Citrus Sinensis ID: 017939

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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-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360---
Protein Sequence
MASSDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHESLSQPKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKELLV
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccHHHHHHccHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccccEEcccccccccccccccccccccccHHHEEEcccccccccccccHHHHHccccccccccHHHHccHHHcccHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHccccHHHHHHHHHHHccHHHHcccccccccccccccccccHHHEEcHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEcc
Coil and Loop (DISEMBL)
massdvasmavepskkprsrralkpknslANEAVVMaqtpsqspipnppdaglskenheslsqpKKAAAKGKakqatkkqdtSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQEKLHMELKKLQKMkefkpnmtlpivQCLKDKEqdrkkkgcaerkrpsppyilWCKDQWneakkenpeaEFKEITNILGAkwknvsaeekkpyEEKYQAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADkenkkpkkekdplkpkhpvtayFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKELLV
Flexible Loop (DISEMBL)
massdvasmavepskkprsrralkpknSLANEAVVMAQTPSQSPIPNPPDAGLSKENHESLSQPKKaaakgkakqatkkqdtsfdKDLQEMQEMLEkmklekekteELLKEKDEMLKMKEEELELQGKEQEKLHMELKKLQkmkefkpnmtlpivqclkdkeqdrkkkgcaerkrpsppyilWCKDQWNEAKKENPEAEFKEItnilgakwknvsaeekkpyeekyqAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEadkenkkpkkekdplkpkhpVTAYFLFSSERRAALLADNKNVLEVAKITgeewknmteeqkrpyeeiakknkekynEEMEAYKrrmkellv
Low Complexity Region (SEG)
MASSDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHESLSQPkkaaakgkakqatkkQDTSFDKDlqemqemlekmklekekteellkekdemlkmkeeelelqgkeqeklHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSaeekkpyeekyqaekeayLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFkqeadkenkkpkkekdplkpkHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPyeeiakknkekyneemeaykRRMKELLV
Disordered region (IsUnstruct)
********************************************************************************************************************************************************PIVQC**********************YILWCKDQWNE*********FKEITNILGAKWK********************************************************************************VTAYFLFSSERRAALLADNKNVLEVAKITGE****************************************
Disordered Region (DISOPRED)
*********************************************************************************************************************************************************************************PPYILWCKDQWN************EITNILGAK********************EAYLQV*************LEEEHKQKTAMELLEQYL***********************HPVTAYFLFSS*****************KITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKEL*V
Disordered Region (DISEMBL)
************************PKNSLANEAVVMAQTPSQSPIPNPP*********************************SFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDK*************RPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQ****************KPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKELLV
Disordered Region (DISPRO)
***********************************************************************************FDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCL**********GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEE*KQKTAMELLEQYLQFKQEAD*******KEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKELLV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASSDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHESLSQPKKAAAKGKAKQATKKQDTSFDKDxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYxxxxxxxxxxxxxxxxxxxxxSEAMKLLEEEHKQKTxxxxxxxxxxxxxxxxxxxxxPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYxxxxxxxxxxxxxxxxxxxxxMKELLV
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	363	2.2.26 [Sep-21-2011]
Q9SUP7	456	High mobility group B pro	yes	no	0.845	0.673	0.601	1e-100
Q9T012	446	High mobility group B pro	no	no	0.746	0.607	0.681	9e-97
P26586	271	High mobility group prote	N/A	no	0.393	0.527	0.291	2e-11
P07746	204	High mobility group-T pro	N/A	no	0.407	0.725	0.309	2e-11
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.206	0.503	0.435	7e-10
Q6CC79	103	Non-histone chromosomal p	yes	no	0.212	0.747	0.405	8e-10
P11633	99	Non-histone chromosomal p	yes	no	0.225	0.828	0.391	5e-09
P63159	215	High mobility group prote	no	no	0.407	0.688	0.315	6e-09
A9RA84	215	High mobility group prote	N/A	no	0.407	0.688	0.315	6e-09
P63158	215	High mobility group prote	yes	no	0.407	0.688	0.315	6e-09

>sp|Q9SUP7|HMGB6_ARATH High mobility group B protein 6 OS=Arabidopsis thaliana GN=HMGB6 PE=2 SV=1

 Score =  364 bits (934), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 211/351 (60%), Positives = 263/351 (74%), Gaps = 44/351 (12%)

Query: 13  PSKKPR-SRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHESLSQPKKAAAKG 71
           P+KKPR SR+ALK KN L        +TP     P+P                   + KG
Sbjct: 9   PTKKPRNSRKALKQKNELV-------ETP-----PSP------------------VSVKG 38

Query: 72  KAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQE 131
           K+ +       SF++DL EMQ MLEKMK+EK+KTEELLKEKDE+L+ KEEELE +  EQE
Sbjct: 39  KSAK-------SFEQDLMEMQTMLEKMKIEKDKTEELLKEKDEILRKKEEELETRDAEQE 91

Query: 132 KLHMELKKLQKMKEFKPNMTL-----PIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKD 186
           KL +ELKKLQKMKEFKPNMT       + Q  ++K   +KKK C E KRPS  Y+LWCKD
Sbjct: 92  KLKVELKKLQKMKEFKPNMTFACGQSSLTQAEQEKANKKKKKDCPETKRPSSSYVLWCKD 151

Query: 187 QWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEA 246
           QW E KKENPEA+FKE +NILGAKWK++SAE+KKPYEE+YQ EKEAYLQV+AKE+RE EA
Sbjct: 152 QWTEVKKENPEADFKETSNILGAKWKSLSAEDKKPYEERYQVEKEAYLQVIAKEKREKEA 211

Query: 247 MKLLEEEHKQKTAMELLEQYLQFKQEADKE-NKKPKKEKDPLKPKHPVTAYFLFSSERRA 305
           MKLLE++ KQ+TAMELL+QYL F QEA+++  KK KKEKDPLKPKHPV+A+ ++++ERRA
Sbjct: 212 MKLLEDDQKQRTAMELLDQYLNFVQEAEQDNKKKNKKEKDPLKPKHPVSAFLVYANERRA 271

Query: 306 ALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR 356
           AL  +NK+V+EVAKITGEEWKN+++++K PYE++AKKNKE Y + ME YKR
Sbjct: 272 ALREENKSVVEVAKITGEEWKNLSDKKKAPYEKVAKKNKETYLQAMEEYKR 322

Arabidopsis thaliana (taxid: 3702)

>sp|Q9T012|HMG13_ARATH High mobility group B protein 13 OS=Arabidopsis thaliana GN=HMGB13 PE=2 SV=1

 Score =  353 bits (907), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 193/283 (68%), Positives = 232/283 (81%), Gaps = 12/283 (4%)

Query: 79  KQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQEKLHMELK 138
           K+  SF+KDL EMQ MLEKMK+EKEKTE+LLKEKDE+L+ KE        EQEKL  ELK
Sbjct: 38  KETKSFEKDLMEMQAMLEKMKIEKEKTEDLLKEKDEILRKKE-------VEQEKLKTELK 90

Query: 139 KLQKMKEFKPNMTLPIVQCL----KDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKE 194
           KLQKMKEFKPNMT    Q L    ++K+  +KKK CAE KRPS PYILWCKD WNE KK+
Sbjct: 91  KLQKMKEFKPNMTFAFSQSLAQTEEEKKGKKKKKDCAETKRPSTPYILWCKDNWNEVKKQ 150

Query: 195 NPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEEH 254
           NPEA+FKE +NILGAKWK +SAEEKKPYEEKYQA+KEAYLQV+ KE+RE EAMKLL++E 
Sbjct: 151 NPEADFKETSNILGAKWKGISAEEKKPYEEKYQADKEAYLQVITKEKREREAMKLLDDEQ 210

Query: 255 KQKTAMELLEQYLQFKQEADKEN-KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN 313
           KQKTAMELL+QYL F QEA+ +N KK KK KDPLKPK P++AY ++++ERRAAL  +NK+
Sbjct: 211 KQKTAMELLDQYLHFVQEAEHDNKKKAKKIKDPLKPKQPISAYLIYANERRAALKGENKS 270

Query: 314 VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR 356
           V+EVAK+ GEEWKN++EE+K PY+++AKKNKE Y +EME YKR
Sbjct: 271 VIEVAKMAGEEWKNLSEEKKAPYDQMAKKNKEIYLQEMEGYKR 313

Arabidopsis thaliana (taxid: 3702)

>sp|P26586|HMGL_TRYBR High mobility group protein homolog TDP-1 OS=Trypanosoma brucei rhodesiense PE=2 SV=1

 Score = 70.5 bits (171), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 88/175 (50%), Gaps = 32/175 (18%)

Query: 180 YILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAK 239
           Y+L+  DQ  E K +NP  +   I   LG  W + S + K+ Y +K + +K       A+
Sbjct: 125 YLLFVADQREELKAKNPGMQNTAILQTLGKMWSDASDDVKEHYRKKAEEDK-------AR 177

Query: 240 ERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKE-NKKPKKEKDPLKPKHPVTAYFL 298
            RRE +                      ++K++  KE  +  K +KD   PK  +T++  
Sbjct: 178 FRREVD----------------------EYKRQGGKEYGRGGKIKKDSNAPKRAMTSFMF 215

Query: 299 FSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEA 353
           FSS+ R+     + +++E++K  G  WK +  E+++ YEE+A+K+KE+Y  EM A
Sbjct: 216 FSSDFRSK--HSDLSIVEMSKAAGAAWKELGPEERKVYEEMAEKDKERYKREMAA 268

Unknown. May play a role in transcription and/or DNA replication. It is not known whether this protein is DNA sequence binding-specific or not.

Trypanosoma brucei rhodesiense (taxid: 31286)

>sp|P07746|HMGT_ONCMY High mobility group-T protein OS=Oncorhynchus mykiss PE=2 SV=2

 Score = 70.1 bits (170), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 57/184 (30%), Positives = 90/184 (48%), Gaps = 36/184 (19%)

Query: 180 YILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVM 237
           Y  + + +  E KK++PEA   F E +     +WK +SA+EK  +E+         L  +
Sbjct: 15  YAYFVQTRREEHKKKHPEASVNFSEFSKKCSERWKTMSAKEKGKFED---------LAKL 65

Query: 238 AKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYF 297
            K R E E                 +  Y+  K E      K K+ KDP  PK P +A+F
Sbjct: 66  DKVRYERE-----------------MRSYIPPKGE------KKKRFKDPNAPKRPSSAFF 102

Query: 298 LFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK 355
           +F ++ R  +  +     + +VAK  GE+W N+T E K PYE+ A + KEKY +++ AY+
Sbjct: 103 IFCADFRPQVKGETPGLSIGDVAKKLGEKWNNLTAEDKVPYEKKASRLKEKYEKDITAYR 162

Query: 356 RRMK 359
            + K
Sbjct: 163 NKGK 166

Binds preferentially single-stranded DNA and unwinds double stranded DNA.

Oncorhynchus mykiss (taxid: 8022)

>sp|P40620|HMGL_VICFA HMG1/2-like protein OS=Vicia faba PE=2 SV=1

 Score = 65.5 bits (158), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 51/78 (65%), Gaps = 3/78 (3%)

Query: 284 KDPLKPKHPVTAYFLFSSERRAALLAD---NKNVLEVAKITGEEWKNMTEEQKRPYEEIA 340
           KDP KPK P +A+F+F ++ R     D   NK+V  V K  GEEWK+++EE+K PY + A
Sbjct: 40  KDPNKPKRPPSAFFVFMADFREQYKKDHPNNKSVAAVGKACGEEWKSLSEEEKAPYVDRA 99

Query: 341 KKNKEKYNEEMEAYKRRM 358
            K KE+Y   ++AY +++
Sbjct: 100 LKKKEEYEITLQAYNKKL 117

Vicia faba (taxid: 3906)

>sp|Q6CC79|NHP6_YARLI Non-histone chromosomal protein 6 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=NHP6 PE=3 SV=1

 Score = 65.1 bits (157), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 48/79 (60%), Gaps = 2/79 (2%)

Query: 285 DPLKPKHPVTAYFLFSSERRAALLADNKNVL--EVAKITGEEWKNMTEEQKRPYEEIAKK 342
           DP  PK  ++AY  F+++ R A+ ADN  +   +V K  GE+WK +T+ +K PYEE A  
Sbjct: 21  DPNAPKRALSAYMFFANDNRDAIRADNPGIAFGQVGKALGEKWKTLTDAEKVPYEEKATA 80

Query: 343 NKEKYNEEMEAYKRRMKEL 361
           +K++Y +E  AYK    E 
Sbjct: 81  DKKRYEDEKAAYKANAAEF 99

DNA-binding protein that induces severe bending of DNA. Required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. Also augments the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

>sp|P11633|NHP6B_YEAST Non-histone chromosomal protein 6B OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NHP6B PE=1 SV=3

 Score = 62.4 bits (150), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 56/92 (60%), Gaps = 10/92 (10%)

Query: 273 ADKENKKPK--------KEKDPLKPKHPVTAYFLFSSERRAALLADNKNVL--EVAKITG 322
           A KE K+PK        ++KDP  PK  ++AY  F++E R  + ++N +V   +V +I G
Sbjct: 3   ATKEAKQPKEPKKRTTRRKKDPNAPKRGLSAYMFFANENRDIVRSENPDVTFGQVGRILG 62

Query: 323 EEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAY 354
           E WK +T E+K+PYE  A+ +K++Y  E E Y
Sbjct: 63  ERWKALTAEEKQPYESKAQADKKRYESEKELY 94

DNA-binding protein that induces severe bending of DNA. Required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. Also augments the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. Required for transcriptional initiation fidelity of some but not all tRNA genes. Seems to be functionally redundant with NHP6A.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|P63159|HMGB1_RAT High mobility group protein B1 OS=Rattus norvegicus GN=Hmgb1 PE=1 SV=2

 Score = 62.0 bits (149), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/184 (31%), Positives = 89/184 (48%), Gaps = 36/184 (19%)

Query: 180 YILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVM 237
           Y  + +    E KK++P+A   F E +     +WK +SA+EK  +E+  +A+K  Y    
Sbjct: 16  YAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARY---- 71

Query: 238 AKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYF 297
               RE                   ++ Y+  K E  K      K KDP  PK P +A+F
Sbjct: 72  ---ERE-------------------MKTYIPPKGETKK------KFKDPNAPKRPPSAFF 103

Query: 298 LFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK 355
           LF SE R  +  ++    + +VAK  GE W N   + K+PYE+ A K KEKY +++ AY+
Sbjct: 104 LFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR 163

Query: 356 RRMK 359
            + K
Sbjct: 164 AKGK 167

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes in developing cells.

Rattus norvegicus (taxid: 10116)

>sp|A9RA84|HMGB1_PAPAN High mobility group protein B1 OS=Papio anubis GN=HMGB1 PE=3 SV=1

 Score = 62.0 bits (149), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/184 (31%), Positives = 89/184 (48%), Gaps = 36/184 (19%)

Query: 180 YILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVM 237
           Y  + +    E KK++P+A   F E +     +WK +SA+EK  +E+  +A+K  Y    
Sbjct: 16  YAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARY---- 71

Query: 238 AKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYF 297
               RE                   ++ Y+  K E  K      K KDP  PK P +A+F
Sbjct: 72  ---ERE-------------------MKTYIPPKGETKK------KFKDPNAPKRPPSAFF 103

Query: 298 LFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK 355
           LF SE R  +  ++    + +VAK  GE W N   + K+PYE+ A K KEKY +++ AY+
Sbjct: 104 LFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR 163

Query: 356 RRMK 359
            + K
Sbjct: 164 AKGK 167

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes in developing cells.

Papio anubis (taxid: 9555)

>sp|P63158|HMGB1_MOUSE High mobility group protein B1 OS=Mus musculus GN=Hmgb1 PE=1 SV=2

 Score = 62.0 bits (149), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/184 (31%), Positives = 89/184 (48%), Gaps = 36/184 (19%)

Query: 180 YILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVM 237
           Y  + +    E KK++P+A   F E +     +WK +SA+EK  +E+  +A+K  Y    
Sbjct: 16  YAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARY---- 71

Query: 238 AKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYF 297
               RE                   ++ Y+  K E  K      K KDP  PK P +A+F
Sbjct: 72  ---ERE-------------------MKTYIPPKGETKK------KFKDPNAPKRPPSAFF 103

Query: 298 LFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK 355
           LF SE R  +  ++    + +VAK  GE W N   + K+PYE+ A K KEKY +++ AY+
Sbjct: 104 LFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR 163

Query: 356 RRMK 359
            + K
Sbjct: 164 AKGK 167

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes in developing cells.

Mus musculus (taxid: 10090)

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	363
224058355	498	high mobility group family [Populus tric	0.972	0.708	0.687	1e-121
225426010	505	PREDICTED: high mobility group B protein	0.950	0.683	0.713	1e-119
255537735	514	transcription factor, putative [Ricinus	0.947	0.669	0.674	1e-117
224072172	480	high mobility group family [Populus tric	0.928	0.702	0.654	1e-111
147777965	532	hypothetical protein VITISV_028213 [Viti	0.955	0.652	0.651	1e-106
356523471	478	PREDICTED: high mobility group B protein	0.922	0.700	0.644	1e-103
356523473	467	PREDICTED: high mobility group B protein	0.922	0.717	0.644	1e-103
449505047	500	PREDICTED: LOW QUALITY PROTEIN: high mob	0.950	0.69	0.662	1e-101
449464074	500	PREDICTED: high mobility group B protein	0.950	0.69	0.662	1e-101
255637700	478	unknown [Glycine max]	0.922	0.700	0.635	1e-100

>gi|224058355|ref|XP_002299486.1| high mobility group family [Populus trichocarpa] gi|222846744|gb|EEE84291.1| high mobility group family [Populus trichocarpa]

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 251/365 (68%), Positives = 293/365 (80%), Gaps = 12/365 (3%)

Query: 4   SDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQT---PSQSPIPNPPDAGLSKENHES 60
           +D A     P K   +R+ALK KN   NEA +MAQ    PS + +  P D   SKEN ES
Sbjct: 2   ADTAVAPTVPKKSRNNRKALKQKNPSTNEANIMAQKLPEPSPASVLPPSDTDSSKENLES 61

Query: 61  LSQPKKA-----AAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEM 115
           LSQP+ +     +   KAKQ  +   +SF+KD QEMQEML+++KLEKEKTE LLKEKDEM
Sbjct: 62  LSQPRSSPKKGKSKAAKAKQNKEAAASSFEKDFQEMQEMLQQLKLEKEKTEVLLKEKDEM 121

Query: 116 LKMKEEELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCA-ERK 174
           LK K+EE+E++GKEQEK+  ELKKLQK+KEFKP MTLP VQ L +KEQD+KKK    E K
Sbjct: 122 LKAKDEEIEMKGKEQEKMKTELKKLQKLKEFKPIMTLPFVQVLNEKEQDKKKKKGGNEIK 181

Query: 175 RPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYL 234
           RP PPY LWCKDQWNE KKENP+AEFK+I++ILGAKWK ++AEEKKPYEEKYQ EKEAYL
Sbjct: 182 RPCPPYSLWCKDQWNEVKKENPDAEFKDISHILGAKWKTITAEEKKPYEEKYQVEKEAYL 241

Query: 235 QVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADK---ENKKPKKEKDPLKPKH 291
           ++M KE+RESEAMKLLEEE KQKTAMELLEQYLQFKQEA +   +  K KKEKDPLKPKH
Sbjct: 242 KLMTKEKRESEAMKLLEEEQKQKTAMELLEQYLQFKQEAGQEENKKNKTKKEKDPLKPKH 301

Query: 292 PVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEM 351
           P++A+FLFS+ERRAALLA+NKNVLEVAKI GEEWKNMTE+QKRPYEEIAKKNKEKY +EM
Sbjct: 302 PLSAFFLFSNERRAALLAENKNVLEVAKIAGEEWKNMTEKQKRPYEEIAKKNKEKYTQEM 361

Query: 352 EAYKR 356
           EAYK+
Sbjct: 362 EAYKQ 366

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225426010|ref|XP_002273198.1| PREDICTED: high mobility group B protein 13-like [Vitis vinifera]

 Score =  432 bits (1112), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 256/359 (71%), Positives = 299/359 (83%), Gaps = 14/359 (3%)

Query: 9   MAVEPSKKPR-SRRALKPKNSLANEAVVMAQTPSQS---PIPNPP-DAGLSKENHESLSQ 63
           MAV P KK R SR+ALK K+S  N+A ++A   S+S   P+P P  DAG  KENHESLSQ
Sbjct: 10  MAV-PIKKARTSRKALKEKSSSTNKANILAGQISESSPAPVPTPSEDAG--KENHESLSQ 66

Query: 64  PKKAAAKGKAKQATKK--QDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEE 121
           P     K K  Q  KK  +  SF++DLQEMQE LE+++LEKEKTEELLK +DEMLK+KEE
Sbjct: 67  PLSGKKKSKGAQKGKKSKESQSFERDLQEMQEKLEQLRLEKEKTEELLKARDEMLKIKEE 126

Query: 122 ELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKK---GCAERKRPSP 178
           ELE +G+EQEKL MELKKLQK+KEFKP +T P+   L+DKEQ++K+K   GC E KRPSP
Sbjct: 127 ELETRGREQEKLQMELKKLQKLKEFKPTVTFPL-HSLRDKEQEKKEKNKKGCPETKRPSP 185

Query: 179 PYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMA 238
            Y+LWCKDQWNEAKK NP+A+FKEI+NILGAKWK +SAEEKKPYEEKYQAEKEAYLQ++ 
Sbjct: 186 SYVLWCKDQWNEAKKANPDADFKEISNILGAKWKTISAEEKKPYEEKYQAEKEAYLQIVG 245

Query: 239 KERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFL 298
           KE+RE+EAM+LLEEE KQKTAMELLEQYLQFKQ A+KENKK KKEKDPLKPKHPV+A+FL
Sbjct: 246 KEKRENEAMRLLEEEQKQKTAMELLEQYLQFKQGAEKENKKKKKEKDPLKPKHPVSAFFL 305

Query: 299 FSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR 357
           FS ERRAALL ++KNVLE+AKI GEEWKNMTE+QKRPYEEIAKKNK KY EEME YK++
Sbjct: 306 FSKERRAALLGEDKNVLEIAKIAGEEWKNMTEKQKRPYEEIAKKNKAKYQEEMELYKQQ 364

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537735|ref|XP_002509934.1| transcription factor, putative [Ricinus communis] gi|223549833|gb|EEF51321.1| transcription factor, putative [Ricinus communis]

 Score =  426 bits (1095), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 247/366 (67%), Positives = 289/366 (78%), Gaps = 22/366 (6%)

Query: 13  PSKKPRSRR--ALKPKNSLANEAVVMAQTPSQ-SPIPNPPD--AGLSKENHESLSQPKKA 67
           P+KKPR +R   LK KN   NEA +MAQ  S  SP+P PP   A  SKENHESLSQP+ +
Sbjct: 15  PTKKPRKKRNHPLKEKNPSTNEANIMAQKLSAISPVPAPPSDAADASKENHESLSQPRSS 74

Query: 68  -------------AAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDE 114
                          K  +  +      SF+K++QEMQEML+K+KLEKEKT+ELLKEKDE
Sbjct: 75  PKKLKAKAATKAKQTKQSSSSSATTTTNSFEKEMQEMQEMLQKLKLEKEKTDELLKEKDE 134

Query: 115 MLKMKEEELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERK 174
           +LK K+EELE +GKEQEKL MELKKLQK+KEFKPNM  P++Q   ++EQD+KKK      
Sbjct: 135 ILKAKQEELENKGKEQEKLQMELKKLQKLKEFKPNMNFPLLQSF-NEEQDKKKKKKKGGH 193

Query: 175 ---RPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKE 231
              RPSPPYILWCKDQWNE K ENP AEFKEI+NILGAKWKNVS E+KKPYE+KYQAEKE
Sbjct: 194 EKKRPSPPYILWCKDQWNEVKNENPNAEFKEISNILGAKWKNVSTEDKKPYEDKYQAEKE 253

Query: 232 AYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKH 291
            YLQV+ KE+RESEAMKLLEEE KQKTAMELLEQYLQFKQE +KENKK KKEKDPLKPK 
Sbjct: 254 VYLQVVNKEKRESEAMKLLEEEQKQKTAMELLEQYLQFKQETEKENKKTKKEKDPLKPKQ 313

Query: 292 PVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEM 351
           P++A+FLFS+ERRA+LLA+NKNV EVAKI GE+WKNMTEEQK PYEE+AK+NK +Y +EM
Sbjct: 314 PMSAFFLFSNERRASLLAENKNVREVAKIAGEQWKNMTEEQKGPYEEMAKRNKLRYMQEM 373

Query: 352 EAYKRR 357
           EAYK++
Sbjct: 374 EAYKQK 379

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224072172|ref|XP_002303636.1| high mobility group family [Populus trichocarpa] gi|222841068|gb|EEE78615.1| high mobility group family [Populus trichocarpa]

 Score =  407 bits (1047), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 235/359 (65%), Positives = 282/359 (78%), Gaps = 22/359 (6%)

Query: 1   MASSDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHES 60
           MA + VAS    P K   +R+ALK KN   NE+ +MAQ  S                 E+
Sbjct: 1   MADTAVASTV--PKKSRNNRKALKQKNPSTNESNIMAQKLS-----------------ET 41

Query: 61  LSQPKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKE 120
            +  K  +   KAKQ  +   + F+KD QEMQEML+++KLEKEKTE LLKEKD+MLK K+
Sbjct: 42  STATKGKSKAAKAKQNKEASASLFEKDFQEMQEMLQQLKLEKEKTEVLLKEKDDMLKAKD 101

Query: 121 EELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCA-ERKRPSPP 179
           EE+E++GKEQ+K+ MELKKLQK+KEFKP MTL  VQ + DK+QD+KKK    E KRP PP
Sbjct: 102 EEIEMKGKEQQKMKMELKKLQKLKEFKPTMTLSFVQAMNDKQQDKKKKKGGNEIKRPCPP 161

Query: 180 YILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAK 239
           Y LWCK QWNE KKENP+AEFK+I+NILGAKWK ++AEEKKPYEEKYQAEKEAYL+VM K
Sbjct: 162 YSLWCKAQWNEVKKENPDAEFKDISNILGAKWKTITAEEKKPYEEKYQAEKEAYLKVMTK 221

Query: 240 ERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKE--NKKPKKEKDPLKPKHPVTAYF 297
           E+RESEAMKLLEEE KQKTAMELLEQYLQFKQEAD+E  +KK KKEKDPLKPK P++A+F
Sbjct: 222 EKRESEAMKLLEEEQKQKTAMELLEQYLQFKQEADQEENSKKTKKEKDPLKPKQPLSAFF 281

Query: 298 LFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR 356
           LF +ERRAALLA+NK+VLEVAKI GEEWKNMTE+++ PYEE+AKKN+EKY +EMEAYK+
Sbjct: 282 LFCNERRAALLAENKSVLEVAKIAGEEWKNMTEKRRGPYEEVAKKNREKYMQEMEAYKQ 340

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147777965|emb|CAN70902.1| hypothetical protein VITISV_028213 [Vitis vinifera]

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 250/384 (65%), Positives = 290/384 (75%), Gaps = 37/384 (9%)

Query: 9   MAVEPSKKPR-SRRALKPKNSLANEAVVMA-QTPSQSPIP-NPPDAGLSKENHESLSQP- 64
           MAV P KK R SR+ALK K+S  N+A ++A Q    SP P   P     KENHESLSQP 
Sbjct: 10  MAV-PIKKARTSRKALKEKSSSTNKANILAGQISESSPAPVXTPXEDAXKENHESLSQPL 68

Query: 65  -KKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEEL 123
             K   KG  K    K+  SF++DLQEMQE L +++LEKEKTE LLK +DEMLK+KEEEL
Sbjct: 69  SGKKKXKGAQKGKKSKESQSFERDLQEMQEKLXQLRLEKEKTEGLLKARDEMLKIKEEEL 128

Query: 124 ELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKK---GCAERKRPSPPY 180
           E +G+EQEKL MELKKLQK+KEFKP  T P+   L+DKEQ++K+K   GC E KRPSP Y
Sbjct: 129 ETRGREQEKLQMELKKLQKLKEFKPTXTFPL-HSLRDKEQEKKEKNKKGCPETKRPSPSY 187

Query: 181 ILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE 240
           +LWCKDQWNEAKK NP+A+FKEI+NILG KWK +SAEEKKPYEEKYQAEKEAYLQ++ KE
Sbjct: 188 VLWCKDQWNEAKKANPDADFKEISNILGTKWKTISAEEKKPYEEKYQAEKEAYLQIVGKE 247

Query: 241 RRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFS 300
           +RE+EAM+LLEEE KQKTAMELLEQYLQFKQEA+KENKK KKEKDPLKPKHPV+A+FLFS
Sbjct: 248 KRENEAMRLLEEEQKQKTAMELLEQYLQFKQEAEKENKKKKKEKDPLKPKHPVSAFFLFS 307

Query: 301 SERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEE---------------------- 338
            ERRAALL +BKNVLE+AKI GEEWKNMTE+QKRPYEE                      
Sbjct: 308 KERRAALLXEBKNVLEIAKIAGEEWKNMTEKQKRPYEEVHLMTSLFLSLFLSAAWSLTIS 367

Query: 339 -----IAKKNKEKYNEEMEAYKRR 357
                I KKNK KY EEME YK++
Sbjct: 368 IENLQIXKKNKAKYQEEMELYKQQ 391

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356523471|ref|XP_003530362.1| PREDICTED: high mobility group B protein 13-like isoform 1 [Glycine max]

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 230/357 (64%), Positives = 279/357 (78%), Gaps = 22/357 (6%)

Query: 1   MASSDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHES 60
           M  + VA +   P+K+ R RRALK K    N+A ++  TP  SP                
Sbjct: 1   MGGTVVAEV---PTKRGRGRRALKEKTPSTNDANIIIATPI-SP---------------- 40

Query: 61  LSQPKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKE 120
            S  K A      K+   K+  SF+K+L EMQEML++M+LEKEKTEELLK KDE LK+KE
Sbjct: 41  -SSEKAAQVVPSKKKQDSKKQQSFEKELLEMQEMLQQMRLEKEKTEELLKVKDEALKLKE 99

Query: 121 EELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPY 180
           EELE +G+EQEKL  ELKKLQK+KEFKP M LP+++   ++++D+KKKGC+E+KRPSPPY
Sbjct: 100 EELENRGREQEKLQTELKKLQKLKEFKPTMNLPVLKD-NEEKKDKKKKGCSEKKRPSPPY 158

Query: 181 ILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE 240
           ILW KDQWNE KK NPEAEFKEI+ +LGAKWK VSAEEKKPYE  Y AEKEAYLQV+AKE
Sbjct: 159 ILWMKDQWNEIKKANPEAEFKEISTMLGAKWKTVSAEEKKPYEGIYHAEKEAYLQVIAKE 218

Query: 241 RRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFS 300
           +RE+EAM+LLE+E KQ+TAMELLEQY+QFKQEA+K+ KK KKEKDPLKPKHP++AYFLF+
Sbjct: 219 KRETEAMRLLEDEQKQRTAMELLEQYMQFKQEAEKDGKKNKKEKDPLKPKHPMSAYFLFT 278

Query: 301 SERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR 357
           ++RRAAL A+NKN LEV KIT EEWKNMTEEQKRPYEE+AKKNKE+Y  EMEAYK++
Sbjct: 279 NDRRAALAAENKNFLEVPKITSEEWKNMTEEQKRPYEEMAKKNKEQYALEMEAYKQK 335

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356523473|ref|XP_003530363.1| PREDICTED: high mobility group B protein 13-like isoform 2 [Glycine max]

 Score =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 230/357 (64%), Positives = 279/357 (78%), Gaps = 22/357 (6%)

Query: 1   MASSDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHES 60
           M  + VA +   P+K+ R RRALK K    N+A ++  TP  SP                
Sbjct: 1   MGGTVVAEV---PTKRGRGRRALKEKTPSTNDANIIIATPI-SP---------------- 40

Query: 61  LSQPKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKE 120
            S  K A      K+   K+  SF+K+L EMQEML++M+LEKEKTEELLK KDE LK+KE
Sbjct: 41  -SSEKAAQVVPSKKKQDSKKQQSFEKELLEMQEMLQQMRLEKEKTEELLKVKDEALKLKE 99

Query: 121 EELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPY 180
           EELE +G+EQEKL  ELKKLQK+KEFKP M LP+++   ++++D+KKKGC+E+KRPSPPY
Sbjct: 100 EELENRGREQEKLQTELKKLQKLKEFKPTMNLPVLKD-NEEKKDKKKKGCSEKKRPSPPY 158

Query: 181 ILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE 240
           ILW KDQWNE KK NPEAEFKEI+ +LGAKWK VSAEEKKPYE  Y AEKEAYLQV+AKE
Sbjct: 159 ILWMKDQWNEIKKANPEAEFKEISTMLGAKWKTVSAEEKKPYEGIYHAEKEAYLQVIAKE 218

Query: 241 RRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFS 300
           +RE+EAM+LLE+E KQ+TAMELLEQY+QFKQEA+K+ KK KKEKDPLKPKHP++AYFLF+
Sbjct: 219 KRETEAMRLLEDEQKQRTAMELLEQYMQFKQEAEKDGKKNKKEKDPLKPKHPMSAYFLFT 278

Query: 301 SERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR 357
           ++RRAAL A+NKN LEV KIT EEWKNMTEEQKRPYEE+AKKNKE+Y  EMEAYK++
Sbjct: 279 NDRRAALAAENKNFLEVPKITSEEWKNMTEEQKRPYEEMAKKNKEQYALEMEAYKQK 335

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449505047|ref|XP_004162361.1| PREDICTED: LOW QUALITY PROTEIN: high mobility group B protein 13-like [Cucumis sativus]

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 238/359 (66%), Positives = 284/359 (79%), Gaps = 14/359 (3%)

Query: 6   VASMAVEPSKKPR-SRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHESLSQ- 63
           V      P+KKPR SR+ALK KNS    +  + Q+ S  P    P  G      E LSQ 
Sbjct: 11  VTGAPAGPTKKPRNSRKALKDKNS----SPEVPQSQSMVPKVTAPSEG------EILSQN 60

Query: 64  -PKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEE 122
                  K KA    +  + SFDKDLQEMQ+ML+++KL+KEKTEELLKEKDEMLK K+EE
Sbjct: 61  QTSAKKPKSKAAAKKQPANQSFDKDLQEMQDMLQQLKLDKEKTEELLKEKDEMLKQKDEE 120

Query: 123 LELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERK-RPSPPYI 181
           L+ + KEQEKL +ELKKLQK+KEFKP M  P++Q  KDKEQD+K+K     K RP+PPYI
Sbjct: 121 LKTRDKEQEKLQIELKKLQKLKEFKPTMNFPMIQIFKDKEQDKKEKKKCAEKKRPAPPYI 180

Query: 182 LWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER 241
           LWCKDQWNE KKENPEA+FKE +NILGAKWK +SAEEKKPYEEKYQAEKE YL++ +KE+
Sbjct: 181 LWCKDQWNEIKKENPEADFKETSNILGAKWKTISAEEKKPYEEKYQAEKETYLRITSKEK 240

Query: 242 RESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSS 301
           RESEAMKLLEEE KQKTAMELLEQYLQFK+EA+KENKK KKEKDPLKPK P++A+FLFS+
Sbjct: 241 RESEAMKLLEEEQKQKTAMELLEQYLQFKEEAEKENKKKKKEKDPLKPKQPMSAFFLFSN 300

Query: 302 ERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKE 360
           ERRA+L+A+NKNV+E+AKI GEEWKNMTEEQK PYEE+AKKNKEKY +EME Y+++ +E
Sbjct: 301 ERRASLVAENKNVVELAKIAGEEWKNMTEEQKGPYEEMAKKNKEKYMQEMEIYEQKKEE 359

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464074|ref|XP_004149754.1| PREDICTED: high mobility group B protein 13-like [Cucumis sativus]

 Score =  373 bits (958), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 238/359 (66%), Positives = 284/359 (79%), Gaps = 14/359 (3%)

Query: 6   VASMAVEPSKKPR-SRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHESLSQ- 63
           V      P+KKPR SR+ALK KNS    +  + Q+ S  P    P  G      E LSQ 
Sbjct: 11  VTGAPAGPTKKPRNSRKALKDKNS----SPEVPQSQSMVPKVTAPSEG------EILSQN 60

Query: 64  -PKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEE 122
                  K KA    +  + SFDKDLQEMQ+ML+++KL+KEKTEELLKEKDEMLK K+EE
Sbjct: 61  QTSAKKPKSKAAAKKQPANQSFDKDLQEMQDMLQQLKLDKEKTEELLKEKDEMLKQKDEE 120

Query: 123 LELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERK-RPSPPYI 181
           L+ + KEQEKL +ELKKLQK+KEFKP M  P++Q  KDKEQD+K+K     K RP+PPYI
Sbjct: 121 LKTRDKEQEKLQIELKKLQKLKEFKPTMNFPMIQIFKDKEQDKKEKKKCAEKKRPAPPYI 180

Query: 182 LWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER 241
           LWCKDQWNE KKENPEA+FKE +NILGAKWK +SAEEKKPYEEKYQAEKE YL++ +KE+
Sbjct: 181 LWCKDQWNEIKKENPEADFKETSNILGAKWKTISAEEKKPYEEKYQAEKETYLRITSKEK 240

Query: 242 RESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSS 301
           RESEAMKLLEEE KQKTAMELLEQYLQFK+EA+KENKK KKEKDPLKPK P++A+FLFS+
Sbjct: 241 RESEAMKLLEEEQKQKTAMELLEQYLQFKEEAEKENKKKKKEKDPLKPKQPMSAFFLFSN 300

Query: 302 ERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKE 360
           ERRA+L+A+NKNV+E+AKI GEEWKNMTEEQK PYEE+AKKNKEKY +EME Y+++ +E
Sbjct: 301 ERRASLVAENKNVVELAKIAGEEWKNMTEEQKGPYEEMAKKNKEKYMQEMEIYEQKKEE 359

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637700|gb|ACU19173.1| unknown [Glycine max]

 Score =  373 bits (957), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 227/357 (63%), Positives = 276/357 (77%), Gaps = 22/357 (6%)

Query: 1   MASSDVASMAVEPSKKPRSRRALKPKNSLANEAVVMAQTPSQSPIPNPPDAGLSKENHES 60
           M  + VA +   P+K+ R RRALK K    N+A ++  TP  SP                
Sbjct: 1   MGGTVVAEV---PTKRGRGRRALKEKTPSTNDANIIIATPI-SP---------------- 40

Query: 61  LSQPKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKE 120
            S  K A      K+   K+  SF+K+L EMQEML++M+LEKEKTEELLK KDE LK+KE
Sbjct: 41  -SSEKAAQVVPSKKKQDSKKQQSFEKELLEMQEMLQQMRLEKEKTEELLKVKDEALKLKE 99

Query: 121 EELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPY 180
           EELE +G+EQEKL  ELKKLQK+KEFKP M L +V    ++++D+KKKGC+E+KR SPPY
Sbjct: 100 EELENRGREQEKLQTELKKLQKLKEFKPTMNL-LVLKDNEEKKDKKKKGCSEKKRSSPPY 158

Query: 181 ILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE 240
           ILW KDQWNE KK NPEAEFKEI+ +LGAKWK VSAEEKKPYE  Y AEKEAYLQV+AKE
Sbjct: 159 ILWMKDQWNEIKKANPEAEFKEISTMLGAKWKTVSAEEKKPYEGIYHAEKEAYLQVIAKE 218

Query: 241 RRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFS 300
           +RE+EAM+LLE+E KQ+TAMELLEQY+QFKQEA+K+ KK KKEKDPL+P+HP++AYFLF+
Sbjct: 219 KRETEAMRLLEDEQKQRTAMELLEQYMQFKQEAEKDGKKNKKEKDPLRPRHPMSAYFLFT 278

Query: 301 SERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR 357
           ++RRAAL A+NKN LEV KIT EEWKNMTEEQKRPYEE+AKKNKE+Y  EMEAYK++
Sbjct: 279 NDRRAALAAENKNFLEVPKITSEEWKNMTEEQKRPYEEMAKKNKEQYALEMEAYKQK 335

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	363
TAIR|locus:2136103	446	3xHMG-box1 "3xHigh Mobility Gr	0.550	0.448	0.541	2e-57
TAIR|locus:2128504	456	3xHMG-box2 "3xHigh Mobility Gr	0.553	0.440	0.526	5.4e-57
SGD|S000004676	183	ABF2 "Mitochondrial DNA-bindin	0.112	0.224	0.414	2.2e-05
UNIPROTKB|G4MS97	101	MGG_04489 "Non-histone chromos	0.118	0.425	0.355	2.3e-05
ASPGD|ASPL0000037691	106	AN2885 [Emericella nidulans (t	0.140	0.481	0.352	0.0006
SGD|S000002157	99	NHP6B "High-mobility group (HM	0.118	0.434	0.377	0.00078

TAIR|locus:2136103 3xHMG-box1 "3xHigh Mobility Group-box1" [Arabidopsis thaliana (taxid:3702)]

 Score = 559 (201.8 bits), Expect = 2.0e-57, Sum P(2) = 2.0e-57
 Identities = 111/205 (54%), Positives = 136/205 (66%)

Query:   136 ELKKLQKMKEFKPNMTLPIVQCLKDKEQDRK----KKGCAERKRPSPPYILWCKDQWNEA 191
             ELKKLQKMKEFKPNMT    Q L   E+++K    KK CAE KRPS PYILWCKD WNE 
Sbjct:    88 ELKKLQKMKEFKPNMTFAFSQSLAQTEEEKKGKKKKKDCAETKRPSTPYILWCKDNWNEV 147

Query:   192 KKENPEAEFKEITNILGAKWKNVSXXXXXXXXXXXXXXXXXXLQVMAKERRESEAMKLLE 251
             KK+NPEA+FKE +NILGAKWK +S                  LQV+ KE+RE EAMKLL+
Sbjct:   148 KKQNPEADFKETSNILGAKWKGISAEEKKPYEEKYQADKEAYLQVITKEKREREAMKLLD 207

Query:   252 EEHKQKTAMELLEQYLQFXXXXXXXXXXXXXXXXXXXX-XHPVTAYFLFSSERRAALLAD 310
             +E KQKTAMELL+QYL F                       P++AY ++++ERRAAL  +
Sbjct:   208 DEQKQKTAMELLDQYLHFVQEAEHDNKKKAKKIKDPLKPKQPISAYLIYANERRAALKGE 267

Query:   311 NKNVLEVAKITGEEWKNMTEEQKRP 335
             NK+V+EVAK+ GEEWKN++EE+K P
Sbjct:   268 NKSVIEVAKMAGEEWKNLSEEKKAP 292

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2128504 3xHMG-box2 "3xHigh Mobility Group-box2" [Arabidopsis thaliana (taxid:3702)]

 Score = 545 (196.9 bits), Expect = 5.4e-57, Sum P(2) = 5.4e-57
 Identities = 109/207 (52%), Positives = 139/207 (67%)

Query:   135 MELKKLQKMKEFKPNMTLP-----IVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWN 189
             +ELKKLQKMKEFKPNMT       + Q  ++K   +KKK C E KRPS  Y+LWCKDQW 
Sbjct:    95 VELKKLQKMKEFKPNMTFACGQSSLTQAEQEKANKKKKKDCPETKRPSSSYVLWCKDQWT 154

Query:   190 EAKKENPEAEFKEITNILGAKWKNVSXXXXXXXXXXXXXXXXXXLQVMAKERRESEAMKL 249
             E KKENPEA+FKE +NILGAKWK++S                  LQV+AKE+RE EAMKL
Sbjct:   155 EVKKENPEADFKETSNILGAKWKSLSAEDKKPYEERYQVEKEAYLQVIAKEKREKEAMKL 214

Query:   250 LEEEHKQKTAMELLEQYLQFXXXXXXXXXXXXXXXXXXXX-XHPVTAYFLFSSERRAALL 308
             LE++ KQ+TAMELL+QYL F                      HPV+A+ ++++ERRAAL 
Sbjct:   215 LEDDQKQRTAMELLDQYLNFVQEAEQDNKKKNKKEKDPLKPKHPVSAFLVYANERRAALR 274

Query:   309 ADNKNVLEVAKITGEEWKNMTEEQKRP 335
              +NK+V+EVAKITGEEWKN+++++K P
Sbjct:   275 EENKSVVEVAKITGEEWKNLSDKKKAP 301

GO:0005634 "nucleus" evidence=ISM

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

GO:0003677 "DNA binding" evidence=IDA

GO:0000226 "microtubule cytoskeleton organization" evidence=RCA

GO:0000911 "cytokinesis by cell plate formation" evidence=RCA

GO:0006084 "acetyl-CoA metabolic process" evidence=RCA

GO:0008283 "cell proliferation" evidence=RCA

GO:0010583 "response to cyclopentenone" evidence=RCA

GO:0016572 "histone phosphorylation" evidence=RCA

GO:0042127 "regulation of cell proliferation" evidence=RCA

SGD|S000004676 ABF2 "Mitochondrial DNA-binding protein" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 89 (36.4 bits), Expect = 2.2e-05, Sum P(3) = 2.2e-05
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query:   174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNV 214
             KRP+  Y L+ +D  ++  KENP     EI+ I G KW+N+
Sbjct:    44 KRPTSAYFLYLQDHRSQFVKENPTLRPAEISKIAGEKWQNL 84

GO:0005739 "mitochondrion" evidence=IEA;IDA

GO:0005634 "nucleus" evidence=IEA

GO:0090139 "mitochondrial DNA packaging" evidence=IMP

GO:0000001 "mitochondrion inheritance" evidence=IMP

GO:0000002 "mitochondrial genome maintenance" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA;IDA

GO:0000262 "mitochondrial chromosome" evidence=IDA

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

GO:0042645 "mitochondrial nucleoid" evidence=IDA

UNIPROTKB|G4MS97 MGG_04489 "Non-histone chromosomal protein 6" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 83 (34.3 bits), Expect = 2.3e-05, Sum P(2) = 2.3e-05
 Identities = 16/45 (35%), Positives = 29/45 (64%)

Query:   293 VTAYFLFSSERRAALLADNKNVL--EVAKITGEEWKNMTEEQKRP 335
             ++AY  F++E+R  +  +N  V   +V KI GE WK ++++Q+ P
Sbjct:    28 LSAYMFFANEQRDNVREENPGVTFGQVGKILGERWKALSDKQRAP 72

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000037691 AN2885 [Emericella nidulans (taxid:162425)]

 Score = 91 (37.1 bits), Expect = 0.00060, P = 0.00060
 Identities = 18/51 (35%), Positives = 29/51 (56%)

Query:   165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVS 215
             RKKK     KR    Y+ +  D  ++ ++ENP   F ++  +LG KWK++S
Sbjct:    19 RKKKDPNAPKRGLSAYMFFANDNRDKVREENPGISFGQVGKMLGEKWKSLS 69

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

GO:0008301 "DNA binding, bending" evidence=IEA

GO:0006338 "chromatin remodeling" evidence=IEA

GO:0070898 "RNA polymerase III transcriptional preinitiation complex assembly" evidence=IEA

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

SGD|S000002157 NHP6B "High-mobility group (HMG) protein, binds to and remodels nucleosomes" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 90 (36.7 bits), Expect = 0.00078, P = 0.00078
 Identities = 17/45 (37%), Positives = 30/45 (66%)

Query:   293 VTAYFLFSSERRAALLADNKNVL--EVAKITGEEWKNMTEEQKRP 335
             ++AY  F++E R  + ++N +V   +V +I GE WK +T E+K+P
Sbjct:    31 LSAYMFFANENRDIVRSENPDVTFGQVGRILGERWKALTAEEKQP 75


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.310   0.125   0.354    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      363       243   0.00097  113 3  11 23  0.38    34
                                                     32  0.45    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  611 (65 KB)
  Total size of DFA:  189 KB (2107 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  20.24u 0.27s 20.51t   Elapsed:  00:00:05
  Total cpu time:  20.24u 0.27s 20.51t   Elapsed:  00:00:06
  Start:  Fri May 10 06:51:31 2013   End:  Fri May 10 06:51:37 2013

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0005694 "chromosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

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

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006338 "chromatin remodeling" evidence=IGI

GO:0070898 "RNA polymerase III transcriptional preinitiation complex assembly" evidence=IGI;IDA

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

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

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

GO:0031491 "nucleosome binding" evidence=ISS

---

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)
Q9SUP7	HMGB6_ARATH	No assigned EC number	0.6011	0.8457	0.6732	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: HMGB912 SubName- Full=Putative uncharacterized protein; (458 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	363
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	4e-12
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	6e-12
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	5e-11
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	7e-11
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-10
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	2e-09
smart00398	70	smart00398, HMG, high mobility group	4e-08
smart00398	70	smart00398, HMG, high mobility group	7e-08
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	9e-08
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	3e-07
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	1e-06
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	3e-06
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	2e-05
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	7e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	3e-04
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	5e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003

>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

 Score = 60.3 bits (147), Expect = 4e-12
 Identities = 33/65 (50%), Positives = 43/65 (66%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   Y L+ ++Q  + KKENP+A   E+T ILG KWK +S EEKK YEEK + +KE Y
Sbjct: 2   KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERY 61

Query: 234 LQVMA 238
            + M 
Sbjct: 62  EKEMK 66

These proteins bind the minor groove of 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 members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

 Score = 59.9 bits (146), Expect = 6e-12
 Identities = 30/65 (46%), Positives = 39/65 (60%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   Y L+ ++   E K ENP     EI+ ILG  WK++S EEKK YEEK + +KE Y
Sbjct: 2   KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERY 61

Query: 234 LQVMA 238
            + M 
Sbjct: 62  EKEMP 66

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 members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

 Score = 57.3 bits (139), Expect = 5e-11
 Identities = 35/66 (53%), Positives = 50/66 (75%), Gaps = 2/66 (3%)

Query: 289 PKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEK 346
           PK P++AYFLFS E+R  L  +N +  V EV KI GE+WK ++EE+K+ YEE A+K+KE+
Sbjct: 1   PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKER 60

Query: 347 YNEEME 352
           Y +EM+
Sbjct: 61  YEKEMK 66

These proteins bind the minor groove of 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 members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

 Score = 56.9 bits (138), Expect = 7e-11
 Identities = 35/66 (53%), Positives = 50/66 (75%), Gaps = 2/66 (3%)

Query: 289 PKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEK 346
           PK P++AYFLFS E RA + A+N    V E++KI GE WK+++EE+K+ YEE A+K+KE+
Sbjct: 1   PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKER 60

Query: 347 YNEEME 352
           Y +EM 
Sbjct: 61  YEKEMP 66

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 members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

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

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 36/69 (52%), Positives = 51/69 (73%), Gaps = 2/69 (2%)

Query: 289 PKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEK 346
           PK P++A+FLFS E+RA L A+N      E++KI GE+WKN++EE+K+PYEE A+K K +
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEKAR 60

Query: 347 YNEEMEAYK 355
           Y +   AYK
Sbjct: 61  YEKAYPAYK 69

Length = 69

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   + L+ ++Q  + K ENP  +  EI+ ILG KWKN+S EEKKPYEEK + EK  Y
Sbjct: 2   KRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEKARY 61

Query: 234 LQVMA 238
            +   
Sbjct: 62  EKAYP 66

Length = 69

>gnl|CDD|197700 smart00398, HMG, high mobility group

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 27/68 (39%), Positives = 42/68 (61%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   ++L+ ++   + K ENP+    EI+  LG +WK +S EEK PYEEK + +KE Y
Sbjct: 3   KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERY 62

Query: 234 LQVMAKER 241
            + M + +
Sbjct: 63  EEEMPEYK 70

Length = 70

>gnl|CDD|197700 smart00398, HMG, high mobility group

 Score = 48.9 bits (117), Expect = 7e-08
 Identities = 37/70 (52%), Positives = 50/70 (71%), Gaps = 2/70 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
           KPK P++A+ LFS E RA + A+N +    E++K  GE WK ++EE+K PYEE AKK+KE
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60

Query: 346 KYNEEMEAYK 355
           +Y EEM  YK
Sbjct: 61  RYEEEMPEYK 70

Length = 70

>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 = 48.4 bits (116), Expect = 9e-08
 Identities = 23/62 (37%), Positives = 38/62 (61%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   ++L+ K    +  +E P  E + I+ ILG +WK +S EEK+PY E+ +  KE +
Sbjct: 3   KRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELH 62

Query: 234 LQ 235
           ++
Sbjct: 63  MK 64

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|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 35/91 (38%), Positives = 56/91 (61%), Gaps = 4/91 (4%)

Query: 270 KQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADN----KNVLEVAKITGEEW 325
           KQ      K  +K+KDP  PK  ++AY  F+ E+RA ++A+N    K+V  V K+ GE W
Sbjct: 4   KQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAW 63

Query: 326 KNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR 356
             ++EE+K PYE+ A+++K +Y +E   Y +
Sbjct: 64  NKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Length = 94

>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 = 45.4 bits (108), Expect = 1e-06
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 290 KHPVTAYFLFSSERRAALLADNKNV--LEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           K P+ A+ LFS   R  +L +        ++KI G+ WK ++ E+K+PY E AKK KE +
Sbjct: 3   KRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELH 62

Query: 348 NEEMEAYKRR 357
            +    YK R
Sbjct: 63  MKLYPDYKWR 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|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

 Score = 47.2 bits (112), Expect = 3e-06
 Identities = 36/131 (27%), Positives = 62/131 (47%), Gaps = 2/131 (1%)

Query: 227 QAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDP 286
                     +    +      + +         + L+Q L   ++  K  +  +K+KDP
Sbjct: 9   PYLTLQAPLSLIIFHKMVFMSGIRQLHTTLVELEKPLQQLLTKPRKKTKSKRLVRKKKDP 68

Query: 287 LKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNK 344
             PK P++AYFL+S+E R  +  +N      EV K+  E+WK +T+E+K PY + A  ++
Sbjct: 69  NGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDR 128

Query: 345 EKYNEEMEAYK 355
           E+Y  E E Y 
Sbjct: 129 ERYQREKEEYN 139

Length = 211

>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

 Score = 44.9 bits (106), Expect = 2e-05
 Identities = 47/213 (22%), Positives = 89/213 (41%), Gaps = 41/213 (19%)

Query: 140 LQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAE 199
           L ++++    +     +  K K   RKKK     KRP   Y L+  +  +E +KENP+  
Sbjct: 38  LVELEKPLQQLLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLT 97

Query: 200 FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEEHKQKTA 259
           F E+  +L  KWK ++ EEK+PY ++  +++E Y +               EE +K+   
Sbjct: 98  FGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREK-------------EEYNKKLPN 144

Query: 260 MELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAK 319
              +  +++ + +   + + P  +                            K ++E  K
Sbjct: 145 KAPIGPFIENEPKIRPKVEGPSPD----------------------------KALVEETK 176

Query: 320 ITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEME 352
           I  + W  + E +K+ Y +  KK KE+Y+    
Sbjct: 177 IISKAWSELDESKKKKYIDKYKKLKEEYDSFYP 209

Length = 211

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 22/62 (35%), Positives = 35/62 (56%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
            RP   +IL+ +D+  + K ENP     EI+ I+G  W++ S E K  Y+E  + EKE +
Sbjct: 3   PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERH 62

Query: 234 LQ 235
            +
Sbjct: 63  AR 64

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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.8 bits (100), Expect = 3e-04
 Identities = 77/296 (26%), Positives = 128/296 (43%), Gaps = 27/296 (9%)

Query: 65   KKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELE 124
            K   AK KA++A K  +     +  +  E  +K   E +K +E  K+ +E    K +E +
Sbjct: 1432 KADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEE--AKKADEAK 1489

Query: 125  LQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWC 184
             + +E +K   E KK  + K+          +  + K+ D  KK    +K          
Sbjct: 1490 KKAEEAKKKADEAKKAAEAKKKADEAK----KAEEAKKADEAKKAEEAKK---------- 1535

Query: 185  KDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRES 244
             D+  +A+++    E K+   +  A+ K  + E KK  E+K  A ++A     A+E R  
Sbjct: 1536 ADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIE 1595

Query: 245  EAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERR 304
            E MKL EEE K K       +  + K E  K+ ++ KK+ + LK K         + E++
Sbjct: 1596 EVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKE--------AEEKK 1647

Query: 305  AALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKE 360
             A   + K   E  KI   E     EE K+  EE  K  +++     EA K+  +E
Sbjct: 1648 KA--EELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAA-EALKKEAEE 1700

Length = 2084

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 26/70 (37%), Positives = 43/70 (61%)

Query: 73  AKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQEK 132
           AK+   K    F+K+L+E +  L+K++    + EE L  K E+L+ +EEELE + KE E+
Sbjct: 62  AKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQ 121

Query: 133 LHMELKKLQK 142
              EL+K ++
Sbjct: 122 KQQELEKKEE 131

Length = 520

>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898)

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 286 PLKPKHPVTAYFLFSSERRAALLADNK---NVLEVAKITGEEWKNMTEEQKRPYEEIAKK 342
           P KPK    AYF F    R  L  +      V E +K+  E+WK M+EE+K  YEE A++
Sbjct: 1   PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKARE 60

Query: 343 NKEKYNEEM 351
           +K++Y+ EM
Sbjct: 61  DKKRYDREM 69

This domain is predominantly found in Maelstrom homolog proteins. It has no known function. Length = 69

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.7 bits (92), Expect = 0.003
 Identities = 77/316 (24%), Positives = 124/316 (39%), Gaps = 19/316 (6%)

Query: 51   AGLSKENHESLSQPKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLK 110
            A +  E      + KKA  K KA +A K ++     + ++  E  +K    K+K EE  K
Sbjct: 1270 AAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKK 1329

Query: 111  EKDEMLKMKEE---ELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKK 167
            + D   K  EE     E    E E    E +  ++  E             K KE+ +KK
Sbjct: 1330 KADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAE----------KKKEEAKKK 1379

Query: 168  KGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQ 227
               A++K          K +  E KK+  E +          + K  + E+KK  E K +
Sbjct: 1380 ADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKK 1439

Query: 228  AE---KEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEK 284
            AE   K    +  A+E +++E  K   EE K+    +   +  +   EA K+ ++ KK+ 
Sbjct: 1440 AEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKA 1499

Query: 285  DPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNK 344
            D  K           + +   A  AD     E AK   E  K    E+K+  +E+ K  +
Sbjct: 1500 DEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK---AEEKKKADELKKAEE 1556

Query: 345  EKYNEEMEAYKRRMKE 360
             K  EE +  +   K 
Sbjct: 1557 LKKAEEKKKAEEAKKA 1572

Length = 2084

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	363
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.86
PTZ00199	94	high mobility group protein; Provisional	99.8
PTZ00199	94	high mobility group protein; Provisional	99.73
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.67
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.67
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.66
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.66
smart00398	70	HMG high mobility group.	99.63
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.62
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.58
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.57
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.56
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.55
KOG0381	96	consensus HMG box-containing protein [General func	99.54
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.54
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.53
smart00398	70	HMG high mobility group.	99.51
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.42
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.39
KOG0381	96	consensus HMG box-containing protein [General func	99.37
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.34
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.26
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.26
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.25
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	98.99
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	98.73
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	98.64
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	98.45
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.29
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.16
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	97.93
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	97.61
KOG2746	683	consensus HMG-box transcription factor Capicua and	97.55
KOG2746	683	consensus HMG-box transcription factor Capicua and	97.01
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	96.81
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	95.64
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	93.97
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	92.37
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	91.36
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	87.39

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=99.86  E-value=2e-21  Score=176.71  Aligned_cols=146  Identities=29%  Similarity=0.525  Sum_probs=132.0

Q ss_pred             hhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          164 DRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       164 ~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      .++++||+.||||+|+||+||.++|..|...+|++++++|++.+|++|++|+++||++|...|..++++|..++..|.. 
T Consensus        62 ~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~-  140 (211)
T COG5648          62 VRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNK-  140 (211)
T ss_pred             HHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhc-
Confidence            5678999999999999999999999999999999999999999999999999999999999999999999998765532 


Q ss_pred             HHHHHhhHHHHHHhhHHHHHHHHhhhhHhhhhhcCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHH
Q 017939          244 SEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKIT  321 (363)
Q Consensus       244 ~e~~kll~~eq~~k~~~e~~~~~~~~~~~~~~k~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l  321 (363)
                                                                ..+++.|..+|+-|....+..+...++  ...++++.+
T Consensus       141 ------------------------------------------k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~  178 (211)
T COG5648         141 ------------------------------------------KLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKII  178 (211)
T ss_pred             ------------------------------------------ccCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhh
Confidence                                                      125677888888899999988877776  579999999


Q ss_pred             HHHhccCChHHhHHHHHHHHHHHHHHHHHHH
Q 017939          322 GEEWKNMTEEQKRPYEEIAKKNKEKYNEEME  352 (363)
Q Consensus       322 ~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~  352 (363)
                      |..|.+|+++-|.+|.+.+..++..|...++
T Consensus       179 ~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         179 SKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             hhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            9999999999999999999999999987764

>PTZ00199 high mobility group protein; Provisional

Probab=99.80  E-value=2.8e-19  Score=146.00  Aligned_cols=79  Identities=34%  Similarity=0.555  Sum_probs=74.8

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCC--HHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s--~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      ++++.+||+.||||+|||++||.++|..|..+||+++  +.+|+++||++|++||+++|.+|++.|..++.+|..+|..|
T Consensus        13 ~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y   92 (94)
T PTZ00199         13 NKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEY   92 (94)
T ss_pred             cCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3457899999999999999999999999999999986  89999999999999999999999999999999999999988


Q ss_pred             h
Q 017939          241 R  241 (363)
Q Consensus       241 k  241 (363)
                      .
T Consensus        93 ~   93 (94)
T PTZ00199         93 A   93 (94)
T ss_pred             h
Confidence            4

>PTZ00199 high mobility group protein; Provisional

Probab=99.73  E-value=9.5e-18  Score=136.99  Aligned_cols=78  Identities=40%  Similarity=0.811  Sum_probs=72.4

Q ss_pred             CCCCCCCCCCCCCCccccccccHHHHHHHHhhCCC----hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHH
Q 017939          279 KPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN----VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAY  354 (363)
Q Consensus       279 kkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~----~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~y  354 (363)
                      +++..+||+.||+|+|||++||+++|..+..+||+    +.+|+++||++|++||+++|.+|.++|+.++.+|..+|.+|
T Consensus        13 ~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y   92 (94)
T PTZ00199         13 NKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEY   92 (94)
T ss_pred             cCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44567899999999999999999999999999874    68999999999999999999999999999999999999999


Q ss_pred             Hh
Q 017939          355 KR  356 (363)
Q Consensus       355 k~  356 (363)
                      .+
T Consensus        93 ~~   94 (94)
T PTZ00199         93 AK   94 (94)
T ss_pred             hC
Confidence            63

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

Probab=99.67  E-value=1e-16  Score=125.74  Aligned_cols=70  Identities=31%  Similarity=0.491  Sum_probs=67.4

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      .||||+|||||||++.|..|+.+||++++++|+++||++|++||+++|++|.+.|..++++|..++..|+
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yk   70 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYK   70 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCc
Confidence            3899999999999999999999999999999999999999999999999999999999999999988774

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.

>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=99.67  E-value=2.3e-16  Score=120.13  Aligned_cols=69  Identities=43%  Similarity=0.777  Sum_probs=65.4

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          173 RKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       173 PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      ||||+|||++||.+++..++.+||++++++|+++||.+|++||+++|.+|.+.|..++..|..++..|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            899999999999999999999999999999999999999999999999999999999999999998874

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 ....

>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

Probab=99.66  E-value=3.5e-16  Score=118.02  Aligned_cols=65  Identities=51%  Similarity=0.816  Sum_probs=63.5

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHH
Q 017939          173 RKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVM  237 (363)
Q Consensus       173 PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~  237 (363)
                      ||+|+|||++||.++|..++..||++++.+|++.||.+|++||+++|.+|.+.|..++.+|..+|
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            89999999999999999999999999999999999999999999999999999999999999876

These proteins bind the minor groove of 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 members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

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

Probab=99.66  E-value=2.1e-16  Score=122.49  Aligned_cols=69  Identities=33%  Similarity=0.577  Sum_probs=66.1

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          173 RKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       173 PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      .|||+|||++||.++|..++.+||++++++|++.||++|+.||+++|++|.+.|..++++|.+++..|+
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            589999999999999999999999999999999999999999999999999999999999999887663

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.

>smart00398 HMG high mobility group

Probab=99.63  E-value=1.3e-15  Score=115.64  Aligned_cols=69  Identities=39%  Similarity=0.680  Sum_probs=66.9

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      +|++|+|||++||.+.+..+...||++++++|++.||.+|+.||+++|.+|.+.|..++..|...+..|
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y   69 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY   69 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            589999999999999999999999999999999999999999999999999999999999999998776

>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins

Probab=99.62  E-value=1.7e-15  Score=117.75  Aligned_cols=71  Identities=35%  Similarity=0.634  Sum_probs=63.4

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHH-CCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          170 CAERKRPSPPYILWCKDQWNEAKKE-NPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       170 p~~PKrP~say~lF~~e~r~~ik~e-~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      |+.||+|+|||+|||.+++..++.. ++...++|+++.||..|++||++||.+|++.|+.++.+|..+|..|
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~   72 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEW   72 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6789999999999999999999988 7788999999999999999999999999999999999999999877

It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....

>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins

Probab=99.58  E-value=4.3e-15  Score=115.43  Aligned_cols=70  Identities=44%  Similarity=0.767  Sum_probs=61.9

Q ss_pred             CCCCCCCccccccccHHHHHHHHhhC---CChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          286 PLKPKHPVTAYFLFSSERRAALLADN---KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       286 ~~~PKrP~SAY~lF~~e~r~~~~~e~---p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      |++||+|+|||+||+.+++..+...+   .+..++++.||..|++||++||.+|.++|..++++|..++..|.
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            56899999999999999999988763   37899999999999999999999999999999999999999984

It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....

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

Probab=99.57  E-value=2.9e-15  Score=117.48  Aligned_cols=70  Identities=30%  Similarity=0.542  Sum_probs=66.0

Q ss_pred             CCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      .||||+||||||+++.|..+..++|  ++.+|+++||.+|+.||+++|++|.++|+.++++|..++++|+-.
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   72 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYT   72 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCccc
Confidence            3799999999999999999999887  689999999999999999999999999999999999999999753

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.

>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=99.56  E-value=9.6e-15  Score=111.16  Aligned_cols=67  Identities=46%  Similarity=0.832  Sum_probs=62.7

Q ss_pred             CCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          289 PKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       289 PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      |+||+|||++|+.+.+..+...||  +..+|++.||.+|++||+++|.+|.+.|..++.+|..++.+|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            799999999999999999999887  6899999999999999999999999999999999999999995

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=99.55  E-value=2.2e-14  Score=107.54  Aligned_cols=65  Identities=46%  Similarity=0.746  Sum_probs=62.7

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHH
Q 017939          173 RKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVM  237 (363)
Q Consensus       173 PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~  237 (363)
                      ||+|+|||++||.+.+..++..||++++.+|++.||.+|+.||+++|.+|.+.|..++..|...+
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            78999999999999999999999999999999999999999999999999999999999998763

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

>KOG0381 consensus HMG box-containing protein [General function prediction only]

Probab=99.54  E-value=3.4e-14  Score=115.41  Aligned_cols=74  Identities=36%  Similarity=0.604  Sum_probs=70.6

Q ss_pred             CC--CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHH-HHhh
Q 017939          169 GC--AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMA-KERR  242 (363)
Q Consensus       169 ~p--~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~-~yk~  242 (363)
                      +|  +.|++|++||++||.+.+..++.+||+++++||++.+|++|++|++++|.+|+..+..++++|..+|. .|+.
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~   93 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKA   93 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            66  49999999999999999999999999999999999999999999999999999999999999999998 7754

>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

Probab=99.54  E-value=1.7e-14  Score=108.73  Aligned_cols=64  Identities=55%  Similarity=0.963  Sum_probs=61.1

Q ss_pred             CCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH
Q 017939          289 PKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEME  352 (363)
Q Consensus       289 PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~  352 (363)
                      ||+|+|||++|+++.|..+...|+  ++.+|++.||..|++||+++|.+|.+.|+.++.+|..+|.
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~   66 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK   66 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            899999999999999999998887  6899999999999999999999999999999999999873

These proteins bind the minor groove of 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 members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

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

Probab=99.53  E-value=9.7e-15  Score=113.16  Aligned_cols=67  Identities=37%  Similarity=0.602  Sum_probs=63.9

Q ss_pred             CCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          289 PKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       289 PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      .|||+|||++|++++|..+...||  ++.+|++.||+.|+.||+++|.+|.++|..++++|..++++|+
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            589999999999999999998887  6899999999999999999999999999999999999999885

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.

>smart00398 HMG high mobility group

Probab=99.51  E-value=3.6e-14  Score=107.60  Aligned_cols=68  Identities=54%  Similarity=0.906  Sum_probs=64.4

Q ss_pred             CCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      +|++|+|||++|+++.|..+...++  +..+|++.||..|+.||+++|.+|.+.|+.++.+|..++..|+
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4899999999999999999988886  5899999999999999999999999999999999999999884

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=99.42  E-value=2.4e-13  Score=124.16  Aligned_cols=79  Identities=41%  Similarity=0.802  Sum_probs=74.3

Q ss_pred             CCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017939          281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRM  358 (363)
Q Consensus       281 Kk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~  358 (363)
                      ++.+||+.||||+||||+|+.++|..+...++  ++.++.+.+|++|++|+++||.+|...|..++++|..+.+.|..+.
T Consensus        63 r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~  142 (211)
T COG5648          63 RKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKL  142 (211)
T ss_pred             HHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhccc
Confidence            35679999999999999999999999999887  7899999999999999999999999999999999999999998865


Q ss_pred             h
Q 017939          359 K  359 (363)
Q Consensus       359 ~  359 (363)
                      +
T Consensus       143 ~  143 (211)
T COG5648         143 P  143 (211)
T ss_pred             C
Confidence            4

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

Probab=99.39  E-value=8.7e-13  Score=98.83  Aligned_cols=63  Identities=56%  Similarity=0.952  Sum_probs=59.9

Q ss_pred             CCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHH
Q 017939          289 PKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEM  351 (363)
Q Consensus       289 PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~  351 (363)
                      |++|+|||++|+++.+..+...++  +..+|++.||..|+.||+++|.+|.+.|+.++.+|..++
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            789999999999999999998887  689999999999999999999999999999999999875

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

>KOG0381 consensus HMG box-containing protein [General function prediction only]

Probab=99.37  E-value=1.8e-12  Score=105.30  Aligned_cols=72  Identities=54%  Similarity=0.872  Sum_probs=68.4

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCCC--hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH-HHHhhh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEME-AYKRRM  358 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p~--~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~-~yk~~~  358 (363)
                      +.|++|+|||++|+.+.+..+...||+  +.++++.+|.+|++|++++|.+|...|..++++|..+|. .|+...
T Consensus        21 ~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~   95 (96)
T KOG0381|consen   21 QAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            589999999999999999999999985  899999999999999999999999999999999999999 998754

>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]

Probab=99.34  E-value=1.2e-12  Score=132.84  Aligned_cols=76  Identities=28%  Similarity=0.531  Sum_probs=72.1

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      ..|++|||++|||++||||+|+...|..|+.+  |++++||++.+|++|+.||+  |.+|++.|+.++.+|+.+|..|+.
T Consensus       526 ~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk~  601 (615)
T KOG0526|consen  526 KGKKKKDPNAPKRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYKN  601 (615)
T ss_pred             CcccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhcC
Confidence            34688999999999999999999999999998  99999999999999999999  999999999999999999999874

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.26  E-value=4.3e-12  Score=124.77  Aligned_cols=74  Identities=31%  Similarity=0.539  Sum_probs=69.2

Q ss_pred             CCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          284 KDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       284 kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      ...+..||||||||+|.+..|.++..+||  .+.||+|.||.+|+.|+++||.+|++.|++++.++++|+.+|+-+
T Consensus        58 ~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYR  133 (331)
T KOG0527|consen   58 TSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYR  133 (331)
T ss_pred             CCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccc
Confidence            34567899999999999999999999998  479999999999999999999999999999999999999999864

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.26  E-value=4.9e-12  Score=124.33  Aligned_cols=75  Identities=28%  Similarity=0.534  Sum_probs=71.5

Q ss_pred             hccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          166 KKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       166 k~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      .++.....||||||||+|.+..|.+|..+||++.+.||+|.||.+|+.|+++||.+|++.|++++..+.++...|
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdY  130 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDY  130 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCc
Confidence            566778899999999999999999999999999999999999999999999999999999999999999988777

>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]

Probab=99.25  E-value=7.8e-12  Score=126.94  Aligned_cols=77  Identities=42%  Similarity=0.710  Sum_probs=73.0

Q ss_pred             CCCCCCCCCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          278 KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       278 kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      ++.|+.+||+.|||++||||+|.+..|..++.++.++.++++.+|+.|+.||.  |.+|.+.|+.++.+|+.+|.+|+.
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~dgi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk~  601 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKEDGISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYKN  601 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhcCchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhcC
Confidence            44567889999999999999999999999999999999999999999999999  999999999999999999999984

>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]

Probab=98.99  E-value=1.4e-09  Score=104.43  Aligned_cols=82  Identities=29%  Similarity=0.562  Sum_probs=76.9

Q ss_pred             hhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhhH
Q 017939          165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRES  244 (363)
Q Consensus       165 kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e~  244 (363)
                      ...+.|.+|-+|+-+|+.|....|++|++.||++...||.+++|.+|..|+++||+.|.+.|+.+|..|.+.|..|....
T Consensus        57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp  136 (410)
T KOG4715|consen   57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSP  136 (410)
T ss_pred             cCCCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999998764


Q ss_pred             HH
Q 017939          245 EA  246 (363)
Q Consensus       245 e~  246 (363)
                      ..
T Consensus       137 ~y  138 (410)
T KOG4715|consen  137 AY  138 (410)
T ss_pred             hH
Confidence            33

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=98.73  E-value=1.2e-08  Score=99.08  Aligned_cols=75  Identities=24%  Similarity=0.359  Sum_probs=67.7

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      .....|+|+|||+||++|+|..|.+++.-....+|.++||.+|.+||-+|..+|.+.|.++++.+.+....|-+.
T Consensus       188 KkphiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSAR  262 (421)
T KOG3248|consen  188 KKPHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSAR  262 (421)
T ss_pred             cCccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchh
Confidence            445679999999999999999999998877889999999999999999999999999999999988887777553

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=98.64  E-value=2.2e-08  Score=97.12  Aligned_cols=69  Identities=23%  Similarity=0.498  Sum_probs=63.4

Q ss_pred             CCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      ..|+|+|||++|++|+|..+.++.-  ...+|.++||++|++||-+|.++|.++|.++++-+.+-+..|-+
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSA  261 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA  261 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcch
Confidence            4699999999999999999988753  67999999999999999999999999999999999999888854

>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]

Probab=98.45  E-value=3e-07  Score=88.71  Aligned_cols=74  Identities=30%  Similarity=0.553  Sum_probs=68.0

Q ss_pred             CCCCCCCCccccccccHHHHHHHHhhCCC--hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017939          285 DPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRM  358 (363)
Q Consensus       285 d~~~PKrP~SAY~lF~~e~r~~~~~e~p~--~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~  358 (363)
                      .|.+|-+|+-+||.|++-.|.++++.||.  +.+|.++||.+|..|+++||+.|...++..+..|.+.|..|....
T Consensus        61 pPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp  136 (410)
T KOG4715|consen   61 PPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSP  136 (410)
T ss_pred             CCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCc
Confidence            45567778899999999999999999984  799999999999999999999999999999999999999998753

>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]

Probab=98.29  E-value=2.6e-07  Score=93.65  Aligned_cols=74  Identities=27%  Similarity=0.503  Sum_probs=62.0

Q ss_pred             ccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          167 KKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       167 ~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      ...++..|||+|||+.|.++.|.+|...+||+-+..|+++||..|+.||..||++|.+.-...-..+.+....|
T Consensus       320 ~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdY  393 (511)
T KOG0528|consen  320 ASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDY  393 (511)
T ss_pred             CCCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCccc
Confidence            34456779999999999999999999999999999999999999999999999999876655544444444443

>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]

Probab=98.16  E-value=5.3e-07  Score=91.42  Aligned_cols=70  Identities=24%  Similarity=0.499  Sum_probs=63.4

Q ss_pred             CCCCCccccccccHHHHHHHHhhCCC--hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p~--~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      .-|||+||||+|.++.|..+....|+  ...|+++||.+|+.||..||++|.+.-.++...+.+.+++|+-+
T Consensus       325 HIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYk  396 (511)
T KOG0528|consen  325 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYK  396 (511)
T ss_pred             cccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccC
Confidence            34999999999999999988888775  58999999999999999999999999999999999999988753

>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A

Probab=97.93  E-value=1.4e-05  Score=62.48  Aligned_cols=71  Identities=20%  Similarity=0.347  Sum_probs=57.8

Q ss_pred             CCCCCccccccccHHHHHHHHhhCCC-hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNKN-VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRM  358 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p~-~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~  358 (363)
                      .|..|.++--+|.++....+.+.+++ .....+.+...|++|++.+|-+|+..|.++..+|+.+|.+|+.-+
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~K~~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~   74 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKALKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAP   74 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            57788999999999999999888874 444567899999999999999999999999999999999887644

>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A

Probab=97.61  E-value=0.00017  Score=56.49  Aligned_cols=71  Identities=14%  Similarity=0.264  Sum_probs=59.3

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      .|..|.||--+|.+.....+.+.+++....+ .+.+...|++|++.+|..|+..|.++..+|+.+|.+|+..
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~   73 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSA   73 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-C
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4677899999999999999999999877777 4599999999999999999999999999999999877653

>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]

Probab=97.55  E-value=5.4e-05  Score=79.73  Aligned_cols=71  Identities=23%  Similarity=0.449  Sum_probs=65.9

Q ss_pred             hccCCCCCCCCCChHHHHHHHHH--HHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHH
Q 017939          166 KKKGCAERKRPSPPYILWCKDQW--NEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQV  236 (363)
Q Consensus       166 k~k~p~~PKrP~say~lF~~e~r--~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke  236 (363)
                      .+.+....++||++|++||+-+|  ..+...||+..++-|+++||+.|-.|-..||+.|.+.|.+.++.+-+.
T Consensus       175 nkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  175 NKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             CcCcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            45667778999999999999999  999999999999999999999999999999999999999999887663

>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]

Probab=97.01  E-value=0.00042  Score=73.19  Aligned_cols=68  Identities=24%  Similarity=0.446  Sum_probs=58.9

Q ss_pred             CCCCCCccccccccHHHH--HHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          287 LKPKHPVTAYFLFSSERR--AALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r--~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      ...++|||||++|++-+|  ..+...|+  +.+-|.++||+.|-.|.+.||+.|.++|.+.++.+-+.  +|+.
T Consensus       180 ~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka--e~~k  251 (683)
T KOG2746|consen  180 DHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA--EWKK  251 (683)
T ss_pred             hhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh--hccc
Confidence            346899999999999999  66666666  68999999999999999999999999999999888775  4443

>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]

Probab=96.81  E-value=0.002  Score=58.17  Aligned_cols=49  Identities=24%  Similarity=0.417  Sum_probs=43.8

Q ss_pred             ccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCC
Q 017939          167 KKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVS  215 (363)
Q Consensus       167 ~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS  215 (363)
                      .|.|.+..|-+|||..|+++...+|++.||+++..|++..++..|...+
T Consensus       116 ~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  116 NKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             cCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence            3455566678999999999999999999999999999999999999765

>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta

Probab=95.64  E-value=0.016  Score=52.38  Aligned_cols=48  Identities=13%  Similarity=0.255  Sum_probs=42.4

Q ss_pred             CChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHH
Q 017939          177 SPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQA  228 (363)
Q Consensus       177 ~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~  228 (363)
                      -+||+-|+.+++.    .|.+++..|++...+..|..||+.+|..|..++..
T Consensus        83 nnaYLNFLReFRr----kh~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~  130 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCGLSPQDLIQRAARAWCRLSEAEKNRYRRMAPS  130 (183)
T ss_pred             chHHHHHHHHHHH----HccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcch
Confidence            3799999998875    57899999999999999999999999999886543

The function of this family is unknown.

>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta

Probab=93.97  E-value=0.057  Score=48.92  Aligned_cols=47  Identities=21%  Similarity=0.342  Sum_probs=41.7

Q ss_pred             ccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHH
Q 017939          293 VTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAK  341 (363)
Q Consensus       293 ~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae  341 (363)
                      .+||+-|+.+.+...  .+++..|+....+..|..||+.+|..|..++.
T Consensus        83 nnaYLNFLReFRrkh--~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~  129 (183)
T PF06382_consen   83 NNAYLNFLREFRRKH--CGLSPQDLIQRAARAWCRLSEAEKNRYRRMAP  129 (183)
T ss_pred             chHHHHHHHHHHHHc--cCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence            479999999999875  45788999999999999999999999998654

The function of this family is unknown.

>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases []

Probab=92.37  E-value=0.13  Score=38.15  Aligned_cols=40  Identities=23%  Similarity=0.409  Sum_probs=36.6

Q ss_pred             CChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCCh
Q 017939          177 SPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSA  216 (363)
Q Consensus       177 ~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~  216 (363)
                      +|.|=+|..-.|+.|...||++....++..++.+|+..++
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKAPMSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHh
Confidence            5778899999999999999999999999999999997654

; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]

Probab=91.36  E-value=0.25  Score=44.77  Aligned_cols=44  Identities=23%  Similarity=0.342  Sum_probs=37.8

Q ss_pred             CCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCC
Q 017939          286 PLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMT  329 (363)
Q Consensus       286 ~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls  329 (363)
                      |.+..|-.|||..|+++....++..+|  +.+|++..++..|...+
T Consensus       119 PEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  119 PEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             ccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence            344456679999999999999999998  67999999999998765

>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function

Probab=87.39  E-value=7  Score=33.62  Aligned_cols=48  Identities=19%  Similarity=0.362  Sum_probs=41.8

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCCh
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSA  216 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~  216 (363)
                      |..|-+|-.-+|--|+-.+.+.++.+|||+....+-.+|-..|..-++
T Consensus        69 drHPErR~KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   69 DRHPERRMKAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPE  116 (122)
T ss_pred             CCCcchhHHHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCC
Confidence            444456666899999999999999999999999999999999987665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	363
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		8e-04

>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 40/164 (24%), Positives = 62/164 (37%), Gaps = 34/164 (20%)
Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSXXXXXXXXXXXXXXXXXX 233
           KRP   +I+W +DQ  +   ENP     EI+  LG +WK ++                  
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT-----EAEKWPFFQEAQK 60
Query: 234 LQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFXXXXXXXXXXXXXXXXXXXXXHPV 293
           LQ M +E+  +   +  E + K K                                  P 
Sbjct: 61  LQAMHREKYPNYKYRKGETKKKFKDP---------------------------NAPKRPP 93
Query: 294 TAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRP 335
           +A+FLF SE R  +  ++    + +VAK  GE W N   + K+P
Sbjct: 94  SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQP 137

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	363
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-26
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-10
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-21
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	9e-09
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-04
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-21
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-08
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	4e-20
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	4e-04
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	8e-19
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	4e-12
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	2e-18
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	2e-11
2lhj_A	97	High mobility group protein homolog NHP1; structur	5e-18
2lhj_A	97	High mobility group protein homolog NHP1; structur	4e-09
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	6e-18
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	2e-11
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	7e-18
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	7e-11
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	2e-17
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	2e-12
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	3e-17
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	2e-10
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	1e-15
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	8e-10
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	3e-15
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	2e-10
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	1e-14
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	1e-09
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	2e-14
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	3e-10
1ckt_A	71	High mobility group 1 protein; high-mobility group	2e-14
1ckt_A	71	High mobility group 1 protein; high-mobility group	2e-10
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	3e-14
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	4e-12
1wgf_A	90	Upstream binding factor 1; transcription factor, D	7e-14
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-10
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	8e-10
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	8e-09
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	9e-10
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	1e-05
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	2e-09
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	3e-09
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	7e-09
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	9e-04
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	1e-08
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	3e-07
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	2e-08
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	1e-06
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	2e-08
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	2e-07
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	3e-08
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	6e-08
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	4e-08
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	5e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	2e-07
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	3e-06
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	2e-07
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	1e-06
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	2e-07
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	8e-07
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	3e-07
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	5e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	9e-05

>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 =  102 bits (255), Expect = 2e-26
 Identities = 50/186 (26%), Positives = 82/186 (44%), Gaps = 34/186 (18%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   +I+W +DQ  +   ENP     EI+  LG +WK ++  EK P+ ++ Q  +  +
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65

Query: 234 LQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPV 293
            +     +      K   ++                                   PK P 
Sbjct: 66  REKYPNYKYRKGETKKKFKDPN--------------------------------APKRPP 93

Query: 294 TAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEM 351
           +A+FLF SE R  +  ++    + +VAK  GE W N   + K+PYE+ A K KEKY +++
Sbjct: 94  SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI 153

Query: 352 EAYKRR 357
            AY+ +
Sbjct: 154 AAYRAK 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 = 57.9 bits (140), Expect = 2e-10
 Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKNV--LEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
           + K P+ A+ ++S ++R  +  +N  +   E++K  G +WK +TE +K P+ + A+K + 
Sbjct: 4   RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQA 63

Query: 346 KYNEEMEAYKRRMKE 360
            + E+   YK R  E
Sbjct: 64  MHREKYPNYKYRKGE 78

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 90.6 bits (224), Expect = 1e-21
 Identities = 47/188 (25%), Positives = 96/188 (51%), Gaps = 13/188 (6%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           K+P   Y+ + K+Q    K +NP+A+  E+   +  +W+ +   +KK Y++ Y+AE + Y
Sbjct: 11  KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVY 70

Query: 234 LQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPV 293
            + +++ + +    +++  E +              K    K   K K+     KPK P 
Sbjct: 71  KEEISRFKEQLTPSQIMSLEKEI-----------MDKHLKRKAMTKKKELTLLGKPKRPR 119

Query: 294 TAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEA 353
           +AY ++ +ER      D+    E  K   E WKN+++ +K  Y + AK+++ +Y+ EM++
Sbjct: 120 SAYNVYVAERFQEAKGDSPQ--EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKS 177

Query: 354 YKRRMKEL 361
           ++ +M E+
Sbjct: 178 WEEQMIEV 185

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 54.0 bits (129), Expect = 9e-09
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEE 338
                   PK PV++Y  FS E+     A N +    E+ +   + W+ + + +K+ Y++
Sbjct: 2   GSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQD 61

Query: 339 IAKKNKEKYNEEMEAYKR 356
             +   + Y EE+  +K 
Sbjct: 62  AYRAEWQVYKEEISRFKE 79

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 42.0 bits (98), Expect = 1e-04
 Identities = 28/130 (21%), Positives = 54/130 (41%), Gaps = 6/130 (4%)

Query: 110 KEKDEMLKMKEEELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKG 169
            +K         E ++  +E  +   +L   Q M   K  M   + +    K+++    G
Sbjct: 54  SKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLG 113

Query: 170 CAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAE 229
               KRP   Y ++  +++ EAK ++P    +E    +   WKN+S  EK+ Y +  + +
Sbjct: 114 K--PKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKED 167

Query: 230 KEAYLQVMAK 239
           +  Y   M  
Sbjct: 168 ETRYHNEMKS 177

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173

 Score = 89.7 bits (222), Expect = 1e-21
 Identities = 55/201 (27%), Positives = 88/201 (43%), Gaps = 36/201 (17%)

Query: 161 KEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEE 218
                 K    + +     Y  + +    E KK++P+A   F E +     +WK +SA+E
Sbjct: 4   GSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKE 63

Query: 219 KKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENK 278
           K  +E+  +A+K  Y + M                                K     + +
Sbjct: 64  KGKFEDMAKADKARYEREM--------------------------------KTYIPPKGE 91

Query: 279 KPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPY 336
             KK KDP  PK P +A+FLF SE R  +  ++    + +VAK  GE W N   + K+PY
Sbjct: 92  TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 151

Query: 337 EEIAKKNKEKYNEEMEAYKRR 357
           E+ A K KEKY +++ AY+ +
Sbjct: 152 EKKAAKLKEKYEKDIAAYRAK 172

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173

 Score = 52.3 bits (125), Expect = 2e-08
 Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 4/85 (4%)

Query: 278 KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADN----KNVLEVAKITGEEWKNMTEEQK 333
                + DP KP+  +++Y  F    R      +     N  E +K   E WK M+ ++K
Sbjct: 5   SSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK 64

Query: 334 RPYEEIAKKNKEKYNEEMEAYKRRM 358
             +E++AK +K +Y  EM+ Y    
Sbjct: 65  GKFEDMAKADKARYEREMKTYIPPK 89

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238

 Score = 87.2 bits (215), Expect = 4e-20
 Identities = 48/203 (23%), Positives = 100/203 (49%), Gaps = 13/203 (6%)

Query: 159 KDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEE 218
           +   +       +  K+P   Y+ + K+Q    K +NP+A+  E+   +  +W+ +   +
Sbjct: 28  QQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSK 87

Query: 219 KKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENK 278
           KK Y++ Y+AE + Y + +++ + +    +           +  LE+ +  K    K   
Sbjct: 88  KKIYQDAYRAEWQVYKEEISRFKEQLTPSQ-----------IMSLEKEIMDKHLKRKAMT 136

Query: 279 KPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEE 338
           K K+     KPK P +AY ++ +ER      D+    E  K   E WKN+++ +K  Y +
Sbjct: 137 KKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ--EKLKTVKENWKNLSDSEKELYIQ 194

Query: 339 IAKKNKEKYNEEMEAYKRRMKEL 361
            AK+++ +Y+ EM++++ +M E+
Sbjct: 195 HAKEDETRYHNEMKSWEEQMIEV 217

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238

 Score = 40.6 bits (94), Expect = 4e-04
 Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 4/118 (3%)

Query: 122 ELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYI 181
             E Q  ++E    + +             +      K   + ++     + KRP   Y 
Sbjct: 96  RAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYN 155

Query: 182 LWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAK 239
           ++  +++ EAK ++P    +E    +   WKN+S  EK+ Y +  + ++  Y   M  
Sbjct: 156 VYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKS 209

>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 = 78.8 bits (195), Expect = 8e-19
 Identities = 32/76 (42%), Positives = 47/76 (61%), Gaps = 2/76 (2%)

Query: 284 KDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAK 341
           KDP  PK P +A+FLF SE R  +  ++    + +VAK  GE W N   + K+PYE+ A 
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 61

Query: 342 KNKEKYNEEMEAYKRR 357
           K KEKY +++ AY+ +
Sbjct: 62  KLKEKYEKDIAAYRAK 77

>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 = 60.3 bits (147), Expect = 4e-12
 Identities = 22/65 (33%), Positives = 36/65 (55%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   + L+C +   + K E+P     ++   LG  W N +A++K+PYE+K    KE Y
Sbjct: 8   KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 67

Query: 234 LQVMA 238
            + +A
Sbjct: 68  EKDIA 72

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 102

 Score = 78.2 bits (193), Expect = 2e-18
 Identities = 31/89 (34%), Positives = 53/89 (59%), Gaps = 2/89 (2%)

Query: 273 ADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTE 330
           +   + K KK+KDP +P+ PV+AY LF  + +AA+   N N    EV+KI    W  + E
Sbjct: 2   SSGSSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGE 61

Query: 331 EQKRPYEEIAKKNKEKYNEEMEAYKRRMK 359
           EQK+ Y++  +  K++Y +++ AY+  + 
Sbjct: 62  EQKQVYKKKTEAAKKEYLKQLAAYRASLV 90

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 102

 Score = 59.4 bits (144), Expect = 2e-11
 Identities = 25/78 (32%), Positives = 45/78 (57%)

Query: 161 KEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKK 220
             + +KKK   E ++P   Y L+ +D     K +NP A F E++ I+ + W  +  E+K+
Sbjct: 6   SGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQ 65

Query: 221 PYEEKYQAEKEAYLQVMA 238
            Y++K +A K+ YL+ +A
Sbjct: 66  VYKKKTEAAKKEYLKQLA 83

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

 Score = 77.4 bits (191), Expect = 5e-18
 Identities = 26/92 (28%), Positives = 52/92 (56%), Gaps = 4/92 (4%)

Query: 270 KQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADN----KNVLEVAKITGEEW 325
             +     +  K +KDP  PK  +++Y  F+ E+R  ++A+N    K+V  + K+ G  W
Sbjct: 4   ASDRTGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAW 63

Query: 326 KNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR 357
             +++E+K+PYE ++ +++ +Y  E   Y +R
Sbjct: 64  NALSDEEKKPYERMSDEDRVRYEREKAEYAQR 95

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

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 159 KDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEA--EFKEITNILGAKWKNVSA 216
             +   + KK     KR    Y+ + K++  E   ENPE   +   I  ++GA W  +S 
Sbjct: 9   GVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSD 68

Query: 217 EEKKPYEEKYQAEKEAYLQVMA 238
           EEKKPYE     ++  Y +  A
Sbjct: 69  EEKKPYERMSDEDRVRYEREKA 90

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93

 Score = 77.0 bits (190), Expect = 6e-18
 Identities = 30/91 (32%), Positives = 53/91 (58%), Gaps = 2/91 (2%)

Query: 270 KQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKN 327
               + + +  +K+KDP  PK  ++AY  F++E R  + ++N +    +V K  GE+WK 
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKA 61

Query: 328 MTEEQKRPYEEIAKKNKEKYNEEMEAYKRRM 358
           +T E+K+PYE  A+ +K++Y  E E Y   +
Sbjct: 62  LTPEEKQPYEAKAQADKKRYESEKELYNATL 92

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 28/81 (34%), Positives = 41/81 (50%)

Query: 159 KDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEE 218
             K   RKKK     KR    Y+ +  +  +  + ENP+  F ++   LG KWK ++ EE
Sbjct: 7   PKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEE 66

Query: 219 KKPYEEKYQAEKEAYLQVMAK 239
           K+PYE K QA+K+ Y      
Sbjct: 67  KQPYEAKAQADKKRYESEKEL 87

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86

 Score = 76.6 bits (189), Expect = 7e-18
 Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 278 KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADN----KNVLEVAKITGEEWKNMTEEQK 333
                + DP KPK  ++AY  F    R      N     N  E +K   E WK M+ ++K
Sbjct: 5   SSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEK 64

Query: 334 RPYEEIAKKNKEKYNEEMEAY 354
             ++E+AK +K +Y+ EM+ Y
Sbjct: 65  SKFDEMAKADKVRYDREMKDY 85

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86

 Score = 57.0 bits (138), Expect = 7e-11
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 161 KEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEA--EFKEITNILGAKWKNVSAEE 218
                 K    + K     Y  + +    E KK+NPE    F E +     +WK +S +E
Sbjct: 4   GSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKE 63

Query: 219 KKPYEEKYQAEKEAYLQVMAK 239
           K  ++E  +A+K  Y + M  
Sbjct: 64  KSKFDEMAKADKVRYDREMKD 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 = 75.9 bits (187), Expect = 2e-17
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 284 KDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAK 341
                PK PVT Y  F +ERR  +   + +    E+ K+ G EW  +   +K+ Y + A+
Sbjct: 3   SGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAE 62

Query: 342 KNKEKYNEEMEAYKRRMKE 360
           K K++Y +E+ AY++    
Sbjct: 63  KEKQQYLKELWAYQQSEAY 81

>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 = 62.0 bits (151), Expect = 2e-12
 Identities = 19/65 (29%), Positives = 37/65 (56%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           K P   Y+ +  ++  + +  +P+  F EIT +LGA+W  +   EK+ Y ++ + EK+ Y
Sbjct: 9   KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQY 68

Query: 234 LQVMA 238
           L+ + 
Sbjct: 69  LKELW 73

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83

 Score = 75.0 bits (185), Expect = 3e-17
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 4/81 (4%)

Query: 284 KDPLKPKHPVTAYFLFSSERRAALLADN----KNVLEVAKITGEEWKNMTEEQKRPYEEI 339
            DP KP+  +++Y  F    R      +     N  E +K   E WK M+ ++K  +E++
Sbjct: 3   GDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDM 62

Query: 340 AKKNKEKYNEEMEAYKRRMKE 360
           AK +K +Y  EM+ Y     E
Sbjct: 63  AKADKARYEREMKTYIPPKGE 83

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKE 231
           +     Y  + +    E KK++P+A   F E +     +WK +SA+EK  +E+  +A+K 
Sbjct: 9   RGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 68

Query: 232 AYLQVMA 238
            Y + M 
Sbjct: 69  RYEREMK 75

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67

 Score = 69.6 bits (171), Expect = 1e-15
 Identities = 22/67 (32%), Positives = 40/67 (59%), Gaps = 2/67 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           KPK P +AY ++ +ER      D+    E  K   E WKN+++ +K  Y + AK+++ +Y
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSPQ--EKLKTVKENWKNLSDSEKELYIQHAKEDETRY 59

Query: 348 NEEMEAY 354
           + EM+++
Sbjct: 60  HNEMKSW 66

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67

 Score = 53.4 bits (129), Expect = 8e-10
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   Y ++  +++ EAK ++P    +E    +   WKN+S  EK+ Y +  + ++  Y
Sbjct: 4   KRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRY 59

Query: 234 LQVMA 238
              M 
Sbjct: 60  HNEMK 64

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99

 Score = 69.8 bits (171), Expect = 3e-15
 Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEE 338
           K +K P  PK P+T YF F  E+RA     +     L++ KI  +++K + E++K  Y +
Sbjct: 3   KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQ 62

Query: 339 IAKKNKEKYNEEMEAYKRRMKEL 361
             ++ K+++   +  ++    +L
Sbjct: 63  DFQREKQEFERNLARFREDHPDL 85

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 19/70 (27%), Positives = 39/70 (55%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           K+P  PY  +  ++  +  K +PE    ++T IL  K+K +  ++K  Y + +Q EK+ +
Sbjct: 12  KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEF 71

Query: 234 LQVMAKERRE 243
            + +A+ R +
Sbjct: 72  ERNLARFRED 81

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 25/70 (35%), Positives = 42/70 (60%), Gaps = 4/70 (5%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
            PK   TA+ L+ ++ R ++  +N    V E+AK  GE WK + +  K  +E+ A K+K+
Sbjct: 3   MPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQ 60

Query: 346 KYNEEMEAYK 355
           +Y++EM  YK
Sbjct: 61  RYHDEMRNYK 70

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KR +  ++LW  D     K+ENP  +  EI    G  WK +   +K  +E+    +K+ Y
Sbjct: 5   KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRY 62

Query: 234 LQVMA 238
              M 
Sbjct: 63  HDEMR 67

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73

 Score = 66.5 bits (163), Expect = 2e-14
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
           KPK P++AY L+ +  R ++  +N    V EVAK  GE W+ M +  K  +E  A K K+
Sbjct: 3   KPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKD 60

Query: 346 KYNEEMEAYK 355
            Y+  ++ ++
Sbjct: 61  DYDRAVKEFE 70

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   Y LW        K+ENP  +  E+    G  W+    ++K  +E K    K+ Y
Sbjct: 5   KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRA--MKDKSEWEAKAAKAKDDY 62

Query: 234 LQVMAK 239
            + + +
Sbjct: 63  DRAVKE 68

>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Length = 71

 Score = 66.3 bits (162), Expect = 2e-14
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 288 KPKHPVTAYFLFSSERRAALLADN----KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKN 343
           KP+  +++Y  F    R      +     N  E +K   E WK M+ ++K  +E++AK +
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 344 KEKYNEEMEAY 354
           K +Y  EM+ Y
Sbjct: 61  KARYEREMKTY 71

>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Length = 71

 Score = 55.1 bits (133), Expect = 2e-10
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEA--EFKEITNILGAKWKNVSAEEKKPYEEKYQAEKE 231
           +     Y  + +    E KK++P+A   F E +     +WK +SA+EK  +E+  +A+K 
Sbjct: 3   RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 62

Query: 232 AYLQVMA 238
            Y + M 
Sbjct: 63  RYEREMK 69

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 66.7 bits (163), Expect = 3e-14
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 284 KDPLKPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAK 341
                 K P++A  LF  + R   L +N   ++ +      E WK ++EE+K  YEE A 
Sbjct: 3   SGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKAT 62

Query: 342 KNKEKYNEEMEAYKRRMKE 360
           K+ E+YN +M+    +  +
Sbjct: 63  KDLERYNSQMKRAIEQESQ 81

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 60.9 bits (148), Expect = 4e-12
 Identities = 24/89 (26%), Positives = 38/89 (42%)

Query: 167 KKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKY 226
             G +  K+P     L+ +D   +   ENP+   ++ T  +   WK +S EEK  YEEK 
Sbjct: 2   SSGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKA 61

Query: 227 QAEKEAYLQVMAKERRESEAMKLLEEEHK 255
             + E Y   M +   +   M L +    
Sbjct: 62  TKDLERYNSQMKRAIEQESQMSLKDSGPS 90

>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 = 65.5 bits (160), Expect = 7e-14
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 275 KENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQ 332
            +  +   +    KPK PV+A F+FS E+R  L  +       E+ ++    W +++E++
Sbjct: 7   GKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKK 66

Query: 333 KRPYEEIAKKNKEKYNEEMEAYK 355
           K  Y+      K +   +     
Sbjct: 67  KAKYKAREAALKAQSERKSGPSS 89

>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 = 55.8 bits (135), Expect = 2e-10
 Identities = 18/83 (21%), Positives = 37/83 (44%)

Query: 159 KDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEE 218
               Q+  K G  + KRP     ++ +++  + ++E PE    E+T +L   W ++S ++
Sbjct: 7   GKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKK 66

Query: 219 KKPYEEKYQAEKEAYLQVMAKER 241
           K  Y+ +  A K    +      
Sbjct: 67  KAKYKAREAALKAQSERKSGPSS 89

>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 = 54.3 bits (131), Expect = 8e-10
 Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 2/78 (2%)

Query: 275 KENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQ 332
             +        P K K P+ A+ LF+ + R         K+   ++ I G+ WK M  E+
Sbjct: 4   GSSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEE 63

Query: 333 KRPYEEIAKKNKEKYNEE 350
           +R Y   AK   E+    
Sbjct: 64  RRMYTLEAKALAEEQKRL 81

>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 = 51.3 bits (123), Expect = 8e-09
 Identities = 18/62 (29%), Positives = 32/62 (51%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   ++L+ K    E  +  P  + + I+ ILG +WK +  EE++ Y  + +A  E  
Sbjct: 19  KRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQ 78

Query: 234 LQ 235
            +
Sbjct: 79  KR 80

>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101

 Score = 54.5 bits (131), Expect = 9e-10
 Identities = 14/72 (19%), Positives = 35/72 (48%)

Query: 289 PKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYN 348
            K P+  Y  FS E  +    ++  + E     G  W+ +++ QK  Y+++A++ + +Y 
Sbjct: 9   KKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK 68

Query: 349 EEMEAYKRRMKE 360
             ++ + + +  
Sbjct: 69  VHLDLWVKSLSP 80

>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 13/87 (14%), Positives = 36/87 (41%), Gaps = 4/87 (4%)

Query: 173 RKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEA 232
           +K P   Y  + ++  +  +  +     KE    +G++W+ +S  +K+ Y++  + ++  
Sbjct: 9   KKPPMNGYQKFSQELLSNGELNHLP--LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQ 66

Query: 233 YLQVMA--KERRESEAMKLLEEEHKQK 257
           Y   +    +    +     +E    K
Sbjct: 67  YKVHLDLWVKSLSPQDRAAYKEYISNK 93

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 14/76 (18%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 284 KDPLKPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAK 341
                 + P+ A+ LF    R+ +  ++   +     KI  + W  +  ++K+ Y ++AK
Sbjct: 3   SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAK 62

Query: 342 KNKEKYNEEMEAYKRR 357
           + K+ + +    Y+  
Sbjct: 63  EYKDAFMKANPGYRSG 78

>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 = 52.6 bits (127), Expect = 3e-09
 Identities = 16/62 (25%), Positives = 35/62 (56%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           +RP   ++L+CK   +  ++E+P  + +  T IL   W  +  +EK+ Y +  +  K+A+
Sbjct: 9   RRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAF 68

Query: 234 LQ 235
           ++
Sbjct: 69  MK 70

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108

 Score = 52.3 bits (125), Expect = 7e-09
 Identities = 17/88 (19%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 273 ADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQ 332
           +   + + K + D    K P  +Y L+ +E  A +   +    E   +  ++WK +++++
Sbjct: 2   SSGSSGQLKDKFDGRPTKPPPNSYSLYCAELMANM--KDVPSTERMVLCSQQWKLLSQKE 59

Query: 333 KRPYEEIAKKNKEKYNEEMEAYKRRMKE 360
           K  Y +   + K+ Y  E+  +   + E
Sbjct: 60  KDAYHKKCDQKKKDYEVELLRFLESLPE 87

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108

 Score = 37.6 bits (87), Expect = 9e-04
 Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 4/81 (4%)

Query: 159 KDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEE 218
               Q + K      K P   Y L+C +     K                 +WK +S +E
Sbjct: 4   GSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERMVLC----SQQWKLLSQKE 59

Query: 219 KKPYEEKYQAEKEAYLQVMAK 239
           K  Y +K   +K+ Y   + +
Sbjct: 60  KDAYHKKCDQKKKDYEVELLR 80

>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 = 50.2 bits (121), Expect = 1e-08
 Identities = 20/58 (34%), Positives = 32/58 (55%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKE 231
           KRP   +I+W +DQ  +   ENP     EI+  LG +WK ++  EK P+ ++ Q  + 
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQA 63

>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 = 46.4 bits (111), Expect = 3e-07
 Identities = 20/68 (29%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 290 KHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           K P+ A+ ++S ++R  +  +N      E++K  G +WK +TE +K P+ + A+K +  +
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65

Query: 348 NEEMEAYK 355
            E+   YK
Sbjct: 66  REKYPNYK 73

>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 = 50.3 bits (121), Expect = 2e-08
 Identities = 20/62 (32%), Positives = 34/62 (54%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   +I+W +DQ  +   ENP     EI+  LG +WK ++  EK P+ ++ Q  +  +
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65

Query: 234 LQ 235
            +
Sbjct: 66  RE 67

>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 = 45.3 bits (108), Expect = 1e-06
 Identities = 20/68 (29%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 290 KHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           K P+ A+ ++S ++R  +  +N      E++K  G +WK +TE +K P+ + A+K +  +
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65

Query: 348 NEEMEAYK 355
            E+   YK
Sbjct: 66  REKYPNYK 73

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 13/58 (22%), Positives = 32/58 (55%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKE 231
           KRP   +++W + +  +  +++P+    EI+  LG +WK +   +K P+ ++ +  + 
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRL 61

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 14/63 (22%), Positives = 35/63 (55%), Gaps = 2/63 (3%)

Query: 290 KHPVTAYFLFSSERRAALLADNKNVL--EVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           K P+ A+ ++S   R  ++  + ++   E++K  G+ WK + +  K P+ + A++ + K+
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKH 63

Query: 348 NEE 350
             +
Sbjct: 64  MAD 66

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 17/62 (27%), Positives = 37/62 (59%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           +RP   +++W KD+     ++NP+    E++ +LG  WK ++  EK+P+ E+ +  +  +
Sbjct: 4   RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQH 63

Query: 234 LQ 235
           +Q
Sbjct: 64  MQ 65

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

 Score = 48.4 bits (116), Expect = 6e-08
 Identities = 18/70 (25%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
             + P+ A+ +++ + R  L   N   +  E++K+ G+ WK +T  +KRP+ E A++ + 
Sbjct: 2   SIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 61

Query: 346 KYNEEMEAYK 355
           ++ ++   YK
Sbjct: 62  QHMQDHPNYK 71

>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 = 50.1 bits (120), Expect = 4e-08
 Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 276 ENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQK 333
           EN   +  K+    K P+ A+ +++   R  L       +  E++K  G+ W+ + E +K
Sbjct: 17  ENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEK 76

Query: 334 RPYEEIAKKNKEKYNEE 350
           RP+ E A++ + ++ ++
Sbjct: 77  RPFVEEAERLRVQHKKD 93

>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 = 46.6 bits (111), Expect = 5e-07
 Identities = 13/62 (20%), Positives = 31/62 (50%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   +++W +    +   + P     E++  LG  W+ ++  EK+P+ E+ +  +  +
Sbjct: 31  KRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQH 90

Query: 234 LQ 235
            +
Sbjct: 91  KK 92

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.9 bits (126), Expect = 1e-07
 Identities = 48/304 (15%), Positives = 86/304 (28%), Gaps = 86/304 (28%)

Query: 102 KEKTEELLKEKDEMLKMKEEELELQGKEQEKLHMELKKL--QKMKEFKPNMTLPIVQCLK 159
              T   L      L   +E   L  K    L    + L  + +       T P    + 
Sbjct: 284 ATTTHISLDHHSMTLT-PDEVKSLLLK---YLDCRPQDLPREVLT------TNPRRLSI- 332

Query: 160 DKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEK 219
                      AE  R            W+  K  N      ++T I+ +    +   E 
Sbjct: 333 ----------IAESIRDGL-------ATWDNWKHVN----CDKLTTIIESSLNVLEPAEY 371

Query: 220 KPYEEKYQA----EKEAYL--QVMA-----KERRESEAM------KLLEEEHKQKTAMEL 262
           +     +         A++   +++       + +   +        L E+  +++ + +
Sbjct: 372 RKM---FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428

Query: 263 LEQYLQFKQEADKE-----------NKKPKKEKDPLKPKHPVTAYF-------LFSSER- 303
              YL+ K + + E           N     + D L P   +  YF       L + E  
Sbjct: 429 PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP-YLDQYFYSHIGHHLKNIEHP 487

Query: 304 -RAALLAD---NKNVLEVAKI--TGEEWKNM-----TEEQKRPYEEIAKKNKEKYNEEME 352
            R  L      +   LE  KI      W        T +Q + Y+     N  KY   + 
Sbjct: 488 ERMTLFRMVFLDFRFLE-QKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVN 546

Query: 353 AYKR 356
           A   
Sbjct: 547 AILD 550

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.5 bits (112), Expect = 5e-06
 Identities = 31/268 (11%), Positives = 76/268 (28%), Gaps = 73/268 (27%)

Query: 85  DKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKE--EELELQGKEQEKLHMELKKLQK 142
           + D +++Q+M + + L KE+ + ++  KD +         L  + +E  +  +E + L+ 
Sbjct: 32  NFDCKDVQDMPKSI-LSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE-EVLRI 89

Query: 143 MKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILW--CKDQ-WNEAKKENP--- 196
             +F           L    +        E+++PS    ++   +D+ +N+ +       
Sbjct: 90  NYKF-----------LMSPIK-------TEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 197 --EAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYL----------QVMAKERRES 244
                + ++   L                   +      +            +A +   S
Sbjct: 132 SRLQPYLKLRQAL------------------LELRPAKNVLIDGVLGSGKTWVALDVCLS 173

Query: 245 EAMKLLEEEH-------KQKTAMELLEQ----YLQFKQEADKENKKPKKEKDPLKPKHPV 293
             ++   +            +   +LE       Q        +      K  +      
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233

Query: 294 TAYFLFSSERRAAL--LAD--NKNVLEV 317
               L S      L  L +  N      
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNA 261

>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 = 47.6 bits (114), Expect = 2e-07
 Identities = 19/58 (32%), Positives = 35/58 (60%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKE 231
           KRP   +++W + Q  +  +ENP+    EI+  LGA+WK +S  EK+P+ ++ +  + 
Sbjct: 4   KRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRA 61

>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 = 43.7 bits (104), Expect = 3e-06
 Identities = 19/65 (29%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKNVL--EVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
           + K P+ A+ ++S  +R  +  +N  +   E++K  G EWK ++E +KRP+ + AK+ + 
Sbjct: 2   RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRA 61

Query: 346 KYNEE 350
            + +E
Sbjct: 62  LHMKE 66

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 17/62 (27%), Positives = 37/62 (59%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           +RP   +++W KD+     ++NP+    E++ +LG  WK ++  EK+P+ E+ +  +  +
Sbjct: 8   RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQH 67

Query: 234 LQ 235
           +Q
Sbjct: 68  MQ 69

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 284 KDPLKPKHPVTAYFLFSSERRAALLADNKNVL--EVAKITGEEWKNMTEEQKRPYEEIAK 341
               + + P+ A+ +++ + R  L   N ++   E++K+ G+ WK +T  +KRP+ E A+
Sbjct: 2   SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAE 61

Query: 342 KNKEKYNEEMEAYK 355
           + + ++ ++   YK
Sbjct: 62  RLRVQHMQDHPNYK 75

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 18/62 (29%), Positives = 32/62 (51%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           K+P   ++L+ K+       E+   E   I  ILG +W  +S EE+  Y E  + E++ +
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLH 63

Query: 234 LQ 235
           +Q
Sbjct: 64  MQ 65

>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 = 45.7 bits (109), Expect = 8e-07
 Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 290 KHPVTAYFLFSSERRAALLADNKNV--LEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           K P+ A+ L+  E RA ++A++       + +I G  W  ++ E++  Y E+A+K ++ +
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLH 63

Query: 348 NEEMEAYK 355
            +    + 
Sbjct: 64  MQLYPGWS 71

>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 = 46.8 bits (112), Expect = 3e-07
 Identities = 19/62 (30%), Positives = 36/62 (58%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   +++W KD+  +  +  P+     I+ ILG++WK ++  EK+PY E+     + +
Sbjct: 6   KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQH 65

Query: 234 LQ 235
           L+
Sbjct: 66  LE 67

>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 = 46.0 bits (110), Expect = 5e-07
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 290 KHPVTAYFLFSSERRAALLADNKNV--LEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           K P+ A+ +++ + R  +L    ++    ++KI G  WK MT  +K+PY E   +  +++
Sbjct: 6   KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQH 65

Query: 348 NEEMEAYK 355
            E+   YK
Sbjct: 66  LEKYPDYK 73

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 48.2 bits (115), Expect = 3e-06
 Identities = 30/203 (14%), Positives = 78/203 (38%), Gaps = 29/203 (14%)

Query: 92   QEMLEKMKLEKEKTEELLKEKDEM---LKMKEEELELQGKEQEKLHMELKKLQKMKEFKP 148
            +  L+K+K+E    E   K    +   +   + +++ Q KE + L  ++  L+     + 
Sbjct: 903  KRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTET 962

Query: 149  NMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILG 208
                  V+ L+  E++ K                         +  + + E  ++   L 
Sbjct: 963  EKLRSDVERLRMSEEEAKNA---------------------TNRVLSLQEEIAKLRKELH 1001

Query: 209  AKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQ 268
                  +  EKK  EE     K    Q++++ + ++  +K  +EE  ++   +  E    
Sbjct: 1002 Q-----TQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITET 1056

Query: 269  FKQEADKENKKPKKEKDPLKPKH 291
             +++  +E K+ + + +  + ++
Sbjct: 1057 MEKKLVEETKQLELDLNDERLRY 1079

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 10/71 (14%), Positives = 25/71 (35%)

Query: 72  KAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELELQGKEQE 131
           K     + +     + + E  +  + +  +    E     + E L+   E L +  +E +
Sbjct: 921 KLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAK 980

Query: 132 KLHMELKKLQK 142
                +  LQ+
Sbjct: 981 NATNRVLSLQE 991

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 56/301 (18%), Positives = 117/301 (38%), Gaps = 24/301 (7%)

Query: 65   KKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEKDEMLKMKEEELE 124
            +K     + K   +++  +  +   E +EM  ++  +K++ EE+L E +  ++ +EE  +
Sbjct: 885  QKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQ 944

Query: 125  LQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWC 184
                E++K+  ++  L++  E          +   +K     K    E        IL  
Sbjct: 945  QLQAEKKKMQQQMLDLEEQLE---EEEAARQKLQLEKVTADGKIKKMEDD------ILIM 995

Query: 185  KDQWNEAKKEN--PEAEFKEITNILGAKWKNVSAEEKKPYE-EKYQAEKEAYLQVMAKER 241
            +DQ N+  KE    E    ++T  L  + +      K   + E   +E E  L+   K R
Sbjct: 996  EDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSR 1055

Query: 242  RESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSS 301
            +E E +K  + E +     E + +      E   +  K ++E      +           
Sbjct: 1056 QELEKIK-RKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARL---------- 1104

Query: 302  ERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKEL 361
            E   +   +    +   +    + +   E +K    + A+K K   +EE+EA K  +++ 
Sbjct: 1105 EDETSQKNNALKKIRELESHISDLQEDLESEKAARNK-AEKQKRDLSEELEALKTELEDT 1163

Query: 362  L 362
            L
Sbjct: 1164 L 1164

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 41/226 (18%), Positives = 88/226 (38%), Gaps = 15/226 (6%)

Query: 53   LSKENHESLSQPKKAAAKGKAKQATKKQDTSFDKDLQEMQEMLEKMKLEKEKTEELLKEK 112
            L  E   +  + KK        +    + T   K L+E    L     E+E+  + L + 
Sbjct: 974  LQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKL 1033

Query: 113  DEMLKMKEEELELQGKEQEKLHMELKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAE 172
                +    ELE++ K++EK   EL+K+++  E + +     +  L+ +  + K +    
Sbjct: 1034 KNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQ---L 1090

Query: 173  RKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEA 232
             K+         + +   ++K N   + +E+                   +E  ++EK A
Sbjct: 1091 AKKEEELQAALARLEDETSQKNNALKKIRELE------------SHISDLQEDLESEKAA 1138

Query: 233  YLQVMAKERRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENK 278
              +   ++R  SE ++ L+ E +        +Q L+     D ++K
Sbjct: 1139 RNKAEKQKRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDDDK 1184

>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 39.8 bits (92), Expect = 9e-05
 Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 288 KPKHPVTAYFLFSSERRAALLADN---KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNK 344
               P T + ++  E R+ +L+DN    +  ++ K     ++ ++ E+++ +   AK   
Sbjct: 5   SSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGET 64

Query: 345 EKYNEEMEAYKRRMKE 360
                E +  K     
Sbjct: 65  ASEGTEAKKRKSGPSS 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	363
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	100.0
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	100.0
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	100.0
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	100.0
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.82
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.81
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.81
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.8
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.79
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.78
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.77
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.77
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.77
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.77
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.77
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.77
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.76
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.76
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.76
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.76
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.75
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.75
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.75
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.74
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.74
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.73
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.73
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.73
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.72
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.72
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.72
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.71
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.71
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.71
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.71
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.7
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.7
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.7
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.7
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.7
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.7
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.69
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.69
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.68
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.68
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.68
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.67
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.67
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.66
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.66
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.66
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.66
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.65
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.65
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.65
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.64
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.64
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.63
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.62
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.62
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.62
2cto_A	93	Novel protein; high mobility group box domain, hel	99.62
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.62
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.61
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.6
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.56
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.55
2cto_A	93	Novel protein; high mobility group box domain, hel	99.53
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.48
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.46
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	86.6

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=100.00  E-value=1.2e-36  Score=272.00  Aligned_cols=163  Identities=33%  Similarity=0.556  Sum_probs=149.2

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCC--CCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPE--AEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~--~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      +++.++||++||||+|||+|||.++|..|+.+||+  +++.||+++||++|++||+++|.+|.+.|..++++|..+|..|
T Consensus         6 ~k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y   85 (173)
T 2yrq_A            6 SGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   85 (173)
T ss_dssp             CSSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            34567899999999999999999999999999999  5899999999999999999999999999999999999999877


Q ss_pred             hhhHHHHHhhHHHHHHhhHHHHHHHHhhhhHhhhhhcCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHH
Q 017939          241 RRESEAMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVA  318 (363)
Q Consensus       241 k~e~e~~kll~~eq~~k~~~e~~~~~~~~~~~~~~k~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~  318 (363)
                      ...                                .+.++++.+|++.||||+|||++||+++|..+...+|  ++.+|+
T Consensus        86 ~~~--------------------------------~~~~kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~  133 (173)
T 2yrq_A           86 IPP--------------------------------KGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVA  133 (173)
T ss_dssp             CCC--------------------------------CCCSSCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHH
T ss_pred             hhh--------------------------------hhhhcccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            542                                1123345679999999999999999999999998887  689999


Q ss_pred             HHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          319 KITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       319 k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      +.||.+|++||+++|++|.++|+.++++|..+|++|+.+
T Consensus       134 k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~k  172 (173)
T 2yrq_A          134 KKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK  172 (173)
T ss_dssp             HHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999865

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=100.00  E-value=1.2e-36  Score=281.36  Aligned_cols=180  Identities=27%  Similarity=0.468  Sum_probs=153.3

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMK  248 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e~e~~k  248 (363)
                      .|++||||+|||+|||+++|..|+.+||+++++||+++||++|++||+++|.+|++.|..++++|..+|..|...     
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~-----   80 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQ-----   80 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhccc-----
Confidence            467899999999999999999999999999999999999999999999999999999999999999999999864     


Q ss_pred             hhHHHHHHhhHHHHHHHHhhhhHhhhhhcCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccC
Q 017939          249 LLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNM  328 (363)
Q Consensus       249 ll~~eq~~k~~~e~~~~~~~~~~~~~~k~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~L  328 (363)
                       +++.+......++.+..+..+.     .++++..+|++.||||+|||++||+++|..+...+|  .+|++.||++|++|
T Consensus        81 -~tp~q~~~~~~~~~~~~~krk~-----~kkkk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p--~ei~k~lg~~Wk~l  152 (214)
T 3tq6_A           81 -LTPSQIMSLEKEIMDKHLKRKA-----MTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSP--QEKLKTVKENWKNL  152 (214)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHTTCCCCCCCHHHHHHHHHTTTSSCSSH--HHHHHHHHHHHHTC
T ss_pred             -CCHHHHHHHHHHHHHHHhhhcc-----hhhhhhhccccCcccccchhhhhHHHHHHhhccCCH--HHHHHHHHHHHHcC
Confidence             3445544333334333332211     111234578999999999999999999998765544  59999999999999


Q ss_pred             ChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 017939          329 TEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKEL  361 (363)
Q Consensus       329 s~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E~  361 (363)
                      |+++|++|.++|+.++++|..+|.+|..++++.
T Consensus       153 s~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~~~~~  185 (214)
T 3tq6_A          153 SDSEKELYIQHAKEDETRYHNEMKSWEEQMIEV  185 (214)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            999999999999999999999999999998764

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=100.00  E-value=1.1e-36  Score=285.75  Aligned_cols=183  Identities=26%  Similarity=0.457  Sum_probs=156.1

Q ss_pred             hccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhhHH
Q 017939          166 KKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESE  245 (363)
Q Consensus       166 k~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e~e  245 (363)
                      ..++|++||+|+|||+|||+++|..|+.+||++++.||+++||++|++||++||.+|++.|..++++|..+|..|...  
T Consensus        35 s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~--  112 (238)
T 3tmm_A           35 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQ--  112 (238)
T ss_dssp             CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc--
Confidence            356889999999999999999999999999999999999999999999999999999999999999999999999865  


Q ss_pred             HHHhhHHHHHHhhHHHHHHHHhhhhHhhhhhcCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHh
Q 017939          246 AMKLLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEW  325 (363)
Q Consensus       246 ~~kll~~eq~~k~~~e~~~~~~~~~~~~~~k~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~W  325 (363)
                          +++.+......++.+.++..+.     .++++..+|++.||||+|||++||+++|..+...+|  .+|++.||++|
T Consensus       113 ----~~p~~~~~~~~~~~~k~~krk~-----~~kkk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p--~ei~k~lg~~W  181 (238)
T 3tmm_A          113 ----LTPSQIMSLEKEIMDKHLKRKA-----MTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSP--QEKLKTVKENW  181 (238)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSSH--HHHHHHHHHHH
T ss_pred             ----CCHHHHHHHHHHHhhhhhhhhc-----ccchhhhcccCCCCCCCcHHHHHHHHHHHHHhccCH--HHHHHHHHHHH
Confidence                3445544333344333333211     111234578999999999999999999998765554  59999999999


Q ss_pred             ccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 017939          326 KNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKEL  361 (363)
Q Consensus       326 k~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E~  361 (363)
                      ++||+++|++|.++|+.++++|..+|.+|..++++.
T Consensus       182 k~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k~~~~  217 (238)
T 3tmm_A          182 KNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEV  217 (238)
T ss_dssp             HTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            999999999999999999999999999999998764

>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=100.00  E-value=1.5e-34  Score=254.76  Aligned_cols=156  Identities=35%  Similarity=0.577  Sum_probs=143.5

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRESEAMK  248 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e~e~~k  248 (363)
                      +++.||||+++||+|+.+.+..|..+||++++.||+++||++|++||+++|.+|.+.|..+++.|..++..|...     
T Consensus         1 g~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~-----   75 (159)
T 2gzk_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR-----   75 (159)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCC-----
T ss_pred             CcCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccc-----
Confidence            467899999999999999999999999999999999999999999999999999999999999999988766421     


Q ss_pred             hhHHHHHHhhHHHHHHHHhhhhHhhhhhcCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhc
Q 017939          249 LLEEEHKQKTAMELLEQYLQFKQEADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWK  326 (363)
Q Consensus       249 ll~~eq~~k~~~e~~~~~~~~~~~~~~k~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk  326 (363)
                                                 .+++++..+|++.||+|+|||++||+++|..+..+||  ++.+|++.||++|+
T Consensus        76 ---------------------------k~~~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk  128 (159)
T 2gzk_A           76 ---------------------------KGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWN  128 (159)
T ss_dssp             ---------------------------CCCCGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHH
T ss_pred             ---------------------------cccccccccccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence                                       1233445789999999999999999999999998887  68999999999999


Q ss_pred             cCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          327 NMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       327 ~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      +||+++|++|.+.|..++++|..+|.+|.+
T Consensus       129 ~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A          129 NTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999985

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=3.5e-20  Score=147.25  Aligned_cols=79  Identities=27%  Similarity=0.406  Sum_probs=74.5

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCC--HHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s--~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      +++.++||++||||+|||+|||.++|..|+.+||+++  +.||+++||++|++||+++|.+|++.|..++++|..+|..|
T Consensus         6 ~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   85 (86)
T 2eqz_A            6 SGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY   85 (86)
T ss_dssp             SSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4456789999999999999999999999999999986  69999999999999999999999999999999999999887


Q ss_pred             h
Q 017939          241 R  241 (363)
Q Consensus       241 k  241 (363)
                      +
T Consensus        86 ~   86 (86)
T 2eqz_A           86 G   86 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.81  E-value=5.7e-20  Score=150.78  Aligned_cols=81  Identities=32%  Similarity=0.600  Sum_probs=76.9

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      ++++++||++||||+|||+|||.++|..|+.+||++++.+|+++||++|++||+++|.+|.+.|..++++|..+|..|..
T Consensus         8 ~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   87 (102)
T 2co9_A            8 KKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA   87 (102)
T ss_dssp             SCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             h
Q 017939          243 E  243 (363)
Q Consensus       243 e  243 (363)
                      .
T Consensus        88 ~   88 (102)
T 2co9_A           88 S   88 (102)
T ss_dssp             H
T ss_pred             h
Confidence            3

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

Probab=99.81  E-value=2.4e-20  Score=152.37  Aligned_cols=80  Identities=26%  Similarity=0.432  Sum_probs=76.6

Q ss_pred             hhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          164 DRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       164 ~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      +++++||++||||+|||+|||.++|..|+.+||+++++||+++||++|++||+++|++|.+.|..++++|..+|..|...
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~   81 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45778999999999999999999999999999999999999999999999999999999999999999999999988764

>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=99.80  E-value=5.6e-20  Score=142.74  Aligned_cols=75  Identities=32%  Similarity=0.579  Sum_probs=72.7

Q ss_pred             ccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          167 KKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       167 ~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      ++||++||||+|||+|||.++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..++.+|..+|..|+
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~   75 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR   75 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            479999999999999999999999999999999999999999999999999999999999999999999998875

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

Probab=99.79  E-value=3.2e-19  Score=143.48  Aligned_cols=77  Identities=26%  Similarity=0.558  Sum_probs=74.5

Q ss_pred             ccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          167 KKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       167 ~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      .+||++||||+|||+|||.++|..|+.+||++++.+|+++||++|++||+++|.+|.+.|..++++|..+|..|+..
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~   78 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQS   78 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999764

>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=99.78  E-value=7.8e-19  Score=154.16  Aligned_cols=95  Identities=28%  Similarity=0.485  Sum_probs=85.7

Q ss_pred             HHHhhhhccCCCCCCcccccchhhhhhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChh
Q 017939          138 KKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAE  217 (363)
Q Consensus       138 ~k~r~mk~~~p~~~~p~~~~~~~k~~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~e  217 (363)
                      +..++|..|.+..+.          ++++.+||+.||||+|||+|||.++|..|+.+||++++++|+++||++|++||++
T Consensus        64 ~y~~~~~~y~~~k~~----------~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~  133 (159)
T 2gzk_A           64 MHREKYPNYKYRKGE----------TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAAD  133 (159)
T ss_dssp             HHHHHCSSCSCCCCC----------CGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSCHH
T ss_pred             HHHHHhhcccccccc----------ccccccccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCCHH
Confidence            445678888776442          3456789999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          218 EKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       218 EK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      +|++|.+.|..++++|..+|..|+.
T Consensus       134 eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A          134 DKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999863

>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

Probab=99.77  E-value=7.5e-20  Score=146.72  Aligned_cols=76  Identities=24%  Similarity=0.433  Sum_probs=71.7

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHH
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMA  238 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~  238 (363)
                      ++++++||++||||+|||+|||.++|..|+.+||++++.||+++||++|++||+++|++|++.|..++++|..+|.
T Consensus        11 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A           11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             cCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999999999999999999999999999999999999987653

>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=99.77  E-value=8.3e-19  Score=135.07  Aligned_cols=71  Identities=25%  Similarity=0.482  Sum_probs=68.3

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          170 CAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       170 p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      .++||||+|||+|||+++|..|+.+||+++++||+++||++|++||+  |.+|++.|..++++|..+|..|+.
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~   71 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHh
Confidence            36899999999999999999999999999999999999999999998  999999999999999999999864

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

Probab=99.77  E-value=6.4e-19  Score=141.75  Aligned_cols=76  Identities=29%  Similarity=0.443  Sum_probs=73.1

Q ss_pred             cCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          168 KGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       168 k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      .+|++||||+|||+|||.++|..|+.+||++++.||+++||++|++||+++|.+|.+.|..++++|..+|..|+..
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~   78 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQ   78 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999999999999999999999999999999999999999999999999999988753

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

Probab=99.77  E-value=1.2e-19  Score=147.40  Aligned_cols=80  Identities=31%  Similarity=0.514  Sum_probs=76.4

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCC--HHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s--~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      ++++++||+.||||+|||+|||.++|..|+.+||+++  +.+|+++||++|++||+++|.+|++.|..++++|..+|..|
T Consensus        13 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y   92 (97)
T 2lhj_A           13 PRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEY   92 (97)
T ss_dssp             TTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4457789999999999999999999999999999999  99999999999999999999999999999999999999998


Q ss_pred             hh
Q 017939          241 RR  242 (363)
Q Consensus       241 k~  242 (363)
                      ..
T Consensus        93 ~~   94 (97)
T 2lhj_A           93 AQ   94 (97)
T ss_dssp             HH
T ss_pred             Hh
Confidence            75

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

Probab=99.77  E-value=1.3e-19  Score=142.91  Aligned_cols=76  Identities=26%  Similarity=0.444  Sum_probs=72.3

Q ss_pred             ccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCC--HHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          167 KKGCAERKRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       167 ~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s--~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      ++||++||||+|||+|||.++|..|+.+||+++  +.||+++||++|++||+++|.+|.+.|..++++|..+|..|..
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   79 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   79 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999999999999986  5999999999999999999999999999999999999988754

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.6e-18  Score=154.46  Aligned_cols=96  Identities=29%  Similarity=0.511  Sum_probs=87.9

Q ss_pred             HHHHhhhhccCCCCCCcccccchhhhhhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCCh
Q 017939          137 LKKLQKMKEFKPNMTLPIVQCLKDKEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSA  216 (363)
Q Consensus       137 l~k~r~mk~~~p~~~~p~~~~~~~k~~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~  216 (363)
                      .+..++|..|.+..+.          ++++.+||+.||||+|||+|||.++|..|+.+||++++++|+++||++|++||+
T Consensus        76 ~~y~~e~~~y~~~~~~----------~kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~  145 (173)
T 2yrq_A           76 ARYEREMKTYIPPKGE----------TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAA  145 (173)
T ss_dssp             HHTHHHHHHCCCCCCC----------SSCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCG
T ss_pred             HHHHHHhhhhhhhhhh----------hcccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCH
Confidence            4567789999887653          345678999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          217 EEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       217 eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      ++|++|.+.|..++++|..+|..|+.
T Consensus       146 ~eK~~y~~~A~~~k~~y~~~~~~y~~  171 (173)
T 2yrq_A          146 DDKQPYEKKAAKLKEKYEKDIAAYRA  171 (173)
T ss_dssp             GGHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999864

>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}

Probab=99.76  E-value=3.6e-19  Score=141.81  Aligned_cols=76  Identities=24%  Similarity=0.365  Sum_probs=72.3

Q ss_pred             hhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       165 kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      +..+||+.||||+|||||||.++|..|+.+||++++.||+++||++|++||+++|++|++.|..++++|..++..|
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Y   85 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDC   85 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            4678999999999999999999999999999999999999999999999999999999999999999999876555

>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=99.76  E-value=3.6e-19  Score=137.85  Aligned_cols=73  Identities=27%  Similarity=0.440  Sum_probs=68.7

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      ||+.||||+|||+|||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..++++|..++..|+
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   73 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999887664

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A

Probab=99.76  E-value=1.6e-19  Score=145.58  Aligned_cols=80  Identities=34%  Similarity=0.576  Sum_probs=76.3

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      ++++++||+.||||+|||+|||.++|..|+.+||++++.||+++||++|++||+++|.+|.+.|..++++|..+|..|..
T Consensus        11 ~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~~   90 (93)
T 1cg7_A           11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA   90 (93)
T ss_dssp             CCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHHH
T ss_pred             cCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999865

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1.8e-18  Score=137.30  Aligned_cols=79  Identities=32%  Similarity=0.547  Sum_probs=73.4

Q ss_pred             cCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCCC----hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH
Q 017939          277 NKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN----VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEME  352 (363)
Q Consensus       277 ~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~----~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~  352 (363)
                      |++++..+||+.||+|+|||++||+++|..+...||+    +.+|++.||++|++||+++|.+|.++|+.++++|..+|.
T Consensus         4 g~~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~   83 (86)
T 2eqz_A            4 GSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMK   83 (86)
T ss_dssp             CCSSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556667899999999999999999999999999873    599999999999999999999999999999999999999


Q ss_pred             HHH
Q 017939          353 AYK  355 (363)
Q Consensus       353 ~yk  355 (363)
                      +|+
T Consensus        84 ~Y~   86 (86)
T 2eqz_A           84 DYG   86 (86)
T ss_dssp             HHC
T ss_pred             HcC
Confidence            994

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

Probab=99.75  E-value=3.8e-18  Score=139.83  Aligned_cols=82  Identities=37%  Similarity=0.629  Sum_probs=76.4

Q ss_pred             CCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          279 KPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       279 kkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      ++++.+||+.||+|+|||||||+++|..+...||  ++.+|++.||.+|++||+++|++|.++|+.++++|..+|.+|+.
T Consensus         8 ~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   87 (102)
T 2co9_A            8 KKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA   87 (102)
T ss_dssp             SCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3456789999999999999999999999998887  68999999999999999999999999999999999999999998


Q ss_pred             hhhh
Q 017939          357 RMKE  360 (363)
Q Consensus       357 ~~~E  360 (363)
                      +...
T Consensus        88 ~~~~   91 (102)
T 2co9_A           88 SLVS   91 (102)
T ss_dssp             HHTS
T ss_pred             hccc
Confidence            8754

>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=99.75  E-value=1.6e-18  Score=132.36  Aligned_cols=69  Identities=26%  Similarity=0.466  Sum_probs=65.5

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCH--HHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEF--KEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~--~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      .||||+|||++||.++|..|+.+||++++  +||+++||++|++||+++|.+|.+.|..++++|..+|..|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            59999999999999999999999999964  9999999999999999999999999999999999998654

>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=99.75  E-value=1.9e-18  Score=136.97  Aligned_cols=73  Identities=27%  Similarity=0.439  Sum_probs=70.2

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      .|+.||||+|||+|||.++|..|+.+||+++++||+++||++|++||+++|.+|.+.|..++++|..++..|+
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   73 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            4789999999999999999999999999999999999999999999999999999999999999999988774

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

Probab=99.74  E-value=1.7e-18  Score=133.36  Aligned_cols=71  Identities=27%  Similarity=0.530  Sum_probs=68.5

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          170 CAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       170 p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      |++||||+|||++||.++|..|+.+||+++++||+++||++|++|  ++|.+|.+.|..++++|..+|..|+.
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~   71 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKP   71 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTT
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHc
Confidence            689999999999999999999999999999999999999999999  89999999999999999999988864

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

Probab=99.74  E-value=1.4e-18  Score=141.84  Aligned_cols=82  Identities=27%  Similarity=0.495  Sum_probs=76.6

Q ss_pred             CCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          280 PKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       280 kKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      +++.+||+.||+|+||||+||++.|..+..++|  ++.+|++.||++|++||+++|++|.++|+.++++|..+|.+|..+
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~   81 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345679999999999999999999999999887  689999999999999999999999999999999999999999998


Q ss_pred             hhhh
Q 017939          358 MKEL  361 (363)
Q Consensus       358 ~~E~  361 (363)
                      +++.
T Consensus        82 ~P~~   85 (99)
T 1k99_A           82 HPDL   85 (99)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            8754

>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=99.73  E-value=1.3e-18  Score=136.77  Aligned_cols=74  Identities=24%  Similarity=0.529  Sum_probs=70.9

Q ss_pred             cCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          168 KGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       168 k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      .+++.||||+|||+|||+++|..|+.+||++++.+|+++||++|++||+++|++|.+.|..++++|..++..|+
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk   76 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYR   76 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhh
Confidence            47899999999999999999999999999999999999999999999999999999999999999998887765

>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=99.73  E-value=3.9e-18  Score=134.15  Aligned_cols=73  Identities=23%  Similarity=0.520  Sum_probs=67.2

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      .++.||||+|||+|||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..+++.|..++..|+
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   75 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   75 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            4678999999999999999999999999999999999999999999999999999999999999999988774

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

Probab=99.73  E-value=2.6e-18  Score=130.89  Aligned_cols=70  Identities=24%  Similarity=0.564  Sum_probs=63.0

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      .||||+|||+|||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..++++|..++..|+
T Consensus         2 k~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            2 SIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             ---CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            5899999999999999999999999999999999999999999999999999999999999998887663

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

Probab=99.72  E-value=5.1e-18  Score=140.14  Aligned_cols=77  Identities=18%  Similarity=0.396  Sum_probs=69.6

Q ss_pred             hhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       165 kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      ...++++.||||+|||+|||+++|..|+.+||++++++|+++||++|++||+++|++|.+.|..++++|..++..|+
T Consensus        22 ~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yk   98 (106)
T 4euw_A           22 QSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYK   98 (106)
T ss_dssp             ------CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             hccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999998875

>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=99.72  E-value=5.2e-18  Score=132.64  Aligned_cols=71  Identities=27%  Similarity=0.538  Sum_probs=68.4

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      +.||||+|||+|||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..++++|..++..|+
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK   71 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            46999999999999999999999999999999999999999999999999999999999999999988774

>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=99.72  E-value=3.9e-18  Score=132.33  Aligned_cols=73  Identities=44%  Similarity=0.778  Sum_probs=69.8

Q ss_pred             CCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          284 KDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       284 kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      +||+.||||+|||++|++++|..+...+|  ++.+|++.||.+|++||+++|.+|.++|+.++++|..+|++|++
T Consensus         2 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A            2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999998887  68999999999999999999999999999999999999999865

>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=99.71  E-value=1.2e-17  Score=138.45  Aligned_cols=82  Identities=22%  Similarity=0.385  Sum_probs=75.6

Q ss_pred             CCCCCCCCCCCC-CCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          278 KKPKKEKDPLKP-KHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       278 kkkKk~kd~~~P-KrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      .+.++.+|++.| |||+|||++||+++|..+.  +.++.+|++.||++|++||+++|.+|.++|+.++++|..+|.+|..
T Consensus         6 ~~~kk~kd~~~P~KrP~say~lF~~e~r~~~k--~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~   83 (108)
T 1v64_A            6 SGQLKDKFDGRPTKPPPNSYSLYCAELMANMK--DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             SCCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT--TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345667899999 9999999999999999876  7899999999999999999999999999999999999999999999


Q ss_pred             hhhhh
Q 017939          357 RMKEL  361 (363)
Q Consensus       357 ~~~E~  361 (363)
                      ++.++
T Consensus        84 ~~~~~   88 (108)
T 1v64_A           84 SLPEE   88 (108)
T ss_dssp             HSCHH
T ss_pred             hCCHH
Confidence            87653

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

Probab=99.71  E-value=7.5e-18  Score=135.47  Aligned_cols=78  Identities=29%  Similarity=0.474  Sum_probs=73.5

Q ss_pred             CCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 017939          284 KDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKEL  361 (363)
Q Consensus       284 kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E~  361 (363)
                      .+++.||||+|||++|++++|..+..+||  ++.+|++.||++|++||+++|++|.++|+.++++|..+|.+|..++.+.
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~~~   82 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQM   82 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            46889999999999999999999999987  6799999999999999999999999999999999999999999987654

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

Probab=99.71  E-value=1.7e-17  Score=133.34  Aligned_cols=76  Identities=32%  Similarity=0.559  Sum_probs=71.9

Q ss_pred             CCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017939          283 EKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRM  358 (363)
Q Consensus       283 ~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~  358 (363)
                      .+||+.||||+|||++|++++|..+...+|  ++.+|++.||.+|++||+++|++|.++|+.++++|..+|.+|+.+.
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~   79 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSE   79 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccH
Confidence            368999999999999999999999998887  6899999999999999999999999999999999999999998754

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A

Probab=99.71  E-value=2e-18  Score=139.12  Aligned_cols=83  Identities=36%  Similarity=0.702  Sum_probs=76.5

Q ss_pred             hcCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHH
Q 017939          276 ENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEA  353 (363)
Q Consensus       276 k~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~  353 (363)
                      ++++++..+|++.|++|+|||+|||+++|..+..+||  ++.+|++.||.+|++||+++|.+|.++|+.++++|..+|.+
T Consensus         8 k~~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~   87 (93)
T 1cg7_A            8 KKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKEL   87 (93)
T ss_dssp             CCCCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHH
T ss_pred             CcccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566789999999999999999999999988887  68999999999999999999999999999999999999999


Q ss_pred             HHhhh
Q 017939          354 YKRRM  358 (363)
Q Consensus       354 yk~~~  358 (363)
                      |..+.
T Consensus        88 Y~~~~   92 (93)
T 1cg7_A           88 YNATL   92 (93)
T ss_dssp             HHHHT
T ss_pred             HHHcc
Confidence            99864

>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=99.70  E-value=1.7e-17  Score=137.49  Aligned_cols=77  Identities=23%  Similarity=0.352  Sum_probs=72.6

Q ss_pred             hhhhccCCCCC-CCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          163 QDRKKKGCAER-KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       163 ~~kk~k~p~~P-KrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      +.++.+|++.| |||+|||+|||.++|..|+    ++++.||++.||++|++||+++|.+|.+.|..++++|..+|..|.
T Consensus         7 ~~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~   82 (108)
T 1v64_A            7 GQLKDKFDGRPTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFL   82 (108)
T ss_dssp             CCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34678999999 9999999999999999887    789999999999999999999999999999999999999999998


Q ss_pred             hh
Q 017939          242 RE  243 (363)
Q Consensus       242 ~e  243 (363)
                      ..
T Consensus        83 ~~   84 (108)
T 1v64_A           83 ES   84 (108)
T ss_dssp             HH
T ss_pred             hh
Confidence            74

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

Probab=99.70  E-value=3.9e-18  Score=138.44  Aligned_cols=82  Identities=30%  Similarity=0.741  Sum_probs=75.6

Q ss_pred             cCCCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--C--hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH
Q 017939          277 NKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--N--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEME  352 (363)
Q Consensus       277 ~kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~--~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~  352 (363)
                      +++++..+|++.|++|+|||+|||+++|..+...||  +  +.+|++.||.+|++||+++|.+|.++|+.++++|..+|.
T Consensus        11 ~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   90 (97)
T 2lhj_A           11 RRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKA   90 (97)
T ss_dssp             CCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344566789999999999999999999999998887  4  789999999999999999999999999999999999999


Q ss_pred             HHHhhh
Q 017939          353 AYKRRM  358 (363)
Q Consensus       353 ~yk~~~  358 (363)
                      +|..+.
T Consensus        91 ~y~~~~   96 (97)
T 2lhj_A           91 EYAQRK   96 (97)
T ss_dssp             HHHHHH
T ss_pred             HHHhcC
Confidence            999864

>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=99.70  E-value=1e-17  Score=130.37  Aligned_cols=71  Identities=18%  Similarity=0.424  Sum_probs=67.8

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      +.||||+|||+|||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..+++.|..++..|+
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yk   71 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYK   71 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            36899999999999999999999999999999999999999999999999999999999999999987764

>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=99.70  E-value=8.3e-18  Score=131.87  Aligned_cols=72  Identities=26%  Similarity=0.532  Sum_probs=67.8

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          170 CAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       170 p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      ++.||||+|||||||+++|..|+.+||+++++||+++||++|++||+++|.+|.+.|..+++.|..++..|+
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yk   73 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYK   73 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC-
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            578999999999999999999999999999999999999999999999999999999999999999887764

>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=99.70  E-value=2e-17  Score=131.20  Aligned_cols=70  Identities=26%  Similarity=0.414  Sum_probs=67.8

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      .|+||+|||||||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..++++|..++..|+
T Consensus         2 ~pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (86)
T 2lef_A            2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS   71 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            5899999999999999999999999999999999999999999999999999999999999999988775

>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A

Probab=99.70  E-value=2.7e-17  Score=132.18  Aligned_cols=72  Identities=13%  Similarity=0.231  Sum_probs=69.4

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      +.||||+|||++|+++.|..++..||+ +++||++.||++|++||+++|.+|++.|..++++|+++|..|...
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~   74 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP   74 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            579999999999999999999999999 999999999999999999999999999999999999999998753

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens}

Probab=99.69  E-value=2.2e-17  Score=124.94  Aligned_cols=66  Identities=27%  Similarity=0.524  Sum_probs=62.3

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      +.||||+|||++||+++|..++..||    ++|++.||++|++||+++|.+|.+.|..++++|..+|..|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            47999999999999999999987665    7999999999999999999999999999999999999876

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

Probab=99.69  E-value=5.8e-18  Score=133.34  Aligned_cols=75  Identities=29%  Similarity=0.562  Sum_probs=70.3

Q ss_pred             CCCCCCCCCccccccccHHHHHHHHhhCCC----hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017939          284 KDPLKPKHPVTAYFLFSSERRAALLADNKN----VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRM  358 (363)
Q Consensus       284 kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~----~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~  358 (363)
                      +||+.||+|+|||++||+++|..+...||+    +.+|++.||.+|++||+++|.+|.++|..++++|..+|.+|....
T Consensus         3 kdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~   81 (83)
T 1aab_A            3 GDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK   81 (83)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            689999999999999999999999998873    499999999999999999999999999999999999999997653

>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=99.68  E-value=4.5e-17  Score=125.31  Aligned_cols=70  Identities=34%  Similarity=0.616  Sum_probs=66.4

Q ss_pred             CCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          286 PLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       286 ~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      ++.||||+|||++||+++|..+..+||  ++.+|++.||++|++||+  |++|.++|..++++|..+|++|+.+
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~k   72 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            368999999999999999999999987  689999999999999998  9999999999999999999999875

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens}

Probab=99.68  E-value=3e-17  Score=124.17  Aligned_cols=67  Identities=33%  Similarity=0.579  Sum_probs=62.6

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      |.||||+|||++||+++|..+...+|  .+|++.||++|++||+++|.+|.++|..++++|..+|.+|.
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p--~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y~   67 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP--QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWA   67 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH--HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH--HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            57999999999999999999876665  79999999999999999999999999999999999999983

>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A

Probab=99.68  E-value=3.8e-17  Score=131.31  Aligned_cols=76  Identities=18%  Similarity=0.276  Sum_probs=71.7

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK-NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKELL  362 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p-~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E~~  362 (363)
                      +.|+||+|||++|+++.|..+...++ ++.+|++.||++|++||+++|++|+++|..++++|..+|.+|..+..+..
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~~~~   79 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATN   79 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGSSS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc
Confidence            58999999999999999999999887 78999999999999999999999999999999999999999998877644

>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=99.67  E-value=1.9e-17  Score=128.04  Aligned_cols=72  Identities=28%  Similarity=0.451  Sum_probs=66.7

Q ss_pred             CCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          285 DPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       285 d~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      ||+.||||+|||++|++++|..+..++|  ++.+|++.||.+|++||+++|++|.++|+.++++|..++++|+-
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky   74 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence            5789999999999999999999998887  68999999999999999999999999999999999999998863

>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}

Probab=99.67  E-value=2.5e-17  Score=131.11  Aligned_cols=75  Identities=25%  Similarity=0.362  Sum_probs=70.4

Q ss_pred             CCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       281 Kk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      +..+|++.||||+||||||++++|..+...+|  ++.+|+++||++|++||+++|++|.++|+.++++|..++++|+
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            45679999999999999999999999999887  6899999999999999999999999999999999999998874

>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=6.5e-17  Score=127.49  Aligned_cols=61  Identities=20%  Similarity=0.393  Sum_probs=59.0

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCC-HHHHHHHHhhccccCChhhhhhhHHHHHHH
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAE-FKEITNILGAKWKNVSAEEKKPYEEKYQAE  229 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s-~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~  229 (363)
                      +++.||||+|||+|||+++|..|+.+||+++ ++||+++||++|++||+++|++|++.|..+
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6889999999999999999999999999998 999999999999999999999999999776

>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=99.66  E-value=1.6e-16  Score=130.21  Aligned_cols=77  Identities=18%  Similarity=0.352  Sum_probs=67.4

Q ss_pred             CCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 017939          285 DPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKEL  361 (363)
Q Consensus       285 d~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E~  361 (363)
                      ..++||||+|||++||++++......+.++.||++.||++|++||+++|++|.++|+.++++|..+|.+|..++.++
T Consensus         5 ~~~~PKrP~say~lF~~e~~~~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~~   81 (101)
T 1v63_A            5 SSGPKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHH
Confidence            46789999999999999997632222346899999999999999999999999999999999999999999987653

>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=99.66  E-value=6e-17  Score=123.57  Aligned_cols=67  Identities=30%  Similarity=0.600  Sum_probs=63.3

Q ss_pred             CCCCCccccccccHHHHHHHHhhCCC----hHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHH
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNKN----VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAY  354 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p~----~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~y  354 (363)
                      +||||+|||++|++++|..+...||+    +.+|++.||++|++||+++|.+|.++|+.++++|..+|.+|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            49999999999999999999998873    49999999999999999999999999999999999999876

>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=99.66  E-value=2.6e-16  Score=128.84  Aligned_cols=74  Identities=16%  Similarity=0.304  Sum_probs=66.8

Q ss_pred             cCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          168 KGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       168 k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      ....+||||+|||+|||++++.  ...+++++++||++.||++|++||++||++|++.|..++++|..+|..|...
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~   77 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKS   77 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3567899999999999999974  3345668999999999999999999999999999999999999999999875

>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

Probab=99.65  E-value=2.5e-17  Score=131.96  Aligned_cols=75  Identities=24%  Similarity=0.454  Sum_probs=69.0

Q ss_pred             CCCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHH
Q 017939          278 KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEME  352 (363)
Q Consensus       278 kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~  352 (363)
                      ++.++.+||+.||+|+|||||||+++|..+...||  ++.+|++.||++|++||+++|++|.++|+.++++|..+|.
T Consensus        10 k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A           10 SQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             CSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             CcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456789999999999999999999999999987  6899999999999999999999999999999999987764

>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=99.65  E-value=1.1e-17  Score=134.25  Aligned_cols=69  Identities=22%  Similarity=0.332  Sum_probs=65.1

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCC--HHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHH
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQ  235 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s--~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~k  235 (363)
                      ..+.++||++||||+|||||||+++|+.|+.+||+++  ++||+    ++|++|++++|++|++.|+.+++.|..
T Consensus        13 ~~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~   83 (90)
T 2yuk_A           13 TLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRI   83 (90)
T ss_dssp             HHHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            4567889999999999999999999999999999999  99998    999999999999999999999998864

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

Probab=99.65  E-value=5.3e-17  Score=123.66  Aligned_cols=69  Identities=26%  Similarity=0.520  Sum_probs=60.3

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      |.||||+|||++|+++.|..+...+|  ++.+|++.||++|++||+++|.+|.++|+.++++|..++++|+
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            57899999999999999999998887  6899999999999999999999999999999999999999985

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

Probab=99.64  E-value=7.7e-17  Score=124.01  Aligned_cols=70  Identities=36%  Similarity=0.675  Sum_probs=66.3

Q ss_pred             CCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          286 PLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       286 ~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      |+.||||+|||++|++++|..+...||  ++.+|++.||.+|++|  ++|.+|.++|+.++++|..+|.+|+++
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            678999999999999999999999987  6799999999999999  999999999999999999999999764

>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=99.64  E-value=1.6e-16  Score=125.76  Aligned_cols=72  Identities=29%  Similarity=0.487  Sum_probs=68.2

Q ss_pred             CCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          286 PLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       286 ~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      |+.|+||+||||+||+++|..+...+|  ++.+|++.||.+|++||+++|++|.++|+.++++|..++++|+.+
T Consensus         2 p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~   75 (85)
T 1j46_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             cCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccC
Confidence            688999999999999999999998887  689999999999999999999999999999999999999998753

>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=99.63  E-value=4.9e-17  Score=127.76  Aligned_cols=74  Identities=19%  Similarity=0.443  Sum_probs=69.3

Q ss_pred             CCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          284 KDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       284 kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      .+++.||||+|||++|++++|..+..++|  ++.+|++.||.+|++||+++|++|.++|+.++++|..++++|+.+
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~   78 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSG   78 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcC
Confidence            46889999999999999999999999887  689999999999999999999999999999999999999988654

>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=99.62  E-value=2.8e-16  Score=122.70  Aligned_cols=71  Identities=31%  Similarity=0.531  Sum_probs=66.7

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      +.|++|+|||++|++++|..+...+|  ++.+|++.||.+|++||+++|++|.++|+.++++|..++++|+.+
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~   73 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR   73 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccC
Confidence            46999999999999999999998887  689999999999999999999999999999999999999998753

>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=99.62  E-value=2e-16  Score=124.37  Aligned_cols=72  Identities=25%  Similarity=0.492  Sum_probs=65.2

Q ss_pred             CCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          285 DPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       285 d~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      .++.||||+|||||||+++|..+...+|  ++.+|++.||++|++||+++|++|.++|+.++++|..++++|+-
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky   76 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKY   76 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            3568999999999999999999999887  68999999999999999999999999999999999999999864

>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=99.62  E-value=3.6e-16  Score=123.93  Aligned_cols=70  Identities=23%  Similarity=0.518  Sum_probs=66.4

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      +.|++|+||||||++++|..+..++|  ++.+|++.||.+|++||+++|++|.++|+.++++|..++++|..
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~   72 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA   72 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccC
Confidence            46999999999999999999998887  68999999999999999999999999999999999999999963

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

Probab=99.62  E-value=1.8e-16  Score=128.07  Aligned_cols=69  Identities=17%  Similarity=0.335  Sum_probs=65.7

Q ss_pred             ccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHH---hhccccCChhhhhhhHHHHHHHHHHHHHHH
Q 017939          167 KKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNIL---GAKWKNVSAEEKKPYEEKYQAEKEAYLQVM  237 (363)
Q Consensus       167 ~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~l---ge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~  237 (363)
                      ..+++.||||+|||+|||+++|+.|+.+  +++++||+++|   |++|++||++||++|++.|..+++.|.+++
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            4688999999999999999999999998  89999999999   999999999999999999999999999875

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

Probab=99.62  E-value=2.8e-16  Score=129.68  Aligned_cols=76  Identities=24%  Similarity=0.461  Sum_probs=67.3

Q ss_pred             CCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          282 KEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       282 k~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      ..++++.||||+|||+|||++.|..+...+|  ++.+|++.||++|++||+++|++|.++|+.++++|..++++|+-+
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~  100 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQ  100 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC-
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcC
Confidence            4567899999999999999999999998887  689999999999999999999999999999999999999998653

>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=99.61  E-value=2.4e-16  Score=122.61  Aligned_cols=70  Identities=23%  Similarity=0.426  Sum_probs=66.4

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKR  356 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~  356 (363)
                      |.||||+|||+|||+++|..+..++|  ++.+|++.||++|++||+++|++|.++|+.++++|..++++|+-
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky   72 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKY   72 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            57899999999999999999998887  68999999999999999999999999999999999999998864

>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=99.60  E-value=3.6e-16  Score=122.50  Aligned_cols=72  Identities=26%  Similarity=0.483  Sum_probs=65.3

Q ss_pred             CCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          286 PLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       286 ~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      .+.||||+||||||++++|..+...+|  ++.+|++.||.+|++||+++|++|.+.|+.++++|..++++|+-+
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   75 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYK   75 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC---
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeec
Confidence            468999999999999999999998887  689999999999999999999999999999999999999988754

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=99.56  E-value=1.1e-14  Score=134.15  Aligned_cols=75  Identities=24%  Similarity=0.455  Sum_probs=69.2

Q ss_pred             hhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       165 kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      +..+||+.||||+|||+|||+++|..|++.||    ++|++.||++|++||+++|++|++.|..++++|..+|..|...
T Consensus       107 k~~kdp~~PKrP~say~lF~~e~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~  181 (214)
T 3tq6_A          107 KELTLLGKPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQ  181 (214)
T ss_dssp             HHHHHTTCCCCCCCHHHHHHHHHTTTSSCSSH----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhccccCcccccchhhhhHHHHHHhhccCCH----HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34679999999999999999999998876555    5999999999999999999999999999999999999999875

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=99.55  E-value=1.1e-14  Score=136.33  Aligned_cols=75  Identities=24%  Similarity=0.455  Sum_probs=69.3

Q ss_pred             hhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       165 kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      +..+||++||||+|||+|||+++|..|+..||    ++|++.||++|++||+++|++|++.|..++++|..+|..|+..
T Consensus       139 k~~kdp~~PKrP~say~lF~~e~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k  213 (238)
T 3tmm_A          139 KELTLLGKPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQ  213 (238)
T ss_dssp             HHHHHTTCCCCCCCHHHHHHHHHTTTSCCSSH----HHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCCCCCcHHHHHHHHHHHHHhccCH----HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34689999999999999999999999886655    4999999999999999999999999999999999999999875

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

Probab=99.53  E-value=2.8e-15  Score=121.15  Aligned_cols=69  Identities=23%  Similarity=0.379  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHH---HHHhccCChHHhHHHHHHHHHHHHHHHHHH
Q 017939          283 EKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKIT---GEEWKNMTEEQKRPYEEIAKKNKEKYNEEM  351 (363)
Q Consensus       283 ~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l---~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~  351 (363)
                      ..+++.||||+||||+||+++|..+..++.++.+|++.|   |++|++|+++||++|.++|.+++++|..++
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRRGLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHHTCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            356789999999999999999999988888999999999   999999999999999999999999999875

>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=1.7e-14  Score=113.59  Aligned_cols=59  Identities=19%  Similarity=0.338  Sum_probs=55.8

Q ss_pred             CCCCCCCCccccccccHHHHHHHHhhCC--C-hHHHHHHHHHHhccCChHHhHHHHHHHHHH
Q 017939          285 DPLKPKHPVTAYFLFSSERRAALLADNK--N-VLEVAKITGEEWKNMTEEQKRPYEEIAKKN  343 (363)
Q Consensus       285 d~~~PKrP~SAY~lF~~e~r~~~~~e~p--~-~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~  343 (363)
                      +++.||||+||||+||+++|..+..+||  + +.+|++.||++|++||+++|++|.++|..+
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5789999999999999999999999987  4 899999999999999999999999999876

>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=99.46  E-value=4.1e-15  Score=119.36  Aligned_cols=68  Identities=16%  Similarity=0.266  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHH
Q 017939          283 EKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEE  350 (363)
Q Consensus       283 ~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E  350 (363)
                      .+||+.||||+|||||||++.|..+..+||+..+....|+++|++|++++|++|.+.|++++++|..+
T Consensus        17 ~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIse~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           17 EKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             HHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             cCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            46899999999999999999999999999986655556669999999999999999999999999753

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=86.60  E-value=1.7  Score=32.86  Aligned_cols=36  Identities=25%  Similarity=0.375  Sum_probs=32.0

Q ss_pred             HhhhhHHHhhhhHHHHHhhhHHHHHHHHHHHHHhhh
Q 017939          108 LLKEKDEMLKMKEEELELQGKEQEKLHMELKKLQKM  143 (363)
Q Consensus       108 ~~~e~~~~l~~k~~e~~~~~~~~~~lq~~l~k~r~m  143 (363)
                      -+..+|++|+..+.++..++.+...|+.+|-|+|-+
T Consensus        34 ELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfrSV   69 (72)
T 3nmd_A           34 ELRQRDALIDELELELDQKDELIQMLQNELDKYRSV   69 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            367888899999999999999999999999998753

---

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	363
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	8e-11
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	6e-08
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-10
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	4e-09
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	1e-10
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	3e-09
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	2e-10
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	6e-09
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-10
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-06
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-10
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-08
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	4e-09
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-07
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-09
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-06
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	8e-09
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	3e-07
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	1e-08
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	2e-08
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-08
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	0.001
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	5e-08
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	9e-08

>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 = 55.7 bits (134), Expect = 8e-11
 Identities = 30/83 (36%), Positives = 52/83 (62%), Gaps = 2/83 (2%)

Query: 278 KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVL--EVAKITGEEWKNMTEEQKRP 335
           +  +K+KDP  PK  ++AY  F++E R  + ++N ++   +V K  GE+WK +T E+K+P
Sbjct: 10  RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQP 69

Query: 336 YEEIAKKNKEKYNEEMEAYKRRM 358
           YE  A+ +K++Y  E E Y   +
Sbjct: 70  YEAKAQADKKRYESEKELYNATL 92

>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 = 48.0 bits (114), Expect = 6e-08
 Identities = 28/79 (35%), Positives = 41/79 (51%)

Query: 161 KEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKK 220
           K   RKKK     KR    Y+ +  +  +  + ENP+  F ++   LG KWK ++ EEK+
Sbjct: 9   KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQ 68

Query: 221 PYEEKYQAEKEAYLQVMAK 239
           PYE K QA+K+ Y      
Sbjct: 69  PYEAKAQADKKRYESEKEL 87

>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 = 55.2 bits (133), Expect = 1e-10
 Identities = 30/75 (40%), Positives = 45/75 (60%), Gaps = 2/75 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
            PK P +A+FLF SE R  +  ++    + +VAK  GE W N   + K+PYE+ A K KE
Sbjct: 2   APKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61

Query: 346 KYNEEMEAYKRRMKE 360
           KY +++ AY+ + K 
Sbjct: 62  KYEKDIAAYRAKGKP 76

>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 = 50.6 bits (121), Expect = 4e-09
 Identities = 23/68 (33%), Positives = 37/68 (54%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   + L+C +   + K E+P     ++   LG  W N +A++K+PYE+K    KE Y
Sbjct: 4   KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 63

Query: 234 LQVMAKER 241
            + +A  R
Sbjct: 64  EKDIAAYR 71

>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 = 54.8 bits (132), Expect = 1e-10
 Identities = 19/62 (30%), Positives = 36/62 (58%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   +++W KD+  +  +  P+     I+ ILG++WK ++  EK+PY E+     + +
Sbjct: 4   KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQH 63

Query: 234 LQ 235
           L+
Sbjct: 64  LE 65

>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 = 51.0 bits (122), Expect = 3e-09
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
             K P+ A+ +++ + R  +L      +   ++KI G  WK MT  +K+PY E   +  +
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSK 61

Query: 346 KYNEEMEAY 354
           ++ E+   Y
Sbjct: 62  QHLEKYPDY 70

>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 = 54.4 bits (131), Expect = 2e-10
 Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
           + K P+ A+ ++S  +R  +  +N   +  E++K  G EWK ++E +KRP+ + AK+ + 
Sbjct: 2   RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRA 61

Query: 346 KYNEEMEAYKRR 357
            + +E   YK R
Sbjct: 62  LHMKEHPDYKYR 73

>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 = 50.2 bits (120), Expect = 6e-09
 Identities = 19/65 (29%), Positives = 38/65 (58%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   +++W + Q  +  +ENP+    EI+  LGA+WK +S  EK+P+ ++ +  +  +
Sbjct: 4   KRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALH 63

Query: 234 LQVMA 238
           ++   
Sbjct: 64  MKEHP 68

>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 = 54.9 bits (132), Expect = 2e-10
 Identities = 14/73 (19%), Positives = 35/73 (47%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
             K P+  Y  FS E  +    ++  + E     G  W+ +++ QK  Y+++A++ + +Y
Sbjct: 8   PKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQY 67

Query: 348 NEEMEAYKRRMKE 360
              ++ + + +  
Sbjct: 68  KVHLDLWVKSLSP 80

>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 = 43.0 bits (101), Expect = 4e-06
 Identities = 11/69 (15%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEK 230
             +K P   Y  + ++  +  +  +     KE    +G++W+ +S  +K+ Y++  + ++
Sbjct: 7   GPKKPPMNGYQKFSQELLSNGELNHLP--LKERMVEIGSRWQRISQSQKEHYKKLAEEQQ 64

Query: 231 EAYLQVMAK 239
             Y   +  
Sbjct: 65  RQYKVHLDL 73

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

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 = 53.4 bits (128), Expect = 5e-10
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 278 KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRP 335
            +   +    KPK PV+A F+FS E+R  L  +       E+ ++    W +++E++K  
Sbjct: 10  SQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAK 69

Query: 336 YEEIAKKNKEKYNEEMEAYK 355
           Y+      K +   +     
Sbjct: 70  YKAREAALKAQSERKSGPSS 89

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

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 = 48.4 bits (115), Expect = 3e-08
 Identities = 18/78 (23%), Positives = 37/78 (47%)

Query: 161 KEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKK 220
             Q+  K G  + KRP     ++ +++  + ++E PE    E+T +L   W ++S ++K 
Sbjct: 9   PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKA 68

Query: 221 PYEEKYQAEKEAYLQVMA 238
            Y+ +  A K    +   
Sbjct: 69  KYKAREAALKAQSERKSG 86

>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 = 50.6 bits (121), Expect = 4e-09
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKNVL----EVAKITGEEWKNMTEEQKRPYEEIAKKN 343
           KP+  +++Y  F    R      + +      E +K   E WK M+ ++K  +E++AK +
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 344 KEKYNEEMEAY 354
           K +Y  EM+ Y
Sbjct: 61  KARYEREMKTY 71

>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 = 45.2 bits (107), Expect = 3e-07
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAE--FKEITNILGAKWKNVSAEEKKPYEEKYQAEKE 231
           +     Y  + +    E KK++P+A   F E +     +WK +SA+EK  +E+  +A+K 
Sbjct: 3   RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 62

Query: 232 AYLQVMAK 239
            Y + M  
Sbjct: 63  RYEREMKT 70

>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 = 50.7 bits (121), Expect = 5e-09
 Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEE 338
           K +K P  PK P+T YF F  E+RA     +     L++ KI  +++K + E++K  Y +
Sbjct: 3   KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQ 62

Query: 339 IAKKNKEKYNEEMEAYKRRMKEL 361
             ++ K+++   +  ++    +L
Sbjct: 63  DFQREKQEFERNLARFREDHPDL 85

>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 = 43.0 bits (101), Expect = 3e-06
 Identities = 21/79 (26%), Positives = 42/79 (53%)

Query: 165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEE 224
           + KK     K+P  PY  +  ++  +  K +PE    ++T IL  K+K +  ++K  Y +
Sbjct: 3   KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQ 62

Query: 225 KYQAEKEAYLQVMAKERRE 243
            +Q EK+ + + +A+ R +
Sbjct: 63  DFQREKQEFERNLARFRED 81

>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 = 50.2 bits (120), Expect = 8e-09
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 288 KPKHPVTAYFLFSSERRAALLADN--KNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
           + K P+ A+ ++S ++R  +  +N      E++K  G +WK +TE +K P+ + A+K + 
Sbjct: 4   RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQA 63

Query: 346 KYNEEMEAYKRR 357
            + E+   YK R
Sbjct: 64  MHREKYPNYKYR 75

>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 = 45.6 bits (108), Expect = 3e-07
 Identities = 20/68 (29%), Positives = 35/68 (51%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   +I+W +DQ  +   ENP     EI+  LG +WK ++  EK P+ ++ Q  +  +
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65

Query: 234 LQVMAKER 241
            +     +
Sbjct: 66  REKYPNYK 73

>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 = 49.0 bits (117), Expect = 1e-08
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 288 KPKHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKE 345
           KPK P++AY L+ +  R ++  +N    V EVAK  GE W+ M  + K  +E  A K K+
Sbjct: 3   KPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAKD 60

Query: 346 KYNEEMEAYK 355
            Y+  ++ ++
Sbjct: 61  DYDRAVKEFE 70

>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 = 48.6 bits (116), Expect = 2e-08
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           KRP   Y+LW        K+ENP  +  E+    G  W+  + ++K  +E K    K+ Y
Sbjct: 5   KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWR--AMKDKSEWEAKAAKAKDDY 62

Query: 234 LQVMAK 239
            + + +
Sbjct: 63  DRAVKE 68

>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 = 49.6 bits (118), Expect = 2e-08
 Identities = 17/88 (19%), Positives = 39/88 (44%), Gaps = 2/88 (2%)

Query: 273 ADKENKKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQ 332
           +   + + K + D    K P  +Y L+ +E  A +        E   +  ++WK +++++
Sbjct: 2   SSGSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPST--ERMVLCSQQWKLLSQKE 59

Query: 333 KRPYEEIAKKNKEKYNEEMEAYKRRMKE 360
           K  Y +   + K+ Y  E+  +   + E
Sbjct: 60  KDAYHKKCDQKKKDYEVELLRFLESLPE 87

>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 = 35.7 bits (82), Expect = 0.001
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 4/79 (5%)

Query: 161 KEQDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKK 220
             Q + K      K P   Y L+C +          +    E   +   +WK +S +EK 
Sbjct: 6   SGQLKDKFDGRPTKPPPNSYSLYCAELM----ANMKDVPSTERMVLCSQQWKLLSQKEKD 61

Query: 221 PYEEKYQAEKEAYLQVMAK 239
            Y +K   +K+ Y   + +
Sbjct: 62  AYHKKCDQKKKDYEVELLR 80

>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 = 47.6 bits (113), Expect = 5e-08
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 290 KHPVTAYFLFSSERRAALLADNKN--VLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKY 347
           K P+ A+ L+  E RA ++A++       + +I G  W  ++ E++  Y E+A+K ++ +
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLH 63

Query: 348 NEEMEAYKRRMK 359
            +    +  R  
Sbjct: 64  MQLYPGWSARDN 75

>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 = 47.2 bits (112), Expect = 9e-08
 Identities = 18/65 (27%), Positives = 33/65 (50%)

Query: 174 KRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAY 233
           K+P   ++L+ K+       E+   E   I  ILG +W  +S EE+  Y E  + E++ +
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLH 63

Query: 234 LQVMA 238
           +Q+  
Sbjct: 64  MQLYP 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	363
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.78
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.77
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.75
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.73
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.71
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.71
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.7
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.69
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.68
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.66
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.66
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.63
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.62
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.61
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.6
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.6
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.54
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.5
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	96.87
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	92.7

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

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

Probab=99.78  E-value=2.2e-19  Score=143.01  Aligned_cols=81  Identities=33%  Similarity=0.569  Sum_probs=77.1

Q ss_pred             hhhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          163 QDRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       163 ~~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      ..++.++|+.||||+|||+|||.++|..|+.+||++++.+|++.||++|++||+++|.+|.+.|..++.+|..+|..|+.
T Consensus        11 ~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~~   90 (93)
T d1lwma_          11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA   90 (93)
T ss_dssp             CCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44577899999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             h
Q 017939          243 E  243 (363)
Q Consensus       243 e  243 (363)
                      .
T Consensus        91 ~   91 (93)
T d1lwma_          91 T   91 (93)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=99.77  E-value=2.6e-19  Score=138.23  Aligned_cols=72  Identities=32%  Similarity=0.614  Sum_probs=70.0

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      |+||||+|||+|||.++|..|+.+||+++++||+++||.+|++||+++|.+|.+.|..++.+|..+|..|+.
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~   72 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   72 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            689999999999999999999999999999999999999999999999999999999999999999999864

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

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]

Probab=99.75  E-value=4.8e-19  Score=140.17  Aligned_cols=80  Identities=26%  Similarity=0.432  Sum_probs=76.7

Q ss_pred             hhhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          164 DRKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       164 ~kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      ++.++||+.||||+|||++||.++|..|+..||++++++|++.||+.|+.||+++|.+|.+.|..++.+|..+|..|...
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~   81 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999988765

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

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

Probab=99.73  E-value=4.2e-18  Score=135.47  Aligned_cols=81  Identities=37%  Similarity=0.711  Sum_probs=75.5

Q ss_pred             CCCCCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          278 KKPKKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       278 kkkKk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      +..+..++|+.||+|+|||++|+.++|..+...+|  ++.+|++.||++|++||+++|.+|.+.|..++++|..+|..|+
T Consensus        10 ~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~   89 (93)
T d1lwma_          10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYN   89 (93)
T ss_dssp             CCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456779999999999999999999999988886  6899999999999999999999999999999999999999999


Q ss_pred             hhh
Q 017939          356 RRM  358 (363)
Q Consensus       356 ~~~  358 (363)
                      .++
T Consensus        90 ~~l   92 (93)
T d1lwma_          90 ATL   92 (93)
T ss_dssp             HHH
T ss_pred             hcc
Confidence            886

>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=99.73  E-value=1.9e-18  Score=134.00  Aligned_cols=71  Identities=27%  Similarity=0.538  Sum_probs=68.4

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      +.||||+|||||||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|..+++.|..++..|+
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk   71 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK   71 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999988775

>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=99.72  E-value=3.6e-18  Score=133.80  Aligned_cols=71  Identities=28%  Similarity=0.478  Sum_probs=68.6

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      +.||||+|||||||+++|..|+.+||+++++||+++||.+|++||+++|.+|.+.|..++..|..++..|+
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk   73 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhc
Confidence            57999999999999999999999999999999999999999999999999999999999999999988775

>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=99.71  E-value=2.9e-18  Score=129.55  Aligned_cols=66  Identities=29%  Similarity=0.574  Sum_probs=63.0

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHH
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVM  237 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~  237 (363)
                      .+|||+|||||||+++|..|+.+||++++++|+++||++|++||+++|.+|.+.|+.++++|.+++
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~   67 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKY   67 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            468999999999999999999999999999999999999999999999999999999999997654

>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=99.71  E-value=8e-18  Score=127.09  Aligned_cols=69  Identities=26%  Similarity=0.491  Sum_probs=65.0

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCC--CCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHH
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPE--AEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKE  240 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~--~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~y  240 (363)
                      .||||+|||++||.++|..|+.+||+  +++++|+++||.+|++||+++|.+|.+.|..++++|..+|..|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            48999999999999999999999997  4689999999999999999999999999999999999998654

>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=99.71  E-value=1.1e-17  Score=127.13  Aligned_cols=70  Identities=26%  Similarity=0.518  Sum_probs=66.7

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhh
Q 017939          171 AERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERR  242 (363)
Q Consensus       171 ~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~  242 (363)
                      +.||||+|||+|||.++|..|+.+||++++.||+++||++|++|+  +|++|.+.|..++++|..+|..|+.
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~   71 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            689999999999999999999999999999999999999999986  4999999999999999999998864

>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=99.70  E-value=1e-17  Score=129.18  Aligned_cols=75  Identities=40%  Similarity=0.679  Sum_probs=70.4

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKEL  361 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E~  361 (363)
                      +.||+|+|||++|++++|..+..+||  ++.+|++.||.+|++||+++|.+|.+.|..++++|..+|.+|+.+....
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~~~   77 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPD   77 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence            57999999999999999999999987  6799999999999999999999999999999999999999999876543

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

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]

Probab=99.69  E-value=7.5e-18  Score=133.21  Aligned_cols=81  Identities=27%  Similarity=0.503  Sum_probs=76.7

Q ss_pred             CCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 017939          281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRM  358 (363)
Q Consensus       281 Kk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~  358 (363)
                      +..++|+.|++|+|||++|++++|..+...||  ++.+|++.||+.|+.||+++|.+|.++|+.++.+|..++..|..++
T Consensus         3 k~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~~   82 (91)
T d1k99a_           3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH   82 (91)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            45679999999999999999999999999987  6899999999999999999999999999999999999999999998


Q ss_pred             hhh
Q 017939          359 KEL  361 (363)
Q Consensus       359 ~E~  361 (363)
                      +|.
T Consensus        83 pe~   85 (91)
T d1k99a_          83 PDL   85 (91)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            875

>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=99.68  E-value=3.3e-17  Score=131.72  Aligned_cols=76  Identities=18%  Similarity=0.364  Sum_probs=71.6

Q ss_pred             CCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 017939          285 DPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKE  360 (363)
Q Consensus       285 d~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E  360 (363)
                      ..++||||+|||++||+++|..+...|+++.+|++.||++|++||+++|++|.++|..++++|..+|..|..+..+
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~~~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~   80 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSP   80 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Confidence            4678899999999999999999988899999999999999999999999999999999999999999999987654

>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=99.66  E-value=5.2e-17  Score=127.33  Aligned_cols=70  Identities=26%  Similarity=0.414  Sum_probs=66.7

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHh
Q 017939          172 ERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKER  241 (363)
Q Consensus       172 ~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk  241 (363)
                      ..|||+|||||||.++|..|..+||++++++|+++||.+|++||+++|.+|.+.|..+++.|..++..|+
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk   71 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS   71 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            3689999999999999999999999999999999999999999999999999999999999998887764

>d1wgfa_ 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=99.66  E-value=3.2e-17  Score=129.26  Aligned_cols=72  Identities=24%  Similarity=0.436  Sum_probs=68.2

Q ss_pred             hhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHH
Q 017939          165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQV  236 (363)
Q Consensus       165 kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke  236 (363)
                      ..+++++.||||+|||+|||.++|..|+.+||++++.+|+++||.+|++||+++|.+|.+.|..++..|.++
T Consensus        13 ~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          13 GGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             CCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999999999999999999999999999999888654

>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=99.63  E-value=8.8e-17  Score=121.26  Aligned_cols=67  Identities=31%  Similarity=0.608  Sum_probs=63.1

Q ss_pred             CCCCCccccccccHHHHHHHHhhCC----ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHH
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNK----NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAY  354 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p----~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~y  354 (363)
                      +||||+|||++|++++|..+..+||    ++.+|++.||.+|++||+++|++|.++|..++++|..+|.+|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4899999999999999999998887    357999999999999999999999999999999999999876

>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=99.63  E-value=9.9e-17  Score=124.23  Aligned_cols=71  Identities=31%  Similarity=0.531  Sum_probs=66.8

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      +.||||+||||||++++|..+..+||  ++.+|+++||.+|++||+++|++|.++|..++++|..++++|+.+
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~   73 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR   73 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCC
Confidence            36899999999999999999999987  689999999999999999999999999999999999999999643

>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=99.62  E-value=1.1e-16  Score=125.10  Aligned_cols=71  Identities=30%  Similarity=0.494  Sum_probs=67.5

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      +.||||+||||||++++|..+..+||  ++.+|+++||..|++||+++|.+|.++|..++++|..++++|+.+
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~   75 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccC
Confidence            57899999999999999999999987  689999999999999999999999999999999999999999754

>d1v64a_ 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=99.62  E-value=4.2e-16  Score=126.95  Aligned_cols=78  Identities=22%  Similarity=0.408  Sum_probs=69.9

Q ss_pred             CCCCCCCCCCCCccccccccHHHHHHHHhhCCChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 017939          281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNKNVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRRMKE  360 (363)
Q Consensus       281 Kk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~~~E  360 (363)
                      +...++.+||+|+|||+||++++|..+  .+.++.+|++.||.+|++||+++|++|.++|+.++.+|..+|.+|..++.+
T Consensus        10 k~~~~~~p~K~P~~ay~lF~~~~r~~~--~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~~~~   87 (108)
T d1v64a_          10 KDKFDGRPTKPPPNSYSLYCAELMANM--KDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPE   87 (108)
T ss_dssp             SCCTTTSCCCCCSSHHHHHHHHHHHHC--TTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             cccCCCCCCCCCCcHHHHHHHHHHHHc--cCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            444567777999999999999999875  456889999999999999999999999999999999999999999987664

>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=99.61  E-value=9.2e-17  Score=121.17  Aligned_cols=67  Identities=27%  Similarity=0.508  Sum_probs=62.7

Q ss_pred             CCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHH
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAY  354 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~y  354 (363)
                      .+|||+||||+||+++|..+..++|  ++.+|++.||.+|++||+++|++|.++|+.++++|.+++++|
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            4689999999999999999999987  689999999999999999999999999999999999887765

>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=99.61  E-value=4.2e-16  Score=118.33  Aligned_cols=69  Identities=35%  Similarity=0.633  Sum_probs=64.9

Q ss_pred             CCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          287 LKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       287 ~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      +.||||+|||++|+.++|..+..+||  ++.+|++.||.+|++|+  +|++|.++|+.++++|..+|..|+.+
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~   72 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            68999999999999999999999998  68999999999999986  59999999999999999999999875

>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=99.60  E-value=7.1e-16  Score=123.82  Aligned_cols=73  Identities=15%  Similarity=0.322  Sum_probs=67.0

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          169 GCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       169 ~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      ...+||||+|||+|||.++|..+...  ++++.||++.||++|++||+++|++|.+.|..++.+|..+|..|...
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~--~~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~   77 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELN--HLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKS   77 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTT--TSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45679999999999999999998755  45799999999999999999999999999999999999999999764

>d1v64a_ 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=99.60  E-value=9e-16  Score=124.94  Aligned_cols=75  Identities=21%  Similarity=0.354  Sum_probs=69.1

Q ss_pred             hhccCCCCCCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHHHhhh
Q 017939          165 RKKKGCAERKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAKERRE  243 (363)
Q Consensus       165 kk~k~p~~PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~yk~e  243 (363)
                      +.+.++.+||+|+|||+|||.++|.    ++|++++.||++.||.+|++||+++|++|.+.|..++.+|..+|..|...
T Consensus        10 k~~~~~~p~K~P~~ay~lF~~~~r~----~~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~   84 (108)
T d1v64a_          10 KDKFDGRPTKPPPNSYSLYCAELMA----NMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLES   84 (108)
T ss_dssp             SCCTTTSCCCCCSSHHHHHHHHHHH----HCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCCCCcHHHHHHHHHHH----HccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4457888899999999999999886    46899999999999999999999999999999999999999999999764

>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=99.54  E-value=2.2e-15  Score=117.91  Aligned_cols=70  Identities=24%  Similarity=0.527  Sum_probs=65.9

Q ss_pred             CCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHHhh
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYKRR  357 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk~~  357 (363)
                      ..|||+||||||+++.|..+..+||  ++.+|+++||.+|++||+++|++|.++|+.++++|..++++|+.+
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~   73 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSAR   73 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCC
Confidence            3589999999999999999999997  689999999999999999999999999999999999999999754

>d1wgfa_ 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=99.50  E-value=6.1e-15  Score=115.92  Aligned_cols=70  Identities=26%  Similarity=0.491  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCCCccccccccHHHHHHHHhhCC--ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHH
Q 017939          281 KKEKDPLKPKHPVTAYFLFSSERRAALLADNK--NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEE  350 (363)
Q Consensus       281 Kk~kd~~~PKrP~SAY~lF~~e~r~~~~~e~p--~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E  350 (363)
                      ....+++.||||+|||+|||+++|..+...||  ++.+|++.||.+|+.||+++|++|.++|..++++|.++
T Consensus        13 ~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          13 GGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             CCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34578999999999999999999999999887  68999999999999999999999999999999998754

>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

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]

Probab=96.87  E-value=0.0015  Score=47.78  Aligned_cols=68  Identities=21%  Similarity=0.360  Sum_probs=58.2

Q ss_pred             CCCCCccccccccHHHHHHHHhhCC-ChHHHHHHHHHHhccCChHHhHHHHHHHHHHHHHHHHHHHHHH
Q 017939          288 KPKHPVTAYFLFSSERRAALLADNK-NVLEVAKITGEEWKNMTEEQKRPYEEIAKKNKEKYNEEMEAYK  355 (363)
Q Consensus       288 ~PKrP~SAY~lF~~e~r~~~~~e~p-~~~ei~k~l~~~Wk~Ls~eEK~~Y~~~Ae~~ke~Y~~E~~~yk  355 (363)
                      .|-.|.+|--+|.+.....+.+... +-....+.+-..|++|...||.+|+..|.+|..+|+.|+-+.+
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~DR~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr   71 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMR   71 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence            5778889999999999888887775 4466677778899999999999999999999999999986543

>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

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]

Probab=92.70  E-value=0.28  Score=35.36  Aligned_cols=66  Identities=12%  Similarity=0.259  Sum_probs=51.1

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhccccCChhhhhhhHHHHHHHHHHHHHHHHH
Q 017939          173 RKRPSPPYILWCKDQWNEAKKENPEAEFKEITNILGAKWKNVSAEEKKPYEEKYQAEKEAYLQVMAK  239 (363)
Q Consensus       173 PKrP~say~lF~~e~r~~ik~e~P~~s~~Ei~K~lge~Wk~LS~eEK~~Y~~~a~~~Ke~Y~ke~~~  239 (363)
                      |-.|.++--+|-......+.+.+-+ +-.-..+.+..-|++|...||..|...|.++..+|+.++-+
T Consensus         4 petpktaeeiWQqsvIgdYlA~fk~-DR~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~e   69 (84)
T d1l8ya_           4 PESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSE   69 (84)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHh-hHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            5556777778877666666655544 34555677788899999999999999999999999987643