Psyllid ID: psy13343

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390------
MLTMETDLKGGHIPPHHHLSSYGSMVHSNMMSLSQSPSSVVHHQNIGPHVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRKTKTLLKKDKYPLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQAGHPPEGMPLTHM
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccHHHHHHHHHHccccccHHHHHHHHHHHHHccHHHcccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHcccccccccccccccc
ccccccccccccccccHHccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcHHHHHHHHHHcccccHHHHHHHHHHHHHHccHHHcccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccHHHHHHHHHHcccccccccccccccccccccccccccccc
mltmetdlkgghipphhhlssygsmvhsnmmslsqspssvvhhqnigphvthnpmsnplhpshntnnnnnstnsknqnaidrvkrpmnafmVWSRgqrrkmaqdnpkmhnsEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHmkehpdykyrprrktktllkkdkyplgsgnliqntsssndvtrnsssvttSAQQNSAARESMyqmpngympngymmdpatyqqhsaytthmssgyprydmtgmhpsstslnsymngssygmyttattlpgagspyhsmqpsshspsgssvksepvspssgggiltptpgsgpptglhlvkreygspnglppnstdlhlvkreysspngappnagdlRHMISMYLPEQQEQARLQAMYQQqaghppegmplthm
MLTMETDlkgghippHHHLSSYGSMVHSNMMSLSQSPSSVVHHQNIGPHVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGqrrkmaqdnpkmhnseISKRLGAEWKLLNEQAKRPFIDEAKRLravhmkehpdykyrprrktktllkkdkyplgsgnliqntsssndvtrnsssvttsaqqnsaARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQAghppegmplthm
MLTMETDLKGGHIPPHHHLSSYGSMVHsnmmslsqspssvvhhqnIGPHVTHNPMsnplhpshntnnnnnstnsknqnAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHpdykyrprrktktllkkdkyplGSGNLIQntsssndvtrnsssvttsAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGspyhsmqpsshspsgssvksepvspssgggiltptpgsgpptgLHLVKREYGSPNGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQAGHPPEGMPLTHM
*******************************************************************************************V****************************WKLL********************************************************************************************************************************************************************************************************************************************************************************
**************************************************************************************MNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKY****************************************************************************************************************************************************************************************************************************************************
MLTMETDLKGGHIPPHHHLSSYGSMVHSNMM***********HQNIGPHVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRKTKTLLKKDKYPLGSGNLIQNTS***********************ESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGS***************************GGILTPTPGSGPPTGLHLVKREYGSPNGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQAGHPPEGMPLTHM
***********HIP************HSN*****************************************************VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRK**********************************************SMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYH****S*HSPSGSSVKSEPVSPSSGGGILTPTP******************************************PNAGDLRHMISMYLPE***************************
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MLTMETDLKGGHIPPHHHLSSYGSMVHSNMMSLSQSPSSVVHHQNIGPHVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRKTKTLLKKDKYPLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQAGHPPEGMPLTHM
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 ?
Query396 2.2.26 [Sep-21-2011]
P48430315 Transcription factor SOX- yes N/A 0.651 0.819 0.447 3e-52
P54231320 Transcription factor SOX- N/A N/A 0.674 0.834 0.437 5e-49
P48431317 Transcription factor SOX- yes N/A 0.674 0.842 0.437 5e-49
Q6NVN0311 Transcription factor Sox- yes N/A 0.659 0.839 0.439 5e-49
O42569311 Transcription factor Sox- N/A N/A 0.659 0.839 0.439 7e-49
P48432319 Transcription factor SOX- yes N/A 0.674 0.836 0.431 1e-47
Q6EJB7300 Transcription factor Sox- yes N/A 0.671 0.886 0.420 2e-45
P55863309 Transcription factor Sox- N/A N/A 0.631 0.809 0.452 2e-44
Q68FA4307 Transcription factor Sox- no N/A 0.631 0.814 0.443 2e-44
Q9DDD7292 Transcription factor Sox- no N/A 0.335 0.455 0.647 3e-44
>sp|P48430|SOX2_CHICK Transcription factor SOX-2 OS=Gallus gallus GN=SOX2 PE=1 SV=1 Back     alignment and function desciption
 Score =  206 bits (523), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 142/317 (44%), Positives = 170/317 (53%), Gaps = 59/317 (18%)

Query: 58  PLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRL 117
           P   S     N+NS  +  +N+ DRVKRPMNAFMVWSRGQRRKMAQ+NPKMHNSEISKRL
Sbjct: 14  PQQTSGGGTGNSNSAANNQKNSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRL 73

Query: 118 GAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRKTKTLLKKDKYPLGSGNLIQN 177
           GAEWKLL+E  KRPFIDEAKRLRA+HMKEHPDYKYRPRRKTKTL+KKDKY L  G L   
Sbjct: 74  GAEWKLLSEAEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLLAPG 133

Query: 178 TSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGY--MMDPATYQQHSAYTTHMS 235
           T++        +++     Q    R   Y   NG+   GY  M +   Y QH     H +
Sbjct: 134 TNTMTTGVGVGATLGAGVNQ----RMDSYAHMNGWTNGGYGMMQEQLGYPQHPGLNAHNA 189

Query: 236 SGYP---RYDMTGM-HPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGS 291
           +      RYD++ + + S TS  +YMNG                SP +SM   S+S  G 
Sbjct: 190 AQMQPMHRYDVSALQYNSMTSSQTYMNG----------------SPTYSM---SYSQQG- 229

Query: 292 SVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPNSTDLHLVKREYSSPNG 351
                             TPG    +   +VK E           +         SS + 
Sbjct: 230 ------------------TPGMALGSMGSVVKTE-----------SSSSPPVVTSSSHSR 260

Query: 352 APPNAGDLRHMISMYLP 368
           AP  AGDLR MISMYLP
Sbjct: 261 APCQAGDLRDMISMYLP 277
Transcriptional activator. May function as a switch in neuronal development. Downstream SRRT target that mediates the promotion of neural stem cell self-renewal (By similarity). Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation. In cooperation with other transcription factors, binds to the promoter sequence of the crystallin gene to activate transcription in the lens. Binds to the consensus DNA sequence 5'-TCATTGTTGTTG-3'.
Gallus gallus (taxid: 9031)
>sp|P54231|SOX2_SHEEP Transcription factor SOX-2 OS=Ovis aries GN=SOX2 PE=3 SV=1 Back     alignment and function description
>sp|P48431|SOX2_HUMAN Transcription factor SOX-2 OS=Homo sapiens GN=SOX2 PE=1 SV=1 Back     alignment and function description
>sp|Q6NVN0|SOX2_XENTR Transcription factor Sox-2 OS=Xenopus tropicalis GN=sox2 PE=2 SV=1 Back     alignment and function description
>sp|O42569|SOX2_XENLA Transcription factor Sox-2 OS=Xenopus laevis GN=sox2 PE=2 SV=1 Back     alignment and function description
>sp|P48432|SOX2_MOUSE Transcription factor SOX-2 OS=Mus musculus GN=Sox2 PE=1 SV=2 Back     alignment and function description
>sp|Q6EJB7|SOX3_DANRE Transcription factor Sox-3 OS=Danio rerio GN=sox3 PE=1 SV=1 Back     alignment and function description
>sp|P55863|SOX3A_XENLA Transcription factor Sox-3-A OS=Xenopus laevis GN=sox3-a PE=1 SV=1 Back     alignment and function description
>sp|Q68FA4|SOX3_XENTR Transcription factor Sox-3 OS=Xenopus tropicalis GN=sox3 PE=2 SV=1 Back     alignment and function description
>sp|Q9DDD7|SX19B_DANRE Transcription factor Sox-19b OS=Danio rerio GN=sox19b 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 ?
Query396
242019305448 transcription factor Sox-2, putative [Pe 0.866 0.765 0.508 1e-72
189237171382 PREDICTED: similar to transcription fact 0.825 0.856 0.538 7e-71
270008206336 SoxNeuro [Tribolium castaneum] 0.765 0.901 0.557 1e-70
328778318471 PREDICTED: transcription factor SOX-2-li 0.707 0.594 0.586 3e-70
380013641458 PREDICTED: transcription factor SOX-2-li 0.691 0.598 0.585 5e-70
322793662479 hypothetical protein SINV_03757 [Solenop 0.702 0.580 0.556 4e-68
332024304483 Transcription factor SOX-2 [Acromyrmex e 0.702 0.575 0.546 1e-67
383857369467 PREDICTED: transcription factor SOX-2-li 0.691 0.586 0.563 2e-67
345491074478 PREDICTED: transcription factor SOX-2-li 0.656 0.543 0.571 3e-67
307182716461 Transcription factor SOX-2 [Camponotus f 0.689 0.592 0.576 1e-66
>gi|242019305|ref|XP_002430102.1| transcription factor Sox-2, putative [Pediculus humanus corporis] gi|212515183|gb|EEB17364.1| transcription factor Sox-2, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
 Score =  279 bits (714), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 219/431 (50%), Positives = 262/431 (60%), Gaps = 88/431 (20%)

Query: 1   MLTMETDLKGGHI-------PPHHHLSSYGSM---VHSNMMSLSQSPSSVVHHQNIGPHV 50
           MLTME DLKGG +       P  H +SSYG++   VH +    S SPSS+   Q   PH+
Sbjct: 71  MLTMEADLKGGSLHGNMAPHPGLHQVSSYGTLGGLVHGS----SLSPSSMALGQ---PHL 123

Query: 51  THNPMSNPLHPSHNTNNNNNSTNSK---------NQNA--------------IDRVKRPM 87
            H     PL  S +T ++ +    +         +Q+A              IDRVKRPM
Sbjct: 124 QHMSQHQPLQHSQHTPHHQSHQPPQHHQPPPSSLHQHAPQPNNNNSSNKNQNIDRVKRPM 183

Query: 88  NAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEH 147
           NAFMVWSRGQRRKMAQ+NPKMHNSEISKRLGAEWKLL+E  KRPFIDEAKRLRAVHMKEH
Sbjct: 184 NAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSESEKRPFIDEAKRLRAVHMKEH 243

Query: 148 PDYKYRPRRKTKTLLKKDKYPLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQ 207
           PDYKYRPRRKTKTLLKKDKYPLG       T+     +   S+ +  +Q  +  R+ +YQ
Sbjct: 244 PDYKYRPRRKTKTLLKKDKYPLG------GTTPLIPGSGGESARSPVSQHQTLGRD-VYQ 296

Query: 208 MPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTT 267
           MPNGYMPNGYM+  A YQQH         GY RYD+  M  +      Y+NGSSYGMY  
Sbjct: 297 MPNGYMPNGYMVHDAAYQQHYG-------GY-RYDVGQMQHA-----GYVNGSSYGMY-- 341

Query: 268 ATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREY- 326
             T+PG G+P   +Q SSHSPSGSS+KSEPVSPSS GG+ TPTP +G P     +KREY 
Sbjct: 342 GGTVPG-GAPSPYLQQSSHSPSGSSIKSEPVSPSS-GGLHTPTPTTGAPVS---IKREYS 396

Query: 327 GSPNGLPPNSTDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQAGH 386
           G+P  +P  S             NG+    GDLR MISMYLP   E    Q ++Q Q  H
Sbjct: 397 GTPGAVPAGS-------------NGS---TGDLRQMISMYLPG--EPGAEQRLHQMQY-H 437

Query: 387 PPEGM-PLTHM 396
           P + + PL H+
Sbjct: 438 PSDQLQPLAHI 448

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|189237171|ref|XP_974496.2| PREDICTED: similar to transcription factor SOX-19 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|270008206|gb|EFA04654.1| SoxNeuro [Tribolium castaneum] Back     alignment and taxonomy information
>gi|328778318|ref|XP_003249473.1| PREDICTED: transcription factor SOX-2-like [Apis mellifera] Back     alignment and taxonomy information
>gi|380013641|ref|XP_003690859.1| PREDICTED: transcription factor SOX-2-like [Apis florea] Back     alignment and taxonomy information
>gi|322793662|gb|EFZ17100.1| hypothetical protein SINV_03757 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|332024304|gb|EGI64503.1| Transcription factor SOX-2 [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|383857369|ref|XP_003704177.1| PREDICTED: transcription factor SOX-2-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|345491074|ref|XP_003426523.1| PREDICTED: transcription factor SOX-2-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|307182716|gb|EFN69840.1| Transcription factor SOX-2 [Camponotus floridanus] 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 ?
Query396
FB|FBgn0029123572 SoxN "SoxNeuro" [Drosophila me 0.169 0.117 0.910 1.5e-50
UNIPROTKB|B1PXF9319 Sox2 "Sex determining region Y 0.169 0.210 0.925 7.5e-46
UNIPROTKB|A2VDX8320 SOX2 "Uncharacterized protein" 0.169 0.209 0.925 1.2e-45
UNIPROTKB|E2R1W3324 SOX2 "Uncharacterized protein" 0.169 0.206 0.925 1.2e-45
UNIPROTKB|P48431317 SOX2 "Transcription factor SOX 0.169 0.211 0.925 1.2e-45
UNIPROTKB|P54231320 SOX2 "Transcription factor SOX 0.169 0.209 0.925 1.2e-45
UNIPROTKB|Q6NVN0311 sox2 "Transcription factor Sox 0.169 0.215 0.925 2e-45
UNIPROTKB|O42569311 sox2 "Transcription factor Sox 0.169 0.215 0.925 2.5e-45
RGD|1565646319 Sox2 "SRY (sex determining reg 0.169 0.210 0.925 3.2e-45
ZFIN|ZDB-GENE-030909-1315 sox2 "SRY-box containing gene 0.169 0.212 0.910 6.5e-45
FB|FBgn0029123 SoxN "SoxNeuro" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 324 (119.1 bits), Expect = 1.5e-50, Sum P(4) = 1.5e-50
 Identities = 61/67 (91%), Positives = 63/67 (94%)

Query:    81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
             DRVKRPMNAFMVWSRGQRRKMA DNPKMHNSEISKRLGA+WK L+E  KRPFIDEAKRLR
Sbjct:   177 DRVKRPMNAFMVWSRGQRRKMASDNPKMHNSEISKRLGAQWKDLSESEKRPFIDEAKRLR 236

Query:   141 AVHMKEH 147
             AVHMKEH
Sbjct:   237 AVHMKEH 243
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISS;IDA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0007399 "nervous system development" evidence=IMP
GO:0005515 "protein binding" evidence=IPI
GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA
GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA
GO:0007417 "central nervous system development" evidence=IMP
GO:0007411 "axon guidance" evidence=IMP
GO:0031490 "chromatin DNA binding" evidence=IDA
GO:0030111 "regulation of Wnt receptor signaling pathway" evidence=IMP
UNIPROTKB|B1PXF9 Sox2 "Sex determining region Y-box 2" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|A2VDX8 SOX2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2R1W3 SOX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P48431 SOX2 "Transcription factor SOX-2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P54231 SOX2 "Transcription factor SOX-2" [Ovis aries (taxid:9940)] Back     alignment and assigned GO terms
UNIPROTKB|Q6NVN0 sox2 "Transcription factor Sox-2" [Xenopus (Silurana) tropicalis (taxid:8364)] Back     alignment and assigned GO terms
UNIPROTKB|O42569 sox2 "Transcription factor Sox-2" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
RGD|1565646 Sox2 "SRY (sex determining region Y)-box 2" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030909-1 sox2 "SRY-box containing gene 2" [Danio rerio (taxid:7955)] 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) ?
Q6EJB7SOX3_DANRENo assigned EC number0.42020.67170.8866yesN/A
P48432SOX2_MOUSENo assigned EC number0.43150.67420.8369yesN/A
P48431SOX2_HUMANNo assigned EC number0.43750.67420.8422yesN/A
P48430SOX2_CHICKNo assigned EC number0.44790.65150.8190yesN/A
Q6NVN0SOX2_XENTRNo assigned EC number0.43970.65900.8392yesN/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 ?
Query396
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 1e-35
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 9e-27
smart0039870 smart00398, HMG, high mobility group 1e-23
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 9e-21
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 5e-17
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 2e-14
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 2e-09
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 1e-05
pfam1233684 pfam12336, SOXp, SOX transcription factor 5e-05
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 4e-04
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information 
 Score =  125 bits (315), Expect = 1e-35
 Identities = 37/72 (51%), Positives = 53/72 (73%)

Query: 82  RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
            +KRPMNAFM++S+  RRK+ Q+ P   N  ISK LG  WK L+ + K+P+ +EAK+L+ 
Sbjct: 1   HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKE 60

Query: 142 VHMKEHPDYKYR 153
           +HMK +PDYK+R
Sbjct: 61  LHMKLYPDYKWR 72

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif. Length = 72
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box Back     alignment and domain information
>gnl|CDD|197700 smart00398, HMG, high mobility group Back     alignment and domain information
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors Back     alignment and domain information
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) Back     alignment and domain information
>gnl|CDD|152771 pfam12336, SOXp, SOX transcription factor Back     alignment and domain information
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional 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 ?
Query396
2le4_A81 Solution Structure Of The Hmg Box Dna-Binding Domai 9e-32
1gt0_D80 Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le 1e-31
1o4x_B88 Ternary Complex Of The Dna Binding Domains Of The O 1e-31
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 3e-20
1hrz_A76 The 3d Structure Of The Human Sry-Dna Complex Solve 3e-20
1j46_A85 3d Solution Nmr Structure Of The Wild Type Hmg-Box 5e-20
1j47_A85 3d Solution Nmr Structure Of The M9i Mutant Of The 1e-19
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 7e-19
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 1e-18
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 2e-18
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 3e-18
3u2b_C79 Structure Of The Sox4 Hmg Domain Bound To Dna Lengt 5e-18
1i11_A81 Solution Structure Of The Dna Binding Domain, Sox-5 3e-13
2e6o_A87 Solution Structure Of The Hmg Box Domain From Human 6e-05
1wz6_A82 Solution Structure Of The Hmg_box Domain Of Murine 1e-04
1hma_A73 The Solution Structure And Dynamics Of The Dna Bind 1e-04
1qrv_A73 Crystal Structure Of The Complex Of Hmg-D And Dna L 1e-04
1e7j_A74 Hmg-D Complexed To A Bulge Dna Length = 74 2e-04
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 2e-04
3nm9_A73 Hmgd(M13a)-Dna Complex Length = 73 6e-04
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of Human Stem Cell Transcription Factor Sox2 Length = 81 Back     alignment and structure 
Iteration: 1

 Score =  134 bits (337), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 62/67 (92%), Positives = 65/67 (97%)
Query: 81  DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
           DRVKRPMNAFMVWSRGQRRKMAQ+NPKMHNSEISKRLGAEWKLL+E  KRPFIDEAKRLR
Sbjct: 2   DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 61
Query: 141 AVHMKEH 147
           A+HMKEH
Sbjct: 62  ALHMKEH 68
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80 Back     alignment and structure
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And Sox2 Transcription Factors With A 19mer Oligonucleotide From The Hoxb1 Regulatory Element Length = 88 Back     alignment and structure
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159 Back     alignment and structure
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr Length = 76 Back     alignment and structure
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85 Back     alignment and structure
>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85 Back     alignment and structure
>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription Factor Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS AT 2.77 A RESOLUTION Length = 106 Back     alignment and structure
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 Back     alignment and structure
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription Factor Sox-17 Length = 82 Back     alignment and structure
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17 Length = 71 Back     alignment and structure
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna Length = 79 Back     alignment and structure
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg Box From Mouse Length = 81 Back     alignment and structure
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human Hmg-Box Transcription Factor 1 Length = 87 Back     alignment and structure
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby Sox Homolog Length = 82 Back     alignment and structure
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding Domain Of Hmg-D From Drosophila Melanogaster Length = 73 Back     alignment and structure
>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna Length = 73 Back     alignment and structure
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna Length = 74 Back     alignment and structure
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High Mobility Group Protein B3 Length = 81 Back     alignment and structure
>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex Length = 73 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 ?
Query396
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 5e-45
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 9e-45
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 1e-43
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 1e-43
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 2e-43
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 2e-43
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 2e-43
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 2e-43
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 7e-42
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 4e-39
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 5e-38
1wgf_A90 Upstream binding factor 1; transcription factor, D 2e-33
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 3e-32
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 2e-31
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 3e-29
1hme_A77 High mobility group protein fragment-B; DNA-bindin 6e-27
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 6e-25
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 1e-23
2lhj_A97 High mobility group protein homolog NHP1; structur 2e-23
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 7e-23
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 2e-22
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 1e-21
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 5e-20
1ckt_A71 High mobility group 1 protein; high-mobility group 2e-17
2yrq_A173 High mobility group protein B1; HMG box domain, DN 7e-17
2yrq_A173 High mobility group protein B1; HMG box domain, DN 3e-09
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 1e-16
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 1e-15
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 3e-14
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 5e-12
3tq6_A214 Transcription factor A, mitochondrial; transcripti 2e-13
3tq6_A214 Transcription factor A, mitochondrial; transcripti 1e-09
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 6e-13
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 1e-12
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 5e-08
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 2e-06
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Length = 85 Back     alignment and structure
 Score =  149 bits (378), Expect = 5e-45
 Identities = 55/83 (66%), Positives = 69/83 (83%)

Query: 81  DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
           DRVKRPMNAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E  K PF  EA++L+
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62

Query: 141 AVHMKEHPDYKYRPRRKTKTLLK 163
           A+H +++P+YKYRPRRK K L K
Sbjct: 63  AMHREKYPNYKYRPRRKAKMLPK 85
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Length = 80 Back     alignment and structure
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Length = 81 Back     alignment and structure
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Length = 82 Back     alignment and structure
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Length = 106 Back     alignment and structure
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} PDB: 2yul_A Length = 83 Back     alignment and structure
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Length = 86 Back     alignment and structure
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79 Back     alignment and structure
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Length = 76 Back     alignment and structure
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71 Back     alignment and structure
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Length = 87 Back     alignment and structure
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 90 Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159 Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159 Back     alignment and structure
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92 Back     alignment and structure
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Length = 77 Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 Back     alignment and structure
>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97 Back     alignment and structure
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73 Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99 Back     alignment and structure
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 102 Back     alignment and structure
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93 Back     alignment and structure
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Length = 71 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86 Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214 Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214 Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67 Back     alignment and structure
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81 Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101 Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query396
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.93
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.92
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.92
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.92
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.91
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.91
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.91
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.91
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.91
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.9
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.88
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.87
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.87
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.86
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.86
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.85
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.84
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.84
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.84
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.83
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.83
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.82
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.82
1ckt_A71 High mobility group 1 protein; high-mobility group 99.82
2lhj_A97 High mobility group protein homolog NHP1; structur 99.81
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.81
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.77
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.77
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.77
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.76
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.76
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.76
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.75
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.74
2cto_A93 Novel protein; high mobility group box domain, hel 99.71
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.71
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.71
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.55
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.55
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
Probab=99.93  E-value=1.5e-25  Score=180.77  Aligned_cols=86  Identities=24%  Similarity=0.499  Sum_probs=80.7

Q ss_pred             CCCCCCCchhHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHhhcCHHhhhhHHHHHHHHHHHHHHHCCCCCCCCcccchh
Q psy13343         81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRKTKT  160 (396)
Q Consensus        81 ~kpKRPmNAFmLF~ke~R~kik~enP~~~~~EISK~LGe~WK~LSeeEK~~Y~e~Ak~~Ke~h~ke~P~Yk~rPrkkkk~  160 (396)
                      .+||||+||||||++++|.+|+++||++++.||+++||++|++|+++||++|+++|++++++|.++||+|+|+|++++++
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~~~~k   80 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKK   80 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTTTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCCCCCc
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999988666


Q ss_pred             ccccCC
Q psy13343        161 LLKKDK  166 (396)
Q Consensus       161 ~~kk~k  166 (396)
                      ++||+|
T Consensus        81 krkkd~   86 (86)
T 2lef_A           81 KRKREK   86 (86)
T ss_dssp             CSSCCC
T ss_pred             cccccC
Confidence            655554
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Back     alignment and structure
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A Back     alignment and structure
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Back     alignment and structure
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Back     alignment and structure
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Back     alignment and structure
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Back     alignment and structure
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 Back     alignment and structure
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Back     alignment and structure
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Back     alignment and structure
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Back     alignment and structure
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Back     alignment and structure
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Back     alignment and structure
>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Back     alignment and structure
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A* Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Back     alignment and structure
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A Back     alignment and structure
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {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 396
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 3e-34
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 2e-32
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 2e-30
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 1e-25
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 3e-24
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 6e-22
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 7e-21
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 6e-20
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 2e-19
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 6e-19
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 9e-19
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-17
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80 Back     information, alignment and structure

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  119 bits (300), Expect = 3e-34
 Identities = 75/80 (93%), Positives = 78/80 (97%)

Query: 81  DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
           DRVKRPMNAFMVWSRGQRRKMAQ+NPKMHNSEISKRLGAEWKLL+E  KRPFIDEAKRLR
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60

Query: 141 AVHMKEHPDYKYRPRRKTKT 160
           A+HMKEHPDYKYRPRRKTKT
Sbjct: 61  ALHMKEHPDYKYRPRRKTKT 80
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 Back     information, alignment and structure
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 Back     information, alignment and structure
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 Back     information, alignment and structure
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 Back     information, alignment and structure
>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91 Back     information, alignment and structure
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93 Back     information, alignment and structure
>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108 Back     information, alignment and structure
>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101 Back     information, alignment and structure
>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90 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 ?
Query396
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.92
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.92
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.91
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.88
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.81
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.8
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.79
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.79
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.79
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.77
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.68
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.67
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 95.23
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.92  E-value=1.2e-25  Score=178.66  Aligned_cols=79  Identities=94%  Similarity=1.460  Sum_probs=76.7

Q ss_pred             CCCCCCCchhHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHhhcCHHhhhhHHHHHHHHHHHHHHHCCCCCCCCcccch
Q psy13343         81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRKTK  159 (396)
Q Consensus        81 ~kpKRPmNAFmLF~ke~R~kik~enP~~~~~EISK~LGe~WK~LSeeEK~~Y~e~Ak~~Ke~h~ke~P~Yk~rPrkkkk  159 (396)
                      ++||||+||||||++++|++|+++||++.+.||+++||++|++|+++||++|+++|+++|++|.++||+|+|+|+|+.|
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p~rk~k   79 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTK   79 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCCCCCCC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999988765
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Back     information, alignment and structure
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure