified; only low lysine deacetylation activity has been demonstrated and active site mutant has enhanced activity toward acetylated lysines. HDAC4 does not bind DNA directly, but through transcription factors MEF2C (myocyte enhancer factor-2C) and MEF2D. Other known interaction partners of the protein are 14-3-3 proteins, SMRT and N-CoR co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein, and ANKRA2. It appears to interact in a multiprotein complex with RbAp48 and HDAC3. Furthermore, HDAC4 is required for TGFbeta1-induced myofibroblastic differentiation.


Pssm-ID: 212530 [Multi-domain]  Cd Length: 409  Bit Score: 927.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  651 KPRFTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 730
Cdd:cd10006      1 KPRFTTGLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  731 NRQKLDSKKLLGSLTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 810
Cdd:cd10006     81 NRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  811 PMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 890
Cdd:cd10006    161 PMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  891 NVNMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRL 970
Cdd:cd10006    241 NVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRI 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  971 VLALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKC 1050
Cdd:cd10006    321 VLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQTC 400


                   ....*....
gi 1039728086 1051 EKEEAETVT 1059
Cdd:cd10006    401 ENEEAETVT 409
Hist_deacetyl pfam00850
Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. ...
 677-994 4.78e-126

Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyze the removal of the acetyl group. Histone deacetylases are related to other proteins.


Pssm-ID: 425906 [Multi-domain]  Cd Length: 298  Bit Score: 386.59  E-value: 4.78e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRqkldskklLGSLTSVFVRLPCGGV 756
Cdd:pfam00850    1 HPENPERLKAILEALREAGLLPDLEIIAPRPATEEELLLVHSPEY--------LEF--------LEEAAPEGGALLLLSY 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  757 GVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKI 836
Cdd:pfam00850   65 LSGDDDTPVSPGSYEAALLAAGGTLAAADAVLSGEARNAFALVRPPGHHAERDRASGFCIFNNVAIAAKYLREKYGLKRV 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  837 LIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYdDGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTV 916
Cdd:pfam00850  145 AIVDFDVHHGNGTQEIFYDDPSVLTLSIHQY-PGGFYPGTGFADETGEGKGKGYTLNVP----LPPGTGDAEYLAAFEEI 219

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  917 VMPIANEFAPDVVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA---GGRLVLALEGGHDLTAICDASEACVSA 993
Cdd:pfam00850  220 LLPALEEFQPDLILVSAGFDAHAGD--PLGGLNLTTEGFAEITRILLELAdplCIRVVSVLEGGYNLDALARSATAVLAA 297


                   .
gi 1039728086  994 L 994
Cdd:pfam00850  298 L 298
AcuC COG0123
Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites ...
 656-996 2.36e-101

Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 439893 [Multi-domain]  Cd Length: 308  Bit Score: 321.67  E-value: 2.36e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  656 TGLVYDTLMLKHQCTCGntnsHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnplnrqkl 735
Cdd:COG0123      1 TALIYHPDYLLHDLGPG----HPEPPERLRAILDALEASGLLDDLELVEPPPATEEDLLRVHTPDY-------------- 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  736 dskkllgsLTSVFVRLPCGGVG-VDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGF 814
Cdd:COG0123     63 --------VDALRAASLDGGYGqLDPDTPVSP-GTWEAALLAAGGALAAADAVLEGEARNAFALVRPPGHHAERDRAMGF 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  815 CYFNSVAVAAKLLQQRlNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddgNFFPGSGAPDEVGTGPGVGFNVNM 894
Cdd:COG0123    134 CLFNNAAIAARYLLAK-GLERVAIVDFDVHHGNGTQDIFYDDPDVLTISIHQD---PLYPGTGAADETGEGAGEGSNLNV 209

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  895 AftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLA---GGRLV 971
Cdd:COG0123    210 P----LPPGTGDAEYLAALEEALLPALEAFKPDLIVVSAGFDAHAD--DPLGRLNLTTEGYAWRTRRVLELAdhcGGPVV 283

                          330       340
                   ....*....|....*....|....*
gi 1039728086  972 LALEGGHDLTAICDASEACVSALLG 996
Cdd:COG0123    284 SVLEGGYNLDALARSVAAHLETLLG 308
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
 90-151 7.06e-33

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 122.23  E-value: 7.06e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10162     29 AEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQELLEHQRKLERHRQEQEMEKQQREQKL 90
HDAC4_Gln pfam12203
Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, ...
 90-151 3.94e-25

Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam00850. The domain forms an alpha helix which complexes to form a tetramer. The glutamine rich domains have many intra- and inter-helical interactions which are thought to be involved in reversible assembly and disassembly of proteins. The domain is part of histone deacetylase 4 (HDAC4) which removes acetyl groups from histones. This restores their positive charge to allow stronger DNA binding thus restricting transcriptional activity.


Pssm-ID: 403429 [Multi-domain]  Cd Length: 91  Bit Score: 100.31  E-value: 3.94e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:pfam12203   30 AEFQKQHELLTRQHEAQLQEHIKQQQELLAMKQQQELLEQQRKLEQQRQEEELEKHRREQQL 91
PTZ00063 PTZ00063
histone deacetylase; Provisional
 804-968 1.58e-21

histone deacetylase; Provisional


Pssm-ID: 240251  Cd Length: 436  Bit Score: 98.73  E-value: 1.58e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  804 HHAEESTPMGFCYFNSVAVAA-KLLQQRlnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEV 882
Cdd:PTZ00063   137 HHAKRSEASGFCYINDIVLGIlELLKYH---ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKF--GDFFPGTGDVTDI 211

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  883 GTGPGVGFNVNMAFTGGleppMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYL 958
Cdd:PTZ00063   212 GVAQGKYYSVNVPLNDG----IDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTG--DRLGRFNLTikghAACVEFV 285

                          170
                   ....*....|...
gi 1039728086  959 TK---QLMGLAGG 968
Cdd:PTZ00063   286 RSlniPLLVLGGG 298
fliH PRK06800
flagellar assembly protein H; Validated
 91-196 5.07e-05

flagellar assembly protein H; Validated


Pssm-ID: 180700  Cd Length: 228  Bit Score: 46.02  E-value: 5.07e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   91 EFQRQHEQLsRQHEAQLHEH---IKQQQEMLAMKHQQeLLEHQRKLERHRQEQELEKQHREQKLQQLKnkekgkesavas 167
Cdd:PRK06800    35 EIQKDHEEL-LAQQKSLHKElnqLRQEQQKLERERQQ-LLADREQFQEHVQQQMKEIEAARQQFQKEQ------------ 100

                           90       100
                   ....*....|....*....|....*....
gi 1039728086  168 TEVKMKLQEFVLNKKKALAHRNLNHCISS 196
Cdd:PRK06800   101 QETAYEWTELLWDQSFQLAEKIVNQAVDT 129
FliJ COG2882
Flagellar biosynthesis chaperone FliJ [Cell motility];
105-152 3.88e-04

Flagellar biosynthesis chaperone FliJ [Cell motility];


Pssm-ID: 442129 [Multi-domain]  Cd Length: 142  Bit Score: 41.81  E-value: 3.88e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039728086  105 AQLHEHIKQQQEMLAM------KHQQELLEHQRKL-------ERHRQEQELEKQHREQKLQ 152
Cdd:COG2882     74 ARLDEAIEQQQQQVAQaeqqveQARQAWLEARQERkaleklkERRREEERQEENRREQKEL 134
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 98-188 8.13e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 40.34  E-value: 8.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   98 QLSRQHEAQLHEHIKQQQEMLamkHQQELLEHQRKLErhrQEQELEKQHREQKLQQLKnKEKGKESAVASTEVKMKLQEF 177
Cdd:TIGR00618  605 EAEDMLACEQHALLRKLQPEQ---DLQDVRLHLQQCS---QELALKLTALHALQLTLT-QERVREHALSIRVLPKELLAS 677

                           90
                   ....*....|.
gi 1039728086  178 VLNKKKALAHR 188
Cdd:TIGR00618  678 RQLALQKMQSE 688
 
Name Accession Description Interval E-value
HDAC4 cd10006
Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes ...
 651-1059 0e+00

Histone deacetylase 4; Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis. However, biological substrates for HDAC4 have not been identified; only low lysine deacetylation activity has been demonstrated and active site mutant has enhanced activity toward acetylated lysines. HDAC4 does not bind DNA directly, but through transcription factors MEF2C (myocyte enhancer factor-2C) and MEF2D. Other known interaction partners of the protein are 14-3-3 proteins, SMRT and N-CoR co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein, and ANKRA2. It appears to interact in a multiprotein complex with RbAp48 and HDAC3. Furthermore, HDAC4 is required for TGFbeta1-induced myofibroblastic differentiation.


Pssm-ID: 212530 [Multi-domain]  Cd Length: 409  Bit Score: 927.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  651 KPRFTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 730
Cdd:cd10006      1 KPRFTTGLVYDTLMLKHQCTCGNSNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  731 NRQKLDSKKLLGSLTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 810
Cdd:cd10006     81 NRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEEST 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  811 PMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 890
Cdd:cd10006    161 PMGFCYFNSVAIAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYSDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGF 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  891 NVNMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRL 970
Cdd:cd10006    241 NVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRI 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  971 VLALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKC 1050
Cdd:cd10006    321 VLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIHSKYWRCLQRTTSTAGYSLIEAQTC 400


                   ....*....
gi 1039728086 1051 EKEEAETVT 1059
Cdd:cd10006    401 ENEEAETVT 409
HDAC5 cd10007
Histone deacetylase 5; Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes ...
 654-1067 0e+00

Histone deacetylase 5; Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC5 is involved in integration of chronic drug (cocaine) addiction and depression with changes in chromatin structure and gene expression; cocaine regulates HDAC5 function to antagonize the rewarding impact of cocaine, possibly by blocking drug-stimulated gene expression that supports drug-induced behavioral change. It is also involved in regulation of angiogenesis and cell cycle as well as immune system development. HDAC5 and HDAC9 have been found to be significantly up-regulated in high-risk medulloblastoma compared with low-risk and may potentially be novel drug targets.


Pssm-ID: 212531 [Multi-domain]  Cd Length: 420  Bit Score: 809.21  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd10007      3 FTTGLVYDTFMLKHQCTCGNTNVHPEHAGRIQSVWSRLQETGLLGKCERVRGRKATLDEIQTVHSEHHTLLYGTSPLNRQ 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  734 KLDSKKLLGSLTS-VFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPM 812
Cdd:cd10007     83 KLDSKKLLGPLSQkMYAVLPCGGIGVDSDTVWNEMHSSSAVRMAVGCLIELAFKVAAGELKNGFAVIRPPGHHAEESTAM 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  813 GFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNV 892
Cdd:cd10007    163 GFCFFNSVAIAAKLLQQKLNVGKILIVDWDIHHGNGTQQAFYNDPNVLYISLHRYDDGNFFPGSGAPDEVGAGPGVGFNV 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  893 NMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVL 972
Cdd:cd10007    243 NIAWTGGVDPPIGDVEYLTAFRTVVMPIANEFSPDVVLVSAGFDAVEGHQSPLGGYSVTAKCFGHLTKQLMTLAGGRVVL 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  973 ALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCLQRLSSTVGHSLIEAQKCEK 1052
Cdd:cd10007    323 ALEGGHDLTAICDASEACVSALLGMELTPLDNTVLQQKPNDNAVATLERVIEIQSKHWSCLKRFAATLGFSLLEAQRGEL 402

                          410
                   ....*....|....*
gi 1039728086 1053 EEAETVTAMASLSVG 1067
Cdd:cd10007    403 EEAETVSAMASLSVD 417
HDAC_classIIa cd11681
Histone deacetylases, class IIa; Class IIa histone deacetylases are Zn-dependent enzymes that ...
 654-1030 0e+00

Histone deacetylases, class IIa; Class IIa histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) to yield deacetylated histones. This subclass includes animal HDAC4, HDAC5, HDAC7, and HDCA9. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, they have N-terminal regulatory domain with two or three conserved serine residues, phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC9 is involved in regulation of gene expression and dendritic growth in developing cortical neurons. It also plays a role in hematopoiesis. HDAC7 is involved in regulation of myocyte migration and differentiation. HDAC5 is involved in integration of chronic drug (cocaine) addiction and depression with changes in chromatin structure and gene expression. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis.


Pssm-ID: 212544 [Multi-domain]  Cd Length: 377  Bit Score: 805.03  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd11681      1 FTTGLAYDPLMLKHQCICGNNSSHPEHGGRLQSIWSRLQETGLVNRCERLRGRKATLEELQLVHSEVHTLLYGTNPLSRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  734 KLDSKKLLGSLTSVFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMG 813
Cdd:cd11681     81 KLDPTKLAGLPQKSFVRLPCGGIGVDSDTVWNELHTSNAARMAVGCVIDLAFKVATGELKNGFAVVRPPGHHAEPSQAMG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  814 FCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVN 893
Cdd:cd11681    161 FCFFNSVAIAAKQLQQKLKLRKILIVDWDVHHGNGTQQIFYEDPNVLYISLHRYDDGNFFPGTGAPTEVGSGAGEGFNVN 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  894 MAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLA 973
Cdd:cd11681    241 IAWSGGLDPPMGDAEYLAAFRTVVMPIAREFSPDIVLVSAGFDAAEGHPPPLGGYKVSPACFGYMTRQLMNLAGGKVVLA 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1039728086  974 LEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYW 1030
Cdd:cd11681    321 LEGGYDLTAICDASEACVRALLGDELDPLSEEELERRPNPNAVTSLEKVIAIQSPYW 377
HDAC7 cd10008
Histone deacetylase 7; Histone deacetylase 7 is a class IIa Zn-dependent enzyme that catalyzes ...
 654-1030 0e+00

Histone deacetylase 7; Histone deacetylase 7 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC7 is involved in regulation of myocyte migration and differentiation. Known interaction partners of class IIa HDAC7 are myocyte enhancer factors - MEF2A, -2C, and -2D, 14-3-3 proteins, SMRT and N-CoR co-repressors, HDAC3, ETA (endothelin receptor). This enzyme is also involved in the development of the immune system as well as brain and heart development. Multiple alternatively spliced transcript variants encoding several isoforms have been found for this gene.


Pssm-ID: 212532 [Multi-domain]  Cd Length: 378  Bit Score: 719.87  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd10008      1 FTTGLVYDSVMLKHQCSCGDNSNHPEHAGRIQSIWSRLQERGLRSQCECLRGRKASLEELQSVHSERHVLLYGTNPLSRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  734 KLDSKKLLGSLTS-VFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPM 812
Cdd:cd10008     81 KLDNGKLAGLLAQrMFVMLPCGGVGVDTDTIWNELHSSNAARWAAGSVTDLAFKVASRELKNGFAVVRPPGHHADHSTAM 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  813 GFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNV 892
Cdd:cd10008    161 GFCFFNSVAIACRQLQQQGKASKILIVDWDVHHGNGTQQTFYQDPSVLYISLHRHDDGNFFPGSGAVDEVGAGSGEGFNV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  893 NMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVL 972
Cdd:cd10008    241 NVAWAGGLDPPMGDPEYLAAFRIVVMPIAREFSPDLVLVSAGFDAAEGHPAPLGGYHVSAKCFGYMTQQLMNLAGGAVVL 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1039728086  973 ALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYW 1030
Cdd:cd10008    321 ALEGGHDLTAICDASEACVAALLGNEVDPLSEESWKQKPNLNAIRSLEAVIRVHSKYW 378
HDAC9 cd10009
Histone deacetylase 9; Histone deacetylase 9 is a class IIa Zn-dependent enzyme that catalyzes ...
 654-1031 0e+00

Histone deacetylase 9; Histone deacetylase 9 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, they have N-terminal regulatory domain with two or three conserved serine residues, phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC9 is involved in regulation of gene expression and dendritic growth in developing cortical neurons. It also plays a role in hematopoiesis. Its deregulated expression may be associated with some human cancers. HDAC5 and HDAC9 have been found to be significantly up-regulated in high-risk medulloblastoma compared with low-risk and may potentially be novel drug targets.


Pssm-ID: 212533 [Multi-domain]  Cd Length: 379  Bit Score: 646.69  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  654 FTTGLVYDTLMLKHQCTCGNTNSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQ 733
Cdd:cd10009      1 SATGIAYDPLMLKHQCVCGNSTTHPEHAGRIQSIWSRLQETGLLNKCERIQGRKASLEEIQLVHSEHHSLLYGTNPLDGQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  734 KLDSKKLLGSLTS-VFVRLPCGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPM 812
Cdd:cd10009     81 KLDPRILLGDDSQkFFSSLPCGGLGVDSDTIWNELHSSGAARMAVGCVIELASKVASGELKNGFAVVRPPGHHAEESTAM 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  813 GFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNV 892
Cdd:cd10009    161 GFCFFNSVAITAKYLRDQLNISKILIVDLDVHHGNGTQQAFYADPSILYISLHRYDEGNFFPGSGAPNEVGTGLGEGYNI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  893 NMAFTGGLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGHPTPLGGYNLSAKCFGYLTKQLMGLAGGRLVL 972
Cdd:cd10009    241 NIAWTGGLDPPMGDVEYLEAFRTIVKPVAKEFDPDMVLVSAGFDALEGHTPPLGGYKVTAKCFGHLTKQLMTLADGRVVL 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039728086  973 ALEGGHDLTAICDASEACVSALLGNELEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWR 1031
Cdd:cd10009    321 ALEGGHDLTAICDASEACVNALLGNELEPLAEDILHQSPNMNAVISLQKIIEIQSKYWK 379
HDAC_classII cd09992
Histone deacetylases and histone-like deacetylases, classII; Class II histone deacetylases are ...
 677-995 2.44e-137

Histone deacetylases and histone-like deacetylases, classII; Class II histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. This group includes animal HDAC4,5,6,7,8,9,10, fungal HOS3 and HDA1, plant HDA5 and HDA15 as well as other eukaryotes, archaeal and bacterial histone-like deacetylases. Eukaryotic deacetylases mostly use histones (H2, H3, H4) as substrates for deacetylation; however, non-histone substrates are known (for example, tubulin). Substrates for prokaryotic histone-like deacetylases are not known. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Interaction partners of class II deacetylases include 14-3-3 proteins, MEF2 family of transcriptional factors, CtBP, calmodulin (CaM), SMRT, N-CoR, BCL6, HP1alpha and SUMO. Histone deacetylases play a role in the regulation of cell cycle, cell differentiation and survival. Class II mammalian HDACs are differentially inhibited by structurally diverse compounds with known antitumor activities, thus presenting them as potential drug targets for human diseases resulting from aberrant acetylation.


Pssm-ID: 212518 [Multi-domain]  Cd Length: 291  Bit Score: 415.74  E-value: 2.44e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRQKLDSKKLLGSLtsvfvrlpcggv 756
Cdd:cd09992      1 HPERPERLLAILEALEEEGLLDRLVFVEPRPATEEELLRVHTPEY--------IERVEETCEAGGGYL------------ 60

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  757 gvDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKI 836
Cdd:cd09992     61 --DPDTYVSP-GSYEAALLAAGAALAAVDAVLSGEAENAFALVRPPGHHAEPDRAMGFCLFNNVAIAARYAQKRYGLKRV 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  837 LIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDdgnFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTV 916
Cdd:cd09992    138 LIVDWDVHHGNGTQDIFYDDPSVLYFSIHQYP---FYPGTGAAEETGGGAGEGFTINVP----LPPGSGDAEYLAAFEEV 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  917 VMPIANEFAPDVVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA----GGRLVLALEGGHDLTAICDASEACVS 992
Cdd:cd09992    211 LLPIAREFQPDLVLVSAGFDAHRGD--PLGGMNLTPEGYARLTRLLKELAdehcGGRLVFVLEGGYNLEALAESVLAVLE 288


                   ...
gi 1039728086  993 ALL 995
Cdd:cd09992    289 ALL 291
HDAC6-dom2 cd10003
Histone deacetylase 6, domain 2; Histone deacetylase 6 is a class IIb Zn-dependent enzyme that ...
 660-1033 2.13e-133

Histone deacetylase 6, domain 2; Histone deacetylase 6 is a class IIb Zn-dependent enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. Known interaction partners of HDAC6 are alpha tubulin and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD).


Pssm-ID: 212527 [Multi-domain]  Cd Length: 350  Bit Score: 407.88  E-value: 2.13e-133
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  660 YDTLMLKHqCTCGNTNsHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRQKLDSKK 739
Cdd:cd10003      1 YDQRMMNH-HNLWDPG-HPECPQRISRIYERHNDLGLLERCLRLPSRLATEDELLLCHSEEH--------LDEMKSLEKM 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  740 LLGSLtsvfvrlpcGGVGVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNS 819
Cdd:cd10003     71 KPREL---------NRLGKEYDSIYIHPDSYQCALLAAGCVLQVVEAVLTGESRNGVAIVRPPGHHAEQDTACGFCFFNN 141

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  820 VAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGS--GAPDEVGTGPGVGFNVNMAFT 897
Cdd:cd10003    142 VAIAARYAQKKYGLKRILIVDWDVHHGNGTQHMFESDPSVLYISLHRYDNGSFFPNSpeGNYDVVGKGKGEGFNVNIPWN 221

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  898 GGlepPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGG 977
Cdd:cd10003    222 KG---GMGDAEYIAAFQQVVLPIAYEFNPELVLVSAGFDAARG--DPLGGCKVTPEGYAHMTHMLMSLAGGRVIVILEGG 296

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1039728086  978 HDLTAICDASEACVSALLGnelEPLPEKVLHQRPNANAVHSMEKVMDIHSKYWRCL 1033
Cdd:cd10003    297 YNLTSISESMSMCTKTLLG---DPPPVLDLPRPPCSSALKSINNVLQVHQKYWKSL 349
Hist_deacetyl pfam00850
Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. ...
 677-994 4.78e-126

Histone deacetylase domain; Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyze the removal of the acetyl group. Histone deacetylases are related to other proteins.


Pssm-ID: 425906 [Multi-domain]  Cd Length: 298  Bit Score: 386.59  E-value: 4.78e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRqkldskklLGSLTSVFVRLPCGGV 756
Cdd:pfam00850    1 HPENPERLKAILEALREAGLLPDLEIIAPRPATEEELLLVHSPEY--------LEF--------LEEAAPEGGALLLLSY 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  757 GVDSDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKI 836
Cdd:pfam00850   65 LSGDDDTPVSPGSYEAALLAAGGTLAAADAVLSGEARNAFALVRPPGHHAERDRASGFCIFNNVAIAAKYLREKYGLKRV 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  837 LIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYdDGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTV 916
Cdd:pfam00850  145 AIVDFDVHHGNGTQEIFYDDPSVLTLSIHQY-PGGFYPGTGFADETGEGKGKGYTLNVP----LPPGTGDAEYLAAFEEI 219

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  917 VMPIANEFAPDVVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA---GGRLVLALEGGHDLTAICDASEACVSA 993
Cdd:pfam00850  220 LLPALEEFQPDLILVSAGFDAHAGD--PLGGLNLTTEGFAEITRILLELAdplCIRVVSVLEGGYNLDALARSATAVLAA 297


                   .
gi 1039728086  994 L 994
Cdd:pfam00850  298 L 298
HDAC_Clr3 cd11600
Class II Histone deacetylase Clr3 and similar proteins; Clr3 is a class II Histone ...
 675-1003 8.87e-119

Class II Histone deacetylase Clr3 and similar proteins; Clr3 is a class II Histone deacetylase Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Clr3 is the homolog of the class-II HDAC HdaI in S. cerevisiae, and is essential for silencing in heterochromatin regions, such as centromeric regions, ribosomal DNA, the mating-type region and telomeric loci. Clr3 has also been implicated in the regulation of stress-related genes; the histone acetyltransferase, Gcn5, in S. cerevisiae, preferentially acetylates global histone H3K14 while Clr3 preferentially deacetylates H3K14ac, and therefore, interplay between Gcn5 and Clr3 is crucial for the regulation of many stress-response genes.


Pssm-ID: 212542 [Multi-domain]  Cd Length: 313  Bit Score: 368.21  E-value: 8.87e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  675 NSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNRQKLDSKKLLGSLTSVFVrlpc 753
Cdd:cd11600      1 DPHPEDPSRISRIFEKLKEAGLINRMLRIPIREATKEEILLVHSEEHwDRVEATEKMSDEQLKDRTEIFERDSLYV---- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  754 ggvgvdsdtiwNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRL-- 831
Cdd:cd11600     77 -----------NN-DTAFCARLSCGGAIEACRAVAEGRVKNAFAVVRPPGHHAEPDESMGFCFFNNVAVAAKWLQTEYpd 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  832 NVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGS--GAPDEVGTGPGVGFNVNMAFTgglEPPMGDAEY 909
Cdd:cd11600    145 KIKKILILDWDIHHGNGTQRAFYDDPNVLYISLHRFENGGFYPGTpyGDYESVGEGAGLGFNVNIPWP---QGGMGDADY 221

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  910 LAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEA 989
Cdd:cd11600    222 IYAFQRIVMPIAYEFDPDLVIISAGFDAADG--DELGQCHVTPAGYAHMTHMLMSLAGGKLVVALEGGYNLDAISDSALA 299

                          330
                   ....*....|....
gi 1039728086  990 CVSALLGNELEPLP 1003
Cdd:cd11600    300 VAKVLLGEAPPKLP 313
HDAC cd09301
Histone deacetylase (HDAC) classes I, II, IV and related proteins; The HDAC/HDAC-like family ...
 683-994 7.71e-117

Histone deacetylase (HDAC) classes I, II, IV and related proteins; The HDAC/HDAC-like family includes Zn-dependent histone deacetylase classes I, II and IV (class III HDACs, also called sirtuins, are NAD-dependent and structurally unrelated, and therefore not part of this family). Histone deacetylases catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98), as opposed to the acetylation reaction by some histone acetyltransferases (EC 2.3.1.48). Deacetylases of this family are involved in signal transduction through histone and other protein modification, and can repress/activate transcription of a number of different genes. They usually act via the formation of large multiprotein complexes. They are involved in various cellular processes, including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. In mammals, they are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs.


Pssm-ID: 212512 [Multi-domain]  Cd Length: 279  Bit Score: 361.75  E-value: 7.71e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  683 RIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNPLNRQKLDSKKllgsltsvfvrlpcggvGVDSDT 762
Cdd:cd09301      1 RIRDLIEALKELGLRPKIELIECREATEELLLKVHTEEYLNELKANFAVATITESKP-----------------VIFGPN 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  763 IWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRlNVSKILIVDWD 842
Cdd:cd09301     64 FPVQRHYFRGARLSTGGVVEAAELVAKGELERAFAVVGAGGHHAGKSRAWGFCYFNDVVLAIKFLRER-GISRILIIDTD 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  843 VHHGNGTQQAFYNDPNVLYMSLHRYDDGNFfpgsgapdevGTGPGVGFNVNMAFTGGleppMGDAEYLAAFRTVVMPIAN 922
Cdd:cd09301    143 AHHGDGTREAFYDDDRVLHMSFHNYDIYPF----------GRGKGKGYKINVPLEDG----LGDEEYLDAVERVISKVLE 208

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039728086  923 EFAPDVVLVSSGFDAVEGHptPLGGYNLSAKCFGYLTKQLMGLA-GGRLVLALEGGHDLTAICDASEACVSAL 994
Cdd:cd09301    209 EFEPEVVVLQFGHDTHEGD--RLGGFNLSEKGFVKLAEIVKEFArGGPILMVLGGGYNPEAAARIWTAIIKEL 279
AcuC COG0123
Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites ...
 656-996 2.36e-101

Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 439893 [Multi-domain]  Cd Length: 308  Bit Score: 321.67  E-value: 2.36e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  656 TGLVYDTLMLKHQCTCGntnsHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnplnrqkl 735
Cdd:COG0123      1 TALIYHPDYLLHDLGPG----HPEPPERLRAILDALEASGLLDDLELVEPPPATEEDLLRVHTPDY-------------- 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  736 dskkllgsLTSVFVRLPCGGVG-VDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGF 814
Cdd:COG0123     63 --------VDALRAASLDGGYGqLDPDTPVSP-GTWEAALLAAGGALAAADAVLEGEARNAFALVRPPGHHAERDRAMGF 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  815 CYFNSVAVAAKLLQQRlNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddgNFFPGSGAPDEVGTGPGVGFNVNM 894
Cdd:COG0123    134 CLFNNAAIAARYLLAK-GLERVAIVDFDVHHGNGTQDIFYDDPDVLTISIHQD---PLYPGTGAADETGEGAGEGSNLNV 209

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  895 AftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLA---GGRLV 971
Cdd:COG0123    210 P----LPPGTGDAEYLAALEEALLPALEAFKPDLIVVSAGFDAHAD--DPLGRLNLTTEGYAWRTRRVLELAdhcGGPVV 283

                          330       340
                   ....*....|....*....|....*
gi 1039728086  972 LALEGGHDLTAICDASEACVSALLG 996
Cdd:COG0123    284 SVLEGGYNLDALARSVAAHLETLLG 308
HDAC10_HDAC6-dom1 cd10002
Histone deacetylase 6, domain 1 and histone deacetylase 10; Histone deacetylases 6 and 10 are ...
 676-1030 5.55e-99

Histone deacetylase 6, domain 1 and histone deacetylase 10; Histone deacetylases 6 and 10 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. HDAC10 has an N-terminal deacetylase domain and a C-terminal pseudo-repeat that shares significant similarity with its catalytic domain. It is located in the nucleus and cytoplasm, and is involved in regulation of melanogenesis. It transcriptionally down-regulates thioredoxin-interacting protein (TXNIP), leading to altered reactive oxygen species (ROS) signaling in human gastric cancer cells. Known interaction partners of HDAC6 are alpha tubulin (substrate) and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD) while interaction partners of HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins.


Pssm-ID: 212526 [Multi-domain]  Cd Length: 336  Bit Score: 316.56  E-value: 5.55e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  676 SHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLygtnpLNRQKLDSKKLLGSLTSVFvrlpcgg 755
Cdd:cd10002      6 NHIECPERLEAILERLTQDGLLERCVKIPAREAEEDEILLVHSQEYIDL-----VKSTETMEKEELESLCSGY------- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  756 vgvdsDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSK 835
Cdd:cd10002     74 -----DSVYLCPSTYEAARLAAGSTIELVKAVMAGKIQNGFALIRPPGHHAMRNEANGYCIFNNVAIAAKYAIEKLGLKR 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  836 ILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAP--DEVGTGPGVGFNVNMAF--TGgleppMGDAEYLA 911
Cdd:cd10002    149 ILIVDWDVHHGQGTQQGFYEDPRVLYFSIHRYEHGRFWPHLFESdyDYIGVGHGYGFNVNVPLnqTG-----LGDADYLA 223

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  912 AFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEACV 991
Cdd:cd10002    224 IFHHILLPLALEFQPELVLVSAGFDASIG--DPEGEMAVTPAGYAHLTRLLMGLAGGKLLLVLEGGYLLESLAESVSMTL 301

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1039728086  992 SALLGNELEPLPekvlHQRPNANAVHSMEKVMDIHSKYW 1030
Cdd:cd10002    302 RGLLGDPLPPLA----PPIPIRSVLETILNAIAHLSPRW 336
HDAC_classII_1 cd09996
Histone deacetylases and histone-like deacetylases, classII; This subfamily includes bacterial ...
 656-981 1.02e-88

Histone deacetylases and histone-like deacetylases, classII; This subfamily includes bacterial as well as eukaryotic Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Included in this family is a bacterial HDAC-like amidohydrolase (Bordetella/Alcaligenes species FB18817, denoted as FB188 HDAH) shown to be most similar in sequence and function to class II HDAC6 domain 3 or b (HDAC6b). FB188 HDAH is able to remove the acetyl moiety from acetylated histones, and can be inhibited by common HDAC inhibitors such as SAHA (suberoylanilide hydroxamic acid) as well as class II-specific but not class I specific inhibitors.


Pssm-ID: 212521 [Multi-domain]  Cd Length: 359  Bit Score: 289.46  E-value: 1.02e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  656 TGLVYDTLMLKHqctcgNTNS----------------HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSE 719
Cdd:cd09996      1 TGFVWDERYLWH-----DTGTgalflpvggllvqpgrHPENPETKRRIKNLLEVSGLSDHLVLITPRPATDEELLRVHTP 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  720 AHtllygtnpLNRQKLDSKKllgsltsvfvrlpcGGVGVDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVV 799
Cdd:cd09996     76 EY--------IDRVKAASAA--------------GGGEAGGGTPFGP-GSYEIALLAAGGAIAAVDAVLDGEVDNAYALV 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  800 RPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRydDGNFFPGSGAP 879
Cdd:cd09996    133 RPPGHHAEPDQGMGFCLFNNVAIAARHALAVGGVKRVAVVDWDVHHGNGTQAIFYDDPDVLTISLHQ--DRCFPPDSGAV 210

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  880 DEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAveGHPTPLGGYNLSAKCFGYLT 959
Cdd:cd09996    211 EERGEGAGEGYNLNIP----LPPGSGDGAYLHAFERIVLPALRAFRPELIIVASGFDA--SAFDPLGRMMLTSDGFRALT 284

                          330       340
                   ....*....|....*....|....*.
gi 1039728086  960 KQLMGLA----GGRLVLALEGGHDLT 981
Cdd:cd09996    285 RKLRDLAdelcGGRLVMVHEGGYSEA 310
HDAC6-dom1 cd11682
Histone deacetylase 6, domain 1; Histone deacetylases 6 are class IIb Zn-dependent enzymes ...
 676-1030 3.90e-86

Histone deacetylase 6, domain 1; Histone deacetylases 6 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. Known interaction partners of HDAC6 are alpha tubulin (substrate) and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD).


Pssm-ID: 212545 [Multi-domain]  Cd Length: 337  Bit Score: 281.74  E-value: 3.90e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  676 SHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNplnrQKLdSKKLLGSLTSVFvrlpcgg 755
Cdd:cd11682      6 SFPECPERLHAIREKLIQEGLLERCVSVQAREASEEELLLVHSPEYVALMKST----QYM-TEEELRTLADTY------- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  756 vgvdsDTIWNEVHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSK 835
Cdd:cd11682     74 -----DSVYLHPNSYSCACLAVGSVLQLVDKVLGGEIRNGLAIVRPPGHHAQHDKMDGYCMFNNVAIAARYAQQKHGVQR 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  836 ILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPGSGAPDE--VGTGPGVGFNVNMAFTgglEPPMGDAEYLAAF 913
Cdd:cd11682    149 VLIVDWDVHHGQGTQFIFEQDPSVLYFSIHRYEQGRFWPHLKESDSsaVGFGRGEGYNINVPWN---QVGMRDADYIAAF 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  914 RTVVMPIANEFAPDVVLVSSGFDAVEGHPTplGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEACVSA 993
Cdd:cd11682    226 LHVLLPVALEFQPQLVLVAAGFDAVIGDPK--GEMAATPACFAHLTHLLMGLAGGKLILSLEGGYNLRSLAEGVCASLKA 303

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 1039728086  994 LLGnelEPLPEKVLHQRPNANAVHSMEKVMDIHSKYW 1030
Cdd:cd11682    304 LLG---DPCPMLESPGAPCRSALASVSCTISALEPFW 337
HDAC_classII_2 cd11599
Histone deacetylases and histone-like deacetylases, classII; This subfamily includes ...
 677-995 5.48e-82

Histone deacetylases and histone-like deacetylases, classII; This subfamily includes eukaryotic as well as bacterial Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. In D. discoideum, where four homologs (HdaA, HdaB, HdaC, HdaD) have been identified, HDAC activity is important for regulating the timing of gene expression during development. Also, inhibition of HDAC activity by trichostatin A is shown to cause hyperacetylation of the histone and a delay in cell aggregation and differentiation.


Pssm-ID: 212541 [Multi-domain]  Cd Length: 288  Bit Score: 268.61  E-value: 5.48e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnplnrqkldskkllgsLTSVFVRLPC-GG 755
Cdd:cd11599      1 HPESPERLEAILDALIASGLDRLLRQLEAPPATREQLLRVHDAAY----------------------VDRLEAAAPEeGL 58

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  756 VGVDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSK 835
Cdd:cd11599     59 VQLDPDTAMSP-GSLEAALRAAGAVVAAVDAVMAGEARNAFCAVRPPGHHAERDKAMGFCLFNNVAIAAAHALAHHGLER 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  836 ILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddgNFFPGSGAPDEvgTGPGVGFNVNM-AFTGGleppmgdAEYLAAFR 914
Cdd:cd11599    138 VAIVDFDVHHGNGTEDIFRDDPRVLFCSSHQH---PLYPGTGAPDE--TGHGNIVNVPLpAGTGG-------AEFREAVE 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  915 TVVMPIANEFAPDVVLVSSGFDAvegHPT-PLGGYNLSAKCFGYLTKQLMGLA----GGRLVLALEGGHDLTAICDASEA 989
Cdd:cd11599    206 DRWLPALDAFKPDLILISAGFDA---HRDdPLAQLNLTEEDYAWITEQLMDVAdrycDGRIVSVLEGGYDLSALARSVAA 282


                   ....*.
gi 1039728086  990 CVSALL 995
Cdd:cd11599    283 HVRALM 288
HDAC10 cd11683
Histone deacetylase 10; Histone deacetylases 10 are class IIb Zn-dependent enzymes that ...
 683-1030 5.26e-74

Histone deacetylase 10; Histone deacetylases 10 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC10 has an N-terminal deacetylase domain and a C-terminal pseudo-repeat that shares significant similarity with its catalytic domain. It is located in the nucleus and cytoplasm, and is involved in regulation of melanogenesis. It transcriptionally down-regulates thioredoxin-interacting protein (TXNIP), leading to altered reactive oxygen species (ROS) signaling in human gastric cancer cells. Known interaction partners of HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins.


Pssm-ID: 212546 [Multi-domain]  Cd Length: 337  Bit Score: 248.62  E-value: 5.26e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  683 RIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYGTNP-LNRQKLdsKKLLGSLTSVFVRLpcggvgvdsd 761
Cdd:cd11683     13 RLTASYERLRQYGLVQRCLRLPAREASEEEILLVHSPEYLSLVRETQvMNKEEL--MAISGKYDAVYFHP---------- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  762 tiwNEVHssgAARLAVGCVVELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDW 841
Cdd:cd11683     81 ---NTFH---CARLAAGATLQLVDAVLTGEVQNGMALVRPPGHHSQRNAANGFCVFNNVAIAAEYAKKKYGLHRILIVDW 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  842 DVHHGNGTQQAFYNDPNVLYMSLHRYDDGNFFPG--SGAPDEVGTGPGVGFNVNMAFTgglEPPMGDAEYLAAFRTVVMP 919
Cdd:cd11683    155 DVHHGQGIQYIFEEDPSVLYFSWHRYEHQRFWPFlrESDYDAVGRGKGLGFNINLPWN---KVGMGNADYLAAFFHVLLP 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  920 IANEFAPDVVLVSSGFDAVEGHPTplGGYNLSAKCFGYLTKQLMGLAGGRLVLALEGGHDLTAICDASEACVSALLGnel 999
Cdd:cd11683    232 LAFEFDPELVLVSAGFDSAIGDPE--GQMCATPECFAHLTHLLMVLAGGKLCAVLEGGYHLESLAESVCMTVQTLLG--- 306

                          330       340       350
                   ....*....|....*....|....*....|.
gi 1039728086 1000 EPLPEKVLHQRPNANAVHSMEKVMDIHSKYW 1030
Cdd:cd11683    307 DPLPRLSGEMTPCQSALESIQNVRAAQAPYW 337
HDAC_classII_APAH cd10001
Histone deacetylase class IIa; This subfamily includes bacterial acetylpolyamine ...
 658-996 1.66e-68

Histone deacetylase class IIa; This subfamily includes bacterial acetylpolyamine amidohydrolase (APAH) as well as other Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Mycoplana ramosa APAH exhibits broad substrate specificity and catalyzes the deacetylation of polyamines such as putrescine, spermidine, and spermine by cleavage of a non-peptide amide bond.


Pssm-ID: 212525 [Multi-domain]  Cd Length: 298  Bit Score: 231.66  E-value: 1.66e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  658 LVYDTLMLKHQ----CTCGNTNSHPEHAGRIQSIWSRLQETGLRGKcecIRGRKATLEELQTVHSEAHtllygtnplnrq 733
Cdd:cd10001      2 IVYSEDHLLHHpkteLSRGKLVPHPENPERAEAILDALKRAGLGEV---LPPRDFGLEPILAVHDPDY------------ 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  734 kLDskkllgsltsvFVRlpcggvGVDSDTIWNEvHSSGAARLAVGCVVELVFKVATGElKNGFAVVRPPGHHAEESTPMG 813
Cdd:cd10001     67 -VD-----------FLE------TADTDTPISE-GTWEAALAAADTALTAADLVLEGE-RAAYALCRPPGHHAGRDRAGG 126

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  814 FCYFNSVAVAAKLLQQRlnVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRyDDGNFFPG-SGAPDEVGTGPGVGFNV 892
Cdd:cd10001    127 FCYFNNAAIAAQYLRDR--AGRVAILDVDVHHGNGTQEIFYERPDVLYVSIHG-DPRTFYPFfLGFADETGEGEGEGYNL 203

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  893 NMAftggLEPPMGDAEYLAAFRTVVMPIAnEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLaGGRLVL 972
Cdd:cd10001    204 NLP----LPPGTGDDDYLAALDEALAAIA-AFGPDALVVSLGFDTHEG--DPLSDFKLTTEDYARIGRRIAAL-GLPTVF 275

                          330       340
                   ....*....|....*....|....
gi 1039728086  973 ALEGGHDLTAIcdaSEACVSALLG 996
Cdd:cd10001    276 VQEGGYNVDAL---GRNAVAFLAG 296
HDAC_AcuC_like cd09994
Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes; AcuC (Acetoin ...
 677-980 2.61e-49

Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes; AcuC (Acetoin utilization protein) is a class I deacetylase found only in bacteria and is involved in post-translational control of the acetyl-coenzyme A synthetase (AcsA). Deacetylase AcuC works in coordination with deacetylase SrtN (class III), possibly to maintain AcsA in active (deacetylated) form and let the cell grow under low concentration of acetate. B. subtilis AcuC is a member of operon acuABC; this operon is repressed by the presence of glucose and does not show induction by acetoin; acetoin is a bacterial fermentation product that can be converted to acetate via the butanediol cycle in absence of other carbon sources. Inactivation of AcuC leads to slower growth and lower cell yield under low-acetate conditions in Bacillus subtilis. In general, Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase.


Pssm-ID: 212520 [Multi-domain]  Cd Length: 313  Bit Score: 177.75  E-value: 2.61e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHtllygtnpLNRQKLDSKkllGSLTSVFVRLpcgGV 756
Cdd:cd09994     17 HPFNPPRLSLTKDLLRALGLLPPVDLVPPRPATEEELLLFHTPDY--------IEAVKEASR---GQEPEGRGRL---GL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  757 GVDSDTIWNEVHSsgAARLAVGCVVELVFKVATGElknGFAVVRPPG--HHAEESTPMGFCYFNSVAVAAKLLQqRLNVS 834
Cdd:cd09994     83 GTEDNPVFPGMHE--AAALVVGGTLLAARLVLEGE---ARRAFNPAGglHHAMRGRASGFCVYNDAAVAIERLR-DKGGL 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  835 KILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRyDDGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDAEYLAAFR 914
Cdd:cd09994    157 RVAYVDIDAHHGDGVQAAFYDDPRVLTISLHE-SGRYLFPGTGFVDEIGEGEGYGYAVNIP----LPPGTGDDEFLRAFE 231

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  915 TVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLA----GGRLVLALEGGHDL 980
Cdd:cd09994    232 AVVPPLLRAFRPDVIVSQHGADAHAG--DPLTHLNLSNRAYRAAVRRIRELAdeycGGRWLALGGGGYNP 299
Arginase_HDAC cd09987
Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily ...
 768-994 3.63e-37

Arginase-like and histone-like hydrolases; Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs.


Pssm-ID: 212513  Cd Length: 217  Bit Score: 139.43  E-value: 3.63e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  768 HSSGAARLAVGCVVELVFKVatgelKNGFAVVrppGHHAEestpmgfcyFNSVAVAAKLLQQRlnvskILIVDWDVHHGN 847
Cdd:cd09987      6 RKAEAHELLAGVVVAVLKDG-----KVPVVLG---GDHSI---------ANGAIRAVAELHPD-----LGVIDVDAHHDV 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  848 GTQQAFYN--------------DPNVLYMSLHRYDDGNFFPGsgapdevGTGPGVGFNVNMAFTGGLeppmgDAEYLAAF 913
Cdd:cd09987     64 RTPEAFGKgnhhtprhllceplISDVHIVSIGIRGVSNGEAG-------GAYARKLGVVYFSMTEVD-----KLGLGDVF 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  914 RTVVMPIanEFAPDVVLVSSGFDAVEGHPTP----LGGYNLSAKCFGYLTKQLMGLaGGRLVLALEGGHDL----TAICD 985
Cdd:cd09987    132 EEIVSYL--GDKGDNVYLSVDVDGLDPSFAPgtgtPGPGGLSYREGLYITERIAKT-NLVVGLDIVEVNPLldetGRTAR 208


                   ....*....
gi 1039728086  986 ASEACVSAL 994
Cdd:cd09987    209 LAAALTLEL 217
HDAC_classI cd09991
Class I histone deacetylases; Class I histone deacetylases (HDACs) are Zn-dependent enzymes ...
 677-968 5.67e-34

Class I histone deacetylases; Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. This group includes animal HDAC1, HDAC2, HDAC3, HDAC8, fungal RPD3, HOS1 and HOS2, plant HDA9, protist, archaeal and bacterial (AcuC) deacetylases. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. In mammals, they are known to be involved in progression of various tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs.


Pssm-ID: 212517 [Multi-domain]  Cd Length: 306  Bit Score: 133.09  E-value: 5.67e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNRQKLdskkllgslTSVFVRLpcgG 755
Cdd:cd09991     15 HPMKPHRIRMTHSLILSYGLYKKMEIYRPRPATAEELTKFHSDDYiDFLRSVSPDNMKEF---------KKQLERF---N 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  756 VGVD---SDTIWNEVHSSGAArlAVGCVVELVFKVATgelkngfAVVRPPG--HHAEESTPMGFCYFNSVAVAA-KLLQ- 828
Cdd:cd09991     83 VGEDcpvFDGLYEYCQLYAGG--SIAAAVKLNRGQAD-------IAINWAGglHHAKKSEASGFCYVNDIVLAIlELLKy 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  829 -QRlnvskILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEVGTGPGVGFNVNMAftggLEPPMGDA 907
Cdd:cd09991    154 hQR-----VLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKF--GEYFFPGTGLRDIGAGKGKYYAVNVP----LKDGIDDE 222

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039728086  908 EYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYLTK---QLMGLAGG 968
Cdd:cd09991    223 SYLQIFEPVLSKVMEVFQPSAVVLQCGADSLAG--DRLGCFNLSikghAKCVKFVKSfniPLLVLGGG 288
ClassIIa_HDAC4_Gln-rich-N cd10162
Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This ...
 90-151 7.06e-33

Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197398 [Multi-domain]  Cd Length: 90  Bit Score: 122.23  E-value: 7.06e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10162     29 AEFQRQHEQLSRQHEAQLHEHIKQQQELLAMKHQQELLEHQRKLERHRQEQEMEKQQREQKL 90
HDAC8 cd10000
Histone deacetylase 8 (HDAC8); HDAC8 is a Zn-dependent class I histone deacetylase that ...
 670-1023 1.01e-31

Histone deacetylase 8 (HDAC8); HDAC8 is a Zn-dependent class I histone deacetylase that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. HDAC8 is found in human cytoskeleton-bound protein fraction and insoluble cell pellets. It plays a crucial role in intramembraneous bone formation; germline deletion of HDAC8 is detrimental to skull bone formation. HDAC8 is possibly associated with the smooth muscle actin cytockeleton and may regulate the contractive capacity of smooth muscle cells. HDAC8 is also involved in the metabolic control of the estrogen receptor related receptor (ERR)-alpha/peroxisome proliferator activated receptor (PPAR) gamma coactivator 1 alpha (PGC1-alpha) transcriptional complex as well as in the development of neuroblastoma and T-cell lymphoma. HDAC8-selective small-molecule inhibitors could be a therapeutic drug option for these diseases.


Pssm-ID: 212524 [Multi-domain]  Cd Length: 364  Bit Score: 127.84  E-value: 1.01e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  670 TCGNTNSHPEHAGRIQSIwsrLQETGLRGKCECIRGRKATLEELQTVHSEA--HTLLYGTNPLNRQKLDSKKLlgsltsv 747
Cdd:cd10000     12 LCDRLPKVPNRASMVHSL---IEAYGLLKQLRVVKPRVATEEELASFHSDEyiQFLKKASNEGDNDEEPSEQQ------- 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  748 fvrlpcgGVGVDSDTIWNEvHSSGAARLAVGCVVELVFKVATGELKngFAVVRPPG-HHAEESTPMGFCYFNSVAVAAKL 826
Cdd:cd10000     82 -------EFGLGYDCPIFE-GIYDYAAAVAGATLTAAQLLIDGKCK--VAINWFGGwHHAQRDEASGFCYVNDIVLGILK 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  827 LQQRLnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGnFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgD 906
Cdd:cd10000    152 LREKF--DRVLYVDLDLHHGDGVEDAFSFTSKVMTVSLHKYSPG-FFPGTGDVSDVGLGKGKYYTVNVPLRDGIQ----D 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  907 AEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLMGLAGGRLVLAlEGGHDL--TAIC 984
Cdd:cd10000    225 EQYLQIFTAVVPEIVAAFRPEAVVLQCGADTLAG--DPMGAFNLTPVGIGKCLKYVLGWKLPTLILG-GGGYNLanTARC 301

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1039728086  985 DASeaCVSALLGNELEPL-----------PEKVLH----QRPNANAVHSMEKVM 1023
Cdd:cd10000    302 WTY--LTGLILGEPLSSDipdhefftsygPDYELEispsLRPDLNEDQYIEKIL 353
HDAC_classIV cd09993
Histone deacetylase class IV also known as histone deacetylase 11; Class IV histone ...
 687-952 1.37e-31

Histone deacetylase class IV also known as histone deacetylase 11; Class IV histone deacetylases (HDAC11; EC 3.5.1.98) are predicted Zn-dependent enzymes. This class includes animal HDAC11, plant HDA2 and related bacterial deacetylases. Enzymes in this subfamily participate in regulation of a number of different processes through protein modification (deacetylation). They catalyze hydrolysis of N(6)-acetyl-lysine of histones (or other proteins) to yield a deacetylated proteins. Histone deacetylases often act as members of large multi-protein complexes such as mSin3A or SMRT/N-CoR. Human HDAC11 does not associate with them but can interact with HDAC6 in vivo. It has been suggested that HDAC11 and HDAC6 may use non-histone proteins as their substrates and play a role other than to directly modulate chromatin structure. In normal tissues, expression of HDAC11 is limited to kidney, heart, brain, skeletal muscle and testis, suggesting that its function might be tissue-specific. In mammals, HDAC11 proteins are known to be involved in progression of various tumors. HDAC11 plays an essential role in regulating OX40 ligand (OX40L) expression in Hodgkin lymphoma (HL); selective inhibition of HDAC11 expression significantly up-regulates OX40L and induces apoptosis in HL cell lines. Thus, inhibition of HDAC11 could be a therapeutic drug option for antitumor immune response in HL patients.


Pssm-ID: 212519 [Multi-domain]  Cd Length: 275  Bit Score: 124.92  E-value: 1.37e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  687 IWSRLQETGLRGKCECIRGRKATLEELQTVHSEA--HTLLYGTNPLNRQKL----DSKKLLGSltsvfVRLPCGGvgvds 760
Cdd:cd09993     11 LREALLEEGLVLPEDIVEPEPATREDLLRVHDPEylESLKSGELSREEIRRigfpWSPELVER-----TRLAVGG----- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  761 dTIwnevhssGAARLAvgcvvelvfkvatgeLKNGFAVvRPPG--HHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILI 838
Cdd:cd09993     81 -TI-------LAARLA---------------LEHGLAI-NLAGgtHHAFPDRGEGFCVFNDIAIAARVLLAEGLVRRVLI 136

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  839 VDWDVHHGNGTQQAFYNDPNVLYMSLHrydDGNFFPGSGAPDevgtgpgvGFNVnmaftgGLEPPMGDAEYLAAFRTVVM 918
Cdd:cd09993    137 VDLDVHQGNGTAAIFADDPSVFTFSMH---GEKNYPFRKEPS--------DLDV------PLPDGTGDDEYLAALEEALP 199

                          250       260       270
                   ....*....|....*....|....*....|....
gi 1039728086  919 PIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSA 952
Cdd:cd09993    200 RLLAEFRPDLVFYNAGVDVLAG--DRLGRLSLSL 231
ClassIIa_HDAC_Gln-rich-N cd10149
Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, ...
 90-151 9.32e-30

Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9); This superfamily consists of a glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDAC9; it is missing in HDAC7. It is referred to as the glutamine-rich domain, and confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors. This domain is able to repress transcription independently of the HDAC's C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197397 [Multi-domain]  Cd Length: 90  Bit Score: 113.25  E-value: 9.32e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10149     29 AEFQKQHENLTRQHEAQLQEHIKQQQEMLAIKQQQELLEKQRKLEQQRQEQELEKQRREQQL 90
HDAC_Hos1 cd11680
Class I histone deacetylases Hos1 and related proteins; Saccharomyces cerevisiae Hos1 is ...
 804-984 1.34e-28

Class I histone deacetylases Hos1 and related proteins; Saccharomyces cerevisiae Hos1 is responsible for Smc3 deacetylation. Smc3 is an important player during the establishment of sister chromatid cohesion. Hos1 belongs to the class I histone deacetylases (HDACs). HDACs are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. Other class I HDACs are animal HDAC1, HDAC2, HDAC3, HDAC8, fungal RPD3 and HOS2, plant HDA9, protist, archaeal and bacterial (AcuC) deacetylases. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase.


Pssm-ID: 212543 [Multi-domain]  Cd Length: 294  Bit Score: 116.98  E-value: 1.34e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  804 HHAEESTPMGFCYFNSVAVAAKLLQqRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDGnFFPGSGAPDEvg 883
Cdd:cd11680    115 HHAQKSRASGFCYVNDIVLAILRLR-RARFRRVFYLDLDLHHGDGVESAFFFSKNVLTCSIHRYDPG-FFPGTGSLKN-- 190

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  884 tgPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLM 963
Cdd:cd11680    191 --SSDKGMLNIP----LKRGLSDKTLLRIIDSIVRPLIEKFEPEVIVIQCGCDGLSG--DPHKEWNLTIRGYGSVIELLL 262

                          170       180
                   ....*....|....*....|....
gi 1039728086  964 GLAGGRLVLALEGG---HDLTAIC 984
Cdd:cd11680    263 KEFKDKPTLLLGGGgynHTEAARA 286
HDAC_Hos2 cd11598
Class I histone deacetylases including ScHos2 and SpPhd1; This subfamily includes Class I ...
 804-956 2.33e-28

Class I histone deacetylases including ScHos2 and SpPhd1; This subfamily includes Class I histone deacetylase (HDAC) Hos2 from Saccharomyces cerevisiae as well as a histone deacetylase Phd1 from Schizosaccharomyces pombe. Hos2 binds to the coding regions of genes during gene activation, specifically it deacetylates the lysines in H3 and H4 histone tails. It is preferentially associated with genes of high activity genome-wide and is shown to be necessary for efficient transcription. Thus, Hos2 is directly required for gene activation in contrast to other class I histone deacetylases. Protein encoded by phd1 is inhibited by trichostatin A (TSA), a specific inhibitor of histone deacetylase, and is involved in the meiotic cell cycle in S. pombe. Class 1 HDACs are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98).


Pssm-ID: 212540 [Multi-domain]  Cd Length: 311  Bit Score: 116.79  E-value: 2.33e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  804 HHAEESTPMGFCYFNSVAVAakLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYdDGNFFPGSGAPDEVG 883
Cdd:cd11598    131 HHAKKSEASGFCYVNDIVLA--ILNLLRYFPRVLYIDIDVHHGDGVEEAFYRTDRVMTLSFHKY-NGEFFPGTGDLDDNG 207

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039728086  884 TGPGVGFNVNMAftggLEPPMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFG 956
Cdd:cd11598    208 GTPGKHFALNVP----LEDGIDDEQYNLLFKSIIGPTIEKFQPSAIVLQCGADSLGG--DRLGQFNLNIKAHG 274
RPD3-like cd10004
reduced potassium dependency-3 (RPD3)-like; Proteins of the Rpd3-like family are class I ...
 677-968 1.88e-25

reduced potassium dependency-3 (RPD3)-like; Proteins of the Rpd3-like family are class I Zn-dependent Histone deacetylases that catalyze hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). RPD3 is the yeast homolog of class I HDACs. The main function of RPD3-like group members is regulation of a number of different processes through protein (mostly different histones) modification (deacetylation). This group includes fungal RPD3 and acts via the formation of large multiprotein complexes. Members of this group are involved in cell cycle regulation, DNA damage response, embryonic development and cytokine signaling important for immune response. Histone deacetylation by yeast RPD3 represses genes regulated by the Ash1 and Ume6 DNA-binding proteins. In mammals, they are known to be involved in progression of various tumors. Specific inhibitors of mammalian histone deacetylases could be a therapeutic drug option.


Pssm-ID: 212528 [Multi-domain]  Cd Length: 375  Bit Score: 109.51  E-value: 1.88e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHT-LLYGTNPLNR---QKLDSKKLLGSLTSVFVRLP 752
Cdd:cd10004     21 HPMKPHRIRMAHSLVMNYGLYKKMEIYRAKPATKNEMTQFHTDEYIdFLSRVTPDNMekfQKEQVKYNVGDDCPVFDGLF 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  753 --CGGVGVDSdtiwnevhSSGAARLAVGcvvelvfkvatgelKNGFAVVRPPG-HHAEESTPMGFCYFNSVAVAA-KLLQ 828
Cdd:cd10004    101 efCSISAGGS--------MEGAARLNRG--------------KCDIAVNWAGGlHHAKKSEASGFCYVNDIVLGIlELLR 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  829 QRlnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgDAE 908
Cdd:cd10004    159 YH---QRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKY--GEYFPGTGELRDIGIGTGKNYAVNVPLRDGID----DES 229

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039728086  909 YLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYLTK---QLMGLAGG 968
Cdd:cd10004    230 YKSIFEPVIKHVMEWYQPEAVVLQCGGDSLSG--DRLGCFNLSmkghANCVNFVKSfnlPMLVLGGG 294
HDAC4_Gln pfam12203
Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, ...
 90-151 3.94e-25

Glutamine rich N terminal domain of histone deacetylase 4; This domain is found in eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam00850. The domain forms an alpha helix which complexes to form a tetramer. The glutamine rich domains have many intra- and inter-helical interactions which are thought to be involved in reversible assembly and disassembly of proteins. The domain is part of histone deacetylase 4 (HDAC4) which removes acetyl groups from histones. This restores their positive charge to allow stronger DNA binding thus restricting transcriptional activity.


Pssm-ID: 403429 [Multi-domain]  Cd Length: 91  Bit Score: 100.31  E-value: 3.94e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:pfam12203   30 AEFQKQHELLTRQHEAQLQEHIKQQQELLAMKQQQELLEQQRKLEQQRQEEELEKHRREQQL 91
HDAC1 cd10010
Histone deacetylase 1 (HDAC1); Histone deacetylase 1 (HDAC1) is a Zn-dependent class I enzyme ...
 677-968 6.02e-24

Histone deacetylase 1 (HDAC1); Histone deacetylase 1 (HDAC1) is a Zn-dependent class I enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDAC1 is involved in regulation through association with DNA binding proteins to target specific chromatin regions. In particular, HDAC1 appears to play a major role in pre-implantation embryogenesis in establishing a repressive chromatin state. Its interaction with retinoblastoma tumor-suppressor protein is essential in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2 (MTA2), it deacetylates p53, thereby modulating its effect on cell growth and apoptosis. It participates in DNA-damage response, along with HDAC2; together, they promote DNA non-homologous end-joining. HDAC1 is also involved in tumorogenesis; its overexpression modulates cancer progression. Specific inhibitors of HDAC1 are currently used in cancer therapy.


Pssm-ID: 212534 [Multi-domain]  Cd Length: 371  Bit Score: 105.15  E-value: 6.02e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNRQKLdSKKL----LGSLTSVFvrl 751
Cdd:cd10010     25 HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYiKFLRSIRPDNMSEY-SKQMqrfnVGEDCPVF--- 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  752 pcggvgvdsDTIWNEVHSSGAARLAVGcvvelvfkVATGELKNGFAVVRPPG-HHAEESTPMGFCYFNSVAVAakLLQQR 830
Cdd:cd10010    101 ---------DGLFEFCQLSAGGSVASA--------VKLNKQQTDIAVNWAGGlHHAKKSEASGFCYVNDIVLA--ILELL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  831 LNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmgDAEYL 910
Cdd:cd10010    162 KYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKY--GEYFPGTGDLRDIGAGKGKYYAVNYPLRDGID----DESYE 235

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039728086  911 AAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYLTK---QLMGLAGG 968
Cdd:cd10010    236 AIFKPVMSKVMEMFQPSAVVLQCGADSLSG--DRLGCFNLTikghAKCVEFVKSfnlPMLMLGGG 298
HDAC_Hos3 cd09998
Class II histone deacetylases Hos3 and related proteins; Fungal histone deacetylase Hos3 from ...
 772-994 7.13e-23

Class II histone deacetylases Hos3 and related proteins; Fungal histone deacetylase Hos3 from Saccharomyces cerevisiae is a Zn-dependent enzyme belonging to HDAC class II. It catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Hos3 deacetylase is homodimer, in vitro it shows specificity to H4, H3 and H2A.


Pssm-ID: 212522 [Multi-domain]  Cd Length: 353  Bit Score: 101.37  E-value: 7.13e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  772 AARLAVGCV---VELVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLNVSKILIVDWDVHHGNG 848
Cdd:cd09998     85 AIQGALGAVceaVDSVFKPESPGTKRAFVAIRPPGHHCSESTPSGFCWVNNVHVGAAHAYLTHGITRVVILDIDLHHGNG 164

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  849 TQ------------------------QAFYNDPNVLYMSLHrydDGNFFP-GSGAPDEVGTGpgvgfNVNMAFTGG---- 899
Cdd:cd09998    165 TQdiawrinaeankqalesssyddfkPAGAPGLRIFYSSLH---DINSFPcEDGDPAKVKDA-----SVSIDGAHGqwiw 236

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  900 ---LEPPMGDAEYLAAFR---TVVMPIANEF------APD---VVLVSSGFDAVEGHPTPLG--GYNLSAKCFGYLTKQL 962
Cdd:cd09998    237 nvhLQPWTTEEDFWELYYpkyRILFEKAAEFlrlttaATPfktLVFISAGFDASEHEYESMQrhGVNVPTSFYYRFARDA 316

                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 1039728086  963 MGLA----GGRLVLALEGGHDLTAICDASEACVSAL 994
Cdd:cd09998    317 VRFAdahaHGRLISVLEGGYSDRALCSGVLAHLTGL 352
ClassIIa_HDAC9_Gln-rich-N cd10163
Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase; This ...
 90-151 2.57e-22

Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 9 (HDAC9). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197399 [Multi-domain]  Cd Length: 90  Bit Score: 92.12  E-value: 2.57e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 151
Cdd:cd10163     29 AEFQKQHENLTRQHQAQLQEHLKLQQELLAMKQQQELLEKEQKLEQQRQEQELERHRREQQL 90
PTZ00063 PTZ00063
histone deacetylase; Provisional
 804-968 1.58e-21

histone deacetylase; Provisional


Pssm-ID: 240251  Cd Length: 436  Bit Score: 98.73  E-value: 1.58e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  804 HHAEESTPMGFCYFNSVAVAA-KLLQQRlnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGNFFPGSGAPDEV 882
Cdd:PTZ00063   137 HHAKRSEASGFCYINDIVLGIlELLKYH---ARVMYIDIDVHHGDGVEEAFYVTHRVMTVSFHKF--GDFFPGTGDVTDI 211

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  883 GTGPGVGFNVNMAFTGGleppMGDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLS----AKCFGYL 958
Cdd:PTZ00063   212 GVAQGKYYSVNVPLNDG----IDDDSFVDLFKPVISKCVEVYRPGAIVLQCGADSLTG--DRLGRFNLTikghAACVEFV 285

                          170
                   ....*....|...
gi 1039728086  959 TK---QLMGLAGG 968
Cdd:PTZ00063   286 RSlniPLLVLGGG 298
HDAC3 cd10005
Histone deacetylase 3 (HDAC3); HDAC3 is a Zn-dependent class I histone deacetylase that ...
 804-956 4.75e-21

Histone deacetylase 3 (HDAC3); HDAC3 is a Zn-dependent class I histone deacetylase that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. In order to target specific chromatin regions, HDAC3 can interact with DNA-binding proteins (transcriptional factors) either directly or after forming complexes with a number of other proteins, as observed for the SMPT/N-CoR complex which recruits human HDAC3 to specific chromatin loci and activates deacetylation. Human HDAC3 is also involved in deacetylation of non-histone substrates such as RelA, SPY and p53 factors. This protein can also down-regulate p53 function and subsequently modulate cell growth and apoptosis. This gene is therefore regarded as a potential tumor suppressor gene. HDAC3 plays a role in various physiological processes, including subcellular protein localization, cell cycle progression, cell differentiation, apoptosis and survival. HDAC3 has been found to be overexpressed in some tumors including leukemia, lung carcinoma, colon cancer and maxillary carcinoma. Thus, inhibitors precisely targeting HDAC3 (in some cases together with retinoic acid or hyperthermia) could be a therapeutic drug option.


Pssm-ID: 212529  Cd Length: 381  Bit Score: 96.70  E-value: 4.75e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  804 HHAEESTPMGFCYFNSVAVAA-KLLQQRlnvSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYddGN-FFPGSGAPDE 881
Cdd:cd10005    132 HHAKKFEASGFCYVNDIVIAIlELLKYH---PRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKY--GNyFFPGTGDMYE 206

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1039728086  882 VGTGPGVGFNVNMAFTGGLEppmgDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFG 956
Cdd:cd10005    207 VGAESGRYYSVNVPLKDGID----DQSYLQLFKPVIQQVIDFYQPTCIVLQCGADSLGC--DRLGCFNLSIKGHG 275
HDAC2 cd10011
Histone deacetylase 2 (HDAC2); Histone deacetylase 2 (HDAC2) is a Zn-dependent class I enzyme ...
 677-953 1.34e-19

Histone deacetylase 2 (HDAC2); Histone deacetylase 2 (HDAC2) is a Zn-dependent class I enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDAC2 is involved in regulation through association with DNA binding proteins to target specific chromatin regions. It forms transcriptional repressor complexes by associating with several proteins, including the mammalian zinc-finger transcription factor YY1, thus playing an important role in transcriptional regulation, cell cycle progression and developmental events. Additionally, a few non-histone HDAC2 substrates have been found. HDAC2 plays a role in embryonic development and cytokine signaling important for immune response, and is over-expressed in several solid tumors including oral, prostate, ovarian, endometrial and gastric cancer. It participates in DNA-damage response, along with HDAC1; together, they can promote DNA non-homologous end-joining. HDAC2 is considered an important cancer prognostic marker. Inhibitors specifically targeting HDAC2 could be a therapeutic drug option.


Pssm-ID: 212535 [Multi-domain]  Cd Length: 366  Bit Score: 92.05  E-value: 1.34e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  677 HPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAH-TLLYGTNPLNRQKLdSKKL----LGSLTSVF--- 748
Cdd:cd10011     21 HPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYiKFLRSIRPDNMSEY-SKQMqrfnVGEDCPVFdgl 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  749 ---VRLPCGGvGVDSDTIWNEVHSSGAARLAVGCvvelvfkvatgelkngfavvrppgHHAEESTPMGFCYFNSVAVAak 825
Cdd:cd10011    100 fefCQLSTGG-SVAGAVKLNRQQTDMAVNWAGGL------------------------HHAKKSEASGFCYVNDIVLA-- 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  826 LLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVlyMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLEppmg 905
Cdd:cd10011    153 ILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRV--MTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGID---- 226

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 1039728086  906 DAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAK 953
Cdd:cd10011    227 DESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSG--DRLGCFNLTVK 272
PTZ00346 PTZ00346
histone deacetylase; Provisional
 804-977 1.26e-17

histone deacetylase; Provisional


Pssm-ID: 240374 [Multi-domain]  Cd Length: 429  Bit Score: 86.62  E-value: 1.26e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  804 HHAEESTPMGFCYFNSVAVAakLLQQRLNVSKILIVDWDVHHGNGTQQAFYNDPNVLYMSLHRYDDgNFFPGSGAPDEVG 883
Cdd:PTZ00346   154 HHSKCGECSGFCYVNDIVLG--ILELLKCHDRVLYVDIDMHHGDGVDEAFCTSDRVFTLSLHKFGE-SFFPGTGHPRDVG 230

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086  884 TGPGVGFNVNMAFTGGLEppmgDAEYLAAFRTVVMPIANEFAPDVVLVSSGFDAVEGhpTPLGGYNLSAKCFGYLTKQLM 963
Cdd:PTZ00346   231 YGRGRYYSMNLAVWDGIT----DFYYLGLFEHALHSIVRRYSPDAIVLQCGADSLAG--DRLGLLNLSSFGHGQCVQAVR 304

                          170
                   ....*....|....
gi 1039728086  964 GLagGRLVLALEGG 977
Cdd:PTZ00346   305 DL--GIPMLALGGG 316
ClassIIa_HDAC5_Gln-rich-N cd10164
Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This ...
 62-151 4.23e-15

Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase; This family consists of the glutamine-rich domain of histone deacetylase 5 (HDAC5). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues.


Pssm-ID: 197400 [Multi-domain]  Cd Length: 97  Bit Score: 71.78  E-value: 4.23e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   62 EPALREQQLQQELLALKQKQQIQRQILIAEFQRQHEQLSRQHEAQLHEHIK---------QQQEMLAMKHQQElLEHQRK 132
Cdd:cd10164      1 DPSLREQQLQQELLLLKQQQQLQKQLLFAEFQKQHEHLTRQHEVQLQKHLKvraelfseqQQQEILAAKRQQE-LEQQRK 79

                           90
                   ....*....|....*....
gi 1039728086  133 LERHRQEqELEKQHREQKL 151
Cdd:cd10164     80 REQQRQE-ELEKQRLEQQL 97
GBP_C pfam02841
Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral ...
 90-155 1.30e-06

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.


Pssm-ID: 460721 [Multi-domain]  Cd Length: 297  Bit Score: 51.52  E-value: 1.30e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQEL--------EKQHREQKLQQLK 155
Cdd:pfam02841  224 REKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREQLLAEQERMLEHKLQEQEEllkegfktEAESLQKEIQDLK 297
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 93-157 1.14e-05

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 48.34  E-value: 1.14e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039728086   93 QRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQE-LEKQHREQKLQQLKNK 157
Cdd:cd16269    221 QRELEQKLEDQERSYEEHLRQLKEKMEEERENLLKEQERALESKLKEQEaLLEEGFKEQAELLQEE 286
fliH PRK06800
flagellar assembly protein H; Validated
 91-196 5.07e-05

flagellar assembly protein H; Validated


Pssm-ID: 180700  Cd Length: 228  Bit Score: 46.02  E-value: 5.07e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   91 EFQRQHEQLsRQHEAQLHEH---IKQQQEMLAMKHQQeLLEHQRKLERHRQEQELEKQHREQKLQQLKnkekgkesavas 167
Cdd:PRK06800    35 EIQKDHEEL-LAQQKSLHKElnqLRQEQQKLERERQQ-LLADREQFQEHVQQQMKEIEAARQQFQKEQ------------ 100

                           90       100
                   ....*....|....*....|....*....
gi 1039728086  168 TEVKMKLQEFVLNKKKALAHRNLNHCISS 196
Cdd:PRK06800   101 QETAYEWTELLWDQSFQLAEKIVNQAVDT 129
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 91-186 6.56e-05

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 46.72  E-value: 6.56e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   91 EFQRQHEQLSRQHEAQ-LHEHIKQQQEMLAMKHQQELLEHQRKLERHR-QEQELEKQHREQ-KLQQLKNKEKGKESAVAS 167
Cdd:PRK09510    63 QYNRQQQQQKSAKRAEeQRKKKEQQQAEELQQKQAAEQERLKQLEKERlAAQEQKKQAEEAaKQAALKQKQAEEAAAKAA 142

                           90
                   ....*....|....*....
gi 1039728086  168 TEVKMKLQEfvlnKKKALA 186
Cdd:PRK09510   143 AAAKAKAEA----EAKRAA 157
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 93-190 1.51e-04

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 45.29  E-value: 1.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   93 QRQHEQLSRQHEAQLhEHIKQQQEMLAMKHQQE---LLEHQRKLERHRQEQ-----ELEKQHREQKLQQLKNKEKGKEsa 164
Cdd:pfam13868  231 ARQRQELQQAREEQI-ELKERRLAEEAEREEEEferMLRKQAEDEEIEQEEaekrrMKRLEHRRELEKQIEEREEQRA-- 307

                           90       100
                   ....*....|....*....|....*.
gi 1039728086  165 vasTEVKMKLQEFVLNKKKALAHRNL 190
Cdd:pfam13868  308 ---AEREEELEEGERLREEEAERRER 330
tolA PRK09510
cell envelope integrity inner membrane protein TolA; Provisional
 93-186 3.69e-04

cell envelope integrity inner membrane protein TolA; Provisional


Pssm-ID: 236545 [Multi-domain]  Cd Length: 387  Bit Score: 44.03  E-value: 3.69e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   93 QRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKLQQLKNKEKGK--ESAVASTEV 170
Cdd:PRK09510    86 QQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKraAAAAKKAAA 165

                           90
                   ....*....|....*.
gi 1039728086  171 KMKLQEFVLNKKKALA 186
Cdd:PRK09510   166 EAKKKAEAEAAKKAAA 181
FliJ COG2882
Flagellar biosynthesis chaperone FliJ [Cell motility];
105-152 3.88e-04

Flagellar biosynthesis chaperone FliJ [Cell motility];


Pssm-ID: 442129 [Multi-domain]  Cd Length: 142  Bit Score: 41.81  E-value: 3.88e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1039728086  105 AQLHEHIKQQQEMLAM------KHQQELLEHQRKL-------ERHRQEQELEKQHREQKLQ 152
Cdd:COG2882     74 ARLDEAIEQQQQQVAQaeqqveQARQAWLEARQERkaleklkERRREEERQEENRREQKEL 134
COG1340 COG1340
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];
90-181 7.25e-04

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];


Pssm-ID: 440951 [Multi-domain]  Cd Length: 297  Bit Score: 42.98  E-value: 7.25e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   90 AEFQRQHEQLSRQHEaqlhEHIKQQQEMLAMKHQ-QELLEHQRKLERHRQEQELEKQhREQKLQQLKNKEKgkesavAST 168
Cdd:COG1340    216 KEIVEAQEKADELHE----EIIELQKELRELRKElKKLRKKQRALKREKEKEELEEK-AEEIFEKLKKGEK------LTT 284

                           90
                   ....*....|...
gi 1039728086  169 EVKMKLQEFVLNK 181
Cdd:COG1340    285 EELKLLQKSGLLE 297
DUF4515 pfam14988
Domain of unknown function (DUF4515); This family of proteins is found in bacteria and ...
 91-187 2.10e-03

Domain of unknown function (DUF4515); This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 198 and 469 amino acids in length. There are two completely conserved L residues that may be functionally important.


Pssm-ID: 405647 [Multi-domain]  Cd Length: 206  Bit Score: 40.91  E-value: 2.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   91 EFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQ-----ELLEHQRKLER--HRQEQELE-----KQHREQKLQQLKNKE 158
Cdd:pfam14988   15 EKQKKIEKLWNQYVQECEEIERRRQELASRYTQQtaelqTQLLQKEKEQAslKKELQALRpfaklKESQEREIQDLEEEK 94

                           90       100
                   ....*....|....*....|....*....
gi 1039728086  159 KGKESAVASTEVKMKLQefVLNKKKALAH 187
Cdd:pfam14988   95 EKVRAETAEKDREAHLQ--FLKEKALLEK 121
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 91-176 2.38e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 42.03  E-value: 2.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   91 EFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQ-RKLERHRQEqELEKQHREQKLQQLKNKEKGKESAVASTE 169
Cdd:pfam17380  405 KILEEERQRKIQQQKVEMEQIRAEQEEARQREVRRLEEERaREMERVRLE-EQERQQQVERLRQQEEERKRKKLELEKEK 483


                   ....*..
gi 1039728086  170 VKMKLQE 176
Cdd:pfam17380  484 RDRKRAE 490
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 90-176 3.41e-03

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 40.64  E-value: 3.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   90 AEFQRQHEQLSRQHEAQLhehikqQQEMLAMKHQQEllEHQRKLERhRQEQELEKQHREQ-KLQQLKNKEKGKESAVAST 168
Cdd:cd16269    207 AEAAEQERKLLEEQQREL------EQKLEDQERSYE--EHLRQLKE-KMEEERENLLKEQeRALESKLKEQEALLEEGFK 277


                   ....*...
gi 1039728086  169 EVKMKLQE 176
Cdd:cd16269    278 EQAELLQE 285
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 91-176 4.94e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 40.88  E-value: 4.94e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   91 EFQRQHEQL--SRQHEAQLHEHIKQQQEMLAMKHQQEL-----LEHQRKLERHRQEQ---ELEKQHREQKLQ---QLKNK 157
Cdd:pfam17380  313 ERRRKLEEAekARQAEMDRQAAIYAEQERMAMERERELerirqEERKRELERIRQEEiamEISRMRELERLQmerQQKNE 392

                           90
                   ....*....|....*....
gi 1039728086  158 EKGKESAVAStevKMKLQE 176
Cdd:pfam17380  393 RVRQELEAAR---KVKILE 408
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
90-176 5.42e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 40.91  E-value: 5.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   90 AEFQRQHEQLSRQHEaQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQeqelEKQHREQKLQQLKNKEKGKESAVASTE 169
Cdd:COG4717    159 RELEEELEELEAELA-ELQEELEELLEQLSLATEEELQDLAEELEELQQ----RLAELEEELEEAQEELEELEEELEQLE 233


                   ....*..
gi 1039728086  170 VKMKLQE 176
Cdd:COG4717    234 NELEAAA 240
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 90-176 5.97e-03

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 38.48  E-value: 5.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   90 AEFQRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQE-----------LEKQHREQKLQQLKNKE 158
Cdd:pfam05672   23 AREQREREEQERLEKEEEERLRKEELRRRAEEERARREEEARRLEEERRREEeerqrkaeeeaEEREQREQEEQERLQKQ 102

                           90
                   ....*....|....*...
gi 1039728086  159 KGKESAVASTEVKMKLQE 176
Cdd:pfam05672  103 KEEAEAKAREEAERQRQE 120
TPH pfam13868
Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of ...
 93-177 8.03e-03

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.


Pssm-ID: 464007 [Multi-domain]  Cd Length: 341  Bit Score: 39.90  E-value: 8.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   93 QRQHEQLSRQHEAQLHEHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKLQQLKNKEKGKEsavasTEVKM 172
Cdd:pfam13868  212 QEEQERKERQKEREEAEKKARQRQELQQAREEQIELKERRLAEEAEREEEEFERMLRKQAEDEEIEQEEA-----EKRRM 286


                   ....*
gi 1039728086  173 KLQEF 177
Cdd:pfam13868  287 KRLEH 291
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 98-188 8.13e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 40.34  E-value: 8.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   98 QLSRQHEAQLHEHIKQQQEMLamkHQQELLEHQRKLErhrQEQELEKQHREQKLQQLKnKEKGKESAVASTEVKMKLQEF 177
Cdd:TIGR00618  605 EAEDMLACEQHALLRKLQPEQ---DLQDVRLHLQQCS---QELALKLTALHALQLTLT-QERVREHALSIRVLPKELLAS 677

                           90
                   ....*....|.
gi 1039728086  178 VLNKKKALAHR 188
Cdd:TIGR00618  678 RQLALQKMQSE 688
DDRGK pfam09756
DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and ...
 93-176 9.06e-03

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.


Pssm-ID: 370664 [Multi-domain]  Cd Length: 188  Bit Score: 38.48  E-value: 9.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039728086   93 QRQHeqlsRQHEAQLHEHIKQQQEMLAMKHQQEllEHQRKLERHRQEQELEKQHREQKLQQLKNKEKGKESAVASTEVKM 172
Cdd:pfam09756   17 KRQQ----REAEEEEREEREKLEEKREEEYKER--EEREEEAEKEKEEEERKQEEEQERKEQEEYEKLKSQFVVEEEGTD 90


                   ....
gi 1039728086  173 KLQE 176
Cdd:pfam09756   91 KLSA 94
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH