Citrus Sinensis ID: 020330

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-------
MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPDHPGPSTSFCQSNDVGAIIPYTPNSKRRYGRRRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLKLRQGEGANS
cccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccEEcccccHHHHHHHHHHHcccHHHHcccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccc
ccccccccccccccccccccccccHHcccccccHHHHHHHHHHHHHHcccccEEEEEcccEEcHHHHHHHHHHcccHHHHHcHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHcccccccccccccccccccccccEEEEEcccccccEEEEEEEccccccEEEEcccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccHHHHHHHHHHcHccccccHHHHHHHHHHHHcccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHccccccccc
msqssaaktkgrsvvedklypaplsshedvskdpivFWDTLRRFHFImgtkfmipviggkeLDLHVLYVEATTRGGYEKVVAEKKWrevgavfkfsptttsasFVLRKHYLTLLYHYEQVHFfkmqgppcvpsasfsvhspscrpglalveyspkrindhpdshiegqscftavgridgkfdcGYLVSVKLGsetlsgvlyhpdhpgpstsfcqsndvgaiipytpnskrrygrrrrskrrgdpsypkpnrsgynfffAEKHYKLKSLYPNREREFTKMIgeswtnlspeERKVYQNIGLKDKERYNRELKEYKERLKLRQGEGANS
msqssaaktkgrsvvedklypaplsshedvskdpiVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEAttrggyekvvAEKKWREVGAvfkfsptttsasfVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPDHPGPSTSFCQSNDVGaiipytpnskrrygrrrrskrrgdpsypkpnrsgynffFAEKHYKLKSLYPNREREFTKMIgeswtnlspeerKVYQniglkdkerynRELKEYKerlklrqgegans
MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPDHPGPSTSFCQSNDVGAIIPYTPNskrrygrrrrskrrgDPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLKLRQGEGANS
********************************DPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYS**********HIEGQSCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHP********FCQSNDVGAIIPY****************************GYNFFFAEKHYKLKSLYPNREREFTKMIGESWTN********Y********************************
*******************************KD*IVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFK*********************************************************************************************************************************YNFFFAEKH*************FTKMIGESWTN************GLKDKERYNR*******************
*************VVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPDHPGPSTSFCQSNDVGAIIPYTPNS*****************YPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK*********
******************LYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF*********************************************SCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPD**************************************DPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKEYKERLK*********
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MSQSSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGKFDCGYLVSVKLGSETLSGVLYHPDHPGPSTSFCQSNDVGAIIPYTPNSKRRYGRRRRSKRRGDPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGxxxxxxxxxxxxxxxxxxxxxxxxGANS
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 ?
Query327 2.2.26 [Sep-21-2011]
Q9SGS2338 High mobility group B pro yes no 0.932 0.902 0.694 1e-113
Q9MAT6 448 High mobility group B pro no no 0.932 0.680 0.416 5e-66
Q9LTT3319 High mobility group B pro no no 0.825 0.846 0.414 8e-54
Q9LG02337 Putative high mobility gr no no 0.798 0.774 0.355 6e-46
Q68CP9 1835 AT-rich interactive domai yes no 0.290 0.051 0.437 8e-16
Q6GQD7539 AT-rich interactive domai N/A no 0.250 0.152 0.397 1e-09
Q5XGD9541 AT-rich interactive domai no no 0.250 0.151 0.397 1e-09
Q99856593 AT-rich interactive domai no no 0.250 0.138 0.397 3e-09
P29375 1690 Lysine-specific demethyla no no 0.287 0.055 0.357 4e-09
Q62431601 AT-rich interactive domai no no 0.250 0.136 0.397 4e-09
>sp|Q9SGS2|HMGB9_ARATH High mobility group B protein 9 OS=Arabidopsis thaliana GN=HMGB9 PE=2 SV=1 Back     alignment and function desciption
 Score =  407 bits (1045), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 218/314 (69%), Positives = 245/314 (78%), Gaps = 9/314 (2%)

Query: 18  KLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGY 77
           K YP PL+ HE V KD  VFWDTLRRFH IM TKFMIPVIGGKELDLHVLYVE T RGGY
Sbjct: 25  KEYPEPLALHEVVVKDSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGY 84

Query: 78  EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFS 137
           EKVV EKKWREVG VF+FS TTTSASFVLRKHYL LL+HYEQVH F  +GP   P A+F 
Sbjct: 85  EKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYEQVHLFTARGPLLHPIATFH 144

Query: 138 VHSPSCRPGLALVEYSPKRI---NDHPDSHIEGQSCFTAVGRIDGKFDCGYLVSVKLGSE 194
             +PS    +ALVEY+P  I   N HP S  +G S FTA+G I+GKFDCGYLV VKLGSE
Sbjct: 145 A-NPSTSKEMALVEYTPPSIRYHNTHPPS--QGSSSFTAIGTIEGKFDCGYLVKVKLGSE 201

Query: 195 TLSGVLYHPDHPGPSTSFCQSNDVGAIIPY--TPNSKRRYGRRRRSKRRGDPSYPKPNRS 252
            L+GVLYH   PGPS+S     +  A++PY  T   +RR G+RRRS+RR DP+YPKPNRS
Sbjct: 202 ILNGVLYHSAQPGPSSSPTAVLN-NAVVPYVETGRRRRRLGKRRRSRRREDPNYPKPNRS 260

Query: 253 GYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKE 312
           GYNFFFAEKH KLKSLYPN+EREFTK+IGESW+NLS EER VYQ+IGLKDKERY REL E
Sbjct: 261 GYNFFFAEKHCKLKSLYPNKEREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNE 320

Query: 313 YKERLKLRQGEGAN 326
           Y+E L+LR G+  N
Sbjct: 321 YRETLRLRDGDMTN 334
Binds preferentially DNA with A/T-rich content.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9MAT6|HMG15_ARATH High mobility group B protein 15 OS=Arabidopsis thaliana GN=HMGB15 PE=2 SV=1 Back     alignment and function description
>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|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|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|Q99856|ARI3A_HUMAN AT-rich interactive domain-containing protein 3A OS=Homo sapiens GN=ARID3A PE=1 SV=2 Back     alignment and function description
>sp|P29375|KDM5A_HUMAN Lysine-specific demethylase 5A OS=Homo sapiens GN=KDM5A PE=1 SV=3 Back     alignment and function description
>sp|Q62431|ARI3A_MOUSE AT-rich interactive domain-containing protein 3A OS=Mus musculus GN=Arid3a 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 ?
Query327
356508987322 PREDICTED: high mobility group B protein 0.957 0.972 0.708 1e-123
224085968329 high mobility group family [Populus tric 0.960 0.954 0.730 1e-123
118487139317 unknown [Populus trichocarpa] 0.926 0.955 0.746 1e-122
255539100338 transcription factor, putative [Ricinus 0.978 0.946 0.701 1e-122
307136305324 high mobility group family [Cucumis melo 0.966 0.975 0.687 1e-116
449455571324 PREDICTED: high mobility group B protein 0.966 0.975 0.687 1e-115
297842355338 high mobility group family protein [Arab 0.981 0.949 0.680 1e-112
15222957338 high mobility group-box and ARID domain- 0.932 0.902 0.694 1e-111
147780606324 hypothetical protein VITISV_031839 [Viti 0.883 0.891 0.561 5e-83
225459781324 PREDICTED: high mobility group B protein 0.883 0.891 0.561 5e-83
>gi|356508987|ref|XP_003523234.1| PREDICTED: high mobility group B protein 9-like [Glycine max] Back     alignment and taxonomy information
 Score =  448 bits (1152), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 226/319 (70%), Positives = 256/319 (80%), Gaps = 6/319 (1%)

Query: 4   SSAAKTKGRSVVEDKLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELD 63
           SSAA+T G    E K YPAPL+ HE V KD  +FWDTLRRFHF+MGTKFMIPVIGGKELD
Sbjct: 2   SSAARTPGGE--EGKHYPAPLAPHEGVVKDSTLFWDTLRRFHFVMGTKFMIPVIGGKELD 59

Query: 64  LHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
           LHVLYVE T R GYEKVVAEKKWREVG+VFKF+ TTTSASFVLRKHY +LLYHYEQVHFF
Sbjct: 60  LHVLYVEVTRRSGYEKVVAEKKWREVGSVFKFAATTTSASFVLRKHYFSLLYHYEQVHFF 119

Query: 124 KMQGPPCVPSA-SFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGKFD 182
           K +GP   PSA +FS +SPS RP LA+VEYSPK +++ P+S  E  SC +  G I+GKFD
Sbjct: 120 KARGPIYTPSADAFSGNSPSWRPELAIVEYSPKPMDNSPESRAEDTSCLSGNGTIEGKFD 179

Query: 183 CGYLVSVKLGSETLSGVLYHPDHPGPSTSFCQSNDVGAIIPYTPNSKRRYGRRRRSKRRG 242
           CGYLVSVKLGSE L GVLYHP+   P  S  +     AI+P       R GRR+++KRR 
Sbjct: 180 CGYLVSVKLGSEVLRGVLYHPEQLVPPPSIPKHES--AIVPIN-RKPHRSGRRKKNKRRW 236

Query: 243 DPSYPKPNRSGYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKD 302
           DP+YPKPNRSGYNFFFAEKHY LK+LYPNREREFTKMIG+SW +LSPEER VYQNIGL+D
Sbjct: 237 DPNYPKPNRSGYNFFFAEKHYTLKTLYPNREREFTKMIGQSWNSLSPEERMVYQNIGLRD 296

Query: 303 KERYNRELKEYKERLKLRQ 321
           KERY REL EYKE++KLRQ
Sbjct: 297 KERYKRELTEYKEKMKLRQ 315

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224085968|ref|XP_002307758.1| high mobility group family [Populus trichocarpa] gi|222857207|gb|EEE94754.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|118487139|gb|ABK95398.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255539100|ref|XP_002510615.1| transcription factor, putative [Ricinus communis] gi|223551316|gb|EEF52802.1| transcription factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|307136305|gb|ADN34129.1| high mobility group family [Cucumis melo subsp. melo] Back     alignment and taxonomy information
>gi|449455571|ref|XP_004145526.1| PREDICTED: high mobility group B protein 9-like [Cucumis sativus] gi|449519744|ref|XP_004166894.1| PREDICTED: high mobility group B protein 9-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297842355|ref|XP_002889059.1| high mobility group family protein [Arabidopsis lyrata subsp. lyrata] gi|297334900|gb|EFH65318.1| high mobility group family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|15222957|ref|NP_177738.1| high mobility group-box and ARID domain-binding domain-containing protein [Arabidopsis thaliana] gi|75265821|sp|Q9SGS2.1|HMGB9_ARATH RecName: Full=High mobility group B protein 9; AltName: Full=Nucleosome/chromatin assembly factor group D 09; Short=Nucleosome/chromatin assembly factor group D 9 gi|6573729|gb|AAF17649.1|AC009978_25 T23E18.4 [Arabidopsis thaliana] gi|20466328|gb|AAM20481.1| unknown protein [Arabidopsis thaliana] gi|31711812|gb|AAP68262.1| At1g76110 [Arabidopsis thaliana] gi|332197676|gb|AEE35797.1| high mobility group-box and ARID domain-binding domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|147780606|emb|CAN69112.1| hypothetical protein VITISV_031839 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225459781|ref|XP_002284786.1| PREDICTED: high mobility group B protein 9 [Vitis vinifera] gi|302141699|emb|CBI18902.3| unnamed protein product [Vitis vinifera] 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 ?
Query327
TAIR|locus:2199824338 AT1G76110 [Arabidopsis thalian 0.932 0.902 0.665 2.8e-105
TAIR|locus:2020517337 AT1G55650 [Arabidopsis thalian 0.498 0.483 0.397 1.1e-44
TAIR|locus:2010587 448 AT1G04880 [Arabidopsis thalian 0.675 0.493 0.417 2.3e-39
TAIR|locus:2088160319 AT3G13350 [Arabidopsis thalian 0.541 0.554 0.403 5.4e-31
UNIPROTKB|E1C9H0 1831 ARID2 "Uncharacterized protein 0.299 0.053 0.444 1.2e-16
UNIPROTKB|Q68CP9 1835 ARID2 "AT-rich interactive dom 0.290 0.051 0.437 2.1e-14
ZFIN|ZDB-GENE-030131-6311 1573 arid2 "AT rich interactive dom 0.266 0.055 0.454 7.4e-13
UNIPROTKB|E2RFL8 1836 ARID2 "Uncharacterized protein 0.290 0.051 0.375 2.2e-09
POMBASE|SPAC57A10.09c108 nhp6 "High-mobility group non- 0.241 0.731 0.390 2.4e-09
UNIPROTKB|E1BIU3186 LOC532409 "Uncharacterized pro 0.253 0.446 0.369 5.1e-09
TAIR|locus:2199824 AT1G76110 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1042 (371.9 bits), Expect = 2.8e-105, P = 2.8e-105
 Identities = 209/314 (66%), Positives = 233/314 (74%)

Query:    18 KLYPAPLSSHEDVSKDPIVFWDTLRRFHFIMGTKFMIPVIGGKELDLHVLYVEATTRGGY 77
             K YP PL+ HE V KD  VFWDTLRRFH IM TKFMIPVIGGKELDLHVLYVE T RGGY
Sbjct:    25 KEYPEPLALHEVVVKDSSVFWDTLRRFHSIMSTKFMIPVIGGKELDLHVLYVEVTRRGGY 84

Query:    78 EKVVAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFS 137
             EKVV EKKWREVG VF+FS TTTSASFVLRKHYL LL+HYEQVH F  +GP   P A+F 
Sbjct:    85 EKVVVEKKWREVGGVFRFSATTTSASFVLRKHYLNLLFHYEQVHLFTARGPLLHPIATFH 144

Query:   138 VHSPSCRPGLALVEYSPKRI---NDHPDSHIEGQSCFTAVGRIDGKFDCGYLVSVKLGSE 194
              + PS    +ALVEY+P  I   N HP S  +G S FTA+G I+GKFDCGYLV VKLGSE
Sbjct:   145 AN-PSTSKEMALVEYTPPSIRYHNTHPPS--QGSSSFTAIGTIEGKFDCGYLVKVKLGSE 201

Query:   195 TLSGVLYHPDHPGPSTSFCQSNDVGAIIPY--TPNXXXXXXXXXXXXXXXDPSYPKPNRS 252
              L+GVLYH   PGPS+S     +  A++PY  T                 DP+YPKPNRS
Sbjct:   202 ILNGVLYHSAQPGPSSSPTAVLN-NAVVPYVETGRRRRRLGKRRRSRRREDPNYPKPNRS 260

Query:   253 GYNFFFAEKHYKLKSLYPNREREFTKMIGESWTNLSPEERKVYQNIGLKDKERYNRELKE 312
             GYNFFFAEKH KLKSLYPN+EREFTK+IGESW+NLS EER VYQ+IGLKDKERY REL E
Sbjct:   261 GYNFFFAEKHCKLKSLYPNKEREFTKLIGESWSNLSTEERMVYQDIGLKDKERYQRELNE 320

Query:   313 YKERLKLRQGEGAN 326
             Y+E L+LR G+  N
Sbjct:   321 YRETLRLRDGDMTN 334
GO:0003677 "DNA binding" evidence=IEA;IDA
GO:0005634 "nucleus" evidence=ISM;IDA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS
GO:0000165 "MAPK cascade" evidence=RCA
GO:0006333 "chromatin assembly or disassembly" evidence=RCA
GO:0006612 "protein targeting to membrane" evidence=RCA
GO:0009617 "response to bacterium" evidence=RCA
GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA
GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA
GO:0009965 "leaf morphogenesis" evidence=RCA
GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA
GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA
GO:0030154 "cell differentiation" evidence=RCA
GO:0031348 "negative regulation of defense response" evidence=RCA
GO:0035304 "regulation of protein dephosphorylation" evidence=RCA
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA
TAIR|locus:2020517 AT1G55650 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010587 AT1G04880 [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|E1C9H0 ARID2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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
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|E2RFL8 ARID2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
POMBASE|SPAC57A10.09c nhp6 "High-mobility group non-histone chromatin protein (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|E1BIU3 LOC532409 "Uncharacterized protein" [Bos taurus (taxid:9913)] 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) ?
Q9SGS2HMGB9_ARATHNo assigned EC number0.69420.93270.9023yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query327
smart0050193 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interac 3e-29
smart0101488 smart01014, ARID, ARID/BRIGHT DNA binding domain 1e-26
pfam0138890 pfam01388, ARID, ARID/BRIGHT DNA binding domain 2e-21
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 2e-17
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 8e-16
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 3e-13
smart0039870 smart00398, HMG, high mobility group 4e-13
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 7e-13
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 2e-11
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 6e-08
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 0.001
>gnl|CDD|128777 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interaction domain) domain Back     alignment and domain information 
 Score =  107 bits (269), Expect = 3e-29
 Identities = 38/93 (40%), Positives = 53/93 (56%), Gaps = 1/93 (1%)

Query: 32  KDPIVFWDTLRRFHFIMGTK-FMIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVG 90
           ++ ++F D L +F    G+    IPVIGGK LDL+ LY     RGGY++V  +KKW+E+ 
Sbjct: 1   RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIA 60

Query: 91  AVFKFSPTTTSASFVLRKHYLTLLYHYEQVHFF 123
                  T+TSA+  LRKHY   L  YE+    
Sbjct: 61  RELGIPDTSTSAASSLRKHYERYLLPYERFLRG 93

DNA-binding domain containing a helix-turn-helix structure. Length = 93
>gnl|CDD|198082 smart01014, ARID, ARID/BRIGHT DNA binding domain Back     alignment and domain information
>gnl|CDD|216473 pfam01388, ARID, ARID/BRIGHT DNA binding 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|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional Back     alignment and domain information
>gnl|CDD|197700 smart00398, HMG, high mobility group Back     alignment and domain information
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box 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|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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 327
KOG2744512 consensus DNA-binding proteins Bright/BRCAA1/RBP1 99.96
smart0050193 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) 99.94
PF0138892 ARID: ARID/BRIGHT DNA binding domain; InterPro: IP 99.92
PTZ0019994 high mobility group protein; Provisional 99.87
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.76
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.74
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.73
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.72
COG5648211 NHP6B Chromatin-associated proteins containing the 99.71
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.71
smart0039870 HMG high mobility group. 99.69
KOG038196 consensus HMG box-containing protein [General func 99.68
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.61
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.6
KOG0527 331 consensus HMG-box transcription factor [Transcript 99.56
KOG3248 421 consensus Transcription factor TCF-4 [Transcriptio 99.25
KOG2510532 consensus SWI-SNF chromatin-remodeling complex pro 99.18
KOG0528 511 consensus HMG-box transcription factor SOX5 [Trans 99.0
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 98.93
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.32
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 97.86
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 96.81
COG5648211 NHP6B Chromatin-associated proteins containing the 96.52
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 95.8
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 89.84
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 87.48
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 84.89
TIGR0162450 LRP1_Cterm LRP1 C-terminal domain. This model repr 82.94
PF0024948 Myb_DNA-binding: Myb-like DNA-binding domain; Inte 81.86
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription] Back     alignment and domain information 
Probab=99.96  E-value=2.8e-29  Score=253.36  Aligned_cols=185  Identities=40%  Similarity=0.495  Sum_probs=152.7

Q ss_pred             CCCCCCcccCChHHHHHHHHHHHhhcCCCCC-CCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCC-CCC
Q 020330           23 PLSSHEDVSKDPIVFWDTLRRFHFIMGTKFM-IPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSP-TTT  100 (327)
Q Consensus        23 ~~~~~e~~~~~~~~F~~~L~~F~~~~G~~~~-~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~-~~~  100 (327)
                      ++...|.+..+++.||++|+.||+.+|++|+ +|+|+|++||||.||.+|+++||+++|+..++|++|+..|+||. ++|
T Consensus       153 ~~~~~e~~~~~~eeF~~dl~~f~~~~~~~~~~iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wrev~~~l~~pt~tiT  232 (512)
T KOG2744|consen  153 PLYETEGVPKSSEEFMEDLRRFMKKRGTKVKSIPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWREVIDGLNFPTPTIT  232 (512)
T ss_pred             cccccccccccHHHHHHHHHHHHHHhCCcceeccccCCCcchHHHHHHHHhcCCchhHhhhhhhHHHHhccccCCCcccc
Confidence            6667777778999999999999999999996 99999999999999999999999999999999999999999999 999


Q ss_pred             cHHHHHHHHHHHhhhhhhhhhhhcccCCCCCCCCcccCCCCCCCCCcccccCCcccccCCCCCCcCCCCCceeeeeeccc
Q 020330          101 SASFVLRKHYLTLLYHYEQVHFFKMQGPPCVPSASFSVHSPSCRPGLALVEYSPKRINDHPDSHIEGQSCFTAVGRIDGK  180 (327)
Q Consensus       101 ~~s~~Lk~~Y~k~L~~yE~~~~~~~~~~~~~p~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~g~Idgk  180 (327)
                      +++|.|+++|+++|++|||.+++.+..+...|.......+++-..+....+.+++.......+....++...+.++|+|+
T Consensus       233 saaf~lr~~y~K~L~~ye~~~~~~~~~pln~p~~~~~~a~~~~~rE~~~~~~~~~~~~~~~~~~~~~~~~~~aa~~~~g~  312 (512)
T KOG2744|consen  233 SAAFTLRKQYLKLLFEYECEFEKNRHVPLNSPAELSEEASSSNRREGRRHELSPSKEFQANGPSEEEPAEAEAAPEILGN  312 (512)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcccccccccccccccccccccCcchhhccCCcccccccccccchhhhcc
Confidence            99999999999999999999999877666666543321233333333444444543333322333334466789999999


Q ss_pred             cCCCceeEEeeccccccccccCCCCCC
Q 020330          181 FDCGYLVSVKLGSETLSGVLYHPDHPG  207 (327)
Q Consensus       181 fd~gylvtv~~gse~~~g~ly~~~~~~  207 (327)
                      |++||+|++.+|++.++|++|+.++..
T Consensus       313 f~~~~~~~~~~~s~~ln~~~~~~~~~~  339 (512)
T KOG2744|consen  313 FLQGLLVFMKDGSEPLNGVLYLGPPDL  339 (512)
T ss_pred             ccccCceeccCcchhccCccccccCcc
Confidence            999999999999999999999997765

>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain 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
>PTZ00199 high mobility group protein; Provisional 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
>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
>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
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] 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
>smart00398 HMG high mobility group 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
>KOG0527 consensus HMG-box transcription factor [Transcription] Back     alignment and domain information
>KOG3248 consensus Transcription factor TCF-4 [Transcription] Back     alignment and domain information
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics] Back     alignment and domain information
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription] 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
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription] 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
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function Back     alignment and domain information
>TIGR01624 LRP1_Cterm LRP1 C-terminal domain Back     alignment and domain information
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins 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 ?
Query327
2kk0_A145 Solution Structure Of Dead Ringer-Like Protein 1 (A 2e-09
2jxj_A96 Nmr Structure Of The Arid Domain From The Histone H 3e-09
2lhj_A97 Nmr Structure Of The High Mobility Group Protein-Li 5e-08
1c20_A128 Solution Structure Of The Dna-Binding Domain From T 5e-07
1kqq_A139 Solution Structure Of The Dead Ringer Arid-Dna Comp 2e-06
2jrz_A117 Solution Structure Of The BrightARID DOMAIN FROM TH 2e-06
2lm1_A107 Solution Nmr Structure Of Lysine-Specific Demethyla 2e-06
2yqe_A100 Solution Structure Of The Arid Domain Of Jarid1d Pr 3e-06
1ig6_A107 Human Mrf-2 Domain, Nmr, 11 Structures Length = 107 7e-06
1ryu_A120 Solution Structure Of The Swi1 Arid Length = 120 4e-05
1aab_A83 Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83 5e-05
1j3x_A77 Solution Structure Of The N-Terminal Domain Of The 5e-05
2crj_A92 Solution Structure Of The Hmg Domain Of Mouse Hmg D 5e-05
3tq6_A214 Crystal Structure Of Human Mitochondrial Transcript 6e-05
2ly4_A83 Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-Bo 7e-05
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 9e-05
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 1e-04
2yrq_A173 Solution Structure Of The Tandem Hmg Box Domain Fro 1e-04
3tmm_A238 Tfam Imposes A U-Turn On Mitochondrial Dna Length = 3e-04
2eqy_A122 Solution Structure Of The Arid Domain Of Jarid1b Pr 3e-04
2cxy_A125 Crystal Structure Of The Hbaf250b At-Rich Interacti 4e-04
3fgh_A67 Human Mitochondrial Transcription Factor A Box B Le 4e-04
2eqz_A86 Solution Structure Of The First Hmg-Box Domain From 9e-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 = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           F D L  F    GT    IP++  + LDL +LYV  T +GG  +V+ +K WRE+      
Sbjct: 38  FLDDLFSFMQKRGTPVNRIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNL 97
Query: 96  SPTTTSASFVLRKHYLTLLYHYE 118
             + TSA+F LR  Y+  LY YE
Sbjct: 98  PTSITSAAFTLRTQYMKYLYPYE 120
>pdb|2JXJ|A Chain A, Nmr Structure Of The Arid Domain From The Histone H3k4 Demethylase Rbp2 Length = 96 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|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|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN Jarid1c Protein Length = 117 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
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein Length = 100 Back     alignment and structure
>pdb|1IG6|A Chain A, Human Mrf-2 Domain, Nmr, 11 Structures Length = 107 Back     alignment and structure
>pdb|1RYU|A Chain A, Solution Structure Of The Swi1 Arid Length = 120 Back     alignment and structure
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83 Back     alignment and structure
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2 Length = 77 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|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription Factor A, Tfam Or Mttfa, Bound To The Light Strand Promoter Lsp Length = 214 Back     alignment and structure
>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53 Transactivation Domain Interaction And Is Regulated By The Acidic Tail Length = 83 Back     alignment and structure
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna Length = 93 Back     alignment and structure
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93 Back     alignment and structure
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human High Mobility Group Protein B1 Length = 173 Back     alignment and structure
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna Length = 238 Back     alignment and structure
>pdb|2EQY|A Chain A, Solution Structure Of The Arid Domain Of Jarid1b Protein Length = 122 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|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B Length = 67 Back     alignment and structure
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High Mobility Group Protein B3 Length = 86 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 ?
Query327
2rq5_A121 Protein jumonji; developmental protein, nucleus, r 4e-29
2eqy_A122 RBP2 like, jumonji, at rich interactive domain 1B; 4e-27
2jrz_A117 Histone demethylase jarid1C; bright/ARID domain, h 2e-26
2lm1_A107 Lysine-specific demethylase LID; structural genomi 4e-26
1ig6_A107 MRF-2, modulator recognition factor 2; DNA binding 1e-25
2lhj_A97 High mobility group protein homolog NHP1; structur 1e-25
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 5e-25
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 9e-25
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 4e-24
2jxj_A96 Histone demethylase jarid1A; ARID domain, chromati 7e-24
2cxy_A125 BAF250B subunit, HBAF250B; DNA-binding domain, str 9e-24
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 2e-23
1hme_A77 High mobility group protein fragment-B; DNA-bindin 1e-21
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 3e-21
2li6_A116 SWI/SNF chromatin-remodeling complex subunit SWI1; 5e-21
1c20_A128 DEAD ringer protein; DNA-binding domain, ARID, AT- 2e-20
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 3e-20
1kkx_A123 Transcription regulatory protein ADR6; ARID, DNA-b 3e-20
1ckt_A71 High mobility group 1 protein; high-mobility group 2e-19
2kk0_A145 AT-rich interactive domain-containing protein 3A; 6e-19
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 1e-18
2yrq_A173 High mobility group protein B1; HMG box domain, DN 2e-18
2yrq_A173 High mobility group protein B1; HMG box domain, DN 1e-11
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 2e-17
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 1e-16
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 1e-15
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 1e-16
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 3e-16
3tq6_A214 Transcription factor A, mitochondrial; transcripti 1e-15
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 7e-16
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 5e-13
1wgf_A90 Upstream binding factor 1; transcription factor, D 6e-13
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 2e-12
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 6e-11
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 7e-09
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 3e-06
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 1e-04
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 5e-04
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 7e-04
>2rq5_A Protein jumonji; developmental protein, nucleus, repressor, transcription, transcription regulation; NMR {Mus musculus} Length = 121 Back     alignment and structure
 Score =  107 bits (268), Expect = 4e-29
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 1/101 (0%)

Query: 22  APLSSHEDVSKDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKV 80
            PL S        +     +++     G     +P+IGG ELDL   +      GG ++V
Sbjct: 1   GPLGSLGRRWGPNVQRLACIKKHLRSQGITMDELPLIGGCELDLACFFRLINEMGGMQQV 60

Query: 81  VAEKKWREVGAVFKFSPTTTSASFVLRKHYLTLLYHYEQVH 121
              KKW ++  + +   T       L++ Y   L  Y+ + 
Sbjct: 61  TDLKKWNKLADMLRIPKTAQDRLAKLQEAYCQYLLSYDSLS 101
>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
>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
>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
>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
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 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
>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
>2li6_A SWI/SNF chromatin-remodeling complex subunit SWI1; ligand binding, DNA binding protein; NMR {Saccharomyces cerevisiae} Length = 116 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
>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
>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
>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
>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
>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
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92 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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query327
1ig6_A107 MRF-2, modulator recognition factor 2; DNA binding 99.95
2jrz_A117 Histone demethylase jarid1C; bright/ARID domain, h 99.94
2eqy_A122 RBP2 like, jumonji, at rich interactive domain 1B; 99.94
2rq5_A121 Protein jumonji; developmental protein, nucleus, r 99.94
2cxy_A125 BAF250B subunit, HBAF250B; DNA-binding domain, str 99.94
2lm1_A107 Lysine-specific demethylase LID; structural genomi 99.94
2jxj_A96 Histone demethylase jarid1A; ARID domain, chromati 99.94
1c20_A128 DEAD ringer protein; DNA-binding domain, ARID, AT- 99.93
2li6_A116 SWI/SNF chromatin-remodeling complex subunit SWI1; 99.93
1kkx_A123 Transcription regulatory protein ADR6; ARID, DNA-b 99.92
2kk0_A145 AT-rich interactive domain-containing protein 3A; 99.92
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.89
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.88
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.87
2lhj_A97 High mobility group protein homolog NHP1; structur 99.86
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.85
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.85
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.85
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.85
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.84
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.84
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.84
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.83
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.83
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.82
1ckt_A71 High mobility group 1 protein; high-mobility group 99.81
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.81
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.81
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.81
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.8
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.8
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.8
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.79
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.79
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.79
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.79
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.79
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.78
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.78
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.78
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.76
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.75
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.72
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.71
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.71
2cto_A93 Novel protein; high mobility group box domain, hel 99.7
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.7
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 99.69
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 99.68
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.56
>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
Probab=99.95  E-value=9.9e-29  Score=201.30  Aligned_cols=101  Identities=28%  Similarity=0.471  Sum_probs=93.6

Q ss_pred             CChHHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHH
Q 020330           32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY  110 (327)
Q Consensus        32 ~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y  110 (327)
                      ++++.|+++|.+||+.+|+++ ++|+|+|++||||+||.+|+++|||++||.+++|.+|++.||++++++++++.|+++|
T Consensus         2 ~e~~~Fl~~L~~F~~~rg~~~~~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~~Va~~lg~~~~~~s~~~~Lk~~Y   81 (107)
T 1ig6_A            2 ADEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHY   81 (107)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCGGGCCCSSSSSCCHHHHHHHHHHTTHHHHHHHHTTHHHHHHHHTCCTTCTTTTTTHHHHH
T ss_pred             chHHHHHHHHHHHHHHcCCCCCcCceECCEeecHHHHHHHHHHhcCHHHhcccCcHHHHHHHhCCCCCCCcHHHHHHHHH
Confidence            478999999999999999999 7999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhhhhhcccCCCCCCC
Q 020330          111 LTLLYHYEQVHFFKMQGPPCVPS  133 (327)
Q Consensus       111 ~k~L~~yE~~~~~~~~~~~~~p~  133 (327)
                      .+||++||+ ++.++++.+.+++
T Consensus        82 ~k~L~~yE~-~~~~~~~~~~p~~  103 (107)
T 1ig6_A           82 ERLILPYER-FIKGEEDKPLPPI  103 (107)
T ss_dssp             HHHTTTTHH-HHHHHTSSSSCTT
T ss_pred             HHHHHHHHH-HHcCCCCCCCCCC
Confidence            999999999 5567766666553
>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
>2eqy_A RBP2 like, jumonji, at rich interactive domain 1B; ARID domain, structural genomics, NPPSFA; NMR {Mus musculus} 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
>2lm1_A Lysine-specific demethylase LID; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Drosophila melanogaster} 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
>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
>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
>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
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; 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
>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
>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
>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
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 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
>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
>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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>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
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {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
>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
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {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 327
d1ryua_120 a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 1e-27
d1c20a_128 a.4.3.1 (A:) DNA-binding domain from the dead ring 7e-27
d1ig6a_107 a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo 2e-25
d1kkxa_102 a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) { 3e-21
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 2e-18
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 6e-17
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 1e-16
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-15
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-15
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 6e-14
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 6e-14
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 9e-12
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 2e-10
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 6e-10
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 7e-10
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 4e-09
>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 120 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: SWI-SNF complex protein p270, SMARCF1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  102 bits (255), Expect = 1e-27
 Identities = 30/96 (31%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 37  FWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKF 95
           + D    F          +P +G K LDL+ LYV     GG  +V   KKWRE+      
Sbjct: 24  WVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNV 83

Query: 96  SPTTTSASFVLRKHYLTLLYHYEQVHFFKMQGPPCV 131
             T++SA+  L+K Y+  LY +E         PP +
Sbjct: 84  -GTSSSAASSLKKQYIQCLYAFECKIERGEDPPPDI 118
>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
>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 102 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
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 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
>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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 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
>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 ?
Query327
d1ig6a_107 MRF-2 DNA-binding domain {Human (Homo sapiens) [Ta 99.94
d1ryua_120 SWI-SNF complex protein p270, SMARCF1 {Human (Homo 99.94
d1c20a_128 DNA-binding domain from the dead ringer protein {F 99.92
d1kkxa_102 Transcription regulator Adr6 (Swi1) {Baker's yeast 99.9
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.87
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.84
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.82
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.8
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.8
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.79
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.79
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.78
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.76
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.75
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.72
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.72
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 96.15
d1guua_50 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 83.42
>d1ig6a_ a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: MRF-2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=3.1e-28  Score=196.48  Aligned_cols=94  Identities=28%  Similarity=0.445  Sum_probs=88.5

Q ss_pred             CChHHHHHHHHHHHhhcCCCC-CCCeeCCeecchhhhHHHHHhcCchhhhhcccchHHhHhhhcCCCCCCcHHHHHHHHH
Q 020330           32 KDPIVFWDTLRRFHFIMGTKF-MIPVIGGKELDLHVLYVEATTRGGYEKVVAEKKWREVGAVFKFSPTTTSASFVLRKHY  110 (327)
Q Consensus        32 ~~~~~F~~~L~~F~~~~G~~~-~~P~i~gk~lDL~~Ly~~V~~~GG~~~V~~~~~W~eV~~~l~~p~~~~~~s~~Lk~~Y  110 (327)
                      .|++.|++.|..||+.+|+++ ++|+|+|++||||.||.+|+++|||++|+.+++|.+||+.||+|++++++++.|+++|
T Consensus         2 ~e~~~Fl~~L~~F~~~rg~~~~~~P~i~gk~vDL~~Ly~~V~~~GG~~~V~~~~~W~~ia~~lg~~~~~~~~~~~Lk~~Y   81 (107)
T d1ig6a_           2 ADEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHY   81 (107)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCGGGCCCSSSSSCCHHHHHHHHHHTTHHHHHHHHTTHHHHHHHHTCCTTCTTTTTTHHHHH
T ss_pred             ccHHHHHHHHHHHHHHcCCCCCcCCeECCccccHHHHHHHHHHhCChhhccccccHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence            368999999999999999999 6999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhhhhhhhcc
Q 020330          111 LTLLYHYEQVHFFKM  125 (327)
Q Consensus       111 ~k~L~~yE~~~~~~~  125 (327)
                      .+||++||+++..+.
T Consensus        82 ~~~L~~yE~~~~~~~   96 (107)
T d1ig6a_          82 ERLILPYERFIKGEE   96 (107)
T ss_dssp             HHHTTTTHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCC
Confidence            999999999655443
>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {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
>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {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
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} 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
>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