Citrus Sinensis ID: 028144

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210---
Protein Sequence
MSSSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQEGEDVLMKDGFFASANVGVSPY
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEEEcccccEEEEEccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEEEEccccEEEEEEcccHHHHcEEEEEccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccEEEccccccccccccccccccccccccccccEEccccccccc
Coil and Loop (DISEMBL)
mssssttlsldqfptseqlcyvhcnlcdtvlavsvpctslfktvtvrcghctnllpvnmrglllpsanqfhlghnffspshnlreeipnpspnflinqtntndfivptrgvvdelprppatsrppekrqrvpsaYNRFIKDEIQrikagnpdisHREAFSAAAKnwahfphihfglvpdhqpvkkanvrqqegedvlmkdgffasanvgvspy
Flexible Loop (DISEMBL)
mssssttlsldqfpTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVdelprppatsrppekrqrvpsaynrfIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQEGEDVLMKDGFfasanvgvspy
Low Complexity Region (SEG)
MSSSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQEGEDVLMKDGFFASANVGVSPY
Disordered region (IsUnstruct)
***************SEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFS***************FLINQTNTNDFIVPTRGV*************************RFIKDEIQRIKA****ISHREAFSAAAKNWAHFPHIHFGLVPDH*********************F***********
Disordered Region (DISOPRED)
**************TSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLL*************************************************************************FIKD**********DISHREAFSAAAKNWAHFP*****************************DGFFASANVGVS**
Disordered Region (DISEMBL)
***********QFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELP**************VPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQEGEDVLMKDGFFASANVGVSPY
Disordered Region (DISPRO)
************FPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSA***************************************************PATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPD****************VLMK**FF*S*NVGVSPY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQEGEDVLMKDGFFASANVGVSPY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	213	2.2.26 [Sep-21-2011]
O22152	229	Axial regulator YABBY 1 O	yes	no	0.962	0.895	0.632	5e-67
Q9XFB1	240	Axial regulator YABBY 3 O	no	no	0.934	0.829	0.616	9e-63
Q0JBF0	266	Protein YABBY 5 OS=Oryza	yes	no	0.995	0.796	0.5	1e-59
Q01JG2	266	Protein YABBY 5 OS=Oryza	N/A	no	0.995	0.796	0.5	1e-59
Q6H668	256	Protein YABBY 4 OS=Oryza	no	no	0.924	0.769	0.555	2e-59
A2X7Q3	256	Protein YABBY 4 OS=Oryza	N/A	no	0.924	0.769	0.555	2e-59
Q8L556	313	Protein YABBY 3 OS=Oryza	no	no	0.924	0.629	0.488	2e-47
Q2QM17	207	Protein YABBY 6 OS=Oryza	no	no	0.807	0.830	0.513	1e-43
Q8GW46	164	Axial regulator YABBY 5 O	no	no	0.690	0.896	0.549	2e-43
Q10FZ7	186	Protein YABBY 2 OS=Oryza	no	no	0.793	0.908	0.522	2e-42

>sp|O22152|YAB1_ARATH Axial regulator YABBY 1 OS=Arabidopsis thaliana GN=YAB1 PE=1 SV=1

 Score =  253 bits (647), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 136/215 (63%), Positives = 163/215 (75%), Gaps = 10/215 (4%)

Query: 9   SLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSAN 68
           S D F  S+ LCYV CN C T+LAV+VP TSLFKTVTVRCG CTNLL VNMR  +LP++N
Sbjct: 15  SPDHFSPSDHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYVLPASN 74

Query: 69  QFHLG---HNFFSPSHNLRE--EIPNPSPNFLINQTNTNDFIVPTRGV--VDELPRPPAT 121
           Q  L    H++F+P   L E  + P+     ++NQ  T + I     +    E+P+ P  
Sbjct: 75  QLQLQLGPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAPPV 134

Query: 122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQ 181
           +RPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPD+Q
Sbjct: 135 NRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDNQ 194

Query: 182 PVKKANVRQQEGED-VLMKDGFF--ASANVGVSPY 213
           PVKK N+ QQEGED ++MK+GF+  A+ANVGV+PY
Sbjct: 195 PVKKTNMPQQEGEDNMVMKEGFYAPAAANVGVTPY 229

Involved in the abaxial cell fate determination during embryogenesis and organogenesis. Required during flower formation and development, particularly for the patterning of floral organs. Positive regulator of class B (AP3 and PI) activity in whorls 2 and 3. Negative regulator of class B activity in whorl 1 and of SUP activity in whorl 3. Interacts with class A proteins (AP1, AP2 and LUG) to repress class C (AG) activity in whorls 1 and 2. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity. In vitro, can compete and displace the AP1 protein binding to DNA containing CArG box.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9XFB1|YAB3_ARATH Axial regulator YABBY 3 OS=Arabidopsis thaliana GN=YAB3 PE=1 SV=1

 Score =  239 bits (610), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 138/224 (61%), Positives = 164/224 (73%), Gaps = 25/224 (11%)

Query: 11  DQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPV--NMRGLLLPSAN 68
           D F +++QLCYVHC+ CDTVLAVSVP +SLFKTVTVRCGHC+NLL V  +MR LLLPS +
Sbjct: 17  DHFSSTDQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVSMRALLLPSVS 76

Query: 69  QFHLGHNFFSPSH-----NLREEIPNPSPNFLINQTNTND---------FIVPTRGV--- 111
              LGH+F  P       NL EE+ +   N  +N   ++           ++ TR     
Sbjct: 77  N--LGHSFLPPPPPPPPPNLLEEMRSGGQNINMNMMMSHHASAHHPNEHLVMATRNGRSV 134

Query: 112 --VDELPRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 169
             + E+PRPP  +RPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAAKNWAHF
Sbjct: 135 DHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHF 194

Query: 170 PHIHFGLVPDHQPVKKANVRQQEGEDVLM-KDGFFAS-ANVGVS 211
           PHIHFGL+ DH P KKANVRQQEGED +M ++GF+ S ANVGV+
Sbjct: 195 PHIHFGLMADHPPTKKANVRQQEGEDGMMGREGFYGSAANVGVA 238

Involved in the abaxial cell fate determination during embryogenesis and organogenesis. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity.

Arabidopsis thaliana (taxid: 3702)

>sp|Q0JBF0|YAB5_ORYSJ Protein YABBY 5 OS=Oryza sativa subsp. japonica GN=YAB5 PE=2 SV=1

 Score =  229 bits (583), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 133/266 (50%), Positives = 161/266 (60%), Gaps = 54/266 (20%)

Query: 1   MSSSSTTLSLDQFPT-----------SEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCG 49
           MSS+  T SLD                EQLCYVHCN CDT+LAV VPC+SLFKTVTVRCG
Sbjct: 2   MSSAPETFSLDHLSQHQQQQPPPLAEQEQLCYVHCNFCDTILAVGVPCSSLFKTVTVRCG 61

Query: 50  HCTNLLPVNMRGLLLPSA----NQFHLGHNFFSPS--HNLREEIPN-----------PSP 92
           HC NLL VN+RGLLLP+A    NQ   G    SP+  H L +E+P+            SP
Sbjct: 62  HCANLLSVNLRGLLLPAAASTANQLPFGQALLSPTSPHGLLDEVPSFQAPASLMTEQASP 121

Query: 93  NFLI----------NQTNTNDFIVPTRGVVDELPRP---PATSRPPEKRQRVPSAYNRFI 139
           N             N   T+      +    E  +P   P+ +R  EKRQRVPSAYNRFI
Sbjct: 122 NVSSITSSNSSCANNAPATSMASAANKATQREPQQPKNAPSANRTSEKRQRVPSAYNRFI 181

Query: 140 KDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQE--GEDVL 197
           KDEIQRIKA NPDI+HREAFSAAAKNWAHFPHIHFGL+PD Q +KK  ++ Q+  GE +L
Sbjct: 182 KDEIQRIKASNPDITHREAFSAAAKNWAHFPHIHFGLMPD-QGLKKTGIQSQDGAGECML 240

Query: 198 MKDGFF----------ASANVGVSPY 213
            KDG +          A++++GV+P+
Sbjct: 241 FKDGLYAAAAAAAAATAASSMGVTPF 266

May be involved in leaf cell growth and differentiation, rather than abaxial cell fate determination.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q01JG2|YAB5_ORYSI Protein YABBY 5 OS=Oryza sativa subsp. indica GN=YAB5 PE=2 SV=2

 Score =  229 bits (583), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 133/266 (50%), Positives = 161/266 (60%), Gaps = 54/266 (20%)

Query: 1   MSSSSTTLSLDQFPT-----------SEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCG 49
           MSS+  T SLD                EQLCYVHCN CDT+LAV VPC+SLFKTVTVRCG
Sbjct: 2   MSSAPETFSLDHLSQHQQQQPPPLAEQEQLCYVHCNFCDTILAVGVPCSSLFKTVTVRCG 61

Query: 50  HCTNLLPVNMRGLLLPSA----NQFHLGHNFFSPS--HNLREEIPN-----------PSP 92
           HC NLL VN+RGLLLP+A    NQ   G    SP+  H L +E+P+            SP
Sbjct: 62  HCANLLSVNLRGLLLPAAASTANQLPFGQALLSPTSPHGLLDEVPSFQAPASLMTEQASP 121

Query: 93  NFLI----------NQTNTNDFIVPTRGVVDELPRP---PATSRPPEKRQRVPSAYNRFI 139
           N             N   T+      +    E  +P   P+ +R  EKRQRVPSAYNRFI
Sbjct: 122 NVSSITSSNSSCANNAPATSMASAANKATQREPQQPKNAPSANRTSEKRQRVPSAYNRFI 181

Query: 140 KDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQE--GEDVL 197
           KDEIQRIKA NPDI+HREAFSAAAKNWAHFPHIHFGL+PD Q +KK  ++ Q+  GE +L
Sbjct: 182 KDEIQRIKASNPDITHREAFSAAAKNWAHFPHIHFGLMPD-QGLKKTGIQSQDGAGECML 240

Query: 198 MKDGFF----------ASANVGVSPY 213
            KDG +          A++++GV+P+
Sbjct: 241 FKDGLYAAAAAAAAATAASSMGVTPF 266

May be involved in leaf cell growth and differentiation, rather than abaxial cell fate determination.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q6H668|YAB4_ORYSJ Protein YABBY 4 OS=Oryza sativa subsp. japonica GN=YAB4 PE=2 SV=1

 Score =  228 bits (582), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 131/236 (55%), Positives = 157/236 (66%), Gaps = 39/236 (16%)

Query: 16  SEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSA-----NQF 70
           +EQLCYVHCN CDT+LAV VPC+SLFKTVTVRCGHC NLL VN+RGLLLP+      NQ 
Sbjct: 22  TEQLCYVHCNCCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQL 81

Query: 71  HLGHNFFSPS--HNLREEIPNPSPNFLINQTNTNDF-------------------IVPTR 109
           H G +  SP+  H L +E+   +P+ L+ Q  +                      + P +
Sbjct: 82  HFGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAK 141

Query: 110 GVVDE--LPR--PPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN 165
            V  E  LP+  P + +RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN
Sbjct: 142 PVQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN 201

Query: 166 WAHFPHIHFGLVPDHQPVKKANVRQQEGEDVLMKDGFF--------ASANVGVSPY 213
           WAHFPHIHFGL+PD Q  KK    Q   ED+L+KD  +        A+AN+GV+P+
Sbjct: 202 WAHFPHIHFGLMPD-QGFKKTFKPQDGSEDILLKDSLYAAAAAAAAAAANMGVTPF 256

Seems to be associated with phloem cell differentiation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2X7Q3|YAB4_ORYSI Protein YABBY 4 OS=Oryza sativa subsp. indica GN=YAB4 PE=2 SV=1

 Score =  228 bits (582), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 131/236 (55%), Positives = 157/236 (66%), Gaps = 39/236 (16%)

Query: 16  SEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSA-----NQF 70
           +EQLCYVHCN CDT+LAV VPC+SLFKTVTVRCGHC NLL VN+RGLLLP+      NQ 
Sbjct: 22  TEQLCYVHCNCCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQL 81

Query: 71  HLGHNFFSPS--HNLREEIPNPSPNFLINQTNTNDF-------------------IVPTR 109
           H G +  SP+  H L +E+   +P+ L+ Q  +                      + P +
Sbjct: 82  HFGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAK 141

Query: 110 GVVDE--LPR--PPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN 165
            V  E  LP+  P + +RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN
Sbjct: 142 PVQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN 201

Query: 166 WAHFPHIHFGLVPDHQPVKKANVRQQEGEDVLMKDGFF--------ASANVGVSPY 213
           WAHFPHIHFGL+PD Q  KK    Q   ED+L+KD  +        A+AN+GV+P+
Sbjct: 202 WAHFPHIHFGLMPD-QGFKKTFKPQDGSEDILLKDSLYAAAAAAAAAAANMGVTPF 256

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q8L556|YAB3_ORYSJ Protein YABBY 3 OS=Oryza sativa subsp. japonica GN=YAB3 PE=2 SV=1

 Score =  188 bits (478), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 125/256 (48%), Positives = 153/256 (59%), Gaps = 59/256 (23%)

Query: 17  EQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQF------ 70
           EQLCYVHC+ CDTVL VSVP +SLF+TVTVRCGHC++LL VNMRGLLLP+          
Sbjct: 58  EQLCYVHCHYCDTVLVVSVPSSSLFETVTVRCGHCSSLLTVNMRGLLLPTTAAAAPPPPP 117

Query: 71  -----------HLGHNF-FSPS-----HNLREEI--PNPSPNFLINQTNTNDFIVP---- 107
                      H  H+   +P+     H+L +EI   N     L+ Q      +      
Sbjct: 118 PPPPPPPPPAAHFPHSLNLAPANPPHHHSLLDEISTANSPTQLLLEQHGLGGLMASAASC 177

Query: 108 ----------------TRGVVDELPRPPATS-----RPPEKRQRVPSAYNRFIKDEIQRI 146
                           ++G        P T+     RPPEKRQRVPSAYNRFIKDEIQRI
Sbjct: 178 RNNNSPAAAAAPPPPTSQGKAAAKEPSPRTNTAVINRPPEKRQRVPSAYNRFIKDEIQRI 237

Query: 147 KAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQEGE--DVLMKDGFF- 203
           KAGNPDISHREAFSAAAKNWAHFPHIHFGL+PDHQ +KK ++  Q+ +  D L+K+G + 
Sbjct: 238 KAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDHQGLKKTSLLPQDHQRKDGLLKEGLYA 297

Query: 204 ------ASANVGVSPY 213
                 A+AN+GV+PY
Sbjct: 298 AAAAAAAAANMGVAPY 313

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2QM17|YAB6_ORYSJ Protein YABBY 6 OS=Oryza sativa subsp. japonica GN=YAB6 PE=2 SV=1

 Score =  176 bits (446), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 95/185 (51%), Positives = 119/185 (64%), Gaps = 13/185 (7%)

Query: 12  QFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLL-----LPS 66
           Q   +EQ+CYVHCN C+T+LAVSVP  S+   VTVRCGHCTNLL VN+RGL+     L  
Sbjct: 4   QIAPAEQVCYVHCNFCNTILAVSVPGNSMLNIVTVRCGHCTNLLSVNLRGLMHSAPALQD 63

Query: 67  ANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVV------DELPRPPA 120
            +  HL  +  S     R++   P   F    +++   + P    +      ++      
Sbjct: 64  HHHHHLQESGLSGC--FRDQSGYPEFGFSAASSSSKLRLPPAAAAMVSYSQQNQQLEQAL 121

Query: 121 TSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDH 180
            +RPPEKRQRVPSAYNRFIK+EI+RIKA NPDISHREAFS AAKNWAH+P+IHFGL P H
Sbjct: 122 HARPPEKRQRVPSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHYPNIHFGLSPGH 181

Query: 181 QPVKK 185
           +  KK
Sbjct: 182 EGGKK 186

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8GW46|YAB5_ARATH Axial regulator YABBY 5 OS=Arabidopsis thaliana GN=YAB5 PE=2 SV=1

 Score =  175 bits (444), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 89/162 (54%), Positives = 105/162 (64%), Gaps = 15/162 (9%)

Query: 16  SEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHN 75
           +EQLCY+ CN C+ +LAV+VPC+SLF  VTVRCGHCTNL  VNM   L   +       N
Sbjct: 8   TEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQSLSRPNFQATN 67

Query: 76  FFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEKRQRVPSAY 135
           +  P +          P+ +  +T T   IV               +RPPEKRQRVPSAY
Sbjct: 68  YAVPEYGSSSRSHTKIPSRISTRTITEQRIV---------------NRPPEKRQRVPSAY 112

Query: 136 NRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV 177
           N+FIK+EIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL+
Sbjct: 113 NQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLM 154

Arabidopsis thaliana (taxid: 3702)

>sp|Q10FZ7|YAB2_ORYSJ Protein YABBY 2 OS=Oryza sativa subsp. japonica GN=YAB2 PE=2 SV=1

 Score =  172 bits (435), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 93/178 (52%), Positives = 114/178 (64%), Gaps = 9/178 (5%)

Query: 8   LSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSA 67
           +S    P  E +CYVHCN C+T+ AVSVP  S+   VTVRCGHCT+LL VN+RGL+    
Sbjct: 1   MSAQIVPAPEHVCYVHCNFCNTIFAVSVPSNSMLNIVTVRCGHCTSLLSVNLRGLVQALP 60

Query: 68  NQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEK 127
            + HL  N    + + RE       N+    +++    VP     ++        RPPEK
Sbjct: 61  AEDHLQDNLKMHNMSFRE-------NYSEYGSSSRYGRVPMMFSKNDTEHMLHV-RPPEK 112

Query: 128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKK 185
           RQRVPSAYNRFIK+EI+RIKA NPDISHREAFS AAKNWAHFP+IHFGL   H+  KK
Sbjct: 113 RQRVPSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHFPNIHFGL-GSHESSKK 169

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
225426944	211	PREDICTED: axial regulator YABBY 1 [Viti	0.985	0.995	0.881	1e-105
255583636	214	Axial regulator YABBY1, putative [Ricinu	0.985	0.981	0.869	1e-104
224074691	213	predicted protein [Populus trichocarpa]	0.920	0.920	0.889	1e-98
356563296	215	PREDICTED: protein YABBY 5-like [Glycine	0.995	0.986	0.828	6e-96
356514214	214	PREDICTED: protein YABBY 5-like [Glycine	0.990	0.985	0.837	2e-94
224125000	214	predicted protein [Populus trichocarpa]	0.948	0.943	0.830	3e-93
225453975	210	PREDICTED: axial regulator YABBY 1 [Viti	0.976	0.990	0.806	5e-93
147839790	210	hypothetical protein VITISV_031595 [Viti	0.976	0.990	0.801	1e-92
444247303	210	transcription factor YABBY1 [Vitis pseud	0.976	0.990	0.801	1e-91
41745624	211	YABBY-like transcription factor GRAMINIF	0.976	0.985	0.779	8e-88

>gi|225426944|ref|XP_002266233.1| PREDICTED: axial regulator YABBY 1 [Vitis vinifera] gi|297741152|emb|CBI31883.3| unnamed protein product [Vitis vinifera]

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 186/211 (88%), Positives = 193/211 (91%), Gaps = 1/211 (0%)

Query: 3   SSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGL 62
           SSS+TLSLD  P SEQLCYVHCN+CDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVN+RGL
Sbjct: 2   SSSSTLSLDHLPPSEQLCYVHCNICDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNLRGL 61

Query: 63  LLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATS 122
           LLPSANQ HLGH FFSPSHNL EEIPNPSPNFLINQT  NDF V  RG  DELPRPP  +
Sbjct: 62  LLPSANQLHLGHAFFSPSHNLLEEIPNPSPNFLINQTTANDFSVSARGGADELPRPPVIN 121

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQP 182
           RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDI+HREAFSAAAKNWAHFPHIHFGL+PD Q 
Sbjct: 122 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDITHREAFSAAAKNWAHFPHIHFGLMPD-QT 180

Query: 183 VKKANVRQQEGEDVLMKDGFFASANVGVSPY 213
           +KK NVRQQEGEDVLMKDGFFASANVGVSPY
Sbjct: 181 MKKTNVRQQEGEDVLMKDGFFASANVGVSPY 211

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583636|ref|XP_002532573.1| Axial regulator YABBY1, putative [Ricinus communis] gi|223527700|gb|EEF29807.1| Axial regulator YABBY1, putative [Ricinus communis]

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 186/214 (86%), Positives = 198/214 (92%), Gaps = 4/214 (1%)

Query: 3   SSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGL 62
           SSS+TLSLD  PTSEQLCYVHCN+CDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGL
Sbjct: 2   SSSSTLSLDHLPTSEQLCYVHCNICDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGL 61

Query: 63  LLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATS 122
           +LPSANQFHLGH+FFSP HN+ +EIPNPSPNFLINQTN NDF +PTRG+ DELPRPP  +
Sbjct: 62  ILPSANQFHLGHSFFSPHHNILDEIPNPSPNFLINQTNVNDFSIPTRGMTDELPRPPVIN 121

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQP 182
           RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL+PD Q 
Sbjct: 122 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPD-QT 180

Query: 183 VKKANVRQ--QEGEDVLMKDGFFASANVGV-SPY 213
           VKK NVRQ   EGEDV+MKDGFFASANVGV +PY
Sbjct: 181 VKKTNVRQVTYEGEDVMMKDGFFASANVGVTTPY 214

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224074691|ref|XP_002304427.1| predicted protein [Populus trichocarpa] gi|222841859|gb|EEE79406.1| predicted protein [Populus trichocarpa]

 Score =  364 bits (934), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 177/199 (88%), Positives = 186/199 (93%), Gaps = 3/199 (1%)

Query: 17  EQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNF 76
           EQLCYVHCN+CDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGH+F
Sbjct: 16  EQLCYVHCNICDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHSF 75

Query: 77  FSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVD-ELPRPPATSRPPEKRQRVPSAY 135
           FSPSHNL +EIPNP+PNFLINQTN NDF VP RG+ D ELPRPP  +RPPEKRQRVPSAY
Sbjct: 76  FSPSHNLLDEIPNPTPNFLINQTNVNDFSVPVRGMADHELPRPPVINRPPEKRQRVPSAY 135

Query: 136 NRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANVRQQEGED 195
           NRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL+PD Q VKK NVRQQEGED
Sbjct: 136 NRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPD-QMVKKTNVRQQEGED 194

Query: 196 VLMKDGFFASANVGV-SPY 213
           VLMKDGFF+SAN GV +PY
Sbjct: 195 VLMKDGFFSSANAGVPTPY 213

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356563296|ref|XP_003549900.1| PREDICTED: protein YABBY 5-like [Glycine max]

 Score =  355 bits (911), Expect = 6e-96,   Method: Compositional matrix adjust.
 Identities = 179/216 (82%), Positives = 196/216 (90%), Gaps = 4/216 (1%)

Query: 1   MSSSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMR 60
           MSSSS+TLSLD  P SEQLCYVHCN+CDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMR
Sbjct: 1   MSSSSSTLSLDHLPPSEQLCYVHCNICDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMR 60

Query: 61  GLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTN---TNDFIVPTRGVVDELPR 117
           GLL+PS  QFHLGH+FFSPSHNL EEIPNP+PNFL+NQTN   +++F +P R   DELPR
Sbjct: 61  GLLMPSPTQFHLGHSFFSPSHNLLEEIPNPTPNFLMNQTNFSASHEFSMPARTAADELPR 120

Query: 118 PPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV 177
           PP T+RPPEKRQRVPSAYNRFIKDEIQRIK+ NPDI+HREAFSAAAKNWAHFPHIHFGL+
Sbjct: 121 PPITNRPPEKRQRVPSAYNRFIKDEIQRIKSVNPDITHREAFSAAAKNWAHFPHIHFGLM 180

Query: 178 PDHQPVKKANVRQQEGEDVLMKDGFFASANVGVSPY 213
           PD Q VKK NV QQ+GE+VLMKDGF+ASANVGVSPY
Sbjct: 181 PD-QTVKKTNVCQQDGEEVLMKDGFYASANVGVSPY 215

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356514214|ref|XP_003525801.1| PREDICTED: protein YABBY 5-like [Glycine max]

 Score =  350 bits (899), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 181/216 (83%), Positives = 194/216 (89%), Gaps = 5/216 (2%)

Query: 1   MSSSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMR 60
           MSSSSTTLSLD  P SEQLCYVHCN+CDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMR
Sbjct: 1   MSSSSTTLSLDHLPPSEQLCYVHCNICDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMR 60

Query: 61  GLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTN---TNDFIVPTRGVVDELPR 117
           GLL+PS  QFHLGH+FFSPSHNL EEIPNPSPNFL+NQTN   +N+F +P R   DELPR
Sbjct: 61  GLLMPSPTQFHLGHSFFSPSHNLLEEIPNPSPNFLMNQTNLSASNEFSMPARIAADELPR 120

Query: 118 PPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV 177
            P  +RPPEKRQRVPSAYNRFIKDEIQRIK+ NPDI+HREAFSAAAKNWAHFPHIHFGL+
Sbjct: 121 -PIMNRPPEKRQRVPSAYNRFIKDEIQRIKSVNPDITHREAFSAAAKNWAHFPHIHFGLM 179

Query: 178 PDHQPVKKANVRQQEGEDVLMKDGFFASANVGVSPY 213
           PD Q VKK NV QQEGE+VLMKDGF+ASANVGVSPY
Sbjct: 180 PD-QTVKKTNVCQQEGEEVLMKDGFYASANVGVSPY 214

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125000|ref|XP_002329866.1| predicted protein [Populus trichocarpa] gi|222871103|gb|EEF08234.1| predicted protein [Populus trichocarpa]

 Score =  346 bits (888), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 171/206 (83%), Positives = 184/206 (89%), Gaps = 4/206 (1%)

Query: 11  DQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQF 70
           D  P SEQLCYVHCN+CDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGL LPSA+QF
Sbjct: 10  DHLPPSEQLCYVHCNICDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLFLPSASQF 69

Query: 71  HLGHNFFSPSHN-LREEIPNPSPNFLINQTNTNDFIVPTRGVVD-ELPRPPATSRPPEKR 128
            LGHN +SPSHN L ++IPNP+PNFLINQT+ NDF V  RG+ D ELPRPP   RPPEKR
Sbjct: 70  PLGHNLYSPSHNLLDDQIPNPTPNFLINQTHVNDFSVTVRGMADHELPRPPVIHRPPEKR 129

Query: 129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQPVKKANV 188
           QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL+PD Q +KK NV
Sbjct: 130 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPD-QAMKKNNV 188

Query: 189 RQQEGEDVLMKDGFFASANVGV-SPY 213
           RQQEGEDVL+ DGFFAS+NVGV +PY
Sbjct: 189 RQQEGEDVLINDGFFASSNVGVTTPY 214

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453975|ref|XP_002280334.1| PREDICTED: axial regulator YABBY 1 [Vitis vinifera] gi|296089181|emb|CBI38884.3| unnamed protein product [Vitis vinifera]

 Score =  345 bits (886), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 171/212 (80%), Positives = 186/212 (87%), Gaps = 4/212 (1%)

Query: 3   SSSTTLSLDQF-PTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRG 61
           SSS+  S D   PTS+QLCYVHCN CDTVLAVSVPCTSLFKTVTVRCGHCTNLL VNMRG
Sbjct: 2   SSSSAFSPDHLSPTSDQLCYVHCNFCDTVLAVSVPCTSLFKTVTVRCGHCTNLLSVNMRG 61

Query: 62  LLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPAT 121
           LLLP+ANQ HLGH+ FSP HN+ EEI +P  + LINQ N N+ ++P RG VDE+P+PP  
Sbjct: 62  LLLPAANQLHLGHSLFSP-HNILEEIRSPPSSMLINQPNPNEAVMPVRG-VDEIPKPPVV 119

Query: 122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQ 181
           +RPPEKRQRVPSAYNRFIKDEIQRIKAGNP ISHREAFSAAAKNWAHFPHIHFGL+PD Q
Sbjct: 120 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPGISHREAFSAAAKNWAHFPHIHFGLMPD-Q 178

Query: 182 PVKKANVRQQEGEDVLMKDGFFASANVGVSPY 213
           PVKKANVRQQEGED+LMKDGFFA ANVGVSPY
Sbjct: 179 PVKKANVRQQEGEDMLMKDGFFAPANVGVSPY 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147839790|emb|CAN70458.1| hypothetical protein VITISV_031595 [Vitis vinifera]

 Score =  344 bits (883), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 170/212 (80%), Positives = 185/212 (87%), Gaps = 4/212 (1%)

Query: 3   SSSTTLSLDQF-PTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRG 61
           SSS+  S D   PTS+QLCYVHCN CDTVLAVSVPCTSLFKTVTVRCGHCTNLL VNMRG
Sbjct: 2   SSSSAFSPDHLSPTSDQLCYVHCNFCDTVLAVSVPCTSLFKTVTVRCGHCTNLLSVNMRG 61

Query: 62  LLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPAT 121
           LLLP+ANQ HLGH+ FSP HNJ EEI +P  + L NQ N N+ ++P RG VDE+P+PP  
Sbjct: 62  LLLPAANQLHLGHSLFSP-HNJLEEIRSPPSSMLTNQPNPNEAVMPVRG-VDEIPKPPVV 119

Query: 122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQ 181
           +RPPEKRQRVPSAYNRFIKDEIQRIKAGNP ISHREAFSAAAKNWAHFPHIHFGL+PD Q
Sbjct: 120 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPGISHREAFSAAAKNWAHFPHIHFGLMPD-Q 178

Query: 182 PVKKANVRQQEGEDVLMKDGFFASANVGVSPY 213
           PVKKANVRQQEGED+LMKDGFFA ANVGVSPY
Sbjct: 179 PVKKANVRQQEGEDMLMKDGFFAPANVGVSPY 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|444247303|gb|AGD94962.1| transcription factor YABBY1 [Vitis pseudoreticulata]

 Score =  341 bits (874), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 170/212 (80%), Positives = 184/212 (86%), Gaps = 4/212 (1%)

Query: 3   SSSTTLSLDQF-PTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRG 61
           SSS+  S D   PTS+QLCYVHCN CDT LAVSVPCTSLFKTVTVRCGHCTNLL VNMRG
Sbjct: 2   SSSSAFSPDHLSPTSDQLCYVHCNFCDTALAVSVPCTSLFKTVTVRCGHCTNLLSVNMRG 61

Query: 62  LLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPAT 121
           LLLP+ANQ HLGH+ FSP HNL EEI +P  + L NQ N N+ ++P RG VDE+P+PP  
Sbjct: 62  LLLPAANQLHLGHSPFSP-HNLLEEIRSPPSSMLTNQPNPNEAVMPVRG-VDEIPKPPVV 119

Query: 122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDHQ 181
           +RPPEKRQRVPSAYNRFIKDEIQRIKAGNP ISHREAFSAAAKNWAHFPHIHFGL+PD Q
Sbjct: 120 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPGISHREAFSAAAKNWAHFPHIHFGLMPD-Q 178

Query: 182 PVKKANVRQQEGEDVLMKDGFFASANVGVSPY 213
           PVKKANVRQQEGED+LMKDGFFA ANVGVSPY
Sbjct: 179 PVKKANVRQQEGEDMLMKDGFFAPANVGVSPY 210

Source: Vitis pseudoreticulata

Species: Vitis pseudoreticulata

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|41745624|gb|AAS10177.1| YABBY-like transcription factor GRAMINIFOLIA [Antirrhinum majus]

 Score =  328 bits (841), Expect = 8e-88,   Method: Compositional matrix adjust.
 Identities = 166/213 (77%), Positives = 179/213 (84%), Gaps = 5/213 (2%)

Query: 3   SSSTTLSLDQ--FPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMR 60
           SSS+  + D      SEQLCYVHCN CDTVLAVSVPCTSL KTVTVRCGHCTNLL VNMR
Sbjct: 2   SSSSAFAPDHHHITPSEQLCYVHCNFCDTVLAVSVPCTSLIKTVTVRCGHCTNLLSVNMR 61

Query: 61  GLLLPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPA 120
           GLLLP+ANQ HLGH+FFSP  NL EEI N   N L+NQ N ND ++P RG +DELP+PP 
Sbjct: 62  GLLLPAANQLHLGHSFFSP-QNLLEEIRNSPSNLLMNQPNPNDSMMPVRG-LDELPKPPV 119

Query: 121 TSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDH 180
            +RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL+PD 
Sbjct: 120 ANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPD- 178

Query: 181 QPVKKANVRQQEGEDVLMKDGFFASANVGVSPY 213
           QPVKK NV +Q G+DVLMKDGF A ANVGVSPY
Sbjct: 179 QPVKKPNVCRQHGDDVLMKDGFLAPANVGVSPY 211

Source: Antirrhinum majus

Species: Antirrhinum majus

Genus: Antirrhinum

Family: Plantaginaceae

Order: Lamiales

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	213
TAIR|locus:2005492	229	AFO "AT2G45190" [Arabidopsis t	0.990	0.921	0.637	5.6e-68
TAIR|locus:2126931	240	YAB3 "YABBY3" [Arabidopsis tha	0.943	0.837	0.497	1.2e-42
TAIR|locus:2826731	184	YAB2 "YABBY2" [Arabidopsis tha	0.765	0.885	0.558	1.7e-41
TAIR|locus:2066311	164	YAB5 "YABBY5" [Arabidopsis tha	0.690	0.896	0.549	7.5e-41
UNIPROTKB|Q7XIM7	169	YAB1 "Protein YABBY 1" [Oryza	0.723	0.911	0.503	1.1e-34
TAIR|locus:2028020	231	INO "INNER NO OUTER" [Arabidop	0.779	0.718	0.451	1.3e-31
UNIPROTKB|Q76EJ0	194	DL "Protein DROOPING LEAF" [Or	0.666	0.731	0.481	1.4e-30
TAIR|locus:2026418	181	CRC "AT1G69180" [Arabidopsis t	0.661	0.779	0.435	2.2e-27

TAIR|locus:2005492 AFO "AT2G45190" [Arabidopsis thaliana (taxid:3702)]

 Score = 690 (248.0 bits), Expect = 5.6e-68, P = 5.6e-68
 Identities = 144/226 (63%), Positives = 172/226 (76%)

Query:     1 MSS-SSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNM 59
             MSS SS   S D F  S+ LCYV CN C T+LAV+VP TSLFKTVTVRCG CTNLL VNM
Sbjct:     6 MSSPSSAVCSPDHFSPSDHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNM 65

Query:    60 RGLLLPSANQFHL--G-HNFFSPSHNLRE--EIPNPSPNFLINQTNT-NDFIVPTRGVVD 113
             R  +LP++NQ  L  G H++F+P   L E  + P+     ++NQ  T ND  +P+   + 
Sbjct:    66 RSYVLPASNQLQLQLGPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMND--IPSFMDLH 123

Query:   114 ---ELPRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 170
                E+P+ P  +RPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAAKNWAHFP
Sbjct:   124 QQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFP 183

Query:   171 HIHFGLVPDHQPVKKANVRQQEGED-VLMKDGFFA--SANVGVSPY 213
             HIHFGLVPD+QPVKK N+ QQEGED ++MK+GF+A  +ANVGV+PY
Sbjct:   184 HIHFGLVPDNQPVKKTNMPQQEGEDNMVMKEGFYAPAAANVGVTPY 229

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

GO:0005634 "nucleus" evidence=ISM;TAS

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=ISS

GO:0009909 "regulation of flower development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

GO:0010158 "abaxial cell fate specification" evidence=IGI

GO:0010159 "specification of organ position" evidence=IMP

GO:0010093 "specification of floral organ identity" evidence=IMP

GO:0010450 "inflorescence meristem growth" evidence=IMP

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0009737 "response to abscisic acid stimulus" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=IMP

GO:0045165 "cell fate commitment" evidence=IMP

TAIR|locus:2126931 YAB3 "YABBY3" [Arabidopsis thaliana (taxid:3702)]

 Score = 451 (163.8 bits), Expect = 1.2e-42, P = 1.2e-42
 Identities = 108/217 (49%), Positives = 132/217 (60%)

Query:     2 SSSSTTLSLDQFPTSE-QLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHC--TNLLPVN 58
             S   T L++   P+S  +   V C  C  +L+V+V   +L        GH       P  
Sbjct:    31 SFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVSMRALLLPSVSNLGHSFLPPPPPPP 90

Query:    59 MRGLL--LPSANQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELP 116
                LL  + S  Q ++  N    SH+     PN     L+  T     +      + E+P
Sbjct:    91 PPNLLEEMRSGGQ-NINMNMMM-SHHASAHHPN---EHLVMATRNGRSV----DHLQEMP 141

Query:   117 RPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 176
             RPP  +RPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL
Sbjct:   142 RPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 201

Query:   177 VPDHQPVKKANVRQQEGEDVLM-KDGFFASA-NVGVS 211
             + DH P KKANVRQQEGED +M ++GF+ SA NVGV+
Sbjct:   202 MADHPPTKKANVRQQEGEDGMMGREGFYGSAANVGVA 238

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

GO:0010158 "abaxial cell fate specification" evidence=IGI

TAIR|locus:2826731 YAB2 "YABBY2" [Arabidopsis thaliana (taxid:3702)]

 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 96/172 (55%), Positives = 116/172 (67%)

Query:     8 LSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSA 67
             +S+D F +SE++CYVHC+ C T+LAVSVP  SLF  VTVRCGHCTNLL +N+ G+ L   
Sbjct:     1 MSVD-F-SSERVCYVHCSFCTTILAVSVPYASLFTLVTVRCGHCTNLLSLNI-GVSLHQT 57

Query:    68 NQFHLGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEK 127
             +   + H    P H           +   +  +TN+    +  +  E PR P   RPPEK
Sbjct:    58 SAPPI-HQDLQP-HRQHTTSLVTRKDCASSSRSTNNL---SENIDREAPRMPPI-RPPEK 111

Query:   128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPD 179
             RQRVPSAYNRFIK+EIQRIKA NP+ISHREAFS AAKNWAHFPHIHFGL  D
Sbjct:   112 RQRVPSAYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLD 163

GO:0005634 "nucleus" evidence=ISM

GO:0010158 "abaxial cell fate specification" evidence=IDA

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

TAIR|locus:2066311 YAB5 "YABBY5" [Arabidopsis thaliana (taxid:3702)]

 Score = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 89/162 (54%), Positives = 105/162 (64%)

Query:    16 SEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHN 75
             +EQLCY+ CN C+ +LAV+VPC+SLF  VTVRCGHCTNL  VNM   L   +       N
Sbjct:     8 TEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQSLSRPNFQATN 67

Query:    76 FFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEKRQRVPSAY 135
             +  P +          P+ +  +T T   IV               +RPPEKRQRVPSAY
Sbjct:    68 YAVPEYGSSSRSHTKIPSRISTRTITEQRIV---------------NRPPEKRQRVPSAY 112

Query:   136 NRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV 177
             N+FIK+EIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL+
Sbjct:   113 NQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLM 154

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0006417 "regulation of translation" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

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

UNIPROTKB|Q7XIM7 YAB1 "Protein YABBY 1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 376 (137.4 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 83/165 (50%), Positives = 103/165 (62%)

Query:    12 QFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFH 71
             QF TSE +CYV+CN C+T+L V+VP    +  VTVRCGHCT +L +++         Q H
Sbjct:     4 QF-TSEHVCYVNCNYCNTILVVNVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQDH 62

Query:    72 LGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEKRQRV 131
                N     +N        S N    +T+T  + +PT        +  +  RPPEKRQRV
Sbjct:    63 QVQNRGFQGNNFGS-YDIASRN---QRTSTAMYPMPTS------QQQVSPIRPPEKRQRV 112

Query:   132 PSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 176
             PSAYNRFIK+EIQRIK  NP+ISHREAFSAAAKNWAH P +HFGL
Sbjct:   113 PSAYNRFIKEEIQRIKTSNPEISHREAFSAAAKNWAHLPRLHFGL 157

GO:0005634 "nucleus" evidence=IDA

GO:0048833 "specification of floral organ number" evidence=IMP

TAIR|locus:2028020 INO "INNER NO OUTER" [Arabidopsis thaliana (taxid:3702)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 83/184 (45%), Positives = 110/184 (59%)

Query:     1 MSSSSTTLSLDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVN-M 59
             + + +TTL+   F    Q+C+V C  C T+L VSVP TSL   VTVRCGHCT+LL VN M
Sbjct:     4 LPNMTTTLN-HLFDLPGQICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCTSLLSVNLM 62

Query:    60 RGLLLPS---ANQFHL---GHNFFSPSHNLREEIPNPSPNFLINQTNTND--FIVPTRGV 111
             +   +P    A+  HL   G    + +  + EE       + +NQ   N    +V +   
Sbjct:    63 KASFIPLHLLASLSHLDETGKEEVAATDGVEEEA------WKVNQEKENSPTTLVSSSDN 116

Query:   112 VDE-LPRP-PATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 169
              DE + R     ++PPEKRQR PSAYN FIK+EI+R+KA NP ++H+EAFS AAKNWAHF
Sbjct:   117 EDEDVSRVYQVVNKPPEKRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHF 176

Query:   170 PHIH 173
             P  H
Sbjct:   177 PPAH 180

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=IDA

GO:0048481 "ovule development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

UNIPROTKB|Q76EJ0 DL "Protein DROOPING LEAF" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 77/160 (48%), Positives = 96/160 (60%)

Query:    10 LDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRG-LLLPSAN 68
             +D    SE LCYV C  C+TVLAV VPC  L  TVTV+CGHC NL  ++ R  ++ P + 
Sbjct:     1 MDLVSPSEHLCYVRCTYCNTVLAVGVPCKRLMDTVTVKCGHCNNLSFLSPRPPMVQPLSP 60

Query:    69 QFH-LGHNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEK 127
               H LG  F  P  + R   P P    L++ T+            +  PR P   +PPEK
Sbjct:    61 TDHPLGP-FQGPCTDCRRNQPLP----LVSPTSN-----------EGSPRAPFVVKPPEK 104

Query:   128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWA 167
             + R+PSAYNRF+++EIQRIKA  PDI HREAFS AAKNWA
Sbjct:   105 KHRLPSAYNRFMREEIQRIKAAKPDIPHREAFSMAAKNWA 144

GO:0010022 "meristem determinacy" evidence=IGI;IMP

GO:0048366 "leaf development" evidence=IMP

GO:0048440 "carpel development" evidence=IMP

TAIR|locus:2026418 CRC "AT1G69180" [Arabidopsis thaliana (taxid:3702)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 68/156 (43%), Positives = 93/156 (59%)

Query:    14 PTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLG 73
             P +E L YV C++C+T+LAV +P   +  TVTV+CGHC NL  +     L     Q H+ 
Sbjct:    16 PQAEHLYYVRCSICNTILAVGIPLKRMLDTVTVKCGHCGNLSFLTTTPPL-----QGHVS 70

Query:    74 HNFFSPSHNLREEIPNPSPNFLINQTNTNDFIVPTRGVVDELPRPPATSRPPEKRQRVPS 133
                   S    +     S +   + ++T+    P+       P PP   +PPEK+QR+PS
Sbjct:    71 LTLQMQSFGGSDYKKGSSSS---SSSSTSSDQPPS-------PSPPFVVKPPEKKQRLPS 120

Query:   134 AYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 169
             AYNRF++DEIQRIK+ NP+I HREAFSAAAKNWA +
Sbjct:   121 AYNRFMRDEIQRIKSANPEIPHREAFSAAAKNWAKY 156


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        0.320   0.134   0.418    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      213       213   0.00084  112 3  11 22  0.36    33
                                                     31  0.49    35


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:  8
  No. of states in DFA:  595 (63 KB)
  Total size of DFA:  180 KB (2104 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:  21.11u 0.08s 21.19t   Elapsed:  00:00:02
  Total cpu time:  21.11u 0.08s 21.19t   Elapsed:  00:00:02
  Start:  Fri May 10 04:38:41 2013   End:  Fri May 10 04:38:43 2013

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

GO:0005634 "nucleus" evidence=ISM

GO:0010254 "nectary development" evidence=IMP

GO:0048440 "carpel development" evidence=RCA;IMP

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

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=TAS

GO:0010582 "floral meristem determinacy" evidence=IGI

GO:0048479 "style development" evidence=IMP

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0009827 "plant-type cell wall modification" evidence=RCA

GO:0009860 "pollen tube growth" evidence=RCA

GO:0009886 "post-embryonic morphogenesis" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010093 "specification of floral organ identity" evidence=RCA

GO:0031540 "regulation of anthocyanin biosynthetic process" evidence=RCA

GO:0048441 "petal development" evidence=RCA

GO:0048443 "stamen development" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0048507 "meristem development" evidence=RCA

---

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)
O22152	YAB1_ARATH	No assigned EC number	0.6325	0.9624	0.8951	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: GSVIVG00007291001 SubName- Full=Chromosome chr2 scaffold_187, whole genome shotgun sequence; (211 aa) (Vitis vinifera)

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	213
pfam04690	170	pfam04690, YABBY, YABBY protein	4e-74
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	9e-05
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	2e-04

>gnl|CDD|113458 pfam04690, YABBY, YABBY protein

 Score =  221 bits (564), Expect = 4e-74
 Identities = 98/169 (57%), Positives = 110/169 (65%), Gaps = 3/169 (1%)

Query: 11  DQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQF 70
             F +SE +CYVHCN C T+LAVSVP TSLF  VTVRCGHCTNLL VN+           
Sbjct: 2   SVFFSSEHVCYVHCNFCTTILAVSVPYTSLFNIVTVRCGHCTNLLSVNLMMRSHLLPALS 61

Query: 71  HLGHNFFSPSH-NLREEIPNPSPNFLINQTNTNDFIVPTRGVVD--ELPRPPATSRPPEK 127
           HL          NL     N + N + + + +              E+PR P  +RPPEK
Sbjct: 62  HLDETGKPELLQNLGVHGQNFNSNMMKSHSASTSVSSYMMSDNQDEEMPRVPPVNRPPEK 121

Query: 128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 176
           RQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL
Sbjct: 122 RQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 170

YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs. Length = 170

>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 = 39.1 bits (92), Expect = 9e-05
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           R  SAY  F +++  ++K  NPD S  E      + W
Sbjct: 3   RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKW 39

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 = 38.0 bits (89), Expect = 2e-04
 Identities = 12/37 (32%), Positives = 17/37 (45%)

Query: 130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           R  SAY  F ++    +KA NP +S  E      + W
Sbjct: 3   RPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMW 39

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	100.0
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.18
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	97.75
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.7
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	97.68
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	97.66
smart00398	70	HMG high mobility group.	97.56
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	97.51
PTZ00199	94	high mobility group protein; Provisional	97.41
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	96.65
KOG0381	96	consensus HMG box-containing protein [General func	96.38
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	93.64
KOG3223	221	consensus Uncharacterized conserved protein [Funct	93.51
KOG4684	275	consensus Uncharacterized conserved protein, conta	83.27
PRK14892	99	putative transcription elongation factor Elf1; Pro	82.26
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	81.1

>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=100.00  E-value=3.1e-83  Score=536.44  Aligned_cols=167  Identities=62%  Similarity=1.023  Sum_probs=130.2

Q ss_pred             CCCCCCCCceeEEeCCCcceeEEecccCCCCcceeeeecCCcCCCcccccccCCCCCCccccccCcccCCCCcccccCCC
Q 028144           10 LDQFPTSEQLCYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPSANQFHLGHNFFSPSHNLREEIPN   89 (213)
Q Consensus        10 ~d~~~~~E~lCYV~CnfCnTILaVsVPcssL~~~VTVRCGHCtnLlSVNm~~ll~p~~~q~~~~~~~~~~~~~~~~~~~~   89 (213)
                      ||+++++|||||||||||||||||||||+|||+|||||||||+|||||||++++++++.|++++++++.+.....+....
T Consensus         1 ~~~~~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~   80 (170)
T PF04690_consen    1 MDLFSPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPE   80 (170)
T ss_pred             CCccCCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhcccccccccccccccc
Confidence            67788899999999999999999999999999999999999999999999999988888777655544221110000000


Q ss_pred             CCcccccccCCCCCc-cc--cCCCCCCCCCCCCCCCCCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 028144           90 PSPNFLINQTNTNDF-IV--PTRGVVDELPRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW  166 (213)
Q Consensus        90 ~~~~~~~~~~~~~~~-~~--~~~~~~~~~p~~~~v~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW  166 (213)
                      .......+....+.+ ..  ...+.+++.|+.++|+||||||||+|||||+||||||||||++||||+|||||++|||||
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW  160 (170)
T PF04690_consen   81 NFGSNSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNW  160 (170)
T ss_pred             ccccccccCCCccccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Confidence            000000111111111 11  123445788998889999999999999999999999999999999999999999999999


Q ss_pred             ccCCcccccc
Q 028144          167 AHFPHIHFGL  176 (213)
Q Consensus       167 ~~~PhihfGL  176 (213)
                      ||+|||||||
T Consensus       161 ~h~phihfgl  170 (170)
T PF04690_consen  161 AHFPHIHFGL  170 (170)
T ss_pred             hhCcccccCC
Confidence            9999999998

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

Probab=98.18  E-value=2.3e-06  Score=61.17  Aligned_cols=45  Identities=33%  Similarity=0.622  Sum_probs=38.4

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhc-CCCCCHHHHHHHHHHhhccC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAG-NPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~-~P~i~HkEaFs~aAknW~~~  169 (213)
                      |.|-.|.+|||+.||++.+.++|+. .+.++.+|++..++..|+..
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~L   46 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSL   46 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhc
Confidence            5666899999999999999999999 88899999999999999975

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 ....

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

Probab=97.75  E-value=5.7e-05  Score=51.43  Aligned_cols=42  Identities=29%  Similarity=0.471  Sum_probs=38.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|-+|+|..|+++....+++++|+++..|....++..|+..+
T Consensus         2 krp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls   43 (66)
T cd01390           2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS   43 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            367899999999999999999999999999999999999753

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.

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

Probab=97.70  E-value=7.9e-05  Score=50.11  Aligned_cols=42  Identities=29%  Similarity=0.412  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|-+++|..|++++...+++.+|+++..|....+++.|+..+
T Consensus         2 krp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~   43 (66)
T cd00084           2 KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLS   43 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            467899999999999999999999999999999999999754

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

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

Probab=97.68  E-value=7.7e-05  Score=53.19  Aligned_cols=42  Identities=17%  Similarity=0.269  Sum_probs=38.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|-++||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus         3 KrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls   44 (72)
T cd01388           3 KRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALS   44 (72)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            467899999999999999999999999999999999998753

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.

>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=97.66  E-value=7.1e-05  Score=51.49  Aligned_cols=41  Identities=32%  Similarity=0.619  Sum_probs=36.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .|-++||..|+++....||+++|+++..|.-+.+++.|+..
T Consensus         2 krP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l   42 (69)
T PF00505_consen    2 KRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNL   42 (69)
T ss_dssp             SSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCS
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcC
Confidence            47889999999999999999999999999999999999974

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 ....

>smart00398 HMG high mobility group

Probab=97.56  E-value=0.00017  Score=49.01  Aligned_cols=42  Identities=31%  Similarity=0.501  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|-+++|..|+++....+++++|+++..|....++..|+..+
T Consensus         3 krp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~   44 (70)
T smart00398        3 KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLS   44 (70)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCC
Confidence            467899999999999999999999999999999999999753

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

Probab=97.51  E-value=0.0002  Score=51.50  Aligned_cols=42  Identities=19%  Similarity=0.371  Sum_probs=39.5

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|-++||-.|+++....|+++||++++.|.-+.++..|+..+
T Consensus         3 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls   44 (77)
T cd01389           3 PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSES   44 (77)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            578999999999999999999999999999999999999754

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.

>PTZ00199 high mobility group protein; Provisional

Probab=97.41  E-value=0.00036  Score=52.94  Aligned_cols=48  Identities=25%  Similarity=0.438  Sum_probs=41.8

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCC--HHHHHHHHHHhhccCC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDIS--HREAFSAAAKNWAHFP  170 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~--HkEaFs~aAknW~~~P  170 (213)
                      +.|.+-.|-+|||..|+++.-..|+++||+++  -.|.-+.++..|+..+
T Consensus        18 kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls   67 (94)
T PTZ00199         18 KDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLS   67 (94)
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCC
Confidence            55666678899999999999999999999986  5788889999999764

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

Probab=96.65  E-value=0.0021  Score=52.32  Aligned_cols=50  Identities=26%  Similarity=0.509  Sum_probs=44.8

Q ss_pred             CCCCCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCCc
Q 028144          120 ATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPH  171 (213)
Q Consensus       120 ~v~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  171 (213)
                      .+-|.||||-+  -||..|--.+|.+||++||++.+-+-=-..=|.|..+|.
T Consensus        67 ~~drHPErR~K--AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   67 PIDRHPERRMK--AAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPE  116 (122)
T ss_pred             CCCCCcchhHH--HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCC
Confidence            45689999875  599999999999999999999999988888999999874

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

Probab=96.38  E-value=0.0072  Score=44.44  Aligned_cols=43  Identities=30%  Similarity=0.442  Sum_probs=39.3

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          127 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       127 KRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .-+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|...
T Consensus        22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l   64 (96)
T KOG0381|consen   22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNL   64 (96)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC
Confidence            4567888999999999999999999999999999999999875

>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function

Probab=93.64  E-value=0.033  Score=38.79  Aligned_cols=38  Identities=26%  Similarity=0.718  Sum_probs=29.5

Q ss_pred             EEeCCCcceeEEecccCCCCcc---eeeeecCCcCCCcccccc
Q 028144           21 YVHCNLCDTVLAVSVPCTSLFK---TVTVRCGHCTNLLPVNMR   60 (213)
Q Consensus        21 YV~CnfCnTILaVsVPcssL~~---~VTVRCGHCtnLlSVNm~   60 (213)
                      ||-|.-|...|-  +|-+.+..   .-.+|||.|+.++++.++
T Consensus         6 Fv~C~~C~~lLq--lP~~~~~~~k~~~klrCGaCs~vl~~s~~   46 (46)
T PF11331_consen    6 FVVCSSCFELLQ--LPAKFSLSKKNQQKLRCGACSEVLSFSLP   46 (46)
T ss_pred             EeECccHHHHHc--CCCccCCCccceeEEeCCCCceeEEEecC
Confidence            789999977765  47775443   568999999999988753

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.51  E-value=0.041  Score=48.85  Aligned_cols=50  Identities=30%  Similarity=0.521  Sum_probs=43.8

Q ss_pred             CCCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCCccc
Q 028144          122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIH  173 (213)
Q Consensus       122 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Phih  173 (213)
                      -|-||||=|.  ||--|=..++-|||.++|+++|-+-=-..-|.|...|.=-
T Consensus       161 drHPEkRmrA--A~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP  210 (221)
T KOG3223|consen  161 DRHPEKRMRA--AFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNP  210 (221)
T ss_pred             ccChHHHHHH--HHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCCh
Confidence            4899999885  8999999999999999999999987777888999887533

>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]

Probab=83.27  E-value=1.2  Score=40.67  Aligned_cols=17  Identities=35%  Similarity=0.852  Sum_probs=12.3

Q ss_pred             eeeeecCCcCCCccccc
Q 028144           43 TVTVRCGHCTNLLPVNM   59 (213)
Q Consensus        43 ~VTVRCGHCtnLlSVNm   59 (213)
                      .+-|+||||.+..--|.
T Consensus       168 gcRV~CgHC~~tFLfnt  184 (275)
T KOG4684|consen  168 GCRVKCGHCNETFLFNT  184 (275)
T ss_pred             ceEEEecCccceeehhh
Confidence            47888999988655543

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=82.26  E-value=1.9  Score=34.14  Aligned_cols=44  Identities=16%  Similarity=0.403  Sum_probs=36.0

Q ss_pred             eEEeCCCcceeEEecccCCCCcceeeeecCCcCCCcccccccCCCCC
Q 028144           20 CYVHCNLCDTVLAVSVPCTSLFKTVTVRCGHCTNLLPVNMRGLLLPS   66 (213)
Q Consensus        20 CYV~CnfCnTILaVsVPcssL~~~VTVRCGHCtnLlSVNm~~ll~p~   66 (213)
                      =++.|.||+. ..|+||...  ++..+.|..|.---.-.+..|.+|.
T Consensus        20 t~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epI   63 (99)
T PRK14892         20 KIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEV   63 (99)
T ss_pred             cEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccch
Confidence            3789999995 789999988  7999999999987776666666663

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=81.10  E-value=1.7  Score=27.57  Aligned_cols=35  Identities=29%  Similarity=0.553  Sum_probs=24.4

Q ss_pred             EEeCCCcceeEEecccCCCCc-ceeeeecCCcCCCccc
Q 028144           21 YVHCNLCDTVLAVSVPCTSLF-KTVTVRCGHCTNLLPV   57 (213)
Q Consensus        21 YV~CnfCnTILaVsVPcssL~-~~VTVRCGHCtnLlSV   57 (213)
                      .+.|..|.+..-|..  +.+- +...|+|++|.+.+.+
T Consensus         2 ~~~CP~C~~~~~v~~--~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         2 RIQCPNCKTSFRVVD--SQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             EEECCCCCCEEEeCH--HHcCCCCCEEECCCCCCEEEe
Confidence            378999999877653  2221 3347999999987654

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	9e-07
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-06
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	6e-05
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-04
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	7e-05
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	2e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	3e-04
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	4e-04
1wgf_A	90	Upstream binding factor 1; transcription factor, D	6e-04
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	6e-04
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	8e-04

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

 Score = 47.1 bits (111), Expect = 9e-07
 Identities = 15/50 (30%), Positives = 23/50 (46%)

Query: 121 TSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 170
           +S      ++  S+Y RF K+++   KA NPD    E     A+ W   P
Sbjct: 3   SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 52

>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 = 46.8 bits (110), Expect = 1e-06
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 170
           S      ++  S+Y RF K+++   KA NPD    E     A+ W   P
Sbjct: 36  SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 84

>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 = 41.1 bits (96), Expect = 6e-05
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           + P   +R PSA+  F  +   +IK  +P +S  +      + W
Sbjct: 97  KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 140

>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 = 40.0 bits (93), Expect = 1e-04
 Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPD--ISHREAFSAAAKNWAHFP 170
             P+K +   S+Y  F++   +  K  +PD  ++  E     ++ W    
Sbjct: 11  GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 60

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

 Score = 39.7 bits (93), Expect = 7e-05
 Identities = 7/44 (15%), Positives = 22/44 (50%)

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           + P+  ++  + Y RF  ++  +    +P++S+ +     +K +
Sbjct: 6   KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKY 49

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 14/44 (31%), Positives = 20/44 (45%)

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           + P + Q+  SAY  F +D    IK  NP+ +  E     A  W
Sbjct: 13  KDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMW 56

>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 = 37.7 bits (88), Expect = 3e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           + P   +R  SAY  F  +    +++ NPDI+  +      + W
Sbjct: 16  KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

>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 = 36.8 bits (86), Expect = 4e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           + P   +R PSA+  F  +   +IK  +P +S  +      + W
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 45

>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 = 37.0 bits (86), Expect = 6e-04
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 116 PRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           P         EK +R  SA   F +++ ++++   P++S  E     A+ W
Sbjct: 9   PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMW 59

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

 Score = 37.0 bits (86), Expect = 6e-04
 Identities = 10/45 (22%), Positives = 17/45 (37%)

Query: 122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           S      ++  SA   F++D   +    NP  S  +A     + W
Sbjct: 2   SSGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELW 46

>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 = 36.6 bits (85), Expect = 8e-04
 Identities = 9/45 (20%), Positives = 18/45 (40%)

Query: 122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           S      +   + Y RF+ +  ++I+  +PD+   E        W
Sbjct: 2   SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEW 46

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	97.88
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	97.82
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	97.72
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	97.72
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	97.71
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	97.71
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	97.7
1wgf_A	90	Upstream binding factor 1; transcription factor, D	97.7
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	97.67
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	97.64
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	97.63
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	97.59
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	97.58
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	97.56
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	97.55
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	97.54
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	97.53
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	97.48
1ckt_A	71	High mobility group 1 protein; high-mobility group	97.45
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	97.4
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.38
2lhj_A	97	High mobility group protein homolog NHP1; structur	97.32
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	97.32
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	97.31
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.28
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	97.21
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	97.19
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.11
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	96.83
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	96.78
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	96.61
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	96.34
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	96.21
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	95.33
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	95.21
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	94.38
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	94.37
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	93.82
2cto_A	93	Novel protein; high mobility group box domain, hel	90.07

>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=97.88  E-value=1.9e-05  Score=55.29  Aligned_cols=47  Identities=23%  Similarity=0.432  Sum_probs=42.7

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |-|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..
T Consensus         2 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   48 (77)
T 1hme_A            2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNT   48 (77)
T ss_dssp             CCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            34666678899999999999999999999999999999999999964

>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=97.82  E-value=2.4e-05  Score=55.64  Aligned_cols=47  Identities=21%  Similarity=0.306  Sum_probs=43.0

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .+|.+-.|-+|||..|+++.-.+|++++|++++.|.-+.++..|+..
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   49 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVL   49 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhC
Confidence            35666778899999999999999999999999999999999999964

>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=97.72  E-value=4.5e-05  Score=53.24  Aligned_cols=43  Identities=26%  Similarity=0.397  Sum_probs=40.1

Q ss_pred             cCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       128 RQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      -.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         4 PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   46 (73)
T 3nm9_A            4 PKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK   46 (73)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            3578999999999999999999999999999999999999864

>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=97.72  E-value=4.1e-05  Score=55.34  Aligned_cols=47  Identities=19%  Similarity=0.260  Sum_probs=43.5

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      +-|.+-.|-++||..|+++.-++|++++|+++..|.-+.++..|+..
T Consensus        13 kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~l   59 (87)
T 2e6o_A           13 TSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKM   59 (87)
T ss_dssp             CCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhC
Confidence            56677788999999999999999999999999999999999999965

>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=97.71  E-value=3.6e-05  Score=53.74  Aligned_cols=45  Identities=16%  Similarity=0.359  Sum_probs=40.8

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |.+-.|-+|||..|+++.-++|++++|+++..|.-+.++..|+..
T Consensus         2 p~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   46 (76)
T 1hry_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKML   46 (76)
T ss_dssp             -CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhC
Confidence            455567899999999999999999999999999999999999965

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

Probab=97.71  E-value=5.7e-05  Score=55.10  Aligned_cols=46  Identities=20%  Similarity=0.249  Sum_probs=41.4

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          124 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       124 PPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .|.+-.|-+|||..|+++.-.+||++||+++..|.-+.++..|+..
T Consensus         4 ~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   49 (92)
T 2cs1_A            4 GSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTL   49 (92)
T ss_dssp             CCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcC
Confidence            3455567899999999999999999999999999999999999964

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

Probab=97.70  E-value=6.3e-05  Score=54.87  Aligned_cols=47  Identities=17%  Similarity=0.431  Sum_probs=42.8

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |-|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..
T Consensus         3 kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   49 (92)
T 2crj_A            3 SGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKL   49 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcC
Confidence            45666678899999999999999999999999999999999999965

>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=97.70  E-value=9.1e-05  Score=53.93  Aligned_cols=48  Identities=23%  Similarity=0.365  Sum_probs=43.6

Q ss_pred             CCCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       122 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .+.|.+-.|-++||..|+++.-++|+++||++++.|.-+.++..|+..
T Consensus        15 ~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~l   62 (90)
T 1wgf_A           15 KGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDL   62 (90)
T ss_dssp             SSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            356666778899999999999999999999999999999999999964

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

Probab=97.67  E-value=6.8e-05  Score=55.87  Aligned_cols=47  Identities=30%  Similarity=0.498  Sum_probs=43.2

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      +.|.+-.|-++||..|+++.-.+|+++||+++..|.-+.++..|+..
T Consensus        13 kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~l   59 (102)
T 2co9_A           13 KDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGL   59 (102)
T ss_dssp             CCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccC
Confidence            55666778899999999999999999999999999999999999975

>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=97.64  E-value=7.7e-05  Score=53.56  Aligned_cols=45  Identities=16%  Similarity=0.359  Sum_probs=40.9

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |.+-.|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..
T Consensus         2 p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~l   46 (85)
T 1j46_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKML   46 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTS
T ss_pred             cCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC
Confidence            445567899999999999999999999999999999999999965

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

Probab=97.63  E-value=7.6e-05  Score=52.07  Aligned_cols=45  Identities=22%  Similarity=0.416  Sum_probs=40.9

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |.+-.|-+|||..|+++.-.+|+++||+++..|.-+.++..|+..
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   45 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL   45 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh
Confidence            344567899999999999999999999999999999999999975

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

Probab=97.59  E-value=9e-05  Score=55.78  Aligned_cols=48  Identities=13%  Similarity=0.243  Sum_probs=42.0

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |.|.+-.|-++||..|+++.-.+|++++|++++.|.-+.++..|+..+
T Consensus        25 k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   72 (106)
T 4euw_A           25 KNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLN   72 (106)
T ss_dssp             ---CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             CCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            567777889999999999999999999999999999999999998753

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

Probab=97.58  E-value=8e-05  Score=55.45  Aligned_cols=47  Identities=15%  Similarity=0.338  Sum_probs=43.0

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |.|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..
T Consensus         6 kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~l   52 (99)
T 1k99_A            6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKEL   52 (99)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            45666678899999999999999999999999999999999999964

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

Probab=97.56  E-value=0.00011  Score=52.95  Aligned_cols=47  Identities=23%  Similarity=0.383  Sum_probs=41.3

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISH--REAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~H--kEaFs~aAknW~~~  169 (213)
                      +-|.+-.|-+|||..|+++.-++|++++|+++.  .|.-+.++..|+..
T Consensus        11 kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~l   59 (86)
T 2eqz_A           11 GDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTM   59 (86)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhC
Confidence            345556778999999999999999999999974  99999999999864

>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=97.55  E-value=9e-05  Score=52.48  Aligned_cols=44  Identities=27%  Similarity=0.476  Sum_probs=39.4

Q ss_pred             cccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          126 EKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       126 EKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .|-.|-++||..|+++.-..|++++|++++.|.-+.++..|+..
T Consensus         5 ~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   48 (83)
T 3f27_D            5 SRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKAL   48 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcC
Confidence            34467899999999999999999999999999999999999864

>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=97.54  E-value=0.00014  Score=51.46  Aligned_cols=43  Identities=21%  Similarity=0.359  Sum_probs=39.5

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          127 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       127 KRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      +-.|-++||..|+++.-+.|++++|++++.|.-+.++..|+..
T Consensus         4 ~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   46 (81)
T 1i11_A            4 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAM   46 (81)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhC
Confidence            3457799999999999999999999999999999999999964

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

Probab=97.53  E-value=0.00011  Score=50.26  Aligned_cols=42  Identities=29%  Similarity=0.476  Sum_probs=38.2

Q ss_pred             cCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       128 RQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      -.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..
T Consensus         3 ~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   44 (71)
T 4a3n_A            3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKAL   44 (71)
T ss_dssp             --CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcC
Confidence            357889999999999999999999999999999999999864

>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=97.48  E-value=0.00018  Score=50.67  Aligned_cols=42  Identities=14%  Similarity=0.333  Sum_probs=39.1

Q ss_pred             cCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       128 RQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      -.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..
T Consensus         3 pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   44 (80)
T 1gt0_D            3 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLL   44 (80)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            357899999999999999999999999999999999999964

>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=97.45  E-value=0.00017  Score=49.59  Aligned_cols=42  Identities=21%  Similarity=0.319  Sum_probs=38.2

Q ss_pred             cCCCchhhhHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhccC
Q 028144          128 RQRVPSAYNRFIKDEIQRIKAGNPDISH--REAFSAAAKNWAHF  169 (213)
Q Consensus       128 RQR~psayN~fmK~ei~riK~~~P~i~H--kEaFs~aAknW~~~  169 (213)
                      -.|-+|||..|+++.-+.||++||+++.  .|.-+.++..|+..
T Consensus         2 PKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~l   45 (71)
T 1ckt_A            2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTM   45 (71)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTC
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhC
Confidence            3578999999999999999999999976  99999999999864

>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=97.40  E-value=0.0002  Score=50.12  Aligned_cols=41  Identities=22%  Similarity=0.367  Sum_probs=38.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .|-++||..|+++.-..|++++|++++.|.-+.++..|+..
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   44 (79)
T 3u2b_C            4 KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLL   44 (79)
T ss_dssp             CCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhC
Confidence            47889999999999999999999999999999999999864

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1

Probab=97.38  E-value=0.00023  Score=55.84  Aligned_cols=47  Identities=23%  Similarity=0.432  Sum_probs=42.6

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      +-|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..
T Consensus        84 kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~l  130 (159)
T 2gzk_A           84 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNT  130 (159)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHS
T ss_pred             cccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhC
Confidence            44566678899999999999999999999999999999999999964

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

Probab=97.32  E-value=0.00011  Score=54.00  Aligned_cols=48  Identities=25%  Similarity=0.393  Sum_probs=43.9

Q ss_pred             CCCCcccCCCchhhhHHHHHHHHHHHhcCCCCC--HHHHHHHHHHhhccC
Q 028144          122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDIS--HREAFSAAAKNWAHF  169 (213)
Q Consensus       122 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~--HkEaFs~aAknW~~~  169 (213)
                      .+.|.+-.|-+|||..|+++.-.+|+++||+++  ..|.-+.++..|+..
T Consensus        17 ~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~l   66 (97)
T 2lhj_A           17 KKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNAL   66 (97)
T ss_dssp             TSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhC
Confidence            356777788999999999999999999999999  999999999999975

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

Probab=97.32  E-value=0.00015  Score=51.61  Aligned_cols=47  Identities=23%  Similarity=0.381  Sum_probs=41.1

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISH--REAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~H--kEaFs~aAknW~~~  169 (213)
                      +-|.+-.|-+|||..|+++.-..|++++|+++.  .|.-+.++..|+..
T Consensus         3 kdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~l   51 (83)
T 1aab_A            3 GDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTM   51 (83)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhC
Confidence            345566788999999999999999999999875  99999999999864

>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=97.31  E-value=7.2e-05  Score=54.77  Aligned_cols=47  Identities=23%  Similarity=0.470  Sum_probs=43.0

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      +.|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..
T Consensus        16 kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~l   62 (93)
T 1cg7_A           16 KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKAL   62 (93)
T ss_dssp             CCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            45666778899999999999999999999999999999999999965

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

Probab=97.28  E-value=0.00031  Score=56.03  Aligned_cols=47  Identities=23%  Similarity=0.432  Sum_probs=42.8

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      +-|.+-.|-+|||..|+++...+|++++|+++..|.-+.++..|+..
T Consensus        97 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~l  143 (173)
T 2yrq_A           97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNT  143 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHS
T ss_pred             cCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            35666678899999999999999999999999999999999999975

>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=97.21  E-value=0.0005  Score=49.25  Aligned_cols=41  Identities=10%  Similarity=0.189  Sum_probs=38.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~l   44 (86)
T 2lef_A            4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHAL   44 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcC
Confidence            47799999999999999999999999999999999999965

>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=97.19  E-value=0.00061  Score=49.56  Aligned_cols=42  Identities=14%  Similarity=0.340  Sum_probs=38.7

Q ss_pred             cCCCchhhhHHHHHHHHHHHhcCCCCC-HHHHHHHHHHhhccC
Q 028144          128 RQRVPSAYNRFIKDEIQRIKAGNPDIS-HREAFSAAAKNWAHF  169 (213)
Q Consensus       128 RQR~psayN~fmK~ei~riK~~~P~i~-HkEaFs~aAknW~~~  169 (213)
                      -.|-+|||..|+++.-.+||++||+++ ..|.-+.++..|+..
T Consensus         6 PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~l   48 (81)
T 2d7l_A            6 SGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVL   48 (81)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcC
Confidence            356799999999999999999999998 999999999999864

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

Probab=97.11  E-value=0.00063  Score=54.21  Aligned_cols=48  Identities=21%  Similarity=0.385  Sum_probs=42.9

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCC--CCHHHHHHHHHHhhccCC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPD--ISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~--i~HkEaFs~aAknW~~~P  170 (213)
                      +-|.+-.|-+|||..|+++....|+++||+  ++-.|..+.++..|+..+
T Consensus        11 ~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   60 (173)
T 2yrq_A           11 GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   60 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCC
Confidence            456666889999999999999999999999  689999999999998753

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

Probab=96.83  E-value=0.00082  Score=56.14  Aligned_cols=46  Identities=30%  Similarity=0.532  Sum_probs=41.4

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |.+-.|-+|||..|+++....|+++||+++..|..+.++..|+..+
T Consensus         7 p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   52 (214)
T 3tq6_A            7 ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   52 (214)
T ss_dssp             HHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccC
Confidence            4455678999999999999999999999999999999999998753

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

Probab=96.78  E-value=0.0009  Score=56.72  Aligned_cols=47  Identities=28%  Similarity=0.437  Sum_probs=42.9

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      +-|.+-.|-+|||..|+++....||++||+++..|..+.++..|+..
T Consensus        37 ~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~L   83 (238)
T 3tmm_A           37 VLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWREL   83 (238)
T ss_dssp             HHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhC
Confidence            34667778999999999999999999999999999999999999875

>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=96.61  E-value=0.0025  Score=49.89  Aligned_cols=46  Identities=15%  Similarity=0.352  Sum_probs=41.8

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |++..|-++||-.|++++-.+|++++|+++..|.-+.++..|+..+
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls   47 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhh
Confidence            5566788999999999999999999999999999999999998653

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

Probab=96.34  E-value=0.003  Score=43.10  Aligned_cols=38  Identities=29%  Similarity=0.647  Sum_probs=34.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|-+|||..|+++.-..+|..+|    .|..+.++..|+..+
T Consensus         4 KrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls   41 (67)
T 3fgh_A            4 KRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLS   41 (67)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCC
Confidence            57789999999999999999987    599999999999753

>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=96.21  E-value=0.0058  Score=46.20  Aligned_cols=41  Identities=15%  Similarity=0.165  Sum_probs=37.4

Q ss_pred             cCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          128 RQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       128 RQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      ..|-+|||+.|+.+.+.++++++|+ ...|.-+.+...|+..
T Consensus         5 PKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~l   45 (91)
T 1l8y_A            5 PESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNM   45 (91)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcC
Confidence            3467999999999999999999999 9999999999999874

>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=95.33  E-value=0.025  Score=42.17  Aligned_cols=38  Identities=11%  Similarity=0.330  Sum_probs=31.3

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       130 R~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |-+|||..|+++.++  +..+++++..|.-+.++..|+..
T Consensus        11 rP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~l   48 (101)
T 1v63_A           11 PPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRI   48 (101)
T ss_dssp             CCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTS
T ss_pred             CCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhC
Confidence            468999999999964  44455678899999999999975

>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=95.21  E-value=0.021  Score=43.09  Aligned_cols=42  Identities=14%  Similarity=0.440  Sum_probs=36.2

Q ss_pred             Cccc-CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          125 PEKR-QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       125 PEKR-QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |.+- .|-+|||..|+++.-++||    +++..|.-+.++..|+..+
T Consensus        14 ~~~P~KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls   56 (108)
T 1v64_A           14 DGRPTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLS   56 (108)
T ss_dssp             TTSCCCCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCC
Confidence            3343 5679999999999999998    8999999999999999753

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

Probab=94.38  E-value=0.011  Score=49.98  Aligned_cols=42  Identities=29%  Similarity=0.574  Sum_probs=36.6

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |.+-.|-+|||+.|+++...+||.++|+    |..+.++..|+..+
T Consensus       144 p~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls  185 (238)
T 3tmm_A          144 LGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLS  185 (238)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSCCSSHH----HHHHHHHHHHHTCC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHhccCHH----HHHHHHHHHHHhCC
Confidence            4555788999999999999999998886    89999999999753

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

Probab=94.37  E-value=0.012  Score=49.14  Aligned_cols=42  Identities=29%  Similarity=0.574  Sum_probs=36.5

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |.+-.|-+|||..|+++...+||.++|+    |..+.++..|+..+
T Consensus       112 p~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls  153 (214)
T 3tq6_A          112 LGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLS  153 (214)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSSCSSHH----HHHHHHHHHHHTCC
T ss_pred             ccCcccccchhhhhHHHHHHhhccCCHH----HHHHHHHHHHHcCC
Confidence            4455678999999999999999998886    89999999999753

>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=93.82  E-value=0.0085  Score=44.99  Aligned_cols=43  Identities=16%  Similarity=0.166  Sum_probs=34.7

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          125 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       125 PEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |-+-.|.||||-.|+.++-.+||++||+++  +.|..+|+.|+..
T Consensus        20 pnaPKRp~sAf~lf~~e~R~kik~enP~~s--~~~~eIse~Wk~l   62 (90)
T 2yuk_A           20 EALGEMATVAPVLYTNINFPNLKEEFPDWT--TRVKQIAKLWRKA   62 (90)
T ss_dssp             HHHGGGCSSSHHHHHHHHCTTHHHHCCSHH--HHHHHHHHHHHHS
T ss_pred             CCCCCCCccHHHHHHHHhHHHHHHHCcCcc--chHHHHHHHHHcC
Confidence            334478899999999999999999999985  3355566999864

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

Probab=90.07  E-value=0.11  Score=38.91  Aligned_cols=39  Identities=18%  Similarity=0.430  Sum_probs=33.7

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHH---HHhhccC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAA---AKNWAHF  169 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~a---AknW~~~  169 (213)
                      .|-+|||..|+++.-.+||.+  +++-.|.=+..   ...|+..
T Consensus        12 KRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~l   53 (93)
T 2cto_A           12 KASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWALL   53 (93)
T ss_dssp             CSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHcC
Confidence            578999999999999999998  78888877777   9999864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	213
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-05
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	6e-04
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	0.001
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	0.001

>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 = 39.9 bits (93), Expect = 2e-05
 Identities = 8/48 (16%), Positives = 23/48 (47%)

Query: 123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 170
           + P+  ++  + Y RF  ++  +    +P++S+ +     +K +   P
Sbjct: 6   KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP 53

>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 = 36.4 bits (84), Expect = 2e-04
 Identities = 10/41 (24%), Positives = 18/41 (43%)

Query: 130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 170
           R PSA+  F  +   +IK  +P +S  +      + W +  
Sbjct: 5   RPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 45

>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 = 35.7 bits (82), Expect = 6e-04
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 116 PRPPATSRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           P         EK +R  SA   F +++ ++++   P++S  E     A+ W
Sbjct: 9   PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMW 59

>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 = 34.9 bits (80), Expect = 0.001
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 5/56 (8%)

Query: 116 PRPPATS-----RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           PR P        + P   +R  SAY  F  +    +++ NPDI+  +      + W
Sbjct: 4   PREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

>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 = 34.4 bits (79), Expect = 0.001
 Identities = 11/37 (29%), Positives = 15/37 (40%)

Query: 130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 166
           R  SAY  ++    + IK  NP I   E      + W
Sbjct: 6   RPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELW 42

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	213
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.06
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	97.94
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	97.85
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	97.77
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.65
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	97.6
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.4
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.38
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	97.12
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	97.04
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	96.49
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	95.88

>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=98.06  E-value=4.5e-06  Score=58.91  Aligned_cols=48  Identities=23%  Similarity=0.367  Sum_probs=42.4

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          123 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       123 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      +.|.+..|-++||..|+++..++|++++|++++.|.-..++..|+..+
T Consensus        16 ~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls   63 (90)
T d1wgfa_          16 GGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLS   63 (90)
T ss_dssp             SCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            345555678899999999999999999999999999999999999753

>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=97.94  E-value=5.6e-06  Score=58.49  Aligned_cols=48  Identities=15%  Similarity=0.332  Sum_probs=44.3

Q ss_pred             CCCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       122 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      .|.|++-.|-+|+|..|+++....|++.+|+++..|.-+.++..|+..
T Consensus         5 kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~l   52 (91)
T d1k99a_           5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKEL   52 (91)
T ss_dssp             CSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCC
Confidence            466777788999999999999999999999999999999999999974

>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=97.85  E-value=1.1e-05  Score=57.56  Aligned_cols=49  Identities=22%  Similarity=0.452  Sum_probs=44.3

Q ss_pred             CCCCcccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          122 SRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       122 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|.|.+-.|-+|||..|+++....||+++|++++.|.-..++..|+..+
T Consensus        15 ~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls   63 (93)
T d1lwma_          15 KKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALT   63 (93)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSC
T ss_pred             CCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCC
Confidence            3566667788999999999999999999999999999999999999754

>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=97.77  E-value=8.3e-06  Score=56.37  Aligned_cols=41  Identities=24%  Similarity=0.410  Sum_probs=38.6

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       130 R~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |-+|||..|+++....||+++|++++.|.-+.++..|+..+
T Consensus         5 rP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls   45 (79)
T d1hsma_           5 RPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA   45 (79)
T ss_dssp             CCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSC
T ss_pred             CCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCC
Confidence            56899999999999999999999999999999999999864

>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=97.65  E-value=3.1e-05  Score=52.84  Aligned_cols=40  Identities=28%  Similarity=0.410  Sum_probs=37.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcc
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAH  168 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~  168 (213)
                      .|-+|||..|+++.-+.||++||++++.|.-+.++..|+.
T Consensus         5 KrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~   44 (73)
T d1qrva_           5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA   44 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcC
Confidence            4679999999999999999999999999999999999984

>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=97.60  E-value=4.4e-05  Score=51.48  Aligned_cols=42  Identities=19%  Similarity=0.365  Sum_probs=37.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCC--CCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPD--ISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~--i~HkEaFs~aAknW~~~P  170 (213)
                      .|-+|||..|+++.-++||++||+  +.+.|.-+.++..|+..+
T Consensus         3 KrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls   46 (71)
T d1ckta_           3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   46 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCC
Confidence            477899999999999999999996  667899999999999754

>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=97.40  E-value=0.00012  Score=51.33  Aligned_cols=44  Identities=14%  Similarity=0.342  Sum_probs=40.4

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          127 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       127 KRQR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |-.|-++||-.|+++.-++|++++|++++.|.=+.++..|+..+
T Consensus         2 kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~   45 (80)
T d1gt0d_           2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCC
Confidence            44678899999999999999999999999999999999999753

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

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

Probab=97.38  E-value=0.00012  Score=51.38  Aligned_cols=42  Identities=17%  Similarity=0.360  Sum_probs=39.3

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          129 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       129 QR~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      .|-+|||..|+++.-.+|+++||++++.|.=+.++..|+..+
T Consensus         6 KRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~   47 (85)
T d1j46a_           6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (85)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCC
Confidence            577899999999999999999999999999999999999753

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

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

Probab=97.12  E-value=0.00039  Score=47.03  Aligned_cols=40  Identities=23%  Similarity=0.388  Sum_probs=37.8

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       130 R~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |-+|||-.|+++.-++|++++|++++.|.=+.++..|+..
T Consensus         5 RP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~l   44 (70)
T d1i11a_           5 RPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAM   44 (70)
T ss_dssp             CSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTS
T ss_pred             CCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhC
Confidence            5689999999999999999999999999999999999975

>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=97.04  E-value=0.00037  Score=48.87  Aligned_cols=40  Identities=10%  Similarity=0.181  Sum_probs=37.4

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 028144          130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  169 (213)
Q Consensus       130 R~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  169 (213)
                      |-++||-.|+++.-++|+++||+++..|.=..++..|+..
T Consensus         5 RP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~l   44 (86)
T d2lefa_           5 KPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHAL   44 (86)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTS
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            4569999999999999999999999999999999999964

>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=96.49  E-value=0.0014  Score=47.33  Aligned_cols=37  Identities=14%  Similarity=0.407  Sum_probs=31.5

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       130 R~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |-++||..|+++..+.    .|+++.+|.+..+++.|+..+
T Consensus        20 ~P~~ay~lF~~~~r~~----~~~~~~~e~~k~ig~~W~~Ls   56 (108)
T d1v64a_          20 PPPNSYSLYCAELMAN----MKDVPSTERMVLCSQQWKLLS   56 (108)
T ss_dssp             CCSSHHHHHHHHHHHH----CTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCcHHHHHHHHHHHH----ccCCCHHHHHHHHHHHHccCC
Confidence            4579999999986654    578999999999999999864

>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=95.88  E-value=0.0038  Score=44.05  Aligned_cols=39  Identities=10%  Similarity=0.328  Sum_probs=33.8

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 028144          130 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  170 (213)
Q Consensus       130 R~psayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  170 (213)
                      |-++||..|+++.++.|+..+  ++.+|.-+.++..|+..+
T Consensus        11 rP~~ay~~F~~e~r~~~~~~~--~~~~ei~k~~g~~Wk~ls   49 (101)
T d1v63a_          11 PPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRIS   49 (101)
T ss_dssp             CCSSSHHHHHHHHHHHCTTTT--SCHHHHHHHHHHHHTTSC
T ss_pred             CCCCHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHhhCC
Confidence            457999999999999998766  468999999999999864