Citrus Sinensis ID: 021735

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-------31
MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKERR
cccEEEEEEEEcccccEEEEEcccccccHHHHHHHHHHHHHHcccccccccEEEEccEEEEEEEEccEEEEEEEcccccHHHHHHHHHHHHHHHcHHccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHccccccccccccccccccccccccccccccccccEEEEEEEEEEEEEEcccccEEEEEEEEEEEEEEEccccccEEEEEcccHHHHcccccccccEEEEccccccccccccccccccEEEEEccccEEEEEEEEEcccccccEEEEEEEEEcccEEEEEEEEEEEcccccc
ccccEEEEEEEcccccEEEEEcccccccHHHHHHHHHHHHHHHHcccccccEEEEccEEEEEEEcccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccccccccccHHcccEcccccccEEcccEEEEEHHHHEEEEEcccccEEEEEEEEEEEEEEEcccccccEEccccEEEEEcccccccccEEEEEccEEEEEEEEcccccccEEEEEcccccEEEEEEEccccccccEEEEEEEEEccccEEEEEEEEEEcccccc
MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFiekegdpqsqnpvvfdngvTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEImdfgfpqftEAKILSEFIKTdayrmevtqrppmavTNAVSWrsegirykkneVFLDVVESVNILVnsngqivrSDVVGALKMRTylsgmpecklglndrVLLEAqgrstkgkaidlddikfhQCVRLArfendrtisfippdgsfdlmTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKERR
MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFiekegdpqsqnPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEeleeeslrDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAyrmevtqrppmavtnavswrsegiRYKKNEVFLDVVESVNilvnsngqivrsdvVGALKMRTYLSGMPECKLGLNDRVLLEAQGRstkgkaidlddiKFHQCVRLarfendrtisfippdgsFDLMTYRLSTQVKPLIWVEAqierhsrsrieIMVKARSQFKERR
MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKERR
******ALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEK*******NPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERH*******************
*AGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIK***************************RYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLE*******GKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKA*SQF****
MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKA********
*AGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAY***VTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQF****
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MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKERR
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 ?
Query308 2.2.26 [Sep-21-2011]
Q9BXS5 423 AP-1 complex subunit mu-1 yes no 0.980 0.713 0.596 1e-111
Q2KJ81 423 AP-1 complex subunit mu-1 yes no 0.980 0.713 0.596 1e-111
P35585 423 AP-1 complex subunit mu-1 yes no 0.980 0.713 0.596 1e-111
Q32Q06 423 AP-1 complex subunit mu-1 yes no 0.980 0.713 0.596 1e-111
Q54HS9 428 AP-1 complex subunit mu O yes no 0.980 0.705 0.582 1e-109
P35602 422 AP-1 complex subunit mu-1 yes no 0.980 0.715 0.578 1e-109
Q9HFE5 426 AP-1 complex subunit mu-1 yes no 0.983 0.711 0.574 1e-106
Q9Y6Q5 423 AP-1 complex subunit mu-2 no no 0.980 0.713 0.580 1e-106
Q3SYW1 423 AP-1 complex subunit mu-2 no no 0.980 0.713 0.573 1e-105
Q9WVP1 423 AP-1 complex subunit mu-2 no no 0.980 0.713 0.573 1e-104
>sp|Q9BXS5|AP1M1_HUMAN AP-1 complex subunit mu-1 OS=Homo sapiens GN=AP1M1 PE=1 SV=3 Back     alignment and function desciption
 Score =  401 bits (1030), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 182/305 (59%), Positives = 249/305 (81%), Gaps = 3/305 (0%)

Query: 4   AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFI 63
           +ASA+++LD+KG+VLI R+YRGDV   + E F    +EKE +    +P++   GV +M+I
Sbjct: 2   SASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGM-LSPILAHGGVRFMWI 60

Query: 64  QHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDF 123
           +HNN+YL+A S++N   + +  FL++V  VF  YF+ELEEES+RDNFV++YELLDE+MDF
Sbjct: 61  KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF 120

Query: 124 GFPQFTEAKILSEFIKTDAYRMEV-TQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVN 182
           G+PQ T++KIL E+I  + +++E    RPP  VTNAVSWRSEGI+Y+KNEVFLDV+ESVN
Sbjct: 121 GYPQTTDSKILQEYITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIESVN 180

Query: 183 ILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFH 242
           +LV++NG ++RS++VG++KMR +LSGMPE +LGLND+VL +  GR  K K+++L+D+KFH
Sbjct: 181 LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRG-KSKSVELEDVKFH 239

Query: 243 QCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARS 302
           QCVRL+RFENDRTISFIPPDG F+LM+YRL+T VKPLIW+E+ IE+HS SRIE M+KA+S
Sbjct: 240 QCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMIKAKS 299

Query: 303 QFKER 307
           QFK R
Sbjct: 300 QFKRR 304
Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the trans-Golgi network (TGN) and endosomes. The AP complexes mediate the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules.
Homo sapiens (taxid: 9606)
>sp|Q2KJ81|AP1M1_BOVIN AP-1 complex subunit mu-1 OS=Bos taurus GN=AP1M1 PE=1 SV=3 Back     alignment and function description
>sp|P35585|AP1M1_MOUSE AP-1 complex subunit mu-1 OS=Mus musculus GN=Ap1m1 PE=1 SV=3 Back     alignment and function description
>sp|Q32Q06|AP1M1_RAT AP-1 complex subunit mu-1 OS=Rattus norvegicus GN=Ap1m1 PE=1 SV=3 Back     alignment and function description
>sp|Q54HS9|AP1M_DICDI AP-1 complex subunit mu OS=Dictyostelium discoideum GN=apm1 PE=1 SV=1 Back     alignment and function description
>sp|P35602|AP1M_CAEEL AP-1 complex subunit mu-1-I OS=Caenorhabditis elegans GN=unc-101 PE=2 SV=2 Back     alignment and function description
>sp|Q9HFE5|AP1M1_SCHPO AP-1 complex subunit mu-1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=apm1 PE=1 SV=1 Back     alignment and function description
>sp|Q9Y6Q5|AP1M2_HUMAN AP-1 complex subunit mu-2 OS=Homo sapiens GN=AP1M2 PE=1 SV=4 Back     alignment and function description
>sp|Q3SYW1|AP1M2_BOVIN AP-1 complex subunit mu-2 OS=Bos taurus GN=AP1M2 PE=1 SV=3 Back     alignment and function description
>sp|Q9WVP1|AP1M2_MOUSE AP-1 complex subunit mu-2 OS=Mus musculus GN=Ap1m2 PE=1 SV=3 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 ?
Query308
255540561 428 clathrin coat assembly protein ap-1, put 0.996 0.717 0.954 1e-175
343172625 428 AP-1 complex subunit mu, partial [Silene 0.996 0.717 0.947 1e-174
225470599 428 PREDICTED: AP-1 complex subunit mu-1 [Vi 0.996 0.717 0.941 1e-173
224100165 428 predicted protein [Populus trichocarpa] 0.996 0.717 0.915 1e-171
449434961 428 PREDICTED: AP-1 complex subunit mu-1-lik 0.996 0.717 0.928 1e-171
224107797 428 predicted protein [Populus trichocarpa] 0.996 0.717 0.915 1e-170
356567664 428 PREDICTED: AP-1 complex subunit mu-1-I-l 0.996 0.717 0.915 1e-170
356526771 428 PREDICTED: AP-1 complex subunit mu-1-I-l 0.996 0.717 0.915 1e-170
449478746 428 PREDICTED: AP-1 complex subunit mu-1-lik 0.993 0.714 0.924 1e-170
356497456 428 PREDICTED: AP-1 complex subunit mu-1-lik 0.996 0.717 0.915 1e-169
>gi|255540561|ref|XP_002511345.1| clathrin coat assembly protein ap-1, putative [Ricinus communis] gi|223550460|gb|EEF51947.1| clathrin coat assembly protein ap-1, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  620 bits (1600), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 293/307 (95%), Positives = 304/307 (99%)

Query: 1   MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTY 60
           MAGAASALFLLDIKGRVLIWRDYRGDVSA+QAERFFTK IEKEGDPQSQ+PVV+DNGVTY
Sbjct: 1   MAGAASALFLLDIKGRVLIWRDYRGDVSAVQAERFFTKLIEKEGDPQSQDPVVYDNGVTY 60

Query: 61  MFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEI 120
           MFIQH+N+YLM+ASRQNCNAASILLFLHR+ DVFKHYFEELEEESLRDNFVVVYELLDEI
Sbjct: 61  MFIQHSNIYLMSASRQNCNAASILLFLHRLVDVFKHYFEELEEESLRDNFVVVYELLDEI 120

Query: 121 MDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVES 180
           MDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVES
Sbjct: 121 MDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVES 180

Query: 181 VNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIK 240
           VNILVNSNGQI+RSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGR+TKGKAIDLDDIK
Sbjct: 181 VNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRATKGKAIDLDDIK 240

Query: 241 FHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKA 300
           FHQCVRLARFENDRTISFIPPDG+FDLMTYRLSTQVKPLIWVEAQ+ERHSRSRIE MVKA
Sbjct: 241 FHQCVRLARFENDRTISFIPPDGAFDLMTYRLSTQVKPLIWVEAQVERHSRSRIEFMVKA 300

Query: 301 RSQFKER 307
           RSQFKER
Sbjct: 301 RSQFKER 307

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|343172625|gb|AEL99016.1| AP-1 complex subunit mu, partial [Silene latifolia] gi|343172627|gb|AEL99017.1| AP-1 complex subunit mu, partial [Silene latifolia] Back     alignment and taxonomy information
>gi|225470599|ref|XP_002274463.1| PREDICTED: AP-1 complex subunit mu-1 [Vitis vinifera] gi|296083422|emb|CBI23375.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224100165|ref|XP_002311769.1| predicted protein [Populus trichocarpa] gi|222851589|gb|EEE89136.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449434961|ref|XP_004135264.1| PREDICTED: AP-1 complex subunit mu-1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224107797|ref|XP_002314604.1| predicted protein [Populus trichocarpa] gi|222863644|gb|EEF00775.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356567664|ref|XP_003552037.1| PREDICTED: AP-1 complex subunit mu-1-I-like [Glycine max] Back     alignment and taxonomy information
>gi|356526771|ref|XP_003531990.1| PREDICTED: AP-1 complex subunit mu-1-I-like [Glycine max] Back     alignment and taxonomy information
>gi|449478746|ref|XP_004155408.1| PREDICTED: AP-1 complex subunit mu-1-like, partial [Cucumis sativus] Back     alignment and taxonomy information
>gi|356497456|ref|XP_003517576.1| PREDICTED: AP-1 complex subunit mu-1-like [Glycine max] 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 ?
Query308
TAIR|locus:2036606 428 HAP13 "HAPLESS 13" [Arabidopsi 0.996 0.717 0.902 5.4e-150
TAIR|locus:2019913 428 AT1G10730 [Arabidopsis thalian 0.996 0.717 0.889 1.6e-148
ASPGD|ASPL0000077433 446 AN8795 [Emericella nidulans (t 0.983 0.679 0.597 1.4e-103
UNIPROTKB|F1NZQ2 416 AP1M1 "Uncharacterized protein 0.980 0.725 0.596 1.8e-101
UNIPROTKB|Q2KJ81 423 AP1M1 "AP-1 complex subunit mu 0.980 0.713 0.596 3e-101
UNIPROTKB|J9P1I0 423 AP1M1 "Uncharacterized protein 0.980 0.713 0.596 3e-101
UNIPROTKB|Q9BXS5 423 AP1M1 "AP-1 complex subunit mu 0.980 0.713 0.596 3e-101
UNIPROTKB|F2Z5I7 423 AP1M1 "Uncharacterized protein 0.980 0.713 0.596 3e-101
MGI|MGI:102776 423 Ap1m1 "adaptor-related protein 0.980 0.713 0.596 4.9e-101
RGD|1307653 423 Ap1m1 "adaptor-related protein 0.980 0.713 0.596 4.9e-101
TAIR|locus:2036606 HAP13 "HAPLESS 13" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1464 (520.4 bits), Expect = 5.4e-150, P = 5.4e-150
 Identities = 277/307 (90%), Positives = 298/307 (97%)

Query:     1 MAGAASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTY 60
             MAGAASALFLLDIKGRVL+WRDYRGDVSA QAERFFTK IEKEGD QS +PV +DNGVTY
Sbjct:     1 MAGAASALFLLDIKGRVLVWRDYRGDVSAAQAERFFTKLIEKEGDSQSNDPVAYDNGVTY 60

Query:    61 MFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEI 120
             MF+QH+NVYLM ASRQNCNAAS+L FLHRV DVFKHYFEELEEESLRDNFVVVYELLDE+
Sbjct:    61 MFVQHSNVYLMIASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEM 120

Query:   121 MDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVES 180
             MDFG+PQ+TEA+ILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGI+YKKNEVFLDV+E+
Sbjct:   121 MDFGYPQYTEARILSEFIKTDAYRMEVTQRPPMAVTNAVSWRSEGIQYKKNEVFLDVIEN 180

Query:   181 VNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIK 240
             VNILVNSNGQIVRSDVVGALKMRTYL+GMPECKLGLNDRVLLEAQGR+TKGKAIDL+DIK
Sbjct:   181 VNILVNSNGQIVRSDVVGALKMRTYLTGMPECKLGLNDRVLLEAQGRATKGKAIDLEDIK 240

Query:   241 FHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKA 300
             FHQCVRLARFENDRTISFIPPDG+FDLMTYRLSTQVKPLIWVEAQIE HSRSR+E+++KA
Sbjct:   241 FHQCVRLARFENDRTISFIPPDGAFDLMTYRLSTQVKPLIWVEAQIESHSRSRVEMLIKA 300

Query:   301 RSQFKER 307
             RSQFKER
Sbjct:   301 RSQFKER 307
GO:0006810 "transport" evidence=IEA
GO:0006886 "intracellular protein transport" evidence=IEA;ISS
GO:0016192 "vesicle-mediated transport" evidence=IEA
GO:0030125 "clathrin vesicle coat" evidence=ISS
GO:0030131 "clathrin adaptor complex" evidence=IEA
GO:0005829 "cytosol" evidence=IDA
TAIR|locus:2019913 AT1G10730 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ASPGD|ASPL0000077433 AN8795 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
UNIPROTKB|F1NZQ2 AP1M1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q2KJ81 AP1M1 "AP-1 complex subunit mu-1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|J9P1I0 AP1M1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q9BXS5 AP1M1 "AP-1 complex subunit mu-1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z5I7 AP1M1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:102776 Ap1m1 "adaptor-related protein complex AP-1, mu subunit 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1307653 Ap1m1 "adaptor-related protein complex 1, mu 1 subunit" [Rattus norvegicus (taxid:10116)] 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) ?
P35585AP1M1_MOUSENo assigned EC number0.59670.98050.7139yesno
Q54HS9AP1M_DICDINo assigned EC number0.58250.98050.7056yesno
P35602AP1M_CAEELNo assigned EC number0.57890.98050.7156yesno
Q32Q06AP1M1_RATNo assigned EC number0.59670.98050.7139yesno
Q9BXS5AP1M1_HUMANNo assigned EC number0.59670.98050.7139yesno
Q2KJ81AP1M1_BOVINNo assigned EC number0.59670.98050.7139yesno
Q9HFE5AP1M1_SCHPONo assigned EC number0.57420.98370.7112yesno

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 ?
Query308
cd09250 268 cd09250, AP-1_Mu1_Cterm, C-terminal domain of medi 1e-107
cd09258 270 cd09258, AP-1_Mu1A_Cterm, C-terminal domain of med 3e-91
cd09259 264 cd09259, AP-1_Mu1B_Cterm, C-terminal domain of med 1e-84
cd09251 263 cd09251, AP-2_Mu2_Cterm, C-terminal domain of medi 8e-68
pfam00928228 pfam00928, Adap_comp_sub, Adaptor complexes medium 2e-57
cd09253 271 cd09253, AP-4_Mu4_Cterm, C-terminal domain of medi 8e-45
cd09252 248 cd09252, AP-3_Mu3_Cterm, C-terminal domain of medi 7e-43
cd07954 239 cd07954, AP_MHD_Cterm, C-terminal domain of adapto 8e-40
cd09261 254 cd09261, AP-3_Mu3B_Cterm, C-terminal domain of med 1e-24
cd09260 254 cd09260, AP-3_Mu3A_Cterm, C-terminal domain of med 1e-24
cd09255 308 cd09255, AP-like_stonins_MHD, Mu homology domain ( 5e-22
cd09263 314 cd09263, AP_stonin-2_MHD, Mu homology domain (MHD) 3e-13
cd09262 309 cd09262, AP_stonin-1_MHD, Mu homology domain (MHD) 8e-13
cd09256 271 cd09256, AP_MuD_MHD, Mu-homology domain (MHD) of a 0.003
>gnl|CDD|211361 cd09250, AP-1_Mu1_Cterm, C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex AP-1 Back     alignment and domain information 
 Score =  312 bits (802), Expect = e-107
 Identities = 119/152 (78%), Positives = 142/152 (93%)

Query: 156 TNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLG 215
           TNAVSWR EGI+YKKNEVFLDV+ESVN+LV+ NGQ++RS++VG +KMR+YLSGMPE KLG
Sbjct: 1   TNAVSWRPEGIKYKKNEVFLDVIESVNLLVDLNGQVLRSEIVGTIKMRSYLSGMPELKLG 60

Query: 216 LNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQ 275
           LND+VL EA GRS+KGKA++L+D+KFHQCVRL+RFENDRTISFIPPDG F+LM+YRLSTQ
Sbjct: 61  LNDKVLFEATGRSSKGKAVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLSTQ 120

Query: 276 VKPLIWVEAQIERHSRSRIEIMVKARSQFKER 307
           VKPLIWVE  +ERHSRSR+EIMVKA++QFK R
Sbjct: 121 VKPLIWVEPTVERHSRSRVEIMVKAKTQFKRR 152

AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1 subunit, which includes two closely related homologs, mu1A (encoded by ap1m1) and mu1B (encoded by ap1m2). Mu1A is ubiquitously expressed, but mu1B is expressed exclusively in polarized epithelial cells. AP-1 has been implicated in bi-directional transport between the trans-Golgi network (TGN) and endosomes. It plays an essential role in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Epithelial cell-specific AP-1 is also involved in sorting to the basolateral surface of polarized epithelial cells. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Length = 268
>gnl|CDD|211369 cd09258, AP-1_Mu1A_Cterm, C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-1 Back     alignment and domain information
>gnl|CDD|211370 cd09259, AP-1_Mu1B_Cterm, C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated adaptor protein (AP) complex AP-1 Back     alignment and domain information
>gnl|CDD|211362 cd09251, AP-2_Mu2_Cterm, C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-2 Back     alignment and domain information
>gnl|CDD|216199 pfam00928, Adap_comp_sub, Adaptor complexes medium subunit family Back     alignment and domain information
>gnl|CDD|211364 cd09253, AP-4_Mu4_Cterm, C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4 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
>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|211372 cd09261, AP-3_Mu3B_Cterm, C-terminal domain of medium Mu3B subunit in neuron-specific adaptor protein (AP) complex AP-3 Back     alignment and domain information
>gnl|CDD|211371 cd09260, AP-3_Mu3A_Cterm, C-terminal domain of medium Mu3A subunit in ubiquitously expressed adaptor protein (AP) complex AP-3 Back     alignment and domain information
>gnl|CDD|211366 cd09255, AP-like_stonins_MHD, Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins Back     alignment and domain information
>gnl|CDD|211374 cd09263, AP_stonin-2_MHD, Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2 Back     alignment and domain information
>gnl|CDD|211373 cd09262, AP_stonin-1_MHD, Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor) Back     alignment and domain information
>gnl|CDD|211367 cd09256, AP_MuD_MHD, Mu-homology domain (MHD) of a adaptor protein (AP) encoded by mu-2 related death-inducing gene, MuD (also known as MUDENG) Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 308
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
PF01217141 Clat_adaptor_s: Clathrin adaptor complex small cha 99.97
KOG2635 512 consensus Medium subunit of clathrin adaptor compl 99.96
COG5030152 APS2 Clathrin adaptor complex, small subunit [Intr 99.9
KOG0934145 consensus Clathrin adaptor complex, small subunit 99.86
KOG0936182 consensus Clathrin adaptor complex, small subunit 99.84
KOG0935143 consensus Clathrin adaptor complex, small subunit 99.81
KOG2677 922 consensus Stoned B synaptic vesicle biogenesis pro 99.81
KOG3343175 consensus Vesicle coat complex COPI, zeta subunit 99.78
COG5541187 RET3 Vesicle coat complex COPI, zeta subunit [Post 99.33
PF03164 415 Mon1: Trafficking protein Mon1; InterPro: IPR00435 96.57
PF15001189 AP-5_subunit_s1: AP-5 complex subunit sigma-1 94.98
PF08923119 MAPKK1_Int: Mitogen-activated protein kinase kinas 94.21
KOG0997 523 consensus Uncharacterized conserved protein Sand [ 93.79
COG5122134 TRS23 Transport protein particle (TRAPP) complex s 93.7
PF10291 257 muHD: Muniscin C-terminal mu homology domain; Inte 93.04
PF04099142 Sybindin: Sybindin-like family ; InterPro: IPR0072 92.85
PF1377483 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3 92.62
KOG0859217 consensus Synaptobrevin/VAMP-like protein [Intrace 92.0
PF09201148 SRX: SRX; InterPro: IPR015284 The signal recogniti 88.67
KOG0781 587 consensus Signal recognition particle receptor, al 87.59
KOG3369199 consensus Transport protein particle (TRAPP) compl 82.67
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information 
Probab=100.00  E-value=7.7e-77  Score=534.50  Aligned_cols=301  Identities=40%  Similarity=0.729  Sum_probs=276.9

Q ss_pred             ceeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHH
Q 021735            4 AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASI   83 (308)
Q Consensus         4 MI~~i~Il~~~G~~ll~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~~   83 (308)
                      ||+++||+|.+|++++.|.||+|..++..+.|+-++.++..   ..+|+..++++.|+|.+.++||+++++.+|.|.+.+
T Consensus         1 misglfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~d---~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v   77 (446)
T KOG0938|consen    1 MISGLFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLD---VRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAV   77 (446)
T ss_pred             CcceEEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhccc---cCCCeeEecceeEEEEeeccEEEEEEecCCCchhhH
Confidence            89999999999999999999999999999999999998743   358999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhcccccccccc----C-----CCC--
Q 021735           84 LLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVT----Q-----RPP--  152 (308)
Q Consensus        84 ~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~----~-----~~~--  152 (308)
                      ++||..+..++..|||+.+|+.|++||.++||+||||+|+||||+|++++|+.+|..+++..+-.    .     .++  
T Consensus        78 ~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~ls~k~s~~sq~~~~  157 (446)
T KOG0938|consen   78 FEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVLSSKSSPTSQATEL  157 (446)
T ss_pred             HHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhccccccCCcCCCCcccccc
Confidence            99999999999999999999999999999999999999999999999999999999988765411    1     111  


Q ss_pred             --CcccCCCcCcccCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhh-cc---
Q 021735          153 --MAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEA-QG---  226 (308)
Q Consensus       153 --~~~~~~~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~-~~---  226 (308)
                        ++.++.++||++|++|+|||+|+||+|+++.+++++|++++++|+|.|.|+++|||||+|++||||.+.+.. ++   
T Consensus       158 ~ssqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmPeckfGlNDkl~~e~kq~esk  237 (446)
T KOG0938|consen  158 RSSQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMPECKFGLNDKLGMESKQSESK  237 (446)
T ss_pred             cccccccccccccccceeccceeEeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCcccccccCcccceeecccccc
Confidence              334567999999999999999999999999999999999999999999999999999999999999987762 21   


Q ss_pred             --------CC-CCCceeecccccccccccccCccCCCeEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEcCceEEEEE
Q 021735          227 --------RS-TKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIM  297 (308)
Q Consensus       227 --------~~-~~~~~~~l~~~~fH~cV~~~~f~~~~~i~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~~~  297 (308)
                              ++ +....+.|+||+||+||++++|++++.|+|+||||+|+||+||++.+.++||+|.|.+++.+.+++++.
T Consensus       238 s~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enInlPFrV~PiV~el~r~kie~r  317 (446)
T KOG0938|consen  238 SDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENINLPFRVTPIVTELGRTKIEYR  317 (446)
T ss_pred             ccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCcccceEeeeheecccceeEEEE
Confidence                    11 133458899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeeccCCC
Q 021735          298 VKARSQFKER  307 (308)
Q Consensus       298 i~l~~~~~~~  307 (308)
                      +++|++||++
T Consensus       318 i~iks~f~~k  327 (446)
T KOG0938|consen  318 ITIKSLFPPK  327 (446)
T ss_pred             EEEeccCCch
Confidence            9999999875

>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
>KOG2635 consensus Medium subunit of clathrin adaptor complex [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
>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
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport] 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
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1 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
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown] Back     alignment and domain information
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion] 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
>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
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PF09201 SRX: SRX; InterPro: IPR015284 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ] Back     alignment and domain information
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport] 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 ?
Query308
1w63_M 423 Ap1 Clathrin Adaptor Core Length = 423 1e-112
2bp5_M 435 Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second D 7e-68
2xa7_M 446 Ap2 Clathrin Adaptor Core In Active Complex With Ca 1e-66
4en2_M 266 Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain 8e-62
4emz_A 266 Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain 1e-58
1i31_A 314 Mu2 Adaptin Subunit (Ap50) Of Ap2 Clathrin Adaptor, 2e-40
1bw8_A 321 Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second D 2e-40
1bxx_A 285 Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second D 3e-39
2pr9_A 299 Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second D 3e-39
1h6e_A 288 Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second D 3e-37
3ml6_A 385 A Complex Between Dishevlled2 And Clathrin Adaptor 4e-34
4ikn_A 261 Crystal Structure Of Adaptor Protein Complex 3 (ap- 2e-21
3l81_A 301 Crystal Structure Of Adaptor Protein Complex 4 (Ap- 6e-17
>pdb|1W63|M Chain M, Ap1 Clathrin Adaptor Core Length = 423 Back     alignment and structure 
Iteration: 1

 Score =  401 bits (1031), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 183/305 (60%), Positives = 249/305 (81%), Gaps = 3/305 (0%)
Query: 4   AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFI 63
           +ASA+++LD+KG+VLI R+YRGDV   + E F    +EKE +    +P++   GV +M+I
Sbjct: 2   SASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKE-EEGMLSPILAHGGVRFMWI 60
Query: 64  QHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDF 123
           +HNN+YL+A S++N   + +  FL++V  VF  YF+ELEEES+RDNFV++YELLDE+MDF
Sbjct: 61  KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF 120
Query: 124 GFPQFTEAKILSEFIKTDAYRMEV-TQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVESVN 182
           G+PQ T++KIL EFI  + +++E    RPP  VTNAVSWRSEGI+Y+KNEVFLDV+E+VN
Sbjct: 121 GYPQTTDSKILQEFITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN 180
Query: 183 ILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFH 242
           +LV++NG ++RS++VG++KMR +LSGMPE +LGLND+VL +  GR  K K+++L+D+KFH
Sbjct: 181 LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRG-KSKSVELEDVKFH 239
Query: 243 QCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARS 302
           QCVRL+RFENDRTISFIPPDG F+LM+YRL+T VKPLIW+E+ IE+HS SRIE MVKA+S
Sbjct: 240 QCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKS 299
Query: 303 QFKER 307
           QFK R
Sbjct: 300 QFKRR 304
>pdb|2BP5|M Chain M, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain), Complexed With Non-Canonical Internalization Peptide Vedyeqglsg Length = 435 Back     alignment and structure
>pdb|2XA7|M Chain M, Ap2 Clathrin Adaptor Core In Active Complex With Cargo Peptides Length = 446 Back     alignment and structure
>pdb|4EN2|M Chain M, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1 Adaptin Subunit Of Ap1 Adaptor (Second Domain) Length = 266 Back     alignment and structure
>pdb|4EMZ|A Chain A, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1 Adaptin Subunit Of Ap1 Adaptor (Second Domain) Length = 266 Back     alignment and structure
>pdb|1I31|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Clathrin Adaptor, Complexed With Egfr Internalization Peptide Fyralm At 2.5 A Resolution Length = 314 Back     alignment and structure
>pdb|1BW8|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain), Complexed With Egfr Internalization Peptide Fyralm Length = 321 Back     alignment and structure
>pdb|1BXX|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain), Complexed With Tgn38 Internalization Peptide Dyqrln Length = 285 Back     alignment and structure
>pdb|2PR9|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain), Complexed With Gabaa Receptor-Gamma2 Subunit-Derived Internalization Peptide Deeygyecl Length = 299 Back     alignment and structure
>pdb|1H6E|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain), Complexed With Ctla-4 Internalization Peptide Ttgvyvkmppt Length = 288 Back     alignment and structure
>pdb|3ML6|A Chain A, A Complex Between Dishevlled2 And Clathrin Adaptor Ap-2 Length = 385 Back     alignment and structure
>pdb|4IKN|A Chain A, Crystal Structure Of Adaptor Protein Complex 3 (ap-3) Mu3a Subunit C- Terminal Domain, In Complex With A Sorting Peptide From Tgn38 Length = 261 Back     alignment and structure
>pdb|3L81|A Chain A, Crystal Structure Of Adaptor Protein Complex 4 (Ap-4) Mu4 Su Terminal Domain, In Complex With A Sorting Peptide From The Precursor Protein (App) Length = 301 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 ?
Query308
2vgl_M 435 AP-2 complex subunit MU-1; cytoplasmic vesicle, al 6e-88
1w63_M 423 Adaptor-related protein complex 1, MU 1 subunit; e 2e-85
1i31_A 314 Clathrin coat assembly protein AP50; beta-sandwich 3e-57
3l81_A 301 AP-4 complex subunit MU-1; immunoglobulin-like bet 2e-50
4en2_M 266 AP-1 complex subunit MU-1; human immunodeficiency 3e-50
3ml6_A 385 Chimeric complex between protein dishevlled2 HOMO 6e-50
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 8e-27
1w63_Q158 Adapter-related protein complex 1 sigma 1A subunit 2e-26
3tjz_C153 Coatomer subunit zeta-1; protein trafficking, golg 1e-18
>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
 Score =  268 bits (686), Expect = 6e-88
 Identities = 125/315 (39%), Positives = 195/315 (61%), Gaps = 14/315 (4%)

Query: 6   SALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQH 65
             LF+ + KG VLI R YR D+     + F    I      +S  PV      ++  ++ 
Sbjct: 3   GGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRS--PVTNIARTSFFHVKR 60

Query: 66  NNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGF 125
           +N++L A ++QN NAA +  FL+++ DV   YF ++ EE++++NFV++YELLDEI+DFG+
Sbjct: 61  SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY 120

Query: 126 PQFTEAKILSEFI-----KTDAYRMEVTQRPPMAVTNAVSWRSEGIRYKKNEVFLDVVES 180
           PQ +E   L  FI     K+     E   +    VT  + WR EGI+Y++NE+FLDV+ES
Sbjct: 121 PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES 180

Query: 181 VNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRST-------KGKA 233
           VN+L++  GQ++ + V G + M++YLSGMPECK G+ND++++E QG+ T         ++
Sbjct: 181 VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQS 240

Query: 234 IDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSR 293
           I +DD  FHQCVRL++F+++R+ISFIPPDG F+LM YR +  +     V   +    R++
Sbjct: 241 IAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTK 300

Query: 294 IEIMVKARSQFKERR 308
           +E+ V  +S FK   
Sbjct: 301 LEVKVVIKSNFKPSL 315
>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
>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
>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
>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
>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_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
>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
>3tjz_C Coatomer subunit zeta-1; protein trafficking, golgi membrane, protein transport-prote binding complex; HET: GNP; 2.90A {Bos taurus} PDB: 2hf6_A Length = 153 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query308
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
3l81_A 301 AP-4 complex subunit MU-1; immunoglobulin-like bet 100.0
3ml6_A 385 Chimeric complex between protein dishevlled2 HOMO 100.0
1w63_Q158 Adapter-related protein complex 1 sigma 1A subunit 100.0
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 100.0
3tjz_C153 Coatomer subunit zeta-1; protein trafficking, golg 99.98
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 95.34
4b93_A189 Vesicle-associated membrane protein 7; endocytosis 93.41
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 93.37
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 93.35
3cpt_A143 Mitogen-activated protein kinase kinase 1- interac 92.81
3cue_A219 Transport protein particle 23 kDa subunit; membran 92.8
1nrj_A158 Signal recognition particle receptor alpha subunit 92.31
3g9h_A 328 Suppressor of yeast profilin deletion; SYP1, MU, a 91.7
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 91.62
2fh5_A185 Signal recognition particle receptor alpha subunit 90.41
2j3t_C145 Trafficking protein particle complex subunit 1, tr 89.8
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 83.77
2j3w_A142 Sedlin, trafficking protein particle complex prote 83.19
3cue_C159 Transport protein particle 18 kDa subunit; membran 81.18
>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=8e-74  Score=556.00  Aligned_cols=302  Identities=40%  Similarity=0.775  Sum_probs=261.9

Q ss_pred             ceeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHH
Q 021735            4 AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASI   83 (308)
Q Consensus         4 MI~~i~Il~~~G~~ll~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~~   83 (308)
                      ||+++||+|++|+++++|+|+++.++...+.|.+.+....+.  ..+|++++++++|+|+++++|||+|+++.++||+++
T Consensus         1 MI~~i~I~~~~Gk~~l~k~y~~~~~~~~~~~f~~~v~~~~~~--~~~~ii~~~~~~~vy~~~~~Lyfv~~~~~~~n~l~~   78 (435)
T 2vgl_M            1 MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQ--VRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMV   78 (435)
T ss_dssp             CCCEEEEECTTCCEEEEEECSSSCCHHHHHHHHHHTTTCSSC--CCCSEEEETTEEEEEEEETTEEEEEEESSCCCHHHH
T ss_pred             CeEEEEEECCCCCEEEEEecCCCCChhHHHHHHHHHhccccC--CCCCEEEECCEEEEEEEECCEEEEEEecCCCCHHHH
Confidence            899999999999999999999988888889999998865422  468999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhccccccccc-----cCCCCCcccCC
Q 021735           84 LLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEV-----TQRPPMAVTNA  158 (308)
Q Consensus        84 ~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~-----~~~~~~~~~~~  158 (308)
                      ++|||+++++|++||++++|++|++||++||++||||+|+|+||+|+++.|++++.++++..+.     .+.+|++++++
T Consensus        79 le~L~~~v~vl~~yf~~v~E~~I~~Nf~~vy~lLDE~id~G~~~~t~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  158 (435)
T 2vgl_M           79 FEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQ  158 (435)
T ss_dssp             HHHHHHHHHHHHHHHSSCCHHHHHHTHHHHHHHHHHHEETTEECCCCHHHHGGGCCCCCCCCC-----------------
T ss_pred             HHHHHHHHHHHHHHHhccCHHHHHHhHHHHHHHHHHHhcCCEEEecCHHHHHHHhccccccccccccccccccccccccc
Confidence            9999999999999999999999999999999999999999999999999999999999987643     12345566778


Q ss_pred             CcCcccCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhhccCC-----C--CC
Q 021735          159 VSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRS-----T--KG  231 (308)
Q Consensus       159 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~-----~--~~  231 (308)
                      +|||+.|++|++|||||||+|+++++++++|.+++++|.|+|.|+|+|+|+|+|+|+||++..++..++.     +  ..
T Consensus       159 i~wr~~gi~~~~nei~vdV~E~v~~~~~~~G~v~~~eV~G~I~~~~~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~~~~  238 (435)
T 2vgl_M          159 IGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGK  238 (435)
T ss_dssp             CCSSCSCCCCSSCEEEEEEEEEEEEEECTTCCEEEEEEEEEEEEEEECSSCCEEEEEECSSSCC----------------
T ss_pred             cccccccCCcCcceEEEEEEEEEEEEEcCCCCEEEEEEEEEEEEEEEeCCCCeEEEEeCchhhccccccccccccccccc
Confidence            9999999999999999999999999999999999999999999999999999999999998766543211     0  12


Q ss_pred             ceeecccccccccccccCccCCCeEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEcCceEEEEEEEEeeccCCC
Q 021735          232 KAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKER  307 (308)
Q Consensus       232 ~~~~l~~~~fH~cV~~~~f~~~~~i~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~~~i~l~~~~~~~  307 (308)
                      .++.|+||+|||||++++|+++|+|+|+||||+|+||+||++.+..|||.+.||+++.+++++|+.++++++|+++
T Consensus       239 ~~~~l~d~~fH~cV~~~~f~~~r~isF~PPdg~F~Lm~Yr~~~~~~~P~~i~~~~~~~~~~~ve~~l~~~~~~~~~  314 (435)
T 2vgl_M          239 QSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPS  314 (435)
T ss_dssp             -CCCCCEEEECTTEEEC-----CCEEECCCSEEEEEEEEEECSSCCCSEEEEEEEECCTTTEEEEEEEEEECSCTT
T ss_pred             CceEccccccceeecHhHhccCceEEEECCCCcEEEEEEEecCCcCCCeEEEEEEEecCCCEEEEEEEEeCCCCCC
Confidence            4678999999999999999999999999999999999999998889999999999987778999999999999865
>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
>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
>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
>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
>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
>4b93_A Vesicle-associated membrane protein 7; endocytosis, exocytosis, snare; 2.00A {Mus musculus} PDB: 2dmw_A 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
>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
>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
>3cue_A Transport protein particle 23 kDa subunit; membrane traffic, GEF, tethering complex, RAB activation, GU nucleotide exchange factor; HET: PLM; 3.70A {Saccharomyces cerevisiae} Back     alignment and structure
>1nrj_A Signal recognition particle receptor alpha subunit homolog; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: d.110.4.4 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
>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
>2fh5_A Signal recognition particle receptor alpha subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Homo sapiens} SCOP: d.110.4.4 PDB: 2go5_1 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
>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
>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
>3cue_C Transport protein particle 18 kDa subunit; membrane traffic, GEF, tethering complex, RAB activation, GU nucleotide exchange factor; HET: PLM; 3.70A {Saccharomyces cerevisiae} 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 308
d2pr9a1 277 b.2.7.1 (A:159-435) Second domain of Mu2 adaptin s 1e-55
d2vglm2141 d.110.4.2 (M:1-141) Mu2 adaptin (clathrin coat ass 2e-37
d2vgls_142 d.110.4.2 (S:) Sigma2 adaptin (clathrin coat assem 9e-22
>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 =  179 bits (455), Expect = 1e-55
 Identities = 69/156 (44%), Positives = 109/156 (69%), Gaps = 7/156 (4%)

Query: 159 VSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLND 218
           + WR EGI+Y++NE+FLDV+ESVN+L++  GQ++ + V G + M++YLSGMPECK G+ND
Sbjct: 1   IGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMND 60

Query: 219 RVLLEAQGRS-------TKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYR 271
           ++++E QG+        +  ++I +DD  FHQCVRL++F+++R+ISFIPPDG F+LM YR
Sbjct: 61  KIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYR 120

Query: 272 LSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKER 307
            +  +     V   +    R+++E+ V  +S FK  
Sbjct: 121 TTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPS 156

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query308
d2pr9a1 277 Second domain of Mu2 adaptin subunit (ap50) of ap2 100.0
d2vglm2141 Mu2 adaptin (clathrin coat assembly protein AP50) 100.0
d2vgls_142 Sigma2 adaptin (clathrin coat assembly protein AP1 99.97
d3cpta1116 MEK binding partner 1, MP1 {Human (Homo sapiens) [ 95.79
d2fh5a1129 Signal recognition particle receptor alpha subunit 93.47
d1nrja_155 Srx domain of the signal recognition particle rece 88.71
d1ifqa_127 Sec22b {Mouse (Mus musculus) [TaxId: 10090]} 88.03
>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=4e-40  Score=299.55  Aligned_cols=149  Identities=46%  Similarity=0.932  Sum_probs=128.1

Q ss_pred             CcCcccCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhhcc-------CCCCC
Q 021735          159 VSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQG-------RSTKG  231 (308)
Q Consensus       159 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~-------~~~~~  231 (308)
                      +|||+.|++|++|||||||+|+++|+++++|.++.++|+|+|.|+|+|+|+|+|+|+||++..++...       +.+..
T Consensus         1 i~WR~~~i~y~~NEi~vDV~E~i~~~~~~~G~~~~~~V~G~I~~~s~LsG~P~~~l~Ln~~~~~~~~~~~~~~~~~~~~~   80 (277)
T d2pr9a1           1 IGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGK   80 (277)
T ss_dssp             CTTSCSCCCCSSCEEEEEEEEEEEEEECTTSCEEEEEEEEEEEEEEECSSSCEEEEEESBC------------------C
T ss_pred             CCccCCCCcccCCEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEecCCCCeEEEEecchhhccccccccccccccccc
Confidence            68999999999999999999999999999999999999999999999999999999999987665432       12345


Q ss_pred             ceeecccccccccccccCccCCCeEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEcCceEEEEEEEEeeccCCC
Q 021735          232 KAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKER  307 (308)
Q Consensus       232 ~~~~l~~~~fH~cV~~~~f~~~~~i~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~~~i~l~~~~~~~  307 (308)
                      .++.|+||+||+|||+++|+++|+|+|+||||+|+||+||++.+..+||.+.++++..+++++++.++++++++.+
T Consensus        81 ~~~~l~d~~fH~cV~~~~f~~~~~i~F~PPdG~F~Lm~Y~~~~~~~~P~~i~~~~~~~~~~~~~~~i~l~~~~~~~  156 (277)
T d2pr9a1          81 QSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPS  156 (277)
T ss_dssp             CCBCCSEEEECTTSBCC-----CCEEECCCSEEEEEEEEEECSSCCCCEEEEEEEEEETTTEEEEEEEEEECSCTT
T ss_pred             CceEccceeeeeccccccccccceEeecCCCCcEEEEEEEcCCCcCCCcEEEEEEEeccCcEEEEEEEEEeccCCC
Confidence            7889999999999999999999999999999999999999998889999999999988888999999999999864
>d3cpta1 d.110.7.1 (A:3-118) MEK binding partner 1, MP1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2fh5a1 d.110.4.4 (A:1-129) Signal recognition particle receptor alpha subunit, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1nrja_ d.110.4.4 (A:) Srx domain of the signal recognition particle receptor alpha-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ifqa_ d.110.4.1 (A:) Sec22b {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure