Psyllid ID: psy16713

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------
SQAATPHKYKKGDIVTTPTGIRKKFNGKQWRRLCSKDGCSKESQRRGYCSRHLSLKGAGSATGLRSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWCSKDKRKSSTGSGRGKLGSMDEGTGEGFMPDDLEHFENSLEMVTSSNETTVQYLLHPTGRLSNIYSTGFQIPISSESLGNVKQPTTPTVIVSKQSNIEMQNASVAAANAELMQQADKNKDSEQQKYRNFNLSQQQQQQVHQQQQQNSSQPSQNHQEQRHMDSGAPNVPYQRSHEMDTSEPPGGGQENKGTGPQTSHFKKDKDLETEPMAKSFLFSFKQ
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccHHHHHHHHHHccccccHHHHHHHHHHHHccccHHcccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccHHHHHcccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccc
ccccccccccccccccccccccccccHcccccHHHHHHHcHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccHHccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccc
sqaatphkykkgdivttptgirkkfngkqwrrlcskdgcskesqrrgycsrhlslkgagsatglrskdrirrPMNAFMIFSKRhrakvhqihpnqdnrtVSKILGEWWYSLGPEEKQKYHELASEVKEAhfkahpewkwcskdkrksstgsgrgklgsmdegtgegfmpddlEHFENSLEMVTSSNETTVQYLLhptgrlsniystgfqipisseslgnvkqpttptVIVSKQSNIEMQNASVAAANAELMQQADKNKDSEQQKYRNFNLSQQQQQQVHQQqqqnssqpsqnhqeqrhmdsgapnvpyqrshemdtseppgggqenkgtgpqtshfkkdkdletepmaKSFLFSFKQ
sqaatphkykkgdivttptgirkkfngkqwrrlcskdgcskesqrrgycsrhlslkgagsatglrskdrirRPMNAFMIFSKrhrakvhqihpnqdnrtvsKILGEWWYSLGPEEKQKYHELASEVKEAHfkahpewkwcskdkrksstgsgrgklgsmdegtGEGFMPDDLEHFENSLEMVTSSNETTVQYLLHPTGRLSNIYSTGFQIPISseslgnvkqpttPTVIVSKQSNIEMQNASVAAANAELMQQADKNKDSEQQKYRNFNLSQQQQQQVHQQQQQNSSQPSQNHQEQRHMDSGAPNVPYQRSHEMDTSEPPGGGQENKGTGPQTShfkkdkdletepMAKSFLFSFKQ
SQAATPHKYKKGDIVTTPTGIRKKFNGKQWRRLCSKDGCSKESQRRGYCSRHLSLKGAGSATGLRSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWCSKDKRKSSTGSGRGKLGSMDEGTGEGFMPDDLEHFENSLEMVTSSNETTVQYLLHPTGRLSNIYSTGFQIPISSESLGNVKQPTTPTVIVSKQSNIEMQNASVAAANAELMQQADKNKDSEQQKYRNFNLsqqqqqqvhqqqqqnssqpsqnhqeqRHMDSGAPNVPYQRSHEMDTSEPPGGGQENKGTGPQTSHFKKDKDLETEPMAKSFLFSFKQ
**************VTTPTGIRKKFNGKQWRRLC****************************************NAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGP*****Y**L*****EAHFKAHPEWKWC***********************************************TTVQYLLHPTGRLSNIYSTGFQIPI*************************************************************************************************************************************************
**************************************************************************NAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWK**********************************************************************************************************************************************************************************************************DLETEPMAKSFLFSF**
**********KGDIVTTPTGIRKKFNGKQWRRLCSK*************SRHLSLKGAGSATGLRSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWCSK**************GSMDEGTGEGFMPDDLEHFENSLEMVTSSNETTVQYLLHPTGRLSNIYSTGFQIPISSESLGNVKQPTTPTVIVSKQSNIEMQNASVAAANAELMQQ**********KYRNFN********************************GAPNVPY******************************DKDLETEPMAKSFLFSFKQ
*****************************WRRLCSKDGCSKESQRRGYCSRHLSLK************RIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWCSK************************************************************************************************QNASVAAANAELMQQADKNKDSEQQKYRNFNL***************************************************************************************
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SQAATPHKYKKGDIVTTPTGIRKKFNGKQWRRLCSKDGCSKESQRRGYCSRHLSLKGAGSATGLRSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWCSKDKRKSSTGSGRGKLGSMDEGTGEGFMPDDLEHFENSLEMVTSSNETTVQYLLHPTGRLSNIYSTGFQIPISSESLGNVKQPTTPTVIVSKQSNIEMQNASxxxxxxxxxxxxxxxxxxxxxKYRNFNLSQQQQQQVHQQQQQNSSQPSQNHQEQRHMDSGAPNVPYQRSHEMDTSEPPGGGQENKGTGPQTSHFKKDKDLETEPMAKSFLFSFKQ
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 ?
Query357 2.2.26 [Sep-21-2011]
Q924A2 2510 Protein capicua homolog O no N/A 0.260 0.037 0.784 6e-42
Q96RK0 1608 Protein capicua homolog O yes N/A 0.260 0.057 0.784 6e-42
Q9U1H0 1832 Putative transcription fa yes N/A 0.274 0.053 0.717 7e-39
Q8WY36 941 HMG box transcription fac no N/A 0.201 0.076 0.583 4e-21
Q8VBW5 907 HMG box transcription fac no N/A 0.201 0.079 0.569 7e-21
Q04891613 Transcription factor SOX- no N/A 0.260 0.151 0.365 7e-13
Q9UN79622 Transcription factor SOX- no N/A 0.260 0.149 0.365 1e-12
Q5RCU4787 Transcription factor SOX- no N/A 0.257 0.116 0.358 1e-12
P40645827 Transcription factor SOX- no N/A 0.257 0.111 0.358 1e-12
P35712828 Transcription factor SOX- no N/A 0.257 0.111 0.358 2e-12
>sp|Q924A2|CIC_MOUSE Protein capicua homolog OS=Mus musculus GN=Cic PE=1 SV=2 Back     alignment and function desciption
 Score =  171 bits (434), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 73/93 (78%), Positives = 83/93 (89%)

Query: 65   RSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELAS 124
            R KD IRRPMNAFMIFSKRHRA VHQ HPNQDNRTVSKILGEWWY+LGP+EKQKYH+LA 
Sbjct: 1102 REKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAF 1161

Query: 125  EVKEAHFKAHPEWKWCSKDKRKSSTGSGRGKLG 157
            +VKEAHFKAHP+WKWC+KD++KSS+ +    LG
Sbjct: 1162 QVKEAHFKAHPDWKWCNKDRKKSSSEAKPASLG 1194
Transcriptional repressor which may play a role in development of the central nervous system (CNS).
Mus musculus (taxid: 10090)
>sp|Q96RK0|CIC_HUMAN Protein capicua homolog OS=Homo sapiens GN=CIC PE=1 SV=2 Back     alignment and function description
>sp|Q9U1H0|CIC_DROME Putative transcription factor capicua OS=Drosophila melanogaster GN=cic PE=1 SV=2 Back     alignment and function description
>sp|Q8WY36|BBX_HUMAN HMG box transcription factor BBX OS=Homo sapiens GN=BBX PE=1 SV=1 Back     alignment and function description
>sp|Q8VBW5|BBX_MOUSE HMG box transcription factor BBX OS=Mus musculus GN=Bbx PE=1 SV=2 Back     alignment and function description
>sp|Q04891|SOX13_MOUSE Transcription factor SOX-13 OS=Mus musculus GN=Sox13 PE=2 SV=4 Back     alignment and function description
>sp|Q9UN79|SOX13_HUMAN Transcription factor SOX-13 OS=Homo sapiens GN=SOX13 PE=1 SV=3 Back     alignment and function description
>sp|Q5RCU4|SOX6_PONAB Transcription factor SOX-6 OS=Pongo abelii GN=SOX6 PE=2 SV=1 Back     alignment and function description
>sp|P40645|SOX6_MOUSE Transcription factor SOX-6 OS=Mus musculus GN=Sox6 PE=1 SV=2 Back     alignment and function description
>sp|P35712|SOX6_HUMAN Transcription factor SOX-6 OS=Homo sapiens GN=SOX6 PE=1 SV=3 Back     alignment and function description

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 ?
Query357
242005681 1731 capicua protein, putative [Pediculus hum 0.282 0.058 0.847 1e-46
383861656 1917 PREDICTED: uncharacterized protein LOC10 0.383 0.071 0.659 1e-46
350413831 1915 PREDICTED: hypothetical protein LOC10074 0.336 0.062 0.72 1e-46
380027952 1944 PREDICTED: uncharacterized protein LOC10 0.383 0.070 0.659 1e-46
340710023 1915 PREDICTED: hypothetical protein LOC10064 0.336 0.062 0.72 1e-46
332025908 1953 Putative transcription factor capicua [A 0.428 0.078 0.609 2e-46
340710021 1802 PREDICTED: hypothetical protein LOC10064 0.336 0.066 0.72 2e-46
328778092 1912 PREDICTED: hypothetical protein LOC10057 0.383 0.071 0.659 2e-46
328702153 1704 PREDICTED: hypothetical protein LOC10016 0.274 0.057 0.868 3e-46
328702151 1695 PREDICTED: hypothetical protein LOC10016 0.274 0.057 0.868 4e-46
>gi|242005681|ref|XP_002423691.1| capicua protein, putative [Pediculus humanus corporis] gi|212506867|gb|EEB10953.1| capicua protein, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
 Score =  193 bits (490), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 89/105 (84%), Positives = 94/105 (89%), Gaps = 4/105 (3%)

Query: 66   SKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASE 125
            S+DRIRRPMNAFMIFSKRHRA VHQ HPNQDNRTVSKILGEWWY+LG EEKQKYHELA+E
Sbjct: 976  SRDRIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGSEEKQKYHELATE 1035

Query: 126  VKEAHFKAHPEWKWCSKDKRKSSTGS---GRGKLGSMDEGTGEGF 167
            VKEAHFKAHPEWKWCSKD+RKSST S   GR KLGS DEG  +GF
Sbjct: 1036 VKEAHFKAHPEWKWCSKDRRKSSTSSVKEGRSKLGSSDEGI-DGF 1079

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|383861656|ref|XP_003706301.1| PREDICTED: uncharacterized protein LOC100880203 [Megachile rotundata] Back     alignment and taxonomy information
>gi|350413831|ref|XP_003490126.1| PREDICTED: hypothetical protein LOC100747566 [Bombus impatiens] Back     alignment and taxonomy information
>gi|380027952|ref|XP_003697676.1| PREDICTED: uncharacterized protein LOC100868625 [Apis florea] Back     alignment and taxonomy information
>gi|340710023|ref|XP_003393598.1| PREDICTED: hypothetical protein LOC100645977 isoform 2 [Bombus terrestris] Back     alignment and taxonomy information
>gi|332025908|gb|EGI66064.1| Putative transcription factor capicua [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|340710021|ref|XP_003393597.1| PREDICTED: hypothetical protein LOC100645977 isoform 1 [Bombus terrestris] Back     alignment and taxonomy information
>gi|328778092|ref|XP_003249448.1| PREDICTED: hypothetical protein LOC100578885 [Apis mellifera] Back     alignment and taxonomy information
>gi|328702153|ref|XP_001952681.2| PREDICTED: hypothetical protein LOC100163586 isoform 1 [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|328702151|ref|XP_003241821.1| PREDICTED: hypothetical protein LOC100163586 isoform 2 [Acyrthosiphon pisum] 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 ?
Query357
MGI|MGI:1918972 2510 Cic "capicua homolog (Drosophi 0.299 0.042 0.710 1.9e-60
UNIPROTKB|Q96RK0 1608 CIC "Protein capicua homolog" 0.299 0.066 0.710 1.1e-38
FB|FBgn0262582 1832 cic "capicua" [Drosophila mela 0.302 0.058 0.688 3.4e-38
UNIPROTKB|Q8WY36 941 BBX "HMG box transcription fac 0.232 0.088 0.529 4e-21
MGI|MGI:1917758 907 Bbx "bobby sox homolog (Drosop 0.232 0.091 0.517 7.4e-19
WB|WBGene00004950212 sox-3 [Caenorhabditis elegans 0.319 0.537 0.358 2.9e-16
UNIPROTKB|B4DWU7178 SOX15 "Protein SOX-15" [Homo s 0.313 0.629 0.358 7.4e-14
UNIPROTKB|O60248233 SOX15 "Protein SOX-15" [Homo s 0.313 0.480 0.358 7.4e-14
UNIPROTKB|F1ST29233 SOX15 "Uncharacterized protein 0.308 0.472 0.345 7.4e-14
UNIPROTKB|A6PVD3213 SOX10 "Transcription factor SO 0.274 0.460 0.3 8.6e-14
MGI|MGI:1918972 Cic "capicua homolog (Drosophila)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
 Score = 422 (153.6 bits), Expect = 1.9e-60, Sum P(2) = 1.9e-60
 Identities = 76/107 (71%), Positives = 88/107 (82%)

Query:    51 RHLSLKGAGSATGLRSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYS 110
             R  S +  G +   R KD IRRPMNAFMIFSKRHRA VHQ HPNQDNRTVSKILGEWWY+
Sbjct:  1088 RDSSSEKDGRSPNKREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYA 1147

Query:   111 LGPEEKQKYHELASEVKEAHFKAHPEWKWCSKDKRKSSTGSGRGKLG 157
             LGP+EKQKYH+LA +VKEAHFKAHP+WKWC+KD++KSS+ +    LG
Sbjct:  1148 LGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKKSSSEAKPASLG 1194
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=IEA
GO:0006351 "transcription, DNA-dependent" evidence=IEA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA
UNIPROTKB|Q96RK0 CIC "Protein capicua homolog" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
FB|FBgn0262582 cic "capicua" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|Q8WY36 BBX "HMG box transcription factor BBX" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1917758 Bbx "bobby sox homolog (Drosophila)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
WB|WBGene00004950 sox-3 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|B4DWU7 SOX15 "Protein SOX-15" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|O60248 SOX15 "Protein SOX-15" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1ST29 SOX15 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|A6PVD3 SOX10 "Transcription factor SOX-10" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query357
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 3e-38
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 1e-21
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 2e-18
smart0039870 smart00398, HMG, high mobility group 1e-17
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 2e-16
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 3e-13
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 6e-05
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 7e-05
>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 =  130 bits (330), Expect = 3e-38
 Identities = 41/72 (56%), Positives = 55/72 (76%)

Query: 69  RIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKE 128
            I+RPMNAFM+FSKRHR KV Q +P ++NR +SKILG+ W +L  EEKQ Y+E A ++KE
Sbjct: 1   HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKE 60

Query: 129 AHFKAHPEWKWC 140
            H K +P++KW 
Sbjct: 61  LHMKLYPDYKWR 72

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif. Length = 72
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors Back     alignment and domain information
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box Back     alignment and domain information
>gnl|CDD|197700 smart00398, HMG, high mobility group Back     alignment and domain information
>gnl|CDD|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
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional Back     alignment and domain information
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 357
KOG0527|consensus331 99.92
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.9
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.87
PTZ0019994 high mobility group protein; Provisional 99.82
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.76
smart0039870 HMG high mobility group. 99.74
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.72
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.68
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.65
KOG0528|consensus511 99.61
KOG0381|consensus96 99.59
COG5648211 NHP6B Chromatin-associated proteins containing the 99.58
KOG3248|consensus421 99.45
KOG0526|consensus615 99.43
KOG4715|consensus410 98.9
KOG2746|consensus 683 98.86
COG5648211 NHP6B Chromatin-associated proteins containing the 98.85
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 97.35
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 96.16
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 96.02
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 95.08
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 93.06
KOG0527|consensus331 92.01
PTZ0019994 high mobility group protein; Provisional 89.42
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 88.65
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 88.49
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 86.14
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 83.86
KOG0526|consensus615 82.68
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 81.89
>KOG0527|consensus Back     alignment and domain information 
Probab=99.92  E-value=3.1e-25  Score=217.93  Aligned_cols=91  Identities=35%  Similarity=0.606  Sum_probs=85.6

Q ss_pred             CCCCCCCCCCCCCCchhHhHHHHHHHHHHhhCCCCChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHcccCccC
Q psy16713         61 ATGLRSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWC  140 (357)
Q Consensus        61 ~~kkkdp~~PKRP~nAFmLF~~e~R~~ik~e~P~ls~~EISK~Lge~Wk~LSeeEK~~Y~e~A~~~Keky~ke~p~YKy~  140 (357)
                      ...++..++|||||||||+|++..|.+|..+||+|+|.||||+||.+||.|+++||.+|+++|+++|.+|+++||||||+
T Consensus        54 ~~~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYR  133 (331)
T KOG0527|consen   54 MKDKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYR  133 (331)
T ss_pred             ccCCCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccc
Confidence            34678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCC
Q psy16713        141 SKDKRKSSTGS  151 (357)
Q Consensus       141 PrkKkk~~k~~  151 (357)
                      ||||+|.....
T Consensus       134 PRRKkk~~~~~  144 (331)
T KOG0527|consen  134 PRRKKKKRPKL  144 (331)
T ss_pred             ccccccccccc
Confidence            99887766554

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information
>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
>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
>KOG0528|consensus 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
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A Back     alignment and domain information
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ] Back     alignment and domain information
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta Back     alignment and domain information
>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
>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
>KOG0527|consensus Back     alignment and domain information
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>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
>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
>KOG0526|consensus Back     alignment and domain information
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query357
1wz6_A82 Solution Structure Of The Hmg_box Domain Of Murine 4e-18
1i11_A81 Solution Structure Of The Dna Binding Domain, Sox-5 6e-11
2e6o_A87 Solution Structure Of The Hmg Box Domain From Human 8e-11
1o4x_B88 Ternary Complex Of The Dna Binding Domains Of The O 5e-10
2le4_A81 Solution Structure Of The Hmg Box Dna-Binding Domai 6e-10
1gt0_D80 Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le 7e-10
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 1e-09
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 2e-09
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 6e-09
2lef_A86 Lef1 Hmg Domain (From Mouse), Complexed With Dna (1 9e-09
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 8e-08
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 1e-06
1j46_A85 3d Solution Nmr Structure Of The Wild Type Hmg-Box 2e-06
1hrz_A76 The 3d Structure Of The Human Sry-Dna Complex Solve 3e-06
3u2b_C79 Structure Of The Sox4 Hmg Domain Bound To Dna Lengt 4e-06
1j47_A85 3d Solution Nmr Structure Of The M9i Mutant Of The 7e-06
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 7e-05
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 1e-04
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 3e-04
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby Sox Homolog Length = 82 Back     alignment and structure 
Iteration: 1

 Score = 88.6 bits (218), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 38/68 (55%), Positives = 50/68 (73%)
Query: 71  RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAH 130
           RRPMNAF++F KRHR+ V Q HP  DNR  +KIL +WW  L P+EKQKY ++A E K+A 
Sbjct: 9   RRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAF 68
Query: 131 FKAHPEWK 138
            KA+P ++
Sbjct: 69  MKANPGYR 76
>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|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human Hmg-Box Transcription Factor 1 Length = 87 Back     alignment and structure
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And Sox2 Transcription Factors With A 19mer Oligonucleotide From The Hoxb1 Regulatory Element Length = 88 Back     alignment and structure
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of Human Stem Cell Transcription Factor Sox2 Length = 81 Back     alignment and structure
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80 Back     alignment and structure
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 Back     alignment and structure
>pdb|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|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp), Nmr, 12 Structures Length = 86 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|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|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|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna Length = 79 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|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|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78 Back     alignment and structure
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query357
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 2e-34
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 2e-33
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 3e-33
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 3e-32
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 4e-32
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 9e-32
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 2e-31
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 2e-31
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 2e-31
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 5e-31
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 1e-30
1wgf_A90 Upstream binding factor 1; transcription factor, D 3e-21
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 3e-20
1hme_A77 High mobility group protein fragment-B; DNA-bindin 7e-19
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 5e-18
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 3e-17
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 2e-15
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 1e-16
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 6e-16
2lhj_A97 High mobility group protein homolog NHP1; structur 8e-16
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 3e-15
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 4e-15
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 3e-14
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 5e-14
2yrq_A173 High mobility group protein B1; HMG box domain, DN 6e-14
2yrq_A173 High mobility group protein B1; HMG box domain, DN 7e-09
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 2e-13
1ckt_A71 High mobility group 1 protein; high-mobility group 4e-13
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 5e-13
3tq6_A214 Transcription factor A, mitochondrial; transcripti 2e-10
3tq6_A214 Transcription factor A, mitochondrial; transcripti 2e-08
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 3e-09
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 6e-09
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 5e-08
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 8e-07
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 4e-06
>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
 Score =  120 bits (304), Expect = 2e-34
 Identities = 39/78 (50%), Positives = 51/78 (65%)

Query: 63  GLRSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHEL 122
           G       RRPMNAF++F KRHR+ V Q HP  DNR  +KIL +WW  L P+EKQKY ++
Sbjct: 1   GSSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDM 60

Query: 123 ASEVKEAHFKAHPEWKWC 140
           A E K+A  KA+P ++  
Sbjct: 61  AKEYKDAFMKANPGYRSG 78
>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
>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
>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
>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
>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
>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
>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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71 Back     alignment and structure
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 90 Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99 Back     alignment and structure
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 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
>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
>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
>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
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214 Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214 Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101 Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108 Back     alignment and structure
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query357
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.92
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.92
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.92
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.92
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.92
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.91
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.91
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.91
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.91
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.91
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.91
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.9
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.89
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.88
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.88
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.87
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.87
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.87
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.85
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.85
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.85
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.84
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.83
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.83
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.83
1ckt_A71 High mobility group 1 protein; high-mobility group 99.83
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.82
2lhj_A97 High mobility group protein homolog NHP1; structur 99.82
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.79
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.79
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.78
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.78
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.78
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.75
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.73
2cto_A93 Novel protein; high mobility group box domain, hel 99.73
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.71
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.67
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.66
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 95.36
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 95.3
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 95.23
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 94.94
1ckt_A71 High mobility group 1 protein; high-mobility group 94.68
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 94.34
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 93.92
1wgf_A90 Upstream binding factor 1; transcription factor, D 93.88
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 93.49
1hme_A77 High mobility group protein fragment-B; DNA-bindin 93.21
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 93.07
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 93.06
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 93.0
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 92.89
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 92.6
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 92.54
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 92.39
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 92.31
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 92.3
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 92.29
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 92.27
2lhj_A97 High mobility group protein homolog NHP1; structur 91.87
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 91.79
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 90.57
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 90.34
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 90.22
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 89.83
2cto_A93 Novel protein; high mobility group box domain, hel 88.23
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 86.94
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 86.82
>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
Probab=99.92  E-value=3.2e-25  Score=172.86  Aligned_cols=78  Identities=32%  Similarity=0.591  Sum_probs=74.8

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHhhCCCCChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHcccCccCcCCCC
Q psy16713         68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWCSKDKR  145 (357)
Q Consensus        68 ~~PKRP~nAFmLF~~e~R~~ik~e~P~ls~~EISK~Lge~Wk~LSeeEK~~Y~e~A~~~Keky~ke~p~YKy~PrkKk  145 (357)
                      |+||||+|||||||+++|..|+.+||++++.+|+++||++|++|++++|++|.++|+.++++|.++||+|+|+|+++.
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~Prk~~   78 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRPRKKV   78 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCC--
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCCCCCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999999998654
>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
>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
>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
>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
>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
>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
>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
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Back     alignment and structure
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Back     alignment and structure
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Back     alignment and structure
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A* Back     alignment and structure
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Back     alignment and structure
>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
>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
>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
>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
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Back     alignment and structure
>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
>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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Back     alignment and structure
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Back     alignment and structure
>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Back     alignment and structure
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 Back     alignment and structure
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Back     alignment and structure
>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
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, 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
>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
>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
>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
>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
>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
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Back     alignment and structure
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Back     alignment and structure
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, 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
>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

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 357
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 3e-25
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 2e-23
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 3e-23
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 2e-22
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 1e-19
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 6e-18
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 2e-17
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-17
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 4e-17
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-15
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 3e-15
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-14
>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 = 95.3 bits (237), Expect = 3e-25
 Identities = 31/80 (38%), Positives = 49/80 (61%)

Query: 68  DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
           DR++RPMNAFM++S+  R K+ Q +P   N  +SK LG  W  L   EK+ + + A  ++
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60

Query: 128 EAHFKAHPEWKWCSKDKRKS 147
             H K HP++K+  + K K+
Sbjct: 61  ALHMKEHPDYKYRPRRKTKT 80
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 Back     information, alignment and structure
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 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
>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
>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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 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 ?
Query357
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]} 99.9
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.87
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.83
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.82
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.81
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.8
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.79
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.78
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.7
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.69
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 92.69
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 92.61
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 92.36
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 92.34
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 92.31
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 92.15
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 90.72
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 89.29
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 82.65
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 82.26
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 81.49
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 80.3
>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=6.3e-25  Score=172.20  Aligned_cols=79  Identities=39%  Similarity=0.717  Sum_probs=75.7

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHhhCCCCChHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHcccCccCcCCCCC
Q psy16713         68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFKAHPEWKWCSKDKRK  146 (357)
Q Consensus        68 ~~PKRP~nAFmLF~~e~R~~ik~e~P~ls~~EISK~Lge~Wk~LSeeEK~~Y~e~A~~~Keky~ke~p~YKy~PrkKkk  146 (357)
                      ++||||+|||||||+++|..|+.+||++++.+|+++||++|++|++++|++|+++|+.++++|.++||+|+|+|+++.+
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p~rk~k   79 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTK   79 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCCCCCCC
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999999975543
>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
>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
>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
>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>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
>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
>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
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure