Psyllid ID: psy15636

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 (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-
MNSKLGLHSLHLGHHHSEGHIKRPMNALSLHSLHLGHHHSEGHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR
cccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccHHHHHHHcc
ccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcHHHHHHHHHHccccccHHHHHHHHHHHHHccHHccccHHHHHHHcc
mnsklglhslhlghhhseghikrpmnalslhslhlghhhseghikrpmnafMVWSRgqrrkmaldnpkmhnsEISKRLGAEWKLLTEMEKRPFIDEAKRLR
mnsklglhSLHLGHHHSEGHIKRPMNALSLHSLHLGHHHSEGHIKRPMNAFMVWSRGQRRKMAldnpkmhnseiSKRLGAEWKLLtemekrpfideakrlr
MNsklglhslhlghhhseghIKRPMNAlslhslhlghhhseghIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR
********************************LHLG*******I**PMNAFMVW***************************W*******************
***********************************************MNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRL*
MNSKLGLHSLHLGHHHSEGHIKRPMNALSLHSLHLGHHHSEGHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR
******************************************HIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MNSKLGLHSLHLGHHHSEGHIKRPMNALSLHSLHLGHHHSEGHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR
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 ?
Query101 2.2.26 [Sep-21-2011]
Q6EJB7 300 Transcription factor Sox- yes N/A 0.831 0.28 0.678 1e-27
P53784 375 Transcription factor SOX- no N/A 0.574 0.154 0.913 3e-27
Q9W7R6 240 Transcription factor SOX- yes N/A 0.584 0.245 0.915 5e-27
P41225 446 Transcription factor SOX- yes N/A 0.574 0.130 0.913 5e-27
Q04892 240 Transcription factor SOX- no N/A 0.584 0.245 0.915 5e-27
P61259 240 Transcription factor SOX- N/A N/A 0.584 0.245 0.915 6e-27
O95416 240 Transcription factor SOX- no N/A 0.584 0.245 0.915 6e-27
Q24533 382 SOX domain-containing pro no N/A 0.603 0.159 0.901 6e-27
A4QNG3 239 Transcription factor Sox- yes N/A 0.584 0.246 0.915 7e-27
B0ZTE2 239 Transcription factor Sox- N/A N/A 0.584 0.246 0.915 7e-27
>sp|Q6EJB7|SOX3_DANRE Transcription factor Sox-3 OS=Danio rerio GN=sox3 PE=1 SV=1 Back     alignment and function desciption
 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 59/87 (67%), Positives = 69/87 (79%), Gaps = 3/87 (3%)

Query: 18  EGHIKRPMNALSLHSLHLGHHHS---EGHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEI 74
           E  IK P+   +  S+  G ++S   +  +KRPMNAFMVWSRGQRRKMA +NPKMHNSEI
Sbjct: 6   ETEIKSPIPQSNTGSVTGGKNNSANDQDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 65

Query: 75  SKRLGAEWKLLTEMEKRPFIDEAKRLR 101
           SKRLGA+WKLLT+ EKRPFIDEAKRLR
Sbjct: 66  SKRLGADWKLLTDAEKRPFIDEAKRLR 92
Transcriptional activator.
Danio rerio (taxid: 7955)
>sp|P53784|SOX3_MOUSE Transcription factor SOX-3 OS=Mus musculus GN=Sox3 PE=1 SV=2 Back     alignment and function description
>sp|Q9W7R6|SOX14_CHICK Transcription factor SOX-14 OS=Gallus gallus GN=SOX14 PE=2 SV=1 Back     alignment and function description
>sp|P41225|SOX3_HUMAN Transcription factor SOX-3 OS=Homo sapiens GN=SOX3 PE=1 SV=2 Back     alignment and function description
>sp|Q04892|SOX14_MOUSE Transcription factor SOX-14 OS=Mus musculus GN=Sox14 PE=2 SV=2 Back     alignment and function description
>sp|P61259|SOX14_MACFA Transcription factor SOX-14 OS=Macaca fascicularis GN=SOX14 PE=2 SV=1 Back     alignment and function description
>sp|O95416|SOX14_HUMAN Transcription factor SOX-14 OS=Homo sapiens GN=SOX14 PE=2 SV=1 Back     alignment and function description
>sp|Q24533|DICH_DROME SOX domain-containing protein dichaete OS=Drosophila melanogaster GN=D PE=2 SV=1 Back     alignment and function description
>sp|A4QNG3|SOX14_XENTR Transcription factor Sox-14 OS=Xenopus tropicalis GN=sox14 PE=2 SV=1 Back     alignment and function description
>sp|B0ZTE2|SOX14_XENLA Transcription factor Sox-14 OS=Xenopus laevis GN=sox14 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 ?
Query101
194870738 403 GG13735 [Drosophila erecta] gi|190654494 0.653 0.163 0.909 4e-28
195590200 385 GD12630 [Drosophila simulans] gi|1941968 0.643 0.168 0.907 1e-27
442632261 407 Sox21a, isoform B [Drosophila melanogast 0.643 0.159 0.907 1e-27
21357779 388 Sox21a, isoform A [Drosophila melanogast 0.643 0.167 0.907 1e-27
195327516 386 GM24557 [Drosophila sechellia] gi|194119 0.871 0.227 0.755 2e-27
194747994 355 GF25206 [Drosophila ananassae] gi|190623 0.653 0.185 0.893 2e-27
195494275 397 GE20029 [Drosophila yakuba] gi|194180868 0.643 0.163 0.907 2e-27
357607461 222 hypothetical protein KGM_19699 [Danaus p 0.623 0.283 0.920 3e-27
339246705 313 SOX-1 protein [Trichinella spiralis] gi| 0.613 0.198 0.919 6e-27
242007459 264 predicted protein [Pediculus humanus cor 0.584 0.223 0.966 7e-27
>gi|194870738|ref|XP_001972711.1| GG13735 [Drosophila erecta] gi|190654494|gb|EDV51737.1| GG13735 [Drosophila erecta] Back     alignment and taxonomy information
 Score =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 60/66 (90%), Positives = 62/66 (93%)

Query: 36  GHHHSEGHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFID 95
           GHH+S  HIKRPMNAFMVWSRGQRRKMA DNPKMHNSEISKRLGAEWKLLTE +KRPFID
Sbjct: 125 GHHNSHDHIKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLTEGQKRPFID 184

Query: 96  EAKRLR 101
           EAKRLR
Sbjct: 185 EAKRLR 190

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|195590200|ref|XP_002084834.1| GD12630 [Drosophila simulans] gi|194196843|gb|EDX10419.1| GD12630 [Drosophila simulans] Back     alignment and taxonomy information
>gi|442632261|ref|NP_001261827.1| Sox21a, isoform B [Drosophila melanogaster] gi|440215766|gb|AGB94520.1| Sox21a, isoform B [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|21357779|ref|NP_648694.1| Sox21a, isoform A [Drosophila melanogaster] gi|7294410|gb|AAF49756.1| Sox21a, isoform A [Drosophila melanogaster] gi|66571134|gb|AAY51532.1| IP01552p [Drosophila melanogaster] gi|220943374|gb|ACL84230.1| Sox21a-PA [synthetic construct] gi|220953338|gb|ACL89212.1| Sox21a-PA [synthetic construct] Back     alignment and taxonomy information
>gi|195327516|ref|XP_002030464.1| GM24557 [Drosophila sechellia] gi|194119407|gb|EDW41450.1| GM24557 [Drosophila sechellia] Back     alignment and taxonomy information
>gi|194747994|ref|XP_001956434.1| GF25206 [Drosophila ananassae] gi|190623716|gb|EDV39240.1| GF25206 [Drosophila ananassae] Back     alignment and taxonomy information
>gi|195494275|ref|XP_002094767.1| GE20029 [Drosophila yakuba] gi|194180868|gb|EDW94479.1| GE20029 [Drosophila yakuba] Back     alignment and taxonomy information
>gi|357607461|gb|EHJ65502.1| hypothetical protein KGM_19699 [Danaus plexippus] Back     alignment and taxonomy information
>gi|339246705|ref|XP_003374986.1| SOX-1 protein [Trichinella spiralis] gi|316971748|gb|EFV55488.1| SOX-1 protein [Trichinella spiralis] Back     alignment and taxonomy information
>gi|242007459|ref|XP_002424557.1| predicted protein [Pediculus humanus corporis] gi|212508000|gb|EEB11819.1| predicted protein [Pediculus humanus corporis] 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 ?
Query101
FB|FBgn0036411 388 Sox21a "Sox21a" [Drosophila me 0.574 0.149 0.948 2.9e-25
MGI|MGI:98365 375 Sox3 "SRY-box containing gene 0.574 0.154 0.913 2.9e-25
ZFIN|ZDB-GENE-010111-1 293 sox19b "SRY-box containing gen 0.574 0.197 0.913 3.6e-25
UNIPROTKB|E2R800 444 SOX3 "Uncharacterized protein" 0.574 0.130 0.913 4.6e-25
UNIPROTKB|P41225 446 SOX3 "Transcription factor SOX 0.574 0.130 0.913 4.8e-25
UNIPROTKB|I3LG51 448 LOC100623770 "Uncharacterized 0.574 0.129 0.913 5e-25
ZFIN|ZDB-GENE-030909-1 315 sox2 "SRY-box containing gene 0.574 0.184 0.931 5.9e-25
ZFIN|ZDB-GENE-980526-102 314 sox19a "SRY-box containing gen 0.574 0.184 0.913 5.9e-25
UNIPROTKB|P48430 315 SOX2 "Transcription factor SOX 0.574 0.184 0.913 7.6e-25
UNIPROTKB|A2VDX8 320 SOX2 "Uncharacterized protein" 0.574 0.181 0.913 7.6e-25
FB|FBgn0036411 Sox21a "Sox21a" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 287 (106.1 bits), Expect = 2.9e-25, P = 2.9e-25
 Identities = 55/58 (94%), Positives = 56/58 (96%)

Query:    44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
             IKRPMNAFMVWSRGQRRKMA DNPKMHNSEISKRLGAEWKLLTE +KRPFIDEAKRLR
Sbjct:   121 IKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLTEGQKRPFIDEAKRLR 178
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
GO:0006911 "phagocytosis, engulfment" evidence=IMP
MGI|MGI:98365 Sox3 "SRY-box containing gene 3" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-010111-1 sox19b "SRY-box containing gene 19b" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|E2R800 SOX3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P41225 SOX3 "Transcription factor SOX-3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3LG51 LOC100623770 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030909-1 sox2 "SRY-box containing gene 2" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-980526-102 sox19a "SRY-box containing gene 19a" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|P48430 SOX2 "Transcription factor SOX-2" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|A2VDX8 SOX2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P41225SOX3_HUMANNo assigned EC number0.91370.57420.1300yesN/A
Q6EJB7SOX3_DANRENo assigned EC number0.67810.83160.28yesN/A
P61259SOX14_MACFANo assigned EC number0.91520.58410.2458N/AN/A
P53784SOX3_MOUSENo assigned EC number0.91370.57420.1546noN/A
Q6RVD7SX21B_DANRENo assigned EC number0.91520.58410.2408noN/A
O95416SOX14_HUMANNo assigned EC number0.91520.58410.2458noN/A
Q9W7R6SOX14_CHICKNo assigned EC number0.91520.58410.2458yesN/A
Q32PP9SOX14_DANRENo assigned EC number0.91520.58410.2478noN/A
O42569SOX2_XENLANo assigned EC number0.91370.57420.1864N/AN/A
Q04892SOX14_MOUSENo assigned EC number0.91520.58410.2458noN/A
Q811W0SOX21_MOUSENo assigned EC number0.91520.58410.2137noN/A
Q9Y651SOX21_HUMANNo assigned EC number0.91520.58410.2137noN/A
B0ZTE1SOX21_XENLANo assigned EC number0.91520.58410.2251N/AN/A
Q6NVN0SOX2_XENTRNo assigned EC number0.91370.57420.1864noN/A
A4QNG3SOX14_XENTRNo assigned EC number0.91520.58410.2468yesN/A
B0ZTE2SOX14_XENLANo assigned EC number0.91520.58410.2468N/AN/A
P47792SX19A_DANRENo assigned EC number0.91370.57420.1952noN/A
Q24533DICH_DROMENo assigned EC number0.90160.60390.1596noN/A
Q9DDD7SX19B_DANRENo assigned EC number0.91370.57420.1986noN/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 ?
Query101
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 2e-25
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 7e-20
smart0039870 smart00398, HMG, high mobility group 1e-18
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 2e-17
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 1e-14
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 4e-10
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 2e-07
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 5e-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 = 90.1 bits (224), Expect = 2e-25
 Identities = 31/59 (52%), Positives = 42/59 (71%)

Query: 43  HIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
           HIKRPMNAFM++S+  RRK+  + P   N  ISK LG  WK L+  EK+P+ +EAK+L+
Sbjct: 1   HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLK 59

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|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) Back     alignment and domain information
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 101
PTZ0019994 high mobility group protein; Provisional 99.86
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 99.85
KOG0527|consensus 331 99.83
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.82
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.8
smart0039870 HMG high mobility group. 99.79
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.78
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.74
COG5648211 NHP6B Chromatin-associated proteins containing the 99.69
KOG0381|consensus96 99.64
KOG3248|consensus 421 99.53
KOG0528|consensus 511 99.48
KOG0526|consensus615 99.38
KOG4715|consensus 410 99.15
KOG2746|consensus 683 98.97
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 97.99
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 97.84
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 97.49
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 96.89
PF04769 201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 96.71
COG5648211 NHP6B Chromatin-associated proteins containing the 96.71
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 94.73
PF12881328 NUT_N: NUT protein N terminus; InterPro: IPR024309 90.73
PRK15117 211 ABC transporter periplasmic binding protein MlaC; 86.38
TIGR03481 198 HpnM hopanoid biosynthesis associated membrane pro 85.55
KOG3223|consensus221 82.71
PF0135241 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-a 82.11
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information 
Probab=99.86  E-value=2.4e-21  Score=121.09  Aligned_cols=68  Identities=24%  Similarity=0.516  Sum_probs=62.8

Q ss_pred             CCCCCCCCCCCCCCCcHHHHHHHHHHHHHHhhCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q psy15636         34 HLGHHHSEGHIKRPMNAFMVWSRGQRRKMALDNPKMH--NSEISKRLGAEWKLLTEMEKRPFIDEAKRLR  101 (101)
Q Consensus        34 ~~~~~~~~~~pkRP~saf~lf~~~~r~~~~~~~p~~~--~~eisk~~~~~W~~ls~~eK~~y~~~A~~~k  101 (101)
                      .....++++.||||+|||++||.++|..|..+||++.  +.+|+++||++|+.|++++|++|+++|+.+|
T Consensus        13 ~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk   82 (94)
T PTZ00199         13 NKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDK   82 (94)
T ss_pred             cCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            3456678999999999999999999999999999986  8999999999999999999999999998864

>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
>KOG0527|consensus Back     alignment and domain information
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin Back     alignment and domain information
>smart00398 HMG high mobility group Back     alignment and domain information
>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
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>KOG0381|consensus Back     alignment and domain information
>KOG3248|consensus Back     alignment and domain information
>KOG0528|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
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ] Back     alignment and domain information
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta Back     alignment and domain information
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A Back     alignment and domain information
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [] Back     alignment and domain information
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT) Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] 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
>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins Back     alignment and domain information
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional Back     alignment and domain information
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM Back     alignment and domain information
>KOG3223|consensus Back     alignment and domain information
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) [] 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 ?
Query101
2le4_A81 Solution Structure Of The Hmg Box Dna-Binding Domai 5e-26
1gt0_D80 Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le 5e-26
1o4x_B88 Ternary Complex Of The Dna Binding Domains Of The O 6e-26
1hrz_A76 The 3d Structure Of The Human Sry-Dna Complex Solve 2e-19
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 2e-19
1j46_A85 3d Solution Nmr Structure Of The Wild Type Hmg-Box 3e-19
1j47_A85 3d Solution Nmr Structure Of The M9i Mutant Of The 7e-19
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 6e-17
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 1e-16
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 1e-16
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 1e-16
3u2b_C79 Structure Of The Sox4 Hmg Domain Bound To Dna Lengt 2e-16
1i11_A81 Solution Structure Of The Dna Binding Domain, Sox-5 4e-14
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 5e-05
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 3e-04
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 3e-04
2e6o_A87 Solution Structure Of The Hmg Box Domain From Human 5e-04
>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 
Iteration: 1

 Score =  112 bits (280), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/58 (91%), Positives = 56/58 (96%)
Query: 44  IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
           +KRPMNAFMVWSRGQRRKMA +NPKMHNSEISKRLGAEWKLL+E EKRPFIDEAKRLR
Sbjct: 4   VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 61
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80 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|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|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|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|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|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 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|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg Box From Mouse Length = 81 Back     alignment and structure
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High Mobility Group Protein B3 Length = 81 Back     alignment and structure
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93 Back     alignment and structure
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna Length = 93 Back     alignment and structure
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human Hmg-Box Transcription Factor 1 Length = 87 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 ?
Query101
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 3e-31
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 4e-31
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 7e-31
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 1e-30
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 2e-30
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 1e-29
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 1e-29
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 2e-29
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 5e-29
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 5e-29
1wgf_A90 Upstream binding factor 1; transcription factor, D 8e-29
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 2e-28
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 7e-27
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 3e-23
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 3e-24
1hme_A77 High mobility group protein fragment-B; DNA-bindin 2e-22
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 4e-22
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 9e-20
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 6e-19
2lhj_A97 High mobility group protein homolog NHP1; structur 9e-19
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 4e-18
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 6e-18
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 2e-17
2yrq_A173 High mobility group protein B1; HMG box domain, DN 4e-16
2yrq_A173 High mobility group protein B1; HMG box domain, DN 2e-09
1ckt_A71 High mobility group 1 protein; high-mobility group 2e-15
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 3e-15
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 2e-14
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 1e-12
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 3e-12
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 3e-10
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 3e-12
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 5e-11
3tq6_A214 Transcription factor A, mitochondrial; transcripti 8e-09
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 6e-09
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 7e-07
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71 Back     alignment and structure
 Score =  104 bits (261), Expect = 3e-31
 Identities = 36/60 (60%), Positives = 49/60 (81%)

Query: 42  GHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
           G I+RPMNAFMVW++ +R+++A  NP +HN+E+SK LG  WK LT  EKRPF++EA+RLR
Sbjct: 1   GSIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLR 60
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86 Back     alignment and structure
>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
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>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
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214 Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101 Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query101
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.91
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.9
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.9
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.89
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.89
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.89
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.88
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.88
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.88
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.88
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.88
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.88
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.88
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.88
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.88
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.88
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.87
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.87
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.87
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.86
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.86
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.86
1ckt_A71 High mobility group 1 protein; high-mobility group 99.86
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.85
2lhj_A97 High mobility group protein homolog NHP1; structur 99.84
2cto_A93 Novel protein; high mobility group box domain, hel 99.83
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.82
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.82
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.82
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.81
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.81
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.81
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.8
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 99.8
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.79
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 99.76
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.74
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.65
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.62
>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
Probab=99.91  E-value=6.2e-24  Score=130.67  Aligned_cols=68  Identities=25%  Similarity=0.508  Sum_probs=64.0

Q ss_pred             CCCCCCCCCCCCCCCcHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q psy15636         34 HLGHHHSEGHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR  101 (101)
Q Consensus        34 ~~~~~~~~~~pkRP~saf~lf~~~~r~~~~~~~p~~~~~eisk~~~~~W~~ls~~eK~~y~~~A~~~k  101 (101)
                      .....++++.||||+|||||||+++|..|+.++|++++.+|+++||++|+.|++++|++|+++|+++|
T Consensus        11 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k   78 (90)
T 1wgf_A           11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALK   78 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHT
T ss_pred             cCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            34556789999999999999999999999999999999999999999999999999999999999875
>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
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>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
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>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
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A Back     alignment and structure
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} 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
>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
>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
>2cto_A Novel protein; 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
>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
>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
>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
>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
>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
>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
>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
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Back     alignment and structure
>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 101
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 2e-19
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 4e-19
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 8e-19
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 2e-17
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 5e-17
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-16
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 3e-15
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-15
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 2e-14
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 3e-14
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 7e-14
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-12
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 Back     information, alignment and structure

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 72.9 bits (179), Expect = 2e-19
 Identities = 34/59 (57%), Positives = 44/59 (74%)

Query: 43  HIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
           HIKRPMNAFMVW++ +RRK+    P MHNS ISK LG+ WK +T +EK+P+ +E  RL 
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLS 60
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80 Back     information, alignment and structure
>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
>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
>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
>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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query101
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.89
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.88
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.88
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.88
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.87
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.86
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.85
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.84
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.83
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.82
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.75
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.73
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 92.19
>d1i11a_ a.21.1.1 (A:) Sox-5 {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-5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=9.9e-24  Score=123.05  Aligned_cols=60  Identities=57%  Similarity=1.010  Sum_probs=57.5

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q psy15636         42 GHIKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR  101 (101)
Q Consensus        42 ~~pkRP~saf~lf~~~~r~~~~~~~p~~~~~eisk~~~~~W~~ls~~eK~~y~~~A~~~k  101 (101)
                      .++|||+|||||||++.|..|+.++|++++.+|+++||++|+.|++++|++|+++|+++|
T Consensus         1 p~iKRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   60 (70)
T d1i11a_           1 PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLS   60 (70)
T ss_dssp             CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999999999999999999999999999999999864
>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
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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
>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