Citrus Sinensis ID: 042402

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---

MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEIDKSKIEKNRGDKGGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRPPSSANAPPKGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV

ccEEEEEEEcccccEEEEEccccccHHHHHHHHHHHcccccccccccEEEEccEEEEEEEcccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHcccccHHHHHccccEEEEEHHHHHHcccccEEcHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccEEEEEEEEEEEEEcccEEEEEEEEEEEEEEEcccccEEEEEEEccccccccccccccccccccccccEEEEcccccccccccEEEEcccccccccEEEEEEEcccccEEEEEEEEEEcccccEEEEEEEEEccccccccEEEcccccEEEEccccEEEEEEEEEccccccEEEEEEEccccccccccEEEEEEEccEEccEEEEEEEEccccccccEEEEEEEEEEcEEEc

cEEEEEEEEcccccEEEEHHHHHccHHHHHHHHHHcHHHccccccEEEEEcccEEEEEccHHHEEEEEEEccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccEEEEEEEEEEEEEEcccccEEEEEEEEEEEEEEcccccEEEEEEEccccccEEEEccccccHHHHccccEEEEccccccccccccEEEEccccccccEEEEEEcccccccEEEEEEEEEccccccccEEEEEEcccccccccEccccEEEEEcccccEEEEEEEEEcccccccEEEEEEccccccccccEEEEEEEcccEEEEEEEEEEEcccccccccEEEEEEEEcEEEEc

MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFpklvgtgkqhtyvetenvRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKlvpeysysldeegICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEidkskieknrgdkggfmslqsmgsgriessfsdmsissggggfgsgsgfglattdvetfsskskgrppssanappkglgmqlgksqrTNQFLESLKAEGEViledvkpiagqsraaaaappltdpitlTVEEKINVSLkrdggmsnfdvqGTLSLQILNQEDGLIQVQietggnpgilfkthpnmnkelfthenilglkdpnrpfpqAKLWRmqsadesmvpltincwpsvsgnetYVSIEYEASTMFDLRNvvisvplpalreapsvrqidgewrydsrnsVLEWTILLIdnsnrsgsmefvvppadsssffpisvrfsatstysdlkvvniiplrggappkfsqrtvLITENYQVV

MVVLAASivsksgkilvsrqfvDMSRIRIEGLLAafpklvgtgkqhtyvetENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQskinetkdvmkrkaseidkskieknrgdkggfmSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVEtfsskskgrppssanappkGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRaaaaappltdpitlTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVplpalreapsvrqidgewrydsrnsvLEWTILLIDNSNRSGSMEFVVPPADSSSFFPISVRFSAtstysdlkvvniiplrggappkfsqrtvlitenyqvv

MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEIDKSKIEKNRGDKGGFMSLQSMGSGRIEssfsdmsissggggfgsgsgfgLATTDVETFSSKSKGRPPSSANAPPKGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRaaaaappLTDPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV

***LAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEME********LV**********************************************************************************************************************VILE*******************DPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDP**PFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSN****MEFVVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLIT******

MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVG**K*HTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESH******************************************************************************************************************************************************PITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV

MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEIDKSKIEKNRGDKGGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVE******************KGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV

MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEIDKSKIE******************************************************************************************************************LTDPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV

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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		523	2.2.26 [Sep-21-2011]
Q93Y22		527	Coatomer subunit delta OS	yes	no	0.988	0.981	0.752	0.0
Q0DJ99		523	Coatomer subunit delta-2	yes	no	0.988	0.988	0.725	0.0
Q0DJA0		524	Coatomer subunit delta-1	yes	no	0.988	0.986	0.726	0.0
P49661		518	Coatomer subunit delta-3	no	no	0.973	0.982	0.706	0.0
Q66H80		511	Coatomer subunit delta OS	yes	no	0.954	0.976	0.422	1e-124
Q5XJY5		511	Coatomer subunit delta OS	yes	no	0.954	0.976	0.420	1e-123
Q5RA77		511	Coatomer subunit delta OS	yes	no	0.954	0.976	0.418	1e-122
P48444		511	Coatomer subunit delta OS	yes	no	0.954	0.976	0.418	1e-122
P53619		511	Coatomer subunit delta OS	yes	no	0.954	0.976	0.413	1e-122
Q5ZL57		510	Coatomer subunit delta OS	yes	no	0.952	0.976	0.422	1e-122

>sp\|Q93Y22\|COPD_ARATH Coatomer subunit delta OS=Arabidopsis thaliana GN=At5g05010 PE=1 SV=2	Back alignment and function desciption

 Score =  786 bits (2031), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 401/533 (75%), Positives = 455/533 (85%), Gaps = 16/533 (3%)

Query: 1   MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQP 60
           MVVLAA+IV KSGK++VSR +VDMSRIRIEGLLAAFPKLVG GKQHTY+ETENVRYVYQP
Sbjct: 1   MVVLAAAIVVKSGKVIVSRHYVDMSRIRIEGLLAAFPKLVGMGKQHTYIETENVRYVYQP 60

Query: 61  IEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLG 120
           IEAL+LLLVT KQSNILEDL TL LLSKLVPEYS SLDEEGI + +FEL+FAFDEVISLG
Sbjct: 61  IEALFLLLVTTKQSNILEDLATLTLLSKLVPEYSMSLDEEGISRASFELIFAFDEVISLG 120

Query: 121 HKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEIDKSKIEKNRGDKGG 180
           HKE+VTVAQVKQYCEMESHEEKLHKLV+QSKIN+TKDVMKRKA+EIDKSKIEKN+   GG
Sbjct: 121 HKESVTVAQVKQYCEMESHEEKLHKLVMQSKINDTKDVMKRKANEIDKSKIEKNK--PGG 178

Query: 181 FMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRPPSSANAPP 240
           F S+ SMGSGR+ES F+++SISSGGGG           +DV+  ++K K R  SS  APP
Sbjct: 179 FSSMGSMGSGRLESGFNELSISSGGGGGYGSGSGFGMISDVDPINTKPKDRSRSSVTAPP 238

Query: 241 KGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKIN 300
           K  GM+LGKS + NQ +ESLKAEGE ++EDVKP  GQS+  AAAPP TDP TLTVEEK+N
Sbjct: 239 KSSGMKLGKSGK-NQLMESLKAEGEDVIEDVKP-TGQSK--AAAPPPTDPFTLTVEEKLN 294

Query: 301 VSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENI 360
           V+L+RDGG+S+FD+QGTLSLQILNQEDG +QVQI TG NP ILFKTHPN+N+++F +ENI
Sbjct: 295 VALRRDGGLSSFDMQGTLSLQILNQEDGFVQVQIATGENPEILFKTHPNINRDMFNNENI 354

Query: 361 LGLKDPNRPFPQAK--------LWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTM 412
           LGLK P++PFP  +         WRMQ ADESMVPLTINCWPSVSGNETYVS+EYEAS+M
Sbjct: 355 LGLKRPDQPFPTGQGGDGVGLLRWRMQRADESMVPLTINCWPSVSGNETYVSLEYEASSM 414

Query: 413 FDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVPPA 472
           FDL NV+ISVPLPALREAPSVRQ DGEWRYD RNSVLEW+ILLIDNSNRSGSMEFVVPP 
Sbjct: 415 FDLTNVIISVPLPALREAPSVRQCDGEWRYDPRNSVLEWSILLIDNSNRSGSMEFVVPPV 474

Query: 473 DSSSFFPISVRFSATSTYSDLKVVNIIPLR--GGAPPKFSQRTVLITENYQVV 523
           DSS FFPISV+F+ATSTYS LKV  +IPLR  GGA P+F QRT LI +NYQV+
Sbjct: 475 DSSVFFPISVQFAATSTYSGLKVTGMIPLRGGGGATPRFVQRTQLIAQNYQVI 527

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q0DJ99\|COPD2_ORYSJ Coatomer subunit delta-2 OS=Oryza sativa subsp. japonica GN=Os05g0311000 PE=2 SV=1	Back alignment and function description

>sp\|Q0DJA0\|COPD1_ORYSJ Coatomer subunit delta-1 OS=Oryza sativa subsp. japonica GN=Os05g0310800 PE=2 SV=1	Back alignment and function description

>sp\|P49661\|COPD3_ORYSJ Coatomer subunit delta-3 OS=Oryza sativa subsp. japonica GN=Os01g0833700 PE=2 SV=2	Back alignment and function description

>sp\|Q66H80\|COPD_RAT Coatomer subunit delta OS=Rattus norvegicus GN=Arcn1 PE=2 SV=1	Back alignment and function description

>sp\|Q5XJY5\|COPD_MOUSE Coatomer subunit delta OS=Mus musculus GN=Arcn1 PE=2 SV=2	Back alignment and function description

>sp\|Q5RA77\|COPD_PONAB Coatomer subunit delta OS=Pongo abelii GN=ARCN1 PE=2 SV=1	Back alignment and function description

>sp\|P48444\|COPD_HUMAN Coatomer subunit delta OS=Homo sapiens GN=ARCN1 PE=1 SV=1	Back alignment and function description

>sp\|P53619\|COPD_BOVIN Coatomer subunit delta OS=Bos taurus GN=ARCN1 PE=1 SV=1	Back alignment and function description

>sp\|Q5ZL57\|COPD_CHICK Coatomer subunit delta OS=Gallus gallus GN=ARCN1 PE=2 SV=1	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		523
147770771		531	hypothetical protein VITISV_008875 [Viti	0.996	0.981	0.855	0.0
297737988		561	unnamed protein product [Vitis vinifera]	0.996	0.928	0.855	0.0
449439976		530	PREDICTED: coatomer subunit delta-like [	0.996	0.983	0.864	0.0
449483403		530	PREDICTED: coatomer subunit delta-like [	0.996	0.983	0.860	0.0
449433869		530	PREDICTED: coatomer subunit delta-like [	0.996	0.983	0.857	0.0
255571263		530	coatomer delta subunit, putative [Ricinu	0.996	0.983	0.859	0.0
357454817		531	Coatomer subunit delta-3 [Medicago trunc	0.996	0.981	0.825	0.0
359473067		508	PREDICTED: coatomer subunit delta [Vitis	0.952	0.980	0.850	0.0
356575506		530	PREDICTED: coatomer subunit delta-2-like	0.994	0.981	0.853	0.0
224136702		529	predicted protein [Populus trichocarpa]	0.994	0.982	0.812	0.0

>gi\|147770771\|emb\|CAN60953.1\| hypothetical protein VITISV_008875 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  925 bits (2391), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 456/533 (85%), Positives = 489/533 (91%), Gaps = 12/533 (2%)

Query: 1   MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQP 60
           MVVLAASIVSKSGK+LVSRQFVDM+RIRIE LLAAFPKLVGTGKQHTYVETENVRYVYQP
Sbjct: 1   MVVLAASIVSKSGKVLVSRQFVDMTRIRIEALLAAFPKLVGTGKQHTYVETENVRYVYQP 60

Query: 61  IEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLG 120
           IEALYLLLVTNKQSNILEDLETLRLLSKLVPEYS SLDEEG+CKTAFEL+FAFDEVISLG
Sbjct: 61  IEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSVSLDEEGVCKTAFELIFAFDEVISLG 120

Query: 121 HKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEIDKSKIEKNRGDKGG 180
           HKENVTVAQVKQYCEMESHEEKLHKLV+QSKINETKDVMKRKASEIDKSKIEKNRG+KGG
Sbjct: 121 HKENVTVAQVKQYCEMESHEEKLHKLVLQSKINETKDVMKRKASEIDKSKIEKNRGEKGG 180

Query: 181 FMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRPPSSANAPP 240
           FMSLQSMGSGRIES+F+DMSISS GGG          TTD+++FS+KSKGRP SSA APP
Sbjct: 181 FMSLQSMGSGRIESTFNDMSISSSGGGGFGSGSGFGLTTDIDSFSTKSKGRPSSSATAPP 240

Query: 241 KGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKIN 300
           KGLGMQL K+Q+ NQFLESLKAEGEVILEDV P AG +R  +AAPPLTDPITL+ EE++N
Sbjct: 241 KGLGMQLNKTQKANQFLESLKAEGEVILEDVHPKAGPTR--SAAPPLTDPITLSAEERLN 298

Query: 301 VSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENI 360
           V+LKRDGG+SNFDVQGTLSLQILNQEDGLIQVQIETG NPGILFKTHPN+NKELF++ENI
Sbjct: 299 VTLKRDGGVSNFDVQGTLSLQILNQEDGLIQVQIETGSNPGILFKTHPNINKELFSNENI 358

Query: 361 LGLKDPNRPFPQAK----------LWRMQSADESMVPLTINCWPSVSGNETYVSIEYEAS 410
           LGLKDPNRPFP  +           WRMQS DES VPLTINCWPSVSGNETYVSIEYEAS
Sbjct: 359 LGLKDPNRPFPTGQGGDAAGVGLLKWRMQSVDESDVPLTINCWPSVSGNETYVSIEYEAS 418

Query: 411 TMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVP 470
           +MFDLRNVVISVPLPALREAP+VRQIDGEWRYDSRNS+LEW+ILLIDNSNRSGSMEFVVP
Sbjct: 419 SMFDLRNVVISVPLPALREAPNVRQIDGEWRYDSRNSILEWSILLIDNSNRSGSMEFVVP 478

Query: 471 PADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV 523
           PADSS FFPISVRF+A  T+SDLKVVN++PLRGG PPKFSQRT LITENYQVV
Sbjct: 479 PADSSVFFPISVRFTAAKTFSDLKVVNVLPLRGGPPPKFSQRTTLITENYQVV 531

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297737988\|emb\|CBI27189.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449439976\|ref\|XP_004137761.1\| PREDICTED: coatomer subunit delta-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449483403\|ref\|XP_004156581.1\| PREDICTED: coatomer subunit delta-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449433869\|ref\|XP_004134719.1\| PREDICTED: coatomer subunit delta-like [Cucumis sativus] gi\|449479321\|ref\|XP_004155568.1\| PREDICTED: coatomer subunit delta-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255571263\|ref\|XP_002526581.1\| coatomer delta subunit, putative [Ricinus communis] gi\|223534075\|gb\|EEF35793.1\| coatomer delta subunit, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|357454817\|ref\|XP_003597689.1\| Coatomer subunit delta-3 [Medicago truncatula] gi\|355486737\|gb\|AES67940.1\| Coatomer subunit delta-3 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|359473067\|ref\|XP_002276172.2\| PREDICTED: coatomer subunit delta [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356575506\|ref\|XP_003555881.1\| PREDICTED: coatomer subunit delta-2-like [Glycine max]	Back alignment and taxonomy information

>gi\|224136702\|ref\|XP_002322394.1\| predicted protein [Populus trichocarpa] gi\|222869390\|gb\|EEF06521.1\| predicted protein [Populus trichocarpa]	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		523
TAIR\|locus:2175269		527	AT5G05010 [Arabidopsis thalian	0.988	0.981	0.724	2.3e-197
UNIPROTKB\|P49661		518	LOC_Os01g61710 "Coatomer subun	0.575	0.581	0.668	1.7e-191
ZFIN\|ZDB-GENE-021031-2		509	arcn1a "archain 1a" [Danio rer	0.579	0.595	0.361	1.1e-112
MGI\|MGI:2387591		511	Arcn1 "archain 1" [Mus musculu	0.579	0.592	0.362	5.5e-111
RGD\|1359110		511	Arcn1 "archain 1" [Rattus norv	0.579	0.592	0.362	5.5e-111
UNIPROTKB\|Q5ZL57		510	ARCN1 "Coatomer subunit delta"	0.579	0.594	0.363	3.9e-110
UNIPROTKB\|I3LBY0		511	ARCN1 "Uncharacterized protein	0.361	0.369	0.556	3.9e-110
UNIPROTKB\|P53619		511	ARCN1 "Coatomer subunit delta"	0.579	0.592	0.359	4.9e-110
UNIPROTKB\|P48444		511	ARCN1 "Coatomer subunit delta"	0.579	0.592	0.359	4.9e-110
UNIPROTKB\|F1PRT4		511	ARCN1 "Uncharacterized protein	0.579	0.592	0.356	6.3e-110

TAIR\|locus:2175269 AT5G05010 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1911 (677.8 bits), Expect = 2.3e-197, P = 2.3e-197
 Identities = 386/533 (72%), Positives = 437/533 (81%)

Query:     1 MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQP 60
             MVVLAA+IV KSGK++VSR +VDMSRIRIEGLLAAFPKLVG GKQHTY+ETENVRYVYQP
Sbjct:     1 MVVLAAAIVVKSGKVIVSRHYVDMSRIRIEGLLAAFPKLVGMGKQHTYIETENVRYVYQP 60

Query:    61 IEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLG 120
             IEAL+LLLVT KQSNILEDL TL LLSKLVPEYS SLDEEGI + +FEL+FAFDEVISLG
Sbjct:    61 IEALFLLLVTTKQSNILEDLATLTLLSKLVPEYSMSLDEEGISRASFELIFAFDEVISLG 120

Query:   121 HKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMKRKASEIDKSKIEKNRGDKGG 180
             HKE+VTVAQVKQYCEMESHEEKLHKLV+QSKIN+TKDVMKRKA+EIDKSKIEKN+   GG
Sbjct:   121 HKESVTVAQVKQYCEMESHEEKLHKLVMQSKINDTKDVMKRKANEIDKSKIEKNK--PGG 178

Query:   181 FMSLQSMGSGRIEXXXXXXXXXXXXXXXXXXXXXXLATTDVETFSSKSKGRPPSSANAPP 240
             F S+ SMGSGR+E                         +DV+  ++K K R  SS  APP
Sbjct:   179 FSSMGSMGSGRLESGFNELSISSGGGGGYGSGSGFGMISDVDPINTKPKDRSRSSVTAPP 238

Query:   241 KGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRXXXXXXXLTDPITLTVEEKIN 300
             K  GM+LGKS + NQ +ESLKAEGE ++EDVKP  GQS+        TDP TLTVEEK+N
Sbjct:   239 KSSGMKLGKSGK-NQLMESLKAEGEDVIEDVKP-TGQSKAAAPPP--TDPFTLTVEEKLN 294

Query:   301 VSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENI 360
             V+L+RDGG+S+FD+QGTLSLQILNQEDG +QVQI TG NP ILFKTHPN+N+++F +ENI
Sbjct:   295 VALRRDGGLSSFDMQGTLSLQILNQEDGFVQVQIATGENPEILFKTHPNINRDMFNNENI 354

Query:   361 LGLKDPNRPFPQAK--------LWRMQSADESMVPLTINCWPSVSGNETYVSIEYEASTM 412
             LGLK P++PFP  +         WRMQ ADESMVPLTINCWPSVSGNETYVS+EYEAS+M
Sbjct:   355 LGLKRPDQPFPTGQGGDGVGLLRWRMQRADESMVPLTINCWPSVSGNETYVSLEYEASSM 414

Query:   413 FDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEFVVPPA 472
             FDL NV+ISVPLPALREAPSVRQ DGEWRYD RNSVLEW+ILLIDNSNRSGSMEFVVPP 
Sbjct:   415 FDLTNVIISVPLPALREAPSVRQCDGEWRYDPRNSVLEWSILLIDNSNRSGSMEFVVPPV 474

Query:   473 DSSSFFPISVRFSATSTYSDLKVVNIIPLRGG--APPKFSQRTVLITENYQVV 523
             DSS FFPISV+F+ATSTYS LKV  +IPLRGG  A P+F QRT LI +NYQV+
Sbjct:   475 DSSVFFPISVQFAATSTYSGLKVTGMIPLRGGGGATPRFVQRTQLIAQNYQVI 527

GO:0006810 "transport" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0030131 "clathrin adaptor complex" evidence=IEA

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

UNIPROTKB\|P49661 LOC_Os01g61710 "Coatomer subunit delta-3" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-021031-2 arcn1a "archain 1a" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

MGI\|MGI:2387591 Arcn1 "archain 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1359110 Arcn1 "archain 1" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5ZL57 ARCN1 "Coatomer subunit delta" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LBY0 ARCN1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|P53619 ARCN1 "Coatomer subunit delta" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|P48444 ARCN1 "Coatomer subunit delta" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PRT4 ARCN1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q0DJA0	COPD1_ORYSJ	No assigned EC number	0.7264	0.9885	0.9866	yes	no
Q0DJ99	COPD2_ORYSJ	No assigned EC number	0.7258	0.9885	0.9885	yes	no
Q5ZL57	COPD_CHICK	No assigned EC number	0.4224	0.9521	0.9764	yes	no
Q93Y22	COPD_ARATH	No assigned EC number	0.7523	0.9885	0.9810	yes	no
Q5RA77	COPD_PONAB	No assigned EC number	0.4186	0.9541	0.9765	yes	no
Q09236	COPD_CAEEL	No assigned EC number	0.3669	0.9426	0.9572	yes	no
P49661	COPD3_ORYSJ	No assigned EC number	0.7067	0.9732	0.9826	no	no
P48444	COPD_HUMAN	No assigned EC number	0.4186	0.9541	0.9765	yes	no
P53619	COPD_BOVIN	No assigned EC number	0.4130	0.9541	0.9765	yes	no
Q5XJY5	COPD_MOUSE	No assigned EC number	0.4205	0.9541	0.9765	yes	no
Q66H80	COPD_RAT	No assigned EC number	0.4224	0.9541	0.9765	yes	no

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

Your Input:
	GSVIVG00030145001	SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (568 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00036398001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (889 aa)	•	•	•	•	0.893
	GSVIVG00032317001	SubName- Full=Putative uncharacterized protein (Chromosome chr4 scaffold_6, whole genome shotgu [...] (948 aa)	•	•	•	•	0.719
	GSVIVG00025293001	SubName- Full=Chromosome chr9 scaffold_33, whole genome shotgun sequence; (949 aa)	•	•	•	•	0.703
	GSVIVG00029848001	SubName- Full=Chromosome chr10 scaffold_50, whole genome shotgun sequence; (241 aa)	•		•	•	0.624
	GSVIVG00004883001	SubName- Full=Chromosome undetermined scaffold_840, whole genome shotgun sequence; (1218 aa)	•	•	•	•	0.548
	GSVIVG00014508001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (1217 aa)	•	•	•	•	0.543
	GSVIVG00016769001	SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (899 aa)	•	•	•	•	0.508
	GSVIVG00003398001	SubName- Full=Chromosome undetermined scaffold_143, whole genome shotgun sequence; (183 aa)		•	•	•	0.487
	GSVIVG00034130001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (183 aa)		•	•	•	0.462
	GSVIVG00034434001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (1017 aa)	•	•	•	•	0.433

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		523
cd09254		232	cd09254, AP_delta-COPI_MHD, Mu homology domain (MH	1e-100
cd07954		239	cd07954, AP_MHD_Cterm, C-terminal domain of adapto	4e-24
pfam00928		228	pfam00928, Adap_comp_sub, Adaptor complexes medium	5e-17
cd09252		248	cd09252, AP-3_Mu3_Cterm, C-terminal domain of medi	4e-05

>gnl\|CDD\|211365 cd09254, AP_delta-COPI_MHD, Mu homology domain (MHD) of adaptor protein (AP) coat protein I (COPI) delta subunit	Back alignment and domain information

 Score =  302 bits (776), Expect = e-100
 Identities = 112/233 (48%), Positives = 157/233 (67%), Gaps = 7/233 (3%)

Query: 289 DPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHP 348
           + + +TVEEKI+ +L RDGG+ + +V+GTLSL+I ++E   I++Q+    + G  FKTHP
Sbjct: 1   EGVHITVEEKISATLSRDGGLESLEVKGTLSLRINDEELAKIKIQLANNDDKGFQFKTHP 60

Query: 349 NMNKELFTHENILGLKDPNRPFPQAKL-----WRMQSADESMVPLTINCWPSVSGNETYV 403
           N++K+LFT +++LGLKDP++PFP         WR+QS DES++PLTINCWPS SG  T V
Sbjct: 61  NVDKKLFTSDSVLGLKDPSKPFPVNDPVGVLKWRLQSKDESLLPLTINCWPSESGGGTDV 120

Query: 404 SIEYEAS-TMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRS 462
           +IEYE +    +L +VVIS+PLP+   AP V   DGE+ YD R + L W I LID SN S
Sbjct: 121 TIEYELNRDDLELNDVVISIPLPS-GSAPVVNSDDGEYEYDGRKNGLIWKIPLIDASNSS 179

Query: 463 GSMEFVVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVL 515
           GS+EF +  +D   FFPISV F+++ T+  +KV  ++    G P  FS  T L
Sbjct: 180 GSLEFSIAASDEDDFFPISVSFTSSKTFCGVKVTEVVSAEDGEPVPFSVETKL 232

COPI complex-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. COPI complex-coated vesicles consist of a small GTPase, ADP-ribosylation factor 1 (ARF1) and a heteroheptameric coatomer composed of two subcomplexes, F-COPI and B-COPI. ARF1 regulates COPI vesicle formation by recruiting the coatomer onto Golgi membranes to initiate its coat function. Coatomer complexes then bind cargo molecules and self-assemble to form spherical cages that yield COPI-coated vesicles. The heterotetrameric F-COPI subcomplex contains beta-, gamma-, delta-, and zeta-COP subunits, where beta- and gamma-COP subunits are related to the large AP subunits, and delta- and zeta-COP subunits are related to the medium and small AP subunits, respectively. Due to the sequence similarity to the AP complexes, the F-COPI subcomplex might play a role in the cargo-binding. The heterotrimeric B-COPI contains alpha-, beta-, and epsilon-COP subunits, which are not related to the adaptins. This subcomplex is thought to participate in the cage-forming and might serve a function similar to that of clathrin. This family corresponds to the mu homology domain of delta-subunit of COPI complex (delta-COP), which is distantly related to the C-terminal domain of mu chains among AP complexes. The delta-COP subunit appears tightly associated with the beta-COP subunit to confer its interaction with ARF1. In addition, both delta- and beta-COP subunits contribute to a common binding site for arginine (R)-based signals, which are sorting motifs conferring transient endoplasmic reticulum (ER) localization to unassembled subunits of multimeric membrane proteins. Length = 232

>gnl\|CDD\|211360 cd07954, AP_MHD_Cterm, C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD)	Back alignment and domain information

>gnl\|CDD\|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family	Back alignment and domain information

>gnl\|CDD\|211363 cd09252, AP-3_Mu3_Cterm, C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		523
KOG2635		512	consensus Medium subunit of clathrin adaptor compl	100.0
KOG0938		446	consensus Adaptor complexes medium subunit family	100.0
KOG0937		424	consensus Adaptor complexes medium subunit family	100.0
KOG2740		418	consensus Clathrin-associated protein medium chain	100.0
PF00928		262	Adap_comp_sub: Adaptor complexes medium subunit fa	100.0
PF01217		141	Clat_adaptor_s: Clathrin adaptor complex small cha	99.92
KOG2677		922	consensus Stoned B synaptic vesicle biogenesis pro	99.82
COG5030		152	APS2 Clathrin adaptor complex, small subunit [Intr	99.81
KOG0935		143	consensus Clathrin adaptor complex, small subunit	99.72
KOG0934		145	consensus Clathrin adaptor complex, small subunit	99.7
KOG0936		182	consensus Clathrin adaptor complex, small subunit	99.52
PF10291		257	muHD: Muniscin C-terminal mu homology domain; Inte	99.15
KOG3343		175	consensus Vesicle coat complex COPI, zeta subunit	98.74
COG5541		187	RET3 Vesicle coat complex COPI, zeta subunit [Post	97.22
PF03164		415	Mon1: Trafficking protein Mon1; InterPro: IPR00435	92.03
PF08923		119	MAPKK1_Int: Mitogen-activated protein kinase kinas	91.34
PF04099		142	Sybindin: Sybindin-like family ; InterPro: IPR0072	87.51
PF13774		83	Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3	86.12
COG5122		134	TRS23 Transport protein particle (TRAPP) complex s	80.86

>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

Probab=100.00  E-value=1.1e-96  Score=741.63  Aligned_cols=499  Identities=50%  Similarity=0.820  Sum_probs=434.9

Q ss_pred             CeEEEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcCCCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHH
Q 042402            1 MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDL   80 (523)
Q Consensus         1 m~v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~l   80 (523)
                      |||++|+|++++|+.+|+||||+|+|.++|++|++|++++..+++|+++|.+.+||||++.++||+|++|++++|++++|
T Consensus         1 Mvvlaa~i~t~~Gk~ivsRqf~~Msr~RIEgLl~aFpkLv~~~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl   80 (512)
T KOG2635|consen    1 MVVLAASINTKTGKAIVSRQFREMSRSRIEGLLAAFPKLVSAGKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNILEDL   80 (512)
T ss_pred             CeEEEEEEeecCCceeeehHhHhhhHHHHHHHHHHhHHhhccCCCccEEecccEEEEEEecccEEEEEEeccccchhhHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhhccchHHHHHHHHhhhcchhhhHHHH
Q 042402           81 ETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMK  160 (523)
Q Consensus        81 e~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~m~s~ee~i~~~~~~~ke~eak~~~k  160 (523)
                      ++|++|.+++..||..++|+.|.+|+|||+|+|||++..||.++.++.|||+|++|||||||+|++++++||.||+++||
T Consensus        81 ~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~v~~nke~ea~q~mk  160 (512)
T KOG2635|consen   81 ETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHELVMRNKEREAKQEMK  160 (512)
T ss_pred             HHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHHHHHhhhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhhhhhhccCCC---CCccccccCCCCccccccccccccCCCCCCCCCCCcccccccccccccCCCCCC-CCCC
Q 042402          161 RKASEIDKSKIEKNRGDK---GGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRP-PSSA  236 (523)
Q Consensus       161 ~~a~e~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~p-~~~~  236 (523)
                      ||||||+++|.+..+++.   ++|...|++|-...+                    .+.+....++...+.+..+ ...+
T Consensus       161 rKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s--------------------~~~~~~~~~~~~~~~~~~sa~~~~  220 (512)
T KOG2635|consen  161 RKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVS--------------------TTNAINRVESIAQKPKQQSAAKAS  220 (512)
T ss_pred             HHHHHHHHHHHhhhccccccCCCccccccccccCCc--------------------ccchhhccccccccccccccccCC
Confidence            999999999999877651   233222221110000                    0011111111111111111 1222


Q ss_pred             CCCCCCcCccccccCCc-hhhhhhhhhccceeecccCccc-c--ccccccCCCCCCCCeEEEEEEEEEEEEecCCCeEEE
Q 042402          237 NAPPKGLGMQLGKSQRT-NQFLESLKAEGEVILEDVKPIA-G--QSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNF  312 (523)
Q Consensus       237 ~~~~~~~gm~lgk~~~~-n~~~~~l~~e~~~~~~~~~~~~-~--~~~~~~~~~~~~neI~vdV~Ekv~~~~~~~G~v~~~  312 (523)
                      ++|  .+||+|||+.+. +.++++|++||+.+...+.+.. +  .+++.+......|.||+.++|+|++.++|||.+.+.
T Consensus       221 s~p--ak~mklG~k~~~s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~  298 (512)
T KOG2635|consen  221 SAP--AKAMKLGKKTKNSDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSG  298 (512)
T ss_pred             CCC--chhhhhcccccchhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccce
Confidence            334  569999976655 4899999999998765422211 1  111122235667779999999999999999999999


Q ss_pred             EEEEEEEEEEecCCCceEEEEeeCCCCCCCCcccccccCcccccccceEEEeCCCCCcccccc-----ccccCCCCCcCC
Q 042402          313 DVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKL-----WRMQSADESMVP  387 (523)
Q Consensus       313 eV~G~i~~~~~lsg~p~~~l~ln~~~~~~~d~~fHpcVd~~~f~~~r~Isf~pPdg~F~L~~~-----yr~~~~d~~~lP  387 (523)
                      |++|.|.+++.+..+.++.|.|.+...++.++++||++||+.|.+.++|.+++|+++||+++.     ||....|+..+|
T Consensus       299 E~qG~lsLrI~d~e~~~i~lkl~n~~~~g~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iP  378 (512)
T KOG2635|consen  299 EVQGTLSLRIKDEEYGDIELKLANGRDKGTQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIP  378 (512)
T ss_pred             eeeeeEEEEEccccccceEEEEcCCCCcceeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCc
Confidence            999999999999999999999998777889999999999999999999999999999999954     999998999999


Q ss_pred             eEEEEEEEeeCCeEEEEEEEEecCCceeeeEEEEecCCCCCCCCeEEeecceEEEECCCCEEEEEEceecCCCceEEEEE
Q 042402          388 LTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEF  467 (523)
Q Consensus       388 ~~i~~~~~~~~~~~~v~i~~~~~~~~~~~~V~V~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~i~~~~~s~s~ef  467 (523)
                      |+++|||++++..+.|+|||++.....++||.|.||+|.+. .|++..++|+|.|++.++.+.|+|+.| .+|.+|++||
T Consensus       379 lTincWPSes~~g~dV~iEYe~~~~~eL~dV~i~iPlP~~i-apsv~~~Dge~~~~~~~~~leW~I~~I-a~N~SGslEF  456 (512)
T KOG2635|consen  379 LTINCWPSESGNGYDVNIEYEAVLECELNDVIITIPLPANI-APSVGECDGEYRYDERKNVLEWSIGVI-AKNFSGSLEF  456 (512)
T ss_pred             eEEEeccccCCCCeEEEEEEeehhcccccceEEEeeccccc-CCccceecceEEeccccceeEEEeeee-ccCCCCcEEE
Confidence            99999999999889999999997778899999999999977 899999999999999999999999999 6789999999


Q ss_pred             EeCCCCCCCCCCeEEEEEecccccCceEeEEEECCCCCCCeeeEEEEEEeeceEEC
Q 042402          468 VVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV  523 (523)
Q Consensus       468 ~~~~~~~~~~~Pi~v~F~ip~t~Sgl~V~~l~i~~~~~~i~~~~~~~~~~~~y~i~  523 (523)
                      +|++.+++.|||++|.|....+++||.|..|...+++++++|++++.|.+|+|+|+
T Consensus       457 s~~~~~~~~fFPl~VsF~s~~~ftgl~vqkVv~~~~~~~~~y~~~t~f~~dky~Vv  512 (512)
T KOG2635|consen  457 SCPASDPDGFFPLSVSFTSDTVFTGLFVQKVVRNDGHAPVRYSVETTFEVDKYEVV  512 (512)
T ss_pred             eecCCCCCceeeEEEEEEecccccceEEEEEEEcCCCCCceeEEEEEEEeeeeEeC
Confidence            99999999999999999999999999999998888889999999999999999996

>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 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

>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 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

>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]	Back alignment and domain information

>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF10291 muHD: Muniscin C-terminal mu homology domain; InterPro: IPR018808 The muniscins are a family of endocytic adaptors that is conserved from yeast to humans	Back alignment and domain information

>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain	Back alignment and domain information

>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases	Back alignment and domain information

>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses	Back alignment and domain information

>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D	Back alignment and domain information

>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		523
2vgl_S		142	AP-2 complex subunit sigma-1; cytoplasmic vesicle,	6e-35
4en2_M		266	AP-1 complex subunit MU-1; human immunodeficiency	2e-28
3l81_A		301	AP-4 complex subunit MU-1; immunoglobulin-like bet	9e-28
1i31_A		314	Clathrin coat assembly protein AP50; beta-sandwich	5e-26
1w63_M		423	Adaptor-related protein complex 1, MU 1 subunit; e	4e-25
1w63_M		423	Adaptor-related protein complex 1, MU 1 subunit; e	2e-22
3ml6_A		385	Chimeric complex between protein dishevlled2 HOMO	3e-19
2vgl_M		435	AP-2 complex subunit MU-1; cytoplasmic vesicle, al	1e-18
2vgl_M		435	AP-2 complex subunit MU-1; cytoplasmic vesicle, al	3e-12
1w63_Q		158	Adapter-related protein complex 1 sigma 1A subunit	3e-15
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>2vgl_S AP-2 complex subunit sigma-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Mus musculus} SCOP: i.23.1.1 PDB: 2jkt_I 2jkr_I* 2xa7_S Length = 142	Back alignment and structure

 Score =  126 bits (319), Expect = 6e-35
 Identities = 27/136 (19%), Positives = 60/136 (44%), Gaps = 3/136 (2%)

Query: 8   IVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT--GKQHTYVETENVRYVYQPIEALY 65
           I +++GK  +++ ++       + L+     +V     K   +VE  N + +Y+    LY
Sbjct: 7   IQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLY 66

Query: 66  LLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENV 125
             +  +   N L  LE +    +++ EY +++ E  +    +++    DE+   G     
Sbjct: 67  FCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRET 126

Query: 126 TVAQV-KQYCEMESHE 140
           +  +V KQ   ++S E
Sbjct: 127 SQTKVLKQLLMLQSLE 142

PyMOL of 2vgl

>4en2_M AP-1 complex subunit MU-1; human immunodeficiency virus 1, HIV, NEF, antigen presentation, HOST defense, adaptor protein complex 1, MU1 subunit; 2.58A {Mus musculus} PDB: 4emz_A Length = 266	Back alignment and structure

>3l81_A AP-4 complex subunit MU-1; immunoglobulin-like beta-sandwich, coated PIT, golgi apparat membrane, phosphoprotein, protein transport, transport; 1.60A {Homo sapiens} Length = 301	Back alignment and structure

>1i31_A Clathrin coat assembly protein AP50; beta-sandwich, peptide-binding site, protein-peptide complex, clathrin adaptor; 2.50A {Rattus norvegicus} SCOP: b.2.7.1 PDB: 1bw8_A 2pr9_A 3h85_A 1bxx_A 1hes_A 1h6e_A Length = 314	Back alignment and structure

>1w63_M Adaptor-related protein complex 1, MU 1 subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1 Length = 423	Back alignment and structure

>1w63_M Adaptor-related protein complex 1, MU 1 subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1 Length = 423	Back alignment and structure

>3ml6_A Chimeric complex between protein dishevlled2 HOMO and clathrin adaptor AP-2 complex...; dishevelled, frizzled internalization; 3.50A {Mus musculus} Length = 385	Back alignment and structure

>2vgl_M AP-2 complex subunit MU-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Rattus norvegicus} PDB: 2jkr_M 2jkt_M 2bp5_M* 2xa7_M Length = 435	Back alignment and structure

>2vgl_M AP-2 complex subunit MU-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Rattus norvegicus} PDB: 2jkr_M 2jkt_M 2bp5_M* 2xa7_M Length = 435	Back alignment and structure

>1w63_Q Adapter-related protein complex 1 sigma 1A subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1 Length = 158	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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		523
2vgl_M		435	AP-2 complex subunit MU-1; cytoplasmic vesicle, al	100.0
1w63_M		423	Adaptor-related protein complex 1, MU 1 subunit; e	100.0
1i31_A		314	Clathrin coat assembly protein AP50; beta-sandwich	100.0
4en2_M		266	AP-1 complex subunit MU-1; human immunodeficiency	100.0
3ml6_A		385	Chimeric complex between protein dishevlled2 HOMO	100.0
3l81_A		301	AP-4 complex subunit MU-1; immunoglobulin-like bet	100.0
1w63_Q		158	Adapter-related protein complex 1 sigma 1A subunit	99.97
2vgl_S		142	AP-2 complex subunit sigma-1; cytoplasmic vesicle,	99.96
3tjz_C		153	Coatomer subunit zeta-1; protein trafficking, golg	99.94
3g9h_A		328	Suppressor of yeast profilin deletion; SYP1, MU, a	98.93
4b93_A		189	Vesicle-associated membrane protein 7; endocytosis	92.86
3kyq_A		199	YKT6, synaptobrevin homolog YKT6; V-snare homolog,	92.72
3bw6_A		144	Synaptobrevin homolog YKT6; YKT6P, farnesylation,	92.04
2nut_C		196	Vesicle-trafficking protein SEC22B; human copii SE	91.63
4afi_A		173	AP-3 complex subunit delta-1, vesicle-associated p	90.14
2vx8_A		169	Nucleoporin-like protein RIP, vesicle-associated m	89.36
2j3w_A		142	Sedlin, trafficking protein particle complex prote	87.75
3cpt_A		143	Mitogen-activated protein kinase kinase 1- interac	86.43
2j3t_C		145	Trafficking protein particle complex subunit 1, tr	83.98

>2vgl_M AP-2 complex subunit MU-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Rattus norvegicus} PDB: 2jkr_M 2jkt_M 2bp5_M* 2xa7_M	Back alignment and structure

Probab=100.00  E-value=8.6e-79  Score=649.20  Aligned_cols=396  Identities=16%  Similarity=0.203  Sum_probs=331.0

Q ss_pred             EEEEEEEcCCCCEEEEEcce-ecchHHHHHHHhhhchhhcCC---CCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHH
Q 042402            3 VLAASIVSKSGKILVSRQFV-DMSRIRIEGLLAAFPKLVGTG---KQHTYVETENVRYVYQPIEALYLLLVTNKQSNILE   78 (523)
Q Consensus         3 v~s~~Il~~~G~~lisR~yr-~~~r~~~e~~l~~F~~~i~~~---~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~   78 (523)
                      |.+++|+|++|+++++|+|+ +++|..++.    |++++...   .++|++++++++|+|+++++|||+++++.|+|++.
T Consensus         2 I~~i~I~~~~Gk~~l~k~y~~~~~~~~~~~----f~~~v~~~~~~~~~~ii~~~~~~~vy~~~~~Lyfv~~~~~~~n~l~   77 (435)
T 2vgl_M            2 IGGLFIYNHKGEVLISRVYRDDIGRNAVDA----FRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAM   77 (435)
T ss_dssp             CCEEEEECTTCCEEEEEECSSSCCHHHHHH----HHHHTTTCSSCCCCSEEEETTEEEEEEEETTEEEEEEESSCCCHHH
T ss_pred             eEEEEEECCCCCEEEEEecCCCCChhHHHH----HHHHHhccccCCCCCEEEECCEEEEEEEECCEEEEEEecCCCCHHH
Confidence            58999999999999999999 788877666    88888762   67899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhhccchHHHHHHHHhhhcchhhhHH
Q 042402           79 DLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDV  158 (523)
Q Consensus        79 ~le~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~m~s~ee~i~~~~~~~ke~eak~~  158 (523)
                      ++||||+|+++|++|||.++|++|++|+..++++||||+|+||||+|++++|+.++.|++|+++++.             
T Consensus        78 ~le~L~~~v~vl~~yf~~v~E~~I~~Nf~~vy~lLDE~id~G~~~~t~~~~l~~~i~~~~~~~~~~~-------------  144 (435)
T 2vgl_M           78 VFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKSQHQT-------------  144 (435)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCHHHHHHTHHHHHHHHHHHEETTEECCCCHHHHGGGCCCCCCCCC----------------
T ss_pred             HHHHHHHHHHHHHHHHhccCHHHHHHhHHHHHHHHHHHhcCCEEEecCHHHHHHHhccccccccccc-------------
Confidence            9999999999999999999999999995555555999999999999999999999999999876420             


Q ss_pred             HHhhhhhhhhhhhhhccCCCCCccccccCCCCccccccccccccCCCCCCCCCCCcccccccccccccCCCCCCCCCCCC
Q 042402          159 MKRKASEIDKSKIEKNRGDKGGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRPPSSANA  238 (523)
Q Consensus       159 ~k~~a~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~p~~~~~~  238 (523)
                           ++  .    ....      +                      ++         +            ..     ..
T Consensus       145 -----~~--~----~~~~------~----------------------~~---------~------------~~-----~i  159 (435)
T 2vgl_M          145 -----KE--E----QSQI------T----------------------SQ---------V------------TG-----QI  159 (435)
T ss_dssp             -------------------------------------------------------------------------------C
T ss_pred             -----cc--c----cccc------c----------------------cc---------c------------cc-----cc
Confidence                 00  0    0000      0                      00         0            00     23


Q ss_pred             CCCCcCccccccCCchhhhhhhhhccceeecccCccccccccccCCCCCCCCeEEEEEEEEEEEEecCCCeEEEEEEEEE
Q 042402          239 PPKGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNFDVQGTL  318 (523)
Q Consensus       239 ~~~~~gm~lgk~~~~n~~~~~l~~e~~~~~~~~~~~~~~~~~~~~~~~~~neI~vdV~Ekv~~~~~~~G~v~~~eV~G~i  318 (523)
                      |||..|+                                       .+.+|||||||+|+|+++++++|.+++++|+|+|
T Consensus       160 ~wr~~gi---------------------------------------~~~~nei~vdV~E~v~~~~~~~G~v~~~eV~G~I  200 (435)
T 2vgl_M          160 GWRREGI---------------------------------------KYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRV  200 (435)
T ss_dssp             CSSCSCC---------------------------------------CCSSCEEEEEEEEEEEEEECTTCCEEEEEEEEEE
T ss_pred             ccccccC---------------------------------------CcCcceEEEEEEEEEEEEEcCCCCEEEEEEEEEE
Confidence            6887776                                       3455799999999999999999999999999999


Q ss_pred             EEEEecCCCceEEEEeeCCC--------------------CCCCCcccccccCcccccccceEEEeCCCCCccccccccc
Q 042402          319 SLQILNQEDGLIQVQIETGG--------------------NPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRM  378 (523)
Q Consensus       319 ~~~~~lsg~p~~~l~ln~~~--------------------~~~~d~~fHpcVd~~~f~~~r~Isf~pPdg~F~L~~~yr~  378 (523)
                      +|+++|+|||+|+|+||++.                    ...+||+||||||+++|+++|+|+|+||||+|+|| +||+
T Consensus       201 ~~~~~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~fH~cV~~~~f~~~r~isF~PPdg~F~Lm-~Yr~  279 (435)
T 2vgl_M          201 VMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELM-RYRT  279 (435)
T ss_dssp             EEEEECSSCCEEEEEECSSSCC-----------------CCCCCEEEECTTEEEC-----CCEEECCCSEEEEEE-EEEE
T ss_pred             EEEEEeCCCCeEEEEeCchhhcccccccccccccccccCceEccccccceeecHhHhccCceEEEECCCCcEEEE-EEEe
Confidence            99999999999999998740                    12379999999999999999999999999999999 8999


Q ss_pred             cCCCCCcCCeEEEEEEEeeCC---eEEEEEEEEecCCceeeeEEEEecCCCCCCCCeEEeecceEEEECCCCEEEEEEce
Q 042402          379 QSADESMVPLTINCWPSVSGN---ETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILL  455 (523)
Q Consensus       379 ~~~d~~~lP~~i~~~~~~~~~---~~~v~i~~~~~~~~~~~~V~V~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~  455 (523)
                      +.  +..+||++.||+++.++   ++.++++.+++....++||.|+||+|+.+..+.+.+..|+++|++.++.|+|+|++
T Consensus       280 ~~--~~~~P~~i~~~~~~~~~~~ve~~l~~~~~~~~~~~~~~V~I~IP~P~~~~~~~~~~~~G~~~y~~~~~~l~W~I~~  357 (435)
T 2vgl_M          280 TK--DIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKR  357 (435)
T ss_dssp             CS--SCCCSEEEEEEEECCTTTEEEEEEEEEECSCTTSEEEEEEEEEECCSSCCCEEEEESSSEEEEETTTTEEEEEEEE
T ss_pred             cC--CcCCCeEEEEEEEecCCCEEEEEEEEeCCCCCCceeeEEEEEEECCCCCCCceEEecceeEEEccCCCEEEEEecc
Confidence            87  57899999999998653   45555555666667899999999999988899999999999999999999999999


Q ss_pred             ecC-CCceEEEEEEeCC---CCCCCCCCeEEEEEecccccCceEeEEEECCC----CCCCee-eEEEEEEeeceEE
Q 042402          456 IDN-SNRSGSMEFVVPP---ADSSSFFPISVRFSATSTYSDLKVVNIIPLRG----GAPPKF-SQRTVLITENYQV  522 (523)
Q Consensus       456 i~~-~~~s~s~ef~~~~---~~~~~~~Pi~v~F~ip~t~Sgl~V~~l~i~~~----~~~i~~-~~~~~~~~~~y~i  522 (523)
                      ++| ++.+++++|.++.   ...+.++||+|+|++|.++|||+|++|++.+.    ...-+| ++++..++++|+|
T Consensus       358 ~~~~~~~~l~~~~~l~~~~~~~~~~~~pi~v~F~i~~t~Sgl~V~~l~v~~~~~~~~~y~~~kwVrY~t~sg~y~~  433 (435)
T 2vgl_M          358 MAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYET  433 (435)
T ss_dssp             EETTCEEEEEEEEECCCCSCSCCCCCCCEEEEEEESSCTTCCCEEEEEEECSSSSCBGGGSEEEEEEEEEEEEEEE
T ss_pred             CCCCCCEEEEEEEEecCCCcCcccCCCcEEEEEEEEecccccEEEEEEEeccccccCCCCCcCceEEEEeCCeEEE
Confidence            998 5566777777643   34567999999999999999999999999885    122244 5899999999997

PyMOL of 2vgl

>1w63_M Adaptor-related protein complex 1, MU 1 subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1	Back alignment and structure

>1i31_A Clathrin coat assembly protein AP50; beta-sandwich, peptide-binding site, protein-peptide complex, clathrin adaptor; 2.50A {Rattus norvegicus} SCOP: b.2.7.1 PDB: 1bw8_A 2pr9_A 3h85_A 1bxx_A 1hes_A 1h6e_A	Back alignment and structure

>4en2_M AP-1 complex subunit MU-1; human immunodeficiency virus 1, HIV, NEF, antigen presentation, HOST defense, adaptor protein complex 1, MU1 subunit; 2.58A {Mus musculus} PDB: 4emz_A	Back alignment and structure

>3ml6_A Chimeric complex between protein dishevlled2 HOMO and clathrin adaptor AP-2 complex...; dishevelled, frizzled internalization; 3.50A {Mus musculus}	Back alignment and structure

>3l81_A AP-4 complex subunit MU-1; immunoglobulin-like beta-sandwich, coated PIT, golgi apparat membrane, phosphoprotein, protein transport, transport; 1.60A {Homo sapiens}	Back alignment and structure

>1w63_Q Adapter-related protein complex 1 sigma 1A subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} SCOP: i.23.1.1	Back alignment and structure

>2vgl_S AP-2 complex subunit sigma-1; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Mus musculus} SCOP: i.23.1.1 PDB: 2jkt_I 2jkr_I* 2xa7_S	Back alignment and structure

>3tjz_C Coatomer subunit zeta-1; protein trafficking, golgi membrane, protein transport-prote binding complex; HET: GNP; 2.90A {Bos taurus} PDB: 2hf6_A	Back alignment and structure

>3g9h_A Suppressor of yeast profilin deletion; SYP1, MU, adaptor, endocytosis, phosphoprotein; HET: 1PG; 2.80A {Saccharomyces cerevisiae}	Back alignment and structure

>4b93_A Vesicle-associated membrane protein 7; endocytosis, exocytosis, snare; 2.00A {Mus musculus} PDB: 2dmw_A	Back alignment and structure

>3kyq_A YKT6, synaptobrevin homolog YKT6; V-snare homolog, lipid binding, cytoplasmic vesicle, ER-GOLG transport, golgi apparatus, lipoprotein; HET: DPV; 2.44A {Rattus norvegicus}	Back alignment and structure

>3bw6_A Synaptobrevin homolog YKT6; YKT6P, farnesylation, vacuole fusion, snare, coiled coil, lipoprotein, membrane, phosphoprotein; 2.50A {Saccharomyces cerevisiae} PDB: 1h8m_A 1iou_A	Back alignment and structure

>2nut_C Vesicle-trafficking protein SEC22B; human copii SEC23/24 complexed with SEC22, protein transport; 2.30A {Homo sapiens} PDB: 2nup_C 3egd_C 3egx_C 1ifq_A	Back alignment and structure

>4afi_A AP-3 complex subunit delta-1, vesicle-associated protein 7; endocytosis, exocytosis, clathrin adaptor, chimera, fusion P; 2.80A {Homo sapiens}	Back alignment and structure

>2vx8_A Nucleoporin-like protein RIP, vesicle-associated membrane protein 7; endocytosis,exocytosis, endocytosis, exocytosis, acetylation, coiled coil; 2.2A {Homo sapiens} PDB: 2dmw_A	Back alignment and structure

>2j3w_A Sedlin, trafficking protein particle complex protein 2; multisubunit tethering factor, trapp, palmitate, transport, lipoprotein; HET: PLM; 2.1A {Mus musculus} SCOP: d.110.4.3 PDB: 1h3q_A	Back alignment and structure

>3cpt_A Mitogen-activated protein kinase kinase 1- interacting protein 1; scaffold, complex, alpha/beta, endosome, membrane, lysosome; 1.90A {Homo sapiens} SCOP: d.110.7.1 PDB: 1sko_A 2zl1_A 1vet_A 1veu_A	Back alignment and structure

>2j3t_C Trafficking protein particle complex subunit 1, trafficking protein particle complex subunit 3; trapp, palmitate, transport, lipoprotein, ER-golgi transport apparatus, protein transport; HET: PLM; 2.4A {Mus musculus}	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		523
d2pr9a1		277	b.2.7.1 (A:159-435) Second domain of Mu2 adaptin s	1e-34
d2vgls_		142	d.110.4.2 (S:) Sigma2 adaptin (clathrin coat assem	2e-28
d2vglm2		141	d.110.4.2 (M:1-141) Mu2 adaptin (clathrin coat ass	4e-27

>d2pr9a1 b.2.7.1 (A:159-435) Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 277	Back information, alignment and structure


class: All beta proteins
fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
superfamily: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
family: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
domain: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score =  129 bits (325), Expect = 1e-34
 Identities = 39/232 (16%), Positives = 75/232 (32%), Gaps = 30/232 (12%)

Query: 291 ITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIE--------------- 335
           + L V E +N+ +   G + +  V G + ++         +  +                
Sbjct: 15  LFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADE 74

Query: 336 --TGGNPGILF---KTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTI 390
               G   I       H  +    F  E  +    P+  F    L R ++  + ++P  +
Sbjct: 75  TSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFE---LMRYRTTKDIILPFRV 131

Query: 391 NCWPSVSGN---ETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNS 447
                  G    E  V I+         + + + +P P       V  + G+ +Y +  +
Sbjct: 132 IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN 191

Query: 448 VLEWTILLID---NSNRSGSMEFV-VPPADSSSFFPISVRFSATSTYSDLKV 495
            + W I  +     S  S  +E +        +  PIS+ F      S LKV
Sbjct: 192 AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKV 243

PyMOL of d2pr9a1

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		523
d2pr9a1		277	Second domain of Mu2 adaptin subunit (ap50) of ap2	100.0
d2vglm2		141	Mu2 adaptin (clathrin coat assembly protein AP50)	99.97
d2vgls_		142	Sigma2 adaptin (clathrin coat assembly protein AP1	99.95
d3cpta1		116	MEK binding partner 1, MP1 {Human (Homo sapiens) [	93.5
d1ioua_		140	Synaptobrevin homolog 1 ykt6 {Baker's yeast (Sacch	89.8

>d2pr9a1 b.2.7.1 (A:159-435) Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

class: All beta proteins
fold: Common fold of diphtheria toxin/transcription factors/cytochrome f
superfamily: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
family: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
domain: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=100.00  E-value=8.6e-49  Score=391.98  Aligned_cols=235  Identities=16%  Similarity=0.177  Sum_probs=199.5

Q ss_pred             CCCCCCeEEEEEEEEEEEEecCCCeEEEEEEEEEEEEEecCCCceEEEEeeCCCC--------------------CCCCc
Q 042402          285 PPLTDPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGN--------------------PGILF  344 (523)
Q Consensus       285 ~~~~neI~vdV~Ekv~~~~~~~G~v~~~eV~G~i~~~~~lsg~p~~~l~ln~~~~--------------------~~~d~  344 (523)
                      .|.+|||||||+|+++++++++|.+++++|+|+|.|+++|+|+|+|+|+||++..                    ..+||
T Consensus         9 ~y~~NEi~vDV~E~i~~~~~~~G~~~~~~V~G~I~~~s~LsG~P~~~l~Ln~~~~~~~~~~~~~~~~~~~~~~~~~l~d~   88 (277)
T d2pr9a1           9 KYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDC   88 (277)
T ss_dssp             CCSSCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEEEECSSSCEEEEEESBC------------------CCCBCCSEE
T ss_pred             cccCCEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEecCCCCeEEEEecchhhcccccccccccccccccCceEccce
Confidence            4556799999999999999999999999999999999999999999999987521                    24899


Q ss_pred             ccccccCcccccccceEEEeCCCCCccccccccccCCCCCcCCeEEEEEEEeeCC---eEEEEEEEEecCCceeeeEEEE
Q 042402          345 KTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSGN---ETYVSIEYEASTMFDLRNVVIS  421 (523)
Q Consensus       345 ~fHpcVd~~~f~~~r~Isf~pPdg~F~L~~~yr~~~~d~~~lP~~i~~~~~~~~~---~~~v~i~~~~~~~~~~~~V~V~  421 (523)
                      +||||||++.|+++|+|+|+||||+|+|| +||++.  +..+||.+.+|++..++   ++.++++++++....++||.|.
T Consensus        89 ~fH~cV~~~~f~~~~~i~F~PPdG~F~Lm-~Y~~~~--~~~~P~~i~~~~~~~~~~~~~~~i~l~~~~~~~~~~~~v~I~  165 (277)
T d2pr9a1          89 TFHQCVRLSKFDSERSISFIPPDGEFELM-RYRTTK--DIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVR  165 (277)
T ss_dssp             EECTTSBCC-----CCEEECCCSEEEEEE-EEEECS--SCCCCEEEEEEEEEETTTEEEEEEEEEECSCTTCEEEEEEEE
T ss_pred             eeeeccccccccccceEeecCCCCcEEEE-EEEcCC--CcCCCcEEEEEEEeccCcEEEEEEEEEeccCCCeeeeEEEEE
Confidence            99999999999999999999999999999 899976  67899999999988764   4556666666777889999999


Q ss_pred             ecCCCCCCCCeEEeecceEEEECCCCEEEEEEceecC-CCceEEEEEEeCC---CCCCCCCCeEEEEEecccccCceEeE
Q 042402          422 VPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDN-SNRSGSMEFVVPP---ADSSSFFPISVRFSATSTYSDLKVVN  497 (523)
Q Consensus       422 iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~i~~-~~~s~s~ef~~~~---~~~~~~~Pi~v~F~ip~t~Sgl~V~~  497 (523)
                      ||+|+.+..+++.+..|+++|++.+++++|+|+++++ ++.++++++++..   ...+.++||+|+|++|+++|||+|++
T Consensus       166 iP~P~~~~~~~~~~~~G~~~y~~~~~~l~W~I~k~~~~~~~~l~~~~~~~~~~~~~~~~~~pi~v~F~ip~t~Sgl~V~~  245 (277)
T d2pr9a1         166 IPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRY  245 (277)
T ss_dssp             EECCTTEEEEEEEESSSEEEEEGGGTEEEEEEEEEETTCEEEEEEEEEECCCCSSSCCCCCCEEEEEEESSCTTCCCEEE
T ss_pred             eeCCCcccCceEEecCceEEEeccCCEEEEecccccCCccceEEEEEEeccCCCCccccCCcEEEEEEecccccceEEEE
Confidence            9999988888999999999999999999999999998 5567777777642   34466899999999999999999999


Q ss_pred             EEECCCC-CC---Cee-eEEEEEEeeceEE
Q 042402          498 IIPLRGG-AP---PKF-SQRTVLITENYQV  522 (523)
Q Consensus       498 l~i~~~~-~~---i~~-~~~~~~~~~~y~i  522 (523)
                      |++.+.. ..   -.| ++++..++++|+|
T Consensus       246 l~v~~~~~~~~~~~~~k~vrY~t~sg~Y~~  275 (277)
T d2pr9a1         246 LKVFEPKLNYSDHDVIKWVRYIGRSGIYET  275 (277)
T ss_dssp             EEEECSSSSCCGGGSEEEEEEEEEEEEEEE
T ss_pred             EEEeccccCCCCCCCCCCEEEEEECCCEEE
Confidence            9998742 21   233 5899999999997

PyMOL of d2pr9a1

>d3cpta1 d.110.7.1 (A:3-118) MEK binding partner 1, MP1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ioua_ d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure