Psyllid ID: psy6707

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-------
MDKSVILSSLKLASESQQKQQMEIHRFHQEQFKRQQEHLLQQQHKIQELQVFNYSSLSSSAGKMSMSSPGKEKTPEYNMHGMYSPHHDKNMYSPHDKNMYSPHDKNMYSPHHDKSEEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMRQLWCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSPGSPGSMDSHDED
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccc
ccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHcccccccccccccccEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHcHHHHHHHHHHcccccHHHHHHcHHHccccHHHHHHHHHHHHHHccccccccccccEEEEcccEEEcHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccc
MDKSVILSSLKLASESQQKQQMEIHRFHQEQFKRQQEHLLQQQHKIQElqvfnysslsssagkmsmsspgkektpeynmhgmysphhdknmysphdknmysphdknmysphhdkseeQDLLMSVWgaggespykmpeetpdkgARWKAMSNAEKQPYYEEQSRLSKlhmekhpdyryrprpkrtcivdgkkmrISEYKTLMRQRRNEMRQLwcrgeagpsgsggpafpfpgdgslspsdmmpfspgspgsmdshded
MDKSVILSSLKLASESQQKQQMEIHRFHQEQFKRQQEHLLQQQHKIQELQVFNYSSLSSSAGKMSMSSPGKEKTPEYNMHGMYSPHHDKNMYSPHDKNMYSPHDKNMYSPHHDKSEEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHmekhpdyryrprpkrtcivdgkkmriseykTLMRQRRNEMRQLWCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSpgspgsmdshded
MDKSVILSSLKLASESQQKQQMEIHRFHQEQFKRQQEHLLQQQHKIQELQVFNYsslsssagkmsmssPGKEKTPEYNMHGMYSPHHDKNMYSPHDKNMYSPHDKNMYSPHHDKSEEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMRQLWCRGEagpsgsggpafpfpgDGSLSPSDMMPFSPGSPGSMDSHDED
***************************************************************************************************************************************************************************************TCIVDGKKMRISEY*************LWC********************************************
*****IL******************************************************************************************************************MSVWGAG****************RWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRY********************************************************************************
********SLKL***********IHRFHQEQFKRQQEHLLQQQHKIQELQVFNYSSL***************KTPEYNMHGMYSPHHDKNMYSPHDKNMYSPHDKNMYSPHHDKSEEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMRQLWCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSP************
************ASESQQKQQMEIHRFHQEQFKRQQEHLLQQQHKIQEL****************************************************************KSEEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMRQLWCRGEAGPSGSGGPA*******SL*P********************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MDKSVILSSLKLASESQQKQQMEIHRFHQEQFKRQQEHLLQQQHKIQELQVFNYSSLSSSAGKMSMSSPGKEKTPEYNMHGMYSPHHDKNMYSPHDKNMYSPHDKNMYSPHHDKSEEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMRQLWCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSPGSPGSMDSHDED
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 ?
Query257 2.2.26 [Sep-21-2011]
B1H349777 Transcription factor Sox- yes N/A 0.287 0.095 0.743 2e-29
P35711763 Transcription factor SOX- yes N/A 0.334 0.112 0.636 3e-29
P35710763 Transcription factor SOX- yes N/A 0.334 0.112 0.636 3e-29
Q5RCU4787 Transcription factor SOX- no N/A 0.287 0.094 0.729 5e-29
P35712828 Transcription factor SOX- no N/A 0.287 0.089 0.729 5e-29
P40645827 Transcription factor SOX- no N/A 0.287 0.089 0.729 6e-29
Q28EW4566 Transcription factor Sox- no N/A 0.315 0.143 0.604 1e-25
P40649567 Transcription factor Sox- N/A N/A 0.373 0.169 0.556 1e-25
B3DM43753 Transcription factor Sox- no N/A 0.252 0.086 0.738 3e-25
P40647757 Transcription factor Sox- N/A N/A 0.245 0.083 0.746 6e-25
>sp|B1H349|SOX6_XENTR Transcription factor Sox-6 OS=Xenopus tropicalis GN=sox6 PE=2 SV=1 Back     alignment and function desciption
 Score =  129 bits (325), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 55/74 (74%), Positives = 66/74 (89%)

Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMR 202
           G+RWKAMSN EKQPYYEEQ+RLSK+H+EK+P+Y+Y+PRPKRTCIVDGKK+RI EYK LMR
Sbjct: 605 GSRWKAMSNQEKQPYYEEQARLSKIHLEKYPNYKYKPRPKRTCIVDGKKLRIGEYKQLMR 664

Query: 203 QRRNEMRQLWCRGE 216
            RR EMRQ +  G+
Sbjct: 665 SRRQEMRQFFTVGQ 678
Transcriptional activator. Binds specifically to the DNA sequence 5'-AACAAT-3'. Plays a key role in several developmental processes, including neurogenesis and skeleton formation.
Xenopus tropicalis (taxid: 8364)
>sp|P35711|SOX5_HUMAN Transcription factor SOX-5 OS=Homo sapiens GN=SOX5 PE=1 SV=3 Back     alignment and function description
>sp|P35710|SOX5_MOUSE Transcription factor SOX-5 OS=Mus musculus GN=Sox5 PE=1 SV=2 Back     alignment and function description
>sp|Q5RCU4|SOX6_PONAB Transcription factor SOX-6 OS=Pongo abelii GN=SOX6 PE=2 SV=1 Back     alignment and function description
>sp|P35712|SOX6_HUMAN Transcription factor SOX-6 OS=Homo sapiens GN=SOX6 PE=1 SV=3 Back     alignment and function description
>sp|P40645|SOX6_MOUSE Transcription factor SOX-6 OS=Mus musculus GN=Sox6 PE=1 SV=2 Back     alignment and function description
>sp|Q28EW4|SOX13_XENTR Transcription factor Sox-13 OS=Xenopus tropicalis GN=sox13 PE=2 SV=1 Back     alignment and function description
>sp|P40649|SOX13_XENLA Transcription factor Sox-13 OS=Xenopus laevis GN=sox13 PE=2 SV=3 Back     alignment and function description
>sp|B3DM43|SOX5_XENTR Transcription factor Sox-5 OS=Xenopus tropicalis GN=sox5 PE=2 SV=1 Back     alignment and function description
>sp|P40647|SOX5_XENLA Transcription factor Sox-5 OS=Xenopus laevis GN=sox5 PE=2 SV=2 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 ?
Query257
328698811 965 PREDICTED: hypothetical protein LOC10016 0.447 0.119 0.738 2e-43
350417222 848 PREDICTED: hypothetical protein LOC10074 0.439 0.133 0.593 3e-39
340715248 844 PREDICTED: hypothetical protein LOC10065 0.439 0.133 0.593 3e-39
307174178 523 Transcription factor SOX-5 [Camponotus f 0.443 0.217 0.586 3e-39
380019991 522 PREDICTED: uncharacterized protein LOC10 0.431 0.212 0.589 5e-39
328785651 522 PREDICTED: hypothetical protein LOC40888 0.431 0.212 0.589 5e-39
322794627 513 hypothetical protein SINV_12661 [Solenop 0.431 0.216 0.578 4e-38
345496351 655 PREDICTED: hypothetical protein LOC10011 0.420 0.164 0.594 4e-38
332025343 524 Transcription factor SOX-6 [Acromyrmex e 0.435 0.213 0.569 2e-37
263359663 690 hypothetical protein DVIR88_6g0036 [Dros 0.357 0.133 0.804 9e-37
>gi|328698811|ref|XP_001951971.2| PREDICTED: hypothetical protein LOC100168120 [Acyrthosiphon pisum] Back     alignment and taxonomy information
 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 99/134 (73%), Positives = 104/134 (77%), Gaps = 19/134 (14%)

Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMR 202
           G RWKAMSNA+KQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMR
Sbjct: 832 GGRWKAMSNADKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMR 891

Query: 203 QRRNEMRQLWCRG-EAGPSGSG----------GPAFPFPGDGSLSPSDM--MPFSPG--- 246
           QRRNEMRQLW RG E+GPSGSG          G +F FP DGS+SP  M  M  SP    
Sbjct: 892 QRRNEMRQLWYRGEESGPSGSGLDGVAEPDVAGTSFRFPADGSVSPIVMYSMANSPANSQ 951

Query: 247 --SPG-SMDSHDED 257
             SP  S+DSHDED
Sbjct: 952 ANSPSFSVDSHDED 965

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|350417222|ref|XP_003491316.1| PREDICTED: hypothetical protein LOC100741472 [Bombus impatiens] Back     alignment and taxonomy information
>gi|340715248|ref|XP_003396129.1| PREDICTED: hypothetical protein LOC100650599 [Bombus terrestris] Back     alignment and taxonomy information
>gi|307174178|gb|EFN64823.1| Transcription factor SOX-5 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|380019991|ref|XP_003693882.1| PREDICTED: uncharacterized protein LOC100863610 [Apis florea] Back     alignment and taxonomy information
>gi|328785651|ref|XP_392414.4| PREDICTED: hypothetical protein LOC408884 [Apis mellifera] Back     alignment and taxonomy information
>gi|322794627|gb|EFZ17635.1| hypothetical protein SINV_12661 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|345496351|ref|XP_001603143.2| PREDICTED: hypothetical protein LOC100119354 [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|332025343|gb|EGI65511.1| Transcription factor SOX-6 [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|263359663|gb|ACY70499.1| hypothetical protein DVIR88_6g0036 [Drosophila virilis] 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 ?
Query257
FB|FBgn0039938618 Sox102F "Sox102F" [Drosophila 0.280 0.116 0.930 7.5e-36
ZFIN|ZDB-GENE-081120-6785 sox6 "SRY-box containing gene 0.287 0.094 0.702 1.3e-35
UNIPROTKB|F1NAU5783 SOX6 "Uncharacterized protein" 0.287 0.094 0.729 1.7e-35
RGD|1309000787 Sox6 "SRY (sex determining reg 0.287 0.094 0.729 1.7e-35
UNIPROTKB|F1MAJ5789 Sox6 "Protein Sox6" [Rattus no 0.287 0.093 0.729 1.7e-35
UNIPROTKB|F6UQM4793 SOX6 "Uncharacterized protein" 0.287 0.093 0.729 1.8e-35
MGI|MGI:98368827 Sox6 "SRY-box containing gene 0.287 0.089 0.729 2.1e-35
UNIPROTKB|P35712828 SOX6 "Transcription factor SOX 0.287 0.089 0.729 2.1e-35
UNIPROTKB|E2QTS7829 SOX6 "Uncharacterized protein" 0.287 0.089 0.729 2.1e-35
UNIPROTKB|E1BE01841 SOX6 "Uncharacterized protein" 0.287 0.087 0.729 2.3e-35
FB|FBgn0039938 Sox102F "Sox102F" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 371 (135.7 bits), Expect = 7.5e-36, Sum P(2) = 7.5e-36
 Identities = 67/72 (93%), Positives = 69/72 (95%)

Query:   143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMR 202
             GARWKAMSNA+KQPYYEEQSRLSKLHME+HPDYRYRPRPKRTCIVDGKKMRISEYK LMR
Sbjct:   458 GARWKAMSNADKQPYYEEQSRLSKLHMEQHPDYRYRPRPKRTCIVDGKKMRISEYKVLMR 517

Query:   203 QRRNEMRQLWCR 214
              RR EMRQLWCR
Sbjct:   518 NRRAEMRQLWCR 529
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISS
ZFIN|ZDB-GENE-081120-6 sox6 "SRY-box containing gene 6" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1NAU5 SOX6 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
RGD|1309000 Sox6 "SRY (sex determining region Y)-box 6" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1MAJ5 Sox6 "Protein Sox6" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F6UQM4 SOX6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:98368 Sox6 "SRY-box containing gene 6" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|P35712 SOX6 "Transcription factor SOX-6" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2QTS7 SOX6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|E1BE01 SOX6 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query257
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 3e-12
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 2e-04
smart0039870 smart00398, HMG, high mobility group 8e-04
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 0.001
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information 
 Score = 60.0 bits (146), Expect = 3e-12
 Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 9/54 (16%)

Query: 134 KMPEETPDK---------GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYR 178
           K+ +E P K         G RWKA+SN EKQPYYEE  +L +LHM+ +PDY++R
Sbjct: 19  KVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKWR 72

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif. Length = 72
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box Back     alignment and domain information
>gnl|CDD|197700 smart00398, HMG, high mobility group Back     alignment and domain information
>gnl|CDD|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 257
KOG0528|consensus511 100.0
KOG0527|consensus 331 99.95
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.86
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.79
PTZ0019994 high mobility group protein; Provisional 99.61
smart0039870 HMG high mobility group. 99.51
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.5
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.42
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.42
KOG3248|consensus421 99.41
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.29
KOG0381|consensus96 99.24
COG5648211 NHP6B Chromatin-associated proteins containing the 99.24
KOG0526|consensus615 99.23
KOG2746|consensus 683 98.58
COG5648211 NHP6B Chromatin-associated proteins containing the 97.68
KOG4715|consensus 410 97.52
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 92.67
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 91.68
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 91.21
>KOG0528|consensus Back     alignment and domain information 
Probab=100.00  E-value=2.5e-37  Score=298.69  Aligned_cols=131  Identities=51%  Similarity=0.824  Sum_probs=118.2

Q ss_pred             CCCCCCCCCCCCCccchhhhcccCCCC-------CCCCCccHHHhhhhccCChhhhhhhHHHHHHHHHHHHHhCCCCccc
Q psy6707         106 NMYSPHHDKSEEQDLLMSVWGAGGESP-------YKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYR  178 (257)
Q Consensus       106 ~~kdP~~pKRP~nAnaFmlF~~e~R~~-------l~n~eISKiLGe~Wk~LS~eeK~pY~e~A~~lKe~H~k~yPdYKY~  178 (257)
                      +...+.||||||||  ||+|.++.|++       ++|.+||||||.+|+.||..||+||+++.++|...|.++||||||+
T Consensus       319 ~~ss~PHIKRPMNA--FMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYk  396 (511)
T KOG0528|consen  319 RASSEPHIKRPMNA--FMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYK  396 (511)
T ss_pred             cCCCCccccCCcch--hhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccC
Confidence            45677899999999  99999999975       7899999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCcccchhhHHHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCCC---CCCCCcc
Q psy6707         179 PRPKRTCIVDGKKMRISEYKTLMRQRRNEMRQLWCRGEAGPSGSGGPAFPFPG---DGSLSPS  238 (257)
Q Consensus       179 Prrk~k~~~~gkk~~~s~y~~l~~~rr~E~r~~w~~~~~~~s~~~~~s~~~~~---~gs~s~~  238 (257)
                      ||.||||+++|||+++++|+.+|+.||+|||++||.+..+....+.+.+++|+   +|..+++
T Consensus       397 PRPKRTCvvdGKklRigEYK~lMr~rrqemrq~~~i~~q~q~~~s~a~v~~~ga~~a~~~s~~  459 (511)
T KOG0528|consen  397 PRPKRTCVVDGKKLRIGEYKALMRNRRQEMRQFFDIGSQAQIPISLAGVVYPGAAMAGMPSPH  459 (511)
T ss_pred             CCCCceeeecCceeehHHHHHHHHhHHHHhhcccccCCccCccccccccccccccccCCCCcc
Confidence            99999999999999999999999999999999999998776555566667775   3444443

>KOG0527|consensus 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
>PTZ00199 high mobility group protein; Provisional 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
>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
>KOG3248|consensus 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
>KOG0381|consensus Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>KOG0526|consensus Back     alignment and domain information
>KOG2746|consensus Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>KOG4715|consensus 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
>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
>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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query257
1i11_A81 Solution Structure Of The Dna Binding Domain, Sox-5 1e-14
1o4x_B88 Ternary Complex Of The Dna Binding Domains Of The O 1e-08
2le4_A81 Solution Structure Of The Hmg Box Dna-Binding Domai 2e-08
1gt0_D80 Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le 2e-08
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 1e-06
1j47_A85 3d Solution Nmr Structure Of The M9i Mutant Of The 6e-06
1j46_A85 3d Solution Nmr Structure Of The Wild Type Hmg-Box 6e-06
3u2b_C79 Structure Of The Sox4 Hmg Domain Bound To Dna Lengt 2e-05
1hrz_A76 The 3d Structure Of The Human Sry-Dna Complex Solve 2e-05
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 2e-04
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 2e-04
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 3e-04
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 5e-04
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg Box From Mouse Length = 81 Back     alignment and structure 
Iteration: 1

 Score = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 40/42 (95%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRT 184
           G+RWKAM+N EKQPYYEEQ+RLSK H+EK+PDY+Y+PRPKRT
Sbjct: 40  GSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKPRPKRT 81
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And Sox2 Transcription Factors With A 19mer Oligonucleotide From The Hoxb1 Regulatory Element Length = 88 Back     alignment and structure
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of Human Stem Cell Transcription Factor Sox2 Length = 81 Back     alignment and structure
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80 Back     alignment and structure
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 Back     alignment and structure
>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85 Back     alignment and structure
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85 Back     alignment and structure
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna Length = 79 Back     alignment and structure
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr Length = 76 Back     alignment and structure
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159 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|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription Factor Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS AT 2.77 A RESOLUTION Length = 106 Back     alignment and structure
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17 Length = 71 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 ?
Query257
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 7e-16
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 1e-14
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 2e-14
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 3e-14
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 6e-14
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 1e-13
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 1e-13
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 3e-13
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 4e-13
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 2e-10
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 2e-09
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 5e-07
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 6e-09
1wgf_A90 Upstream binding factor 1; transcription factor, D 2e-06
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 8e-06
1hme_A77 High mobility group protein fragment-B; DNA-bindin 9e-06
2lhj_A97 High mobility group protein homolog NHP1; structur 5e-05
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 4e-04
>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
 Score = 69.5 bits (171), Expect = 7e-16
 Identities = 33/42 (78%), Positives = 40/42 (95%)

Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRT 184
           G+RWKAM+N EKQPYYEEQ+RLSK H+EK+PDY+Y+PRPKRT
Sbjct: 40  GSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKPRPKRT 81
>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
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79 Back     alignment and structure
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Length = 85 Back     alignment and structure
>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
>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
>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
>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
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Length = 76 Back     alignment and structure
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71 Back     alignment and structure
>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
>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
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92 Back     alignment and structure
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Length = 77 Back     alignment and structure
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query257
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.89
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.88
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.88
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.88
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.88
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.88
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.87
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.86
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.86
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.85
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.85
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.84
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.84
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.81
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.79
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.79
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.79
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.77
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.77
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.76
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.75
2lhj_A97 High mobility group protein homolog NHP1; structur 99.75
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.75
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.75
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.73
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.73
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.72
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.69
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.69
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.66
1ckt_A71 High mobility group 1 protein; high-mobility group 99.65
2cto_A93 Novel protein; high mobility group box domain, hel 99.65
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.64
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.62
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.61
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.57
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.56
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.53
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.5
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 94.45
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 91.72
1ckt_A71 High mobility group 1 protein; high-mobility group 91.02
1wgf_A90 Upstream binding factor 1; transcription factor, D 89.44
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 86.23
2lhj_A97 High mobility group protein homolog NHP1; structur 85.48
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 84.97
>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
Probab=99.89  E-value=5.3e-25  Score=164.63  Aligned_cols=73  Identities=51%  Similarity=0.843  Sum_probs=60.2

Q ss_pred             CCCCCCCCCccchhhhcccCCC-------CCCCCCccHHHhhhhccCChhhhhhhHHHHHHHHHHHHHhCCCCcccCCCC
Q psy6707         110 PHHDKSEEQDLLMSVWGAGGES-------PYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPK  182 (257)
Q Consensus       110 P~~pKRP~nAnaFmlF~~e~R~-------~l~n~eISKiLGe~Wk~LS~eeK~pY~e~A~~lKe~H~k~yPdYKY~Prrk  182 (257)
                      +++||||+||  ||||++++|.       .++++|||++||++|+.||+++|++|.++|++++++|.++||+|+|+|+++
T Consensus         2 ~~~pkRP~na--f~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~pr~~   79 (81)
T 1i11_A            2 SPHIKRPMNA--FMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKPRPK   79 (81)
T ss_dssp             -CCSCCSCCH--HHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC-------
T ss_pred             cCCCCCCCCH--HHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeccCCC
Confidence            5899999999  9999999985       277899999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy6707         183 RT  184 (257)
Q Consensus       183 ~k  184 (257)
                      +|
T Consensus        80 ~~   81 (81)
T 1i11_A           80 RT   81 (81)
T ss_dssp             --
T ss_pred             CC
Confidence            75
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; 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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; 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
>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
>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
>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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {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
>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
>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
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} 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
>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
>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
>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
>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

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 257
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 1e-08
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 4e-08
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 4e-08
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 2e-07
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 2e-06
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-04
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 9e-04
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 0.001
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 0.003
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80 Back     information, alignment and structure

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

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 23/41 (56%), Positives = 30/41 (73%)

Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
           GA WK +S  EK+P+ +E  RL  LHM++HPDY+YRPR K 
Sbjct: 38  GAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKT 78
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 Back     information, alignment and structure
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 Back     information, alignment and structure
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 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 ?
Query257
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.86
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.85
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.84
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.79
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.66
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.64
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.62
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.58
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.57
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.52
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.5
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.5
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 83.34
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=1.5e-23  Score=156.97  Aligned_cols=72  Identities=39%  Similarity=0.736  Sum_probs=67.4

Q ss_pred             CCCCCCCCccchhhhcccCCCC-------CCCCCccHHHhhhhccCChhhhhhhHHHHHHHHHHHHHhCCCCcccCCCCC
Q psy6707         111 HHDKSEEQDLLMSVWGAGGESP-------YKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR  183 (257)
Q Consensus       111 ~~pKRP~nAnaFmlF~~e~R~~-------l~n~eISKiLGe~Wk~LS~eeK~pY~e~A~~lKe~H~k~yPdYKY~Prrk~  183 (257)
                      |+||||+||  ||||++++|..       ++++|||++||++|++|++++|++|.++|+.++++|.++||+|+|+|+++.
T Consensus         1 ~kiKRP~nA--y~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p~rk~   78 (80)
T d1gt0d_           1 DRVKRPMNA--FMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKT   78 (80)
T ss_dssp             CCCCCCCCH--HHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCCCC
T ss_pred             CCCCCCCcH--HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCCCCCC
Confidence            689999999  99999999952       678999999999999999999999999999999999999999999998765


Q ss_pred             C
Q psy6707         184 T  184 (257)
Q Consensus       184 k  184 (257)
                      +
T Consensus        79 k   79 (80)
T d1gt0d_          79 K   79 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>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
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} 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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure