WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1183517071 176 EVSVFVQCFTDFATLVYNAVHFATQGEPLEHlttiasDIRSLYSPFSSRPTSAA-----GSPRRQQQSTPTPASArpmrs 250
Cdd:PTZ00421  352 QVDVYPPTFADHPAITADEYFSGGNAEPLVY------DMSAVFDGTSPELMGASalspsGKPRHSGVSVPASTSA----- 420

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1183517071 251 gsmpiaSSHPRTPRSATVATPTTHSRIRPSPSLNDTTMGLLNELEDLIEKQEEIRERRRTYLHNKERELLARLSD 325
Cdd:PTZ00421  421 ------MTHSFDDNTSKHADPCAMGVKRMDEGILDERLGRLQALSEKLRTQHEEIKRCREALQKKESIVMETLEK 489

coronin; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1183517071 176 EVSVFVQCFTDFATLVYNAVHFATQGEPLEHlttiasDIRSLYSPFSSRPTSAA-----GSPRRQQQSTPTPASArpmrs 250
Cdd:PTZ00421  352 QVDVYPPTFADHPAITADEYFSGGNAEPLVY------DMSAVFDGTSPELMGASalspsGKPRHSGVSVPASTSA----- 420

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1183517071 251 gsmpiaSSHPRTPRSATVATPTTHSRIRPSPSLNDTTMGLLNELEDLIEKQEEIRERRRTYLHNKERELLARLSD 325
Cdd:PTZ00421  421 ------MTHSFDDNTSKHADPCAMGVKRMDEGILDERLGRLQALSEKLRTQHEEIKRCREALQKKESIVMETLEK 489

FYVE-type zinc finger; This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A and regulating synaptic membrane exocytosis protein 2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1183517071 440 DLTDRTEKHCRMCSQGFGFL-EKRVVCKDCRLTIHKDCYGTGHPER 484
Cdd:pfam02318  48 NQAHLGETHCIRCLQPFGFLvNSKRQCLDCRKNVCKKCGVYNKPEQ 93

protein kinase C conserved region 1 (C1 domain) found in the unconventional myosin-IX family; Myosins IX (Myo9) is a class of unique motor proteins with a common structure of an N-terminal extension preceding a myosin head homologous to the Ras-association (RA) domain, a head (motor) domain, a neck with IQ motifs that bind light chains, and a C-terminal tail containing cysteine-rich zinc binding (C1) and Rho-GTPase activating protein (RhoGAP) domains. There are two genes for myosins IX in humans, IXa and IXb, that are different in their expression and localization. IXa is expressed abundantly in brain and testis, and IXb is expressed abundantly in tissues of the immune system. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1183517071 430 NRHRFTVTRVDLTdrteKHCRMCSQGFGFLEKRVVCKDCRLTIHKDCY 477
Cdd:cd20818     2 NGHKFATVQFNIP----TYCEVCNSFIWLMEKGLVCQVCKFTCHKKCY 45

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1183517071  37 NSSTVRTAEHSRGS-TQQPEYSFLQLDAMASELLAD-TLSTPLSAPAGIPLATALLMEGSQQSRMMLAALAEAvevSVTN 114
Cdd:pfam17823  82 NSTEVTAEHTPHGTdLSEPATREGAADGAASRALAAaASSSPSSAAQSLPAAIAALPSEAFSAPRAAACRANA---SAAP 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1183517071 115 ASAILDPISDHLAPGSSHDIALSAQSVLESVRALIHPDSPTRSLPASVPPSSPLAMRHVQR------EVSVFVQCFTDFA 188
Cdd:pfam17823 159 RAAIAAASAPHAASPAPRTAASSTTAASSTTAASSAPTTAASSAPATLTPARGISTAATATghpaagTALAAVGNSSPAA 238

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1183517071 189 TLVYNAVHF---ATQGEPLEHLTTIAS--DIRSLYSPFSSRPTSAagsprrqqQSTPTPASARPmrsgsmPIASSHPRTP 263
Cdd:pfam17823 239 GTVTAAVGTvtpAALATLAAAAGTVASaaGTINMGDPHARRLSPA--------KHMPSDTMARN------PAAPMGAQAQ 304

                         250       260
                  ....*....|....*....|....*...
gi 1183517071 264 ---RSATVATPTTHSRIRPSPSLNDTTM 288
Cdd:pfam17823 305 gpiIQVSTDQPVHNTAGEPTPSPSNTTL 332

protein kinase C conserved region 1 (C1 domain) superfamily; The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains. It contains the motif HX12CX2CXnCX2CX4HX2CX7C, where C and H are cysteine and histidine, respectively; X represents other residues; and n is either 13 or 14. C1 has a globular fold with two separate Zn(2+)-binding sites. It was originally discovered as lipid-binding modules in protein kinase C (PKC) isoforms. C1 domains that bind and respond to phorbol esters (PE) and diacylglycerol (DAG) are referred to as typical, and those that do not respond to PE and DAG are deemed atypical. A C1 domain may also be referred to as PKC or non-PKC C1, based on the parent protein's activity. Most C1 domain-containing non-PKC proteins act as lipid kinases and scaffolds, except PKD which acts as a protein kinase. PKC C1 domains play roles in membrane translocation and activation of the enzyme.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1183517071 432 HRFtvtrVDLTDRTEKHCRMCSQGF-GFLEKRVVCKDCRLTIHKDC 476
Cdd:cd00029     1 HRF----VPTTFSSPTFCDVCGKLIwGLFKQGLKCSDCGLVCHKKC 42

FYVE domain like superfamily; FYVE domain is a 60-80 residue double zinc finger motif-containing module named after the four proteins, Fab1, YOTB, Vac1, and EEA1. The canonical FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif, which form a compact phosphatidylinositol 3-phosphate (PtdIns3P, also termed PI3P)-binding site. They are found in many membrane trafficking regulators, including EEA1, Hrs, Vac1p, Vps27p, and FENS-1, which locate to early endosomes, specifically bind PtdIns3P, and play important roles in vesicular traffic and in signal transduction. Some proteins, such as rabphilin-3A and alpha-Rab3-interacting molecules (RIMs), are also involved in membrane trafficking and bind to members of the Rab subfamily of GTP hydrolases. However, they contain FYVE-related domains that are structurally similar to the canonical FYVE domains but lack the three signature sequences. At this point, they may not bind to phosphoinositides. In addition, this superfamily also contains the third group of proteins, caspase-associated ring proteins CARP1 and CARP2. They do not localize to membranes in the cell and are involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10, which are distinguished from other FYVE-type proteins. Moreover, these proteins have an altered sequence in the basic ligand binding patch and lack the WxxD motif that is conserved only in phosphoinositide binding FYVE domains. Thus they constitute a family of unique FYVE-type domains called FYVE-like domains. The FYVE domain is structurally similar to the RING domain and the PHD finger. This superfamily also includes ADDz zinc finger domain, which is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1183517071 448 HCRMCSQGFGFLEKRVVCKDCRLTIHKDC---------YGTGHPERYACECF 490
Cdd:cd00065     1 RCMLCGKKFSLFRRRHHCRRCGRVFCSKCsskklplpsFGSGKPVRVCDSCY 52