Citrus Sinensis ID: 006008

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-----

MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDLGQFSNSIDRTTALGEEWTGSSSNGTDDPDTSGSLDEESGSNYDSQQSIPGLSDNSGTGDSASEGDRNCDPLIQISDAGIACSNENGASHSGFPDLEGMMSKRALESWLDEQPGSSSPSASEQIQVRQSSARISIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLVESSLNT

cHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccccccHHHHccccccccHHHHHHHHcccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccHHHHHHHcccccEEEccccccccccEEEEcccccccccEEEEEEEccccccccccEEEEEEEEEcccccEEEEEEEcccccccccHHHHHHHcccccccccccccccccccccccccccccEEEEEEEEEcccccccEEEEEEccccccEEEEcccccccccccccHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccEEEEEcccccccccccccccEEEEEEcccccccEEEEEEEEcccccccccEEEEEEcccHHHHHHHHHHHHHHHHHccccc

ccHHHHHHHHHHHHHcccccHcHcccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccccHcHHHcccccccccHHHHHHHHHHccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccHcccccccHHHHHccccccccccccHcccccccccEEEEEcccccccccEEEEEcccccccEEEEEEEccccccccccEEEEEEEEEEcccccccEEEEcccccccccccccccccccccccccccccccEccHHHHHHccccccEEEEEEEEcccccccEEEEEEEcccEEEEEEcccccEEEccccccHHHHHHHHHcccccHHHHHEcccccHHHccccccccccHcHHHHHHHHHHHHHHHHHHccEEEEEcccccccccccccccEEEEEEEEccccccEEEEEEEEcccccccEEEEEEccHHHHHHHHHHHHHHHHHHcccccc

MANTCVEGLLALIRQELLTsdiesgngeADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSldsikvpeARVMIIWMVGeyssvgvkIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCakggdmwtITRLFSYLLELAECDLNYDVRDRARFFKKLFShnlcsqvpeetnalqenkdlpLVLVECIFRKqenlaasepindrfylpgslsqivlhaapgyeplpkpcsslcddlgqfsnsidRTTAlgeewtgsssngtddpdtsgsldeesgsnydsqqsipglsdnsgtgdsasegdrncdpliqisdagiacsnengashsgfpdlegMMSKRALESwldeqpgssspsaseQIQVRQSSArisignigrqvkaksytlldpangnglKVYYSfsseastispqLVCLETFFENcssetmsevtlvdeeshkaldlADLTLATTassltsqsdlptlvpmeeitslepgqTMKRILEVRFHHHLLPLKLALhcngkklpvklrpdigyfikpvpmdMETFIEMESRLpgmfeyarsctftdhlgevdkdtdessllkdKYLVICESLASKMLSNANIFLVSVdmpvaakfddasglslrfsseilgnsvpCLITITvegkcseplkvsakvnceetVFGLNLLNRIVNFLVESSLNT

MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLfrsldsikvpEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDLGQFSNSIDRTTALgeewtgsssngtddpdtSGSLDEESGSNYDSQQSIPGLSDNSGTGDSASEGDRNCDPLIQISDAGIACSNENGASHSGFPDLEGMMSKRALESWLDEQPGSSSPSASEQIQVRQSsarisignigrqVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASsltsqsdlptlvPMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLgevdkdtdessllkDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLVESSLNT

MANTCVEGLLALIRQELLTSDIESGNGEADVLiqsiisiksiikqDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDLGQFSNSIDRTTALGEEWTGSSSNGTDDPDTSGSLDEESGSNYDSQQSIPGLSDNSGTGDSASEGDRNCDPLIQISDAGIACSNENGASHSGFPDLEGMMSKRALESWLDEQPGSSSPSASEQIQVRQSSARISIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKaldladltlattassltsqsdlPTLVPMEEITSLEPGQTMKRILEVRFhhhllplklalhCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLVESSLNT

****CVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDLGQF*********************************************************************************************************************************SIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLV*******LDLADLTL*****************************TMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLV******

*ANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCS**********ENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEP*P******************************************************************************************************************************************************VKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLV*****************************************PGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLV*S****

MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDLGQFSNSIDRTTALGE*************************************************DRNCDPLIQISDAGIACSNENGASHSGFPDLEGMMSKRALES**********************SARISIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLVESSLNT

MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDL*********************************************************************PL***S*AGI************************************************SSARISIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDE*********************SQSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLVES****

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SSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		665	2.2.26 [Sep-21-2011]
Q9M2T1		987	AP3-complex subunit beta-	no	no	0.948	0.639	0.530	0.0
Q13367		1082	AP-3 complex subunit beta	yes	no	0.285	0.175	0.327	2e-21
Q9JME5		1082	AP-3 complex subunit beta	yes	no	0.285	0.175	0.323	7e-21
Q9Z1T1		1105	AP-3 complex subunit beta	no	no	0.284	0.171	0.314	1e-19
Q32PG1		1084	AP-3 complex subunit beta	no	no	0.338	0.207	0.291	1e-19
Q7YRF1		1091	AP-3 complex subunit beta	no	no	0.290	0.176	0.311	9e-19
O00203		1094	AP-3 complex subunit beta	no	no	0.293	0.178	0.309	9e-19
Q556J8		1108	AP-3 complex subunit beta	yes	no	0.245	0.147	0.293	6e-14
O13939		745	AP-3 complex subunit beta	yes	no	0.264	0.236	0.275	5e-13
Q759E2		781	AP-3 complex subunit beta	yes	no	0.198	0.169	0.344	9e-13

>sp\|Q9M2T1\|AP3BA_ARATH AP3-complex subunit beta-A OS=Arabidopsis thaliana GN=AP3BA PE=2 SV=2	Back alignment and function desciption

 Score =  670 bits (1728), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/666 (53%), Positives = 464/666 (69%), Gaps = 35/666 (5%)

Query: 1   MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRS 60
           +  TC++GLLAL+RQE    D ES +GEA VL+Q+++SI+++I++DP  HEKV+IQLFRS
Sbjct: 349 IPTTCLDGLLALVRQESFAGDFESADGEAGVLVQAVMSIQTMIERDPLRHEKVLIQLFRS 408

Query: 61  LDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKV 120
           LDSIKV  AR  IIWMVG Y S+G  IPRMLTT+ KYLAW FKSEA ETKLQILNT  KV
Sbjct: 409 LDSIKVAAARATIIWMVGVYCSLGHIIPRMLTTITKYLAWSFKSEASETKLQILNTIAKV 468

Query: 121 LLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVP-EETNALQE 179
           L+ A+ GD   + R+  Y+ EL E DL+YD+RDR RF KKL S  L S  P E++ A QE
Sbjct: 469 LISAEAGDFHMLKRIVVYVFELGEYDLSYDIRDRTRFLKKLLSCKLASHEPAEDSVASQE 528

Query: 180 NKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDL 239
           N  +   +VE +F ++    +   +++RFYLPGSLSQIVLHAAPGYEPLPKPCS + ++ 
Sbjct: 529 N--IAAHVVEHVFGRKLKSVSPITLHNRFYLPGSLSQIVLHAAPGYEPLPKPCSFVYEEQ 586

Query: 240 GQFSNSIDRTTALGEEWTGSSSNGTDDPDTSGSLDEESGSNYDSQQSIPGLSDNSGTGDS 299
            Q S+ +D+      +  GS        ++S + DE   S+YDS+ S    SD S  GD 
Sbjct: 587 DQLSD-LDKQREAAADLDGSE-------ESSETGDENGSSDYDSESS--NGSDFSSEGDE 636

Query: 300 ASEGDRNCD---PLIQISDAGIACSNENGASHSGFPDLEGMMSKRALESWLDEQPGSSSP 356
            +  +   D   PLIQIS+  ++             D E + S+RAL+ WLD+QP +S+ 
Sbjct: 637 RTVSNDANDPAAPLIQISETSVSA------------DQEELRSRRALDLWLDDQPSTSNQ 684

Query: 357 SASEQIQVRQSSARISIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCL 416
           + S     + S A+ISIG++G +VK KSY+L+DP NG+GLKV Y+F SE S +SP  VC+
Sbjct: 685 TPSALNSNQSSYAKISIGDVGSRVKPKSYSLVDPGNGSGLKVDYAFLSEVSNVSPLHVCV 744

Query: 417 ETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEP 476
           E  FEN S+E + EV L DEES K  D ++ TL   A++  S +++PTL+PMEEI+ LEP
Sbjct: 745 EVLFENSSAEPILEVNLEDEESMKVADSSEQTLVGKANA--SYNNIPTLIPMEEISCLEP 802

Query: 477 GQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLP 536
            Q+ KR+++VRFHHHLLP++L LH N KK+PVKLRPD+GY +KP  M +E F+  ESRLP
Sbjct: 803 HQSTKRLIQVRFHHHLLPMRLTLHYNEKKVPVKLRPDLGYLVKPFSMSIEEFLATESRLP 862

Query: 537 GMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAA 596
           GMFEY+R CTF DH+   D  T+     KDK+L ICES+  K+LSN+N+ LVSVD+PVA 
Sbjct: 863 GMFEYSRRCTFDDHVK--DSRTENG---KDKFLSICESITLKVLSNSNLHLVSVDLPVAN 917

Query: 597 KFDDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVN 656
             +DA+GL LRFSS+IL + +P LITITVEGKC+E L ++ K+NCEETVFGLNLLNRI N
Sbjct: 918 SLEDATGLRLRFSSKILSSEIPLLITITVEGKCTEVLNLTVKINCEETVFGLNLLNRIAN 977

Query: 657 FLVESS 662
           F+VE S
Sbjct: 978 FMVEPS 983

Subunit of non-clathrin- and clathrin-associated adaptor protein complex 3 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. AP-3 appears to be involved in the sorting of a subset of transmembrane proteins targeted to lysosomes and lysosome-related organelles.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q13367\|AP3B2_HUMAN AP-3 complex subunit beta-2 OS=Homo sapiens GN=AP3B2 PE=1 SV=2	Back alignment and function description

>sp\|Q9JME5\|AP3B2_MOUSE AP-3 complex subunit beta-2 OS=Mus musculus GN=Ap3b2 PE=1 SV=2	Back alignment and function description

>sp\|Q9Z1T1\|AP3B1_MOUSE AP-3 complex subunit beta-1 OS=Mus musculus GN=Ap3b1 PE=1 SV=2	Back alignment and function description

>sp\|Q32PG1\|AP3B1_BOVIN AP-3 complex subunit beta-1 OS=Bos taurus GN=AP3B1 PE=2 SV=1	Back alignment and function description

>sp\|Q7YRF1\|AP3B1_CANFA AP-3 complex subunit beta-1 OS=Canis familiaris GN=AP3B1 PE=2 SV=1	Back alignment and function description

>sp\|O00203\|AP3B1_HUMAN AP-3 complex subunit beta-1 OS=Homo sapiens GN=AP3B1 PE=1 SV=3	Back alignment and function description

>sp\|Q556J8\|AP3B_DICDI AP-3 complex subunit beta OS=Dictyostelium discoideum GN=ap3b-1 PE=3 SV=1	Back alignment and function description

>sp\|O13939\|AP3B_SCHPO AP-3 complex subunit beta OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=apl6 PE=1 SV=1	Back alignment and function description

>sp\|Q759E2\|AP3B_ASHGO AP-3 complex subunit beta OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=APL6 PE=3 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		665
359486795		1140	PREDICTED: AP3-complex subunit beta-A-li	0.993	0.579	0.659	0.0
224109508		991	predicted protein [Populus trichocarpa]	0.963	0.646	0.634	0.0
356501063		1129	PREDICTED: AP3-complex subunit beta-A-li	0.977	0.575	0.619	0.0
255584875		1121	conserved hypothetical protein [Ricinus	0.963	0.571	0.638	0.0
357492243		1126	AP-3 complex subunit beta-2 [Medicago tr	0.968	0.571	0.617	0.0
356551707		1129	PREDICTED: AP3-complex subunit beta-A-li	0.977	0.575	0.620	0.0
449459904		1127	PREDICTED: AP3-complex subunit beta-A-li	0.968	0.571	0.559	0.0
240255649		1115	AP3-complex subunit beta-A [Arabidopsis	0.948	0.565	0.530	0.0
18410287		987	AP3-complex subunit beta-A [Arabidopsis	0.948	0.639	0.530	0.0
16604671		987	putative AP3-complex beta-3A adaptin sub	0.948	0.639	0.527	0.0

>gi\|359486795\|ref\|XP_002278568.2\| PREDICTED: AP3-complex subunit beta-A-like [Vitis vinifera] gi\|296086225\|emb\|CBI31666.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  824 bits (2129), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 438/664 (65%), Positives = 514/664 (77%), Gaps = 3/664 (0%)

Query: 1    MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRS 60
            +AN C+EGLLAL R+E L  D    + E ++LIQ+I+SI++I+KQDP  HEKVI+QL RS
Sbjct: 476  VANICLEGLLALTREEYLIGDFVCMDEETNILIQAIMSIEAILKQDPPAHEKVIVQLVRS 535

Query: 61   LDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKV 120
            LDSIKVP AR +IIW++GEY+++G  IPRMLTTVL YLA CF SEA ETKLQILNT +KV
Sbjct: 536  LDSIKVPAARAIIIWIIGEYNTIGEIIPRMLTTVLTYLARCFASEAQETKLQILNTAVKV 595

Query: 121  LLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQEN 180
            LLCAKG D+WT   + SY+LELA+CDL+YDVRDRA   K+L S  L   + EET+ L + 
Sbjct: 596  LLCAKGKDLWTFKSVLSYVLELAKCDLSYDVRDRAHILKELMSCYLGQDLEEETDCLPQ- 654

Query: 181  KDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDLG 240
            KD+P +L ECIFR Q    + EPIN RFYLPGSLSQIVLHAAPGYEPLPKPCS LC+DL 
Sbjct: 655  KDIPQILAECIFRGQRKPMSPEPINFRFYLPGSLSQIVLHAAPGYEPLPKPCSLLCNDLH 714

Query: 241  QFSNSIDRTTALGEEWTGSSSNGTDDPDT-SGSLDEESGSNYDSQQSIPGLSDNSGTGDS 299
            Q  N +      GE  T S S  TDDPD  S S +EES S Y SQ SI   S +   G S
Sbjct: 715  QRLNVVQGIEGSGEGATNSDSYETDDPDMLSQSANEESTSGYSSQNSISRSSGSDEPG-S 773

Query: 300  ASEGDRNCDPLIQISDAGIACSNENGASHSGFPDLEGMMSKRALESWLDEQPGSSSPSAS 359
             SE D N DPLIQ SD GI+   + G S SG   +E +MSK+ LESWLDEQPG S P+ S
Sbjct: 774  ESEDDDNVDPLIQFSDVGISNKKQTGVSQSGSDSMEELMSKQTLESWLDEQPGLSDPNLS 833

Query: 360  EQIQVRQSSARISIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETF 419
            +Q QVR+SSARISIG+IG +VK K Y LLDP NGNGL+V YSFSSE S++SPQLVC+E  
Sbjct: 834  KQSQVRRSSARISIGDIGGRVKPKIYGLLDPTNGNGLRVNYSFSSEVSSMSPQLVCVELI 893

Query: 420  FENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQT 479
            FENCS+E+MS+V LVDEES+K LD  D +L  T SS+ SQ+D+P LV MEEI S+EPGQ+
Sbjct: 894  FENCSAESMSKVLLVDEESNKGLDSEDQSLVATESSMPSQNDVPNLVYMEEIASIEPGQS 953

Query: 480  MKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGMF 539
             K IL+V FHHHLLP+KLAL CNGKK PVKLRPDIGYFIKP+PMD+E F+  ES LPGMF
Sbjct: 954  TKCILQVCFHHHLLPVKLALWCNGKKYPVKLRPDIGYFIKPLPMDVEVFVNKESHLPGMF 1013

Query: 540  EYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFD 599
            EY R CTFTDH+ E++ D  +SSL KDK+LVIC+SLA KMLSNAN+FLVSVDMPVA+  D
Sbjct: 1014 EYERRCTFTDHIREMNSDKGDSSLTKDKFLVICKSLAVKMLSNANLFLVSVDMPVASNLD 1073

Query: 600  DASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLV 659
            DASGL LRFSSEIL NS+PCLITIT+EG CSEPL V+ KVNCEETVFGLNLLNRIVNFLV
Sbjct: 1074 DASGLRLRFSSEILSNSIPCLITITIEGNCSEPLNVTIKVNCEETVFGLNLLNRIVNFLV 1133

Query: 660  ESSL 663
            E S+
Sbjct: 1134 EPSI 1137

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224109508\|ref\|XP_002315219.1\| predicted protein [Populus trichocarpa] gi\|222864259\|gb\|EEF01390.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356501063\|ref\|XP_003519348.1\| PREDICTED: AP3-complex subunit beta-A-like [Glycine max]	Back alignment and taxonomy information

>gi\|255584875\|ref\|XP_002533153.1\| conserved hypothetical protein [Ricinus communis] gi\|223527048\|gb\|EEF29234.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|357492243\|ref\|XP_003616410.1\| AP-3 complex subunit beta-2 [Medicago truncatula] gi\|355517745\|gb\|AES99368.1\| AP-3 complex subunit beta-2 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356551707\|ref\|XP_003544215.1\| PREDICTED: AP3-complex subunit beta-A-like [Glycine max]	Back alignment and taxonomy information

>gi\|449459904\|ref\|XP_004147686.1\| PREDICTED: AP3-complex subunit beta-A-like [Cucumis sativus] gi\|449503249\|ref\|XP_004161908.1\| PREDICTED: AP3-complex subunit beta-A-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|240255649\|ref\|NP_974443.4\| AP3-complex subunit beta-A [Arabidopsis thaliana] gi\|332645870\|gb\|AEE79391.1\| AP3-complex subunit beta-A [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi|18410287|ref|NP_567022.1| AP3-complex subunit beta-A [Arabidopsis thaliana] gi|306531058|sp|Q9M2T1.2|AP3BA_ARATH RecName: Full=AP3-complex subunit beta-A; AltName: Full=Adapter-related protein complex 3 subunit beta-A; AltName: Full=Adaptor protein complex AP-3 subunit beta-A; AltName: Full=Beta-3B-adaptin; AltName: Full=Clathrin assembly protein complex 3 beta-A large chain gi|332645869|gb|AEE79390.1| AP3-complex subunit beta-A [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|16604671\|gb\|AAL24128.1\| putative AP3-complex beta-3A adaptin subunit [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		665
TAIR\|locus:2099961		1115	PAT2 "protein affected traf	0.574	0.342	0.489	2.5e-88
UNIPROTKB\|F1RI97		1082	F1RI97 "Uncharacterized protei	0.446	0.274	0.306	2.9e-25
UNIPROTKB\|J9P1J6		1102	AP3B2 "Uncharacterized protein	0.533	0.322	0.286	4.2e-23
UNIPROTKB\|Q32PG1		1084	AP3B1 "AP-3 complex subunit be	0.219	0.134	0.319	1.1e-19
UNIPROTKB\|B7ZKR7		1050	AP3B2 "AP3B2 protein" [Homo sa	0.476	0.301	0.286	2.2e-19
UNIPROTKB\|Q13367		1082	AP3B2 "AP-3 complex subunit be	0.476	0.292	0.286	2.4e-19
UNIPROTKB\|E1BME2		1085	AP3B2 "Uncharacterized protein	0.351	0.215	0.308	6.9e-19
UNIPROTKB\|F1P7W8		1084	AP3B2 "Uncharacterized protein	0.539	0.331	0.271	1.3e-18
RGD\|1308950		1082	Ap3b2 "adaptor-related protein	0.481	0.295	0.280	2.2e-18
UNIPROTKB\|B7ZKS0		1101	AP3B2 "AP-3 complex subunit be	0.547	0.330	0.261	5.7e-18

TAIR\|locus:2099961 PAT2 "protein affected trafﬁcking 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 882 (315.5 bits), Expect = 2.5e-88, P = 2.5e-88
 Identities = 194/396 (48%), Positives = 249/396 (62%)

Query:   268 DTSGSLDEESGSNYDSQQSIPGLSDNSGTGDSASEGD-RNCDPLIQISDAGIACSNENGA 326
             D  GS  EES    D   S    S++S   D +SEGD R          A +   +E   
Sbjct:   729 DLDGS--EESSETGDENGSSDYDSESSNGSDFSSEGDERTVSNDANDPAAPLIQISETSV 786

Query:   327 SHSGFPDLEGMMSKRALESWLDEQPGSSSPSASEQIQVRQSSARISIGNIGRQVKAKSYT 386
             S     D E + S+RAL+ WLD+QP +S+ + S     + S A+ISIG++G +VK KSY+
Sbjct:   787 S----ADQEELRSRRALDLWLDDQPSTSNQTPSALNSNQSSYAKISIGDVGSRVKPKSYS 842

Query:   387 LLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKXXXXXX 446
             L+DP NG+GLKV Y+F SE S +SP  VC+E  FEN S+E + EV L DEES K      
Sbjct:   843 LVDPGNGSGLKVDYAFLSEVSNVSPLHVCVEVLFENSSAEPILEVNLEDEESMKVADSSE 902

Query:   447 XXXXXXXXXXXXXXXXPTLVPMEEITSLEPGQTMKRILEVRFXXXXXXXXXXXXCNGKKL 506
                             PTL+PMEEI+ LEP Q+ KR+++VRF             N KK+
Sbjct:   903 QTLVGKANASYNNI--PTLIPMEEISCLEPHQSTKRLIQVRFHHHLLPMRLTLHYNEKKV 960

Query:   507 PVKLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKD 566
             PVKLRPD+GY +KP  M +E F+  ESRLPGMFEY+R CTF DH+   D  T+     KD
Sbjct:   961 PVKLRPDLGYLVKPFSMSIEEFLATESRLPGMFEYSRRCTFDDHVK--DSRTENG---KD 1015

Query:   567 KYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVPCLITITVE 626
             K+L ICES+  K+LSN+N+ LVSVD+PVA   +DA+GL LRFSS+IL + +P LITITVE
Sbjct:  1016 KFLSICESITLKVLSNSNLHLVSVDLPVANSLEDATGLRLRFSSKILSSEIPLLITITVE 1075

Query:   627 GKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLVESS 662
             GKC+E L ++ K+NCEETVFGLNLLNRI NF+VE S
Sbjct:  1076 GKCTEVLNLTVKINCEETVFGLNLLNRIANFMVEPS 1111

GO:0005634 "nucleus" evidence=ISM

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008565 "protein transporter activity" evidence=IEA

GO:0030117 "membrane coat" evidence=IEA

GO:0080171 "lytic vacuole organization" evidence=IMP

GO:0006896 "Golgi to vacuole transport" evidence=IMP

GO:0051453 "regulation of intracellular pH" evidence=IMP

UNIPROTKB\|F1RI97 F1RI97 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|J9P1J6 AP3B2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q32PG1 AP3B1 "AP-3 complex subunit beta-1" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|B7ZKR7 AP3B2 "AP3B2 protein" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q13367 AP3B2 "AP-3 complex subunit beta-2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BME2 AP3B2 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1P7W8 AP3B2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

RGD\|1308950 Ap3b2 "adaptor-related protein complex 3, beta 2 subunit" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|B7ZKS0 AP3B2 "AP-3 complex subunit beta-2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		665
pfam01602		522	pfam01602, Adaptin_N, Adaptin N terminal region	5e-19
COG5096		757	COG5096, COG5096, Vesicle coat complex, various su	1e-04

>gnl\|CDD\|216598 pfam01602, Adaptin_N, Adaptin N terminal region	Back alignment and domain information

 Score = 90.4 bits (225), Expect = 5e-19
 Identities = 43/165 (26%), Positives = 76/165 (46%), Gaps = 17/165 (10%)

Query: 1   MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRS 60
            A  C++ LL     ELL+        E       +  I+ II++ P   E ++  L   
Sbjct: 372 DAEWCIDVLL-----ELLSLAGSYVVDEI------VEVIRDIIRKYPELREYILEHLCEL 420

Query: 61  LDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKV 120
           L+ I+ PEAR   +W++GEY  +   IP   + +L+ +   F  E+++ +L +L   +K 
Sbjct: 421 LEDIESPEARAAALWILGEYGEL---IPNSPSDLLRSILEVFVLESLKVRLALLTALVK- 476

Query: 121 LLCAKGGDMWTITRLFSYLLELA-ECDLNYDVRDRARFFKKLFSH 164
            L     D      +   +L LA +   + ++RDRA  + +L S 
Sbjct: 477 -LSLTFPDEEVQNLIVQVVLSLATQDSSDLELRDRAVEYLRLLSL 520

This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles. Length = 522

>gnl\|CDD\|227427 COG5096, COG5096, Vesicle coat complex, various subunits [Intracellular trafficking and secretion]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		665
KOG1060		968	consensus Vesicle coat complex AP-3, beta subunit	100.0
PF14796		145	AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit	100.0
PTZ00429		746	beta-adaptin; Provisional	99.97
KOG1061		734	consensus Vesicle coat complex AP-1/AP-2/AP-4, bet	99.96
PF01602		526	Adaptin_N: Adaptin N terminal region; InterPro: IP	99.81
COG5096		757	Vesicle coat complex, various subunits [Intracellu	99.59
KOG1060		968	consensus Vesicle coat complex AP-3, beta subunit	98.44
KOG1062		866	consensus Vesicle coat complex AP-1, gamma subunit	97.22
PF14807		104	AP4E_app_platf: Adaptin AP4 complex epsilon append	95.41
smart00809		104	Alpha_adaptinC2 Adaptin C-terminal domain. Adaptin	94.98
KOG1058		948	consensus Vesicle coat complex COPI, beta subunit	93.04
PF12717		178	Cnd1: non-SMC mitotic condensation complex subunit	91.66
PF13646		88	HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2I	91.36
COG5240		898	SEC21 Vesicle coat complex COPI, gamma subunit [In	90.08
PF14764		459	SPG48: AP-5 complex subunit, vesicle trafficking	89.35
KOG1078		865	consensus Vesicle coat complex COPI, gamma subunit	88.86
PF14797		130	SEEEED: Serine-rich region of AP3B1, clathrin-adap	88.02
PF02883		115	Alpha_adaptinC2: Adaptin C-terminal domain; InterP	87.99
PF10633		78	NPCBM_assoc: NPCBM-associated, NEW3 domain of alph	86.1
KOG0413		1529	consensus Uncharacterized conserved protein relate	84.3
PRK09687		280	putative lyase; Provisional	82.88
PF02296		113	Alpha_adaptin_C: Alpha adaptin AP2, C-terminal dom	81.66

>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

Probab=100.00  E-value=1.2e-113  Score=953.94  Aligned_cols=521  Identities=30%  Similarity=0.423  Sum_probs=412.9

Q ss_pred             ChhHHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccc
Q 006008            1 MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEY   80 (665)
Q Consensus         1 va~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY   80 (665)
                      |+++|++||++||+           +.++.||+|+|+|||.|||++|.+|.+||.+|++++|+|.+|.|||+||||||||
T Consensus       426 v~~tCL~gLv~Lls-----------shde~Vv~eaV~vIk~Llq~~p~~h~~ii~~La~lldti~vp~ARA~IiWLige~  494 (968)
T KOG1060|consen  426 VTDTCLNGLVQLLS-----------SHDELVVAEAVVVIKRLLQKDPAEHLEILFQLARLLDTILVPAARAGIIWLIGEY  494 (968)
T ss_pred             hhhHHHHHHHHHHh-----------cccchhHHHHHHHHHHHHhhChHHHHHHHHHHHHHhhhhhhhhhhceeeeeehhh
Confidence            68999999999999           4678999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHH
Q 006008           81 SSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKK  160 (665)
Q Consensus        81 ~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~r  160 (665)
                      |   +.+|+|||||||+|||+|++|.++||||||+++||||++++.    ++++++|||++||+||+|||||||||||+.
T Consensus       495 ~---e~vpri~PDVLR~laksFs~E~~evKlQILnL~aKLyl~~~~----~~kll~~Yv~~L~~yD~sYDiRDRaRF~r~  567 (968)
T KOG1060|consen  495 C---EIVPRIAPDVLRKLAKSFSDEGDEVKLQILNLSAKLYLTNID----QTKLLVQYVFELARYDLSYDIRDRARFLRQ  567 (968)
T ss_pred             h---hhcchhchHHHHHHHHhhccccchhhHHHHHhhhhheEechh----hHHHHHHHHHHHhccCCCcchhHHHHHHHH
Confidence            9   479999999999999999999999999999999999999986    689999999999999999999999999999


Q ss_pred             hhcCCCCCCCCcccchhcccCcchHHHHHhhhccCCCCCC-CCCCcccccccccHHHHhhccCCCCccCCCCCCccCccc
Q 006008          161 LFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAA-SEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDL  239 (665)
Q Consensus       161 LLs~~~~~~~~~~~~~~s~~~~~~~~~a~~if~~k~p~~~-~~~~~~r~~~lGSLSh~l~~~~~GY~~LP~p~~~~~~~~  239 (665)
                      |+++..                ..++|++.+|.++||++. ++.|++++|++||+||+++++++||+|||+|+...++. 
T Consensus       568 l~~~~~----------------~Ls~h~~ei~l~~Kpa~~~es~f~~~~~~~gslS~lLn~~a~GY~~lp~~~~~~~d~-  630 (968)
T KOG1060|consen  568 LISPLE----------------ALSKHAREIFLASKPAPVLESSFKDRHYQLGSLSLLLNAPAPGYEPLPNWPAVAPDP-  630 (968)
T ss_pred             HhccHH----------------HHHHHHHHHhhccCCCccCcccccCCCcccchHHHHhcCcCcCCccCCCccccCCCC-
Confidence            999741                347899999999998888 66899899999999999999999999999999998861 


Q ss_pred             CccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc-ccccccccc
Q 006008          240 GQFSNSIDRTTALGEEWTGSSSNGTDDPDTSGSLDEESGSNYDSQQSIPGLSDNSGTGDSASEGDRNCDP-LIQISDAGI  318 (665)
Q Consensus       240 ~~~~~~~~~~~k~~~~~f~S~se~~d~~~~s~ss~~es~s~~~se~~~~~~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~  318 (665)
                          .+..    .+++.|++++|++++..+++.++++++++++++.+.++++     +..++++.++++. .-+.+.++.
T Consensus       631 ----~~~~----~~a~~~~~~~e~~e~~~~~~~s~~~ses~~~~~~~~e~ge-----~~dsn~~~~~~~d~sdqss~~~s  697 (968)
T KOG1060|consen  631 ----FPDS----ERAKLLDSDSEEEETGDDESWSDPESESGESSNFSREGGE-----ENDSNEEKDSEDDFSDQSSYEES  697 (968)
T ss_pred             ----Ccch----hhcccccCCccccccccccCCCCCccccccCCcccccccc-----cccccccccccccccccchhccc
Confidence                1111    2355688888877554444434444333322222211111     0111111111000 000000100


Q ss_pred             ccCCCCCCCCCCCCCcccc--------cchhcccccccCCCCCCC-C------Cchhhh-----hhhcccceeeecccCc
Q 006008          319 ACSNENGASHSGFPDLEGM--------MSKRALESWLDEQPGSSS-P------SASEQI-----QVRQSSARISIGNIGR  378 (665)
Q Consensus       319 ~~~~~~~~~~s~s~~~~e~--------~s~~~l~~~LD~~p~~~~-~------~~s~~~-----~~~~s~~~~s~~~~~~  378 (665)
                      +.++    ..++|+++.+.        .+.++..+.+++..+.+. |      .+.++.     ++..+..+..+.. |.
T Consensus       698 s~~d----~~s~se~e~e~~~e~~k~~pet~~~sl~l~d~~~~n~~P~~~~~~~~~l~~d~~~~~~~~s~~~~~~~~-p~  772 (968)
T KOG1060|consen  698 SAED----SESSSEAESEPTPEKLKEKPETKDVSLDLNDFTPQNGKPVLPERNDPDLAADDEFFSLTGSRNSKPLKI-PT  772 (968)
T ss_pred             cccc----cccccccccccCCCccCCCcccccccccccccCCCCCCCCCCCCCChhhhccccccccccccccccccC-Cc
Confidence            0000    01111111111        011122246666544332 1      122221     3334444455554 55


Q ss_pred             cccCceeecccccCCCCeeEEEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhccccccc
Q 006008          379 QVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTS  458 (665)
Q Consensus       379 ~v~~k~~eLL~~~~G~GL~v~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~  458 (665)
                      .++.|++||||++.|+||.++|+|+|+|    +  |+|+++|+|.++.++.+||+      |+|.||+            
T Consensus       773 ~i~~~~~ell~~~~g~gl~~~y~f~r~~----~--~~i~~~~~n~~~~~~~~~~l------~~p~gm~------------  828 (968)
T KOG1060|consen  773 HIEEKSIELLNEVEGSGLDLEYSFSRLP----D--VSISLHFTNKSDLELLGIHL------KLPAGMS------------  828 (968)
T ss_pred             cCcchhHhhhhhcccCCcceeeeccCCC----C--eeEEEecccCCCccccccee------ecccccc------------
Confidence            6899999999999999999999999999    2  99999999999999999999      6799995            


Q ss_pred             CCCCCCcccCCCccccCCCCeeEEEEEEecCCCCccceEEEEEcCceeeeEEecCcccccccccCCHHHHHHHhccCCCC
Q 006008          459 QSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGM  538 (665)
Q Consensus       459 ~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~dstq~~~f~l~~~~~~f~V~i~PpvGElv~Pv~mse~~F~~eq~kL~GM  538 (665)
                            |++|.+|++|+||+++++.|||||||+||++.|+||+.+|  +|+++|||||+++||.|++++|+||||+|+||
T Consensus       829 ------i~ef~~i~s~~pg~~~~~~~~i~F~dst~~~~~~l~~~~g--~~~~~~pvge~~~~v~~~~~~~~~E~~~L~gl  900 (968)
T KOG1060|consen  829 ------IKEFSPIESLPPGASASVVLGIDFCDSTQAAEWQLLTDDG--RVRFQPPVGELVQPVRMSEEDFKKERGKLGGL  900 (968)
T ss_pred             ------ccccccccccCCCcceeeeeeeeccccccceeEEEEeccC--cEEecCchhhhhccccCCHHHHHhhhhhhccc
Confidence                  9999999999999999999999999999999999999999  99999999999999999999999999999999


Q ss_pred             cccceeeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCccccccCCCCCceeeeeeccccCCce
Q 006008          539 FEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVP  618 (665)
Q Consensus       539 nE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~~~~~d~~~~~~rFa~~tlss~s~  618 (665)
                      |||  .|.+..                             ++..||++.|+++            ..+||||||+|+++|
T Consensus       901 n~~--~~~l~~-----------------------------~~~~an~~~~~~g------------~~~rFa~~tlss~~~  937 (968)
T KOG1060|consen  901 NEH--VIQLEN-----------------------------PNPSANVLFVPSG------------SSHRFAGQTLSSKSL  937 (968)
T ss_pred             chh--heeeec-----------------------------ccchhhhhcccCC------------cceeeeeeeccCCce
Confidence            999  444431                             0568999999874            349999999999999


Q ss_pred             EEEEEEeccccCCCcceEEEEcccchHHHHHHHHHHHHhh
Q 006008          619 CLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFL  658 (665)
Q Consensus       619 ~LiTi~~~~~~~~~~~~~l~vNcEk~ViGs~Ll~~~~~~l  658 (665)
                      |||||++  +       ||+|||||||||+||||+|.++|
T Consensus       938 ~llT~~~--k-------~l~ince~~ViG~~ll~~~~~~~  968 (968)
T KOG1060|consen  938 VLLTVDE--K-------TLEINCEKTVIGSMLLNEVSNAL  968 (968)
T ss_pred             EEEEeeh--h-------eeEecchhhhHHHHHHHHHHhhC
Confidence            9999998  3       69999999999999999999986

>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal	Back alignment and domain information

>PTZ00429 beta-adaptin; Provisional	Back alignment and domain information

>KOG1061 consensus Vesicle coat complex AP-1/AP-2/AP-4, beta subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]	Back alignment and domain information

>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG1062 consensus Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform	Back alignment and domain information

>smart00809 Alpha_adaptinC2 Adaptin C-terminal domain	Back alignment and domain information

>KOG1058 consensus Vesicle coat complex COPI, beta subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1	Back alignment and domain information

>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A	Back alignment and domain information

>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]	Back alignment and domain information

>PF14764 SPG48: AP-5 complex subunit, vesicle trafficking	Back alignment and domain information

>KOG1078 consensus Vesicle coat complex COPI, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF14797 SEEEED: Serine-rich region of AP3B1, clathrin-adaptor complex	Back alignment and domain information

>PF02883 Alpha_adaptinC2: Adaptin C-terminal domain; InterPro: IPR008152 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known	Back alignment and domain information

>KOG0413 consensus Uncharacterized conserved protein related to condensin complex subunit 1 [Function unknown]	Back alignment and domain information

>PRK09687 putative lyase; Provisional	Back alignment and domain information

>PF02296 Alpha_adaptin_C: Alpha adaptin AP2, C-terminal domain; InterPro: IPR003164 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		665
1w63_B		584	Ap1 Clathrin Adaptor Core Length = 584		8e-07
2xa7_B		592	Ap2 Clathrin Adaptor Core In Active Complex With Ca		4e-06
2vgl_B		591	Ap2 Clathrin Adaptor Core Length = 591		4e-06

>pdb|1W63|B Chain B, Ap1 Clathrin Adaptor Core Length = 584

Back alignment and structure

Iteration: 1

Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust. Identities = 37/117 (31%), Positives = 58/117 (49%), Gaps = 7/117 (5%) Query: 47 PSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEA 106 P+ +E VI L +LDS PEAR +IW+VGEY+ +L + L F E+ Sbjct: 422 PNKYESVIATLCENLDSDDEPEARAAMIWIVGEYAERSDNADELLESFLD----GFHDES 477 Query: 107 VETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFS 163 + +LQ+L +K+ L + ++ S L + D N D+RDR + +L S Sbjct: 478 TQVQLQLLTAIVKLFLKKPTETQELVQQVLS--LATQDSD-NPDLRDRGYIYWRLLS 531

PyMOL of 1w63

>pdb|2XA7|B Chain B, Ap2 Clathrin Adaptor Core In Active Complex With Cargo Peptides Length = 592

Back alignment and structure

>pdb|2VGL|B Chain B, Ap2 Clathrin Adaptor Core Length = 591

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		665
2vgl_B		591	AP-2 complex subunit beta-1; cytoplasmic vesicle,	7e-22
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-07
2vgl_A		621	Adaptor protein complex AP-2, alpha 2 subunit; cyt	1e-09
1w63_A		618	Adapter-related protein complex 1 gamma 1 subunit;	8e-07

>2vgl_B AP-2 complex subunit beta-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Homo sapiens} SCOP: i.23.1.1 PDB: 2jkt_B 2jkr_B* 2xa7_B 1w63_B Length = 591	Back alignment and structure

 Score = 99.1 bits (247), Expect = 7e-22
 Identities = 46/165 (27%), Positives = 76/165 (46%), Gaps = 20/165 (12%)

Query: 2   ANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSL 61
           A  CV  LL LI+                V+ ++I+ I+ I ++ P+ +E +I  L  +L
Sbjct: 388 AERCVSTLLDLIQ-----------TKVNYVVQEAIVVIRDIFRKYPNKYESIIATLCENL 436

Query: 62  DSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVL 121
           DS+  P+AR  +IW+VGEY+            +L+     F  E+ + +L +L   +K+ 
Sbjct: 437 DSLDEPDARAAMIWIVGEYAERIDNADE----LLESFLEGFHDESTQVQLTLLTAIVKLF 492

Query: 122 LCAKGGDMWTITRLFSYLLELAECD-LNYDVRDRARFFKKLFSHN 165
           L            L   +L LA  D  N D+RDR   + +L S +
Sbjct: 493 LKKPS----ETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTD 533

PyMOL of 2vgl

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>2vgl_A Adaptor protein complex AP-2, alpha 2 subunit; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Rattus norvegicus} PDB: 2xa7_A 2jkr_A 2jkt_A Length = 621	Back alignment and structure

>1w63_A Adapter-related protein complex 1 gamma 1 subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1 Length = 618	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		665
2vgl_B		591	AP-2 complex subunit beta-1; cytoplasmic vesicle,	99.9
2g30_A		258	AP-2 complex subunit beta-1; alpha-helical ARH pep	99.89
2vgl_A		621	Adaptor protein complex AP-2, alpha 2 subunit; cyt	99.82
1w63_A		618	Adapter-related protein complex 1 gamma 1 subunit;	99.78
3hs8_A		273	Adaptor protein complex AP-2, alpha 2 subunit; ada	97.8
1kyf_A		247	Alpha-adaptin C; protein-peptide complex, endocyto	97.51
1r4x_A		275	Gamma1-COP, coatomer gamma subunit; appendage, bet	95.15
1pzd_A		322	Coatomer gamma subunit; platform domain, appendage	94.63
3mnm_A		123	ADP-ribosylation factor-binding protein GGA2; IG-l	93.15
1p4u_A		153	ADP-ribosylation factor binding protein GGA3; prot	92.68
3zy7_A		122	AP-1 complex subunit gamma-1; endocytosis, protein	91.68
1iu1_A		146	Gamma1-adaptin; coated PITS, endocytosis; 1.80A {H	91.53
1gyu_A		140	Adapter-related protein complex 1 gamma 1 subunit;	91.38
2e9g_A		131	AP-1 complex subunit gamma-2; beta-sandwich, immun	91.05
2vgl_B		591	AP-2 complex subunit beta-1; cytoplasmic vesicle,	90.09
4fdd_A		852	Transportin-1; heat repeats, karyopherin, nuclear	89.05
1b3u_A		588	Protein (protein phosphatase PP2A); scaffold prote	88.8
2qk2_A		242	LP04448P; mini spindles, MSPS, XMAP215, DIS1, STU2	84.53
4db6_A		210	Armadillo repeat protein; solenoid repeat, armadil	83.94
4fdd_A		852	Transportin-1; heat repeats, karyopherin, nuclear	83.9

>2vgl_B AP-2 complex subunit beta-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Homo sapiens} SCOP: i.23.1.1 PDB: 2jkt_B 2jkr_B* 2xa7_B 1w63_B	Back alignment and structure

Probab=99.90  E-value=1.9e-24  Score=239.59  Aligned_cols=182  Identities=28%  Similarity=0.477  Sum_probs=151.1

Q ss_pred             hhHHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeecccc
Q 006008            2 ANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYS   81 (665)
Q Consensus         2 a~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~   81 (665)
                      +..|++.|+++++.           ...+|+.|++.+|++|+|++|+.+..+|.+|++.++.+..|.+|++++|++|||+
T Consensus       388 ~~~~v~~Ll~ll~~-----------~~~~v~~e~i~~l~~ii~~~p~~~~~~v~~L~~~l~~~~~~~~~~~~~wilGey~  456 (591)
T 2vgl_B          388 AERCVSTLLDLIQT-----------KVNYVVQEAIVVIRDIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYA  456 (591)
T ss_dssp             HHHHHHHHHHHHHT-----------CCHHHHHHHHHHHHHHHHHSCSSCCTTHHHHHHTTTTCCSHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHcc-----------cchHHHHHHHHHHHHHHHHCcchHHHHHHHHHHHHHhccCHHHHHHHHHHHHccc
Confidence            47899999999983           4568899999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccC-CCccchhhHHHHHH
Q 006008           82 SVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECD-LNYDVRDRARFFKK  160 (665)
Q Consensus        82 ~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD-~nyDVRDRARfy~r  160 (665)
                      .   .+++ ++++||.++++|.+|+..||+++|++++|+|.+.|..    ...+++++|+.+++| .|+||||||++||+
T Consensus       457 ~---~~~~-~~~~l~~l~~~~~~~~~~vr~~~l~a~~Kl~~~~p~~----~~~~i~~ll~~~~~d~~d~evrdRA~~y~~  528 (591)
T 2vgl_B          457 E---RIDN-ADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSE----TQELVQQVLSLATQDSDNPDLRDRGYIYWR  528 (591)
T ss_dssp             T---TCTT-HHHHHHHHSTTCSSSCHHHHHHHHHHHHHHHTTCCST----THHHHHHHHHHHHTTCCCHHHHHHHHHHHT
T ss_pred             c---cccC-HHHHHHHHHHhhccCCHHHHHHHHHHHHHHHhcCchH----HHHHHHHHHHHhhhcCCChHHHHHHHHHHH
Confidence            5   4555 7899999999999999999999999999999998863    357889999999888 59999999999999


Q ss_pred             hhcCCCCCCCCcccchhcccCcchHHHHH-hhhccCCCCCCCCCC-cc----c-ccccccHHHHhhcc
Q 006008          161 LFSHNLCSQVPEETNALQENKDLPLVLVE-CIFRKQENLAASEPI-ND----R-FYLPGSLSQIVLHA  221 (665)
Q Consensus       161 LLs~~~~~~~~~~~~~~s~~~~~~~~~a~-~if~~k~p~~~~~~~-~~----r-~~~lGSLSh~l~~~  221 (665)
                      ||..+.                   ..++ .++.++||++..++. ..    . ...+||||++++.+
T Consensus       529 ll~~~~-------------------~~~~~~v~~~~p~~~~~~~~~~~~~~~~~~~~~~tl~~~~~~~  577 (591)
T 2vgl_B          529 LLSTDP-------------------VTAKEVVLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKP  577 (591)
T ss_dssp             TTTTCT-------------------THHHHHHTSCCCCCCSCSSCCCHHHHHHHHTTTTSSHHHHTSC
T ss_pred             HHCcCH-------------------HHHHHHHcCCCCCCCCCccccCHHHHHHHHHHhCcchhhhcCC
Confidence            997531                   1234 444555544443322 22    1 34689999999854

PyMOL of 2vgl

>2g30_A AP-2 complex subunit beta-1; alpha-helical ARH peptide, platform domain, sandwich domain, endocytosis, adaptor, endocytosis/exocytosis complex; 1.60A {Homo sapiens} SCOP: b.1.10.1 d.105.1.1 PDB: 1e42_A 3h1z_A 3hs9_A 2iv9_A 2iv8_A	Back alignment and structure

>2vgl_A Adaptor protein complex AP-2, alpha 2 subunit; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Rattus norvegicus} PDB: 2xa7_A 2jkr_A 2jkt_A	Back alignment and structure

>1w63_A Adapter-related protein complex 1 gamma 1 subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1	Back alignment and structure

>3hs8_A Adaptor protein complex AP-2, alpha 2 subunit; adaptor complex AP-2, endocytosis, cell membrane, coated PIT binding, membrane, disease mutation; 1.90A {Mus musculus}	Back alignment and structure

>1kyf_A Alpha-adaptin C; protein-peptide complex, endocytosis, endocytosis/exocytosis complex; 1.22A {Mus musculus} SCOP: b.1.10.1 d.105.1.1 PDB: 1ky7_A 1kyd_A 1ky6_A 1kyu_A 1qtp_A 1qts_A 2vj0_A 1w80_A 1b9k_A	Back alignment and structure

>1r4x_A Gamma1-COP, coatomer gamma subunit; appendage, beta sandwich, ADP-ribosylation factors, protein transport; 1.90A {Homo sapiens} SCOP: b.1.10.3 d.105.1.2	Back alignment and structure

>1pzd_A Coatomer gamma subunit; platform domain, appendage domain, EAR domain, endocytosis/exocytosis complex; 2.31A {Bos taurus} SCOP: b.1.10.3 d.105.1.2	Back alignment and structure

>3mnm_A ADP-ribosylation factor-binding protein GGA2; IG-like, beta sandwich, protein transport; HET: MLY; 1.73A {Saccharomyces cerevisiae}	Back alignment and structure

>1p4u_A ADP-ribosylation factor binding protein GGA3; protein transport; 2.20A {Homo sapiens} SCOP: b.1.10.2 PDB: 1om9_A 1na8_A 2dwy_A 2dwx_A	Back alignment and structure

>3zy7_A AP-1 complex subunit gamma-1; endocytosis, protein design, computational design; 1.09A {Mus musculus} PDB: 2a7b_A 1gyv_A 1gyw_A	Back alignment and structure

>1iu1_A Gamma1-adaptin; coated PITS, endocytosis; 1.80A {Homo sapiens} SCOP: b.1.10.2	Back alignment and structure

>1gyu_A Adapter-related protein complex 1 gamma 1 subunit; clathrin, golgi, adaptin, endocytosis, adaptor; 1.81A {Mus musculus} SCOP: b.1.10.2	Back alignment and structure

>2e9g_A AP-1 complex subunit gamma-2; beta-sandwich, immunoglobulin-like fold, adaptin, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2vgl_B AP-2 complex subunit beta-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Homo sapiens} SCOP: i.23.1.1 PDB: 2jkt_B 2jkr_B* 2xa7_B 1w63_B	Back alignment and structure

>4fdd_A Transportin-1; heat repeats, karyopherin, nuclear import, protein transport importin, transportin, transport protein; 2.30A {Homo sapiens} PDB: 2ot8_A 2h4m_A 2z5k_A 2z5j_A 2qmr_A 2z5m_A 2z5n_A 2z5o_A 1qbk_B*	Back alignment and structure

>1b3u_A Protein (protein phosphatase PP2A); scaffold protein, phosphorylation, heat repeat; 2.30A {Homo sapiens} SCOP: a.118.1.2 PDB: 2ie4_A* 2ie3_A* 2npp_A* 3k7v_A* 3k7w_A* 3fga_A* 2pf4_A 2iae_A 2nym_A* 2nyl_A* 3dw8_A* 2pkg_A 3c5w_A	Back alignment and structure

>2qk2_A LP04448P; mini spindles, MSPS, XMAP215, DIS1, STU2, heat repeat, micro plus END, +TIP, protein binding; 2.10A {Drosophila melanogaster}	Back alignment and structure

>4db6_A Armadillo repeat protein; solenoid repeat, armadillo repeat motif, de novo protein; 1.80A {Synthetic construct} PDB: 4db9_A 4dba_A	Back alignment and structure

>4fdd_A Transportin-1; heat repeats, karyopherin, nuclear import, protein transport importin, transportin, transport protein; 2.30A {Homo sapiens} PDB: 2ot8_A 2h4m_A 2z5k_A 2z5j_A 2qmr_A 2z5m_A 2z5n_A 2z5o_A 1qbk_B*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		665
d2vglb_		579	a.118.1.10 (B:) Adaptin beta subunit N-terminal fr	9e-14
d2vgla_		584	a.118.1.10 (A:) Adaptin alpha C subunit N-terminal	4e-07

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		665
d2vglb_		579	Adaptin beta subunit N-terminal fragment {Human (H	99.94
d2vgla_		584	Adaptin alpha C subunit N-terminal fragment {Mouse	97.28
d1e42a1		120	Beta2-adaptin AP2 ear domain, N-terminal subdomain	97.17
d2dwya1		129	ADP-ribosylation factor binding protein Gga1 domai	95.19
d1p4ua_		145	ADP-ribosylation factor binding protein Gga3 domai	94.82
d1gyva_		120	Gamma1-adaptin domain {Human (Homo sapiens) [TaxId	90.56
d1kyfa2		114	Alpa-adaptin AP2, C-terminal subdomain {Mouse (Mus	86.09
d1oyza_		276	Hypothetical protein YibA {Escherichia coli [TaxId	81.58
d1w8oa1		103	Sialidase, "linker" domain {Micromonospora viridif	80.71

>d1e42a1 b.1.10.1 (A:705-824) Beta2-adaptin AP2 ear domain, N-terminal subdomain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All beta proteins
fold: Immunoglobulin-like beta-sandwich
superfamily: Clathrin adaptor appendage domain
family: Alpha-adaptin ear subdomain-like
domain: Beta2-adaptin AP2 ear domain, N-terminal subdomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.17  E-value=0.0014  Score=58.04  Aligned_cols=108  Identities=19%  Similarity=0.198  Sum_probs=79.1

Q ss_pred             ccccCceeecccccCCCCeeEEEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEee-ccccccchhhhhhhhhhccccc
Q 006008          378 RQVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLV-DEESHKALDLADLTLATTASSL  456 (665)
Q Consensus       378 ~~v~~k~~eLL~~~~G~GL~v~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~-~~~~~~~~~g~~~~l~~~~~~~  456 (665)
                      ++++||. .+|.-..|+||.|.=.|.|+     ...+..+|+|+|++..+|.+.-|- .|++-    |+.          
T Consensus         2 ~~~~p~~-~~lp~~~g~GLeI~g~f~r~-----~g~i~l~l~itN~s~~~ls~faIQfNKNsF----GL~----------   61 (120)
T d1e42a1           2 GYVAPKA-VWLPAVKAKGLEISGTFTHR-----QGHIYMEMNFTNKALQHMTDFAIQFNKNSF----GVI----------   61 (120)
T ss_dssp             CCCCCCE-EEECGGGTTTEEEEEEEEEE-----TTEEEEEEEEEECSSSCBCCCEEEECCBTT----CCE----------
T ss_pred             CccCcee-EEeecccCCcEEEEEEEEEe-----CCEEEEEEEEecCCCCccchheEEEccccc----ccc----------
Confidence            4567764 88888999999999999996     457889999999999999998775 34332    221          


Q ss_pred             ccCCCCCCcccCCCc-cccCCCCeeEEEEEEecCCCCc------cceEEEEEcCceeeeEEecC
Q 006008          457 TSQSDLPTLVPMEEI-TSLEPGQTMKRILEVRFHHHLL------PLKLALHCNGKKLPVKLRPD  513 (665)
Q Consensus       457 ~~~~~~~~i~~f~eI-~sL~Pg~s~t~~lgIdF~dstq------~~~f~l~~~~~~f~V~i~Pp  513 (665)
                              ...+... ..|.||+|+.+.+=|.|....+      .+.+.|.++-+-|+....-|
T Consensus        62 --------P~~~l~~p~~l~pgqS~~~~lpl~~~~~~~~~~p~~~LQVAIKnn~dvfYF~~~ip  117 (120)
T d1e42a1          62 --------PSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIP  117 (120)
T ss_dssp             --------ESSCCCCCSCBCTTCEEEEEEEEESCSCBCCCSSTTEEEEEEECSSCEEEEEEECC
T ss_pred             --------cCCcccCCCccCCCCEEEEEEEEecCCcccCCCCCCeeEEEEEcCCceEEEeeeec
Confidence                    1112223 2599999999999999976544      35566677877777766544

PyMOL of d1e42a1

>d2dwya1 b.1.10.2 (A:511-639) ADP-ribosylation factor binding protein Gga1 domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1p4ua_ b.1.10.2 (A:) ADP-ribosylation factor binding protein Gga3 domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1gyva_ b.1.10.2 (A:) Gamma1-adaptin domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1kyfa2 d.105.1.1 (A:825-938) Alpa-adaptin AP2, C-terminal subdomain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Subdomain of clathrin and coatomer appendage domain
superfamily: Subdomain of clathrin and coatomer appendage domain
family: Clathrin adaptor appendage, alpha and beta chain-specific domain
domain: Alpa-adaptin AP2, C-terminal subdomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.09  E-value=3.3  Score=35.14  Aligned_cols=107  Identities=13%  Similarity=0.222  Sum_probs=67.3

Q ss_pred             ccccccCCHHHHHHHhccCCCC-cccceeeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCccc
Q 006008          517 FIKPVPMDMETFIEMESRLPGM-FEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVA  595 (665)
Q Consensus       517 lv~Pv~mse~~F~~eq~kL~GM-nE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~  595 (665)
                      |+.|+.|+-++|.+.=..|.|= .|.  +.+|... .+.           +      ....+++++--++++++      
T Consensus         1 F~~p~~l~~~dFf~rW~qig~~~~E~--q~if~~~-~~~-----------~------~~~~~~~l~~~g~~v~~------   54 (114)
T d1kyfa2           1 FFQPTEMASQDFFQRWKQLSNPQQEV--QNIFKAK-HPM-----------D------TEITKAKIIGFGSALLE------   54 (114)
T ss_dssp             GEEECCCCHHHHHHHHTTCCSGGGEE--EEEEECS-SCC-----------C------HHHHHHHHHHHTSEEEC------
T ss_pred             CCCCccCCHHHHHHHHHHhCCCccee--eeeecCC-CCC-----------C------HHHHHHHHhhCCeEecC------
Confidence            6789999999999999999874 466  5555431 111           1      23445677777888775      


Q ss_pred             cccCCCCCceeeeeecccc---CCceEEEEEEeccccCCCcceEEEEcccchHHHHHHHHHHH
Q 006008          596 AKFDDASGLSLRFSSEILG---NSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIV  655 (665)
Q Consensus       596 ~~~~d~~~~~~rFa~~tls---s~s~~LiTi~~~~~~~~~~~~~l~vNcEk~ViGs~Ll~~~~  655 (665)
                       +.|+-..+  =++|-+++   ....||+.|+-... +.  ...|||-|-+-.+--.|++-|+
T Consensus        55 -~~Dpnp~n--lv~agi~~t~~~~~gcL~Rle~n~~-~~--~~rlTvRst~~~vs~~l~~~l~  111 (114)
T d1kyfa2          55 -EVDPNPAN--FVGAGIIHTKTTQIGCLLRLEPNLQ-AQ--MYRLTLRTSKDTVSQRLCELLS  111 (114)
T ss_dssp             -SSSSSTTS--EEEEEEEECSSCEEEEEEEEEEETT-TT--EEEEEEEESSHHHHHHHHHHHH
T ss_pred             -CCCCChhh--EEEEEEEEcCCceEeEEEEEEECCC-Cc--EEEEEEEeCCccHHHHHHHHHH
Confidence             23332222  24555554   34789999985221 21  3689999999777555555443

PyMOL of d1kyfa2

>d1oyza_ a.118.1.16 (A:) Hypothetical protein YibA {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: PBS lyase HEAT-like repeat
domain: Hypothetical protein YibA
species: Escherichia coli [TaxId: 562]

Probab=81.58  E-value=1.1  Score=40.07  Aligned_cols=124  Identities=9%  Similarity=0.037  Sum_probs=75.8

Q ss_pred             HHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccccCCCCC
Q 006008            7 EGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVK   86 (665)
Q Consensus         7 ~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~e~   86 (665)
                      +.|+.+|.           +.++.|-..|+.++..   ...   ..++..|.+.+.. .++.-|...+|.+|+.......
T Consensus        22 ~~L~~~L~-----------d~~~~vR~~A~~~L~~---~~~---~~~~~~l~~~l~d-~~~~vr~~a~~aL~~l~~~~~~   83 (276)
T d1oyza_          22 DELFRLLD-----------DHNSLKRISSARVLQL---RGG---QDAVRLAIEFCSD-KNYIRRDIGAFILGQIKICKKC   83 (276)
T ss_dssp             HHHHHHTT-----------CSSHHHHHHHHHHHHH---HCC---HHHHHHHHHHHTC-SSHHHHHHHHHHHHHSCCCTTT
T ss_pred             HHHHHHhc-----------CCCHHHHHHHHHHHHh---hCC---HhHHHHHHHHHcC-CCHHHHHHHHHHHHHhcccccc
Confidence            45788887           4555555555555443   333   4567777776653 4677888889988887532222


Q ss_pred             cccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHH
Q 006008           87 IPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRAR  156 (665)
Q Consensus        87 ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRAR  156 (665)
                      .+.+.+.+++.+   -.++...|+.+.+.+..++.-..+.    ....++.++... -+|.++++|-.|-
T Consensus        84 ~~~~~~~l~~~~---l~d~~~~vr~~a~~aL~~~~~~~~~----~~~~~~~~l~~~-~~d~~~~vr~~a~  145 (276)
T d1oyza_          84 EDNVFNILNNMA---LNDKSACVRATAIESTAQRCKKNPI----YSPKIVEQSQIT-AFDKSTNVRRATA  145 (276)
T ss_dssp             HHHHHHHHHHHH---HHCSCHHHHHHHHHHHHHHHHHCGG----GHHHHHHHHHHH-TTCSCHHHHHHHH
T ss_pred             ccchHHHHHHHH---hcCCChhHHHHHHHHHHHHccccch----hhHHHHHHHHHH-hcCcchHHHHHHH
Confidence            222333333333   3478899999999999887654432    234566665554 4566788875543

PyMOL of d1oyza_

>d1w8oa1 b.1.18.2 (A:403-505) Sialidase, "linker" domain {Micromonospora viridifaciens [TaxId: 1881]}	Back information, alignment and structure