Citrus Sinensis ID: 034314

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTKPEEEEESEKSMSEVNDEDDDEEGSGEEDDDE
Secondary Structure (PSIPRED)
cHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
meefreqykkdhpknksVAAVGKAggekwksmseadkapyvaKAEKRKVEYEKDMKNYnrrqaegtkpeeeeeseksmsevndedddeegsgeeddde
Flexible Loop (DISEMBL)
MEEFREqykkdhpknksvaavgkaggekwksmseadkapyvakaekrkveyekdmknynrrqaegtkpeeeeeseksmsevndedddeegsgeeddde
Low Complexity Region (SEG)
MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTKPeeeeeseksmseVNdedddeegsgeeddde
Disordered region (IsUnstruct)
**************************************************************************************************
Disordered Region (DISOPRED)
***FREQ*KKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEK*********************************************
Disordered Region (DISEMBL)
*********************************EADKAPYVAKAEKRKVEYEKDMKNYNR**************************************
Disordered Region (DISPRO)
MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR*************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYxxxxxxxxxxxxxxxxxxxxxQAEGTKPEEEEESEKSMSEVNDEDDDEEGSGEEDDDE
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	98	2.2.26 [Sep-21-2011]
P93047	141	High mobility group B pro	yes	no	0.816	0.567	0.731	1e-26
O49596	144	High mobility group B pro	no	no	0.816	0.555	0.695	3e-25
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.877	0.597	0.625	1e-21
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.663	0.427	0.707	2e-21
O49595	178	High mobility group B pro	no	no	0.857	0.471	0.586	9e-20
Q42344	138	High mobility group B pro	no	no	0.948	0.673	0.525	3e-19
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.806	0.530	0.634	1e-18
P27347	157	DNA-binding protein MNB1B	N/A	no	0.683	0.426	0.611	4e-17
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.612	0.372	0.666	4e-16
O49597	125	High mobility group B pro	no	no	0.765	0.6	0.413	2e-12

>sp|P93047|HMGB3_ARATH High mobility group B protein 3 OS=Arabidopsis thaliana GN=HMGB3 PE=1 SV=1

 Score =  118 bits (295), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 75/82 (91%), Gaps = 2/82 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FR  YK++HPKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN+
Sbjct: 46  MEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNK 105

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           +  EG  P+E+EES+KS+SEVN
Sbjct: 106 KLEEG--PKEDEESDKSVSEVN 125

Binds preferentially double-stranded DNA.
Arabidopsis thaliana (taxid: 3702)

>sp|O49596|HMGB2_ARATH High mobility group B protein 2 OS=Arabidopsis thaliana GN=HMGB2 PE=1 SV=1

 Score =  113 bits (283), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 57/82 (69%), Positives = 74/82 (90%), Gaps = 2/82 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FRE +KK++PKNKSVA VGKA G+KWKS+S+++KAPYVAKAEKRKVEYEK++K YN+
Sbjct: 49  MEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYNK 108

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           +  EG  P+E+EES+KS+SEVN
Sbjct: 109 KLEEG--PKEDEESDKSVSEVN 128

Binds preferentially double-stranded DNA. Confers sensitivity to salt and drought stresses.

Arabidopsis thaliana (taxid: 3702)

>sp|P40619|HMGL_IPONI HMG1/2-like protein OS=Ipomoea nil PE=2 SV=1

 Score =  101 bits (251), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 55/88 (62%), Positives = 74/88 (84%), Gaps = 2/88 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FR+ YK+ HP NKSVA VGKAGG+KWK ++ A+KAP+++KAEKRK EYEK+++ YN+
Sbjct: 47  MEDFRKTYKEKHPNNKSVAVVGKAGGDKWKQLTAAEKAPFISKAEKRKQEYEKNLQAYNK 106

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDE 88
           +QA G    EEEES+KS SEVND+D+D+
Sbjct: 107 KQAAGA--AEEEESDKSRSEVNDDDEDQ 132

Ipomoea nil (taxid: 35883)

>sp|P26585|HMGL_SOYBN HMG1/2-like protein OS=Glycine max PE=2 SV=1

 Score =  100 bits (249), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 46/65 (70%), Positives = 60/65 (92%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           MEEFR+ + K+HP+NK+V+AVGKA G KWK+MS+A+KAPYVAK+EKRKVEYEK+M+ YN+
Sbjct: 55  MEEFRKVFNKEHPENKAVSAVGKAAGAKWKTMSDAEKAPYVAKSEKRKVEYEKNMRAYNK 114

Query: 61  RQAEG 65
           +QAEG
Sbjct: 115 KQAEG 119

Glycine max (taxid: 3847)

>sp|O49595|HMGB1_ARATH High mobility group B protein 1 OS=Arabidopsis thaliana GN=HMGB1 PE=1 SV=1

 Score = 95.5 bits (236), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 54/92 (58%), Positives = 68/92 (73%), Gaps = 8/92 (8%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           +E+FR  +KK++P  K+V+AVGKAGG+KWKSMS+A+KAPY  KA KRK EYEK M  YN+
Sbjct: 64  LEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKQMDAYNK 123

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDEEGSG 92
              EG+     +ESEKS SE+NDED   E SG
Sbjct: 124 NLEEGS-----DESEKSRSEINDED---EASG 147

Binds preferentially double-stranded DNA. Modulates general plant growth and stress tolerance. Confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses.

Arabidopsis thaliana (taxid: 3702)

>sp|Q42344|HMGB4_ARATH High mobility group B protein 4 OS=Arabidopsis thaliana GN=HMGB4 PE=1 SV=1

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 51/97 (52%), Positives = 71/97 (73%), Gaps = 4/97 (4%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           +E+FR+++   +P NKSVA VGKA G +WK+M++ DKAPYVAKAE RK EY K+++ YN 
Sbjct: 46  LEDFRKEFNLANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYNL 105

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDEEGSGEEDDD 97
           + A GT   EE++S+KS SEV++   +EE    EDDD
Sbjct: 106 KLASGTN-REEDDSDKSKSEVDEAVSEEEA---EDDD 138

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 52/82 (63%), Positives = 65/82 (79%), Gaps = 3/82 (3%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           M +FREQYKKDHP NKSVAAVGKA GE+WKS+SE +KAPYV +A K+K EYE  ++ YN+
Sbjct: 56  MADFREQYKKDHPNNKSVAAVGKACGEEWKSLSEEEKAPYVDRALKKKEEYEITLQAYNK 115

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           +  EG   ++EE S+KS SEVN
Sbjct: 116 K-LEGK--DDEEGSDKSKSEVN 134

Vicia faba (taxid: 3906)

>sp|P27347|MNB1B_MAIZE DNA-binding protein MNB1B OS=Zea mays GN=MNB1B PE=1 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 41/67 (61%), Positives = 55/67 (82%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           MEEFR+++K+ +PKNKSVAAVGKA G++WKS+SE+DKAPYVAKA K K+EY K +  YN+
Sbjct: 52  MEEFRKEFKEKNPKNKSVAAVGKAAGDRWKSLSESDKAPYVAKANKLKLEYNKAIAAYNK 111

Query: 61  RQAEGTK 67
            ++   K
Sbjct: 112 GESTAAK 118

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

>sp|P40621|HMGL_WHEAT HMG1/2-like protein OS=Triticum aestivum PE=2 SV=1

 Score = 83.2 bits (204), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 50/60 (83%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           M EFRE++K+ +PKNKSVAAVGKA GE+WKS+SE++KAPYVAKA K K EY K +  YN+
Sbjct: 53  MGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSESEKAPYVAKANKLKGEYNKAIAAYNK 112

Triticum aestivum (taxid: 4565)

>sp|O49597|HMGB5_ARATH High mobility group B protein 5 OS=Arabidopsis thaliana GN=HMGB5 PE=2 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 52/75 (69%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           +++FR+++   +P NKSV  VG+A G+KWK+M+E ++AP+VAK++ +K EY   M+ YN 
Sbjct: 45  LDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTEEERAPFVAKSQSKKTEYAVTMQQYNM 104

Query: 61  RQAEGTKPEEEEESE 75
             A G K   ++E +
Sbjct: 105 ELANGNKTTGDDEKQ 119

Binds preferentially double-stranded DNA. Confers resistance to salt and drought stresses.

Arabidopsis thaliana (taxid: 3702)

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	98
297845042	141	hypothetical protein ARALYDRAFT_472304 [	0.908	0.631	0.758	8e-30
308569660	142	high mobility group box 1 protein [Gossy	0.826	0.570	0.841	1e-29
145323962	140	high mobility group B3 protein [Arabidop	0.908	0.635	0.736	1e-28
79318286	142	high mobility group B2 protein [Arabidop	0.959	0.661	0.711	1e-28
225457566	153	PREDICTED: high mobility group-like isof	0.836	0.535	0.807	2e-28
8886929	662	F2D10.18 [Arabidopsis thaliana]	0.908	0.134	0.703	2e-27
359476973	156	PREDICTED: high mobility group B2 protei	0.836	0.525	0.731	2e-25
296088654	154	unnamed protein product [Vitis vinifera]	0.836	0.532	0.731	2e-25
312281681	144	unnamed protein product [Thellungiella h	0.816	0.555	0.731	2e-25
18394900	141	high mobility group B3 protein [Arabidop	0.816	0.567	0.731	5e-25

>gi|297845042|ref|XP_002890402.1| hypothetical protein ARALYDRAFT_472304 [Arabidopsis lyrata subsp. lyrata] gi|297336244|gb|EFH66661.1| hypothetical protein ARALYDRAFT_472304 [Arabidopsis lyrata subsp. lyrata]

 Score =  134 bits (336), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 69/91 (75%), Positives = 84/91 (92%), Gaps = 2/91 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FRE YKK+HPKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN+
Sbjct: 48  MEDFRETYKKEHPKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNK 107

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDEEGS 91
           +  EG  P+E+EES+KS+SEVNDEDD E+GS
Sbjct: 108 KLEEG--PKEDEESDKSVSEVNDEDDAEDGS 136

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|308569660|gb|ADO34795.1| high mobility group box 1 protein [Gossypium hirsutum]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 69/82 (84%), Positives = 78/82 (95%), Gaps = 1/82 (1%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           MEEFREQYKKDHPKNKSVAAVGKAGG+KWKS+SEA+KAPYVAKAEKRKVEYEK+MK YN+
Sbjct: 46  MEEFREQYKKDHPKNKSVAAVGKAGGDKWKSLSEAEKAPYVAKAEKRKVEYEKNMKAYNK 105

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           RQAEG K +E+ ES+KS+SEVN
Sbjct: 106 RQAEGPK-DEDVESDKSVSEVN 126

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145323962|ref|NP_001077570.1| high mobility group B3 protein [Arabidopsis thaliana] gi|332191890|gb|AEE30011.1| high mobility group B3 protein [Arabidopsis thaliana]

 Score =  130 bits (327), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 67/91 (73%), Positives = 83/91 (91%), Gaps = 2/91 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FR  YK++HPKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN+
Sbjct: 46  MEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNK 105

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDEEGS 91
           +  EG  P+E+EES+KS+SEVNDEDD E+GS
Sbjct: 106 KLEEG--PKEDEESDKSVSEVNDEDDAEDGS 134

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79318286|ref|NP_001031074.1| high mobility group B2 protein [Arabidopsis thaliana] gi|297845040|ref|XP_002890401.1| hypothetical protein ARALYDRAFT_472301 [Arabidopsis lyrata subsp. lyrata] gi|297336243|gb|EFH66660.1| hypothetical protein ARALYDRAFT_472301 [Arabidopsis lyrata subsp. lyrata] gi|332191886|gb|AEE30007.1| high mobility group B2 protein [Arabidopsis thaliana]

 Score =  130 bits (326), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 69/97 (71%), Positives = 87/97 (89%), Gaps = 3/97 (3%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FRE +KK++PKNKSVA VGKA G+KWKS+S+++KAPYVAKAEKRKVEYEK++K YN+
Sbjct: 49  MEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYNK 108

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDEEGSGEEDDD 97
           +  EG  P+E+EES+KS+SEVNDEDD E+GS EEDDD
Sbjct: 109 KLEEG--PKEDEESDKSVSEVNDEDDAEDGS-EEDDD 142

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457566|ref|XP_002272299.1| PREDICTED: high mobility group-like isoform 1 [Vitis vinifera] gi|359491843|ref|XP_003634333.1| PREDICTED: high mobility group-like isoform 2 [Vitis vinifera] gi|297745562|emb|CBI40727.3| unnamed protein product [Vitis vinifera]

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 67/83 (80%), Positives = 77/83 (92%), Gaps = 1/83 (1%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           MEEFR+QYK+ HP NKSV+ VGKAGG+KWKSMSEA+KAPYVAKAEKRKVEYEK+MK YN+
Sbjct: 55  MEEFRKQYKEKHPSNKSVSVVGKAGGDKWKSMSEAEKAPYVAKAEKRKVEYEKNMKAYNK 114

Query: 61  RQAEGTK-PEEEEESEKSMSEVN 82
           +QAEGTK  EEE+ESEKS+SEVN
Sbjct: 115 KQAEGTKVVEEEDESEKSLSEVN 137

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8886929|gb|AAF80615.1|AC069251_8 F2D10.18 [Arabidopsis thaliana]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/91 (70%), Positives = 82/91 (90%), Gaps = 2/91 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FRE +KK++PKNKSVA VGKA G+KWKS+S+++KAPYVAKAEKRKVEYEK++K YN+
Sbjct: 426 MEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYNK 485

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDEEGS 91
           +  EG  P+E+EES+KS+SEVNDEDD E+GS
Sbjct: 486 KLEEG--PKEDEESDKSVSEVNDEDDAEDGS 514

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359476973|ref|XP_002280084.2| PREDICTED: high mobility group B2 protein-like isoform 1 [Vitis vinifera]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 69/82 (84%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           MEEFR+QYK+ HP NKSV+ VGKAGG+KWKS+SEA+KAPYVAKAEKRK EY K M+ YN+
Sbjct: 58  MEEFRKQYKEKHPANKSVSVVGKAGGDKWKSLSEAEKAPYVAKAEKRKTEYNKSMQAYNK 117

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           R AEG    EEEES+KS SEVN
Sbjct: 118 RMAEGPTAAEEEESDKSRSEVN 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088654|emb|CBI37645.3| unnamed protein product [Vitis vinifera]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 69/82 (84%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           MEEFR+QYK+ HP NKSV+ VGKAGG+KWKS+SEA+KAPYVAKAEKRK EY K M+ YN+
Sbjct: 56  MEEFRKQYKEKHPANKSVSVVGKAGGDKWKSLSEAEKAPYVAKAEKRKTEYNKSMQAYNK 115

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           R AEG    EEEES+KS SEVN
Sbjct: 116 RMAEGPTAAEEEESDKSRSEVN 137

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312281681|dbj|BAJ33706.1| unnamed protein product [Thellungiella halophila]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 75/82 (91%), Gaps = 2/82 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FRE +KK+HPKNKSVAAVGKA G+KWKS+S+A+KAPYVAKAEKRKV+YEK+MK YN+
Sbjct: 49  MEDFRETFKKEHPKNKSVAAVGKAAGDKWKSLSDAEKAPYVAKAEKRKVDYEKNMKAYNK 108

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           +  EG  P+E+EES+KS+SEVN
Sbjct: 109 KLEEG--PKEDEESDKSVSEVN 128

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18394900|ref|NP_564124.1| high mobility group B3 protein [Arabidopsis thaliana] gi|75220405|sp|P93047.1|HMGB3_ARATH RecName: Full=High mobility group B protein 3; AltName: Full=High mobility group protein B 2; Short=AtHMGbeta2; Short=HMG beta 2; AltName: Full=Nucleosome/chromatin assembly factor group D 03; Short=Nucleosome/chromatin assembly factor group D 3 gi|15724174|gb|AAL06479.1|AF411789_1 At1g20690/F2D10_15 [Arabidopsis thaliana] gi|1694976|emb|CAA70691.1| HMG1 [Arabidopsis thaliana] gi|2832361|emb|CAA74402.1| HMG protein [Arabidopsis thaliana] gi|20453325|gb|AAM19901.1| At1g20690/F2D10_15 [Arabidopsis thaliana] gi|21537072|gb|AAM61413.1| unknown [Arabidopsis thaliana] gi|22530942|gb|AAM96975.1| expressed protein [Arabidopsis thaliana] gi|23198424|gb|AAN15739.1| expressed protein [Arabidopsis thaliana] gi|332191888|gb|AEE30009.1| high mobility group B3 protein [Arabidopsis thaliana]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 60/82 (73%), Positives = 75/82 (91%), Gaps = 2/82 (2%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           ME+FR  YK++HPKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN+
Sbjct: 46  MEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNK 105

Query: 61  RQAEGTKPEEEEESEKSMSEVN 82
           +  EG  P+E+EES+KS+SEVN
Sbjct: 106 KLEEG--PKEDEESDKSVSEVN 125

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	98
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.683	0.465	0.701	1.6e-22
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.673	0.478	0.560	8.6e-17
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.683	0.536	0.447	1e-13
MGI|MGI:1098219	200	Hmgb3 "high mobility group box	0.653	0.32	0.409	3.3e-08
UNIPROTKB|F1RQ19	202	LOC100517745 "Uncharacterized	0.653	0.316	0.393	3.3e-08
RGD|1564407	200	Hmgb3 "high mobility group box	0.653	0.32	0.393	4.2e-08
UNIPROTKB|Q32L31	200	HMGB3 "High mobility group pro	0.653	0.32	0.393	4.2e-08
UNIPROTKB|E7EQU1	193	HMGB3 "High mobility group pro	0.653	0.331	0.378	4.2e-08
UNIPROTKB|E7ES08	188	HMGB3 "High mobility group pro	0.653	0.340	0.378	4.2e-08
UNIPROTKB|O15347	200	HMGB3 "High mobility group pro	0.653	0.32	0.378	4.2e-08

TAIR|locus:505006135 HMGB2 "high mobility group B2" [Arabidopsis thaliana (taxid:3702)]

 Score = 261 (96.9 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 47/67 (70%), Positives = 60/67 (89%)

Query:     1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
             ME+FRE +KK++PKNKSVA VGKA G+KWKS+S+++KAPYVAKAEKRKVEYEK++K YN+
Sbjct:    49 MEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYNK 108

Query:    61 RQAEGTK 67
             +  EG K
Sbjct:   109 KLEEGPK 115

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0000785 "chromatin" evidence=TAS

GO:0003682 "chromatin binding" evidence=TAS

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

GO:0030527 "structural constituent of chromatin" evidence=TAS

GO:0006096 "glycolysis" evidence=RCA

GO:0006833 "water transport" evidence=RCA

GO:0006972 "hyperosmotic response" evidence=RCA

GO:0007030 "Golgi organization" evidence=RCA

GO:0009266 "response to temperature stimulus" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0046686 "response to cadmium ion" evidence=RCA

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

TAIR|locus:2053893 HMGB4 "high mobility group B4" [Arabidopsis thaliana (taxid:3702)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 37/66 (56%), Positives = 51/66 (77%)

Query:     1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
             +E+FR+++   +P NKSVA VGKA G +WK+M++ DKAPYVAKAE RK EY K+++ YN 
Sbjct:    46 LEDFRKEFNLANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYNL 105

Query:    61 RQAEGT 66
             + A GT
Sbjct:   106 KLASGT 111

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0000785 "chromatin" evidence=TAS

GO:0003682 "chromatin binding" evidence=TAS

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

GO:0030527 "structural constituent of chromatin" evidence=TAS

GO:0005737 "cytoplasm" evidence=IDA

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

GO:0006342 "chromatin silencing" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0008283 "cell proliferation" evidence=RCA

GO:0016572 "histone phosphorylation" evidence=RCA

GO:0051567 "histone H3-K9 methylation" evidence=RCA

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

TAIR|locus:2128003 HMGB5 "high mobility group B5" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 30/67 (44%), Positives = 48/67 (71%)

Query:     1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
             +++FR+++   +P NKSV  VG+A G+KWK+M+E ++AP+VAK++ +K EY   M+ YN 
Sbjct:    45 LDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTEEERAPFVAKSQSKKTEYAVTMQQYNM 104

Query:    61 RQAEGTK 67
               A G K
Sbjct:   105 ELANGNK 111

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0000785 "chromatin" evidence=TAS

GO:0003682 "chromatin binding" evidence=TAS

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

GO:0030527 "structural constituent of chromatin" evidence=TAS

GO:0005737 "cytoplasm" evidence=IDA

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

MGI|MGI:1098219 Hmgb3 "high mobility group box 3" [Mus musculus (taxid:10090)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 27/66 (40%), Positives = 40/66 (60%)

Query:     3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR- 61
             EFR + K  +P   S+  V K  GE W ++S+ +K PYV KA K K +YEKD+ +Y  + 
Sbjct:   106 EFRPKIKSTNP-GISIGDVAKKLGEMWNNLSDNEKQPYVTKAAKLKEKYEKDVADYKSKG 164

Query:    62 QAEGTK 67
             + +G K
Sbjct:   165 KFDGAK 170

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005694 "chromosome" evidence=IEA

GO:0045578 "negative regulation of B cell differentiation" evidence=IDA

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=IDA

UNIPROTKB|F1RQ19 LOC100517745 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 26/66 (39%), Positives = 41/66 (62%)

Query:     3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR- 61
             EFR + K  +P   S+  V K  GE W ++S+++K PY+ KA K K +YEKD+ +Y  + 
Sbjct:   106 EFRPKIKSTNP-GISIGDVAKKLGEMWNNLSDSEKQPYINKAAKLKEKYEKDVADYKSKG 164

Query:    62 QAEGTK 67
             + +G K
Sbjct:   165 KFDGAK 170

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

RGD|1564407 Hmgb3 "high mobility group box 3" [Rattus norvegicus (taxid:10116)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 26/66 (39%), Positives = 41/66 (62%)

Query:     3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR- 61
             EFR + K  +P   S+  V K  GE W ++S+++K PY+ KA K K +YEKD+ +Y  + 
Sbjct:   106 EFRPKIKSANP-GISIGDVAKKLGEMWNNLSDSEKQPYMTKAAKLKEKYEKDVADYKSKG 164

Query:    62 QAEGTK 67
             + +G K
Sbjct:   165 KFDGAK 170

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0045578 "negative regulation of B cell differentiation" evidence=ISO

GO:0045638 "negative regulation of myeloid cell differentiation" evidence=ISO

UNIPROTKB|Q32L31 HMGB3 "High mobility group protein B3" [Bos taurus (taxid:9913)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 26/66 (39%), Positives = 41/66 (62%)

Query:     3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR- 61
             EFR + K  +P   S+  V K  GE W ++S+++K PY+ KA K K +YEKD+ +Y  + 
Sbjct:   106 EFRPKIKSANP-GISIGDVAKKLGEMWNNLSDSEKQPYINKAAKLKEKYEKDVADYKSKG 164

Query:    62 QAEGTK 67
             + +G K
Sbjct:   165 KFDGAK 170

GO:0003690 "double-stranded DNA binding" evidence=IDA

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

GO:0006310 "DNA recombination" evidence=IDA

GO:0005694 "chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E7EQU1 HMGB3 "High mobility group protein B3" [Homo sapiens (taxid:9606)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR- 61
             EFR + K  +P   S+  V K  GE W ++++++K PY+ KA K K +YEKD+ +Y  + 
Sbjct:   106 EFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYKSKG 164

Query:    62 QAEGTK 67
             + +G K
Sbjct:   165 KFDGAK 170

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E7ES08 HMGB3 "High mobility group protein B3" [Homo sapiens (taxid:9606)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR- 61
             EFR + K  +P   S+  V K  GE W ++++++K PY+ KA K K +YEKD+ +Y  + 
Sbjct:   106 EFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYKSKG 164

Query:    62 QAEGTK 67
             + +G K
Sbjct:   165 KFDGAK 170

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|O15347 HMGB3 "High mobility group protein B3" [Homo sapiens (taxid:9606)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR- 61
             EFR + K  +P   S+  V K  GE W ++++++K PY+ KA K K +YEKD+ +Y  + 
Sbjct:   106 EFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYKSKG 164

Query:    62 QAEGTK 67
             + +G K
Sbjct:   165 KFDGAK 170

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006310 "DNA recombination" evidence=ISS

GO:0003690 "double-stranded DNA binding" evidence=ISS

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

GO:0007275 "multicellular organismal development" evidence=TAS

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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)
P93047	HMGB3_ARATH	No assigned EC number	0.7317	0.8163	0.5673	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	98
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	2e-11
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	2e-09
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	1e-08
smart00398	70	smart00398, HMG, high mobility group	1e-07
PHA03237	424	PHA03237, PHA03237, envelope glycoprotein M; Provi	0.001

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

 Score = 54.2 bits (131), Expect = 2e-11
 Identities = 26/59 (44%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
           +E R + K ++P  K  A + K  GEKWK++SE +K PY  KAEK K  YEK    Y 
Sbjct: 12 SQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69

Length = 69

>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 = 48.8 bits (117), Expect = 2e-09
 Identities = 28/56 (50%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK 56
           +E R + KK++P + SV  V K  GEKWK +SE +K  Y  KAEK K  YEK+MK
Sbjct: 12 SQEQRPKLKKENP-DASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 66

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

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

 Score = 46.8 bits (112), Expect = 1e-08
 Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK 56
           +E R + K ++P   SV  + K  GE WKS+SE +K  Y  KAEK K  YEK+M 
Sbjct: 12 SQEHRAEVKAENP-GLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP 66

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

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

 Score = 44.2 bits (105), Expect = 1e-07
 Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
           +E R + K ++P     A + K  GE+WK +SE +KAPY  KA+K K  YE++M  Y 
Sbjct: 13 SQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

Length = 70

>gnl|CDD|223019 PHA03237, PHA03237, envelope glycoprotein M; Provisional

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 9/60 (15%)

Query: 48  KVEYEKD-MKNY-NRRQAEGTKPEEEEESEKSMSEVND-EDDDEE------GSGEEDDDE 98
           +V+  +  +K Y NR +    +P+   E E+ +    D E DDEE       S  E +  
Sbjct: 364 RVKTVQQKVKRYLNRVRGGRRRPKSLVEDERGLLLTEDSETDDEEPIYDVVYSEFESEWY 423

Length = 424

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	98
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.68
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.66
PTZ00199	94	high mobility group protein; Provisional	99.66
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.59
smart00398	70	HMG high mobility group.	99.57
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.56
KOG0381	96	consensus HMG box-containing protein [General func	99.49
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.45
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.42
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.42
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.4
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	98.93
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	98.84
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	98.36
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.28
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.22
KOG2746	683	consensus HMG-box transcription factor Capicua and	97.29
COG5648	211	NHP6B Chromatin-associated proteins containing the	97.07
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	95.9
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	95.85
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	94.37
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	93.21
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	84.75
PF05494	170	Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro:	82.82
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	80.86

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

Probab=99.68  E-value=7.8e-17  Score=100.40  Aligned_cols=58  Identities=29%  Similarity=0.468  Sum_probs=56.3

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |+++|+.|+.+||+ +++++|+++||.+|+.||+++|++|.++|..++.+|.+++++|+
T Consensus        13 ~~~~r~~~~~~~p~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388          13 SKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            57899999999999 99999999999999999999999999999999999999999986

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.

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

Probab=99.66  E-value=2.6e-16  Score=99.05  Aligned_cols=61  Identities=23%  Similarity=0.343  Sum_probs=58.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|..|+.+||+ +++++||++||.+|+.||+++|.+|.++|..++.+|.+++++|+-..
T Consensus        13 ~~~~r~~~~~~~p~-~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p   73 (77)
T cd01389          13 RQDKHAQLKTENPG-LTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTP   73 (77)
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccC
Confidence            57899999999999 99999999999999999999999999999999999999999997653

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=99.66  E-value=4.3e-16  Score=102.27  Aligned_cols=58  Identities=45%  Similarity=0.731  Sum_probs=55.5

Q ss_pred             ChHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s--~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |+++|..|+.+||+ ++  +++|+++||++|++||+++|.+|+.+|..++.+|..+|..|+
T Consensus        34 ~~~~R~~i~~~~P~-~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~   93 (94)
T PTZ00199         34 AKEKRAEIIAENPE-LAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA   93 (94)
T ss_pred             HHHHHHHHHHHCcC-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            57899999999999 65  899999999999999999999999999999999999999995

>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin

Probab=99.59  E-value=6.3e-15  Score=89.69  Aligned_cols=58  Identities=38%  Similarity=0.649  Sum_probs=56.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |+++|..|+..||+ +++++|+++||.+|++||+++|.+|...|...+.+|..+|+.|+
T Consensus        12 ~~~~~~~~k~~~p~-~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen   12 CKEKRAKLKEENPD-LSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             HHHHHHHHHHHSTT-STHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc-cccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            56889999999999 99999999999999999999999999999999999999999996

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=99.57  E-value=1.1e-14  Score=88.02  Aligned_cols=58  Identities=43%  Similarity=0.700  Sum_probs=55.8

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |+++|..++.+||+ +++++|+++||.+|+.||+++|.+|.++|..++.+|...++.|+
T Consensus        13 ~~~~r~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398       13 SQENRAKIKAENPD-LSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             HHHHHHHHHHHCcC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            57899999999999 99999999999999999999999999999999999999999884

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

Probab=99.56  E-value=1.4e-14  Score=87.32  Aligned_cols=54  Identities=50%  Similarity=0.724  Sum_probs=52.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDM   55 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~   55 (98)
                      |+++|..++..||+ +++++|+++||.+|++||+++|.+|.++|..++.+|..+|
T Consensus        12 ~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390          12 SQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             HHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            57899999999999 9999999999999999999999999999999999999876

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.

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

Probab=99.49  E-value=1.4e-13  Score=89.06  Aligned_cols=61  Identities=41%  Similarity=0.644  Sum_probs=57.5

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHH-HHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK-NYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~-~Y~~~~   62 (98)
                      |++.|..++.+||+ +++.+|+++||++|++|++++|.+|+..|..++.+|..+|. .|+...
T Consensus        34 ~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~   95 (96)
T KOG0381|consen   34 SSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             HHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            46789999999999 99999999999999999999999999999999999999999 888754

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

Probab=99.45  E-value=3.6e-13  Score=83.99  Aligned_cols=58  Identities=41%  Similarity=0.713  Sum_probs=51.5

Q ss_pred             ChHHHHHHHHh-CCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKD-HPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~e-nP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |++++..++.. +|. .++.++++.||.+|++||+++|.+|+++|..++.+|..+|..|+
T Consensus        15 ~~~~~~~~k~~G~~~-~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen   15 MKEMRKEVKEEGGQK-QSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             HHHHHHHHHHHT-T--SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHhcccC-CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            56889999999 777 88999999999999999999999999999999999999999985

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 ....

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

Probab=99.42  E-value=6.8e-13  Score=79.32  Aligned_cols=54  Identities=46%  Similarity=0.685  Sum_probs=51.6

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDM   55 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~   55 (98)
                      |+++|..++..||+ +++.+|+++||.+|+.|++++|.+|.++|...+.+|...+
T Consensus        12 ~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084          12 SQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             HHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            57899999999999 9999999999999999999999999999999999999875

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

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

Probab=99.42  E-value=5.9e-13  Score=98.72  Aligned_cols=66  Identities=29%  Similarity=0.626  Sum_probs=63.9

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK   67 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~~   67 (98)
                      ++.+|.+|+..||. ++|++|+++||++|++||+++|.+|...|..++++|++++..|..+.+++.+
T Consensus        82 ~~~~R~ei~~~~p~-l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~~  147 (211)
T COG5648          82 SAENRDEIRKENPK-LTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAP  147 (211)
T ss_pred             HHHHHHHHHHhCCC-CChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCCC
Confidence            46899999999999 8999999999999999999999999999999999999999999999999988

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.40  E-value=3e-13  Score=106.16  Aligned_cols=59  Identities=31%  Similarity=0.561  Sum_probs=56.2

Q ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         2 qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      +..|.+|..+||. +.++||||.||.+||.|++++|.||.+.|+++|+.|++++++|+-+
T Consensus        75 q~~RRkma~qnP~-mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYR  133 (331)
T KOG0527|consen   75 QGQRRKLAKQNPK-MHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYR  133 (331)
T ss_pred             HHHHHHHHHhCcc-hhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccc
Confidence            5789999999999 9999999999999999999999999999999999999999998644

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

Probab=98.93  E-value=1.1e-09  Score=86.08  Aligned_cols=62  Identities=27%  Similarity=0.500  Sum_probs=58.0

Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCC
Q 034314            3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEG   65 (98)
Q Consensus         3 e~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~   65 (98)
                      .+|.+|++.||. +...+|+|+||.+|..|++++|+.|...+...|..|.+.|+.|.......
T Consensus        78 kvWd~VkA~nPe-~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~  139 (410)
T KOG4715|consen   78 KVWDQVKASNPE-LKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYL  139 (410)
T ss_pred             hhhhhhhccCcc-hHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHH
Confidence            478999999999 99999999999999999999999999999999999999999998776543

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

Probab=98.84  E-value=4e-09  Score=87.24  Aligned_cols=56  Identities=45%  Similarity=0.633  Sum_probs=51.8

Q ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         2 qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      +.-|..||..  + +++++|+|.+|++|+.|+.  |.+|+.+|+.+|.||..+|+.|+...
T Consensus       548 ~~~r~~ik~d--g-i~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk~g~  603 (615)
T KOG0526|consen  548 NASRESIKED--G-ISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYKNGQ  603 (615)
T ss_pred             HhhhhhHhhc--C-chHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhcCCC
Confidence            5678899988  7 8999999999999999999  99999999999999999999999444

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=98.36  E-value=4.4e-07  Score=72.08  Aligned_cols=65  Identities=23%  Similarity=0.376  Sum_probs=58.7

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      |.++|..|.++.-- .-..+|.++||.+|..||-+|..+|.++|+++|.-|...++.|-++-..+.
T Consensus       203 MKEmRa~vvaEctl-KeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYgK  267 (421)
T KOG3248|consen  203 MKEMRAKVVAECTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGK  267 (421)
T ss_pred             HHHHHHHHHHHhhh-hhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhh
Confidence            67899999999965 678999999999999999999999999999999999999999977766653

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

Probab=98.28  E-value=2.4e-07  Score=75.92  Aligned_cols=64  Identities=19%  Similarity=0.361  Sum_probs=57.7

Q ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314            2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus         2 qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      ++-|..|...+|+ +.+..|||+||-+|+.||..+|+||.+.-.++-..|...++.|+-+..++-
T Consensus       338 kDERRKILqA~PD-MHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPRPKR  401 (511)
T KOG0528|consen  338 KDERRKILQAFPD-MHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPRPKR  401 (511)
T ss_pred             chhhhhhhhcCcc-ccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCCCCc
Confidence            4668899999999 999999999999999999999999999999998899999999987765543

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

Probab=98.22  E-value=7.7e-06  Score=52.83  Aligned_cols=63  Identities=19%  Similarity=0.364  Sum_probs=52.3

Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCCC
Q 034314            3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK   67 (98)
Q Consensus         3 e~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~~   67 (98)
                      ..+..+.+.+|+ -+..+ -+.+...|++|+..+|-+|+..|.++..+|..+|..|+...+..+.
T Consensus        17 ~vi~dYla~~~~-dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~~~~   79 (85)
T PF14887_consen   17 SVIGDYLAKFRN-DRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPADANS   79 (85)
T ss_dssp             HHHHHHHHHTTS-THHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCTTTT
T ss_pred             HHHHHHHHHhhH-hHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence            344556778888 56666 4599999999999999999999999999999999999988777654

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

Probab=97.29  E-value=0.0002  Score=60.83  Aligned_cols=52  Identities=23%  Similarity=0.326  Sum_probs=47.9

Q ss_pred             hHHH--HHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHH
Q 034314            2 EEFR--EQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKD   54 (98)
Q Consensus         2 qe~R--~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e   54 (98)
                      +.+|  ..++..||+ ..+.-|++|||+.|-+|.+.||+.|.++|...|..|.+.
T Consensus       194 krhr~~g~vhq~~pn-~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  194 KRHRGEGRVHQRHPN-QDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             hhcCCccchhccCcc-ccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            4566  778899999 999999999999999999999999999999999999875

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

Probab=97.07  E-value=0.00039  Score=52.00  Aligned_cols=54  Identities=24%  Similarity=0.403  Sum_probs=49.0

Q ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHH
Q 034314            2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK   56 (98)
Q Consensus         2 qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~   56 (98)
                      +.+|+++...+|. .+..++++++|..|+.|++.-|.+|.+.++.++..|...|+
T Consensus       156 ~~~r~~~~~~~~~-~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         156 PKIRPKVEGPSPD-KALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             HHhccccCCCCcc-hhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            4577888888898 88999999999999999999999999999999999987765

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

Probab=95.90  E-value=0.017  Score=34.93  Aligned_cols=31  Identities=19%  Similarity=0.367  Sum_probs=27.7

Q ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCC
Q 034314            2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS   33 (98)
Q Consensus         2 qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls   33 (98)
                      +-.||.|.+.||+ +..+-|..+++.+||.-+
T Consensus        21 q~vRP~l~~~NPk-~~~sKl~~l~~AKwrEF~   51 (55)
T PF08073_consen   21 QHVRPLLAKANPK-APMSKLMMLLQAKWREFQ   51 (55)
T ss_pred             HHHHHHHHHHCCC-CcHHHHHHHHHHHHHHHH
Confidence            4579999999999 899999999999998643

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

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

Probab=95.85  E-value=0.019  Score=42.17  Aligned_cols=42  Identities=24%  Similarity=0.393  Sum_probs=37.4

Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHH
Q 034314            4 FREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK   46 (98)
Q Consensus         4 ~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~   46 (98)
                      +-..++..|.+ ++..++....+..|..||+.+|..|..++-.
T Consensus        89 FLReFRrkh~~-L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~  130 (183)
T PF06382_consen   89 FLREFRRKHCG-LSPQDLIQRAARAWCRLSEAEKNRYRRMAPS  130 (183)
T ss_pred             HHHHHHHHccC-CCHHHHHHHHHHHHHhCCHHHHHHHHhhcch
Confidence            45678889999 9999999999999999999999999997553

The function of this family is unknown.

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=94.37  E-value=0.11  Score=37.98  Aligned_cols=45  Identities=18%  Similarity=0.438  Sum_probs=39.8

Q ss_pred             CCHHHHHH-HHHHHhhcCChhHhhhhHHHHHH-HHHHHHHHHHHHhh
Q 034314           16 KSVAAVGK-AGGEKWKSMSEADKAPYVAKAEK-RKVEYEKDMKNYNR   60 (98)
Q Consensus        16 ~s~~eIsK-~ige~Wk~ls~eeK~~Ye~~A~~-dK~rY~~e~~~Y~~   60 (98)
                      +.|..|++ .||..|+.+|+++|+.|...... ....|-..+..|..
T Consensus        64 ~Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~  110 (198)
T TIGR03481        64 FDLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAG  110 (198)
T ss_pred             CCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            67888988 78999999999999999998777 88889999988864

The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.

>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional

Probab=93.21  E-value=0.29  Score=36.14  Aligned_cols=48  Identities=23%  Similarity=0.367  Sum_probs=40.5

Q ss_pred             CCCCCHHHHHH-HHHHHhhcCChhHhhhhHHHHHH-HHHHHHHHHHHHhhh
Q 034314           13 PKNKSVAAVGK-AGGEKWKSMSEADKAPYVAKAEK-RKVEYEKDMKNYNRR   61 (98)
Q Consensus        13 P~~~s~~eIsK-~ige~Wk~ls~eeK~~Ye~~A~~-dK~rY~~e~~~Y~~~   61 (98)
                      |. +.|..||+ .||..|+.+|+++|..|...... +..-|-..+..|...
T Consensus        66 p~-~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q  115 (211)
T PRK15117         66 PY-VQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQ  115 (211)
T ss_pred             cc-CCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence            66 68888887 67899999999999999998655 777899999999643

>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=84.75  E-value=1.4  Score=32.12  Aligned_cols=32  Identities=22%  Similarity=0.353  Sum_probs=28.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS   33 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls   33 (98)
                      |.+.-++||+.||+ ++-.|+-+..+..|...+
T Consensus       133 ~k~ei~rik~~~p~-ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  133 MKEEIQRIKAENPD-ISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             HHHHHHHHHhcCCC-CCHHHHHHHHHHhhhhCc
Confidence            34566889999999 999999999999998764

>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []

Probab=82.82  E-value=3.6  Score=28.73  Aligned_cols=47  Identities=19%  Similarity=0.391  Sum_probs=35.8

Q ss_pred             CCCCCHHHHHHH-HHHHhhcCChhHhhhhHHHHHH-HHHHHHHHHHHHhh
Q 034314           13 PKNKSVAAVGKA-GGEKWKSMSEADKAPYVAKAEK-RKVEYEKDMKNYNR   60 (98)
Q Consensus        13 P~~~s~~eIsK~-ige~Wk~ls~eeK~~Ye~~A~~-dK~rY~~e~~~Y~~   60 (98)
                      |. +.+..|++. ||.-|+.||++++..|...... ....|-..+..|..
T Consensus        36 ~~-~D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~   84 (170)
T PF05494_consen   36 PY-FDFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG   84 (170)
T ss_dssp             GG-B-HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred             Hh-CCHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            45 678888875 5678999999999999998655 67778888888874

Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.

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

Probab=80.86  E-value=2.6  Score=29.11  Aligned_cols=30  Identities=13%  Similarity=0.246  Sum_probs=26.7

Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHhhcCCh
Q 034314            4 FREQYKKDHPKNKSVAAVGKAGGEKWKSMSE   34 (98)
Q Consensus         4 ~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~   34 (98)
                      .-+.|+.+||| +..+.+--+|-..|..-++
T Consensus        87 ~Lp~lK~E~Pg-LrlsQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   87 RLPELKEENPG-LRLSQYKQMLWKEWQKSPE  116 (122)
T ss_pred             HhHHHHhhCCC-chHHHHHHHHHHHHhcCCC
Confidence            45899999999 9999999999999987654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	98
2yqi_A	81	Solution Structure Of The Second Hmg-Box Domain Fro		7e-06
1j3c_A	79	Solution Structure Of The C-Terminal Domain Of The		3e-04
1j3d_A	78	Solution Structure Of The C-Terminal Domain Of The		8e-04

>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High Mobility Group Protein B3 Length = 81

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
            EFR + K  +P   S+  V K  GE W ++++++K PY+ KA K K +YEKD+ +Y
Sbjct: 21 CSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADY 77

>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          E+R + K +HP   S+    K  GE W   S  DK PY  KA K K +YEKD+  Y
Sbjct: 22 EYRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAY 76

>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          E R + K +HP   S+    K  GE W   S  DK PY  KA K K +YEKD+  Y
Sbjct: 21 EHRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAY 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	98
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	5e-13
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	2e-12
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	7e-12
2lhj_A	97	High mobility group protein homolog NHP1; structur	1e-11
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	2e-11
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	2e-11
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	4e-11
1ckt_A	71	High mobility group 1 protein; high-mobility group	7e-11
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-10
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-10
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	2e-10
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	2e-10
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	3e-10
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	9e-10
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-06
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	7e-09
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-08
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	9e-06
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	2e-05
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	3e-05
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	3e-05
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	5e-04
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	5e-05
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-04
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	1e-04
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	2e-04
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	3e-04
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	5e-04
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	5e-04
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	5e-04
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	8e-04

>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 = 57.6 bits (140), Expect = 5e-13
 Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            E+R + K +HP   S+  V K  GE W + +  DK PY  KA K K +YEKD+  Y  
Sbjct: 18 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 76

Query: 61 R 61
          +
Sbjct: 77 K 77

>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 = 57.0 bits (138), Expect = 2e-12
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
          + E REQ +  HP +     + K  G +W  +  A+K  Y+ +AEK K +Y K++  Y +
Sbjct: 19 LNERREQIRTRHP-DLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQ 77

Query: 61 RQAEGTKPEEEEES 74
           +A     E    S
Sbjct: 78 SEAYKVCTESGPSS 91

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

 Score = 55.0 bits (133), Expect = 7e-12
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 1  MEEFREQYKKDHP-KNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
          ++  RE++KK HP  + + +   K   E+WK+MS  +K  +   A+  K  YE++MK Y 
Sbjct: 19 VQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYI 78

Query: 60 RRQAE 64
            + E
Sbjct: 79 PPKGE 83

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

 Score = 54.7 bits (132), Expect = 1e-11
 Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 1  MEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
           +E R +   ++P+  K VAA+GK  G  W ++S+ +K PY   +++ +V YE++   Y 
Sbjct: 34 AKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYA 93

Query: 60 RRQ 62
          +R+
Sbjct: 94 QRK 96

>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 = 54.2 bits (131), Expect = 2e-11
 Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            E R+  + ++P + +   VGK  GEKWK+++  +K PY AKA+  K  YE + + YN 
Sbjct: 32 ANENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA 90

Query: 61 RQA 63
            A
Sbjct: 91 TLA 93

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

 Score = 54.3 bits (131), Expect = 2e-11
 Identities = 17/74 (22%), Positives = 25/74 (33%), Gaps = 1/74 (1%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
             + +   K  +P N +   V K     W  + E  K  Y  K E  K EY K +  Y  
Sbjct: 29  FRDTQAAIKGQNP-NATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA 87

Query: 61  RQAEGTKPEEEEES 74
                +  +    S
Sbjct: 88  SLVSKSYTDSGPSS 101

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

 Score = 53.1 bits (128), Expect = 4e-11
 Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 1  MEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          ++  RE++KK +P+   + A   K   E+WK+MS  +K+ +   A+  KV Y+++MK+Y
Sbjct: 27 VQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY 85

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

 Score = 52.4 bits (126), Expect = 7e-11
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 1  MEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          ++  RE++KK HP    + +   K   E+WK+MS  +K  +   A+  K  YE++MK Y
Sbjct: 13 VQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71

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

 Score = 51.7 bits (124), Expect = 2e-10
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
          +++ R Q+  ++P   S+        E WK++SE +K  Y  KA K    Y   MK    
Sbjct: 19 VQDHRPQFLIENP-KTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIE 77

Query: 61 RQAEGTKPEEEEES 74
          ++++ +  +    S
Sbjct: 78 QESQMSLKDSGPSS 91

>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 = 53.5 bits (128), Expect = 2e-10
 Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
             E+R + K +HP   S+  V K  GE W + +  DK PY  KA K K +YEKD+  Y  
Sbjct: 113 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 171

Query: 61  R 61
           +
Sbjct: 172 K 172

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

 Score = 51.1 bits (123), Expect = 2e-10
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 3/59 (5%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
          + + RE  K+++P    V  + K GGE WK +   DK+ +   A K K  Y  +M+NY 
Sbjct: 15 LNDTRESIKRENP-GIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYK 70

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

 Score = 50.7 bits (122), Expect = 2e-10
 Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 3/59 (5%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
          +   RE  K+++P    V  V K GGE W++M   DK+ + AKA K K +Y++ +K + 
Sbjct: 15 LNSARESIKRENP-GIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFE 70

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

 Score = 51.3 bits (123), Expect = 3e-10
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            E R +Y K HP   S   + K   +K+K + E  K  Y+   ++ K E+E+++  +  
Sbjct: 22 FMEKRAKYAKLHP-EMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE 80

Query: 61 RQAEGTKPEEEEESEKSM 78
             +  +  ++ E     
Sbjct: 81 DHPDLIQNAKKLEHHHHH 98

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159

 Score = 51.4 bits (123), Expect = 9e-10
 Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
             E+R + K +HP   S+  V K  GE W + +  DK PY  KA K K +YEKD+  Y  
Sbjct: 100 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 158

Query: 61  R 61
           +
Sbjct: 159 K 159

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159

 Score = 42.5 bits (100), Expect = 2e-06
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ 62
          + R +   ++P     + + K  G +WK ++EA+K P+  +A+K +  + +   NY  R+
Sbjct: 18 DQRRKMALENP-RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRK 76

Query: 63 AEGTKPEEEEESEKSM 78
           E  K  ++  + K  
Sbjct: 77 GETKKKFKDPNAPKRP 92

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

 Score = 46.9 bits (112), Expect = 7e-09
 Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 5/58 (8%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          + E  ++ K D P+        K   E WK++S+++K  Y+  A++ +  Y  +MK++
Sbjct: 14 VAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66

>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 = 46.6 bits (111), Expect = 2e-08
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
           EE R Q +++ P   S + + +     W  +SE  KA Y A+    K + E+     +
Sbjct: 32 SEEKRRQLQEERP-ELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPSS 89

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Length = 82

 Score = 39.5 bits (93), Expect = 9e-06
 Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
            R   +++HP         K   + W  +   +K  Y   A++ K  + K    Y
Sbjct: 21 RHRSLVRQEHP-RLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGY 75

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

 Score = 38.0 bits (89), Expect = 2e-05
 Identities = 17/56 (30%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          + R++  + +P +   A + K  G+ WK+++ A+K P+V +AE+ +V++ +D  NY
Sbjct: 16 DERKRLAQQNP-DLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY 70

>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Length = 87

 Score = 38.2 bits (89), Expect = 3e-05
 Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKD 54
          ++R +Y + +P  K   A+    G++WK M   ++  Y  +A+    E ++ 
Sbjct: 31 KYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRL 81

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

 Score = 39.7 bits (92), Expect = 3e-05
 Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
           + E  ++ K D P+        K   E WK++S+++K  Y+  A++ +  Y  +MK++  
Sbjct: 126 VAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE 180

Query: 61  RQAEGTKPEEEEESEK 76
           +  E  + +    + K
Sbjct: 181 QMIEVGRKDLLRRTIK 196

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

 Score = 36.3 bits (83), Expect = 5e-04
 Identities = 9/88 (10%), Positives = 30/88 (34%), Gaps = 1/88 (1%)

Query: 1   MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            +E    +K  +P +     + +   ++W+ + ++ K  Y          Y++++  +  
Sbjct: 21  SKEQLPIFKAQNP-DAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKE 79

Query: 61  RQAEGTKPEEEEESEKSMSEVNDEDDDE 88
           +         E+E      +       +
Sbjct: 80  QLTPSQIMSLEKEIMDKHLKRKAMTKKK 107

>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Length = 76

 Score = 37.1 bits (87), Expect = 5e-05
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          + R +   ++P     + + K  G +WK ++EA+K P+  +A+K +  + +   NY
Sbjct: 18 DQRRKMALENP-RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNY 72

>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 = 38.3 bits (88), Expect = 1e-04
 Identities = 16/72 (22%), Positives = 34/72 (47%)

Query: 14  KNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTKPEEEEE 73
           K  S     K   E WK++S+++K  Y+  A++ +  Y  +MK++  +  E  + +    
Sbjct: 166 KGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRR 225

Query: 74  SEKSMSEVNDED 85
           + K   +   E+
Sbjct: 226 TIKKQRKYGAEE 237

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

 Score = 36.4 bits (85), Expect = 1e-04
 Identities = 14/56 (25%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
            R +  +  P +   A + K  G++WK + ++DK P++ +AE+ ++++  D  +Y
Sbjct: 16 IERRKIMEQSP-DMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDY 70

>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Length = 85

 Score = 36.0 bits (84), Expect = 2e-04
 Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          + R +   ++P+    + + K  G +WK ++EA+K P+  +A+K +  + +   NY
Sbjct: 18 DQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNY 72

>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Length = 86

 Score = 35.3 bits (82), Expect = 3e-04
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          M+E R     +    +S AA+ +  G +W ++S  ++A Y   A K +  + +    +
Sbjct: 14 MKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGW 70

>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} PDB: 2yul_A Length = 83

 Score = 34.9 bits (81), Expect = 5e-04
 Identities = 17/56 (30%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          + R++  + +P +   A + K  G+ WK+++ A+K P+V +AE+ +V++ +D  NY
Sbjct: 20 DERKRLAQQNP-DLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY 74

>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Length = 81

 Score = 34.9 bits (81), Expect = 5e-04
 Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          + R +  +  P +   + + K  G +WK+M+  +K PY  +  +   ++ +   +Y
Sbjct: 18 DERRKILQAFP-DMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY 72

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

 Score = 35.3 bits (81), Expect = 5e-04
 Identities = 10/73 (13%), Positives = 29/73 (39%)

Query: 4  FREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQA 63
           +E        +  +       G +W+ +S++ K  Y   AE+++ +Y+  +  + +  +
Sbjct: 20 SQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLS 79

Query: 64 EGTKPEEEEESEK 76
             +   +E    
Sbjct: 80 PQDRAAYKEYISN 92

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Length = 80

 Score = 34.1 bits (79), Expect = 8e-04
 Identities = 13/56 (23%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 3  EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
            R +  +++P     + + K  G +WK +SE +K P++ +A++ +  + K+  +Y
Sbjct: 16 GQRRKMAQENP-KMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDY 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	98
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.74
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.73
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.72
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.72
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.71
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.71
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.71
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.71
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.7
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.7
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.7
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.69
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.69
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.69
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.68
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.68
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.68
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.67
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.67
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.67
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.66
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.65
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.65
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.65
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.63
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.62
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.59
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.59
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.59
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.56
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.56
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.56
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.53
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.48
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.45
2cto_A	93	Novel protein; high mobility group box domain, hel	99.39
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.3
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.28
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.27
2qgu_A	211	Probable signal peptide protein; NESG, RSR89, Q8XV	86.71

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=99.74  E-value=5.3e-18  Score=104.82  Aligned_cols=59  Identities=34%  Similarity=0.661  Sum_probs=56.4

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++|++  |++|+++|..++++|..+|+.|++++
T Consensus        15 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~kg   73 (73)
T 3nm9_A           15 LNSARESIKRENPG-IKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEANG   73 (73)
T ss_dssp             HHHHHHHHHHHSSS-CCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            57899999999999 9999999999999999998  99999999999999999999999864

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

Probab=99.73  E-value=5.3e-18  Score=109.15  Aligned_cols=65  Identities=28%  Similarity=0.433  Sum_probs=61.1

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      |+++|..|+.+||+ +++++|+++||++|++|++++|++|.++|..++++|..+|+.|+..+....
T Consensus        19 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~~~~   83 (92)
T 2cs1_A           19 VQDHRPQFLIENPK-TSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMS   83 (92)
T ss_dssp             HHHHHHHHHHHCCS-SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTTCCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence            57899999999999 999999999999999999999999999999999999999999998765543

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

Probab=99.72  E-value=1.7e-17  Score=108.77  Aligned_cols=66  Identities=23%  Similarity=0.387  Sum_probs=63.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK   67 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~~   67 (98)
                      |+++|..|+.+||+ +++++|+++||++|++|++++|++|+++|..++++|..+|+.|+........
T Consensus        29 ~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~~   94 (102)
T 2co9_A           29 FRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSY   94 (102)
T ss_dssp             HHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            57899999999999 9999999999999999999999999999999999999999999999887765

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A

Probab=99.72  E-value=7e-18  Score=104.80  Aligned_cols=59  Identities=41%  Similarity=0.675  Sum_probs=56.9

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR   60 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~   60 (98)
                      |+++|..|+..||+ +++++|+++||++|++||+++|.+|.++|..++.+|..+|+.|+.
T Consensus        18 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A           18 CSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             HHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            57899999999999 999999999999999999999999999999999999999999975

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

Probab=99.71  E-value=2e-17  Score=106.43  Aligned_cols=65  Identities=31%  Similarity=0.540  Sum_probs=60.4

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      |+++|..|+.+||+ +++++|+++||++|++||+++|++|.++|..++++|..+|+.|+.+.....
T Consensus        19 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~   83 (92)
T 2crj_A           19 LNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKV   83 (92)
T ss_dssp             HHHHHHHHHHHCTT-CCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHH
Confidence            57899999999999 999999999999999999999999999999999999999999997654433

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

Probab=99.71  E-value=7.1e-18  Score=103.19  Aligned_cols=57  Identities=37%  Similarity=0.665  Sum_probs=54.0

Q ss_pred             ChHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY   58 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s--~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y   58 (98)
                      |+++|+.|+..||+ ++  |++|+++||++|++||+++|++|.++|..++++|..+|..|
T Consensus        13 ~~~~r~~~~~~~p~-~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A           13 VQTCREEHKKKHPD-ASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             HHHHHHHHHHHCTT-CCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHCCC-CCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            57899999999999 75  69999999999999999999999999999999999999877

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

Probab=99.71  E-value=2.6e-17  Score=104.65  Aligned_cols=58  Identities=34%  Similarity=0.641  Sum_probs=55.3

Q ss_pred             ChHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s--~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |+++|+.|+.+||+ ++  |++|+++||++|++||+++|++|+++|..++++|..+|+.|+
T Consensus        27 ~~~~r~~~k~~~p~-~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A           27 VQTCREEHKKKNPE-VPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             HHHHHHHHHHHCTT-SCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHCCC-CCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            57899999999999 65  799999999999999999999999999999999999999994

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

Probab=99.71  E-value=5.7e-18  Score=103.35  Aligned_cols=58  Identities=29%  Similarity=0.552  Sum_probs=53.6

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |+++|+.|+..||+ +++++|+++||++|++||+++|.+|.++|..++.+|..+|+.|+
T Consensus        14 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A           14 AKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             HHHHHHHHHTTCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            57899999999999 99999999999999999999999999999999999999999985

>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.70  E-value=1.7e-17  Score=105.31  Aligned_cols=64  Identities=23%  Similarity=0.383  Sum_probs=59.5

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEG   65 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~   65 (98)
                      |+++|+.|+.+||+ +++++||++||++|++||+++|++|.++|..++++|..+|+.|+.....+
T Consensus        14 ~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~~   77 (86)
T 2lef_A           14 MKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG   77 (86)
T ss_dssp             HHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTT
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCCC
Confidence            57899999999999 99999999999999999999999999999999999999999998654433

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

Probab=99.70  E-value=3.1e-17  Score=107.03  Aligned_cols=65  Identities=17%  Similarity=0.284  Sum_probs=60.3

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK   67 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~~   67 (98)
                      ++.+|..++..||+  ++++|+|+||++|++||+.+|+||+++|..+|++|.++|..|+.++...+.
T Consensus        16 ~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~~~~~   80 (91)
T 1l8y_A           16 QQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNS   80 (91)
T ss_dssp             HHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGSSSS
T ss_pred             HHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc
Confidence            47899999999999  699999999999999999999999999999999999999999988776443

>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A*

Probab=99.70  E-value=1e-17  Score=103.77  Aligned_cols=59  Identities=24%  Similarity=0.446  Sum_probs=56.7

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR   60 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~   60 (98)
                      |+++|..|+.+||+ +++++|+++||++|++||+++|++|.++|..++++|..+|+.|+-
T Consensus        16 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky   74 (76)
T 1hry_A           16 SRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (76)
T ss_dssp             HHHHHHHHHHHCSC-CSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             HHHHHHHHHHHCcC-CCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence            57899999999999 999999999999999999999999999999999999999999874

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

Probab=99.69  E-value=2.1e-17  Score=103.47  Aligned_cols=61  Identities=25%  Similarity=0.485  Sum_probs=57.9

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|..|+..||+ +++++|+++||++|++||+++|++|.++|..++++|..+|+.|+...
T Consensus        14 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   74 (80)
T 1gt0_D           14 SRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRP   74 (80)
T ss_dssp             HHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccCC
Confidence            57899999999999 99999999999999999999999999999999999999999997543

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

Probab=99.69  E-value=2.4e-17  Score=101.86  Aligned_cols=58  Identities=34%  Similarity=0.688  Sum_probs=55.5

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++|  ++|++|+++|..++++|..+|+.|+.+
T Consensus        15 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A           15 LNDTRESIKRENPG-IKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             HHHHHHHHHHHSTT-CCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            57899999999999 99999999999999999  889999999999999999999999865

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

Probab=99.69  E-value=3.1e-17  Score=107.23  Aligned_cols=65  Identities=25%  Similarity=0.434  Sum_probs=61.1

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++||+++|++|.++|..++++|..+|..|....+.-.
T Consensus        22 ~~~~r~~ik~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~~P~~~   86 (99)
T 1k99_A           22 FMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLI   86 (99)
T ss_dssp             HHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCCCCCS
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcc
Confidence            57899999999999 999999999999999999999999999999999999999999998866543

>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A

Probab=99.68  E-value=3.3e-17  Score=103.01  Aligned_cols=60  Identities=30%  Similarity=0.550  Sum_probs=57.5

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      |+++|..|+.+||+ +++++|+++||++|++|++++|.+|.++|..++++|..+|+.|+-.
T Consensus        18 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~   77 (83)
T 3f27_D           18 AKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYR   77 (83)
T ss_dssp             HHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeC
Confidence            57899999999999 9999999999999999999999999999999999999999999754

>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A

Probab=99.68  E-value=4.1e-17  Score=103.50  Aligned_cols=61  Identities=25%  Similarity=0.456  Sum_probs=58.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|..|+.+||+ +++++||++||++|++||+++|.+|.++|..++++|..+|+.|+...
T Consensus        16 ~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   76 (85)
T 1j46_A           16 SRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             HHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccCC
Confidence            57899999999999 99999999999999999999999999999999999999999997654

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

Probab=99.68  E-value=2.9e-17  Score=102.30  Aligned_cols=60  Identities=25%  Similarity=0.501  Sum_probs=57.3

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++||+++|.+|.++|..++++|..+|+.|+-.
T Consensus        14 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~   73 (79)
T 3u2b_C           14 SQIERRKIMEQSPD-MHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYR   73 (79)
T ss_dssp             HHHHHHHHHTTSTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCC
T ss_pred             HHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeC
Confidence            57899999999999 9999999999999999999999999999999999999999998754

>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-17  Score=104.77  Aligned_cols=58  Identities=21%  Similarity=0.362  Sum_probs=56.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN   59 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~   59 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++||+++|++|+++|..++++|.++++.|+
T Consensus        29 ~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           29 AKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             HHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            57899999999999 99999999999999999999999999999999999999999885

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

Probab=99.67  E-value=1.2e-17  Score=105.37  Aligned_cols=61  Identities=34%  Similarity=0.594  Sum_probs=57.5

Q ss_pred             ChHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s--~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|++|+.+||+ ++  |++|+++||++|++||+++|++|.++|..++++|..+|+.|+...
T Consensus        19 ~~~~r~~~~~~~p~-~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~   81 (83)
T 1aab_A           19 VQTSREEHKKKHPD-ASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK   81 (83)
T ss_dssp             HHHHHHHHTTSCTT-TCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCCS
T ss_pred             HHHHHHHHHHHCCC-CCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            57899999999999 75  699999999999999999999999999999999999999998764

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

Probab=99.67  E-value=1.7e-17  Score=104.45  Aligned_cols=61  Identities=18%  Similarity=0.323  Sum_probs=58.1

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|..|+.+||+ +++++|+++||++|++||+++|++|.++|..++++|..+|+.|+...
T Consensus        19 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~p   79 (82)
T 1wz6_A           19 CKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSGP   79 (82)
T ss_dssp             HHHHHHHHHHHCSS-SCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCCT
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcCC
Confidence            57899999999999 99999999999999999999999999999999999999999998654

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

Probab=99.66  E-value=1e-16  Score=105.96  Aligned_cols=60  Identities=27%  Similarity=0.518  Sum_probs=57.1

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++|++++|++|.++|..++++|.++|+.|+-.
T Consensus        41 ~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~  100 (106)
T 4euw_A           41 AQAARRKLADQYPH-LHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQ  100 (106)
T ss_dssp             HHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC-
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcC
Confidence            57899999999999 9999999999999999999999999999999999999999999754

>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.65  E-value=5.8e-17  Score=101.75  Aligned_cols=60  Identities=18%  Similarity=0.409  Sum_probs=55.4

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      |+++|..|+..||+ +++++||++||++|++||+++|++|.++|..++.+|..++++|+-.
T Consensus        16 ~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   75 (81)
T 1i11_A           16 AKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYK   75 (81)
T ss_dssp             HHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC---
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeec
Confidence            57899999999999 9999999999999999999999999999999999999999998754

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

Probab=99.65  E-value=1.4e-17  Score=107.46  Aligned_cols=61  Identities=36%  Similarity=0.624  Sum_probs=58.4

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|..|+.+||+ +++++|+++||++|++||+++|++|.++|..++++|..+|+.|+.++
T Consensus        32 ~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~~~~   92 (93)
T 1cg7_A           32 ANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATL   92 (93)
T ss_dssp             HHHHTSTTTTTCTT-SCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            57889999999999 99999999999999999999999999999999999999999999875

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

Probab=99.65  E-value=2.8e-17  Score=106.67  Aligned_cols=61  Identities=31%  Similarity=0.651  Sum_probs=58.0

Q ss_pred             ChHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s--~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|..|+.+||+ ++  +++|+++||++|++||+++|++|+++|..++.+|..+|+.|+.+.
T Consensus        34 ~~~~r~~~k~~~p~-~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~   96 (97)
T 2lhj_A           34 AKEKRVEIIAENPE-IAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQRK   96 (97)
T ss_dssp             HHGGGGGHHHHCTT-STTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCC-CCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            57889999999999 88  999999999999999999999999999999999999999998764

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

Probab=99.63  E-value=5.9e-16  Score=107.35  Aligned_cols=60  Identities=40%  Similarity=0.679  Sum_probs=57.7

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++||+++|++|.++|..++++|..+|+.|+++
T Consensus       100 ~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~  159 (159)
T 2gzk_A          100 CSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK  159 (159)
T ss_dssp             HHHHHHHHHHHCSC-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hHhhHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            57899999999999 9999999999999999999999999999999999999999999863

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

Probab=99.62  E-value=8.1e-16  Score=108.21  Aligned_cols=61  Identities=39%  Similarity=0.662  Sum_probs=58.5

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++||+++|++|.++|..++.+|..+|+.|+.++
T Consensus       113 ~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~k~  173 (173)
T 2yrq_A          113 CSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG  173 (173)
T ss_dssp             HHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            57899999999999 99999999999999999999999999999999999999999998763

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

Probab=99.59  E-value=3.6e-15  Score=97.86  Aligned_cols=56  Identities=14%  Similarity=0.303  Sum_probs=51.2

Q ss_pred             hCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCCC
Q 034314           11 DHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK   67 (98)
Q Consensus        11 enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~~   67 (98)
                      .+|+ +++++|+|+||++|++|++++|++|+++|..++++|.++|+.|..+++....
T Consensus        28 ~~~~-~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~~~~   83 (101)
T 1v63_A           28 ELNH-LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDR   83 (101)
T ss_dssp             TTTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTHH
T ss_pred             CCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHHHH
Confidence            4556 7899999999999999999999999999999999999999999999876554

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

Probab=99.59  E-value=1.2e-16  Score=102.54  Aligned_cols=56  Identities=27%  Similarity=0.394  Sum_probs=52.8

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKN   57 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~   57 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++||+++|++|+++|..++++|.++|..
T Consensus        32 ~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~   87 (90)
T 1wgf_A           32 SEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGP   87 (90)
T ss_dssp             HHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSS
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999 999999999999999999999999999999999999877654

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

Probab=99.59  E-value=8.2e-16  Score=93.37  Aligned_cols=53  Identities=28%  Similarity=0.529  Sum_probs=49.5

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY   58 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y   58 (98)
                      |+++|+.|+..||     ++|+++||++|++||+++|.+|+++|..++.+|.++|..|
T Consensus        14 ~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A           14 VAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             HHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5789999987776     4999999999999999999999999999999999999988

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

Probab=99.56  E-value=7.8e-15  Score=107.09  Aligned_cols=63  Identities=11%  Similarity=0.310  Sum_probs=59.8

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAE   64 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~   64 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++||+++|.+|+++|..++++|..+|+.|....+.
T Consensus        21 ~~~~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~tp   83 (214)
T 3tq6_A           21 SKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTP   83 (214)
T ss_dssp             HHHHHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred             HHHHHHHHHHhCCC-CCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCCH
Confidence            58999999999999 9999999999999999999999999999999999999999999876643

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

Probab=99.56  E-value=7.9e-15  Score=108.53  Aligned_cols=63  Identities=11%  Similarity=0.310  Sum_probs=59.9

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAE   64 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~   64 (98)
                      |+++|+.|+.+||+ +++++|+++||++|++|++++|.+|+++|..++++|..+|+.|......
T Consensus        53 ~~e~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~~p  115 (238)
T 3tmm_A           53 SKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTP  115 (238)
T ss_dssp             HHHHHHHHHHHSTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred             HHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Confidence            58999999999999 9999999999999999999999999999999999999999999877653

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

Probab=99.56  E-value=5.2e-15  Score=98.24  Aligned_cols=58  Identities=19%  Similarity=0.351  Sum_probs=54.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQA   63 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~   63 (98)
                      |+++|+.|+    + +++++|+++||++|++|++++|++|.++|..++++|..+|+.|..++.
T Consensus        29 ~~e~r~~~k----~-~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~   86 (108)
T 1v64_A           29 CAELMANMK----D-VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLP   86 (108)
T ss_dssp             HHHHHHHCT----T-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHh----C-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            567888877    6 899999999999999999999999999999999999999999999864

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

Probab=99.53  E-value=1.3e-14  Score=101.95  Aligned_cols=62  Identities=32%  Similarity=0.580  Sum_probs=58.0

Q ss_pred             ChHHHHHHHHhCCCC-CCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKN-KSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~-~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|++|+..||+. +++++|+++||++|++||+++|.+|.++|..++++|..+|+.|....
T Consensus        27 ~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~   89 (173)
T 2yrq_A           27 VQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK   89 (173)
T ss_dssp             HHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCCCC
T ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence            588999999999994 48999999999999999999999999999999999999999998643

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

Probab=99.48  E-value=1.6e-14  Score=91.75  Aligned_cols=47  Identities=26%  Similarity=0.365  Sum_probs=44.6

Q ss_pred             ChHHHHHHHHhCCCCCC-HHHHHHHHHHHhhcCChhHhhhhHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKS-VAAVGKAGGEKWKSMSEADKAPYVAKAEKRK   48 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s-~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK   48 (98)
                      |+++|++|+.+||+ ++ +++|+|+||++|++||+++|++|+++|..+.
T Consensus        17 ~~e~R~~ik~~~P~-~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A           17 LEENRSNILSDNPD-FSDEADIIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             HHHHHHHHHHHCTT-CCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             HHHHHHHHHHHCCC-CchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            58999999999999 88 9999999999999999999999999998873

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

Probab=99.45  E-value=5.7e-14  Score=97.27  Aligned_cols=59  Identities=25%  Similarity=0.481  Sum_probs=55.6

Q ss_pred             hHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhh
Q 034314            2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR   61 (98)
Q Consensus         2 qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~   61 (98)
                      +..|..|+..||+ +++++||++||++|++||+++|.+|.++|..++++|..+|+.|...
T Consensus        17 ~~~~~ki~~~~P~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~   75 (159)
T 2gzk_A           17 RDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (159)
T ss_dssp             HHHHHHHHHHCSS-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCC
T ss_pred             HHHHHHHHHHCCC-CCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccc
Confidence            5678889999999 9999999999999999999999999999999999999999999653

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

Probab=99.39  E-value=7.4e-14  Score=91.03  Aligned_cols=52  Identities=23%  Similarity=0.330  Sum_probs=49.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHH---HHHhhcCChhHhhhhHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAG---GEKWKSMSEADKAPYVAKAEKRKVEYEKDM   55 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~i---ge~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~   55 (98)
                      |+++|++|+.+  + +++++|+++|   |++|++|++++|++|+++|..+|++|.+.+
T Consensus        22 ~~e~R~~ik~e--~-~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A           22 VQEKIPELRRR--G-LPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             HHTTHHHHHHH--T-CCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHc--C-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            57899999999  6 8899999999   999999999999999999999999999876

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

Probab=99.30  E-value=8.3e-13  Score=85.75  Aligned_cols=48  Identities=23%  Similarity=0.438  Sum_probs=45.9

Q ss_pred             ChHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEK   53 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s--~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~   53 (98)
                      |+++|++|+.+||+ ++  +++|+    ++|++|++++|+||+++|..+|++|+.
T Consensus        34 ~~e~R~kik~enP~-~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~   83 (90)
T 2yuk_A           34 TNINFPNLKEEFPD-WTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRI   83 (90)
T ss_dssp             HHHHCTTHHHHCCS-HHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHCcC-ccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            68899999999999 99  99999    999999999999999999999999985

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

Probab=99.28  E-value=7.5e-13  Score=96.54  Aligned_cols=60  Identities=27%  Similarity=0.475  Sum_probs=51.6

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEG   65 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~   65 (98)
                      |+++|+.|+..||     ++|+++||++|++||+++|++|+.+|..++++|..+|+.|+.+++..
T Consensus       126 ~~e~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~~~~~  185 (214)
T 3tq6_A          126 VAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEV  185 (214)
T ss_dssp             HHHHTTTSSCSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhhccCCH-----HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            4566666655554     49999999999999999999999999999999999999999987443

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

Probab=99.27  E-value=7.4e-13  Score=97.91  Aligned_cols=60  Identities=27%  Similarity=0.484  Sum_probs=52.1

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEG   65 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~   65 (98)
                      |+++|+.|+..||+     +|+++||++|++|++++|++|+++|..++++|..+|+.|+.+++..
T Consensus       158 ~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k~~~~  217 (238)
T 3tmm_A          158 VAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEV  217 (238)
T ss_dssp             HHHHTTTSCCSSHH-----HHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhccCHH-----HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            45667666655554     9999999999999999999999999999999999999999987543

>2qgu_A Probable signal peptide protein; NESG, RSR89, Q8XV73, structural genomics, PSI-2, protein STR initiative; HET: MSE PEF; 1.50A {Ralstonia solanacearum}

Probab=86.71  E-value=0.93  Score=32.25  Aligned_cols=49  Identities=10%  Similarity=0.184  Sum_probs=39.0

Q ss_pred             CCCCCCHHHHHHH-HHHHhhcCChhHhhhhHHHHHH-HHHHHHHHHHHHhhh
Q 034314           12 HPKNKSVAAVGKA-GGEKWKSMSEADKAPYVAKAEK-RKVEYEKDMKNYNRR   61 (98)
Q Consensus        12 nP~~~s~~eIsK~-ige~Wk~ls~eeK~~Ye~~A~~-dK~rY~~e~~~Y~~~   61 (98)
                      .|- +.+..|++. ||..|+.+|+++|+.|.+.... ...-|-..+..|...
T Consensus        69 ~p~-~D~~~~a~~vLG~~wr~at~~Qr~~F~~~F~~~L~~tY~~~l~~y~~q  119 (211)
T 2qgu_A           69 VPR-ADFKRTTQIAMGRFWSQATPEQQQQIQDGFKSLLIRTYAGALANVRNQ  119 (211)
T ss_dssp             GGG-BCHHHHHHHHHGGGTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTCSSC
T ss_pred             hhh-cCHHHHHHHHHhHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence            355 678888876 4899999999999999997554 667788888888743

---

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	98
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	5e-07
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	2e-06
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	2e-06
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-06
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	3e-06
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	7e-06
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	1e-05
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-05
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	4e-05
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-04

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

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

 Score = 41.4 bits (97), Expect = 5e-07
 Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            E+R + K +HP   S+  V K  GE W + +  DK PY  KA K K +YEKD+  Y  
Sbjct: 14 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 72

Query: 61 R 61
          +
Sbjct: 73 K 73

>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 = 40.7 bits (95), Expect = 2e-06
 Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            E R+  + ++P + +   VGK  GEKWK+++  +K PY AKA+  K  YE + + YN 
Sbjct: 32 ANENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA 90

Query: 61 RQA 63
            A
Sbjct: 91 TLA 93

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

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

 Score = 39.8 bits (93), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
              R +  +++P     + + K  G +WK +SE +K P++ +A++ +  + K+  +Y
Sbjct: 14 SRGQRRKMAQENP-KMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDY 70

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

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

 Score = 39.5 bits (92), Expect = 3e-06
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 1  MEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
          ++  RE++KK HP    + +   K   E+WK+MS  +K  +   A+  K  YE++MK Y
Sbjct: 13 VQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71

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

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

 Score = 39.4 bits (92), Expect = 3e-06
 Identities = 11/58 (18%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
           ++ R +  +  P +   + + K  G +WK+M+  +K PY  +  +   ++ +   +Y
Sbjct: 14 AKDERRKILQAFP-DMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY 70

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

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

 Score = 38.7 bits (90), Expect = 7e-06
 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
          M+E R     +    K  AA+ +  G +W ++S  ++A Y   A K +  + +    ++ 
Sbjct: 14 MKEMRANVVAEST-LKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA 72

Query: 61 RQAEGTKP 68
          R   G K 
Sbjct: 73 RDNYGKKK 80

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

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

 Score = 38.3 bits (89), Expect = 1e-05
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            + R +   ++P     + + K  G +WK ++EA+K P+  +A+K +  + +   NY  
Sbjct: 16 SRDQRRKMALENP-RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY 74

Query: 61 RQAEGTKP 68
          R     K 
Sbjct: 75 RPRRKAKM 82

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

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

 Score = 37.2 bits (86), Expect = 3e-05
 Identities = 10/73 (13%), Positives = 29/73 (39%)

Query: 4  FREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQA 63
           +E        +  +       G +W+ +S++ K  Y   AE+++ +Y+  +  + +  +
Sbjct: 20 SQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLS 79

Query: 64 EGTKPEEEEESEK 76
             +   +E    
Sbjct: 80 PQDRAAYKEYISN 92

>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 = 36.3 bits (84), Expect = 4e-05
 Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 3/59 (5%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
          +   RE  K+++P    V  V K GGE W++M +  K+ + AKA K K +Y++ +K + 
Sbjct: 15 LNSARESIKRENP-GIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFE 70

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

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

 Score = 34.5 bits (79), Expect = 2e-04
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
            E R +Y K HP   S   + K   +K+K + E  K  Y+   ++ K E+E+++  +  
Sbjct: 22 FMEKRAKYAKLHP-EMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE 80

Query: 61 RQAE 64
             +
Sbjct: 81 DHPD 84

>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 = 34.2 bits (78), Expect = 4e-04
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 1  MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
           EE R Q +++ P   S + + +     W  +SE  KA Y A+    K + E+     +
Sbjct: 32 SEEKRRQLQEERP-ELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPSS 89

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	98
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.73
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.68
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.68
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.66
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.65
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.63
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.56
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.49
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.41
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.4
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	96.76

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

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

Probab=99.73  E-value=2.4e-18  Score=106.54  Aligned_cols=65  Identities=37%  Similarity=0.620  Sum_probs=61.4

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      |+++|.+|+.+||+ +++++|+++||.+|++||+++|.+|.++|..++.+|..+|+.|+.++...+
T Consensus        14 ~~~~r~~i~~~~p~-~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~~~a   78 (79)
T d1hsma_          14 CSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDA   78 (79)
T ss_dssp             HHHHHHHHHHHCTT-CCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCC
Confidence            57899999999999 999999999999999999999999999999999999999999998876554

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

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

Probab=99.69  E-value=5.2e-18  Score=103.30  Aligned_cols=57  Identities=19%  Similarity=0.421  Sum_probs=54.6

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY   58 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y   58 (98)
                      |+++|+.|+.+||+ +++++||++||.+|++||+++|++|.++|..++++|.+++++|
T Consensus        14 ~~~~r~~i~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_          14 AKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             HHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             HHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            57899999999999 9999999999999999999999999999999999999888776

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

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

Probab=99.69  E-value=1.5e-17  Score=103.85  Aligned_cols=61  Identities=25%  Similarity=0.485  Sum_probs=58.0

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|++|+.+||+ +++++||++||++|++||+++|++|+.+|..++++|..+|+.|+.+.
T Consensus        14 ~~~~r~~~~~~~p~-~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p   74 (80)
T d1gt0d_          14 SRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRP   74 (80)
T ss_dssp             HHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCC
Confidence            57899999999999 99999999999999999999999999999999999999999997553

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

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

Probab=99.68  E-value=2.4e-17  Score=103.80  Aligned_cols=65  Identities=23%  Similarity=0.378  Sum_probs=59.9

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      |+++|++|+.+||+ +++++||++||.+|++||+++|.+|.++|..++++|...+++|+.....+.
T Consensus        14 ~~~~r~~~~~~~P~-~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~~~   78 (86)
T d2lefa_          14 MKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGK   78 (86)
T ss_dssp             HHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTTT
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCCCC
Confidence            47899999999999 999999999999999999999999999999999999999999986544443

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

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

Probab=99.68  E-value=2.3e-17  Score=103.69  Aligned_cols=61  Identities=25%  Similarity=0.456  Sum_probs=58.4

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|.+|+.+||+ +++++||++||.+|++||+++|.+|+++|..++.+|..+|+.|+.+.
T Consensus        16 ~~~~r~~i~~~~p~-~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p   76 (85)
T d1j46a_          16 SRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             HHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHHhcc-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCC
Confidence            57899999999999 99999999999999999999999999999999999999999998654

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

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

Probab=99.66  E-value=1.3e-16  Score=101.56  Aligned_cols=62  Identities=37%  Similarity=0.627  Sum_probs=59.1

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQA   63 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~   63 (98)
                      |+++|..|+.+||+ +++++|++.||.+|++||+++|.+|.++|..++.+|..+|..|+..++
T Consensus        32 ~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~~~l~   93 (93)
T d1lwma_          32 ANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA   93 (93)
T ss_dssp             HHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            57899999999999 999999999999999999999999999999999999999999998753

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

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

Probab=99.65  E-value=1.3e-16  Score=97.49  Aligned_cols=59  Identities=36%  Similarity=0.672  Sum_probs=55.5

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ   62 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~   62 (98)
                      |+++|+.|+.+||+ +++++|+++||.+|++|+  +|++|.++|..++.+|..+|+.|+.+|
T Consensus        15 ~~~~r~~~k~~~p~-~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~g   73 (73)
T d1qrva_          15 LNSARESIKRENPG-IKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEANG   73 (73)
T ss_dssp             HHHHHHHHHHTSTT-CCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            57899999999999 999999999999999986  599999999999999999999998875

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

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

Probab=99.63  E-value=2.2e-16  Score=95.65  Aligned_cols=58  Identities=34%  Similarity=0.637  Sum_probs=54.0

Q ss_pred             ChHHHHHHHHhCCCC-CCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKN-KSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY   58 (98)
Q Consensus         1 ~qe~R~~vk~enP~~-~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y   58 (98)
                      |+++|+.|+.+||+. +++++|+++||.+|++||+++|.+|.++|..++++|..+|+.|
T Consensus        13 ~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_          13 VQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             HHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            578999999999972 4689999999999999999999999999999999999999887

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

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

Probab=99.56  E-value=2e-15  Score=95.22  Aligned_cols=64  Identities=25%  Similarity=0.444  Sum_probs=60.2

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEG   65 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~   65 (98)
                      |+++|..|+..||+ +++++|+++||.+|+.||+++|.+|.++|..++.+|...|..|....+..
T Consensus        22 ~~~~r~~~~~~~p~-~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~~pe~   85 (91)
T d1k99a_          22 FMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDL   85 (91)
T ss_dssp             HHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCCCCC
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCccc
Confidence            57899999999999 99999999999999999999999999999999999999999999876543

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

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

Probab=99.49  E-value=2.1e-14  Score=91.78  Aligned_cols=64  Identities=16%  Similarity=0.304  Sum_probs=56.7

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCCC
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK   67 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~~   67 (98)
                      |+++|..++..|   +++++|+++||.+|+.||+++|++|.++|..++.+|..+|..|.........
T Consensus        20 ~~e~r~~~~~~~---~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~~~~   83 (101)
T d1v63a_          20 SQELLSNGELNH---LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDR   83 (101)
T ss_dssp             HHHHHHHCTTTT---SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTHH
T ss_pred             HHHHHHHHHhcC---CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH
Confidence            578888887555   4599999999999999999999999999999999999999999998766543

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=99.41  E-value=5.7e-14  Score=88.20  Aligned_cols=53  Identities=28%  Similarity=0.438  Sum_probs=49.7

Q ss_pred             ChHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHH
Q 034314            1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKD   54 (98)
Q Consensus         1 ~qe~R~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e   54 (98)
                      |+++|.+|+..||+ +++++|+++||.+|+.|++++|.+|.++|..++++|.++
T Consensus        32 ~~e~r~~~~~~~p~-~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          32 SEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             HHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             HHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999 999999999999999999999999999999999888643

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

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

Probab=99.40  E-value=5.4e-13  Score=86.40  Aligned_cols=57  Identities=16%  Similarity=0.319  Sum_probs=52.3

Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCC
Q 034314            6 EQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQA   63 (98)
Q Consensus         6 ~~vk~enP~~~s~~eIsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~   63 (98)
                      ..++.++|+ +++.+|+++||.+|++||+++|.+|.++|..++.+|..+|+.|....+
T Consensus        30 ~~~r~~~~~-~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~~~   86 (108)
T d1v64a_          30 AELMANMKD-VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLP   86 (108)
T ss_dssp             HHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHccC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            345567899 999999999999999999999999999999999999999999998764

>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.76  E-value=0.0011  Score=40.05  Aligned_cols=46  Identities=22%  Similarity=0.385  Sum_probs=39.3

Q ss_pred             HHHHHHHHhhcCChhHhhhhHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 034314           21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGT   66 (98)
Q Consensus        21 IsK~ige~Wk~ls~eeK~~Ye~~A~~dK~rY~~e~~~Y~~~~~~~~   66 (98)
                      ..+.+-..|++|...+|-+|..+|.++..||.+++...+...+...
T Consensus        33 aqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~~~a~~~   78 (84)
T d1l8ya_          33 ALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATN   78 (84)
T ss_dssp             HHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGSSS
T ss_pred             HHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhccCCCCcC
Confidence            4456677899999999999999999999999999998887655444