Citrus Sinensis ID: 046368

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-------39
IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSLLRDYEQIYFFRSQDSWQGPSTNAVSAPGTAQPSPDIQSAVQQPRINAAVLPEARPASSGGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQYPIHQVPSSYNVINNNNATAHAVSGVQRRRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKTGQVISDAIPLQQRLPGADVDMVEVDTKLDETGGDSPQTPDNESSSGVSDFEDDKTVEKDTEMEESPGVGLGTETSNVDLEISAEEPAFELPKAEENAKDKNVENVSDDIVRNDMVE
cccccccccHHHHHHHHHHHHccHHHHHHHccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccHHHHcHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccHHHHccccc
cccccccEEcHHHHHHHHHHccccHHHHcHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHEccccccccccccccccccccccccccHHHccccccccccccccccccccccccEEEEEEccccccEEEEEEEccccEEEEEEcccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccEccccccc
IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAifnfpstatnASFVLRKYYQSLLRDYEQIYFfrsqdswqgpstnavsapgtaqpspdiqsavqqprinaavlpearpassggspvigvidgkfesGYLVTVTIGSEtlkgvlyqapqypihqvpssynvinnnnatahaVSGVQRRRRRKkseikrrdpahpkpnrsgynfffaeqharlkplhpgkdrEISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKtgqvisdaiplqqrlpgadvdmVEVDtkldetggdspqtpdnesssgvsdfeddktvekdtemeespgvglgtetsnvdleisaeepafelpkaeenakdknvenvsddivrndmve
ipiiggkeldlhrlfvevtarggiekiikerrwKEVTAIfnfpstatnasfVLRKYYQSLLRDYEQIYFFRSQDSWQGPSTNAVSAPGTAQPSPDIQSAVQQPRINAAVLpearpassggsPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQYPIHQVPSSYNVINNNNAtahavsgvqrrrrrkkseikrrdpahpkpnrsgyNFFFAEQHARlkplhpgkdreISRMIGELWNKLKESEKAvyqekalkdkeryrIEMEDYRERlktgqvisdaiplqqrlpgadVDMVEVDTKLdetggdspqtpdnesssgvsdfedDKTVEKDtemeespgvglgtetSNVDLEISAEEPafelpkaeenakdknvenvsddivrndmve
IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSLLRDYEQIYFFRSQDSWQGPSTNAVSAPGTAQPSPDIQSAVQQPRINAAVLPEARPASSGGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQYPIHQVPSSYNVINNNNATAHAVSGVQrrrrrkkseikrrDPAHPKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKTGQVISDAIPLQQRLPGADVDMVEVDTKLDETGGDSPQTPDNESSSGVSDFEDDKTVEKDTEMEESPGVGLGTETSNVDLEISAEEPAFELPKAEENAKDKNVENVSDDIVRNDMVE
***IGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSLLRDYEQIYFFRS**************************************************VIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQYPIHQVPSSYNVINNN***********************************YNFFFAEQH***************RMIGELWNKL*****************************LKTGQVISDAI************************************************************************************************************
IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSLLRDYEQIYFFRSQ*******************************************************************************************************************************KPNRSGYNFFFAEQHARLKP**P***REISRMIGELWNKLKESEKAVYQEKALKDKERYRIEM************************************************************************************************************************ND***
IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSLLRDYEQIYFFRSQDSW**********************AVQQPRINAAVLP********GSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQYPIHQVPSSYNVINNNNATAH***********************PKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKTGQVISDAIPLQQRLPGADVDMVEVDTKLD**************************************VGLGTETSNVDLEISAEEPAFELPKAEENAKDKNVENVSDDIVRNDMVE
IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSLLRDYEQIYFFRSQ*********************************************GGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQ***************************************RDPAHPKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKTGQVISDAIPLQQRLPGADVDMVEVDTKLD***************************************************************************************
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IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSLLRDYEQIYFFRSQDSWQGPSTNAVSAPGTAQPSPDIQSAVQQPRINAAVLPEARPASSGGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQYPIHQVPSSYNVINNNNATAHAVSGVQRRRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHPGKDREISRMIGELWNKLKESEKAVYxxxxxxxxxxxxxxxxxxxxxLKTGQVISDAIPLQQRLPGADVDMVEVDTKLDETGGDSPQTPDNESSSGVSDFEDDKTVEKDTEMEESPGVGLGTETSNVDLEISAEEPAFELPKAEENAKDKNVENVSDDIVRNDMVE
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 ?
Query388 2.2.26 [Sep-21-2011]
Q9MAT6448 High mobility group B pro yes no 0.850 0.736 0.611 1e-101
Q9LTT3319 High mobility group B pro no no 0.652 0.793 0.451 5e-64
Q9SGS2338 High mobility group B pro no no 0.680 0.781 0.461 7e-60
Q9LG02337 Putative high mobility gr no no 0.587 0.676 0.385 1e-46
Q68CP9 1835 AT-rich interactive domai yes no 0.190 0.040 0.445 4e-15
O02326467 AT-rich interactive domai yes no 0.167 0.139 0.446 3e-10
Q6GQD7539 AT-rich interactive domai N/A no 0.167 0.120 0.415 7e-10
Q5XGD9541 AT-rich interactive domai no no 0.167 0.120 0.415 8e-10
A6PWV5409 AT-rich interactive domai no no 0.201 0.190 0.373 1e-09
A6NKF2412 AT-rich interactive domai no no 0.201 0.189 0.373 1e-09
>sp|Q9MAT6|HMG15_ARATH High mobility group B protein 15 OS=Arabidopsis thaliana GN=HMGB15 PE=2 SV=1 Back     alignment and function desciption
 Score =  370 bits (949), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 216/353 (61%), Positives = 252/353 (71%), Gaps = 23/353 (6%)

Query: 1   IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
           +PIIGG++LDLH+LFVEVT+RGGI KI+ ERRWKEVTA F FP TATNAS+VLRKYY SL
Sbjct: 52  VPIIGGRDLDLHKLFVEVTSRGGINKILNERRWKEVTATFVFPPTATNASYVLRKYYFSL 111

Query: 61  LRDYEQIYFFRSQ-----DSWQGPSTNAVSAPGTAQPSPDIQSAV--QQPRINAAVLPEA 113
           L +YEQIYFFRS      DS Q PS       G  +PS ++Q+     QP+IN A   E 
Sbjct: 112 LNNYEQIYFFRSNGQIPPDSMQSPSARPCFIQGAIRPSQELQALTFTPQPKINTA---EF 168

Query: 114 RPASSGGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQ----------APQYPIHQVPS 163
              S  GS V+GVIDGKFESGYLVTVTIGSE LKGVLYQ           PQ     +P+
Sbjct: 169 LGGSLAGSNVVGVIDGKFESGYLVTVTIGSEQLKGVLYQLLPQNTVSYQTPQQSHGVLPN 228

Query: 164 SYNVINNNNATAHAVSGVQRRRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHP 223
           + N+  N    A  V+  +RRRRRKKSEIKRRDP HPKPNRSGYNFFFAEQHARLKPLHP
Sbjct: 229 TLNISANPQGVAGGVT--KRRRRRKKSEIKRRDPDHPKPNRSGYNFFFAEQHARLKPLHP 286

Query: 224 GKDREISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKTGQVISDAIPLQ 283
           GKDR+ISRMIGELWNKL E EK +YQ KA++DKERYR EMEDYRE+ K GQ+IS+A+PLQ
Sbjct: 287 GKDRDISRMIGELWNKLNEDEKLIYQGKAMEDKERYRTEMEDYREKKKNGQLISNAVPLQ 346

Query: 284 QRLPGADVDMVEVDTKLDETGGDSPQTPDNESSSGVSDFEDDKTVEKDTEMEE 336
           QRLP  +VDM E D  +DE   D  +   + SS       DD+++E D E+EE
Sbjct: 347 QRLPEQNVDMAEADLPIDEVEEDDEEGDSSGSSGESEP-HDDQSIETDPELEE 398
Binds preferentially DNA with A/T-rich content.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9LTT3|HMG10_ARATH High mobility group B protein 10 OS=Arabidopsis thaliana GN=HMGB10 PE=2 SV=1 Back     alignment and function description
>sp|Q9SGS2|HMGB9_ARATH High mobility group B protein 9 OS=Arabidopsis thaliana GN=HMGB9 PE=2 SV=1 Back     alignment and function description
>sp|Q9LG02|HMG11_ARATH Putative high mobility group B protein 11 OS=Arabidopsis thaliana GN=HMGB11 PE=3 SV=2 Back     alignment and function description
>sp|Q68CP9|ARID2_HUMAN AT-rich interactive domain-containing protein 2 OS=Homo sapiens GN=ARID2 PE=1 SV=2 Back     alignment and function description
>sp|O02326|CFI1_CAEEL AT-rich interactive domain-containing protein cfi-1 OS=Caenorhabditis elegans GN=cfi-1 PE=1 SV=3 Back     alignment and function description
>sp|Q6GQD7|ARI3A_XENLA AT-rich interactive domain-containing protein 3A OS=Xenopus laevis GN=arid3a PE=2 SV=1 Back     alignment and function description
>sp|Q5XGD9|ARI3A_XENTR AT-rich interactive domain-containing protein 3A OS=Xenopus tropicalis GN=arid3a PE=2 SV=1 Back     alignment and function description
>sp|A6PWV5|ARI3C_MOUSE AT-rich interactive domain-containing protein 3C OS=Mus musculus GN=Arid3c PE=2 SV=2 Back     alignment and function description
>sp|A6NKF2|ARI3C_HUMAN AT-rich interactive domain-containing protein 3C OS=Homo sapiens GN=ARID3C PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query388
356536532425 PREDICTED: high mobility group B protein 0.896 0.818 0.705 1e-137
298205254483 unnamed protein product [Vitis vinifera] 0.930 0.747 0.689 1e-136
225433532482 PREDICTED: high mobility group B protein 0.930 0.748 0.689 1e-136
147855747461 hypothetical protein VITISV_021289 [Viti 0.930 0.783 0.689 1e-136
356575009419 PREDICTED: high mobility group B protein 0.884 0.818 0.691 1e-127
255554110466 transcription factor, putative [Ricinus 0.963 0.802 0.649 1e-126
357445043417 High mobility group protein B3 [Medicago 0.858 0.798 0.639 1e-121
449442473 491 PREDICTED: high mobility group B protein 0.837 0.661 0.658 1e-119
224060381348 high mobility group family [Populus tric 0.768 0.856 0.683 1e-107
357501441437 High mobility group family [Medicago tru 0.814 0.723 0.608 1e-101
>gi|356536532|ref|XP_003536791.1| PREDICTED: high mobility group B protein 15-like [Glycine max] Back     alignment and taxonomy information
 Score =  493 bits (1268), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 256/363 (70%), Positives = 285/363 (78%), Gaps = 15/363 (4%)

Query: 1   IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
           IPI+GG+ELDLHRLFVEVT+RGGI KII+ER+WK+VT++FNFPSTATNASFVLRKYY SL
Sbjct: 59  IPIVGGRELDLHRLFVEVTSRGGIAKIIRERKWKDVTSVFNFPSTATNASFVLRKYYASL 118

Query: 61  LRDYEQIYFFRSQ-------DSWQGPSTNAVSAPGTAQPSP--DIQSAV-QQPRINAAVL 110
           L  YEQIYFF+++       D+ Q  ST  V  P    P P  +IQ AV QQ  INAA L
Sbjct: 119 LYHYEQIYFFKAREWDPTAPDALQNQSTLPVPPPKMQFPQPLSEIQPAVFQQSNINAAKL 178

Query: 111 PEARPASSGGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQYPIHQVPSSYNVINN 170
           PEA  ASS GSPVIGVIDGKFESGYLVTVTIGSE LKGVLYQAPQ P+           N
Sbjct: 179 PEAMAASSAGSPVIGVIDGKFESGYLVTVTIGSEKLKGVLYQAPQNPVLVASHHSASAKN 238

Query: 171 NNATAHAVSGVQRRRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHPGKDREIS 230
           NNA+A    GV RRRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLK LH GKDREIS
Sbjct: 239 NNASASL--GVHRRRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKLLHHGKDREIS 296

Query: 231 RMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKTGQVISDAIPLQQRLPGAD 290
           RMIGELWNKLKESEK VYQEKA+KDKERYR EMEDYRE+ K GQVISDA+PLQQRLP  D
Sbjct: 297 RMIGELWNKLKESEKTVYQEKAMKDKERYRAEMEDYREKQKMGQVISDAVPLQQRLPEPD 356

Query: 291 VDMVEVDTKLDETGGDSPQTPDNESSSGVSDFED-DKTVEKDTEMEESPGVGLGTETSNV 349
            DM++VD K+DE  GDSPQTP  E SSG SD+ED +KT E+  +M+  P +G+G ETS +
Sbjct: 357 ADMLDVDIKMDEAEGDSPQTP--EESSGGSDYEDYNKTAERGFDMDALPVIGMGAETSYL 414

Query: 350 DLE 352
             E
Sbjct: 415 GSE 417

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|298205254|emb|CBI17313.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225433532|ref|XP_002266394.1| PREDICTED: high mobility group B protein 15-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|147855747|emb|CAN83439.1| hypothetical protein VITISV_021289 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356575009|ref|XP_003555635.1| PREDICTED: high mobility group B protein 15-like [Glycine max] Back     alignment and taxonomy information
>gi|255554110|ref|XP_002518095.1| transcription factor, putative [Ricinus communis] gi|223542691|gb|EEF44228.1| transcription factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|357445043|ref|XP_003592799.1| High mobility group protein B3 [Medicago truncatula] gi|355481847|gb|AES63050.1| High mobility group protein B3 [Medicago truncatula] Back     alignment and taxonomy information
>gi|449442473|ref|XP_004139006.1| PREDICTED: high mobility group B protein 15-like [Cucumis sativus] gi|449530303|ref|XP_004172135.1| PREDICTED: high mobility group B protein 15-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224060381|ref|XP_002300171.1| high mobility group family [Populus trichocarpa] gi|222847429|gb|EEE84976.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357501441|ref|XP_003621009.1| High mobility group family [Medicago truncatula] gi|355496024|gb|AES77227.1| High mobility group family [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 ?
Query388
TAIR|locus:2010587448 AT1G04880 [Arabidopsis thalian 0.855 0.741 0.598 7.1e-100
TAIR|locus:2199824338 AT1G76110 [Arabidopsis thalian 0.688 0.789 0.453 9.6e-57
TAIR|locus:2020517337 AT1G55650 [Arabidopsis thalian 0.353 0.406 0.455 7.6e-44
TAIR|locus:2088160319 AT3G13350 [Arabidopsis thalian 0.363 0.442 0.452 6e-32
UNIPROTKB|Q68CP9 1835 ARID2 "AT-rich interactive dom 0.239 0.050 0.408 5.1e-12
UNIPROTKB|E1C9H0 1831 ARID2 "Uncharacterized protein 0.239 0.050 0.397 7.2e-12
ZFIN|ZDB-GENE-030131-6311 1573 arid2 "AT rich interactive dom 0.239 0.059 0.376 3.1e-11
UNIPROTKB|F1N1P2199 F1N1P2 "Uncharacterized protei 0.286 0.557 0.347 3.8e-10
GENEDB_PFALCIPARUM|PFL0145c97 PFL0145c "high mobility group 0.182 0.731 0.445 1.3e-09
UNIPROTKB|Q8I61697 HMGB1 "High mobility group pro 0.182 0.731 0.445 1.3e-09
TAIR|locus:2010587 AT1G04880 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 991 (353.9 bits), Expect = 7.1e-100, P = 7.1e-100
 Identities = 210/351 (59%), Positives = 249/351 (70%)

Query:     1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
             +PIIGG++LDLH+LFVEVT+RGGI KI+ ERRWKEVTA F FP TATNAS+VLRKYY SL
Sbjct:    52 VPIIGGRDLDLHKLFVEVTSRGGINKILNERRWKEVTATFVFPPTATNASYVLRKYYFSL 111

Query:    61 LRDYEQIYFFRSQ-----DSWQGPSTNAVSAPGTAQPSPDIQSAV--QQPRINAAVLPEA 113
             L +YEQIYFFRS      DS Q PS       G  +PS ++Q+     QP+IN A   E 
Sbjct:   112 LNNYEQIYFFRSNGQIPPDSMQSPSARPCFIQGAIRPSQELQALTFTPQPKINTA---EF 168

Query:   114 RPASSGGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQA-PQYPI-HQVPS-SYNVINN 170
                S  GS V+GVIDGKFESGYLVTVTIGSE LKGVLYQ  PQ  + +Q P  S+ V+ N
Sbjct:   169 LGGSLAGSNVVGVIDGKFESGYLVTVTIGSEQLKGVLYQLLPQNTVSYQTPQQSHGVLPN 228

Query:   171 N-NATAH--AVSG--VQXXXXXXXXXXXXXDPAHPKPNRSGYNFFFAEQHARLKPLHPGK 225
               N +A+   V+G   +             DP HPKPNRSGYNFFFAEQHARLKPLHPGK
Sbjct:   229 TLNISANPQGVAGGVTKRRRRRKKSEIKRRDPDHPKPNRSGYNFFFAEQHARLKPLHPGK 288

Query:   226 DREISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRERLKTGQVISDAIPLQQR 285
             DR+ISRMIGELWNKL E EK +YQ KA++DKERYR EMEDYRE+ K GQ+IS+A+PLQQR
Sbjct:   289 DRDISRMIGELWNKLNEDEKLIYQGKAMEDKERYRTEMEDYREKKKNGQLISNAVPLQQR 348

Query:   286 LPGADVDMVEVDTKLDETGGDSPQTPDNESSSGVSDFEDDKTVEKDTEMEE 336
             LP  +VDM E D  +DE   D  +  D+  SSG S+  DD+++E D E+EE
Sbjct:   349 LPEQNVDMAEADLPIDEVEEDDEEG-DSSGSSGESEPHDDQSIETDPELEE 398
GO:0003677 "DNA binding" evidence=IEA
GO:0005622 "intracellular" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS
GO:0006333 "chromatin assembly or disassembly" evidence=RCA
TAIR|locus:2199824 AT1G76110 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2020517 AT1G55650 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2088160 AT3G13350 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q68CP9 ARID2 "AT-rich interactive domain-containing protein 2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E1C9H0 ARID2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-6311 arid2 "AT rich interactive domain 2 (ARID, RFX-like)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1N1P2 F1N1P2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
GENEDB_PFALCIPARUM|PFL0145c PFL0145c "high mobility group protein" [Plasmodium falciparum (taxid:5833)] Back     alignment and assigned GO terms
UNIPROTKB|Q8I616 HMGB1 "High mobility group protein" [Plasmodium falciparum 3D7 (taxid:36329)] 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) ?
Q9MAT6HMG15_ARATHNo assigned EC number0.61180.85050.7366yesno

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:
GSVIVG00031686001
SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_58, whole genome shotgun sequence); (461 aa)
(Vitis vinifera)
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 ?
Query388
smart0101488 smart01014, ARID, ARID/BRIGHT DNA binding domain 2e-22
smart0050193 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interac 8e-22
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 1e-20
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 7e-20
pfam0138890 pfam01388, ARID, ARID/BRIGHT DNA binding domain 2e-18
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 5e-18
smart0039870 smart00398, HMG, high mobility group 1e-17
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 2e-13
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 6e-10
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 9e-10
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 4e-07
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 3e-06
>gnl|CDD|198082 smart01014, ARID, ARID/BRIGHT DNA binding domain Back     alignment and domain information 
 Score = 90.0 bits (224), Expect = 2e-22
 Identities = 31/65 (47%), Positives = 44/65 (67%)

Query: 1  IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
          IP+IGGK LDL+RL+  V  RGG +K+ K+++WK+V      P +AT+A   LRK+Y+  
Sbjct: 24 IPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATSAGTSLRKHYEKY 83

Query: 61 LRDYE 65
          L  YE
Sbjct: 84 LLPYE 88

Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. Length = 88
>gnl|CDD|128777 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interaction domain) domain 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|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|216473 pfam01388, ARID, ARID/BRIGHT DNA binding domain Back     alignment and domain information
>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|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional 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|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|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) Back     alignment and domain information
>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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 388
KOG2744512 consensus DNA-binding proteins Bright/BRCAA1/RBP1 99.87
PTZ0019994 high mobility group protein; Provisional 99.85
smart0050193 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) 99.81
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.77
PF0138892 ARID: ARID/BRIGHT DNA binding domain; InterPro: IP 99.76
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.74
KOG0527331 consensus HMG-box transcription factor [Transcript 99.71
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.71
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.68
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.68
smart0039870 HMG high mobility group. 99.67
KOG3248421 consensus Transcription factor TCF-4 [Transcriptio 99.66
COG5648211 NHP6B Chromatin-associated proteins containing the 99.65
KOG038196 consensus HMG box-containing protein [General func 99.62
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.59
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.46
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 99.35
KOG0528511 consensus HMG-box transcription factor SOX5 [Trans 99.21
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.62
KOG2510532 consensus SWI-SNF chromatin-remodeling complex pro 98.56
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 97.55
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 96.79
COG5648211 NHP6B Chromatin-associated proteins containing the 96.22
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 95.94
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 88.69
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 88.33
TIGR0162450 LRP1_Cterm LRP1 C-terminal domain. This model repr 84.53
PF05142154 DUF702: Domain of unknown function (DUF702) ; Inte 81.82
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription] Back     alignment and domain information 
Probab=99.87  E-value=2.3e-22  Score=209.60  Aligned_cols=150  Identities=35%  Similarity=0.534  Sum_probs=115.8

Q ss_pred             CCccCCeecccchhhHHHHhccchhhhhhccchhhhhhhhCCCC-CCCcHHHHHHHHHHHhHHHHHhHhhhccCCCCCCC
Q 046368            1 IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPS-TATNASFVLRKYYQSLLRDYEQIYFFRSQDSWQGP   79 (388)
Q Consensus         1 iP~i~gk~LDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~-~~tsas~~Lk~~Y~k~L~~yE~~~~~~~~~~~~~p   79 (388)
                      ||+|+|++||||.||.+|+++||+++|+..++|++|+..|+||+ ++|+++|+||++|+++|++|||.+++....++..|
T Consensus       185 iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wrev~~~l~~pt~tiTsaaf~lr~~y~K~L~~ye~~~~~~~~~pln~p  264 (512)
T KOG2744|consen  185 IPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWREVIDGLNFPTPTITSAAFTLRKQYLKLLFEYECEFEKNRHVPLNSP  264 (512)
T ss_pred             ccccCCCcchHHHHHHHHhcCCchhHhhhhhhHHHHhccccCCCcccchHHHHHHHHHHHHHHHHHHHHHHhccCCCCCc
Confidence            79999999999999999999999999999999999999999999 99999999999999999999999999977554444


Q ss_pred             CCCCCCCCCCCCCCccchhh-cccc---cccccCCCCCCCCCCCCCceeeccCCcccCceeEEEEecccccccccccCCC
Q 046368           80 STNAVSAPGTAQPSPDIQSA-VQQP---RINAAVLPEARPASSGGSPVIGVIDGKFESGYLVTVTIGSETLKGVLYQAPQ  155 (388)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~-~~~~---~~~~~~~~g~~~~s~~~~~v~g~idgkf~~gYlvtv~~gse~l~gvLy~~~~  155 (388)
                      .....    .+.++...+.. ....   ..+....   ..+.++...+.|+|+|+|.+||++.+.+|++.|.|++|++++
T Consensus       265 ~~~~~----~a~~~~~rE~~~~~~~~~~~~~~~~~---~~~~~~~~~aa~~~~g~f~~~~~~~~~~~s~~ln~~~~~~~~  337 (512)
T KOG2744|consen  265 AELSE----EASSSNRREGRRHELSPSKEFQANGP---SEEEPAEAEAAPEILGNFLQGLLVFMKDGSEPLNGVLYLGPP  337 (512)
T ss_pred             ccccc----cccccccccccccccCcchhhccCCc---ccccccccccchhhhccccccCceeccCcchhccCccccccC
Confidence            32211    01111111111 0000   1111111   123345678999999999999999999999999999999976


Q ss_pred             CC
Q 046368          156 YP  157 (388)
Q Consensus       156 p~  157 (388)
                      ..
T Consensus       338 ~~  339 (512)
T KOG2744|consen  338 DL  339 (512)
T ss_pred             cc
Confidence            54

>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain Back     alignment and domain information
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans Back     alignment and domain information
>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
>KOG0527 consensus HMG-box transcription factor [Transcription] Back     alignment and domain information
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin Back     alignment and domain information
>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
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins Back     alignment and domain information
>smart00398 HMG high mobility group Back     alignment and domain information
>KOG3248 consensus Transcription factor TCF-4 [Transcription] Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>KOG0381 consensus HMG box-containing protein [General function prediction only] Back     alignment and domain information
>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
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics] Back     alignment and domain information
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics] Back     alignment and domain information
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription] Back     alignment and domain information
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription] Back     alignment and domain information
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics] Back     alignment and domain information
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A Back     alignment and domain information
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ] Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta Back     alignment and domain information
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [] Back     alignment and domain information
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT) Back     alignment and domain information
>TIGR01624 LRP1_Cterm LRP1 C-terminal domain Back     alignment and domain information
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function 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 ?
Query388
2kk0_A145 Solution Structure Of Dead Ringer-Like Protein 1 (A 9e-10
1c20_A128 Solution Structure Of The Dna-Binding Domain From T 4e-08
1kqq_A139 Solution Structure Of The Dead Ringer Arid-Dna Comp 2e-07
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 1e-06
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 6e-05
1ryu_A120 Solution Structure Of The Swi1 Arid Length = 120 2e-04
2jrz_A117 Solution Structure Of The BrightARID DOMAIN FROM TH 2e-04
2cxy_A125 Crystal Structure Of The Hbaf250b At-Rich Interacti 3e-04
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 3e-04
2co9_A102 Solution Structure Of The Hmg_box Domain Of Thymus 3e-04
2yqe_A100 Solution Structure Of The Arid Domain Of Jarid1d Pr 3e-04
2jxj_A96 Nmr Structure Of The Arid Domain From The Histone H 3e-04
2rq5_A121 Solution Structure Of The At-Rich Interaction Domai 4e-04
2crj_A92 Solution Structure Of The Hmg Domain Of Mouse Hmg D 4e-04
2lhj_A97 Nmr Structure Of The High Mobility Group Protein-Li 5e-04
2lm1_A107 Solution Nmr Structure Of Lysine-Specific Demethyla 5e-04
>pdb|2KK0|A Chain A, Solution Structure Of Dead Ringer-Like Protein 1 (At-Rich Interactive Domain-Containing Protein 3a) From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4394c Length = 145 Back     alignment and structure 
Iteration: 1

 Score = 61.2 bits (147), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 42/65 (64%)
Query: 1   IPIIGGKELDLHRLFVEVTARGGIEKIIKERRWKEVTAIFNFPSTATNASFVLRKYYQSL 60
           IPI+  + LDL  L+V VT +GG+ ++I ++ W+E+T   N P++ T+A+F LR  Y   
Sbjct: 56  IPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMKY 115
Query: 61  LRDYE 65
           L  YE
Sbjct: 116 LYPYE 120
>pdb|1C20|A Chain A, Solution Structure Of The Dna-Binding Domain From The Dead Ringer Protein Length = 128 Back     alignment and structure
>pdb|1KQQ|A Chain A, Solution Structure Of The Dead Ringer Arid-Dna Complex Length = 139 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|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78 Back     alignment and structure
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid Length = 120 Back     alignment and structure
>pdb|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN Jarid1c Protein Length = 117 Back     alignment and structure
>pdb|2CXY|A Chain A, Crystal Structure Of The Hbaf250b At-Rich Interaction Domain (Arid) Length = 125 Back     alignment and structure
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79 Back     alignment and structure
>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High Mobility Group Box Protein Tox From Mouse Length = 102 Back     alignment and structure
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein Length = 100 Back     alignment and structure
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4 Demethylase Rbp2 Length = 96 Back     alignment and structure
>pdb|2RQ5|A Chain A, Solution Structure Of The At-Rich Interaction Domain (Arid) Of JumonjiJARID2 Length = 121 Back     alignment and structure
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain Protein Hmgx2 Length = 92 Back     alignment and structure
>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A) Length = 97 Back     alignment and structure
>pdb|2LM1|A Chain A, Solution Nmr Structure Of Lysine-Specific Demethylase Lid From Drosophila Melanogaster, Northeast Structural Genomics Consortium Target Fr824d Length = 107 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 ?
Query388
2lhj_A97 High mobility group protein homolog NHP1; structur 3e-29
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 3e-29
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 3e-27
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 7e-27
1hme_A77 High mobility group protein fragment-B; DNA-bindin 3e-26
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 6e-26
2rq5_A121 Protein jumonji; developmental protein, nucleus, r 2e-23
2yrq_A173 High mobility group protein B1; HMG box domain, DN 6e-23
2yrq_A173 High mobility group protein B1; HMG box domain, DN 6e-14
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 8e-23
1ckt_A71 High mobility group 1 protein; high-mobility group 8e-22
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 2e-21
1ig6_A107 MRF-2, modulator recognition factor 2; DNA binding 3e-21
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 1e-20
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 1e-20
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 4e-20
2eqy_A122 RBP2 like, jumonji, at rich interactive domain 1B; 1e-19
2jrz_A117 Histone demethylase jarid1C; bright/ARID domain, h 7e-19
2lm1_A107 Lysine-specific demethylase LID; structural genomi 2e-18
2cxy_A125 BAF250B subunit, HBAF250B; DNA-binding domain, str 2e-18
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 3e-18
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 9e-18
2jxj_A96 Histone demethylase jarid1A; ARID domain, chromati 4e-18
3tq6_A214 Transcription factor A, mitochondrial; transcripti 2e-17
3tq6_A214 Transcription factor A, mitochondrial; transcripti 8e-17
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 2e-17
1c20_A128 DEAD ringer protein; DNA-binding domain, ARID, AT- 3e-17
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 3e-17
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 6e-17
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 2e-13
1wgf_A90 Upstream binding factor 1; transcription factor, D 7e-17
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 2e-16
1kkx_A123 Transcription regulatory protein ADR6; ARID, DNA-b 8e-16
2kk0_A145 AT-rich interactive domain-containing protein 3A; 1e-15
2li6_A116 SWI/SNF chromatin-remodeling complex subunit SWI1; 7e-14
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 6e-10
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 7e-10
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 1e-09
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 3e-09
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 5e-09
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 7e-09
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 1e-08
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 1e-08
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 1e-08
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 2e-08
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 2e-08
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 8e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
>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
 Score =  108 bits (271), Expect = 3e-29
 Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 3/95 (3%)

Query: 178 VSGVQRRRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHPGKDR---EISRMIG 234
           ++G   R   ++    ++DP  PK   S Y FF  E+   +   +P   +    I +MIG
Sbjct: 1   MAGASDRTGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIG 60

Query: 235 ELWNKLKESEKAVYQEKALKDKERYRIEMEDYRER 269
             WN L + EK  Y+  + +D+ RY  E  +Y +R
Sbjct: 61  AAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR 95
>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
>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
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 Back     alignment and structure
>2rq5_A Protein jumonji; developmental protein, nucleus, repressor, transcription, transcription regulation; NMR {Mus musculus} Length = 121 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
>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
>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
>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
>1ig6_A MRF-2, modulator recognition factor 2; DNA binding protein, DNA-binding motif, protein-DNA interaction; NMR {Homo sapiens} SCOP: a.4.3.1 PDB: 2oeh_A Length = 107 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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92 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
>2eqy_A RBP2 like, jumonji, at rich interactive domain 1B; ARID domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 122 Back     alignment and structure
>2jrz_A Histone demethylase jarid1C; bright/ARID domain, helical, structural genomics, structural genomics consortium, SGC, oxidoreductase; NMR {Homo sapiens} PDB: 2yqe_A Length = 117 Back     alignment and structure
>2lm1_A Lysine-specific demethylase LID; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Drosophila melanogaster} Length = 107 Back     alignment and structure
>2cxy_A BAF250B subunit, HBAF250B; DNA-binding domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.60A {Homo sapiens} PDB: 2eh9_A 1ryu_A Length = 125 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
>2jxj_A Histone demethylase jarid1A; ARID domain, chromatin regulator, developmental protein, dioxygenase, iron, metal-binding, nucleus, oxidoreductase; NMR {Homo sapiens} Length = 96 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
>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
>1c20_A DEAD ringer protein; DNA-binding domain, ARID, AT-rich interaction domain, DNA- binding protein; NMR {Drosophila melanogaster} SCOP: a.4.3.1 PDB: 1kqq_A Length = 128 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
>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
>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
>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
>1kkx_A Transcription regulatory protein ADR6; ARID, DNA-binding domain, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.4.3.1 PDB: 1kn5_A Length = 123 Back     alignment and structure
>2kk0_A AT-rich interactive domain-containing protein 3A; DEAD ringer, AT-rich interaction domain, NESG, ARID, cytopla binding, nucleus, phosphoprotein; NMR {Homo sapiens} Length = 145 Back     alignment and structure
>2li6_A SWI/SNF chromatin-remodeling complex subunit SWI1; ligand binding, DNA binding protein; NMR {Saccharomyces cerevisiae} Length = 116 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
>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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71 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
>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
>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
>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
>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
>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
>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
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query388
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.86
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.85
1ig6_A107 MRF-2, modulator recognition factor 2; DNA binding 99.85
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.84
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.84
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.84
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.84
2rq5_A121 Protein jumonji; developmental protein, nucleus, r 99.83
2cxy_A125 BAF250B subunit, HBAF250B; DNA-binding domain, str 99.83
2lhj_A97 High mobility group protein homolog NHP1; structur 99.83
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.83
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.83
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.82
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.82
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.82
1c20_A128 DEAD ringer protein; DNA-binding domain, ARID, AT- 99.81
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.81
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.81
2jrz_A117 Histone demethylase jarid1C; bright/ARID domain, h 99.8
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.8
2jxj_A96 Histone demethylase jarid1A; ARID domain, chromati 99.8
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.8
2eqy_A122 RBP2 like, jumonji, at rich interactive domain 1B; 99.8
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.8
2kk0_A145 AT-rich interactive domain-containing protein 3A; 99.8
2lm1_A107 Lysine-specific demethylase LID; structural genomi 99.79
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.79
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.79
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.79
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.79
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.79
1ckt_A71 High mobility group 1 protein; high-mobility group 99.78
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.78
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.78
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.77
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.77
2li6_A116 SWI/SNF chromatin-remodeling complex subunit SWI1; 99.77
1kkx_A123 Transcription regulatory protein ADR6; ARID, DNA-b 99.76
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.75
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.75
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.73
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.73
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.7
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.68
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.66
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.66
2cto_A93 Novel protein; high mobility group box domain, hel 99.65
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.64
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.63
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.58
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
Probab=99.86  E-value=8.6e-22  Score=163.55  Aligned_cols=84  Identities=30%  Similarity=0.623  Sum_probs=79.4

Q ss_pred             cccCCCCCCCCCCCChhHHHHHHHHHHhcccCCCCc-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 046368          191 EIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMEDYRER  269 (388)
Q Consensus       191 ~~~~kdp~~PKrP~saY~lF~ke~r~~lk~~~P~~~-~EisK~lge~Wk~LseeeK~~Y~e~A~~dK~rY~~em~~Yk~k  269 (388)
                      +++++||++||||+||||||++++|..|+.+||++. .+|+++||++|++|++++|++|+++|++++++|..+|++|++.
T Consensus         9 kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~   88 (102)
T 2co9_A            9 KKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRAS   88 (102)
T ss_dssp             CSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            355689999999999999999999999999999999 9999999999999999999999999999999999999999998


Q ss_pred             hccCc
Q 046368          270 LKTGQ  274 (388)
Q Consensus       270 ~k~~~  274 (388)
                      .....
T Consensus        89 ~~~~~   93 (102)
T 2co9_A           89 LVSKS   93 (102)
T ss_dssp             HTSSC
T ss_pred             ccccc
Confidence            76654
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1ig6_A MRF-2, modulator recognition factor 2; DNA binding protein, DNA-binding motif, protein-DNA interaction; NMR {Homo sapiens} SCOP: a.4.3.1 PDB: 2oeh_A 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
>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
>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
>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
>2rq5_A Protein jumonji; developmental protein, nucleus, repressor, transcription, transcription regulation; NMR {Mus musculus} Back     alignment and structure
>2cxy_A BAF250B subunit, HBAF250B; DNA-binding domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.60A {Homo sapiens} PDB: 2eh9_A 1ryu_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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {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
>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
>1c20_A DEAD ringer protein; DNA-binding domain, ARID, AT-rich interaction domain, DNA- binding protein; NMR {Drosophila melanogaster} SCOP: a.4.3.1 PDB: 1kqq_A 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
>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
>2jrz_A Histone demethylase jarid1C; bright/ARID domain, helical, structural genomics, structural genomics consortium, SGC, oxidoreductase; NMR {Homo sapiens} PDB: 2yqe_A 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
>2jxj_A Histone demethylase jarid1A; ARID domain, chromatin regulator, developmental protein, dioxygenase, iron, metal-binding, nucleus, oxidoreductase; NMR {Homo sapiens} 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
>2eqy_A RBP2 like, jumonji, at rich interactive domain 1B; ARID domain, structural genomics, NPPSFA; NMR {Mus musculus} 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
>2kk0_A AT-rich interactive domain-containing protein 3A; DEAD ringer, AT-rich interaction domain, NESG, ARID, cytopla binding, nucleus, phosphoprotein; NMR {Homo sapiens} Back     alignment and structure
>2lm1_A Lysine-specific demethylase LID; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Drosophila melanogaster} 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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>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
>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
>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
>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
>2li6_A SWI/SNF chromatin-remodeling complex subunit SWI1; ligand binding, DNA binding protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>1kkx_A Transcription regulatory protein ADR6; ARID, DNA-binding domain, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.4.3.1 PDB: 1kn5_A 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
>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
>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
>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
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {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
>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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {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
>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
>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

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 388
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 5e-22
d1c20a_128 a.4.3.1 (A:) DNA-binding domain from the dead ring 2e-21
d1ig6a_107 a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo 2e-21
d1ryua_120 a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 4e-21
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 4e-19
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 9e-19
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-18
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-18
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 2e-17
d1kkxa_102 a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) { 1e-16
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-16
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 2e-16
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 1e-15
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 4e-15
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 6e-14
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 7e-14
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93 Back     information, alignment and structure

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 87.3 bits (216), Expect = 5e-22
 Identities = 30/88 (34%), Positives = 44/88 (50%), Gaps = 1/88 (1%)

Query: 184 RRRRKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKE 242
           R  +K++  K++DP  PK   S Y FF  E    ++  +P     ++ + +GE W  L  
Sbjct: 5   REPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTP 64

Query: 243 SEKAVYQEKALKDKERYRIEMEDYRERL 270
            EK  Y+ KA  DK+RY  E E Y   L
Sbjct: 65  EEKQPYEAKAQADKKRYESEKELYNATL 92
>d1c20a_ a.4.3.1 (A:) DNA-binding domain from the dead ringer protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 128 Back     information, alignment and structure
>d1ig6a_ a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 107 Back     information, alignment and structure
>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 120 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
>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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure
>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 102 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
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 Back     information, alignment and structure
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80 Back     information, alignment and structure
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query388
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.84
d1ig6a_107 MRF-2 DNA-binding domain {Human (Homo sapiens) [Ta 99.83
d1ryua_120 SWI-SNF complex protein p270, SMARCF1 {Human (Homo 99.82
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.82
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.8
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.79
d1c20a_128 DNA-binding domain from the dead ringer protein {F 99.78
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.78
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.77
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.77
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.77
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.76
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.73
d1kkxa_102 Transcription regulator Adr6 (Swi1) {Baker's yeast 99.71
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.69
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.69
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 94.62
d1guua_50 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 82.27
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=2.7e-21  Score=156.17  Aligned_cols=84  Identities=35%  Similarity=0.604  Sum_probs=78.6

Q ss_pred             hhhccccCCCCCCCCCCCChhHHHHHHHHHHhcccCCCCc-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 046368          187 RKKSEIKRRDPAHPKPNRSGYNFFFAEQHARLKPLHPGKD-REISRMIGELWNKLKESEKAVYQEKALKDKERYRIEMED  265 (388)
Q Consensus       187 kkk~~~~~kdp~~PKrP~saY~lF~ke~r~~lk~~~P~~~-~EisK~lge~Wk~LseeeK~~Y~e~A~~dK~rY~~em~~  265 (388)
                      ++++.++.+||++||||+|||+||++++|.+++.+||+++ .+|++.||++|++|++++|++|+++|++++++|..+|.+
T Consensus         8 ~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~   87 (93)
T d1lwma_           8 KKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKEL   87 (93)
T ss_dssp             TSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444456789999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             HHHhh
Q 046368          266 YRERL  270 (388)
Q Consensus       266 Yk~k~  270 (388)
                      |++++
T Consensus        88 y~~~l   92 (93)
T d1lwma_          88 YNATL   92 (93)
T ss_dssp             HHHHH
T ss_pred             HHhcc
Confidence            99875
>d1ig6a_ a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]} 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
>d1gt0d_ a.21.1.1 (D:) Sox-2 {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
>d1c20a_ a.4.3.1 (A:) DNA-binding domain from the dead ringer protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure