Psyllid ID: psy15631

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210---
Protein Sequence
MEKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQSALELDQLRRPVPVIY
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccHHccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccEEc
Coil and Loop (DISEMBL)
MEKRPFIDEAKRLRAMHmkehpdykyrprrkpktpgqsipnnkspnqgapaptsasnafpsfplppyfanhgggshphpldslsaayppmnmphyfgspfdamnfsklvqgqtsqadtkssnAAAAVVSSFYSslypsvtsaqtktfstpppshlsalfqhptaasshpsqflyglkseqlspssspgesqsqsnnqsaleldqlrrpvpviy
Flexible Loop (DISEMBL)
mekrpfideakrlramhmkehpdykyrprrkPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSspgesqsqsnnqsaleldqlrrpvpviy
Low Complexity Region (SEG)
MEKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTKssnaaaavvssfyssLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHPSQFLYglkseqlspssspgesqsqsnnqsALELDQLRRPVPVIY
Disordered region (IsUnstruct)
**********************************************************************************************YF*********************************SFY*********************************************************************************
Disordered Region (DISOPRED)
*EKRPFIDEAKRLRAMHMKEHPDYK*************************************************************************************************************************************************************************************R******
Disordered Region (DISEMBL)
MEKRPFIDEAKRLRAMHMKEHPDYKYR***************************ASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLV***************AAVVSSFYSSLYPSV*************SHLSALFQHPTAASSHPSQFLYGLKS********************ALELDQLRRPVPVIY
Disordered Region (DISPRO)
**KRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTS*****FST*******A*FQHPT****HPSQFLYGLK*E***********************DQLRRPVPVIY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQSALELDQLRRPVPVIY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	213	2.2.26 [Sep-21-2011]
Q24533	382	SOX domain-containing pro	yes	N/A	0.591	0.329	0.402	2e-16
Q6RVD7	245	Transcription factor Sox-	yes	N/A	0.154	0.134	1.0	2e-13
Q811W0	276	Transcription factor SOX-	yes	N/A	0.154	0.119	1.0	3e-13
Q9Y651	276	Transcription factor SOX-	yes	N/A	0.154	0.119	1.0	3e-13
Q9W7R5	280	Transcription factor SOX-	yes	N/A	0.154	0.117	1.0	5e-13
B0ZTE1	262	Transcription factor Sox-	N/A	N/A	0.154	0.125	0.969	5e-13
P48430	315	Transcription factor SOX-	yes	N/A	0.154	0.104	0.939	8e-13
Q6P0E1	315	Transcription factor Sox-	no	N/A	0.154	0.104	0.939	1e-12
O42569	311	Transcription factor Sox-	N/A	N/A	0.154	0.106	0.939	1e-12
Q6NVN0	311	Transcription factor Sox-	no	N/A	0.154	0.106	0.939	1e-12

>sp|Q24533|DICH_DROME SOX domain-containing protein dichaete OS=Drosophila melanogaster GN=D PE=2 SV=1

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 76/159 (47%), Gaps = 33/159 (20%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGA---------PAP 52
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRKPK P  + P      Q              
Sbjct: 187 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKPKNPLTAGPQGGLQMQAGGMGQQKLGAGPG 246

Query: 53  TSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQ 112
             A    P   LPPYFA         P   L   YP   +P YFG  FD +  SKL Q Q
Sbjct: 247 AGAGGYNPFHQLPPYFA---------PSHHLDQGYP---VP-YFGG-FDPLALSKLHQSQ 292

Query: 113 TSQADTKSSNAAAAV----------VSSFYSSLYPSVTS 141
            + A   ++                +SSFYS +Y  +++
Sbjct: 293 AAAAAAVNNQGQQQGQAPPQLPPTSLSSFYSGIYSGISA 331

Essential for segmentation and CNS development. May modulate the actions of other transcription factors, including gap and pair-rule proteins.
Drosophila melanogaster (taxid: 7227)

>sp|Q6RVD7|SX21B_DANRE Transcription factor Sox-21-B OS=Danio rerio GN=sox21b PE=2 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT
Sbjct: 53 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 85

Acts as a negative regulator of transcription.

Danio rerio (taxid: 7955)

>sp|Q811W0|SOX21_MOUSE Transcription factor SOX-21 OS=Mus musculus GN=Sox21 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT
Sbjct: 53 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 85

May play a role as an activator of transcription of OPRM1. Overexpression of SOX21 can up-regulate the OPRM1 distal promoter activity in mor-expressing neuronal cells.

Mus musculus (taxid: 10090)

>sp|Q9Y651|SOX21_HUMAN Transcription factor SOX-21 OS=Homo sapiens GN=SOX21 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT
Sbjct: 53 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 85

May play a role as an activator of transcription of OPRM1.

Homo sapiens (taxid: 9606)

>sp|Q9W7R5|SOX21_CHICK Transcription factor SOX-21 OS=Gallus gallus GN=SOX21 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/33 (100%), Positives = 33/33 (100%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT
Sbjct: 53 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 85

Acts as a negative regulator of transcription.

Gallus gallus (taxid: 9031)

>sp|B0ZTE1|SOX21_XENLA Transcription factor Sox-21 OS=Xenopus laevis GN=sox21 PE=2 SV=1

 Score = 74.3 bits (181), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 32/33 (96%), Positives = 33/33 (100%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRAMHMK+HPDYKYRPRRKPKT
Sbjct: 53 EKRPFIDEAKRLRAMHMKDHPDYKYRPRRKPKT 85

Acts as a negative regulator of transcription (By similarity). May function as a switch in neuronal development.

Xenopus laevis (taxid: 8355)

>sp|P48430|SOX2_CHICK Transcription factor SOX-2 OS=Gallus gallus GN=SOX2 PE=1 SV=1

 Score = 73.9 bits (180), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 84  EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 116

Transcriptional activator. May function as a switch in neuronal development. Downstream SRRT target that mediates the promotion of neural stem cell self-renewal (By similarity). Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation. In cooperation with other transcription factors, binds to the promoter sequence of the crystallin gene to activate transcription in the lens. Binds to the consensus DNA sequence 5'-TCATTGTTGTTG-3'.

Gallus gallus (taxid: 9031)

>sp|Q6P0E1|SOX2_DANRE Transcription factor Sox-2 OS=Danio rerio GN=sox2 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 83  EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 115

Transcriptional activator. May function as a switch in neuronal development (By similarity). Downstream SRRT target that mediates the promotion of neural stem cell self-renewal.

Danio rerio (taxid: 7955)

>sp|O42569|SOX2_XENLA Transcription factor Sox-2 OS=Xenopus laevis GN=sox2 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 82  EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 114

Transcriptional activator (By similarity). Functions as a switch in neuronal development, participating in the differentiation of embryonic neuroectodermal cells into neural tissues by making the ectodermal cells responsive to FGF-neuralizing signals. Downstream SRRT target that mediates the promotion of neural stem cell self-renewal.

Xenopus laevis (taxid: 8355)

>sp|Q6NVN0|SOX2_XENTR Transcription factor Sox-2 OS=Xenopus tropicalis GN=sox2 PE=2 SV=1

 Score = 73.2 bits (178), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 82  EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 114

Transcriptional activator. Functions as a switch in neuronal development, participating in the differentiation of embryonic neuroectodermal cells into neural tissues by making the ectodermal cells responsive to FGF-neuralizing signals (By similarity). Downstream SRRT target that mediates the promotion of neural stem cell self-renewal.

Xenopus tropicalis (taxid: 8364)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
345494190	339	PREDICTED: transcription factor Sox-14-l	0.873	0.548	0.426	3e-26
350416776	311	PREDICTED: SOX domain-containing protein	0.896	0.614	0.408	4e-22
340721649	311	PREDICTED: SOX domain-containing protein	0.915	0.627	0.415	7e-21
380016546	279	PREDICTED: SOX domain-containing protein	0.737	0.562	0.459	4e-18
157111610	314	sex-determining region y protein, sry [A	0.600	0.407	0.435	2e-17
357607486	202	hypothetical protein KGM_19696 [Danaus p	0.755	0.797	0.448	9e-16
195161050	403	GL24831 [Drosophila persimilis] gi|19411	0.784	0.414	0.369	9e-16
194747990	387	GF25204 [Drosophila ananassae] gi|190623	0.591	0.325	0.412	1e-15
158287886	330	AGAP010919-PA [Anopheles gambiae str. PE	0.582	0.375	0.425	2e-15
195494282	381	GE20027 [Drosophila yakuba] gi|194180871	0.591	0.330	0.411	7e-15

>gi|345494190|ref|XP_003427240.1| PREDICTED: transcription factor Sox-14-like [Nasonia vitripennis]

 Score =  124 bits (311), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 105/246 (42%), Positives = 129/246 (52%), Gaps = 60/246 (24%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
           +K+PFIDEAKRLRA HMKEHPDYKYRPRRKPK P  +IP  K+ + GA        +FPS
Sbjct: 120 QKQPFIDEAKRLRAKHMKEHPDYKYRPRRKPKVPVSAIPGGKNQSMGA--------SFPS 171

Query: 62  FPLPPYFANHGG---GSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADT 118
           F L PYF +  G     HPHPLD     YPP  +P YFGS FDA++  KLV    SQ  +
Sbjct: 172 FTL-PYFGSPAGPVSHHHPHPLD-----YPP--LPGYFGSAFDAVHLGKLVSNTQSQQTS 223

Query: 119 KS--------SNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHPS 170
            +        + +AAAVVSSFYSSLY +  + Q K       + + +LF  P AA  H  
Sbjct: 224 TTAADVANNNAASAAAVVSSFYSSLY-NPAAQQNKVSPYGAATTMGSLF--PGAAHHH-- 278

Query: 171 QFLYGLKSEQLSPSSSPGESQ-----------------------SQSNNQSALELDQLRR 207
                + S  + P S    SQ                       S S    +L+LDQLRR
Sbjct: 279 -----MTSSMMFPGSQLTASQMTHSSSSPSSSPGSTPVSLSHGSSTSPTAPSLDLDQLRR 333

Query: 208 PVPVIY 213
           P+ VIY
Sbjct: 334 PLSVIY 339

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350416776|ref|XP_003491097.1| PREDICTED: SOX domain-containing protein dichaete-like [Bombus impatiens]

 Score =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 101/247 (40%), Positives = 128/247 (51%), Gaps = 56/247 (22%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
           EKRPFIDEAKRLRA+HMK+HPDYKYRPRRKPK P  +I N K+ +         S AF +
Sbjct: 86  EKRPFIDEAKRLRAVHMKQHPDYKYRPRRKPKIP-VAIGNGKTVSIN-------SGAFAN 137

Query: 62  FPLPPYFANHGGG-SHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQA---- 116
           FPLPPYFA      SH HP        PP      FGS FD ++ SKLV G  + +    
Sbjct: 138 FPLPPYFAAPATSVSHHHPHPLDYPPLPPY-----FGSAFDPVHLSKLVAGSGTGSPSTN 192

Query: 117 -----DTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALF---QHPTAASS- 167
                   ++ +AAAVVSSFY+  Y + TS      +T   SHL  LF    H  +A++ 
Sbjct: 193 AAADAANNNAASAAAVVSSFYTGFYSTPTSGAKPYPTT--ASHLGPLFPTGHHSVSATTP 250

Query: 168 HPSQFLYGLKSEQLSPSSSPGESQSQ-------------SNNQSA--------LELDQLR 206
           HP          Q S ++ PG   +              S++Q A        L+++QLR
Sbjct: 251 HPPLVF------QSSAATDPGSIATTSSPGSSPGSTPIPSSHQHAPTSATPTTLDMEQLR 304

Query: 207 RPVPVIY 213
           RPVPVIY
Sbjct: 305 RPVPVIY 311

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721649|ref|XP_003399229.1| PREDICTED: SOX domain-containing protein dichaete-like [Bombus terrestris]

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 101/243 (41%), Positives = 128/243 (52%), Gaps = 48/243 (19%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
           EKRPFIDEAKRLRA+HMK+HPDYKYRPRRKPK    SI N K+ +         S++F S
Sbjct: 86  EKRPFIDEAKRLRAVHMKQHPDYKYRPRRKPKI-AVSIGNGKTVSLN-------SSSFAS 137

Query: 62  FPLPPYFAN-HGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQA---- 116
           FPLPPYFA      SH HP        PP      FGS FDA++FSKLV G  + +    
Sbjct: 138 FPLPPYFAAPATSVSHHHPHPLDYPPLPPY-----FGSAFDAVHFSKLVAGSGTGSPSTN 192

Query: 117 -----DTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHPSQ 171
                   ++ +AAAVVSSFY+ LY + T+      +T   SHL  LF  PT   S P+ 
Sbjct: 193 AAADVANNNAASAAAVVSSFYTGLYSTPTTPTKPYPTT--ASHLGPLF--PTGHHSVPAT 248

Query: 172 FLYGLKSEQLSPSSSPGESQSQ---------------------SNNQSALELDQLRRPVP 210
             +     Q S ++ PG   +                      ++  S L+++QLRRPVP
Sbjct: 249 TPHPPLMFQSSAATGPGSIVTTTSSPGSSPGSTPIPSSHQHVPTSATSTLDMEQLRRPVP 308

Query: 211 VIY 213
           VIY
Sbjct: 309 VIY 311

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380016546|ref|XP_003692243.1| PREDICTED: SOX domain-containing protein dichaete-like [Apis florea]

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 86/187 (45%), Positives = 101/187 (54%), Gaps = 30/187 (16%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
           EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK P   +P       GA   + +   FPS
Sbjct: 89  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKVPVSVVP-------GAKTTSMSPGGFPS 141

Query: 62  FPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLV------------ 109
           FPLPPYFA        H        YPP  +P YFGS FDA++ SKLV            
Sbjct: 142 FPLPPYFAAPAAPVSHHHHHPHPLDYPP--LPSYFGSAFDAVHLSKLVAGGGGTGSTSSS 199

Query: 110 -----QGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALF--QHP 162
                    + A   ++ +AAAVV+SFYS  Y + T+      ST   SHL  LF   H 
Sbjct: 200 AAAAAAAAAADAANNNAASAAAVVNSFYSGFYSTPTTPGKPYPST--ASHLGPLFPPGHH 257

Query: 163 TAASSHP 169
           T A++ P
Sbjct: 258 TMATNTP 264

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157111610|ref|XP_001651645.1| sex-determining region y protein, sry [Aedes aegypti] gi|108883819|gb|EAT48044.1| AAEL000893-PA [Aedes aegypti]

 Score = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/147 (43%), Positives = 79/147 (53%), Gaps = 19/147 (12%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
           +KRPFIDEAKRLRA HMKEHPDYKYRPRRKPK P  +     S      A  +  +++P 
Sbjct: 124 QKRPFIDEAKRLRASHMKEHPDYKYRPRRKPKNPLANAAGGLSLGMQQSAKNALGSSYPF 183

Query: 62  FPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTKSS 121
             LPPYFA        H L  L   YP   +P YFG  FD +  SKL Q Q +   T  +
Sbjct: 184 PQLPPYFAP------THHLQQLEQHYP---VP-YFGG-FDPLTLSKLHQSQQNMQSTSPT 232

Query: 122 NAAA--------AVVSSFYSSLYPSVT 140
              A          +SSFYS++Y  ++
Sbjct: 233 GLEAQKTQQMPPTSLSSFYSNIYSGIS 259

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357607486|gb|EHJ65526.1| hypothetical protein KGM_19696 [Danaus plexippus]

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 96/214 (44%), Positives = 111/214 (51%), Gaps = 53/214 (24%)

Query: 1   MEKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFP 60
           M+KRPFIDEAKRLRA+HMKEHPDYKYRPRRKPK P                    + AFP
Sbjct: 41  MQKRPFIDEAKRLRALHMKEHPDYKYRPRRKPKPPTAGG-------------APGAGAFP 87

Query: 61  SFPLPPYFANHGGGSHPHPLDSLS-AAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTK 119
           SFPL PYFA  G      PLD+LS +A PP     YF    D + FSKL+   T +  T 
Sbjct: 88  SFPL-PYFA--GPAPTVGPLDALSYSAVPP-----YFPHQLDHLQFSKLM-APTEKLPTA 138

Query: 120 SSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAASSHPSQFLYGLKSE 179
           SS AA    SSFYSSLY +  +A  K F +P       LF    AA + P          
Sbjct: 139 SSAAAVV--SSFYSSLY-TQPAAPPKPFPSP-------LFHQYGAAPASP---------- 178

Query: 180 QLSPSSSPGESQSQSNNQSALELDQLRRPVPVIY 213
            +SP +S          Q +   DQLRRPV VIY
Sbjct: 179 -VSPVTS---------TQHSPHDDQLRRPVSVIY 202

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195161050|ref|XP_002021383.1| GL24831 [Drosophila persimilis] gi|194118496|gb|EDW40539.1| GL24831 [Drosophila persimilis]

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 78/211 (36%), Positives = 97/211 (45%), Gaps = 44/211 (20%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP-------GQSIPNNKSPNQGAPAPTS 54
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRKPK P       G  +  N    Q       
Sbjct: 195 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKPKNPMTAGPQGGLQMQANGMGQQKLGGGPG 254

Query: 55  ASNAF--PSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQ 112
           A      P   LPPYFA         P   L   YP   +P YFG  FD +  SKL Q Q
Sbjct: 255 AGAGGYNPFHQLPPYFA---------PSHHLDQPYP---VP-YFGG-FDPLALSKLHQSQ 300

Query: 113 TSQADTKSSNAAAAV-------------VSSFYSSLY-----PSVTSAQTKTFSTPPPSH 154
            + A   ++     +             +SSFYS +Y     PS+ +A +    +  P H
Sbjct: 301 AAAAAAANNQGHKVLESQQAPPQLPPTSLSSFYSGIYSGMSAPSLYAAHSANARSRWPVH 360

Query: 155 LSALFQHPTAASSHPSQF---LYGLKSEQLS 182
           L         A +H +Q+   L+G + E  S
Sbjct: 361 LIVHLLARILAGNHHTQWNGRLHGQRPEATS 391

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194747990|ref|XP_001956432.1| GF25204 [Drosophila ananassae] gi|190623714|gb|EDV39238.1| GF25204 [Drosophila ananassae]

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/160 (41%), Positives = 78/160 (48%), Gaps = 34/160 (21%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAF-- 59
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRKPK P  + P      QG P       A   
Sbjct: 191 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKPKNPLTAGPQGGLQMQGGPMGQQKLGAGAG 250

Query: 60  -------PSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQ 112
                  P   LPPYFA         P   L   YP   +P YFG  FD +  SKL Q Q
Sbjct: 251 AGPGGYNPFHQLPPYFA---------PSHHLDQPYP---VP-YFGG-FDPLALSKLHQSQ 296

Query: 113 TSQADTKSSNAAAAV-----------VSSFYSSLYPSVTS 141
            + A   ++                 +SSFYS +Y  +++
Sbjct: 297 AAAAAAVNNQVHKVEPQAPPQLPPTSLSSFYSGIYSGISA 336

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158287886|ref|XP_001688246.1| AGAP010919-PA [Anopheles gambiae str. PEST] gi|157019404|gb|EDO64436.1| AGAP010919-PA [Anopheles gambiae str. PEST]

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/155 (42%), Positives = 77/155 (49%), Gaps = 31/155 (20%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
           +KRPFIDEAKRLRA HMKEHPDYKYRPRRKPK P  S  N             A +   S
Sbjct: 130 QKRPFIDEAKRLRATHMKEHPDYKYRPRRKPKNPLASAANGLGALGAMQQSGKAGSLGSS 189

Query: 62  FP---LPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKL---------- 108
           +P   LPPYFA        HPL  L   YP   +P YFGS FD +   KL          
Sbjct: 190 YPFPQLPPYFAP------AHPLQQLEQHYP---VP-YFGS-FDPLTLQKLHQSQQQSVHQ 238

Query: 109 -----VQGQTSQADTKSSNAAA--AVVSSFYSSLY 136
                V G    +  +S+        +SSFYS++Y
Sbjct: 239 AGHSPVGGLGGDSGKQSAGQQLPPTSLSSFYSNIY 273

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195494282|ref|XP_002094770.1| GE20027 [Drosophila yakuba] gi|194180871|gb|EDW94482.1| GE20027 [Drosophila yakuba]

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 77/158 (48%), Gaps = 32/158 (20%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQ-GAPAPTSASNAF- 59
           EKRPFIDEAKRLRA+HMKEHPDYKYRPRRKPK P  + P      Q GA           
Sbjct: 187 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKPKNPLTAGPQGGLQMQAGAMGQQKLGAGPA 246

Query: 60  ------PSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQT 113
                 P   LPPYFA         P   L   YP   +P YFG  FD +  SKL Q Q 
Sbjct: 247 GAGGYNPFHQLPPYFA---------PSHHLDQGYP---VP-YFGG-FDPLALSKLHQSQA 292

Query: 114 SQADTKSSNAAAAV----------VSSFYSSLYPSVTS 141
           + A   ++                +SSFYS +Y  +++
Sbjct: 293 AAAAAVNNQGQQQGQAPPQLPPTSLSSFYSGIYSGISA 330

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
FB|FBgn0000411	382	D "Dichaete" [Drosophila melan	0.474	0.264	0.5	7.1e-21
ZFIN|ZDB-GENE-060322-5	340	sox1b "SRY-box containing gene	0.154	0.097	0.969	2.9e-17
ZFIN|ZDB-GENE-040429-1	245	sox21b "SRY-box containing gen	0.154	0.134	1.0	6e-17
ZFIN|ZDB-GENE-990715-6	239	sox21a "SRY-box containing gen	0.150	0.133	0.968	6e-17
UNIPROTKB|Q9Y651	276	SOX21 "Transcription factor SO	0.154	0.119	1.0	1.6e-16
MGI|MGI:2654070	276	Sox21 "SRY-box containing gene	0.154	0.119	1.0	1.6e-16
ZFIN|ZDB-GENE-980526-333	300	sox3 "SRY-box containing gene	0.431	0.306	0.484	2.9e-16
UNIPROTKB|B0ZTE1	262	sox21 "Transcription factor So	0.154	0.125	0.969	3.2e-16
ZFIN|ZDB-GENE-040718-186	336	sox1a "SRY-box containing gene	0.154	0.098	0.969	8.4e-16
UNIPROTKB|F1MIK5	369	SOX1 "Uncharacterized protein"	0.154	0.089	0.939	1.6e-15

FB|FBgn0000411 D "Dichaete" [Drosophila melanogaster (taxid:7227)]

 Score = 222 (83.2 bits), Expect = 7.1e-21, Sum P(2) = 7.1e-21
 Identities = 62/124 (50%), Positives = 67/124 (54%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQ---------GAPAP 52
             EKRPFIDEAKRLRA+HMKEHPDYKYRPRRKPK P  + P      Q         GA   
Sbjct:   187 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKPKNPLTAGPQGGLQMQAGGMGQQKLGAGPG 246

Query:    53 TSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQ 112
               A    P   LPPYFA     SH H    L   YP   +P YFG  FD +  SKL Q Q
Sbjct:   247 AGAGGYNPFHQLPPYFAP----SH-H----LDQGYP---VP-YFGG-FDPLALSKLHQSQ 292

Query:   113 TSQA 116
              + A
Sbjct:   293 AAAA 296

GO:0007350 "blastoderm segmentation" evidence=IMP

GO:0007417 "central nervous system development" evidence=IMP

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0008301 "DNA binding, bending" evidence=NAS;IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0035120 "post-embryonic appendage morphogenesis" evidence=IMP

GO:0002168 "instar larval development" evidence=IMP

GO:0007442 "hindgut morphogenesis" evidence=IMP

GO:0007420 "brain development" evidence=IMP

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0003730 "mRNA 3'-UTR binding" evidence=IDA

GO:0009950 "dorsal/ventral axis specification" evidence=IMP

GO:0060810 "intracellular mRNA localization involved in pattern specification process" evidence=IMP

GO:0008134 "transcription factor binding" evidence=IPI

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

ZFIN|ZDB-GENE-060322-5 sox1b "SRY-box containing gene 1b" [Danio rerio (taxid:7955)]

 Score = 174 (66.3 bits), Expect = 2.9e-17, Sum P(3) = 2.9e-17
 Identities = 32/33 (96%), Positives = 32/33 (96%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
             EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK KT
Sbjct:    82 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKTKT 114

GO:0005667 "transcription factor complex" evidence=IC

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

ZFIN|ZDB-GENE-040429-1 sox21b "SRY-box containing gene 21 b" [Danio rerio (taxid:7955)]

 Score = 182 (69.1 bits), Expect = 6.0e-17, Sum P(2) = 6.0e-17
 Identities = 33/33 (100%), Positives = 33/33 (100%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
             EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT
Sbjct:    53 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 85

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0043565 "sequence-specific DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

ZFIN|ZDB-GENE-990715-6 sox21a "SRY-box containing gene 21a" [Danio rerio (taxid:7955)]

 Score = 173 (66.0 bits), Expect = 6.0e-17, Sum P(2) = 6.0e-17
 Identities = 31/32 (96%), Positives = 32/32 (100%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
             EKRPFIDEAKRLRA+HMKEHPDYKYRPRRKPK
Sbjct:    53 EKRPFIDEAKRLRAVHMKEHPDYKYRPRRKPK 84

GO:0009953 "dorsal/ventral pattern formation" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA;ISS;IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA;IMP

GO:0001071 "nucleic acid binding transcription factor activity" evidence=IMP

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0043565 "sequence-specific DNA binding" evidence=ISS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

UNIPROTKB|Q9Y651 SOX21 "Transcription factor SOX-21" [Homo sapiens (taxid:9606)]

 Score = 182 (69.1 bits), Expect = 1.6e-16, Sum P(2) = 1.6e-16
 Identities = 33/33 (100%), Positives = 33/33 (100%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
             EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT
Sbjct:    53 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 85

GO:0001942 "hair follicle development" evidence=IEA

GO:0043588 "skin development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0048863 "stem cell differentiation" evidence=IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=NAS

GO:0000981 "sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=NAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=NAS

MGI|MGI:2654070 Sox21 "SRY-box containing gene 21" [Mus musculus (taxid:10090)]

 Score = 182 (69.1 bits), Expect = 1.6e-16, Sum P(2) = 1.6e-16
 Identities = 33/33 (100%), Positives = 33/33 (100%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
             EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT
Sbjct:    53 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 85

GO:0001942 "hair follicle development" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0005634 "nucleus" evidence=IC

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IDA

GO:0042633 "hair cycle" evidence=IMP

GO:0043588 "skin development" evidence=IMP

GO:0045665 "negative regulation of neuron differentiation" evidence=ISO

GO:0048863 "stem cell differentiation" evidence=ISO

ZFIN|ZDB-GENE-980526-333 sox3 "SRY-box containing gene 3" [Danio rerio (taxid:7955)]

 Score = 183 (69.5 bits), Expect = 2.9e-16, Sum P(2) = 2.9e-16
 Identities = 46/95 (48%), Positives = 53/95 (55%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
             EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK KT  +    +      AP   + +NA   
Sbjct:    80 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKTKTLLKKDKYSLPGGLLAPGANAVNNAVSV 139

Query:    62 FPLPPYFANHGGGSHPHPLDSLSAAYP--P-MNMP 93
                  Y   +G  +  + L     AYP  P MN P
Sbjct:   140 GQRMDYTHMNGWTNSAYSLMQDQLAYPQHPSMNSP 174

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0043049 "otic placode formation" evidence=IGI;IMP

GO:0007422 "peripheral nervous system development" evidence=IGI;IMP

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0030182 "neuron differentiation" evidence=IMP

GO:0007417 "central nervous system development" evidence=IMP

UNIPROTKB|B0ZTE1 sox21 "Transcription factor Sox-21" [Xenopus laevis (taxid:8355)]

 Score = 179 (68.1 bits), Expect = 3.2e-16, Sum P(2) = 3.2e-16
 Identities = 32/33 (96%), Positives = 33/33 (100%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
             EKRPFIDEAKRLRAMHMK+HPDYKYRPRRKPKT
Sbjct:    53 EKRPFIDEAKRLRAMHMKDHPDYKYRPRRKPKT 85

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0007399 "nervous system development" evidence=IEP

GO:0043565 "sequence-specific DNA binding" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

ZFIN|ZDB-GENE-040718-186 sox1a "SRY-box containing gene 1a" [Danio rerio (taxid:7955)]

 Score = 174 (66.3 bits), Expect = 8.4e-16, Sum P(2) = 8.4e-16
 Identities = 32/33 (96%), Positives = 32/33 (96%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
             EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK KT
Sbjct:    82 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKTKT 114

GO:0051091 "positive regulation of sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0005667 "transcription factor complex" evidence=IC

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

UNIPROTKB|F1MIK5 SOX1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 171 (65.3 bits), Expect = 1.6e-15, Sum P(2) = 1.6e-15
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query:     2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
             EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct:    91 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 123

GO:0021884 "forebrain neuron development" evidence=IEA

GO:0021521 "ventral spinal cord interneuron specification" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0002089 "lens morphogenesis in camera-type eye" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001046 "core promoter sequence-specific DNA binding" evidence=IEA

---

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)
P40670	CH31_CHICK	No assigned EC number	0.9259	0.1267	0.5	no	N/A
P40667	CH03_CHICK	No assigned EC number	0.9259	0.1267	0.5	no	N/A
P40642	AMA2_ALLMI	No assigned EC number	0.9259	0.1267	0.5	N/A	N/A
P40669	CH07_CHICK	No assigned EC number	0.9259	0.1267	0.5	no	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	213
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	3e-09
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	2e-04
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-04

>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 51.1 bits (123), Expect = 3e-09
 Identities = 15/26 (57%), Positives = 23/26 (88%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYR 27
          EK+P+ +EAK+L+ +HMK +PDYK+R
Sbjct: 47 EKQPYYEEAKKLKELHMKLYPDYKWR 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|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP 32
           K  + + A+  +  H +E+PDYKY PR+  
Sbjct: 47 VKAYYKELAEEEKERHAREYPDYKYTPRKSS 77

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11. Length = 77

>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 9/24 (37%), Positives = 18/24 (75%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYK 25
          EK+P+ ++A++ +A + K +P YK
Sbjct: 46 EKKPYEEKAEKEKARYEKAYPAYK 69

Length = 69

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
KOG0527|consensus	331		99.54
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	98.45
KOG0528|consensus	511		98.19
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	97.7
KOG3248|consensus	421		91.58
smart00398	70	HMG high mobility group.	91.56
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	89.76
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	85.46

>KOG0527|consensus

Probab=99.54  E-value=5.9e-15  Score=134.05  Aligned_cols=37  Identities=73%  Similarity=1.137  Sum_probs=34.9

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQS   38 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~~~~~   38 (213)
                      ||+||||||||||++||++|||||||||||+|+....
T Consensus       108 EKrPFi~EAeRLR~~HmkehPdYKYRPRRKkk~~~~~  144 (331)
T KOG0527|consen  108 EKRPFVDEAERLRAQHMKEYPDYKYRPRRKKKKRPKL  144 (331)
T ss_pred             hhccHHHHHHHHHHHHHHhCCCccccccccccccccc
Confidence            8999999999999999999999999999999887764

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=98.45  E-value=1.2e-07  Score=67.72  Aligned_cols=31  Identities=35%  Similarity=0.629  Sum_probs=29.4

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP   32 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~   32 (213)
                      ||.+|.++|++++++|+++||+|+|+|||+.
T Consensus        47 eK~~y~~~A~~~k~~~~~~~p~Yky~p~~~~   77 (77)
T cd01389          47 VKAYYKELAEEEKERHAREYPDYKYTPRKSS   77 (77)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCcccCCCCC
Confidence            6899999999999999999999999999974

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.

>KOG0528|consensus

Probab=98.19  E-value=8.1e-07  Score=85.49  Aligned_cols=37  Identities=38%  Similarity=0.790  Sum_probs=33.7

Q ss_pred             CCcchhHHHHHHHHHHHHhhCCCCcccCCCCCCCCCC
Q psy15631          1 MEKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQ   37 (213)
Q Consensus         1 ~EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~~~~   37 (213)
                      .||+||++|-.||..+|+++|||||||||-|+.|..+
T Consensus       370 ~eKQPYYEEQaRLSk~HlEk~PdYrYkPRPKRTCvvd  406 (511)
T KOG0528|consen  370 TEKQPYYEEQARLSKLHLEKYPDYRYKPRPKRTCVVD  406 (511)
T ss_pred             ccccchHHHHHHHHHhhhccCcccccCCCCCceeeec
Confidence            3899999999999999999999999999988877553

>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=97.70  E-value=2.2e-05  Score=55.62  Aligned_cols=26  Identities=58%  Similarity=1.088  Sum_probs=24.9

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCccc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYR   27 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYr   27 (213)
                      ||.+|.++|++++++|+++||||||+
T Consensus        47 eK~~y~~~a~~~k~~y~~~~p~y~y~   72 (72)
T cd01388          47 EKQPYYEEAKKLKELHMKLYPDYKWR   72 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCCC
Confidence            68999999999999999999999996

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.

>KOG3248|consensus

Probab=91.58  E-value=0.19  Score=48.07  Aligned_cols=28  Identities=25%  Similarity=0.492  Sum_probs=24.8

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPR   29 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPR   29 (213)
                      |..-|+|.|++.|+.||+.||+|.-|-+
T Consensus       237 EQAKYyElArKerqlH~qlYP~WSARdN  264 (421)
T KOG3248|consen  237 EQAKYYELARKERQLHMQLYPGWSARDN  264 (421)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCcchhhh
Confidence            5678999999999999999999986665

>smart00398 HMG high mobility group

Probab=91.56  E-value=0.1  Score=34.89  Aligned_cols=24  Identities=38%  Similarity=0.639  Sum_probs=22.6

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYK   25 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYK   25 (213)
                      ||.+|.++|++.+++|.+++++|+
T Consensus        47 ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398       47 EKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcC
Confidence            689999999999999999999985

>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

Probab=89.76  E-value=0.066  Score=36.35  Aligned_cols=24  Identities=42%  Similarity=0.666  Sum_probs=22.3

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYK   25 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYK   25 (213)
                      ||.+|.++|++.+++|.+++++|+
T Consensus        46 eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen   46 EKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcC
Confidence            689999999999999999998885

HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....

>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

Probab=85.46  E-value=0.57  Score=30.92  Aligned_cols=21  Identities=29%  Similarity=0.436  Sum_probs=19.2

Q ss_pred             CcchhHHHHHHHHHHHHhhCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHP   22 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YP   22 (213)
                      ||.+|+++|++.+++|.+.+|
T Consensus        46 ~k~~y~~~a~~~~~~y~~~~~   66 (66)
T cd00084          46 EKKKYEEKAEKDKERYEKEMP   66 (66)
T ss_pred             HHHHHHHHHHHHHHHHHHhhC
Confidence            689999999999999998875

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	213
2le4_A	81	Solution Structure Of The Hmg Box Dna-Binding Domai		1e-12
1gt0_D	80	Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le		2e-12
1o4x_B	88	Ternary Complex Of The Dna Binding Domains Of The O		2e-12
3f27_D	83	Structure Of Sox17 Bound To Dna Length = 83		7e-08
4euw_A	106	Crystal Structure Of A Hmg Domain Of Transcription		2e-07
3u2b_C	79	Structure Of The Sox4 Hmg Domain Bound To Dna Lengt		2e-05
1j47_A	85	3d Solution Nmr Structure Of The M9i Mutant Of The		3e-05
1j46_A	85	3d Solution Nmr Structure Of The Wild Type Hmg-Box		3e-05
2yul_A	82	Solution Structure Of The Hmg Box Of Human Transcri		6e-05
4a3n_A	71	Crystal Structure Of Hmg-Box Of Human Sox17 Length		1e-04

>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of Human Stem Cell Transcription Factor Sox2 Length = 81

Iteration: 1
 Score = 69.3 bits (168), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 49 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 81

>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 48 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 80

>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

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 31/33 (93%), Positives = 32/33 (96%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 53 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 85

>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83

Iteration: 1
 Score = 53.9 bits (128), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 29/32 (90%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          EKRPF++EA+RLR  HM++HP+YKYRPRR+ +
Sbjct: 52 EKRPFVEEAERLRVQHMQDHPNYKYRPRRRKQ 83

>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

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/30 (70%), Positives = 27/30 (90%)
Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK 31
           EKRPF++EA+RLR  H K+HPDYKY+PRR+
Sbjct: 75  EKRPFVEEAERLRVQHKKDHPDYKYQPRRR 104

>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna Length = 79

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 26/32 (81%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          +K PFI EA+RLR  HM ++PDYKYRPR+K K
Sbjct: 48 DKIPFIQEAERLRLKHMADYPDYKYRPRKKVK 79

>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

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/32 (62%), Positives = 27/32 (84%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          EK PF  EA++L+AMH +++P+YKYRPRRK K
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAK 81

>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

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/32 (62%), Positives = 27/32 (84%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          EK PF  EA++L+AMH +++P+YKYRPRRK K
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAK 81

>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription Factor Sox-17 Length = 82

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 17/27 (62%), Positives = 23/27 (85%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRP 28
          EKRPF++EA+RLR  HM++HP+YK  P
Sbjct: 53 EKRPFVEEAERLRVQHMQDHPNYKSGP 79

>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17 Length = 71

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 16/24 (66%), Positives = 22/24 (91%)
Query: 2  EKRPFIDEAKRLRAMHMKEHPDYK 25
          EKRPF++EA+RLR  HM++HP+YK
Sbjct: 48 EKRPFVEEAERLRVQHMQDHPNYK 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	4e-16
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	4e-16
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	6e-16
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	3e-15
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	1e-14
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	1e-14
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	4e-14
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	9e-14
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	1e-12
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	3e-10
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	1e-09
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	7e-05
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	1e-07
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	8e-06
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-05
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	1e-04
2lhj_A	97	High mobility group protein homolog NHP1; structur	4e-04

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79

 Score = 69.1 bits (170), Expect = 4e-16
 Identities = 21/32 (65%), Positives = 26/32 (81%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          +K PFI EA+RLR  HM ++PDYKYRPR+K K
Sbjct: 48 DKIPFIQEAERLRLKHMADYPDYKYRPRKKVK 79

>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

 Score = 69.1 bits (170), Expect = 4e-16
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 48 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 80

>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

 Score = 69.2 bits (170), Expect = 6e-16
 Identities = 20/33 (60%), Positives = 27/33 (81%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EK PF  EA++L+AMH +++P+YKYRPRRK K 
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKM 82

>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

 Score = 67.2 bits (165), Expect = 3e-15
 Identities = 21/32 (65%), Positives = 29/32 (90%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          EKRPF++EA+RLR  HM++HP+YKYRPRR+ +
Sbjct: 52 EKRPFVEEAERLRVQHMQDHPNYKYRPRRRKQ 83

>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

 Score = 65.7 bits (161), Expect = 1e-14
 Identities = 8/34 (23%), Positives = 17/34 (50%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP 35
          E+  + + A++ R +HM+ +P +  R     K  
Sbjct: 48 EQAKYYELARKERQLHMQLYPGWSARDNYGKKKK 81

>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

 Score = 65.3 bits (160), Expect = 1e-14
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK 31
          EK+P+ +E  RL   H++++PDYKY+PR K
Sbjct: 50 EKQPYYEEQARLSKQHLEKYPDYKYKPRPK 79

>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

 Score = 64.2 bits (157), Expect = 4e-14
 Identities = 10/29 (34%), Positives = 15/29 (51%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRR 30
          EK+ + D AK  +   MK +P Y+  P  
Sbjct: 53 EKQKYTDMAKEYKDAFMKANPGYRSGPSS 81

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Length = 106

 Score = 63.9 bits (156), Expect = 9e-14
 Identities = 21/30 (70%), Positives = 27/30 (90%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK 31
           EKRPF++EA+RLR  H K+HPDYKY+PRR+
Sbjct: 75  EKRPFVEEAERLRVQHKKDHPDYKYQPRRR 104

>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

 Score = 59.9 bits (146), Expect = 1e-12
 Identities = 16/27 (59%), Positives = 23/27 (85%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRP 28
          EK PF  EA++L+AMH +++P+YKYRP
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRP 76

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71

 Score = 53.4 bits (129), Expect = 3e-10
 Identities = 16/24 (66%), Positives = 22/24 (91%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYK 25
          EKRPF++EA+RLR  HM++HP+YK
Sbjct: 48 EKRPFVEEAERLRVQHMQDHPNYK 71

>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

 Score = 54.1 bits (130), Expect = 1e-09
 Identities = 6/26 (23%), Positives = 16/26 (61%)

Query: 2   EKRPFIDEAKRLRAMHMKEHPDYKYR 27
           +K+P+  +A +L+  + K+   Y+ +
Sbjct: 134 DKQPYEKKAAKLKEKYEKDIAAYRAK 159

>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

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 11/61 (18%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
          EK PF  EA++L+AMH +++P+YKYR     K                 AP    +AF  
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDP-----------NAPKRPPSAFFL 98

Query: 62 F 62
          F
Sbjct: 99 F 99

>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

 Score = 46.6 bits (111), Expect = 1e-07
 Identities = 8/22 (36%), Positives = 12/22 (54%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPD 23
          E+R +  EAK L     + +PD
Sbjct: 63 ERRMYTLEAKALAEEQKRLNPD 84

>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

 Score = 42.0 bits (99), Expect = 8e-06
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP 35
          EK+ ++DEA++ +  ++KE   Y+     K  T 
Sbjct: 53 EKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCTE 86

>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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 3/24 (12%), Positives = 8/24 (33%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYK 25
          +K  +      L+A   ++     
Sbjct: 66 KKAKYKAREAALKAQSERKSGPSS 89

>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

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 6/26 (23%), Positives = 16/26 (61%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYR 27
          +K+P+  +A +L+  + K+   Y+ +
Sbjct: 52 DKQPYEKKAAKLKEKYEKDIAAYRAK 77

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 7/26 (26%), Positives = 13/26 (50%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYR 27
          EK+P+   +   R  + +E  +Y  R
Sbjct: 70 EKKPYERMSDEDRVRYEREKAEYAQR 95

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	98.71
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	98.61
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	98.58
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	98.56
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	98.5
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	98.2
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	98.06
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	98.0
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	97.37
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.0
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	96.81
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	95.37
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	95.35
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	95.08
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	93.99
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	93.6
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	92.53
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	89.64
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	89.09
1ckt_A	71	High mobility group 1 protein; high-mobility group	88.75
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	83.76
2cto_A	93	Novel protein; high mobility group box domain, hel	82.21

>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

Probab=98.71  E-value=5.2e-09  Score=74.00  Aligned_cols=31  Identities=48%  Similarity=0.963  Sum_probs=22.5

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP   32 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~   32 (213)
                      ||++|+++|++++++|+++||||+|+||||+
T Consensus        50 eK~~y~~~A~~~k~~~~~~~p~Yky~pr~~~   80 (81)
T 1i11_A           50 EKQPYYEEQARLSKQHLEKYPDYKYKPRPKR   80 (81)
T ss_dssp             GGHHHHHHHHHHHHHHHTTCSCC--------
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCeeccCCCC
Confidence            7999999999999999999999999999875

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1

Probab=98.61  E-value=1.4e-08  Score=70.95  Aligned_cols=32  Identities=66%  Similarity=1.111  Sum_probs=28.3

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK   33 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k   33 (213)
                      ||.+|.++|++++++|.++||+|+|+|||+.|
T Consensus        48 eK~~y~~~A~~~k~~y~~~~p~Yky~Prk~~k   79 (79)
T 3u2b_C           48 DKIPFIQEAERLRLKHMADYPDYKYRPRKKVK   79 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSSCCCCCCC---
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCeeCCCCCCC
Confidence            68999999999999999999999999999865

>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

Probab=98.58  E-value=3.1e-08  Score=70.92  Aligned_cols=35  Identities=57%  Similarity=0.962  Sum_probs=32.8

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPG   36 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~~~   36 (213)
                      ||.+|.++|++++++|.++||+|+|+|||+++...
T Consensus        50 eK~~y~~~A~~~k~~y~~~~~~Yk~~prr~~~~~~   84 (85)
T 1j46_A           50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLP   84 (85)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHCcccccCCCCcccccc
Confidence            68999999999999999999999999999998754

>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

Probab=98.56  E-value=2.4e-08  Score=70.47  Aligned_cols=32  Identities=66%  Similarity=1.311  Sum_probs=28.3

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK   33 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k   33 (213)
                      ||.+|.++|++++++|.+++|+|+|+||||++
T Consensus        52 eK~~y~~~A~~~k~~y~~~~~~Yky~P~~kk~   83 (83)
T 3f27_D           52 EKRPFVEEAERLRVQHMQDHPNYKYRPRRRKQ   83 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCCCCCCC---
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCeeCCccCCC
Confidence            68999999999999999999999999999875

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B

Probab=98.50  E-value=5.5e-08  Score=68.40  Aligned_cols=33  Identities=94%  Similarity=1.487  Sum_probs=30.9

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT   34 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~   34 (213)
                      ||.+|.++|++++++|.+++|+|+|+|||++|+
T Consensus        48 eK~~y~~~A~~~k~~y~~~~~~Yk~~p~r~~k~   80 (80)
T 1gt0_D           48 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT   80 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHCcccccCCCCCCCC
Confidence            689999999999999999999999999999874

>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

Probab=98.20  E-value=8.5e-07  Score=63.36  Aligned_cols=33  Identities=24%  Similarity=0.416  Sum_probs=29.9

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT   34 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~   34 (213)
                      ||.+|.++|++++++|+++||+|+|+|+.++++
T Consensus        48 eK~~y~~~A~~~k~~y~~~~~~Yk~~p~~~~~k   80 (86)
T 2lef_A           48 EQAKYYELARKERQLHMQLYPGWSARDNYGKKK   80 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTCCSCSSTTTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHcccccCCCCCCCCc
Confidence            689999999999999999999999999966543

>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*

Probab=98.06  E-value=1.4e-06  Score=60.47  Aligned_cols=27  Identities=59%  Similarity=1.104  Sum_probs=25.3

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRP   28 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrP   28 (213)
                      ||++|.++|+++|++|+++||+|||+|
T Consensus        50 eK~~y~~~A~~~k~~y~~~~~~Yky~P   76 (76)
T 1hry_A           50 EKWPFFQEAQKLQAMHREKYPNYKYRP   76 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSSCCCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCc
Confidence            689999999999999999999999998

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus}

Probab=98.00  E-value=1.8e-06  Score=60.98  Aligned_cols=29  Identities=34%  Similarity=0.618  Sum_probs=28.1

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRR   30 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRR   30 (213)
                      ||++|.++|++++++|.+++|+|+|+|||
T Consensus        53 eK~~y~~~A~~~k~~y~~~~~~yk~~p~~   81 (82)
T 1wz6_A           53 EKQKYTDMAKEYKDAFMKANPGYRSGPSS   81 (82)
T ss_dssp             HHHHHHHHHHHHHHHHCCSCSSCCCCTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHhhcCCCC
Confidence            68999999999999999999999999997

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1

Probab=97.37  E-value=8.1e-05  Score=55.03  Aligned_cols=30  Identities=20%  Similarity=0.411  Sum_probs=27.8

Q ss_pred             CcchhHHHHHHHHHH-------HHhhCCCCcccCCCC
Q psy15631          2 EKRPFIDEAKRLRAM-------HMKEHPDYKYRPRRK   31 (213)
Q Consensus         2 EK~PyideAkrLKa~-------H~k~YPdYKYrPRRK   31 (213)
                      ||++|.++|++++++       |.++||||+|+||+-
T Consensus        56 eK~~Y~~~A~~~k~~Y~~e~~~y~~~~P~~~~~~~~~   92 (99)
T 1k99_A           56 KKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKKL   92 (99)
T ss_dssp             THHHHHHHHHHHHHHHHHHHGGGGGCCCCCSCCCCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCccCCCccc
Confidence            799999999999999       999999999999864

>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

Probab=97.00  E-value=0.00034  Score=54.29  Aligned_cols=33  Identities=48%  Similarity=0.843  Sum_probs=29.9

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT   34 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~   34 (213)
                      ||.+|.++|++++++|.+++++|+|++|++++.
T Consensus        50 eK~~y~~~A~~~k~~y~~~~~~y~~~k~~~kk~   82 (159)
T 2gzk_A           50 EKWPFFQEAQKLQAMHREKYPNYKYRKGETKKK   82 (159)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSSCSCCCCCCGGG
T ss_pred             HhccHHHHHHHHHHHHHHHhhcccccccccccc
Confidence            689999999999999999999999999876544

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0

Probab=96.81  E-value=0.00044  Score=46.76  Aligned_cols=24  Identities=67%  Similarity=1.288  Sum_probs=20.4

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYK   25 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYK   25 (213)
                      ||.+|.++|++++++|.+++|+||
T Consensus        48 eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A           48 EKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCC---
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCcC
Confidence            689999999999999999999996

>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

Probab=95.37  E-value=0.0075  Score=41.56  Aligned_cols=25  Identities=24%  Similarity=0.493  Sum_probs=23.7

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKY   26 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKY   26 (213)
                      ||.+|.++|++++++|.+++++|+.
T Consensus        52 eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A           52 DKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             GSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            7999999999999999999999974

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=95.35  E-value=0.0031  Score=46.49  Aligned_cols=33  Identities=15%  Similarity=0.212  Sum_probs=29.7

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT   34 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~   34 (213)
                      ||++|.++|++++++|.+++++|+|+...+...
T Consensus        63 eK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~~~   95 (102)
T 2co9_A           63 QKQVYKKKTEAAKKEYLKQLAAYRASLVSKSYT   95 (102)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccccccc
Confidence            689999999999999999999999998876544

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus}

Probab=95.08  E-value=0.0021  Score=46.37  Aligned_cols=31  Identities=29%  Similarity=0.374  Sum_probs=27.9

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP   32 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~   32 (213)
                      ||++|.++|++++++|.+++++|++++..+.
T Consensus        53 eK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~   83 (92)
T 2crj_A           53 EKQRYLDEAEKEKQQYLKELWAYQQSEAYKV   83 (92)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHccHHHHH
Confidence            6899999999999999999999998876543

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.99  E-value=0.009  Score=43.02  Aligned_cols=31  Identities=10%  Similarity=-0.029  Sum_probs=27.1

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP   32 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~   32 (213)
                      ||++|.++|+++|++|.+++++|+++..++.
T Consensus        53 eK~~y~~~A~~~k~~y~~e~~~y~~~~~~~~   83 (92)
T 2cs1_A           53 EKLKYEEKATKDLERYNSQMKRAIEQESQMS   83 (92)
T ss_dssp             HHHHHHHHHHTTTHHHHHHHHHHTSTTTCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence            6899999999999999999999997754443

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster}

Probab=93.60  E-value=0.026  Score=38.76  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=23.0

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYK   25 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYK   25 (213)
                      ||.+|.++|+++|++|.+++++|+
T Consensus        47 eK~~y~~~A~~~k~~y~~e~~~Y~   70 (73)
T 1wxl_A           47 DKSKWEDAAAKDKQRYHDEMRNYK   70 (73)
T ss_dssp             THHHHHHHHHHHHHHHHTTTGGGT
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999999999996

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1

Probab=92.53  E-value=0.06  Score=37.67  Aligned_cols=24  Identities=38%  Similarity=0.314  Sum_probs=23.0

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYK   25 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYK   25 (213)
                      ||.+|.++|++++++|.+++++|+
T Consensus        55 eK~~y~~~A~~~k~~y~~e~~~y~   78 (83)
T 1aab_A           55 EKGKFEDMAKADKARYEREMKTYI   78 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            689999999999999999999995

>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*

Probab=89.64  E-value=0.06  Score=36.94  Aligned_cols=24  Identities=8%  Similarity=0.194  Sum_probs=22.3

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYK   25 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYK   25 (213)
                      +|++|.++|++++++|.+++++|+
T Consensus        47 ~K~~y~~~A~~~k~~y~~~~~~Y~   70 (73)
T 3nm9_A           47 DKSEWEAKAAKAKDDYDRAVKEFE   70 (73)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHH
Confidence            388999999999999999999996

>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

Probab=89.09  E-value=0.052  Score=40.18  Aligned_cols=25  Identities=8%  Similarity=-0.051  Sum_probs=23.3

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKY   26 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKY   26 (213)
                      ||+||.++|+++|++|.+++++|+-
T Consensus        52 eK~~Y~~~A~~~k~~Y~~e~~~Y~~   76 (101)
T 1v63_A           52 QKEHYKKLAEEQQRQYKVHLDLWVK   76 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7899999999999999999999973

>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

Probab=88.75  E-value=0.22  Score=33.43  Aligned_cols=23  Identities=39%  Similarity=0.358  Sum_probs=21.3

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDY   24 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdY   24 (213)
                      ||.+|.++|+++|++|.++...|
T Consensus        49 eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A           49 EKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhC
Confidence            79999999999999999988776

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=83.76  E-value=0.15  Score=38.19  Aligned_cols=26  Identities=12%  Similarity=0.059  Sum_probs=23.9

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCccc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYR   27 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYr   27 (213)
                      ||.+|.++|++++++|.+++++|+-+
T Consensus        59 eK~~Y~~~A~~~k~~Y~~e~~~Y~~~   84 (108)
T 1v64_A           59 EKDAYHKKCDQKKKDYEVELLRFLES   84 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            68999999999999999999999753

>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=82.21  E-value=1.4  Score=32.63  Aligned_cols=19  Identities=32%  Similarity=0.464  Sum_probs=17.5

Q ss_pred             CcchhHHHHHHHHHHHHhh
Q psy15631          2 EKRPFIDEAKRLRAMHMKE   20 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~   20 (213)
                      ||+||.++|+++|++|.++
T Consensus        57 EK~pYe~~A~~~K~~y~kd   75 (93)
T 2cto_A           57 EKEKYAEMAREWRAAQGKD   75 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhcc
Confidence            7999999999999999776

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	213
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	2e-13
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	2e-11
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	2e-10
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	2e-06
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-06
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-05
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	8e-05
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	1e-04
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	0.001
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	0.001
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	0.003

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

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

 Score = 61.4 bits (149), Expect = 2e-13
 Identities = 31/33 (93%), Positives = 32/33 (96%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
          EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 48 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 80

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 2e-11
 Identities = 20/34 (58%), Positives = 27/34 (79%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP 35
          EK PF  EA++L+AMH +++P+YKYRPRRK K  
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKML 83

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.3 bits (128), Expect = 2e-10
 Identities = 8/34 (23%), Positives = 17/34 (50%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP 35
          E+  + + A++ R +HM+ +P +  R     K  
Sbjct: 48 EQAKYYELARKERQLHMQLYPGWSARDNYGKKKK 81

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70

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

 Score = 42.1 bits (99), Expect = 2e-06
 Identities = 10/23 (43%), Positives = 17/23 (73%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDY 24
          EK+P+ +E  RL   H++++PDY
Sbjct: 48 EKQPYYEEQARLSKQHLEKYPDY 70

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 41.8 bits (98), Expect = 3e-06
 Identities = 6/30 (20%), Positives = 17/30 (56%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK 31
          +K+P+  +A +L+  + K+   Y+ + +  
Sbjct: 48 DKQPYEKKAAKLKEKYEKDIAAYRAKGKPD 77

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (90), Expect = 5e-05
 Identities = 3/32 (9%), Positives = 11/32 (34%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          EK  +  +  + +  +  E   +      + +
Sbjct: 59 EKDAYHKKCDQKKKDYEVELLRFLESLPEEEQ 90

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.0 bits (88), Expect = 8e-05
 Identities = 6/36 (16%), Positives = 14/36 (38%), Gaps = 7/36 (19%)

Query: 2  EKRPFIDEAKRLRAMHMKE-------HPDYKYRPRR 30
          +K  +I + +R +    +        HPD     ++
Sbjct: 56 KKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK 91

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

 Score = 37.1 bits (86), Expect = 1e-04
 Identities = 2/25 (8%), Positives = 12/25 (48%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKY 26
          +K  +  +A + +  + +   +++ 
Sbjct: 47 DKSEWEAKAAKAKDDYDRAVKEFEA 71

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 2/32 (6%), Positives = 10/32 (31%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
          +K  +   A+  +  +      +      + +
Sbjct: 52 QKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDR 83

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 34.1 bits (78), Expect = 0.001
 Identities = 9/23 (39%), Positives = 12/23 (52%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDY 24
          EK  F D AK  +A + +E   Y
Sbjct: 49 EKGKFEDMAKADKARYEREMKTY 71

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93

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

 Score = 33.7 bits (77), Expect = 0.003
 Identities = 6/27 (22%), Positives = 12/27 (44%)

Query: 2  EKRPFIDEAKRLRAMHMKEHPDYKYRP 28
          EK+P+  +A+  +  +  E   Y    
Sbjct: 66 EKQPYEAKAQADKKRYESEKELYNATL 92

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	213
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	98.31
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	98.05
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.96
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	97.16
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	90.83
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	86.17
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	83.29
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	80.39

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=98.31  E-value=1.3e-07  Score=66.53  Aligned_cols=33  Identities=94%  Similarity=1.487  Sum_probs=30.6

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT   34 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~   34 (213)
                      ||.+|.++|+++|++|.+++|+|+|+||||.|+
T Consensus        48 eK~~y~~~A~~~k~~y~~~~p~Yk~~p~rk~kt   80 (80)
T d1gt0d_          48 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT   80 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHCccccCCCCCCCCC
Confidence            689999999999999999999999999998764

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.05  E-value=1.3e-06  Score=61.60  Aligned_cols=34  Identities=24%  Similarity=0.398  Sum_probs=31.1

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP   35 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~~   35 (213)
                      ||.+|.++|++++++|+++||+|+|+|+++.+..
T Consensus        48 eK~~y~~~A~~~k~~~~~~~p~yk~~~~~~~~~~   81 (86)
T d2lefa_          48 EQAKYYELARKERQLHMQLYPGWSARDNYGKKKK   81 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTCCSCSSTTTSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCCCCCCCCCcc
Confidence            6899999999999999999999999999877553

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.96  E-value=2.5e-06  Score=59.94  Aligned_cols=34  Identities=59%  Similarity=1.006  Sum_probs=31.2

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCCCCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP   35 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRRK~k~~   35 (213)
                      ||.+|.++|++++++|.+++|+|+|+|+++.+..
T Consensus        50 eK~~y~~~A~~~k~~y~~~~~~yk~~p~~~~k~~   83 (85)
T d1j46a_          50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKML   83 (85)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCCCCCCCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHhccCCCCccccc
Confidence            6899999999999999999999999999877653

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=97.16  E-value=9.8e-05  Score=49.82  Aligned_cols=23  Identities=43%  Similarity=0.901  Sum_probs=22.4

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDY   24 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdY   24 (213)
                      ||++|.++|+++|++|+++||||
T Consensus        48 eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_          48 EKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             GGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCC
Confidence            79999999999999999999998

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

Probab=90.83  E-value=0.02  Score=38.37  Aligned_cols=29  Identities=21%  Similarity=0.458  Sum_probs=26.7

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcccCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRR   30 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYrPRR   30 (213)
                      ||.+|.++|++++++|.++++.|+++++.
T Consensus        48 eK~~y~~~a~~~k~~Y~~e~~~y~~k~~~   76 (79)
T d1hsma_          48 DKQPYEKKAAKLKEKYEKDIAAYRAKGKP   76 (79)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHccCCC
Confidence            79999999999999999999999987653

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

Probab=86.17  E-value=0.074  Score=35.16  Aligned_cols=25  Identities=8%  Similarity=0.157  Sum_probs=23.2

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCcc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKY   26 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKY   26 (213)
                      ||++|.++|++++++|.+++++|+.
T Consensus        47 eK~~y~~~a~~~k~~y~~~~~~y~~   71 (73)
T d1qrva_          47 DKSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7899999999999999999999964

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=83.29  E-value=0.29  Score=31.66  Aligned_cols=23  Identities=39%  Similarity=0.358  Sum_probs=21.7

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCC
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDY   24 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdY   24 (213)
                      ||.+|.++|++.++++.++...|
T Consensus        49 eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_          49 EKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcC
Confidence            79999999999999999998887

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.39  E-value=0.096  Score=36.20  Aligned_cols=26  Identities=8%  Similarity=-0.051  Sum_probs=24.6

Q ss_pred             CcchhHHHHHHHHHHHHhhCCCCccc
Q psy15631          2 EKRPFIDEAKRLRAMHMKEHPDYKYR   27 (213)
Q Consensus         2 EK~PyideAkrLKa~H~k~YPdYKYr   27 (213)
                      ||.+|.++|++++++|.+++..|+++
T Consensus        52 eK~~Y~~~a~~~~~~y~~e~~~y~~~   77 (101)
T d1v63a_          52 QKEHYKKLAEEQQRQYKVHLDLWVKS   77 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999876