Citrus Sinensis ID: 026832

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--
MPSSSKSNAPKPRKRVDAQSASTSSATLMRGRDGSAFARCEECNKNVPVALISMHSCSLDAKIKMNLEAQVVEKPAEINKKKPAERKKPTSTEPRAKRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGNGDYNEVEDKADNEVEDKAENEVEDKAEKEDGDEGGSEKDVAEKEVQQDEENLDDY
cccccccccccccccccccccccccccccccccccccHHHHHHcccccccHHccccccHHHHHccHHHHccccccHHHcccccccccccccccccHHHccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHcHHHHHHHHHHHHHHHHHHHHHcccccccHHHcHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccc
cccccccccccccEEEEEcccccccEEEEEccccccEEEHHHcccccEEEEEEHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHccccHccccccccccccccccccccccccccccc
mpsssksnapkprkrvdaqsastssatlmrgrdgsafarceecnknVPVALISMHSCSLDAKIKMNLEAqvvekpaeinkkkpaerkkptsteprakrlrkkdsdsnkpkrpptafFLFMDDFRKEykeahpdskgvtGVAKEAGEKWknmtdeekkpYLDKAAELKADYSkamegngdynevedkadnevedKAENevedkaekedgdeggsekdVAEKEVQqdeenlddy
mpsssksnapkprkrvdaqsastssatlmrgrdGSAFARCEECNKNVPVALISMHSCSLDAKIKMNLEAQvvekpaeinkkkpaerkkptsteprakrlrkkdsdsnkpkrpptaFFLFMDDFRKEYKeahpdskgvtgvakeagekwknmtdeekkpyLDKAAELKADYSKAmegngdynevedkadnevedkaenevedkaekedgdeggsekdvaekevqqdeenlddy
MPSSSKSNAPKPRKRVDAQSASTSSATLMRGRDGSAFARCEECNKNVPVALISMHSCSLDAKIKMNLEAQVVEKPAEINKKKPAERKKPTSTEPRAKRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGNGDYNEVEDKADNEVEDKAENevedkaekedgdeggsekdVAEKEVQQDEENLDDY
************************************FARCEECNKNVPVALISMHSCSLDAKIKMNL***********************************************AFFLFMDDF*************************************************************************************************************
****************************************************************************************************************PTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAM**********************************************************
******************************GRDGSAFARCEECNKNVPVALISMHSCSLDAKIKMNLEAQVVEKPAEINKK*****************************RPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGNGDYNEVEDKAD********************************************
************RKRVDAQSASTSSATLMRGRDGSAFARCEECNKNVPVALISMHSCSLDAKIKMNLEAQVVEKPAEINKKKPA********************DSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGNGDY****************************************************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MPSSSKSNAPKPRKRVDAQSASTSSATLMRGRDGSAFARCEECNKNVPVALISMHSCSLDAKIKMNLEAQVVEKPAEINKKKPAERKKPTSTEPRAKRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGNGDxxxxxxxxxxxxxxxxxxxxxDKAEKEDGDEGGSEKDVAEKEVQQDEENLDDY
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 ?
Query232 2.2.26 [Sep-21-2011]
Q8LDF9241 High mobility group B pro yes no 0.728 0.701 0.632 1e-48
P40620149 HMG1/2-like protein OS=Vi N/A no 0.396 0.617 0.489 5e-19
P40619144 HMG1/2-like protein OS=Ip N/A no 0.439 0.708 0.467 4e-18
O49595178 High mobility group B pro no no 0.491 0.640 0.450 8e-18
O49597125 High mobility group B pro no no 0.349 0.648 0.469 2e-17
P93047141 High mobility group B pro no no 0.396 0.652 0.494 4e-17
P27347157 DNA-binding protein MNB1B N/A no 0.396 0.585 0.463 4e-17
Q42344138 High mobility group B pro no no 0.370 0.623 0.483 5e-17
P26585152 HMG1/2-like protein OS=Gl no no 0.301 0.460 0.542 8e-17
P40621161 HMG1/2-like protein OS=Tr N/A no 0.336 0.484 0.493 9e-17
>sp|Q8LDF9|HMGB7_ARATH High mobility group B protein 7 OS=Arabidopsis thaliana GN=HMGB7 PE=1 SV=1 Back     alignment and function desciption
 Score =  192 bits (488), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 112/177 (63%), Positives = 136/177 (76%), Gaps = 8/177 (4%)

Query: 4   SSKSNAPKPRKRVDAQSASTSSATLMRGRDGSAFARCEECNKNVPVALISMHSCSLDAKI 63
           S+ SNAPK RKRV+A+++S +S TL R +DGSAFA CE CNK+V VALISMH+CSLDAKI
Sbjct: 5   STTSNAPKQRKRVEAETSSNTSTTLRRAKDGSAFALCEGCNKSVAVALISMHNCSLDAKI 64

Query: 64  KMNLEAQVVEKPAEINKKKPAERKKPTSTEPRAKRLRKKD------SDSNKPKRPPTAFF 117
           ++NLEAQVVE  AE  KKKPAE+KK TS  P+ KRL+K +      S SNKPKRP TAFF
Sbjct: 65  RVNLEAQVVETQAE-AKKKPAEKKKTTSDGPKPKRLKKTNDEKKSSSTSNKPKRPLTAFF 123

Query: 118 LFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAM 174
           +FM DFRK +K  H  S      AK  GEKWK++T+EEKK YLDKAAELKA+Y+K++
Sbjct: 124 IFMSDFRKTFKSEHNGSLA-KDAAKIGGEKWKSLTEEEKKVYLDKAAELKAEYNKSL 179
Binds preferentially double-stranded supercoiled DNA.
Arabidopsis thaliana (taxid: 3702)
>sp|P40620|HMGL_VICFA HMG1/2-like protein OS=Vicia faba PE=2 SV=1 Back     alignment and function description
>sp|P40619|HMGL_IPONI HMG1/2-like protein OS=Ipomoea nil PE=2 SV=1 Back     alignment and function description
>sp|O49595|HMGB1_ARATH High mobility group B protein 1 OS=Arabidopsis thaliana GN=HMGB1 PE=1 SV=1 Back     alignment and function description
>sp|O49597|HMGB5_ARATH High mobility group B protein 5 OS=Arabidopsis thaliana GN=HMGB5 PE=2 SV=1 Back     alignment and function description
>sp|P93047|HMGB3_ARATH High mobility group B protein 3 OS=Arabidopsis thaliana GN=HMGB3 PE=1 SV=1 Back     alignment and function description
>sp|P27347|MNB1B_MAIZE DNA-binding protein MNB1B OS=Zea mays GN=MNB1B PE=1 SV=1 Back     alignment and function description
>sp|Q42344|HMGB4_ARATH High mobility group B protein 4 OS=Arabidopsis thaliana GN=HMGB4 PE=1 SV=1 Back     alignment and function description
>sp|P26585|HMGL_SOYBN HMG1/2-like protein OS=Glycine max PE=2 SV=1 Back     alignment and function description
>sp|P40621|HMGL_WHEAT HMG1/2-like protein OS=Triticum aestivum PE=2 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query232
359484115190 PREDICTED: high mobility group B protein 0.693 0.847 0.704 1e-58
449464956207 PREDICTED: high mobility group B protein 0.702 0.787 0.680 4e-58
255544145196 DNA-binding protein MNB1B, putative [Ric 0.806 0.954 0.602 4e-57
224097317201 high mobility group family [Populus tric 0.827 0.955 0.575 4e-56
388499756197 unknown [Lotus japonicus] 0.715 0.842 0.649 9e-56
351722065209 uncharacterized protein LOC100306558 [Gl 0.754 0.837 0.639 1e-53
346472777208 hypothetical protein [Amblyomma maculatu 0.728 0.812 0.620 3e-53
356536465200 PREDICTED: high mobility group B protein 0.737 0.855 0.648 2e-52
242080163221 hypothetical protein SORBIDRAFT_07g00023 0.887 0.932 0.519 2e-48
297812491193 hypothetical protein ARALYDRAFT_910356 [ 0.741 0.891 0.627 1e-47
>gi|359484115|ref|XP_002267697.2| PREDICTED: high mobility group B protein 7-like [Vitis vinifera] gi|147815109|emb|CAN61363.1| hypothetical protein VITISV_034306 [Vitis vinifera] gi|297742725|emb|CBI35359.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  231 bits (590), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 119/169 (70%), Positives = 139/169 (82%), Gaps = 8/169 (4%)

Query: 9   APKPRKRVDAQSASTSSATLMRGRDGSAFARCEECNKNVPVALISMHSCSLDAKIKMNLE 68
            PK RKRV+A+++S     L R RDGSAF RCEEC K+VPV LI MHSCSL+AKIK+NLE
Sbjct: 3   GPKQRKRVEAETSS-----LKRARDGSAFIRCEECKKDVPVVLIDMHSCSLEAKIKLNLE 57

Query: 69  AQVVEKPAEINKKKPAERKKPTSTEPRAKRLRK--KDSDSNKPKRPPTAFFLFMDDFRKE 126
           AQVVEK  ++ KKKPAE+K  T+TEP+ K+ R+  K  D N PKRPPTAFFLFMDDFRKE
Sbjct: 58  AQVVEKVTDV-KKKPAEKKNATTTEPKPKKSRRLRKVKDPNMPKRPPTAFFLFMDDFRKE 116

Query: 127 YKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAME 175
           YKE++PDSK V+ VAKE GEKWK+MTDEEKKPY+DKAAELKA+Y KAME
Sbjct: 117 YKESNPDSKNVSVVAKEGGEKWKSMTDEEKKPYVDKAAELKAEYDKAME 165

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449464956|ref|XP_004150195.1| PREDICTED: high mobility group B protein 7-like [Cucumis sativus] gi|449531370|ref|XP_004172659.1| PREDICTED: high mobility group B protein 7-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255544145|ref|XP_002513135.1| DNA-binding protein MNB1B, putative [Ricinus communis] gi|223548146|gb|EEF49638.1| DNA-binding protein MNB1B, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224097317|ref|XP_002310906.1| high mobility group family [Populus trichocarpa] gi|118483462|gb|ABK93630.1| unknown [Populus trichocarpa] gi|222853809|gb|EEE91356.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|388499756|gb|AFK37944.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|351722065|ref|NP_001236719.1| uncharacterized protein LOC100306558 [Glycine max] gi|255628875|gb|ACU14782.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|346472777|gb|AEO36233.1| hypothetical protein [Amblyomma maculatum] Back     alignment and taxonomy information
>gi|356536465|ref|XP_003536758.1| PREDICTED: high mobility group B protein 7-like [Glycine max] Back     alignment and taxonomy information
>gi|242080163|ref|XP_002444850.1| hypothetical protein SORBIDRAFT_07g000230 [Sorghum bicolor] gi|241941200|gb|EES14345.1| hypothetical protein SORBIDRAFT_07g000230 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|297812491|ref|XP_002874129.1| hypothetical protein ARALYDRAFT_910356 [Arabidopsis lyrata subsp. lyrata] gi|297319966|gb|EFH50388.1| hypothetical protein ARALYDRAFT_910356 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query232
TAIR|locus:2154433241 HMGB6 "high-mobility group box 0.978 0.941 0.539 1.6e-56
TAIR|locus:2128003125 HMGB5 "high mobility group B5" 0.504 0.936 0.386 4.4e-20
RGD|1585821213 LOC680968 "similar to High mob 0.603 0.657 0.377 7.3e-20
TAIR|locus:505006135144 HMGB2 "high mobility group B2" 0.508 0.819 0.415 9.2e-20
TAIR|locus:2053893138 HMGB4 "high mobility group B4" 0.482 0.811 0.429 1.2e-19
UNIPROTKB|F1RQ19202 LOC100517745 "Uncharacterized 0.534 0.613 0.384 3.1e-19
RGD|1564407200 Hmgb3 "high mobility group box 0.534 0.62 0.392 1.7e-18
MGI|MGI:1098219200 Hmgb3 "high mobility group box 0.534 0.62 0.384 5.5e-18
UNIPROTKB|F1N927214 HMGB1 "High mobility group pro 0.849 0.920 0.319 3.2e-17
UNIPROTKB|Q9YH06215 HMG1 "High mobility group 1 pr 0.849 0.916 0.319 3.2e-17
TAIR|locus:2154433 HMGB6 "high-mobility group box 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 582 (209.9 bits), Expect = 1.6e-56, P = 1.6e-56
 Identities = 129/239 (53%), Positives = 159/239 (66%)

Query:     4 SSKSNAPKPRKRVDAQSASTSSATLMRGRDGSAFARCEECNKNVPVALISMHSCSLDAKI 63
             S+ SNAPK RKRV+A+++S +S TL R +DGSAFA CE CNK+V VALISMH+CSLDAKI
Sbjct:     5 STTSNAPKQRKRVEAETSSNTSTTLRRAKDGSAFALCEGCNKSVAVALISMHNCSLDAKI 64

Query:    64 KMNLEAQVVEKPAEINKKKPAERKKPTSTEPRAKRLRKKD------SDSNKPKRPPTAFF 117
             ++NLEAQVVE  AE  KKKPAE+KK TS  P+ KRL+K +      S SNKPKRP TAFF
Sbjct:    65 RVNLEAQVVETQAEA-KKKPAEKKKTTSDGPKPKRLKKTNDEKKSSSTSNKPKRPLTAFF 123

Query:   118 LFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGN 177
             +FM DFRK +K  H  S      AK  GEKWK++T+EEKK YLDKAAELKA+Y+K++E N
Sbjct:   124 IFMSDFRKTFKSEHNGSLA-KDAAKIGGEKWKSLTEEEKKVYLDKAAELKAEYNKSLESN 182

Query:   178 GDYNEVED--KADNEVEDKAENXXXXXXXXXXXXXXXXXXXVAEKEVQQDEEN--LDDY 232
                 E ED  K  ++V+D  E                      E E +++EE   LDDY
Sbjct:   183 DADEEEEDEEKQSDDVDDAEEKQVDDDDEVEEKEVENTDDDKKEAEGKEEEEEEILDDY 241
GO:0005634 "nucleus" evidence=ISM;IDA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0003677 "DNA binding" evidence=IDA
GO:0006261 "DNA-dependent DNA replication" evidence=RCA
TAIR|locus:2128003 HMGB5 "high mobility group B5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
RGD|1585821 LOC680968 "similar to High mobility group protein 1 (HMG-1) (High mobility group protein B1) (Amphoterin) (Heparin-binding protein p30)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
TAIR|locus:505006135 HMGB2 "high mobility group B2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2053893 HMGB4 "high mobility group B4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|F1RQ19 LOC100517745 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
RGD|1564407 Hmgb3 "high mobility group box 3" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:1098219 Hmgb3 "high mobility group box 3" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1N927 HMGB1 "High mobility group protein B1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q9YH06 HMG1 "High mobility group 1 protein" [Gallus gallus (taxid:9031)] 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) ?
Q8LDF9HMGB7_ARATHNo assigned EC number0.63270.72840.7012yesno

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 ?
Query232
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 1e-18
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 5e-18
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 3e-16
smart0039870 smart00398, HMG, high mobility group 1e-13
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 4e-11
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 9e-10
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 2e-09
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 1e-06
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 2e-05
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 3e-05
>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 
 Score = 76.9 bits (190), Expect = 1e-18
 Identities = 32/67 (47%), Positives = 45/67 (67%), Gaps = 1/67 (1%)

Query: 109 PKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKA 168
           PKRP +A+FLF  + R + K+ +PD+  VT V K  GEKWK +++EEKK Y +KA + K 
Sbjct: 1   PKRPLSAYFLFSQEQRPKLKKENPDAS-VTEVTKILGEKWKELSEEEKKKYEEKAEKDKE 59

Query: 169 DYSKAME 175
            Y K M+
Sbjct: 60  RYEKEMK 66

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66
>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|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) Back     alignment and domain information
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional 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 232
PTZ0019994 high mobility group protein; Provisional 99.86
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.79
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.77
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.75
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.74
smart0039870 HMG high mobility group. 99.73
COG5648211 NHP6B Chromatin-associated proteins containing the 99.72
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.7
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.67
KOG0527 331 consensus HMG-box transcription factor [Transcript 99.62
KOG038196 consensus HMG box-containing protein [General func 99.61
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.46
COG5648211 NHP6B Chromatin-associated proteins containing the 99.28
KOG3248 421 consensus Transcription factor TCF-4 [Transcriptio 99.09
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 99.06
KOG0528511 consensus HMG-box transcription factor SOX5 [Trans 98.99
PTZ0019994 high mobility group protein; Provisional 98.37
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.17
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 98.17
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 97.93
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 97.91
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 97.9
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 97.75
smart0039870 HMG high mobility group. 97.49
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 97.27
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 97.27
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 96.98
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 96.58
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 96.56
KOG0527331 consensus HMG-box transcription factor [Transcript 96.47
KOG038196 consensus HMG box-containing protein [General func 95.86
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 95.66
KOG0528511 consensus HMG-box transcription factor SOX5 [Trans 90.83
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 90.21
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 90.14
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 89.76
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 81.49
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information 
Probab=99.86  E-value=1.1e-21  Score=149.11  Aligned_cols=81  Identities=36%  Similarity=0.648  Sum_probs=75.8

Q ss_pred             hhcccCCCCCCCCCCCCchhhhHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCChhhchHHHHHHHHHHHHHHHHhcC
Q 026832           98 RLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSK-GVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEG  176 (232)
Q Consensus        98 k~kK~~kdp~~PKrP~sAy~lF~~e~R~~~k~~~P~~~-~~~eisK~lge~Wk~Ls~eeK~~Y~~~A~~~k~~Y~ke~~~  176 (232)
                      ++++..+||++||||+||||||++++|..|..+||++. ++.+|+++||++|+.||+++|++|.++|..++.+|..+|. 
T Consensus        12 ~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~-   90 (94)
T PTZ00199         12 KNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKA-   90 (94)
T ss_pred             ccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH-
Confidence            44567899999999999999999999999999999983 3899999999999999999999999999999999999999 


Q ss_pred             Cccch
Q 026832          177 NGDYN  181 (232)
Q Consensus       177 ~~~y~  181 (232)
                        +|+
T Consensus        91 --~Y~   93 (94)
T PTZ00199         91 --EYA   93 (94)
T ss_pred             --HHh
Confidence              985

>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
>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
>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
>smart00398 HMG high mobility group Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] 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
>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
>KOG0381 consensus HMG box-containing protein [General function prediction only] 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
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>KOG3248 consensus Transcription factor TCF-4 [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
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription] Back     alignment and domain information
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription] 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
>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
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins 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
>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
>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
>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
>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
>KOG0527 consensus HMG-box transcription factor [Transcription] Back     alignment and domain information
>KOG0381 consensus HMG box-containing protein [General function prediction only] 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
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription] 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
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query232
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 4e-13
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 3e-10
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 5e-10
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 1e-09
2yrq_A173 Solution Structure Of The Tandem Hmg Box Domain Fro 5e-09
1nhm_A81 The Structure Of The Hmg Box And Its Interaction Wi 2e-08
1hme_A77 Structure Of The Hmg Box Motif In The B-Domain Of H 2e-08
1hsm_A79 The Structure Of The Hmg Box And Its Interaction Wi 2e-07
1e7j_A74 Hmg-D Complexed To A Bulge Dna Length = 74 8e-07
1qrv_A73 Crystal Structure Of The Complex Of Hmg-D And Dna L 8e-07
3nm9_A73 Hmgd(M13a)-Dna Complex Length = 73 2e-06
1hma_A73 The Solution Structure And Dynamics Of The Dna Bind 2e-06
1wxl_A73 Solution Structure Of The Hmg-Box Domain In The Ssr 1e-05
2e6o_A87 Solution Structure Of The Hmg Box Domain From Human 2e-05
2lhj_A97 Nmr Structure Of The High Mobility Group Protein-Li 4e-05
1i11_A81 Solution Structure Of The Dna Binding Domain, Sox-5 6e-05
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 7e-05
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 7e-05
1j3x_A77 Solution Structure Of The N-Terminal Domain Of The 9e-05
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 4e-04
2crj_A92 Solution Structure Of The Hmg Domain Of Mouse Hmg D 4e-04
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 8e-04
2ly4_A83 Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-Bo 9e-04
>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 
Iteration: 1

 Score = 71.2 bits (173), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 34/69 (49%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 104 SDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKA 163
           S  N PKRPP+ FFLF  +FR + K  +P    +  VAK+ GE W N+ D EK+PY+ KA
Sbjct: 5   SSGNAPKRPPSGFFLFCSEFRPKIKSTNPGIS-IGDVAKKLGEMWNNLNDSEKQPYITKA 63
Query: 164 AELKADYSK 172
           A+LK  Y K
Sbjct: 64  AKLKEKYEK 72
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79 Back     alignment and structure
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159 Back     alignment and structure
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78 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|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 81 Back     alignment and structure
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1 Length = 77 Back     alignment and structure
>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 79 Back     alignment and structure
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna Length = 74 Back     alignment and structure
>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna Length = 73 Back     alignment and structure
>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex Length = 73 Back     alignment and structure
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding Domain Of Hmg-D From Drosophila Melanogaster Length = 73 Back     alignment and structure
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1 Subunit Of Fact Length = 73 Back     alignment and structure
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human Hmg-Box Transcription Factor 1 Length = 87 Back     alignment and structure
>pdb|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|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg Box From Mouse Length = 81 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|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2 Length = 77 Back     alignment and structure
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription Factor Sox-17 Length = 82 Back     alignment and structure
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain Protein Hmgx2 Length = 92 Back     alignment and structure
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query232
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 4e-22
2lhj_A97 High mobility group protein homolog NHP1; structur 4e-22
1hme_A77 High mobility group protein fragment-B; DNA-bindin 4e-22
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 4e-21
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 3e-20
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 4e-20
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 7e-20
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 2e-19
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 2e-19
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 3e-19
1ckt_A71 High mobility group 1 protein; high-mobility group 3e-19
1wgf_A90 Upstream binding factor 1; transcription factor, D 7e-19
2yrq_A173 High mobility group protein B1; HMG box domain, DN 6e-18
2yrq_A173 High mobility group protein B1; HMG box domain, DN 3e-13
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 1e-17
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 6e-17
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 6e-15
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 8e-15
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 1e-14
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 4e-14
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 2e-13
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 2e-13
3tq6_A214 Transcription factor A, mitochondrial; transcripti 3e-13
3tq6_A214 Transcription factor A, mitochondrial; transcripti 1e-10
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 3e-13
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 6e-10
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 6e-13
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 9e-13
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 1e-12
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 3e-12
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 1e-11
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 1e-11
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 2e-10
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 4e-10
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 1e-09
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 5e-08
>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
 Score = 85.8 bits (213), Expect = 4e-22
 Identities = 31/86 (36%), Positives = 42/86 (48%), Gaps = 1/86 (1%)

Query: 90  TSTEPRAKRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWK 149
            +     KR  +K  D N PKR  +A+  F ++ R   +  +PD      V K+ GEKWK
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWK 60

Query: 150 NMTDEEKKPYLDKAAELKADYSKAME 175
            +T EEK+PY  KA   K  Y    E
Sbjct: 61  ALTPEEKQPYEAKAQADKKRYESEKE 86
>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
>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
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 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
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73 Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 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
>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
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67 Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92 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
>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
>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
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Length = 106 Back     alignment and structure
>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
>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
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Length = 76 Back     alignment and structure
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} PDB: 2yul_A Length = 83 Back     alignment and structure
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79 Back     alignment and structure
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Length = 80 Back     alignment and structure
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Length = 81 Back     alignment and structure
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Length = 85 Back     alignment and structure
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Length = 86 Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101 Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108 Back     alignment and structure
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query232
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.97
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.96
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.94
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.93
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.88
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.88
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.88
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.87
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.86
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.86
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.86
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.86
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.85
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.85
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.85
2lhj_A97 High mobility group protein homolog NHP1; structur 99.85
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.85
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.84
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.83
1ckt_A71 High mobility group 1 protein; high-mobility group 99.83
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.83
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.82
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.82
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.82
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.82
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.81
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.81
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.81
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.8
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.79
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.78
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.76
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.76
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.75
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.72
2cto_A93 Novel protein; high mobility group box domain, hel 99.72
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.7
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.69
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.63
2lhj_A97 High mobility group protein homolog NHP1; structur 98.59
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 98.56
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 98.56
1wgf_A90 Upstream binding factor 1; transcription factor, D 98.55
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 98.52
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 98.4
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 98.39
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 98.39
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 98.34
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 98.29
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 98.27
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 98.27
1ckt_A71 High mobility group 1 protein; high-mobility group 98.26
1hme_A77 High mobility group protein fragment-B; DNA-bindin 98.25
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 98.23
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 98.1
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 98.09
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 98.09
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 98.08
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 98.06
2cto_A93 Novel protein; high mobility group box domain, hel 98.0
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 97.99
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 97.98
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 97.98
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 97.94
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 97.9
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 97.89
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 97.88
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 97.73
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 97.58
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 97.5
>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
Probab=99.97  E-value=5.2e-31  Score=218.41  Aligned_cols=154  Identities=34%  Similarity=0.513  Sum_probs=132.6

Q ss_pred             CccccccCCCCchhHhh---HhhhcCCcc---chhhh-hhchHHHhhhhHHHhhhhhhhhhhccchhhhhhCCCCCChhh
Q 026832           24 SSATLMRGRDGSAFARC---EECNKNVPV---ALISM-HSCSLDAKIKMNLEAQVVEKPAEINKKKPAERKKPTSTEPRA   96 (232)
Q Consensus        24 ~~~~~~r~~dgsaf~~c---e~~~~~~~v---a~~~~-~~cs~~WK~ls~~Ek~~y~~~a~~~k~~~ye~~~~~~~~~k~   96 (232)
                      +++.++|...+..|...   ..+...+|.   .+.++ ++|+.+|+.||+.||++|.++|+.++ .+|+.++..|.++.+
T Consensus        12 dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k-~~y~~e~~~y~~~~~   90 (173)
T 2yrq_A           12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK-ARYEREMKTYIPPKG   90 (173)
T ss_dssp             CSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH-HHTHHHHHHCCCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH-HHHHHHhhhhhhhhh
Confidence            34678887655444322   333455665   45566 89999999999999999999999999 999999999987755


Q ss_pred             hhhcccCCCCCCCCCCCCchhhhHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCChhhchHHHHHHHHHHHHHHHHhcC
Q 026832           97 KRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEG  176 (232)
Q Consensus        97 kk~kK~~kdp~~PKrP~sAy~lF~~e~R~~~k~~~P~~~~~~eisK~lge~Wk~Ls~eeK~~Y~~~A~~~k~~Y~ke~~~  176 (232)
                      . ++++.++|++||||+|||||||+++|..|+.+||++ ++.+|+++||++|+.||+++|++|.++|..++.+|..+|+ 
T Consensus        91 ~-~kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~-  167 (173)
T 2yrq_A           91 E-TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA-  167 (173)
T ss_dssp             C-SSCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSS-CHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHH-
T ss_pred             h-hcccccCCccccCcccHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH-
Confidence            3 345678999999999999999999999999999999 9999999999999999999999999999999999999999 


Q ss_pred             Cccchhh
Q 026832          177 NGDYNEV  183 (232)
Q Consensus       177 ~~~y~~~  183 (232)
                        +|+.+
T Consensus       168 --~y~~k  172 (173)
T 2yrq_A          168 --AYRAK  172 (173)
T ss_dssp             --HHHCC
T ss_pred             --HHHhc
Confidence              99865
>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
>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
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Back     alignment and structure
>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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 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
>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
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {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
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>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
>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
>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
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, 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
>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
>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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} 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
>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
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Back     alignment and structure
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {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
>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
>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
>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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>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
>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

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 232
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 4e-16
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 7e-16
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 8e-16
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 3e-15
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 1e-14
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 2e-14
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-14
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 5e-14
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 6e-14
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 7e-13
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-12
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-10
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93 Back     information, alignment and structure

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

 Score = 69.2 bits (169), Expect = 4e-16
 Identities = 31/79 (39%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 97  KRLRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEK 156
           KR  +K  D N PKR  +A+  F ++ R   +  +PD      V K+ GEKWK +T EEK
Sbjct: 9   KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEK 67

Query: 157 KPYLDKAAELKADYSKAME 175
           +PY  KA   K  Y    E
Sbjct: 68  QPYEAKAQADKKRYESEKE 86
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80 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
>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
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 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
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 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
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query232
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.85
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.84
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.84
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.83
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.82
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.82
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.81
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.8
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.78
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.77
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.71
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.71
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 98.26
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 98.15
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 98.11
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 98.08
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 98.02
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 98.01
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 97.95
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 97.86
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 97.84
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 97.82
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 97.72
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 97.24
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 96.0
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=9.6e-22  Score=145.94  Aligned_cols=82  Identities=38%  Similarity=0.594  Sum_probs=77.8

Q ss_pred             hcccCCCCCCCCCCCCchhhhHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCChhhchHHHHHHHHHHHHHHHHhcCCc
Q 026832           99 LRKKDSDSNKPKRPPTAFFLFMDDFRKEYKEAHPDSKGVTGVAKEAGEKWKNMTDEEKKPYLDKAAELKADYSKAMEGNG  178 (232)
Q Consensus        99 ~kK~~kdp~~PKrP~sAy~lF~~e~R~~~k~~~P~~~~~~eisK~lge~Wk~Ls~eeK~~Y~~~A~~~k~~Y~ke~~~~~  178 (232)
                      .++..++|++||||+||||||+.++|..|+.+||++ ++.+|++.||++|++||+++|.+|.+.|..++.+|..+|.   
T Consensus        11 ~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~-~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~---   86 (93)
T d1lwma_          11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKE---   86 (93)
T ss_dssp             CCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHH---
T ss_pred             cccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCC-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            345778999999999999999999999999999999 9999999999999999999999999999999999999999   


Q ss_pred             cchhhc
Q 026832          179 DYNEVE  184 (232)
Q Consensus       179 ~y~~~~  184 (232)
                      .|+++.
T Consensus        87 ~y~~~l   92 (93)
T d1lwma_          87 LYNATL   92 (93)
T ss_dssp             HHHHHH
T ss_pred             HHHhcc
Confidence            998764
>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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 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
>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
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} 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