Psyllid ID: psy15590

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-------
MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTGVTNV
ccEEEEEEEEccccEEEEEccccccccccccccccccccccccccEEEEEcccccEEEEEEEEEEccccccccccccccccEEEcccccccccccccccccccccHHHHHHHcccccHHcEEcccccccccccEEEEEEccEEEEEEEccccEEEEEEEccccccHHHHHHHHHHHHHHHHHHcccccccccEEcHHHHHHHHHHHHHHHccccccc
cEEEEEEEEEccccEEEEcccccccEEEEEEccccEEEEEEEcccEEEEEEccccccEEEEEEEEEcccEccccEccccccHHHHHccccccccEEcccccccccHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEccEEEEEEEccccEEEEEEEccccccHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHcccccc
MVIYGVYIVSksgglifnydhnvpkienavtfqfplnikltpenkKIVVSFGQRDGILVGHVLTAVNDAvikngqlddgtdvleflskpesfpvkltftrprmttnEKIFLASMFYPLFaiasqlspepkssgievleadtfkLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADyalknpfyslempircELFDTHLQNLLQQHektgvtnv
MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEflskpesfpvkltftrprMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLqqhektgvtnv
MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTGVTNV
*VIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQL*******GIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLL***********
MVIYGVYIVSKSGGLIFNYDHNVPKI*******FPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVN***************LEFL**************************SMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQHEKT*****
MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQ*********
MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQHEKT*****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTGVTNV
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 ?
Query217 2.2.26 [Sep-21-2011]
Q5R9J9219 Trafficking protein parti yes N/A 0.981 0.972 0.563 1e-70
Q9Y296219 Trafficking protein parti yes N/A 0.981 0.972 0.563 1e-70
Q9ES56219 Trafficking protein parti yes N/A 0.981 0.972 0.558 1e-70
Q2TBL9219 Trafficking protein parti yes N/A 0.981 0.972 0.558 3e-70
Q69BT7219 Trafficking protein parti yes N/A 0.981 0.972 0.549 7e-69
Q54UU1135 Trafficking protein parti yes N/A 0.483 0.777 0.537 3e-26
O43041132 Transport protein particl yes N/A 0.493 0.810 0.495 5e-25
Q03784219 Trafficking protein parti yes N/A 0.806 0.799 0.258 6e-10
Q557G3142 Trafficking protein parti no N/A 0.479 0.732 0.336 1e-09
Q2KMM2145 Trafficking protein parti no N/A 0.465 0.696 0.274 1e-05
>sp|Q5R9J9|TPPC4_PONAB Trafficking protein particle complex subunit 4 OS=Pongo abelii GN=TRAPPC4 PE=2 SV=1 Back     alignment and function desciption
 Score =  266 bits (679), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 120/213 (56%), Positives = 162/213 (76%)

Query: 1   MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVG 60
           M I+ VY+V+K+GGLI+  D   P+ E   TF +PL++ L   +++++V+FGQRDGI VG
Sbjct: 1   MAIFSVYVVNKAGGLIYQLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVG 60

Query: 61  HVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFA 120
           H + A+N   +      DG +VLE+L  P ++PV + F RPR+T+NEK+ LASMF+ LFA
Sbjct: 61  HAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMFHSLFA 120

Query: 121 IASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADY 180
           I SQLSPE  SSGIE+LE DTFKLHCYQTLTG+KF+++ D  Q+G+D +L+KIYE+Y+D+
Sbjct: 121 IGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGIDSLLRKIYEIYSDF 180

Query: 181 ALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTG 213
           ALKNPFYSLEMPIRCELFD +L+  L+  EK G
Sbjct: 181 ALKNPFYSLEMPIRCELFDQNLKLALEVAEKAG 213
May play a role in vesicular transport from endoplasmic reticulum to Golgi.
Pongo abelii (taxid: 9601)
>sp|Q9Y296|TPPC4_HUMAN Trafficking protein particle complex subunit 4 OS=Homo sapiens GN=TRAPPC4 PE=1 SV=1 Back     alignment and function description
>sp|Q9ES56|TPPC4_MOUSE Trafficking protein particle complex subunit 4 OS=Mus musculus GN=Trappc4 PE=1 SV=1 Back     alignment and function description
>sp|Q2TBL9|TPPC4_BOVIN Trafficking protein particle complex subunit 4 OS=Bos taurus GN=TRAPPC4 PE=2 SV=1 Back     alignment and function description
>sp|Q69BT7|TPPC4_RAT Trafficking protein particle complex subunit 4 OS=Rattus norvegicus GN=Trappc4 PE=2 SV=1 Back     alignment and function description
>sp|Q54UU1|TPPC4_DICDI Trafficking protein particle complex subunit 4 OS=Dictyostelium discoideum GN=trappc4 PE=3 SV=1 Back     alignment and function description
>sp|O43041|TRS23_SCHPO Transport protein particle subunit trs23 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=trs23 PE=3 SV=1 Back     alignment and function description
>sp|Q03784|TRS23_YEAST Trafficking protein particle complex subunit 23 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TRS23 PE=1 SV=1 Back     alignment and function description
>sp|Q557G3|TPPC1_DICDI Trafficking protein particle complex subunit 1 OS=Dictyostelium discoideum GN=trappc1-1 PE=3 SV=1 Back     alignment and function description
>sp|Q2KMM2|TPPC1_RAT Trafficking protein particle complex subunit 1 OS=Rattus norvegicus GN=Trappc1 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 ?
Query217
66558617217 PREDICTED: trafficking protein particle 1.0 1.0 0.741 4e-93
350410142217 PREDICTED: trafficking protein particle 1.0 1.0 0.737 7e-93
340718883217 PREDICTED: trafficking protein particle 1.0 1.0 0.737 7e-93
380012539217 PREDICTED: trafficking protein particle 1.0 1.0 0.737 2e-92
332024033217 Trafficking protein particle complex sub 1.0 1.0 0.723 2e-91
156543860217 PREDICTED: trafficking protein particle 1.0 1.0 0.737 7e-91
91081497217 PREDICTED: similar to AGAP008106-PA [Tri 1.0 1.0 0.732 2e-90
307188894217 Trafficking protein particle complex sub 1.0 1.0 0.718 3e-90
307199208217 Trafficking protein particle complex sub 1.0 1.0 0.714 5e-90
383864336217 PREDICTED: trafficking protein particle 1.0 1.0 0.709 2e-89
>gi|66558617|ref|XP_624818.1| PREDICTED: trafficking protein particle complex subunit 4-like [Apis mellifera] Back     alignment and taxonomy information
 Score =  346 bits (887), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 161/217 (74%), Positives = 194/217 (89%)

Query: 1   MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVG 60
           MVIYGVYIVSKSGGLIFN+DHNVP+IEN  TF FPL+IKL  ENKKIVVSFGQ++GI VG
Sbjct: 1   MVIYGVYIVSKSGGLIFNHDHNVPRIENEKTFNFPLDIKLNYENKKIVVSFGQKEGINVG 60

Query: 61  HVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFA 120
           HVLTAVN++ +   +L++G DV+E L +PE+FPV L F+R RMTTNEKIFLASMFYPLFA
Sbjct: 61  HVLTAVNNSPVVGRELENGKDVIELLEQPENFPVLLRFSRARMTTNEKIFLASMFYPLFA 120

Query: 121 IASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADY 180
           IASQLSPEP+ SGIEVLEADTF+LHCYQTLTG+KF++V +  QSG++++LK++YELYADY
Sbjct: 121 IASQLSPEPRCSGIEVLEADTFRLHCYQTLTGIKFIVVAEPTQSGIEILLKRVYELYADY 180

Query: 181 ALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTGVTNV 217
           ALKNPFYSLEMPIRCELF+T+LQ+LL+  EK+G +NV
Sbjct: 181 ALKNPFYSLEMPIRCELFETNLQSLLENIEKSGASNV 217

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|350410142|ref|XP_003488960.1| PREDICTED: trafficking protein particle complex subunit 4-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|340718883|ref|XP_003397892.1| PREDICTED: trafficking protein particle complex subunit 4-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|380012539|ref|XP_003690337.1| PREDICTED: trafficking protein particle complex subunit 4-like [Apis florea] Back     alignment and taxonomy information
>gi|332024033|gb|EGI64251.1| Trafficking protein particle complex subunit 4 [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|156543860|ref|XP_001608154.1| PREDICTED: trafficking protein particle complex subunit 4-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|91081497|ref|XP_974526.1| PREDICTED: similar to AGAP008106-PA [Tribolium castaneum] gi|270005142|gb|EFA01590.1| hypothetical protein TcasGA2_TC007153 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|307188894|gb|EFN73443.1| Trafficking protein particle complex subunit 4 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|307199208|gb|EFN79895.1| Trafficking protein particle complex subunit 4 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|383864336|ref|XP_003707635.1| PREDICTED: trafficking protein particle complex subunit 4-like [Megachile rotundata] 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 ?
Query217
FB|FBgn0260861219 Trs23 [Drosophila melanogaster 1.0 0.990 0.682 2e-79
UNIPROTKB|F1NXY8218 TRAPPC4 "Uncharacterized prote 0.967 0.963 0.580 3.2e-65
UNIPROTKB|Q9Y296219 TRAPPC4 "Trafficking protein p 0.981 0.972 0.563 1.4e-64
UNIPROTKB|Q2TBL9219 TRAPPC4 "Trafficking protein p 0.981 0.972 0.558 2.9e-64
UNIPROTKB|F2Z5G7219 TRAPPC4 "Uncharacterized prote 0.981 0.972 0.558 2.9e-64
MGI|MGI:1926211219 Trappc4 "trafficking protein p 0.981 0.972 0.558 2.9e-64
UNIPROTKB|E2RSA9219 TRAPPC4 "Uncharacterized prote 0.981 0.972 0.553 9.7e-64
ZFIN|ZDB-GENE-040426-1734219 trappc4 "trafficking protein p 0.976 0.968 0.560 1.2e-63
UNIPROTKB|F1NU38210 TRAPPC4 "Uncharacterized prote 0.930 0.961 0.588 2.6e-63
RGD|1302991219 Trappc4 "trafficking protein p 0.981 0.972 0.549 1.1e-62
FB|FBgn0260861 Trs23 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 798 (286.0 bits), Expect = 2.0e-79, P = 2.0e-79
 Identities = 148/217 (68%), Positives = 181/217 (83%)

Query:     1 MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVG 60
             M+IYGVYIVSKSGGLIFN D+NVP+IE+  TF +PL++ L  ++KK+ VSF ++DGI VG
Sbjct:     1 MIIYGVYIVSKSGGLIFNLDNNVPRIEHEKTFTYPLDLVLDYDSKKVSVSFNRKDGINVG 60

Query:    61 HVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFA 120
             HVL AVN   +    LDDG DV   L  PE++P+ L F+RP+MTTNEKIFLASMFYPLFA
Sbjct:    61 HVLVAVNGMPVNGVTLDDGRDVRTTLDAPENYPINLKFSRPKMTTNEKIFLASMFYPLFA 120

Query:   121 IASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADY 180
             IASQLSPEPKSSGIE+LEADTF LHC+QTLTG+KF+I+ +T  +G+DL+L+K+YELY+DY
Sbjct:   121 IASQLSPEPKSSGIEILEADTFTLHCFQTLTGIKFIIISETGLNGIDLLLRKVYELYSDY 180

Query:   181 ALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTGVTNV 217
              LKNPFYSLEMPIRCELFD  LQ LL Q EKTG++N+
Sbjct:   181 VLKNPFYSLEMPIRCELFDNKLQELLAQVEKTGISNI 217
GO:0030008 "TRAPP complex" evidence=ISS
GO:0016192 "vesicle-mediated transport" evidence=ISS
GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=IEA
GO:0005801 "cis-Golgi network" evidence=IEA
UNIPROTKB|F1NXY8 TRAPPC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q9Y296 TRAPPC4 "Trafficking protein particle complex subunit 4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q2TBL9 TRAPPC4 "Trafficking protein particle complex subunit 4" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z5G7 TRAPPC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1926211 Trappc4 "trafficking protein particle complex 4" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E2RSA9 TRAPPC4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040426-1734 trappc4 "trafficking protein particle complex 4" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1NU38 TRAPPC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
RGD|1302991 Trappc4 "trafficking protein particle complex 4" [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) ?
Q9ES56TPPC4_MOUSENo assigned EC number0.55860.98150.9726yesN/A
Q69BT7TPPC4_RATNo assigned EC number0.54920.98150.9726yesN/A
Q9Y296TPPC4_HUMANNo assigned EC number0.56330.98150.9726yesN/A
Q54UU1TPPC4_DICDINo assigned EC number0.53770.48380.7777yesN/A
Q2TBL9TPPC4_BOVINNo assigned EC number0.55860.98150.9726yesN/A
Q5R9J9TPPC4_PONABNo assigned EC number0.56330.98150.9726yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query217
pfam04099135 pfam04099, Sybindin, Sybindin-like family 8e-53
COG5122134 COG5122, TRS23, Transport protein particle (TRAPP) 2e-34
pfam04628127 pfam04628, Sedlin_N, Sedlin, N-terminal conserved 2e-06
>gnl|CDD|146632 pfam04099, Sybindin, Sybindin-like family Back     alignment and domain information 
 Score =  165 bits (421), Expect = 8e-53
 Identities = 66/109 (60%), Positives = 79/109 (72%), Gaps = 1/109 (0%)

Query: 102 RMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDT 161
           ++TTNE   LA M + L AI+S+LSP P SSGIE LE DTFKLHC QTLTG+KF++V D 
Sbjct: 27  KLTTNEYKLLAGMLHSLHAISSKLSPLPGSSGIESLETDTFKLHCLQTLTGIKFVLVTDP 86

Query: 162 NQS-GLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 209
                 D +L+K YELY+DY LKNPFYSLEMPIRCELFD  L   ++  
Sbjct: 87  GTGPNRDSLLRKYYELYSDYVLKNPFYSLEMPIRCELFDEKLDQYVRSL 135

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. Length = 135
>gnl|CDD|227451 COG5122, TRS23, Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion] Back     alignment and domain information
>gnl|CDD|218183 pfam04628, Sedlin_N, Sedlin, N-terminal conserved region Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 217
KOG3369|consensus199 100.0
PF04099142 Sybindin: Sybindin-like family ; InterPro: IPR0072 100.0
KOG3368|consensus140 100.0
COG5122134 TRS23 Transport protein particle (TRAPP) complex s 100.0
PF04628132 Sedlin_N: Sedlin, N-terminal conserved region; Int 99.87
KOG3444|consensus121 99.6
COG5603136 TRS20 Subunit of TRAPP, an ER-Golgi tethering comp 99.56
KOG3487|consensus139 99.44
PF1377483 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3 92.86
PF1468588 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6 88.59
KOG0861|consensus198 86.7
PF08217 604 DUF1712: Fungal domain of unknown function (DUF171 85.58
PF0059581 PDZ: PDZ domain (Also known as DHR or GLGF) Coordi 85.13
cd0098885 PDZ_CTP_protease PDZ domain of C-terminal processi 81.08
cd0013670 PDZ PDZ domain, also called DHR (Dlg homologous re 80.91
>KOG3369|consensus Back     alignment and domain information 
Probab=100.00  E-value=2.1e-68  Score=447.04  Aligned_cols=199  Identities=57%  Similarity=0.947  Sum_probs=195.7

Q ss_pred             CeEEEEEEEeccceeEEecccCCCccccceecccCccccccccCceeEEeeccccceeeeeeEEeeeceeecccccCCCc
Q psy15590          1 MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGT   80 (217)
Q Consensus         1 M~iy~~~i~~~~~~~i~~~d~~~~~~~~~~t~~~p~~~~l~~~~~~~~v~~g~~~~~~~g~~~~~~ng~~~~~~~~~dg~   80 (217)
                      |+||++||+||+|||||++|...|+.|.| ||    |+.|...+.+++|+||++||||+||.+.+|||++|+|+.+.|| 
T Consensus         1 maI~~~~IINKsGgLIfq~e~~~~~~e~e-t~----d~~l~~~~~~~vvaf~~kdgik~~~~~~~vNg~~v~g~~~~~G-   74 (199)
T KOG3369|consen    1 MAIESLFIINKSGGLIFQREFGNPRQELE-TF----DLLLLASDLKVVVAFGSKDGIKVGHLVQAVNGENVNGYILYDG-   74 (199)
T ss_pred             CceEEEEEEecCCcEEEEeecCCcccccc-ch----hhhhhhcccceeEEeecccccchhheeeeecccccccceeccc-
Confidence            89999999999999999999999999999 87    8999999999999999999999999999999999999999999 


Q ss_pred             chhhhccCCCCCCeeeeeCCCCCCchhhHHHhhhhhcHHHHHhhhCCCCCCCceeEEecCcEEEEEEEeCCCcEEEEEec
Q psy15590         81 DVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGD  160 (217)
Q Consensus        81 ~~~~~~~~~~n~Pl~l~~~~~~l~sne~llLag~l~SL~~i~~kLsp~~~s~g~~~~~T~~yklh~yeT~TGiKFVlitd  160 (217)
                           |+.++|||++++|++|++++||+++|+|||||+++|++|+||.++++|++.++|++|++|||||.||+|||++++
T Consensus        75 -----l~~~~~ypv~~~f~~p~~ttNEkL~las~fhsl~aI~~qlsp~~ksSGie~LetdtF~l~~~QTlTG~KFVvis~  149 (199)
T KOG3369|consen   75 -----LSSPRNYPVNGKFGRPKLTTNEKLILASSFHSLFAISTQLSPEPKSSGIEVLETDTFTLHIFQTLTGTKFVVIAE  149 (199)
T ss_pred             -----ccCccccccccccCCCcccccchhhhhhhhcchhheeeccCCCCCCCceEEEEeccEEEEEEEccCCcEEEEEec
Confidence                 999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHHHHHHHHHHHHhhhhcCCCCCCCCcccchhHHHHHHHHHHHhh
Q psy15590        161 TNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQHE  210 (217)
Q Consensus       161 ~~~~~l~~~L~~IYelYvdyVlkNPfy~~~~pI~s~~Fd~~l~~ll~~~~  210 (217)
                      +..+.++.+|++||++|+|||+|||||++||||||++||.+|+.++++.|
T Consensus       150 ~~~~~aD~lLrKiYelYsDyvlKNPfYSlEMPIRc~lFDe~lk~~le~~e  199 (199)
T KOG3369|consen  150 PGTQGADSLLRKIYELYSDYVLKNPFYSLEMPIRCELFDEKLKFLLESAE  199 (199)
T ss_pred             CCchhHHHHHHHHHHHHHHHhhcCCccCcccceeHHHhhHHHHHHHhhcC
Confidence            99999999999999999999999999999999999999999999998764

>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
>KOG3368|consensus Back     alignment and domain information
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion] Back     alignment and domain information
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport Back     alignment and domain information
>KOG3444|consensus Back     alignment and domain information
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion] Back     alignment and domain information
>KOG3487|consensus 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
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A Back     alignment and domain information
>KOG0861|consensus Back     alignment and domain information
>PF08217 DUF1712: Fungal domain of unknown function (DUF1712); InterPro: IPR013176 The function of this fungal family of proteins is unknown Back     alignment and domain information
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ] Back     alignment and domain information
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts Back     alignment and domain information
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif) 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 ?
Query217
2zmv_A227 Crystal Structure Of Synbindin Length = 227 9e-72
2j3t_D219 The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 9e-72
2jsn_A96 Solution Structure Of The Atypical Pdz-Like Domain 4e-17
3cue_A219 Crystal Structure Of A Trapp Subassembly Activating 5e-11
2j3t_C145 The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 1e-06
1h3q_A140 Crystal Sturcture Of Sedl At 2.4 Angstroms Resoluti 8e-04
2j3w_A142 The Crystal Structure Of The Bet3-Trs31-Sedlin Comp 8e-04
>pdb|2ZMV|A Chain A, Crystal Structure Of Synbindin Length = 227 Back     alignment and structure 
Iteration: 1

 Score =  266 bits (679), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 120/213 (56%), Positives = 162/213 (76%)
Query: 1   MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVG 60
           M I+ VY+V+K+GGLI+  D   P+ E   TF +PL++ L   +++++V+FGQRDGI VG
Sbjct: 1   MAIFSVYVVNKAGGLIYQLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVG 60
Query: 61  HVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFA 120
           H + A+N   +      DG +VLE+L  P ++PV + F RPR+T+NEK+ LASMF+ LFA
Sbjct: 61  HAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMFHSLFA 120
Query: 121 IASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADY 180
           I SQLSPE  SSGIE+LE DTFKLHCYQTLTG+KF+++ D  Q+G+D +L+KIYE+Y+D+
Sbjct: 121 IGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGIDSLLRKIYEIYSDF 180
Query: 181 ALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTG 213
           ALKNPFYSLEMPIRCELFD +L+  L+  EK G
Sbjct: 181 ALKNPFYSLEMPIRCELFDQNLKLALEVAEKAG 213
>pdb|2J3T|D Chain D, The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 Complex Length = 219 Back     alignment and structure
>pdb|2JSN|A Chain A, Solution Structure Of The Atypical Pdz-Like Domain Of Synbindin Length = 96 Back     alignment and structure
>pdb|3CUE|A Chain A, Crystal Structure Of A Trapp Subassembly Activating The Rab Ypt1p Length = 219 Back     alignment and structure
>pdb|2J3T|C Chain C, The Crystal Structure Of The Bet3-Trs33-Bet5-Trs23 Complex Length = 145 Back     alignment and structure
>pdb|1H3Q|A Chain A, Crystal Sturcture Of Sedl At 2.4 Angstroms Resolution Length = 140 Back     alignment and structure
>pdb|2J3W|A Chain A, The Crystal Structure Of The Bet3-Trs31-Sedlin Complex. Length = 142 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 ?
Query217
2j3t_D219 Trafficking protein particle complex subunit 4; tr 8e-85
3cue_A219 Transport protein particle 23 kDa subunit; membran 3e-59
2j3t_C145 Trafficking protein particle complex subunit 1, tr 2e-41
3cue_C159 Transport protein particle 18 kDa subunit; membran 2e-37
2j3w_A142 Sedlin, trafficking protein particle complex prote 6e-20
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-06
>2j3t_D Trafficking protein particle complex subunit 4; trapp, palmitate, transport, lipoprotein, ER-golgi transport apparatus, protein transport; HET: PLM; 2.4A {Homo sapiens} PDB: 2zmv_A 2jsn_A Length = 219 Back     alignment and structure
 Score =  249 bits (637), Expect = 8e-85
 Identities = 120/213 (56%), Positives = 162/213 (76%)

Query: 1   MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVG 60
           M I+ VY+V+K+GGLI+  D   P+ E   TF +PL++ L   +++++V+FGQRDGI VG
Sbjct: 1   MAIFSVYVVNKAGGLIYQLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVG 60

Query: 61  HVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFA 120
           H + A+N   +      DG +VLE+L  P ++PV + F RPR+T+NEK+ LASMF+ LFA
Sbjct: 61  HAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMFHSLFA 120

Query: 121 IASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDTNQSGLDLILKKIYELYADY 180
           I SQLSPE  SSGIE+LE DTFKLHCYQTLTG+KF+++ D  Q+G+D +L+KIYE+Y+D+
Sbjct: 121 IGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGIDSLLRKIYEIYSDF 180

Query: 181 ALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTG 213
           ALKNPFYSLEMPIRCELFD +L+  L+  EK G
Sbjct: 181 ALKNPFYSLEMPIRCELFDQNLKLALEVAEKAG 213
>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} Length = 219 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} Length = 145 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} Length = 159 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 Length = 142 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 ?
Query217
2j3t_D219 Trafficking protein particle complex subunit 4; tr 100.0
2j3t_C145 Trafficking protein particle complex subunit 1, tr 100.0
3cue_A219 Transport protein particle 23 kDa subunit; membran 100.0
3cue_C159 Transport protein particle 18 kDa subunit; membran 100.0
2j3w_A142 Sedlin, trafficking protein particle complex prote 100.0
3pr6_A162 Trapp-associated protein TCA17; longin fold, vesic 99.67
2nut_C196 Vesicle-trafficking protein SEC22B; human copii SE 95.2
3bw6_A144 Synaptobrevin homolog YKT6; YKT6P, farnesylation, 94.41
3kyq_A199 YKT6, synaptobrevin homolog YKT6; V-snare homolog, 93.3
4b93_A189 Vesicle-associated membrane protein 7; endocytosis 91.61
2vgl_S142 AP-2 complex subunit sigma-1; cytoplasmic vesicle, 86.62
1r6j_A82 Syntenin 1; PDZ, membrane protein; 0.73A {Homo sap 86.58
2vx8_A169 Nucleoporin-like protein RIP, vesicle-associated m 85.72
1wi4_A109 Synip, syntaxin binding protein 4; syntaxin4-inter 84.3
2vsp_A91 PDZ domain-containing protein 1; membrane, cytopla 83.71
2he4_A90 Na(+)/H(+) exchange regulatory cofactor NHE-RF2; p 83.67
4afi_A173 AP-3 complex subunit delta-1, vesicle-associated p 82.39
1kwa_A88 Hcask/LIN-2 protein; PDZ domain, neurexin, syndeca 82.29
>2j3t_D Trafficking protein particle complex subunit 4; trapp, palmitate, transport, lipoprotein, ER-golgi transport apparatus, protein transport; HET: PLM; 2.4A {Homo sapiens} PDB: 2zmv_A 2jsn_A Back     alignment and structure
Probab=100.00  E-value=7.3e-80  Score=533.20  Aligned_cols=217  Identities=55%  Similarity=0.988  Sum_probs=207.8

Q ss_pred             CeEEEEEEEeccceeEEecccCCCccccceecccCccccccccCceeEEeeccccceeeeeeEEeeeceeecccccCCCc
Q psy15590          1 MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGT   80 (217)
Q Consensus         1 M~iy~~~i~~~~~~~i~~~d~~~~~~~~~~t~~~p~~~~l~~~~~~~~v~~g~~~~~~~g~~~~~~ng~~~~~~~~~dg~   80 (217)
                      |+|||||||||||+|||++||+.|++|+||||+||||++|+.+|+|++|+|||||||++||+++++||.+|+|++++|||
T Consensus         1 m~iy~~yi~~~~~~liy~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~v~~~~~d~~~~~~~~~~~ng~~~~~~~~~d~~   80 (219)
T 2j3t_D            1 MAIFSVYVVNKAGGLIYQLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGK   80 (219)
T ss_dssp             -CEEEEEEECTTSCEEEEEECC----CEEEEECSSCSSEEEECSSSEEEEECCCTTCCTTCEEEEETTEECBTTBCTTSS
T ss_pred             CeEEEEEEEecCCceEEecccCCCCcceeeeccCCcceeeeeccceeEEeecccCCccccceeeecCCccCCCcccccCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhccCCCCCCeeeeeCCCCCCchhhHHHhhhhhcHHHHHhhhCCCCCCCceeEEecCcEEEEEEEeCCCcEEEEEec
Q psy15590         81 DVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGD  160 (217)
Q Consensus        81 ~~~~~~~~~~n~Pl~l~~~~~~l~sne~llLag~l~SL~~i~~kLsp~~~s~g~~~~~T~~yklh~yeT~TGiKFVlitd  160 (217)
                      +|+++|.+++|+||+||++++++++|++++|+|++|||++|++||+|.++++|+++++|++||+|||+|+||+||||+||
T Consensus        81 ~v~~~iigk~N~PLyir~f~~~l~sn~~L~lag~lhSLd~i~~klsp~~~s~g~~~~~T~~ykl~~y~T~TgiKFVLltd  160 (219)
T 2j3t_D           81 EVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLAD  160 (219)
T ss_dssp             BHHHHTTCGGGCSEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHTCSSSSCCSCSEEEESSCEEEEEECTTSCEEEEEEC
T ss_pred             eeeeeeecCCCCceEEEecCCCCChhHHHHHHHHHHHHHHHHHHhCCCCCCCCeeEEecCceEEEEEEcCCCCEEEEEec
Confidence            99999999999999999999999999999999999999999999999877889999999999999999999999999999


Q ss_pred             CCchhHHHHHHHHHHHHHhhhhcCCCCCCCCcccchhHHHHHHHHHHHhhhcCCcCC
Q psy15590        161 TNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQHEKTGVTNV  217 (217)
Q Consensus       161 ~~~~~l~~~L~~IYelYvdyVlkNPfy~~~~pI~s~~Fd~~l~~ll~~~~~~~~~~~  217 (217)
                      +++++++++|++||++|+|||||||||+++|||+|++||++|++++++++++|+.++
T Consensus       161 ~~~~~ir~~l~~IyelYvd~V~kNPFY~~~~pI~s~~Fd~~v~~l~~~~~~~~~~~~  217 (219)
T 2j3t_D          161 PRQAGIDSLLRKIYEIYSDFALKNPFYSLEMPIRCELFDQNLKLALEVAEKAGTFGP  217 (219)
T ss_dssp             TTCCCHHHHHHHHHHHHHHHHTTCTTCCTTSCCCCHHHHHHHHHHHHHHTTSCCC--
T ss_pred             CCchHHHHHHHHHHHHHHHHhccCCCCCCCCccchHHHHHHHHHHHHHhhccCcccc
Confidence            999999999999999999999999999999999999999999999999999998753
>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
>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
>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
>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
>3pr6_A Trapp-associated protein TCA17; longin fold, vesicle tethering regulation, trapp complex, TR network, transport protein; 1.80A {Saccharomyces cerevisiae} 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
>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
>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
>4b93_A Vesicle-associated membrane protein 7; endocytosis, exocytosis, snare; 2.00A {Mus musculus} PDB: 2dmw_A 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
>1r6j_A Syntenin 1; PDZ, membrane protein; 0.73A {Homo sapiens} SCOP: b.36.1.1 PDB: 1nte_A 1obx_A 1oby_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
>1wi4_A Synip, syntaxin binding protein 4; syntaxin4-interacting protein, STXBP4 protein, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: b.36.1.1 Back     alignment and structure
>2vsp_A PDZ domain-containing protein 1; membrane, cytoplasm, phosphoprotein, transport protein, CAsp; 2.60A {Homo sapiens} PDB: 2eej_A Back     alignment and structure
>2he4_A Na(+)/H(+) exchange regulatory cofactor NHE-RF2; phosphorylation, structural genomics, structural genomics consortium, SGC, unknown function; 1.45A {Homo sapiens} PDB: 2ozf_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
>1kwa_A Hcask/LIN-2 protein; PDZ domain, neurexin, syndecan, receptor clustering, kinase; 1.93A {Homo sapiens} SCOP: b.36.1.1 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 217
d2j3wa1140 d.110.4.3 (A:1-140) Sedlin (SEDL) {Mouse (Mus musc 3e-19
>d2j3wa1 d.110.4.3 (A:1-140) Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090]} Length = 140 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: SNARE-like
family: Sedlin (SEDL)
domain: Sedlin (SEDL)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.4 bits (193), Expect = 3e-19
 Identities = 21/115 (18%), Positives = 51/115 (44%), Gaps = 5/115 (4%)

Query: 99  TRPRMTTNEKIFLASMF--YPLFAIASQLSPEPKSSGIEVLEA-DTFKLHCYQTLTGVKF 155
              +  + +     + F  +    +  +      +  ++ ++  + + +  + T   ++F
Sbjct: 24  PPGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEWFVSAFVTAGHMRF 83

Query: 156 MIVGDT-NQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 209
           +++ D   + G+      +Y+LY  +A+ NPFY    PIR   FD  +Q L ++H
Sbjct: 84  IMLHDVRQEDGIKNFFTDVYDLYIKFAM-NPFYEPNSPIRSSAFDRKVQFLGKKH 137

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query217
d2j3wa1140 Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090] 99.97
d1ioua_140 Synaptobrevin homolog 1 ykt6 {Baker's yeast (Sacch 94.81
d1ifqa_127 Sec22b {Mouse (Mus musculus) [TaxId: 10090]} 92.06
d1fc6a392 Photosystem II D1 C-terminal processing protease { 90.9
d1k32a191 Tricorn protease {Archaeon Thermoplasma acidophilu 90.33
d1wi4a196 Syntaxin binding protein 4 {Mouse (Mus musculus) [ 89.95
d1w9ea185 Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]} 88.11
d1vaea_111 Rhophilin-2 {Mouse (Mus musculus) [TaxId: 10090]} 85.59
d1wifa_126 hypothetical PDZ domain containing protein Uqcrc2 84.19
d1i16a_130 Interleukin 16 {Human (Homo sapiens) [TaxId: 9606] 82.63
d1wi2a_104 PDZ domain containing protein 11, Pdzk11 {Mouse (M 81.82
d2fe5a192 Synapse-associated protein 102 {Human (Homo sapien 81.1
>d2j3wa1 d.110.4.3 (A:1-140) Sedlin (SEDL) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: SNARE-like
family: Sedlin (SEDL)
domain: Sedlin (SEDL)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.97  E-value=1e-31  Score=215.72  Aligned_cols=104  Identities=19%  Similarity=0.399  Sum_probs=93.9

Q ss_pred             chhhHHHhhhhhcHHHHHhhhCCCCCCCceeE-EecCcEEEEEEEeCCCcEEEEEecCC-chhHHHHHHHHHHHHHhhhh
Q psy15590        105 TNEKIFLASMFYPLFAIASQLSPEPKSSGIEV-LEADTFKLHCYQTLTGVKFMIVGDTN-QSGLDLILKKIYELYADYAL  182 (217)
Q Consensus       105 sne~llLag~l~SL~~i~~kLsp~~~s~g~~~-~~T~~yklh~yeT~TGiKFVlitd~~-~~~l~~~L~~IYelYvdyVl  182 (217)
                      +++.++...++||...|.++++|.....++.+ .++++|++|||+|+||+||||+||++ ++.++.+|+++|++|+++|+
T Consensus        32 ~~~~~~~~fi~hssLDive~~~~~~~~~~l~~l~~~~~~~v~~y~T~tg~Kfvl~td~~~~~~i~~~~~~v~~lYv~~v~  111 (140)
T d2j3wa1          32 DDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEWFVSAFVTAGHMRFIMLHDVRQEDGIKNFFTDVYDLYIKFAM  111 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHGGGCSCSEEEEEEEETTEEEEEEECTTCCEEEEEESSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHhcccCCCccceeEEecCCEEEEEEEcCCCcEEEEEeCCCcchHHHHHHHHHHHHHHHHhh
Confidence            56777888899998888999988776667766 47999999999999999999999997 55689999999999999998


Q ss_pred             cCCCCCCCCcccchhHHHHHHHHHHHh
Q psy15590        183 KNPFYSLEMPIRCELFDTHLQNLLQQH  209 (217)
Q Consensus       183 kNPfy~~~~pI~s~~Fd~~l~~ll~~~  209 (217)
                       ||||.++|||+|+.||++|+++++++
T Consensus       112 -NPfy~~~~pI~s~~Fd~~v~~~~~~~  137 (140)
T d2j3wa1         112 -NPFYEPNSPIRSSAFDRKVQFLGKKH  137 (140)
T ss_dssp             -STTCCTTCCCCCHHHHHHHHHHHHHH
T ss_pred             -CccCCCCCcccCHHHHHHHHHHHHHH
Confidence             99999999999999999999999986
>d1ioua_ d.110.4.1 (A:) Synaptobrevin homolog 1 ykt6 {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
>d1fc6a3 b.36.1.3 (A:157-248) Photosystem II D1 C-terminal processing protease {Algae (Scenedesmus obliquus) [TaxId: 3088]} Back     information, alignment and structure
>d1k32a1 b.36.1.3 (A:763-853) Tricorn protease {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d1wi4a1 b.36.1.1 (A:8-103) Syntaxin binding protein 4 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1w9ea1 b.36.1.1 (A:110-194) Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vaea_ b.36.1.1 (A:) Rhophilin-2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wifa_ b.36.1.1 (A:) hypothetical PDZ domain containing protein Uqcrc2 (4930408O21Rik) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1i16a_ b.36.1.2 (A:) Interleukin 16 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wi2a_ b.36.1.1 (A:) PDZ domain containing protein 11, Pdzk11 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2fe5a1 b.36.1.1 (A:223-314) Synapse-associated protein 102 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure