Citrus Sinensis ID: 023488

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-
MVSKRQREARKRFKEVHPELFPKPEPTAPKDPSEKKKKKSSKFKRKKAESKDPNRNEKSMKRVFTRHPLRVPGMKPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNKGIQGFTASSKQAMAGGERPTGQVTKFTSGDDLLDDFLTEDANIGNKDKSSIAKVDSTSDSTNAKVKQKKKQGSKVVNFVG
cccHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHcccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccEEcccc
cccHHHHHHHHHHHHHcccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccEEEccccccccccccccccccccccccEEEccccccccccccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcc
MVSKRQREARKRFKevhpelfpkpeptapkdpsekkkkksskfkrkkaeskdpnrneksmkrvftrhplrvpgmkpgescfiCKAKEhiakhcpmkaeweknkiclvcrrrghtlkncpskndetestklcyncgqaghslaqcpqplqdggtkfascfickeqghlskncpqnahgiypkggcckicggvthlardcpnkgiqgftasskqamaggerptgqvtkftsgddllddfltedanignkdkssiakvdstsdstnakvkqkkkqgskvVNFVG
mvskrqrearkrfkevhpelfpkpeptapkdpsekkkkksskfkrkkaeskdpnrneksmkrvftrhplrvpgmkpgESCFICKAKEHIAkhcpmkaeweknkICLVCrrrghtlkncpskndeteSTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNKGIQGFTASSKQAMAGGERPTGQVTKFTSGDDLLDDFLTEdanignkdkssiakvdstsdstnakvkqkkkqgskvvnfvg
MVSKRQREARKRFKEVHPELFPKPEPTapkdpsekkkkksskfkrkkaeskdPNRNEKSMKRVFTRHPLRVPGMKPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNKGIQGFTASSKQAMAGGERPTGQVTKFTSGDDLLDDFLTEDANIGNKDKSSIAKVDSTSDSTNAkvkqkkkqgskvvNFVG
****************************************************************************GESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNC*********TKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNKGIQG****************************************************************************
***************************************************************************PGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPS*******TKLCYNCGQAGHS*****************************************GGCCKICGGVTHLARDCP***************************************************************************KVVNFVG
*************KEVHPELFPKP***********************************MKRVFTRHPLRVPGMKPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNKGIQGFTASS**********TGQVTKFTSGDDLLDDFLTEDANIGNKDKSS******************************
*********RKRFKEVHPELFPKPEPTAP**********************************************************HIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNKGI*********AMA*****************LLD**********NKDKSSI*KVDSTSDSTNAKV**K*KQGSKVVNFVG
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVSKRQREARKRFKEVHPELFPKPEPTAPKDPSEKKKKKSSKFKRKKAESKDPNRNEKSMKRVFTRHPLRVPGMKPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNKGIQGFTASSKQAMAGGERPTGQVTKFTSGDDLLDDFLTEDANIGNKDKSSIAKVDSTSDSTNAKVKQKKKQGSKVVNFVG
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 ?
Query281 2.2.26 [Sep-21-2011]
Q9HFF2218 Uncharacterized protein C yes no 0.327 0.422 0.489 5e-22
Q8N567271 Zinc finger CCHC domain-c yes no 0.341 0.354 0.424 2e-19
Q8R1J3273 Zinc finger CCHC domain-c yes no 0.338 0.347 0.408 3e-18
Q04832271 DNA-binding protein HEXBP yes no 0.498 0.516 0.293 7e-13
Q8T8R1165 CCHC-type zinc finger pro yes no 0.384 0.654 0.344 2e-11
O65639299 Cold shock protein 1 OS=A no no 0.423 0.397 0.288 5e-09
P36627179 Cellular nucleic acid-bin no no 0.387 0.608 0.323 2e-07
O42395172 Cellular nucleic acid-bin no no 0.377 0.616 0.318 6e-06
P53996178 Cellular nucleic acid-bin no no 0.377 0.595 0.310 1e-05
Q966L9 974 ATP-dependent RNA helicas no no 0.320 0.092 0.265 1e-05
>sp|Q9HFF2|YL92_SCHPO Uncharacterized protein C683.02c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC683.02c PE=4 SV=1 Back     alignment and function desciption
 Score =  105 bits (261), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 48/98 (48%), Positives = 61/98 (62%), Gaps = 6/98 (6%)

Query: 101 KNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFI 160
           ++K C  CR++GH +++CP   D   +  +C+ CG   HSL  C +    G  KFA CFI
Sbjct: 75  RDKFCFACRQQGHIVQDCPEAKD---NVSICFRCGSKEHSLNACSKK---GPLKFAKCFI 128

Query: 161 CKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDC 198
           C E GHLS  C QN  G+YPKGGCCK C  V HLA+DC
Sbjct: 129 CHENGHLSGQCEQNPKGLYPKGGCCKFCSSVHHLAKDC 166

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)
>sp|Q8N567|ZCHC9_HUMAN Zinc finger CCHC domain-containing protein 9 OS=Homo sapiens GN=ZCCHC9 PE=2 SV=2 Back     alignment and function description
>sp|Q8R1J3|ZCHC9_MOUSE Zinc finger CCHC domain-containing protein 9 OS=Mus musculus GN=Zcchc9 PE=2 SV=1 Back     alignment and function description
>sp|Q04832|HEXP_LEIMA DNA-binding protein HEXBP OS=Leishmania major GN=HEXBP PE=4 SV=1 Back     alignment and function description
>sp|Q8T8R1|Y3800_DROME CCHC-type zinc finger protein CG3800 OS=Drosophila melanogaster GN=CG3800 PE=1 SV=1 Back     alignment and function description
>sp|O65639|CSP1_ARATH Cold shock protein 1 OS=Arabidopsis thaliana GN=CSP1 PE=2 SV=1 Back     alignment and function description
>sp|P36627|BYR3_SCHPO Cellular nucleic acid-binding protein homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=byr3 PE=4 SV=1 Back     alignment and function description
>sp|O42395|CNBP_CHICK Cellular nucleic acid-binding protein OS=Gallus gallus GN=CNBP PE=2 SV=1 Back     alignment and function description
>sp|P53996|CNBP_MOUSE Cellular nucleic acid-binding protein OS=Mus musculus GN=Cnbp PE=2 SV=2 Back     alignment and function description
>sp|Q966L9|GLH2_CAEEL ATP-dependent RNA helicase glh-2 OS=Caenorhabditis elegans GN=glh-2 PE=1 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 ?
Query281
224137012278 predicted protein [Populus trichocarpa] 0.985 0.996 0.656 3e-97
118485064278 unknown [Populus trichocarpa] 0.985 0.996 0.656 5e-97
302143876279 unnamed protein product [Vitis vinifera] 0.978 0.985 0.687 8e-97
224120076273 predicted protein [Populus trichocarpa] 0.971 1.0 0.647 2e-95
225470195 401 PREDICTED: uncharacterized protein LOC10 0.918 0.643 0.682 5e-91
255539441 498 actin depolymerizing factor, putative [R 0.964 0.544 0.634 1e-90
356574489 1410 PREDICTED: uncharacterized protein LOC10 0.932 0.185 0.641 1e-88
395146534 388 putative actin-depolymerizing factor 12 0.900 0.652 0.608 1e-81
449446157 396 PREDICTED: uncharacterized protein LOC10 0.857 0.608 0.652 1e-81
357444017262 Zinc finger CCHC domain-containing prote 0.911 0.977 0.602 2e-81
>gi|224137012|ref|XP_002322472.1| predicted protein [Populus trichocarpa] gi|222869468|gb|EEF06599.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  360 bits (924), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 185/282 (65%), Positives = 220/282 (78%), Gaps = 5/282 (1%)

Query: 1   MVSKRQREARKRFKEVHPELFPKPEPTAPKDPSEKKKKKSSKFKRK-KAESKDPNRNEKS 59
           MVSKRQ+ ARK +KE HPELFPKPEPT P DP++ KKKK     ++  ++ KDPN   K+
Sbjct: 1   MVSKRQKLARKIYKEDHPELFPKPEPTPPNDPNKMKKKKKKSLFKRKNSDPKDPN---KA 57

Query: 60  MKRVFTRHPLRVPGMKPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCP 119
            K+ F + PLRVPGMKPG+SCFICKAK+HIAK CP K EWEKNKICL+CR RGH+LK CP
Sbjct: 58  NKKGFRKQPLRVPGMKPGDSCFICKAKDHIAKLCPQKDEWEKNKICLLCRHRGHSLKRCP 117

Query: 120 SKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIY 179
            KNDET   KLCYNCG+ GHSL+QCPQP +DGGTKFA+CFIC E+GHLSK+CP+N  GIY
Sbjct: 118 KKNDETMDQKLCYNCGETGHSLSQCPQPREDGGTKFANCFICNERGHLSKDCPKNTRGIY 177

Query: 180 PKGGCCKICGGVTHLARDCPNKGIQGFTASSKQAMAGGERPTGQVTKFTSGDDLLDDFLT 239
           PKGGCCK+CGGVTHLARDCP+KG +G  A  + A+    RPTG+VTKF SGD+L DDF+T
Sbjct: 178 PKGGCCKLCGGVTHLARDCPDKGKRGDAAFGRGAIGREVRPTGRVTKFVSGDELDDDFMT 237

Query: 240 EDANIGNKDKSSIAKVDSTSDSTNAKVKQKKKQGSKVVNFVG 281
           E+     KDKS+ +KV    DS +  VK KKKQG K+VNFVG
Sbjct: 238 ENMYSIPKDKSTDSKV-VPPDSKDGHVKSKKKQGPKIVNFVG 278

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|118485064|gb|ABK94395.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|302143876|emb|CBI22737.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224120076|ref|XP_002318236.1| predicted protein [Populus trichocarpa] gi|222858909|gb|EEE96456.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225470195|ref|XP_002268512.1| PREDICTED: uncharacterized protein LOC100242054 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255539441|ref|XP_002510785.1| actin depolymerizing factor, putative [Ricinus communis] gi|223549900|gb|EEF51387.1| actin depolymerizing factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356574489|ref|XP_003555379.1| PREDICTED: uncharacterized protein LOC100783153 [Glycine max] Back     alignment and taxonomy information
>gi|395146534|gb|AFN53688.1| putative actin-depolymerizing factor 12 [Linum usitatissimum] Back     alignment and taxonomy information
>gi|449446157|ref|XP_004140838.1| PREDICTED: uncharacterized protein LOC101212555 [Cucumis sativus] Back     alignment and taxonomy information
>gi|357444017|ref|XP_003592286.1| Zinc finger CCHC domain-containing protein [Medicago truncatula] gi|355481334|gb|AES62537.1| Zinc finger CCHC domain-containing protein [Medicago truncatula] 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 ?
Query281
TAIR|locus:2156647268 AT5G52380 [Arabidopsis thalian 0.946 0.992 0.540 2.4e-76
WB|WBGene00017210384 F07E5.5 [Caenorhabditis elegan 0.348 0.255 0.45 9.4e-27
POMBASE|SPAC683.02c218 SPAC683.02c "zf-CCHC type zinc 0.327 0.422 0.489 4.6e-25
ZFIN|ZDB-GENE-031030-9256 zcchc9 "zinc finger, CCHC doma 0.355 0.390 0.436 2.6e-24
UNIPROTKB|E1BZR6235 ZCCHC9 "Uncharacterized protei 0.466 0.557 0.357 8.7e-24
UNIPROTKB|F1RF07270 ZCCHC9 "Uncharacterized protei 0.355 0.370 0.423 2.3e-23
UNIPROTKB|F6V033271 ZCCHC9 "Uncharacterized protei 0.355 0.369 0.413 2.9e-23
UNIPROTKB|Q8N567271 ZCCHC9 "Zinc finger CCHC domai 0.355 0.369 0.423 1e-22
UNIPROTKB|F1ML79271 ZCCHC9 "Uncharacterized protei 0.355 0.369 0.413 2.1e-22
RGD|1307450271 Zcchc9 "zinc finger, CCHC doma 0.355 0.369 0.413 4.3e-22
TAIR|locus:2156647 AT5G52380 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 769 (275.8 bits), Expect = 2.4e-76, P = 2.4e-76
 Identities = 153/283 (54%), Positives = 183/283 (64%)

Query:     1 MVSKRQREARKRFKEVHPELFPKPEPTXXXXXXXXXXXXXXXXXXX-XXXXXXPNRNEKS 59
             MV++R+R A+KR+KE +PELFPK EPT                          P R   S
Sbjct:     1 MVNQRRRLAQKRYKEANPELFPKAEPTPPKDPNKKKKKKSLFKKKKPGSSTDRPQRTGSS 60

Query:    60 MKRVFTRHPLRVPGMKPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCP 119
                  TRHPLRVPGMKPGE CFIC +K HIAK CP K+EWE+NKICL CRRRGH+LKNCP
Sbjct:    61 -----TRHPLRVPGMKPGEGCFICHSKTHIAKLCPEKSEWERNKICLQCRRRGHSLKNCP 115

Query:   120 SKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIY 179
              KN+E+   KLCYNCG  GHSL+ CP P++DGGTKFASCFICK QGH+SKNCP+N HGIY
Sbjct:   116 EKNNESSEKKLCYNCGDTGHSLSHCPYPMEDGGTKFASCFICKGQGHISKNCPENKHGIY 175

Query:   180 PKGGCCKICGGVTHLARDCPNKGIQGFTASSKQAMAGGERPTGQVTKFTSGDDLLDDFLT 239
             P GGCCK+CG V HL +DCP+K  Q  +A  K+       P G++TKF SGDDL DDF T
Sbjct:   176 PMGGCCKVCGSVAHLVKDCPDKFNQE-SAQPKKTSRFDATPRGKLTKF-SGDDLEDDF-T 232

Query:   240 EDANIGNKDKSSIAKVDSTSDST-NAXXXXXXXXXXXXXNFVG 281
             E+       KSS  K++++ DS  N+             NFVG
Sbjct:   233 EEP------KSS-KKINTSDDSAQNSVEVKKKKQGPKIVNFVG 268
GO:0003676 "nucleic acid binding" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0008270 "zinc ion binding" evidence=IEA
GO:0009560 "embryo sac egg cell differentiation" evidence=RCA
WB|WBGene00017210 F07E5.5 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
POMBASE|SPAC683.02c SPAC683.02c "zf-CCHC type zinc finger protein" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-031030-9 zcchc9 "zinc finger, CCHC domain containing 9" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|E1BZR6 ZCCHC9 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1RF07 ZCCHC9 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|F6V033 ZCCHC9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q8N567 ZCCHC9 "Zinc finger CCHC domain-containing protein 9" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1ML79 ZCCHC9 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
RGD|1307450 Zcchc9 "zinc finger, CCHC domain containing 9" [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

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
estExt_fgenesh4_pm.C_LG_XV0457
SubName- Full=Putative uncharacterized protein; (278 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query281
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 6e-23
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 9e-18
PTZ00368148 PTZ00368, PTZ00368, universal minicircle sequence 4e-14
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 2e-13
COG5082190 COG5082, AIR1, Arginine methyltransferase-interact 7e-12
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
 Score = 91.4 bits (227), Expect = 6e-23
 Identities = 43/132 (32%), Positives = 61/132 (46%), Gaps = 3/132 (2%)

Query: 70  RVPGMKPGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTK 129
              G      C+ C    H+++ CP        + C  C + GH  + CP     +   +
Sbjct: 20  APAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSG-PR 78

Query: 130 LCYNCGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICG 189
            CYNCGQ GH   +CP     GG    +C+ C  +GH+S++CP NA         C  CG
Sbjct: 79  SCYNCGQTGHISRECPNR-AKGGAARRACYNCGGEGHISRDCP-NAGKRPGGDKTCYNCG 136

Query: 190 GVTHLARDCPNK 201
              HL+RDCP+K
Sbjct: 137 QTGHLSRDCPDK 148

Length = 148
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 281
PTZ00368148 universal minicircle sequence binding protein (UMS 99.91
PTZ00368148 universal minicircle sequence binding protein (UMS 99.88
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.86
COG5082190 AIR1 Arginine methyltransferase-interacting protei 99.67
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.63
KOG4400261 consensus E3 ubiquitin ligase interacting with arg 99.5
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.88
PF0009818 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi 97.66
PF1369632 zf-CCHC_2: Zinc knuckle 96.93
PF1369632 zf-CCHC_2: Zinc knuckle 96.33
KOG0119 554 consensus Splicing factor 1/branch point binding p 95.23
KOG0119554 consensus Splicing factor 1/branch point binding p 94.67
COG5222427 Uncharacterized conserved protein, contains RING Z 93.97
PF1391742 zf-CCHC_3: Zinc knuckle 93.01
smart0034326 ZnF_C2HC zinc finger. 92.37
smart0034326 ZnF_C2HC zinc finger. 91.24
PF1391742 zf-CCHC_3: Zinc knuckle 90.94
PF1439249 zf-CCHC_4: Zinc knuckle 89.31
KOG0314 448 consensus Predicted E3 ubiquitin ligase [Posttrans 89.2
KOG0314 448 consensus Predicted E3 ubiquitin ligase [Posttrans 88.69
PF1528840 zf-CCHC_6: Zinc knuckle 88.35
KOG0109346 consensus RNA-binding protein LARK, contains RRM a 85.37
PF1439249 zf-CCHC_4: Zinc knuckle 85.01
COG5222 427 Uncharacterized conserved protein, contains RING Z 84.63
PF1528840 zf-CCHC_6: Zinc knuckle 84.42
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information 
Probab=99.91  E-value=4.8e-24  Score=179.97  Aligned_cols=123  Identities=32%  Similarity=0.841  Sum_probs=97.1

Q ss_pred             CCccccccCCCCccCCCCCCccccccCccccccCCCCCCCCCCCCCCcCcccccccccccccCCCCCCCCCCCCCCCCCc
Q 023488           76 PGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTKF  155 (281)
Q Consensus        76 ~~~~Cf~Cg~~GH~a~~Cp~~~~~~~~~~C~~Cg~~GH~~~~CP~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~  155 (281)
                      ....||+|++.||++++||..........|++|++.||++++||...... ....||+|++.||++++|++.... +...
T Consensus        26 ~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~-~~~~C~~Cg~~GH~~~~C~~~~~~-~~~~  103 (148)
T PTZ00368         26 KARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGS-GPRSCYNCGQTGHISRECPNRAKG-GAAR  103 (148)
T ss_pred             CCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCC-CCcccCcCCCCCcccccCCCcccc-cccc
Confidence            45689999999999999998654444568999999999999998864221 246899999999999999986533 2344


Q ss_pred             eeeeecCCCCcCCCCCCCCCCCCCccccccccccccCcCCCCCCCC
Q 023488          156 ASCFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNK  201 (281)
Q Consensus       156 ~~C~~Cg~~GH~a~dCp~~~~g~~~~~~~C~~Cg~~GH~a~dCp~~  201 (281)
                      ..||+|++.||++++||+.+.. ......||+|++.|||+.|||+.
T Consensus       104 ~~C~~Cg~~gH~~~~C~~~~~~-~~~~~~C~~Cg~~gH~~~dCp~~  148 (148)
T PTZ00368        104 RACYNCGGEGHISRDCPNAGKR-PGGDKTCYNCGQTGHLSRDCPDK  148 (148)
T ss_pred             hhhcccCcCCcchhcCCCcccc-CCCCCccccCCCcCcccccCCCC
Confidence            6799999999999999997432 23456899999999999999963

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional Back     alignment and domain information
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion] Back     alignment and domain information
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PF13696 zf-CCHC_2: Zinc knuckle Back     alignment and domain information
>PF13696 zf-CCHC_2: Zinc knuckle Back     alignment and domain information
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only] Back     alignment and domain information
>PF13917 zf-CCHC_3: Zinc knuckle Back     alignment and domain information
>smart00343 ZnF_C2HC zinc finger Back     alignment and domain information
>smart00343 ZnF_C2HC zinc finger Back     alignment and domain information
>PF13917 zf-CCHC_3: Zinc knuckle Back     alignment and domain information
>PF14392 zf-CCHC_4: Zinc knuckle Back     alignment and domain information
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF15288 zf-CCHC_6: Zinc knuckle Back     alignment and domain information
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only] Back     alignment and domain information
>PF14392 zf-CCHC_4: Zinc knuckle Back     alignment and domain information
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only] Back     alignment and domain information
>PF15288 zf-CCHC_6: Zinc knuckle Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query281
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 7e-16
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 2e-11
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 1e-08
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 2e-06
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 2e-06
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 3e-07
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 1e-06
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 3e-05
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 4e-05
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 6e-07
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 2e-05
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 1e-06
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 3e-06
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 4e-05
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 4e-04
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
 Score = 71.3 bits (174), Expect = 7e-16
 Identities = 34/142 (23%), Positives = 46/142 (32%), Gaps = 34/142 (23%)

Query: 75  KPGESCFICKAKEHIAKHCPMKAEWEKNKICLVC-RRRGHTLKNCPSKNDETESTKLCYN 133
           +    C  C  + H+ K CP       + IC  C     H  ++CP           C  
Sbjct: 2   EAAPKCNNCSQRGHLKKDCP-------HIICSYCGATDDHYSRHCPKA-------IQCSK 47

Query: 134 CGQAGHSLAQCPQPLQDGGTKFASCFICKEQGHLSKNCPQ--------------NAHGIY 179
           C + GH  +QCP        K   C +CK + H  + CP                   + 
Sbjct: 48  CDEVGHYRSQCPHKW-----KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLP 102

Query: 180 PKGGCCKICGGVTHLARDCPNK 201
                C  CGG  H   DC  K
Sbjct: 103 FHTIYCYNCGGKGHFGDDCKEK 124
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61 Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61 Back     alignment and structure
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60 Back     alignment and structure
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60 Back     alignment and structure
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60 Back     alignment and structure
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60 Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63 Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63 Back     alignment and structure
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* Length = 148 Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74 Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74 Back     alignment and structure
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query281
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.93
2lli_A124 Protein AIR2; RNA surveillance, RNA degradation, R 99.82
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.53
3nyb_B83 Protein AIR2; polya RNA polymerase, zinc knuckle p 99.49
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.32
2li8_A74 Protein LIN-28 homolog A; zinc finger, micro RNA, 99.31
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 99.1
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 99.02
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 99.02
2a51_A39 Nucleocapsid protein; sivlhoest, structure, NCP8, 99.01
2ec7_A49 GAG polyprotein (PR55GAG); nucleocapsid protein, H 99.0
2bl6_A37 Nucleocapsid protein P11; lentivirus, polyprotein, 98.99
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.96
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.95
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.94
2ihx_A61 Nucleocapsid (NC) protein; protein-RNA complex, vi 98.93
2cqf_A63 RNA-binding protein LIN-28; CCHC zinc-finger, stru 98.93
1cl4_A60 Protein (GAG polyprotein); nucleocapsid protein, R 98.93
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 98.9
1a1t_A55 Nucleocapsid protein; stem-loop RNA, viral protein 98.85
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.64
3ts2_A148 Protein LIN-28 homolog A; microrna biogenesis, pro 98.63
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.67
1dsq_A26 Nucleic acid binding protein P14; CCHC type zinc f 97.66
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.41
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.36
1a6b_B40 Momulv, zinc finger protein NCP10; nucleocapsid pr 97.3
1nc8_A29 Nucleocapsid protein; HIV-2, RNA recognition, zinc 97.18
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 97.03
1u6p_A56 GAG polyprotein; MLV, A-minor K-turn, stem loop, b 97.02
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.93
2ysa_A55 Retinoblastoma-binding protein 6; zinc finger, CCH 96.57
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
Probab=99.93  E-value=1.4e-26  Score=188.98  Aligned_cols=106  Identities=30%  Similarity=0.733  Sum_probs=93.6

Q ss_pred             CCccccccCCCCccCCCCCCccccccCccccccCCC-CCCCCCCCCCCcCcccccccccccccCCCCCCCCCCCCCCCCC
Q 023488           76 PGESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRR-GHTLKNCPSKNDETESTKLCYNCGQAGHSLAQCPQPLQDGGTK  154 (281)
Q Consensus        76 ~~~~Cf~Cg~~GH~a~~Cp~~~~~~~~~~C~~Cg~~-GH~~~~CP~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~  154 (281)
                      +...||+|++.||++++||.       ..||+|++. ||++++||..       ..||+|++.||++++||....     
T Consensus         3 ~~~~C~~C~~~GH~~~~Cp~-------~~C~~Cg~~~gH~~~~C~~~-------~~C~~Cg~~GH~~~~C~~~~~-----   63 (124)
T 2lli_A            3 AAPKCNNCSQRGHLKKDCPH-------IICSYCGATDDHYSRHCPKA-------IQCSKCDEVGHYRSQCPHKWK-----   63 (124)
T ss_dssp             CSSCCSSCSSSSCCTTTTTS-------CCCTTTCCTTTCCTTTGGGS-------SCSSSSSCSSSSTTTSCCCCC-----
T ss_pred             CCCcccCCCCCCcCcccCcC-------CcCcCCCCcCCccCcccCCc-------ccccccCCCCCccccCcCccc-----
Confidence            45789999999999999998       489999999 9999999983       689999999999999998642     


Q ss_pred             ceeeeecCCCCcCCCCCCCCCCCCC--------------ccccccccccccCcCCCCCCC
Q 023488          155 FASCFICKEQGHLSKNCPQNAHGIY--------------PKGGCCKICGGVTHLARDCPN  200 (281)
Q Consensus       155 ~~~C~~Cg~~GH~a~dCp~~~~g~~--------------~~~~~C~~Cg~~GH~a~dCp~  200 (281)
                      .+.||+|++.||++++||+.|..+.              ...+.||+|++.|||++|||+
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCC
T ss_pred             CccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcC
Confidence            3679999999999999999986421              135799999999999999996
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Back     alignment and structure
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Back     alignment and structure
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Back     alignment and structure
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1 Back     alignment and structure
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Back     alignment and structure
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Back     alignment and structure
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Back     alignment and structure
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A Back     alignment and structure
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A Back     alignment and structure
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* Back     alignment and structure
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A* Back     alignment and structure
>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1 Back     alignment and structure
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1 Back     alignment and structure
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A Back     alignment and structure
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1 Back     alignment and structure
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A Back     alignment and structure
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A Back     alignment and structure
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A Back     alignment and structure
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} 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 281
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 4e-06
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 5e-06
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 8e-04
d2exfa142 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod 0.002
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 41.0 bits (96), Expect = 4e-06
 Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 6/44 (13%)

Query: 158 CFICKEQGHLSKNCPQNAHGIYPKGGCCKICGGVTHLARDCPNK 201
           CF C ++GH ++NC        P+   C  CG   H  +DC  +
Sbjct: 4   CFNCGKEGHTARNCRA------PRKKGCWKCGKEGHQMKDCTER 41
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query281
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.16
d2exfa142 HIV nucleocapsid {Human immunodeficiency virus typ 99.09
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.5
d1nc8a_29 HIV nucleocapsid {Human immunodeficiency virus typ 97.07
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 96.31
d1dsqa_26 Nucleic acid binding protein p14 {Mouse mammary tu 96.22
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 94.22
d1a6bb_40 Zinc finger protein ncp10 {Moloney murine leukemia 93.37
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Back     information, alignment and structure
class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=99.16  E-value=1e-11  Score=81.30  Aligned_cols=39  Identities=33%  Similarity=0.850  Sum_probs=23.1

Q ss_pred             ccccccCCCCccCCCCCCccccccCccccccCCCCCCCCCCCC
Q 023488           78 ESCFICKAKEHIAKHCPMKAEWEKNKICLVCRRRGHTLKNCPS  120 (281)
Q Consensus        78 ~~Cf~Cg~~GH~a~~Cp~~~~~~~~~~C~~Cg~~GH~~~~CP~  120 (281)
                      +.||+|++.||++++||.+.    ...|+.|++.||++++||+
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~----~~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR----KKGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC----CSSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCcCcCcccCcCCC----cCccccCCCCCeecccCCC
Confidence            46666666666666666532    2345666555565555554
>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Back     information, alignment and structure
>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} Back     information, alignment and structure
>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]} Back     information, alignment and structure
>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]} Back     information, alignment and structure
>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} Back     information, alignment and structure
>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]} Back     information, alignment and structure