Citrus Sinensis ID: 020460

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------
MSSHMLNGQKSSATTSNSNSNSNNNNNNNKASSYYPPPTAKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSGSSLDNGSASPEEGSTINQLGSQGSSKLQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPHAHNVSQSSNNSAAPTHRRRKRSRLALRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDSTVQQ
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccEEcccccHHHHHHHHHHHcccHHHHcccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
ccccccccccccccccccccccccccccccccccccccHHHcccccccHHHHHHHHHHHHHHcccccEEEEEcccEEcHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcEccccEEEEEEEccccccEEEEccccccccccccccccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHcHccccccHHHHHHHHHHHHcccHHHHHHHHHHccHHHHHHHHHHHHHHHHccccccc
msshmlngqkssattsnsnsnsnnnnnnnkassyyppptakyediaqSSDLFWATLEAFHKsfgdkfkvptvggkaldlHRLFVEVtsrgglgkvirdrrWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYfrreapsssmpdavsgssldngsaspeegstinqlgsqgssklqigcsvsgvidgkfdngYLVTVNLGSEQLKGVLyhiphahnvsqssnnsaapthrrrkrsrlalrdpsrpksnrsgynffFAEHyarlkphyygqEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDSTVQQ
msshmlngqkssattsnsnsnsnnnnnnnkaSSYYPPPTAKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLfvevtsrgglgkvirdrrwkeVVVVFnfpttitsasfVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSGSSLDNGSASPEEGSTINQLGSQGSSKLQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPhahnvsqssnnsaapthrrrkrsrlalrdpsrpksnrsgyNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQvyqekglkdkeryksemleyrssydstvqq
MSSHMLNGQkssattsnsnsnsnnnnnnnkassYYPPPTAKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSGSSLDNGSASPEEGSTINQLGSQGSSKLQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPHAHNVSQSSNNSAAPTHrrrkrsrlalrDPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDSTVQQ
********************************************IAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFR****************************************LQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPHA************************************GYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEA*********************************
**************************************************LFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRR*****************************************************************************************************************RSGYNFFFAEHYAR***********ISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKS*M*************
**********************NNNNNNNKASSYYPPPTAKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREA************************************KLQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPHAHNV*****************************SNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEY**********
*********************************YYPPPTAKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREA*****************************************CSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIP*****************************PSRPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSY******
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MSSHMLNGQKSSATTSNSNSNSNNNNNNNKASSYYPPPTAKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSGSSLDNGSASPEEGSTINQLGSQGSSKLQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPHAHNVSQSSNNSAAPTHRRRKRSRLALRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDSTVQQ
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 ?
Query326 2.2.26 [Sep-21-2011]
Q9LTT3319 High mobility group B pro yes no 0.831 0.849 0.567 7e-89
Q9MAT6 448 High mobility group B pro no no 0.852 0.620 0.464 3e-68
Q9LG02337 Putative high mobility gr no no 0.800 0.774 0.444 7e-64
Q9SGS2338 High mobility group B pro no no 0.861 0.831 0.440 7e-60
Q68CP9 1835 AT-rich interactive domai yes no 0.297 0.052 0.427 2e-17
Q6GQD7539 AT-rich interactive domai N/A no 0.251 0.152 0.397 5e-12
Q5XGD9541 AT-rich interactive domai no no 0.251 0.151 0.397 7e-12
Q99856593 AT-rich interactive domai no no 0.251 0.138 0.397 2e-11
A6PWV5409 AT-rich interactive domai no no 0.251 0.200 0.421 3e-11
Q62431601 AT-rich interactive domai no no 0.251 0.136 0.397 3e-11
>sp|Q9LTT3|HMG10_ARATH High mobility group B protein 10 OS=Arabidopsis thaliana GN=HMGB10 PE=2 SV=1 Back     alignment and function desciption
 Score =  327 bits (838), Expect = 7e-89,   Method: Compositional matrix adjust.
 Identities = 164/289 (56%), Positives = 206/289 (71%), Gaps = 18/289 (6%)

Query: 40  AKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDR 99
           AKY+D+ ++S LFW  L AF        KVPTVGG  LDLHRLF+EVTSRGG+ +V++DR
Sbjct: 34  AKYDDLVRNSALFWEKLRAFLGLTSKTLKVPTVGGNTLDLHRLFIEVTSRGGIERVVKDR 93

Query: 100 RWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSG-SSLDN 158
           +WKEV+  F+FPTTITSASFVLRKYYL  L+  E VYY   E P SS+        SL N
Sbjct: 94  KWKEVIGAFSFPTTITSASFVLRKYYLKFLFQLEHVYYL--EKPVSSLQSTDEALKSLAN 151

Query: 159 GSASPEEGSTINQLGSQGSSKLQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPH 218
            S +PEE          G  + Q+G  V G IDGKFD+GYLVT+ LGS++LKGVLYHIP 
Sbjct: 152 ESPNPEE----------GIDEPQVGYEVQGFIDGKFDSGYLVTMKLGSQELKGVLYHIPQ 201

Query: 219 AHNVSQSSNNSAAPT-----HRRRKRSRLALRDPSRPKSNRSGYNFFFAEHYARLKPHYY 273
             + SQ +  + +        R RK+S+LA+ D  +PK +RSGYNFFFAE YARLKP Y+
Sbjct: 202 TPSQSQQTMETPSAIVQSSQRRHRKKSKLAVVDTQKPKCHRSGYNFFFAEQYARLKPEYH 261

Query: 274 GQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDS 322
           GQE++I+KKIG +WSNLTE+EKQVYQ+KG+KD ERY+ EMLEY+SS++S
Sbjct: 262 GQERSITKKIGHMWSNLTESEKQVYQDKGVKDVERYRIEMLEYKSSHES 310
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|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|Q9SGS2|HMGB9_ARATH High mobility group B protein 9 OS=Arabidopsis thaliana GN=HMGB9 PE=2 SV=1 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|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|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 ?
Query326
255581935313 transcription factor, putative [Ricinus 0.953 0.993 0.693 1e-123
224122224316 high mobility group family [Populus tric 0.892 0.920 0.750 1e-119
225463518331 PREDICTED: high mobility group B protein 0.886 0.873 0.680 1e-112
356517796339 PREDICTED: LOW QUALITY PROTEIN: high mob 0.874 0.840 0.540 9e-89
297834160318 high mobility group family protein [Arab 0.883 0.905 0.540 2e-87
18399977319 high mobility group-box and ARID domain- 0.831 0.849 0.567 4e-87
298205254 483 unnamed protein product [Vitis vinifera] 0.923 0.623 0.528 2e-85
225433532 482 PREDICTED: high mobility group B protein 0.923 0.624 0.528 2e-85
147855747 461 hypothetical protein VITISV_021289 [Viti 0.923 0.652 0.528 2e-85
449442473 491 PREDICTED: high mobility group B protein 0.868 0.576 0.527 2e-83
>gi|255581935|ref|XP_002531766.1| transcription factor, putative [Ricinus communis] gi|223528602|gb|EEF30622.1| transcription factor, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  448 bits (1153), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 222/320 (69%), Positives = 260/320 (81%), Gaps = 9/320 (2%)

Query: 1   MSSHMLNGQKSSATTSNSNSNSNNNNNNNKASSYYPPPTAKYEDIAQSSDLFWATLEAFH 60
           MS+H       +AT  ++     +   N ++   YP PTA++ED+ QSSDLFW  L++FH
Sbjct: 1   MSTH-----NPTATVISTQQEVQSETRNCQSFRSYPSPTAQFEDVVQSSDLFWEKLKSFH 55

Query: 61  KSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFV 120
           KSFG KF VPTVGGKALDLH LFVEVTSRGGL KV+RDR+WKEV+  FNFP+TITSASFV
Sbjct: 56  KSFGTKFMVPTVGGKALDLHHLFVEVTSRGGLEKVVRDRKWKEVIAAFNFPSTITSASFV 115

Query: 121 LRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSGSSLDNGSASPEEGSTINQLGSQGSSKL 180
           LRKYYLSLLYHFEQVY F ++ PS S+ D V+G+ L NGSA+ E G T+NQ    GSS+L
Sbjct: 116 LRKYYLSLLYHFEQVYQFHKQVPSVSVSDDVNGN-LVNGSATVE-GVTVNQF--PGSSQL 171

Query: 181 QIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPHAHNVSQSSNNSAAPTHRRRKRS 240
           Q+G SV+G IDGKFDNGYL+TV LGSEQLKGVLYHIP+   +SQSS+NS  P  R RKRS
Sbjct: 172 QLGSSVNGTIDGKFDNGYLITVTLGSEQLKGVLYHIPNEFYMSQSSHNSDLPPRRHRKRS 231

Query: 241 RLALRDPSRPKSNRSGYNFFFAEHYARLKPHYYGQEKAISKKIGVLWSNLTEAEKQVYQE 300
           RL LRDPSRPKS+RSGYNFFFAEHYA+LKP +YGQEK ISKKIG+LW+NLTEAEK++YQE
Sbjct: 232 RLLLRDPSRPKSHRSGYNFFFAEHYAQLKPLHYGQEKVISKKIGLLWNNLTEAEKEIYQE 291

Query: 301 KGLKDKERYKSEMLEYRSSY 320
           KGLKDKERYK+EMLEYRSSY
Sbjct: 292 KGLKDKERYKNEMLEYRSSY 311

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224122224|ref|XP_002330570.1| high mobility group family [Populus trichocarpa] gi|222872128|gb|EEF09259.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225463518|ref|XP_002264357.1| PREDICTED: high mobility group B protein 10 [Vitis vinifera] gi|296090037|emb|CBI39856.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|356517796|ref|XP_003527572.1| PREDICTED: LOW QUALITY PROTEIN: high mobility group B protein 10-like [Glycine max] Back     alignment and taxonomy information
>gi|297834160|ref|XP_002884962.1| high mobility group family protein [Arabidopsis lyrata subsp. lyrata] gi|297330802|gb|EFH61221.1| high mobility group family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|18399977|ref|NP_566454.1| high mobility group-box and ARID domain-binding domain-containing protein [Arabidopsis thaliana] gi|75274126|sp|Q9LTT3.1|HMG10_ARATH RecName: Full=High mobility group B protein 10; AltName: Full=Nucleosome/chromatin assembly factor group D 10 gi|13605513|gb|AAK32750.1|AF361582_1 AT3g13350/MDC11_14 [Arabidopsis thaliana] gi|9294541|dbj|BAB02804.1| high mobility group protein-like [Arabidopsis thaliana] gi|21593357|gb|AAM65306.1| unknown [Arabidopsis thaliana] gi|22137084|gb|AAM91387.1| At3g13350/MDC11_14 [Arabidopsis thaliana] gi|332641816|gb|AEE75337.1| high mobility group-box and ARID domain-binding domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>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|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

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 ?
Query326
TAIR|locus:2088160319 AT3G13350 [Arabidopsis thalian 0.831 0.849 0.557 5.5e-77
TAIR|locus:2010587 448 AT1G04880 [Arabidopsis thalian 0.564 0.410 0.477 6.1e-64
TAIR|locus:2199824338 AT1G76110 [Arabidopsis thalian 0.871 0.840 0.441 1.2e-56
TAIR|locus:2020517337 AT1G55650 [Arabidopsis thalian 0.558 0.540 0.479 1.1e-41
UNIPROTKB|E1C9H0 1831 ARID2 "Uncharacterized protein 0.276 0.049 0.472 1.6e-17
UNIPROTKB|Q68CP9 1835 ARID2 "AT-rich interactive dom 0.297 0.052 0.427 2.1e-15
UNIPROTKB|K7EJ04182 ARID3A "AT-rich interactive do 0.202 0.362 0.439 4.2e-14
ZFIN|ZDB-GENE-030131-6311 1573 arid2 "AT rich interactive dom 0.276 0.057 0.472 3.5e-13
UNIPROTKB|E2RFL8 1836 ARID2 "Uncharacterized protein 0.297 0.052 0.378 2.7e-09
UNIPROTKB|Q99856593 ARID3A "AT-rich interactive do 0.202 0.111 0.439 3.7e-09
TAIR|locus:2088160 AT3G13350 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 775 (277.9 bits), Expect = 5.5e-77, P = 5.5e-77
 Identities = 161/289 (55%), Positives = 200/289 (69%)

Query:    40 AKYEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDR 99
             AKY+D+ ++S LFW  L AF        KVPTVGG  LDLHRLF+EVTSRGG+ +V++DR
Sbjct:    34 AKYDDLVRNSALFWEKLRAFLGLTSKTLKVPTVGGNTLDLHRLFIEVTSRGGIERVVKDR 93

Query:   100 RWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSG-SSLDN 158
             +WKEV+  F+FPTTITSASFVLRKYYL  L+  E VYY   E P SS+        SL N
Sbjct:    94 KWKEVIGAFSFPTTITSASFVLRKYYLKFLFQLEHVYYL--EKPVSSLQSTDEALKSLAN 151

Query:   159 GSASPEEGSTINQLGSQGSSKLQIGCSVSGVIDGKFDNGYLVTVNLGSEQLKGVLYHIPH 218
              S +PEEG  I++         Q+G  V G IDGKFD+GYLVT+ LGS++LKGVLYHIP 
Sbjct:   152 ESPNPEEG--IDEP--------QVGYEVQGFIDGKFDSGYLVTMKLGSQELKGVLYHIPQ 201

Query:   219 AHNVSQSSNN--SA---APTHXXXXXXXXXXXDPSRPKSNRSGYNFFFAEHYARLKPHYY 273
               + SQ +    SA   +              D  +PK +RSGYNFFFAE YARLKP Y+
Sbjct:   202 TPSQSQQTMETPSAIVQSSQRRHRKKSKLAVVDTQKPKCHRSGYNFFFAEQYARLKPEYH 261

Query:   274 GQEKAISKKIGVLWSNLTEAEKQVYQEKGLKDKERYKSEMLEYRSSYDS 322
             GQE++I+KKIG +WSNLTE+EKQVYQ+KG+KD ERY+ EMLEY+SS++S
Sbjct:   262 GQERSITKKIGHMWSNLTESEKQVYQDKGVKDVERYRIEMLEYKSSHES 310
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:0006333 "chromatin assembly or disassembly" evidence=RCA
TAIR|locus:2010587 AT1G04880 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
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
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
UNIPROTKB|K7EJ04 ARID3A "AT-rich interactive domain-containing protein 3A" [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
UNIPROTKB|Q99856 ARID3A "AT-rich interactive domain-containing protein 3A" [Homo sapiens (taxid:9606)] 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) ?
Q9LTT3HMG10_ARATHNo assigned EC number0.56740.83120.8495yesno

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:
HMGB904
high mobility group family (301 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query326
smart0050193 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interac 2e-28
smart0101488 smart01014, ARID, ARID/BRIGHT DNA binding domain 4e-25
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
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 9e-14
smart0039870 smart00398, HMG, high mobility group 2e-12
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 2e-11
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 9e-08
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 8e-07
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 0.001
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 0.004
>gnl|CDD|128777 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interaction domain) domain Back     alignment and domain information 
 Score =  105 bits (264), Expect = 2e-28
 Identities = 35/93 (37%), Positives = 50/93 (53%), Gaps = 1/93 (1%)

Query: 47  QSSDLFWATLEAFHKSFGDK-FKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVV 105
           +   LF   L  F +  G    K+P +GGK LDL+RL+  V  RGG  +V +D++WKE+ 
Sbjct: 1   RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIA 60

Query: 106 VVFNFPTTITSASFVLRKYYLSLLYHFEQVYYF 138
                P T TSA+  LRK+Y   L  +E+    
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|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|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
>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 326
KOG2744512 consensus DNA-binding proteins Bright/BRCAA1/RBP1 99.94
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 99.86
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.77
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.75
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.73
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.71
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.7
smart0039870 HMG high mobility group. 99.7
KOG038196 consensus HMG box-containing protein [General func 99.66
COG5648211 NHP6B Chromatin-associated proteins containing the 99.66
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.61
KOG0527 331 consensus HMG-box transcription factor [Transcript 99.61
KOG3248 421 consensus Transcription factor TCF-4 [Transcriptio 99.53
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.5
KOG2510532 consensus SWI-SNF chromatin-remodeling complex pro 99.22
KOG0528 511 consensus HMG-box transcription factor SOX5 [Trans 98.99
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 98.94
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.26
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 97.85
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 96.88
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 96.63
COG5648211 NHP6B Chromatin-associated proteins containing the 96.17
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 88.16
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 87.38
PF0024948 Myb_DNA-binding: Myb-like DNA-binding domain; Inte 81.77
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription] Back     alignment and domain information 
Probab=99.94  E-value=7.1e-27  Score=236.62  Aligned_cols=179  Identities=39%  Similarity=0.575  Sum_probs=145.2

Q ss_pred             CCCCchhhhhcHHHHHHHHHHHHHhcCCCCC-CCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCC-CCC
Q 020460           38 PTAKYEDIAQSSDLFWATLEAFHKSFGDKFK-VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPT-TIT  115 (326)
Q Consensus        38 p~~~~e~~~~~~~~F~~~L~~F~~~rG~~l~-~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~-~~t  115 (326)
                      +....|.+..+++.||+.|+.||+.+|++|+ +|+|+|++||||.||.+|+++||++.|+..++|++|+..|.||. ++|
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            5666677777999999999999999999997 99999999999999999999999999999999999999999999 999


Q ss_pred             cHHHHHHHHHHHhhHHHHHHHhhhcCCCCCCCCCCCC-CCCCC-CCCCCCCCCcc-ccc---CCCCCCcccccCCceeec
Q 020460          116 SASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVS-GSSLD-NGSASPEEGST-INQ---LGSQGSSKLQIGCSVSGV  189 (326)
Q Consensus       116 ~as~~Lk~~Y~k~L~~fE~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~-~~~---~~~~~~~~~~~~~~v~~~  189 (326)
                      ++++.||++|.++|++||+.+++....+...+.+... ..++. .+...-+.++. ...   .....++    ...+.++
T Consensus       233 saaf~lr~~y~K~L~~ye~~~~~~~~~pln~p~~~~~~a~~~~~rE~~~~~~~~~~~~~~~~~~~~~~~----~~~aa~~  308 (512)
T KOG2744|consen  233 SAAFTLRKQYLKLLFEYECEFEKNRHVPLNSPAELSEEASSSNRREGRRHELSPSKEFQANGPSEEEPA----EAEAAPE  308 (512)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcccccccccccccccccccccCcchhhccCCccccccc----ccccchh
Confidence            9999999999999999999999998777776665433 22222 11112222221 111   1111111    2578999


Q ss_pred             ccCccCCCceEEEeeccccccccccccCCCC
Q 020460          190 IDGKFDNGYLVTVNLGSEQLKGVLYHIPHAH  220 (326)
Q Consensus       190 idgkf~~gy~vtv~~gse~~~g~ly~~p~~~  220 (326)
                      |+|+|+.||++++.++++.+++++|+.+...
T Consensus       309 ~~g~f~~~~~~~~~~~s~~ln~~~~~~~~~~  339 (512)
T KOG2744|consen  309 ILGNFLQGLLVFMKDGSEPLNGVLYLGPPDL  339 (512)
T ss_pred             hhccccccCceeccCcchhccCccccccCcc
Confidence            9999999999999999999999999986644

>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
>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
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] 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
>KOG0527 consensus HMG-box transcription factor [Transcription] Back     alignment and domain information
>KOG3248 consensus Transcription factor TCF-4 [Transcription] 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
>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
>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
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] 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
>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 ?
Query326
2kk0_A145 Solution Structure Of Dead Ringer-Like Protein 1 (A 2e-11
1c20_A128 Solution Structure Of The Dna-Binding Domain From T 1e-09
1kqq_A139 Solution Structure Of The Dead Ringer Arid-Dna Comp 6e-09
1ryu_A120 Solution Structure Of The Swi1 Arid Length = 120 2e-07
2cxy_A125 Crystal Structure Of The Hbaf250b At-Rich Interacti 2e-06
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 4e-06
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 1e-05
2lm1_A107 Solution Nmr Structure Of Lysine-Specific Demethyla 1e-05
2jrz_A117 Solution Structure Of The BrightARID DOMAIN FROM TH 1e-05
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 2e-05
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 4e-05
2lhj_A97 Nmr Structure Of The High Mobility Group Protein-Li 4e-05
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 4e-05
2yqe_A100 Solution Structure Of The Arid Domain Of Jarid1d Pr 6e-05
>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 = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 43/66 (65%)
Query: 68  KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 127
           ++P +  + LDL  L+V VT +GGL +VI  + W+E+    N PT+ITSA+F LR  Y+ 
Sbjct: 55  RIPIMAKQVLDLFMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLRTQYMK 114
Query: 128 LLYHFE 133
            LY +E
Sbjct: 115 YLYPYE 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|1RYU|A Chain A, Solution Structure Of The Swi1 Arid Length = 120 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|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78 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|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|2JRZ|A Chain A, Solution Structure Of The BrightARID DOMAIN FROM THE HUMAN Jarid1c Protein Length = 117 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|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|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|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93 Back     alignment and structure
>pdb|2YQE|A Chain A, Solution Structure Of The Arid Domain Of Jarid1d Protein Length = 100 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 ?
Query326
2rq5_A121 Protein jumonji; developmental protein, nucleus, r 3e-28
2lhj_A97 High mobility group protein homolog NHP1; structur 3e-25
1ig6_A107 MRF-2, modulator recognition factor 2; DNA binding 5e-25
2eqy_A122 RBP2 like, jumonji, at rich interactive domain 1B; 8e-25
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 1e-24
2lm1_A107 Lysine-specific demethylase LID; structural genomi 1e-23
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 2e-23
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 2e-23
2cxy_A125 BAF250B subunit, HBAF250B; DNA-binding domain, str 8e-23
1hme_A77 High mobility group protein fragment-B; DNA-bindin 1e-22
2jxj_A96 Histone demethylase jarid1A; ARID domain, chromati 2e-22
2jrz_A117 Histone demethylase jarid1C; bright/ARID domain, h 3e-22
1c20_A128 DEAD ringer protein; DNA-binding domain, ARID, AT- 2e-21
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 3e-21
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 9e-21
2kk0_A145 AT-rich interactive domain-containing protein 3A; 4e-20
1ckt_A71 High mobility group 1 protein; high-mobility group 2e-19
2yrq_A173 High mobility group protein B1; HMG box domain, DN 6e-19
2yrq_A173 High mobility group protein B1; HMG box domain, DN 1e-10
1kkx_A123 Transcription regulatory protein ADR6; ARID, DNA-b 2e-18
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 2e-17
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 8e-17
2li6_A116 SWI/SNF chromatin-remodeling complex subunit SWI1; 2e-16
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 2e-16
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 3e-16
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 4e-16
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 5e-15
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 1e-14
3tq6_A214 Transcription factor A, mitochondrial; transcripti 1e-14
1wgf_A90 Upstream binding factor 1; transcription factor, D 8e-14
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 2e-13
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 3e-13
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 6e-13
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 4e-12
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 3e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-05
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 6e-05
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 4e-04
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 7e-04
>2rq5_A Protein jumonji; developmental protein, nucleus, repressor, transcription, transcription regulation; NMR {Mus musculus} Length = 121 Back     alignment and structure
 Score =  105 bits (263), Expect = 3e-28
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 1/98 (1%)

Query: 49  SDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVV 107
           +    A ++   +S G    ++P +GG  LDL   F  +   GG+ +V   ++W ++  +
Sbjct: 13  NVQRLACIKKHLRSQGITMDELPLIGGCELDLACFFRLINEMGGMQQVTDLKKWNKLADM 72

Query: 108 FNFPTTITSASFVLRKYYLSLLYHFEQVYYFRREAPSS 145
              P T       L++ Y   L  ++ +          
Sbjct: 73  LRIPKTAQDRLAKLQEAYCQYLLSYDSLSPEEHRRLEK 110
>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
>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
>2eqy_A RBP2 like, jumonji, at rich interactive domain 1B; ARID domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 122 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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Length = 71 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>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
>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
>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
>2li6_A SWI/SNF chromatin-remodeling complex subunit SWI1; ligand binding, DNA binding protein; NMR {Saccharomyces cerevisiae} Length = 116 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
>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
>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
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query326
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
2jxj_A96 Histone demethylase jarid1A; ARID domain, chromati 99.94
2cxy_A125 BAF250B subunit, HBAF250B; DNA-binding domain, str 99.94
2rq5_A121 Protein jumonji; developmental protein, nucleus, r 99.94
2lm1_A107 Lysine-specific demethylase LID; structural genomi 99.94
1c20_A128 DEAD ringer protein; DNA-binding domain, ARID, AT- 99.93
1kkx_A123 Transcription regulatory protein ADR6; ARID, DNA-b 99.93
2li6_A116 SWI/SNF chromatin-remodeling complex subunit SWI1; 99.93
2kk0_A145 AT-rich interactive domain-containing protein 3A; 99.93
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.87
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.87
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.86
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.86
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.85
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.84
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.84
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.83
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.83
2lhj_A97 High mobility group protein homolog NHP1; structur 99.83
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.83
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.83
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.82
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.8
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.8
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.8
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.8
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.8
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.8
1ckt_A71 High mobility group 1 protein; high-mobility group 99.8
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.8
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.79
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.79
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.79
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.79
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.78
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.77
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.77
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.77
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.75
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.74
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.72
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.71
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 99.69
2cto_A93 Novel protein; high mobility group box domain, hel 99.67
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.65
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.65
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 99.65
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.54
>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=9.5e-29  Score=201.99  Aligned_cols=100  Identities=21%  Similarity=0.342  Sum_probs=93.3

Q ss_pred             hcHHHHHHHHHHHHHhcCCCC-CCCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHHH
Q 020460           47 QSSDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYY  125 (326)
Q Consensus        47 ~~~~~F~~~L~~F~~~rG~~l-~~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y  125 (326)
                      +|++.|+++|.+||+.+|+++ ++|+|+|++||||+||.+|+++|||++||++++|.+||+.||++.+++++++.||++|
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            578999999999999999999 7999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhHHHHHHHhhhcCCCCCCC
Q 020460          126 LSLLYHFEQVYYFRREAPSSSM  147 (326)
Q Consensus       126 ~k~L~~fE~~~~~~~~~~~~~~  147 (326)
                      ++||++||+ ++.++++.+.++
T Consensus        82 ~k~L~~yE~-~~~~~~~~~~p~  102 (107)
T 1ig6_A           82 ERLILPYER-FIKGEEDKPLPP  102 (107)
T ss_dssp             HHHTTTTHH-HHHHHTSSSSCT
T ss_pred             HHHHHHHHH-HHcCCCCCCCCC
Confidence            999999999 556776665554
>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
>2jxj_A Histone demethylase jarid1A; ARID domain, chromatin regulator, developmental protein, dioxygenase, iron, metal-binding, nucleus, oxidoreductase; NMR {Homo sapiens} 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
>2rq5_A Protein jumonji; developmental protein, nucleus, repressor, transcription, transcription regulation; NMR {Mus musculus} 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
>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
>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
>2li6_A SWI/SNF chromatin-remodeling complex subunit SWI1; ligand binding, DNA binding protein; NMR {Saccharomyces cerevisiae} 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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {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
>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
>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
>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
>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
>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
>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
>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
>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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, 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
>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 326
d1c20a_128 a.4.3.1 (A:) DNA-binding domain from the dead ring 8e-27
d1ryua_120 a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 2e-25
d1ig6a_107 a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo 1e-24
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 1e-19
d1kkxa_102 a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) { 2e-19
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 4e-16
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 3e-15
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 1e-14
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-14
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 4e-14
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-13
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 1e-12
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 4e-12
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 3e-11
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 1e-10
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 5e-09
>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

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: DNA-binding domain from the dead ringer protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score =  100 bits (250), Expect = 8e-27
 Identities = 32/105 (30%), Positives = 55/105 (52%), Gaps = 3/105 (2%)

Query: 50  DLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVF 108
             F   L +F +  G    ++P +    LDL+ L+  V +RGGL  VI  + W+E++   
Sbjct: 24  KEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGL 83

Query: 109 NFPTTITSASFVLRKYYLSLLYHFEQVYYFRREAPSSSMPDAVSG 153
           + P++ITSA+F LR  Y+  LY +E     +  +  + +  A+ G
Sbjct: 84  HLPSSITSAAFTLRTQYMKYLYPYEC--EKKNLSTPAELQAAIDG 126
>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 120 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
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93 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
>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91 Back     information, alignment and structure
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 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
>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
>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
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query326
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 99.93
d1kkxa_102 Transcription regulator Adr6 (Swi1) {Baker's yeast 99.91
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.86
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.84
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.83
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.8
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.79
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.78
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.78
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.77
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.76
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.73
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.73
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.72
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 95.96
d1guua_50 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 81.02
>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=2.4e-28  Score=197.87  Aligned_cols=97  Identities=22%  Similarity=0.364  Sum_probs=90.7

Q ss_pred             hcHHHHHHHHHHHHHhcCCCC-CCCeeCCeecchhHHHHHHHhcCcchhhcccccHHHHHHHhCCCCCCCcHHHHHHHHH
Q 020460           47 QSSDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYY  125 (326)
Q Consensus        47 ~~~~~F~~~L~~F~~~rG~~l-~~P~i~gk~lDL~~Ly~~V~~rGG~~~V~~~~~W~eVa~~l~~~~~~t~as~~Lk~~Y  125 (326)
                      .|++.|++.|.+||+.+|+++ ++|+|+|++||||.||.+|+++|||++|+.+++|.+||+.||++.+++++++.||++|
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            578999999999999999998 6999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhHHHHHHHhhhcCCC
Q 020460          126 LSLLYHFEQVYYFRREAP  143 (326)
Q Consensus       126 ~k~L~~fE~~~~~~~~~~  143 (326)
                      .+||++||+++..++.++
T Consensus        82 ~~~L~~yE~~~~~~~~~~   99 (107)
T d1ig6a_          82 ERLILPYERFIKGEEDKP   99 (107)
T ss_dssp             HHHTTTTHHHHHHHTSSS
T ss_pred             HHHHHHHHHHHhcCCCCC
Confidence            999999999766555433
>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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} 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