Psyllid ID: psy3437

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--
MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSINSLKKGQLNEQSLQIRRGIRE
cccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHccccc
ccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccccccEEcccccHHHHHccHHccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHccccccccccccc
MNAFMVWAQAARRTLAnqypslhnaELSKTLGVLWKTLKVETHyhhvmspfedtytklsdsdkkpFIEEAERLRQIHksehpnykyqprrrkcsknlgtsannlskstssinslkkgqlneQSLQIRRGIRE
MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHhvmspfedtytklsDSDKKPFIEEAERLrqihksehpnykyqprrrkcsknlgtsannlskstssinslkkgqlneqslqirrgire
MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSINSLKKGQLNEQSLQIRRGIRE
***FMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTY*****************************************************************************
MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDT*****DSDKKPFIEEAERLRQIHKSEHPNYK***********************************************
MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSINSLKKGQLNEQSLQIRRGIRE
*NAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPR*******************************************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSKNLGTSANNLSKSTSSINSLKKGQLNEQSLQIRRGIRE
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 ?
Query132 2.2.26 [Sep-21-2011]
A5A763 469 Transcription factor SOX- yes N/A 0.568 0.159 0.621 6e-27
P56693 466 Transcription factor SOX- yes N/A 0.568 0.160 0.621 7e-27
Q04888 466 Transcription factor SOX- yes N/A 0.568 0.160 0.621 7e-27
Q9W757 461 Transcription factor SOX- yes N/A 0.568 0.162 0.621 7e-27
O55170 466 Transcription factor SOX- yes N/A 0.568 0.160 0.621 8e-27
Q04887 507 Transcription factor SOX- no N/A 0.666 0.173 0.555 9e-27
Q9BG91 509 Transcription factor SOX- no N/A 0.666 0.172 0.555 1e-26
Q8AXX8 446 Transcription factor Sox- N/A N/A 0.719 0.213 0.521 1e-26
O18896 509 Transcription factor SOX- no N/A 0.666 0.172 0.555 1e-26
P61754 509 Transcription factor SOX- N/A N/A 0.666 0.172 0.555 1e-26
>sp|A5A763|SOX10_PIG Transcription factor SOX-10 OS=Sus scrofa GN=SOX10 PE=2 SV=1 Back     alignment and function desciption
 Score =  119 bits (297), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 59/95 (62%), Positives = 66/95 (69%), Gaps = 20/95 (21%)

Query: 1   MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
           MNAFMVWAQAARR LA+QYP LHNAELSKTLG LW+                     L++
Sbjct: 111 MNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRL--------------------LNE 150

Query: 61  SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKCSK 95
           SDK+PFIEEAERLR  HK +HP+YKYQPRRRK  K
Sbjct: 151 SDKRPFIEEAERLRMQHKKDHPDYKYQPRRRKNGK 185
Transcription factor that seems to function synergistically with the POU domain protein TST-1/OCT6/SCIP. Could confer cell specificity to the function of other transcription factors in developing and mature glia.
Sus scrofa (taxid: 9823)
>sp|P56693|SOX10_HUMAN Transcription factor SOX-10 OS=Homo sapiens GN=SOX10 PE=1 SV=1 Back     alignment and function description
>sp|Q04888|SOX10_MOUSE Transcription factor SOX-10 OS=Mus musculus GN=Sox10 PE=2 SV=2 Back     alignment and function description
>sp|Q9W757|SOX10_CHICK Transcription factor SOX-10 OS=Gallus gallus GN=SOX10 PE=2 SV=2 Back     alignment and function description
>sp|O55170|SOX10_RAT Transcription factor SOX-10 OS=Rattus norvegicus GN=Sox10 PE=1 SV=1 Back     alignment and function description
>sp|Q04887|SOX9_MOUSE Transcription factor SOX-9 OS=Mus musculus GN=Sox9 PE=2 SV=2 Back     alignment and function description
>sp|Q9BG91|SOX9_CALJA Transcription factor SOX-9 OS=Callithrix jacchus GN=SOX9 PE=2 SV=1 Back     alignment and function description
>sp|Q8AXX8|SOX10_XENLA Transcription factor Sox-10 OS=Xenopus laevis GN=sox10 PE=1 SV=1 Back     alignment and function description
>sp|O18896|SOX9_PIG Transcription factor SOX-9 OS=Sus scrofa GN=SOX9 PE=2 SV=1 Back     alignment and function description
>sp|P61754|SOX9_PONPY Transcription factor SOX-9 OS=Pongo pygmaeus GN=SOX9 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 ?
Query132
350420702 431 PREDICTED: transcription factor SOX-9-li 0.727 0.222 0.583 4e-27
340724034 431 PREDICTED: transcription factor SOX-9-li 0.727 0.222 0.583 4e-27
307166149 373 Transcription factor SOX-8 [Camponotus f 0.795 0.281 0.538 8e-27
380022084 452 PREDICTED: uncharacterized protein LOC10 0.795 0.232 0.542 8e-27
332019145 431 Transcription factor Sox-10 [Acromyrmex 0.780 0.238 0.537 9e-27
110763018 458 PREDICTED: hypothetical protein LOC72728 0.674 0.194 0.598 2e-26
383854786 423 PREDICTED: transcription factor Sox-9-B- 0.795 0.248 0.514 3e-26
194032520 408 SoxE1 [Acropora millepora] 0.734 0.237 0.555 4e-26
156375336 398 predicted protein [Nematostella vectensi 0.734 0.243 0.555 5e-26
300296645 458 Sox9b [Clarias gariepinus] 0.575 0.165 0.604 2e-25
>gi|350420702|ref|XP_003492595.1| PREDICTED: transcription factor SOX-9-like [Bombus impatiens] Back     alignment and taxonomy information
 Score =  126 bits (316), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 70/120 (58%), Positives = 80/120 (66%), Gaps = 24/120 (20%)

Query: 1   MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
           MNAFMVWAQAARR LA+QYP LHNAELSKTLG LW+                     LSD
Sbjct: 94  MNAFMVWAQAARRILADQYPQLHNAELSKTLGKLWRL--------------------LSD 133

Query: 61  SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK---CSKNLGTSANNLSKSTSSIN-SLKK 116
           SDKKPFIEEA+RLR IHK EHP+YKYQPRRRK    S   G+ + N S  T +++ SLK+
Sbjct: 134 SDKKPFIEEADRLRVIHKREHPDYKYQPRRRKQNGPSGREGSPSRNQSNVTFNVSRSLKQ 193

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|340724034|ref|XP_003400390.1| PREDICTED: transcription factor SOX-9-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|307166149|gb|EFN60398.1| Transcription factor SOX-8 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|380022084|ref|XP_003694885.1| PREDICTED: uncharacterized protein LOC100865918 [Apis florea] Back     alignment and taxonomy information
>gi|332019145|gb|EGI59657.1| Transcription factor Sox-10 [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|110763018|ref|XP_001122993.1| PREDICTED: hypothetical protein LOC727284 [Apis mellifera] Back     alignment and taxonomy information
>gi|383854786|ref|XP_003702901.1| PREDICTED: transcription factor Sox-9-B-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|194032520|gb|ACF33142.1| SoxE1 [Acropora millepora] Back     alignment and taxonomy information
>gi|156375336|ref|XP_001630037.1| predicted protein [Nematostella vectensis] gi|156217050|gb|EDO37974.1| predicted protein [Nematostella vectensis] Back     alignment and taxonomy information
>gi|300296645|gb|ADJ96869.1| Sox9b [Clarias gariepinus] 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 ?
Query132
UNIPROTKB|A6PVD3213 SOX10 "Transcription factor SO 0.287 0.178 0.842 2.2e-27
UNIPROTKB|Q6VVD7 459 sox8 "Transcription factor Sox 0.287 0.082 0.842 3.7e-27
UNIPROTKB|Q7YRJ7 513 SOX9 "Transcription factor SOX 0.287 0.074 0.842 1.8e-26
MGI|MGI:98371 507 Sox9 "SRY-box containing gene 0.287 0.074 0.842 2.7e-26
UNIPROTKB|P48436 509 SOX9 "Transcription factor SOX 0.287 0.074 0.842 2.8e-26
UNIPROTKB|O18896 509 SOX9 "Transcription factor SOX 0.287 0.074 0.842 2.8e-26
UNIPROTKB|P61753 509 SOX9 "Transcription factor SOX 0.287 0.074 0.842 2.8e-26
UNIPROTKB|P61754 509 SOX9 "Transcription factor SOX 0.287 0.074 0.842 2.8e-26
UNIPROTKB|Q9BG91 509 SOX9 "Transcription factor SOX 0.287 0.074 0.842 2.8e-26
UNIPROTKB|F1RV30 511 SOX9 "Transcription factor SOX 0.287 0.074 0.842 2.8e-26
UNIPROTKB|A6PVD3 SOX10 "Transcription factor SOX-10" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
 Score = 167 (63.8 bits), Expect = 2.2e-27, Sum P(2) = 2.2e-27
 Identities = 32/38 (84%), Positives = 34/38 (89%)

Query:     1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTL 38
             MNAFMVWAQAARR LA+QYP LHNAELSKTLG LW+ L
Sbjct:   108 MNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLL 145
GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=IEA
GO:0000980 "RNA polymerase II distal enhancer sequence-specific DNA binding" evidence=IEA
GO:0001701 "in utero embryonic development" evidence=IEA
GO:0001755 "neural crest cell migration" evidence=IEA
GO:0002052 "positive regulation of neuroblast proliferation" evidence=IEA
GO:0003682 "chromatin binding" evidence=IEA
GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IEA
GO:0005634 "nucleus" evidence=IEA
GO:0007422 "peripheral nervous system development" evidence=IEA
GO:0008134 "transcription factor binding" evidence=IEA
GO:0014015 "positive regulation of gliogenesis" evidence=IEA
GO:0030318 "melanocyte differentiation" evidence=IEA
GO:0031315 "extrinsic to mitochondrial outer membrane" evidence=IEA
GO:0043066 "negative regulation of apoptotic process" evidence=IEA
GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA
GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA
GO:0048469 "cell maturation" evidence=IEA
GO:0048484 "enteric nervous system development" evidence=IEA
GO:0048546 "digestive tract morphogenesis" evidence=IEA
GO:0048589 "developmental growth" evidence=IEA
GO:0048709 "oligodendrocyte differentiation" evidence=IEA
GO:0048863 "stem cell differentiation" evidence=IEA
GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA
UNIPROTKB|Q6VVD7 sox8 "Transcription factor Sox-8" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
UNIPROTKB|Q7YRJ7 SOX9 "Transcription factor SOX-9" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:98371 Sox9 "SRY-box containing gene 9" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|P48436 SOX9 "Transcription factor SOX-9" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|O18896 SOX9 "Transcription factor SOX-9" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|P61753 SOX9 "Transcription factor SOX-9" [Macaca mulatta (taxid:9544)] Back     alignment and assigned GO terms
UNIPROTKB|P61754 SOX9 "Transcription factor SOX-9" [Pongo pygmaeus (taxid:9600)] Back     alignment and assigned GO terms
UNIPROTKB|Q9BG91 SOX9 "Transcription factor SOX-9" [Callithrix jacchus (taxid:9483)] Back     alignment and assigned GO terms
UNIPROTKB|F1RV30 SOX9 "Transcription factor SOX-9" [Sus scrofa (taxid:9823)] 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) ?
Q04888SOX10_MOUSENo assigned EC number0.62100.56810.1609yesN/A
O55170SOX10_RATNo assigned EC number0.62100.56810.1609yesN/A
A5A763SOX10_PIGNo assigned EC number0.62100.56810.1599yesN/A
A4IIJ8SOX10_XENTRNo assigned EC number0.52170.71960.2178yesN/A
Q9W757SOX10_CHICKNo assigned EC number0.62100.56810.1626yesN/A
P56693SOX10_HUMANNo assigned EC number0.62100.56810.1609yesN/A

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 ?
Query132
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 6e-17
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 6e-16
smart0039870 smart00398, HMG, high mobility group 2e-11
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 2e-10
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 3e-10
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 4e-07
>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 = 69.6 bits (171), Expect = 6e-17
 Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 20/86 (23%)

Query: 1  MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
          MNAFM++++  RR +  +YP   N  +SK LG  WK                     LS+
Sbjct: 6  MNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWK--------------------ALSN 45

Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKY 86
           +K+P+ EEA++L+++H   +P+YK+
Sbjct: 46 EEKQPYYEEAKKLKELHMKLYPDYKW 71

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|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|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 132
KOG0527|consensus 331 99.94
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.91
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.86
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.7
smart0039870 HMG high mobility group. 99.7
KOG0528|consensus511 99.67
PTZ0019994 high mobility group protein; Provisional 99.66
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.65
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.64
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.43
KOG0381|consensus96 99.4
COG5648211 NHP6B Chromatin-associated proteins containing the 99.23
KOG3248|consensus 421 99.21
KOG0526|consensus615 98.9
KOG4715|consensus 410 98.5
KOG2746|consensus 683 98.44
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 96.95
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 96.44
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 96.34
COG5648211 NHP6B Chromatin-associated proteins containing the 96.12
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 94.84
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 94.77
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 87.11
>KOG0527|consensus Back     alignment and domain information 
Probab=99.94  E-value=4.6e-27  Score=196.67  Aligned_cols=78  Identities=56%  Similarity=0.979  Sum_probs=75.5

Q ss_pred             CchHHHHHHHHHHHHHHhCCCCChHHHHHHHHHhhhhhhhhhccccCCcchhhhcccCChhhchhhHHHHHHHHHHHHhh
Q psy3437           1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSE   80 (132)
Q Consensus         1 lNafilf~~~~r~~i~~~~P~l~~~eIsk~lg~~Wk~~~~~~~~~~~~~~~~~~w~~ls~eeK~py~~~A~~~K~~h~~~   80 (132)
                      |||||||++..|++|.++||+|+|.||||.||..||.                    |+++||.||+++|+++|..|+++
T Consensus        67 MNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~--------------------Lse~EKrPFi~EAeRLR~~Hmke  126 (331)
T KOG0527|consen   67 MNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKL--------------------LSEEEKRPFVDEAERLRAQHMKE  126 (331)
T ss_pred             cchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhh--------------------cCHhhhccHHHHHHHHHHHHHHh
Confidence            8999999999999999999999999999999999999                    99999999999999999999999


Q ss_pred             CCCCCCCCCccccccCCC
Q psy3437          81 HPNYKYQPRRRKCSKNLG   98 (132)
Q Consensus        81 ~p~Yky~p~k~k~~~~~~   98 (132)
                      ||||||+||||++.+...
T Consensus       127 hPdYKYRPRRKkk~~~~~  144 (331)
T KOG0527|consen  127 YPDYKYRPRRKKKKRPKL  144 (331)
T ss_pred             CCCccccccccccccccc
Confidence            999999999998877664

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin Back     alignment and domain information
>smart00398 HMG high mobility group Back     alignment and domain information
>KOG0528|consensus Back     alignment and domain information
>PTZ00199 high mobility group protein; Provisional 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
>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
>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
>KOG3248|consensus Back     alignment and domain information
>KOG0526|consensus Back     alignment and domain information
>KOG4715|consensus Back     alignment and domain information
>KOG2746|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
>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
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [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
>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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query132
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 4e-26
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 3e-20
2le4_A81 Solution Structure Of The Hmg Box Dna-Binding Domai 7e-19
1o4x_B88 Ternary Complex Of The Dna Binding Domains Of The O 7e-19
1gt0_D80 Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le 8e-19
3u2b_C79 Structure Of The Sox4 Hmg Domain Bound To Dna Lengt 9e-19
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 3e-17
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 2e-16
1j46_A85 3d Solution Nmr Structure Of The Wild Type Hmg-Box 6e-14
1j47_A85 3d Solution Nmr Structure Of The M9i Mutant Of The 2e-13
1hrz_A76 The 3d Structure Of The Human Sry-Dna Complex Solve 1e-12
1i11_A81 Solution Structure Of The Dna Binding Domain, Sox-5 4e-12
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 8e-12
1qrv_A73 Crystal Structure Of The Complex Of Hmg-D And Dna L 8e-04
1hma_A73 The Solution Structure And Dynamics Of The Dna Bind 8e-04
1e7j_A74 Hmg-D Complexed To A Bulge Dna Length = 74 9e-04
>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 
Iteration: 1

 Score =  113 bits (282), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 56/93 (60%), Positives = 65/93 (69%), Gaps = 20/93 (21%)
Query: 1   MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
           MNAFMVWAQAARR LA+QYP LHNAELSKTLG LW+                     L++
Sbjct: 34  MNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRL--------------------LNE 73
Query: 61  SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRKC 93
           S+K+PF+EEAERLR  HK +HP+YKYQPRRRK 
Sbjct: 74  SEKRPFVEEAERLRVQHKKDHPDYKYQPRRRKS 106
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 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|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|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80 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|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription Factor Sox-17 Length = 82 Back     alignment and structure
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17 Length = 71 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|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|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|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg Box From Mouse Length = 81 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|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna 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|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna Length = 74 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 ?
Query132
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 1e-31
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 3e-31
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 5e-31
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 6e-31
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 1e-30
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 3e-30
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 5e-30
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 2e-29
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 5e-29
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 2e-27
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 6e-25
1wgf_A90 Upstream binding factor 1; transcription factor, D 3e-21
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 6e-21
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 6e-20
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 7e-18
1hme_A77 High mobility group protein fragment-B; DNA-bindin 2e-16
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 1e-15
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 2e-13
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 6e-13
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 1e-12
2lhj_A97 High mobility group protein homolog NHP1; structur 4e-12
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 5e-11
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 5e-10
2yrq_A173 High mobility group protein B1; HMG box domain, DN 9e-09
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 7e-08
1ckt_A71 High mobility group 1 protein; high-mobility group 9e-08
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 1e-06
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 5e-06
3tq6_A214 Transcription factor A, mitochondrial; transcripti 8e-05
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 8e-05
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 1e-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 =  106 bits (267), Expect = 1e-31
 Identities = 32/92 (34%), Positives = 51/92 (55%), Gaps = 20/92 (21%)

Query: 1  MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
          MNAFMVWA+  RR +   +P +HN+ +SK LG  WK                     +++
Sbjct: 9  MNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWK--------------------AMTN 48

Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
           +K+P+ EE  RL + H  ++P+YKY+PR ++
Sbjct: 49 LEKQPYYEEQARLSKQHLEKYPDYKYKPRPKR 80
>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
>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
>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
>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
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Length = 85 Back     alignment and structure
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Length = 106 Back     alignment and structure
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Length = 76 Back     alignment and structure
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71 Back     alignment and structure
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Length = 87 Back     alignment and structure
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 Back     alignment and structure
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73 Back     alignment and structure
>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
>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97 Back     alignment and structure
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93 Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query132
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.92
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.91
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.91
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.91
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.91
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.9
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.9
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.9
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.88
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.87
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.85
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.84
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.83
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.81
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.8
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.8
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.79
1ckt_A71 High mobility group 1 protein; high-mobility group 99.79
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.77
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.77
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.75
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.75
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.74
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.71
2lhj_A97 High mobility group protein homolog NHP1; structur 99.71
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.69
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.69
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.67
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.65
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.65
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.62
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.61
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.59
2cto_A93 Novel protein; high mobility group box domain, hel 99.59
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.58
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.58
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.57
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.36
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.35
>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=99.92  E-value=3.3e-25  Score=148.88  Aligned_cols=72  Identities=44%  Similarity=0.945  Sum_probs=63.4

Q ss_pred             CchHHHHHHHHHHHHHHhCCCCChHHHHHHHHHhhhhhhhhhccccCCcchhhhcccCChhhchhhHHHHHHHHHHHHhh
Q psy3437           1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSE   80 (132)
Q Consensus         1 lNafilf~~~~r~~i~~~~P~l~~~eIsk~lg~~Wk~~~~~~~~~~~~~~~~~~w~~ls~eeK~py~~~A~~~K~~h~~~   80 (132)
                      ||||||||+++|..|+.+||++++++|+++||.+|+.                    ||+++|++|.++|++++++|.++
T Consensus         9 ~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~--------------------ls~eeK~~y~~~A~~~k~~~~~~   68 (81)
T 1i11_A            9 MNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKA--------------------MTNLEKQPYYEEQARLSKQHLEK   68 (81)
T ss_dssp             CCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTT--------------------SCSGGGHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhh--------------------CCHHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999                    99999999999999999999999


Q ss_pred             CCCCCCCCCccc
Q psy3437          81 HPNYKYQPRRRK   92 (132)
Q Consensus        81 ~p~Yky~p~k~k   92 (132)
                      ||+|+|+|++++
T Consensus        69 ~p~Yky~pr~~~   80 (81)
T 1i11_A           69 YPDYKYKPRPKR   80 (81)
T ss_dssp             CSCC--------
T ss_pred             CCCCeeccCCCC
Confidence            999999998875
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A Back     alignment and structure
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 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
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Back     alignment and structure
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Back     alignment and structure
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 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
>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
>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
>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
>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
>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
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A Back     alignment and structure
>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
>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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Back     alignment and structure
>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
>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

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 132
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 5e-19
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 2e-17
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 3e-16
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 2e-14
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 4e-14
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 3e-12
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 1e-10
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 8e-10
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-09
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-09
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 4e-09
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 5e-08
>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 = 73.3 bits (180), Expect = 5e-19
 Identities = 40/92 (43%), Positives = 57/92 (61%), Gaps = 20/92 (21%)

Query: 1  MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSD 60
          MNAFMVW++  RR +A + P +HN+E+SK LG  WK L                     +
Sbjct: 7  MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS--------------------E 46

Query: 61 SDKKPFIEEAERLRQIHKSEHPNYKYQPRRRK 92
          ++K+PFI+EA+RLR +H  EHP+YKY+PRR+ 
Sbjct: 47 TEKRPFIDEAKRLRALHMKEHPDYKYRPRRKT 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
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 Back     information, alignment and structure
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93 Back     information, alignment and structure
>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101 Back     information, alignment and structure
>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91 Back     information, alignment and structure
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query132
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.91
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.9
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.89
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.87
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.76
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.73
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.7
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.67
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.66
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.65
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.59
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.57
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 88.75
>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=99.91  E-value=1.6e-24  Score=145.25  Aligned_cols=72  Identities=57%  Similarity=1.122  Sum_probs=70.0

Q ss_pred             CchHHHHHHHHHHHHHHhCCCCChHHHHHHHHHhhhhhhhhhccccCCcchhhhcccCChhhchhhHHHHHHHHHHHHhh
Q psy3437           1 MNAFMVWAQAARRTLANQYPSLHNAELSKTLGVLWKTLKVETHYHHVMSPFEDTYTKLSDSDKKPFIEEAERLRQIHKSE   80 (132)
Q Consensus         1 lNafilf~~~~r~~i~~~~P~l~~~eIsk~lg~~Wk~~~~~~~~~~~~~~~~~~w~~ls~eeK~py~~~A~~~K~~h~~~   80 (132)
                      +|||||||+++|..|+.+||++++++||++||.+|+.                    |++++|++|.++|+.++++|.++
T Consensus         7 ~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~--------------------l~~eeK~~y~~~A~~~k~~y~~~   66 (80)
T d1gt0d_           7 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKL--------------------LSETEKRPFIDEAKRLRALHMKE   66 (80)
T ss_dssp             CCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTT--------------------SCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCc--------------------CCHHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999                    99999999999999999999999


Q ss_pred             CCCCCCCCCccc
Q psy3437          81 HPNYKYQPRRRK   92 (132)
Q Consensus        81 ~p~Yky~p~k~k   92 (132)
                      ||+|+|+|+++.
T Consensus        67 ~p~Yk~~p~rk~   78 (80)
T d1gt0d_          67 HPDYKYRPRRKT   78 (80)
T ss_dssp             CTTCCCCCCCCC
T ss_pred             CccccCCCCCCC
Confidence            999999998654
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} 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
>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
>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
>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