Citrus Sinensis ID: 033714

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110---
Protein Sequence
MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQVIY
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHcHHHHHHHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHccccccccccccccccccccccccccccHHEEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEc
Coil and Loop (DISEMBL)
mkggksksdtrnaklsvnkkpakagrksgkaakdpnkpkrpasAFFVFMEEFREQykkdhpknksVAAVGKAggekwksmseadkapyvaKAEKRKVEYEKDMknynrrqviy
Flexible Loop (DISEMBL)
mkggksksdtrnaklsvnkkpakagrksgkaakdpnkpkrpASAFFVFMEEFREqykkdhpknksvAAVGkaggekwksmseadkapyvakaekrkveyekdmknynrrqviy
Low Complexity Region (SEG)
MKGGKSKSDTRNAKLSVNkkpakagrksgkaakDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQVIY
Disordered region (IsUnstruct)
********************************************FFVFME***************************************************************
Disordered Region (DISOPRED)
****************************************PASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR****
Disordered Region (DISEMBL)
***************************************RPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQVIY
Disordered Region (DISPRO)
***********************************NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQVIY
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYxxxxxxxxxxxxxxxxxxxxxQVIY
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	113	2.2.26 [Sep-21-2011]
P93047	141	High mobility group B pro	no	no	0.938	0.751	0.743	2e-39
O49596	144	High mobility group B pro	no	no	0.964	0.756	0.724	3e-39
P26585	152	HMG1/2-like protein OS=Gl	yes	no	0.982	0.730	0.675	7e-35
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.955	0.75	0.645	2e-32
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.964	0.731	0.637	2e-30
P27347	157	DNA-binding protein MNB1B	N/A	no	0.938	0.675	0.654	3e-29
Q42344	138	High mobility group B pro	no	no	0.911	0.746	0.555	1e-26
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.955	0.670	0.633	5e-25
O49595	178	High mobility group B pro	no	no	0.734	0.466	0.674	2e-24
O49597	125	High mobility group B pro	no	no	0.734	0.664	0.518	5e-21

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

 Score =  160 bits (405), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 81/109 (74%), Positives = 97/109 (88%), Gaps = 3/109 (2%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKG KSK++TR+ KLSV KKPAK  +    AAKDPNKPKRP+SAFFVFME+FR  YK++H
Sbjct: 1   MKGAKSKAETRSTKLSVTKKPAKGAKG---AAKDPNKPKRPSSAFFVFMEDFRVTYKEEH 57

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           PKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN++
Sbjct: 58  PKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNKK 106

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 =  160 bits (404), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 79/109 (72%), Positives = 97/109 (88%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKG KSK++TR++KLSV KKPAK   +   AAKDPNKPKRPASAFFVFME+FRE +KK++
Sbjct: 1   MKGAKSKTETRSSKLSVTKKPAKGAGRGKAAAKDPNKPKRPASAFFVFMEDFRETFKKEN 60

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           PKNKSVA VGKA G+KWKS+S+++KAPYVAKAEKRKVEYEK++K YN++
Sbjct: 61  PKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYNKK 109

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  145 bits (366), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 79/117 (67%), Positives = 98/117 (83%), Gaps = 6/117 (5%)

Query: 1   MKGGKSKSDTRNA--KLSVNKKPAKA-GRKS---GKAAKDPNKPKRPASAFFVFMEEFRE 54
           MKGGKSK++++ A  KL+VNKK A    RK    GKAAKDPNKPKRP SAFFVFMEEFR+
Sbjct: 1   MKGGKSKTESKRADPKLAVNKKGAATKARKPAGKGKAAKDPNKPKRPPSAFFVFMEEFRK 60

Query: 55  QYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV 111
            + K+HP+NK+V+AVGKA G KWK+MS+A+KAPYVAK+EKRKVEYEK+M+ YN++Q 
Sbjct: 61  VFNKEHPENKAVSAVGKAAGAKWKTMSDAEKAPYVAKSEKRKVEYEKNMRAYNKKQA 117

Glycine max (taxid: 3847)

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

 Score =  137 bits (344), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 71/110 (64%), Positives = 91/110 (82%), Gaps = 2/110 (1%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKGGKSK+ + N KL+V KK A   +K+ KA KDPNKPKRP SAFFVFME+FR+ YK+ H
Sbjct: 1   MKGGKSKAKSDN-KLAV-KKQAADTKKTKKAVKDPNKPKRPPSAFFVFMEDFRKTYKEKH 58

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ 110
           P NKSVA VGKAGG+KWK ++ A+KAP+++KAEKRK EYEK+++ YN++Q
Sbjct: 59  PNNKSVAVVGKAGGDKWKQLTAAEKAPFISKAEKRKQEYEKNLQAYNKKQ 108

Ipomoea nil (taxid: 35883)

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

 Score =  130 bits (328), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 74/116 (63%), Positives = 89/116 (76%), Gaps = 7/116 (6%)

Query: 1   MKGGKSKSDTRNA--KLSVNKKPAKAGRKSGKAA-----KDPNKPKRPASAFFVFMEEFR 53
           MKGGKSK +++ A  KL+VNKK A A +   K A     KDPNKPKRP SAFFVFM +FR
Sbjct: 1   MKGGKSKGESKKAETKLAVNKKGAAATKGGKKPAKGKEPKDPNKPKRPPSAFFVFMADFR 60

Query: 54  EQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           EQYKKDHP NKSVAAVGKA GE+WKS+SE +KAPYV +A K+K EYE  ++ YN++
Sbjct: 61  EQYKKDHPNNKSVAAVGKACGEEWKSLSEEEKAPYVDRALKKKEEYEITLQAYNKK 116

Vicia faba (taxid: 3906)

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

 Score =  127 bits (318), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 74/113 (65%), Positives = 90/113 (79%), Gaps = 7/113 (6%)

Query: 1   MKGGKSKSDTR-NAKLSVN----KKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQ 55
           MKG KSK   + +AKL+V     +KPAK GRK GKA KDPNKPKR  SAFFVFMEEFR++
Sbjct: 1   MKGAKSKGAAKADAKLAVKSKGAEKPAK-GRK-GKAGKDPNKPKRAPSAFFVFMEEFRKE 58

Query: 56  YKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 108
           +K+ +PKNKSVAAVGKA G++WKS+SE+DKAPYVAKA K K+EY K +  YN+
Sbjct: 59  FKEKNPKNKSVAAVGKAAGDRWKSLSESDKAPYVAKANKLKLEYNKAIAAYNK 111

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

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

 Score =  118 bits (295), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 60/108 (55%), Positives = 81/108 (75%), Gaps = 5/108 (4%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAK-DPNKPKRPASAFFVFMEEFREQYKKD 59
           MKGG+SK++      S +++    GRK+GK  K DPN+PKRP SAFFVF+E+FR+++   
Sbjct: 1   MKGGESKAEA----TSTDQRLKTRGRKAGKKTKKDPNQPKRPPSAFFVFLEDFRKEFNLA 56

Query: 60  HPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 107
           +P NKSVA VGKA G +WK+M++ DKAPYVAKAE RK EY K+++ YN
Sbjct: 57  NPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYN 104

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  112 bits (281), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 71/112 (63%), Positives = 85/112 (75%), Gaps = 4/112 (3%)

Query: 1   MKGGKSKSDTR-NAKLSVNKKPAK---AGRKSGKAAKDPNKPKRPASAFFVFMEEFREQY 56
           MKG KSK   + +AKL+V  K A+   A  K GKA KDPNKPKR  SAFFVFM EFRE++
Sbjct: 1   MKGAKSKGAAKADAKLAVKSKGAEKPAAKGKKGKAGKDPNKPKRAPSAFFVFMGEFREEF 60

Query: 57  KKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 108
           K+ +PKNKSVAAVGKA GE+WKS+SE++KAPYVAKA K K EY K +  YN+
Sbjct: 61  KQKNPKNKSVAAVGKAAGERWKSLSESEKAPYVAKANKLKGEYNKAIAAYNK 112

Triticum aestivum (taxid: 4565)

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

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/83 (67%), Positives = 67/83 (80%)

Query: 26  RKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADK 85
           RK  KA KDPNKPKR  SAFFVF+E+FR  +KK++P  K+V+AVGKAGG+KWKSMS+A+K
Sbjct: 41  RKEKKAKKDPNKPKRAPSAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEK 100

Query: 86  APYVAKAEKRKVEYEKDMKNYNR 108
           APY  KA KRK EYEK M  YN+
Sbjct: 101 APYEEKAAKRKAEYEKQMDAYNK 123

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

 Score = 99.4 bits (246), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 43/83 (51%), Positives = 63/83 (75%)

Query: 25  GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAD 84
           G K GK  KDPN+PK+P S FFVF+++FR+++   +P NKSV  VG+A G+KWK+M+E +
Sbjct: 21  GNKVGKKTKDPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTEEE 80

Query: 85  KAPYVAKAEKRKVEYEKDMKNYN 107
           +AP+VAK++ +K EY   M+ YN
Sbjct: 81  RAPFVAKSQSKKTEYAVTMQQYN 103

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	113
308569654	146	high mobility group box 2 protein [Gossy	0.982	0.760	0.848	1e-44
224083306	160	high mobility group family [Populus tric	0.982	0.693	0.794	3e-44
297845042	141	hypothetical protein ARALYDRAFT_472304 [	0.938	0.751	0.798	2e-41
312281681	144	unnamed protein product [Thellungiella h	0.964	0.756	0.770	1e-40
312282031	141	unnamed protein product [Thellungiella h	0.946	0.758	0.763	3e-40
304651500	146	high mobility group protein [Hevea brasi	0.982	0.760	0.857	4e-40
255539248	145	DNA-binding protein MNB1B, putative [Ric	0.982	0.765	0.810	1e-39
308569660	142	high mobility group box 1 protein [Gossy	0.946	0.753	0.872	1e-39
79318295	147	high mobility group B3 protein [Arabidop	0.964	0.741	0.741	1e-39
118488125	151	unknown [Populus trichocarpa]	0.982	0.735	0.75	1e-38

>gi|308569654|gb|ADO34793.1| high mobility group box 2 protein [Gossypium hirsutum]

 Score =  183 bits (464), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 95/112 (84%), Positives = 104/112 (92%), Gaps = 1/112 (0%)

Query: 1   MKGGKSKSDTRNAKLSVNKK-PAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKD 59
           MKGGKSKSD ++AKLSVNKK   KAG+KSGKAAKDPNKPKRPASAFFVFMEEFREQYKK+
Sbjct: 1   MKGGKSKSDAKSAKLSVNKKSTTKAGKKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKE 60

Query: 60  HPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV 111
           HPKNKSVAAVGKAGG+KWKS+SEA+K PYV KAEKRKVEYEK+MK YN+RQ 
Sbjct: 61  HPKNKSVAAVGKAGGDKWKSLSEAEKRPYVDKAEKRKVEYEKNMKAYNKRQA 112

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224083306|ref|XP_002306980.1| high mobility group family [Populus trichocarpa] gi|222856429|gb|EEE93976.1| high mobility group family [Populus trichocarpa]

 Score =  182 bits (461), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 93/117 (79%), Positives = 105/117 (89%), Gaps = 6/117 (5%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAG------RKSGKAAKDPNKPKRPASAFFVFMEEFRE 54
           MKGG+SKSDT++AKLSV KKP K G      RKSGKAAKDPNKPKRPASAFFVFMEEFRE
Sbjct: 1   MKGGRSKSDTKSAKLSVTKKPTKGGGGGAAARKSGKAAKDPNKPKRPASAFFVFMEEFRE 60

Query: 55  QYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV 111
           QYK++HPKNKSVAAVGKAGG+KWKS+SEA+KAP+VAKA+KRKVEYEK MK YN+ Q+
Sbjct: 61  QYKREHPKNKSVAAVGKAGGDKWKSLSEAEKAPFVAKADKRKVEYEKKMKAYNKEQL 117

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  172 bits (437), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 87/109 (79%), Positives = 101/109 (92%), Gaps = 3/109 (2%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKGGKSK++TRNAKLSV KKPAK G+    AAKDPNKPKRP+SAFFVFME+FRE YKK+H
Sbjct: 3   MKGGKSKTETRNAKLSVTKKPAKGGKG---AAKDPNKPKRPSSAFFVFMEDFRETYKKEH 59

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           PKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN++
Sbjct: 60  PKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNKK 108

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  169 bits (429), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 100/109 (91%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKGGKSK++TR++KLSV KKPAK   +S  AAKDPNKPKRPASAFFVFME+FRE +KK+H
Sbjct: 1   MKGGKSKTETRSSKLSVTKKPAKGAGRSKAAAKDPNKPKRPASAFFVFMEDFRETFKKEH 60

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           PKNKSVAAVGKA G+KWKS+S+A+KAPYVAKAEKRKV+YEK+MK YN++
Sbjct: 61  PKNKSVAAVGKAAGDKWKSLSDAEKAPYVAKAEKRKVDYEKNMKAYNKK 109

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312282031|dbj|BAJ33881.1| unnamed protein product [Thellungiella halophila]

 Score =  168 bits (426), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 84/110 (76%), Positives = 99/110 (90%), Gaps = 3/110 (2%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKGGKSK++TR++KLSVNKKP K G+    AAKDPNKPKRPASAFFVFMEEFRE YKK+H
Sbjct: 1   MKGGKSKTETRSSKLSVNKKPTKGGKG---AAKDPNKPKRPASAFFVFMEEFRETYKKEH 57

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ 110
           P NKSVAAVGKAGG+KWKS+S+++KAPY AKA+KRKVEYEK+M  YN++Q
Sbjct: 58  PNNKSVAAVGKAGGQKWKSLSDSEKAPYQAKADKRKVEYEKNMNAYNKKQ 107

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|304651500|gb|ADM47612.1| high mobility group protein [Hevea brasiliensis]

 Score =  168 bits (426), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 96/112 (85%), Positives = 105/112 (93%), Gaps = 1/112 (0%)

Query: 1   MKGGKSKSDTRNA-KLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKD 59
           MKGGKSKSDT+ A +LSVNKKPAKA +KSGKAAKDPNKPKRPASAFFVFMEEFREQYKK+
Sbjct: 1   MKGGKSKSDTKAANRLSVNKKPAKASKKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKE 60

Query: 60  HPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV 111
           HPKNKSVAAVGKAGG+KWKS+SEA+KAPYVAKAEKRKVEYEK +K YN+ Q 
Sbjct: 61  HPKNKSVAAVGKAGGDKWKSLSEAEKAPYVAKAEKRKVEYEKKLKAYNKGQA 112

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539248|ref|XP_002510689.1| DNA-binding protein MNB1B, putative [Ricinus communis] gi|223551390|gb|EEF52876.1| DNA-binding protein MNB1B, putative [Ricinus communis]

 Score =  166 bits (421), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/111 (81%), Positives = 104/111 (93%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKGGKSK+D +N+KLSVNKKP KA +K+GKAAKDPNKPKRPASAFFVFMEEFREQYKK+H
Sbjct: 1   MKGGKSKADAKNSKLSVNKKPVKATKKAGKAAKDPNKPKRPASAFFVFMEEFREQYKKEH 60

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV 111
           PKNKSVAAVGKAGG++WKSMSE++KAP+VAKAEKRK+EYEK +K YN+ Q 
Sbjct: 61  PKNKSVAAVGKAGGDRWKSMSESEKAPFVAKAEKRKIEYEKKLKAYNKGQA 111

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  166 bits (421), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 96/110 (87%), Positives = 105/110 (95%), Gaps = 3/110 (2%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKGGKSKSDT++AKLSV    +KAG+KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH
Sbjct: 1   MKGGKSKSDTKSAKLSVK---SKAGKKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 57

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ 110
           PKNKSVAAVGKAGG+KWKS+SEA+KAPYVAKAEKRKVEYEK+MK YN+RQ
Sbjct: 58  PKNKSVAAVGKAGGDKWKSLSEAEKAPYVAKAEKRKVEYEKNMKAYNKRQ 107

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79318295|ref|NP_001031075.1| high mobility group B3 protein [Arabidopsis thaliana] gi|332191889|gb|AEE30010.1| high mobility group B3 protein [Arabidopsis thaliana]

 Score =  166 bits (420), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 83/112 (74%), Positives = 99/112 (88%), Gaps = 3/112 (2%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKG KSK++TR+ KLSV KKPAK  +    AAKDPNKPKRP+SAFFVFME+FR  YK++H
Sbjct: 1   MKGAKSKAETRSTKLSVTKKPAKGAKG---AAKDPNKPKRPSSAFFVFMEDFRVTYKEEH 57

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQVI 112
           PKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN++ VI
Sbjct: 58  PKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNKKLVI 109

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488125|gb|ABK95882.1| unknown [Populus trichocarpa]

 Score =  163 bits (412), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 87/116 (75%), Positives = 97/116 (83%), Gaps = 5/116 (4%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAK-----DPNKPKRPASAFFVFMEEFREQ 55
           MKGG+SKSDT++AKLSVNKKP K G  +          DPNKPKRPASAFFVFMEEFREQ
Sbjct: 1   MKGGRSKSDTKSAKLSVNKKPTKGGAAAAAKKSGKAAKDPNKPKRPASAFFVFMEEFREQ 60

Query: 56  YKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV 111
           YKK+HPKNKSVAAVGKAGG+KWKS+S A+KAPYVAKA+KRKVEYEK MK YN+ Q 
Sbjct: 61  YKKEHPKNKSVAAVGKAGGDKWKSLSAAEKAPYVAKADKRKVEYEKKMKAYNKEQA 116

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	113
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.964	0.756	0.651	2.4e-35
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.920	0.753	0.495	3.3e-24
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.654	0.592	0.513	1.9e-19
MGI|MGI:1098219	200	Hmgb3 "high mobility group box	0.663	0.375	0.473	9.8e-17
UNIPROTKB|F1RQ19	202	LOC100517745 "Uncharacterized	0.663	0.371	0.460	9.8e-17
RGD|1564407	200	Hmgb3 "high mobility group box	0.663	0.375	0.460	1.2e-16
UNIPROTKB|Q32L31	200	HMGB3 "High mobility group pro	0.663	0.375	0.460	1.2e-16
UNIPROTKB|E7EQU1	193	HMGB3 "High mobility group pro	0.663	0.388	0.447	1.2e-16
UNIPROTKB|E7ES08	188	HMGB3 "High mobility group pro	0.663	0.398	0.447	1.2e-16
UNIPROTKB|O15347	200	HMGB3 "High mobility group pro	0.663	0.375	0.447	1.2e-16

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

 Score = 382 (139.5 bits), Expect = 2.4e-35, P = 2.4e-35
 Identities = 71/109 (65%), Positives = 88/109 (80%)

Query:     1 MKGGKSKSDTRNAKLSVNXXXXXXXXXXXXXXXDPNKPKRPASAFFVFMEEFREQYKKDH 60
             MKG KSK++TR++KLSV                DPNKPKRPASAFFVFME+FRE +KK++
Sbjct:     1 MKGAKSKTETRSSKLSVTKKPAKGAGRGKAAAKDPNKPKRPASAFFVFMEDFRETFKKEN 60

Query:    61 PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 109
             PKNKSVA VGKA G+KWKS+S+++KAPYVAKAEKRKVEYEK++K YN++
Sbjct:    61 PKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYNKK 109

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 = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 53/107 (49%), Positives = 72/107 (67%)

Query:     1 MKGGKSKSDTRNAKLSVNXXXXXXXXXXXXXXXDPNKPKRPASAFFVFMEEFREQYKKDH 60
             MKGG+SK++  +    +                DPN+PKRP SAFFVF+E+FR+++   +
Sbjct:     1 MKGGESKAEATSTDQRLKTRGRKAGKKTKK---DPNQPKRPPSAFFVFLEDFRKEFNLAN 57

Query:    61 PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 107
             P NKSVA VGKA G +WK+M++ DKAPYVAKAE RK EY K+++ YN
Sbjct:    58 PNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYN 104

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 = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 38/74 (51%), Positives = 58/74 (78%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN+PK+P S FFVF+++FR+++   +P NKSV  VG+A G+KWK+M+E ++AP+VAK++
Sbjct:    30 DPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTEEERAPFVAKSQ 89

Query:    94 KRKVEYEKDMKNYN 107
              +K EY   M+ YN
Sbjct:    90 SKKTEYAVTMQQYN 103

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 = 186 (70.5 bits), Expect = 9.8e-17, Sum P(2) = 9.8e-17
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++S+ +K PYV KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLSDNEKQPYVTKAA 147

Query:    94 KRKVEYEKDMKNYNRR 109
             K K +YEKD+ +Y  +
Sbjct:   148 KLKEKYEKDVADYKSK 163

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 = 186 (70.5 bits), Expect = 9.8e-17, Sum P(2) = 9.8e-17
 Identities = 35/76 (46%), Positives = 49/76 (64%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++S+++K PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLSDSEKQPYINKAA 147

Query:    94 KRKVEYEKDMKNYNRR 109
             K K +YEKD+ +Y  +
Sbjct:   148 KLKEKYEKDVADYKSK 163

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 185 (70.2 bits), Expect = 1.2e-16, Sum P(2) = 1.2e-16
 Identities = 35/76 (46%), Positives = 49/76 (64%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++S+++K PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSANP-GISIGDVAKKLGEMWNNLSDSEKQPYMTKAA 147

Query:    94 KRKVEYEKDMKNYNRR 109
             K K +YEKD+ +Y  +
Sbjct:   148 KLKEKYEKDVADYKSK 163

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 = 185 (70.2 bits), Expect = 1.2e-16, Sum P(2) = 1.2e-16
 Identities = 35/76 (46%), Positives = 49/76 (64%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++S+++K PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSANP-GISIGDVAKKLGEMWNNLSDSEKQPYINKAA 147

Query:    94 KRKVEYEKDMKNYNRR 109
             K K +YEKD+ +Y  +
Sbjct:   148 KLKEKYEKDVADYKSK 163

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 = 185 (70.2 bits), Expect = 1.2e-16, Sum P(2) = 1.2e-16
 Identities = 34/76 (44%), Positives = 49/76 (64%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++++++K PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAA 147

Query:    94 KRKVEYEKDMKNYNRR 109
             K K +YEKD+ +Y  +
Sbjct:   148 KLKEKYEKDVADYKSK 163

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

 Score = 185 (70.2 bits), Expect = 1.2e-16, Sum P(2) = 1.2e-16
 Identities = 34/76 (44%), Positives = 49/76 (64%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++++++K PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAA 147

Query:    94 KRKVEYEKDMKNYNRR 109
             K K +YEKD+ +Y  +
Sbjct:   148 KLKEKYEKDVADYKSK 163

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

 Score = 185 (70.2 bits), Expect = 1.2e-16, Sum P(2) = 1.2e-16
 Identities = 34/76 (44%), Positives = 49/76 (64%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
             DPN PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++++++K PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAA 147

Query:    94 KRKVEYEKDMKNYNRR 109
             K K +YEKD+ +Y  +
Sbjct:   148 KLKEKYEKDVADYKSK 163

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

---

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)
P26585	HMGL_SOYBN	No assigned EC number	0.6752	0.9823	0.7302	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh2_kg.1__2258__AT1G20696.3 annotation not avaliable (141 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	113
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-17
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	5e-16
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	4e-15
smart00398	70	smart00398, HMG, high mobility group	6e-13
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	6e-09
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	7e-09
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	2e-08
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	8e-07

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

 Score = 69.6 bits (171), Expect = 3e-17
 Identities = 35/70 (50%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
           PKRP SAFF+F +E R + K ++P  K  A + K  GEKWK++SE +K PY  KAEK K 
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKPYEEKAEKEKA 59

Query: 98  EYEKDMKNYN 107
            YEK    Y 
Sbjct: 60  RYEKAYPAYK 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 = 66.5 bits (163), Expect = 5e-16
 Identities = 36/67 (53%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
           PKRP SA+F+F +E R + KK++P + SV  V K  GEKWK +SE +K  Y  KAEK K 
Sbjct: 1   PKRPLSAYFLFSQEQRPKLKKENP-DASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKE 59

Query: 98  EYEKDMK 104
            YEK+MK
Sbjct: 60  RYEKEMK 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 = 63.8 bits (156), Expect = 4e-15
 Identities = 33/67 (49%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
           PKRP SA+F+F +E R + K ++P   SV  + K  GE WKS+SE +K  Y  KAEK K 
Sbjct: 1   PKRPLSAYFLFSQEHRAEVKAENP-GLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKE 59

Query: 98  EYEKDMK 104
            YEK+M 
Sbjct: 60  RYEKEMP 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 = 58.5 bits (142), Expect = 6e-13
 Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
           KPKRP SAF +F +E R + K ++P     A + K  GE+WK +SE +KAPY  KA+K K
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDK 59

Query: 97  VEYEKDMKNYN 107
             YE++M  Y 
Sbjct: 60  ERYEEEMPEYK 70

Length = 70

>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional

 Score = 49.1 bits (117), Expect = 6e-09
 Identities = 39/87 (44%), Positives = 53/87 (60%), Gaps = 1/87 (1%)

Query: 23  KAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMS 81
              RK+ +  KDPN PKR  SA+  F +E R +   ++P+  K VAAVGK  GE W  +S
Sbjct: 8   VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLS 67

Query: 82  EADKAPYVAKAEKRKVEYEKDMKNYNR 108
           E +KAPY  KA++ KV YEK+   Y +
Sbjct: 68  EEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Length = 94

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

 Score = 51.0 bits (122), Expect = 7e-09
 Identities = 31/94 (32%), Positives = 55/94 (58%), Gaps = 1/94 (1%)

Query: 14  KLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAG 73
           +L    +     ++  +  KDPN PKRP SA+F++  E R++ +K++PK  +   VGK  
Sbjct: 47  QLLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPK-LTFGEVGKLL 105

Query: 74  GEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 107
            EKWK +++ +K PY  +A   +  Y+++ + YN
Sbjct: 106 SEKWKELTDEEKEPYYKEANSDRERYQREKEEYN 139

Length = 211

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

 Score = 47.0 bits (112), Expect = 2e-08
 Identities = 28/69 (40%), Positives = 42/69 (60%)

Query: 35  PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK 94
           PNKPK   +A+F F++  R + K++ P+   VA   K   EKWK+MSE +K  Y  KA +
Sbjct: 1   PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKARE 60

Query: 95  RKVEYEKDM 103
            K  Y+++M
Sbjct: 61  DKKRYDREM 69

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

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

 Score = 42.7 bits (101), Expect = 8e-07
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           KRP +AF +F +  R +  +++P  K   A+ K  G++WK++S  +K PY  +A+K K  
Sbjct: 3   KRPMNAFMLFSKRHRRKVLQEYP-LKENRAISKILGDRWKALSNEEKQPYYEEAKKLKEL 61

Query: 99  YEKDMKNYNRR 109
           + K   +Y  R
Sbjct: 62  HMKLYPDYKWR 72

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif. Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	113
PTZ00199	94	high mobility group protein; Provisional	99.95
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.89
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.88
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.88
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.86
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.86
smart00398	70	HMG high mobility group.	99.86
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.84
KOG0381	96	consensus HMG box-containing protein [General func	99.81
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.81
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.79
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.73
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	99.47
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	99.34
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	99.24
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.83
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.73
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.7
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.67
COG5648	211	NHP6B Chromatin-associated proteins containing the	97.56
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	96.25
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	94.82
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	94.24
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	92.41
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	90.62
KOG3223	221	consensus Uncharacterized conserved protein [Funct	87.1
PF12881	328	NUT_N: NUT protein N terminus; InterPro: IPR024309	85.96
PF05494	170	Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro:	85.16

>PTZ00199 high mobility group protein; Provisional

Probab=99.95  E-value=1.5e-27  Score=152.81  Aligned_cols=90  Identities=43%  Similarity=0.682  Sum_probs=83.1

Q ss_pred             cCCCCccCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHhhhcCCChhhhhHHHHHHHHHH
Q 033714           18 NKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK   96 (113)
Q Consensus        18 ~k~~~~~~k~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~-~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k   96 (113)
                      ++.+.+.+++++++.+||+.|+||+|||+||++++|..|..+||+.. ++.+|+++||++|+.||+++|.+|+++|+.++
T Consensus         3 ~~~~~~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk   82 (94)
T PTZ00199          3 KKQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDK   82 (94)
T ss_pred             ccccCccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            45566777788888999999999999999999999999999999942 38999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 033714           97 VEYEKDMKNYN  107 (113)
Q Consensus        97 ~~y~~~~~~y~  107 (113)
                      .+|..+|.+|+
T Consensus        83 ~rY~~e~~~Y~   93 (94)
T PTZ00199         83 VRYEKEKAEYA   93 (94)
T ss_pred             HHHHHHHHHHh
Confidence            99999999996

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

Probab=99.89  E-value=3.1e-23  Score=127.98  Aligned_cols=70  Identities=27%  Similarity=0.451  Sum_probs=67.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      .|+||+||||||+++.|..|+.+||+ +++.+|+++||++|+.||+++|++|.++|++++++|..++++|+
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yk   70 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPG-LTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYK   70 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCc
Confidence            48999999999999999999999999 59999999999999999999999999999999999999999986

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.

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

Probab=99.88  E-value=1.8e-22  Score=123.21  Aligned_cols=69  Identities=33%  Similarity=0.552  Sum_probs=66.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        38 PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      .+||+|||++|++++|..++.+||+ +++.+|+++||++|+.||+++|++|.++|+.++++|.+++++|+
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            5899999999999999999999999 59999999999999999999999999999999999999999884

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.

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

Probab=99.88  E-value=4.1e-22  Score=119.80  Aligned_cols=69  Identities=42%  Similarity=0.758  Sum_probs=65.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        38 PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      |+||+|||+||+.+.+..++.+||+ ++..+|+++||++|++||+++|.+|.+.|.+++.+|..+|++|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~-~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPD-LSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTT-STHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcc-cccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            8999999999999999999999999 59999999999999999999999999999999999999999996

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

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

Probab=99.86  E-value=1.6e-21  Score=116.14  Aligned_cols=65  Identities=54%  Similarity=0.844  Sum_probs=63.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHH
Q 033714           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDM  103 (113)
Q Consensus        38 PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~  103 (113)
                      |++|+|||++|++++|..+..+||+ +++.+|++.||++|++||+++|++|.+.|++++.+|..+|
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999999999 5999999999999999999999999999999999999987

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.

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

Probab=99.86  E-value=2.2e-21  Score=118.66  Aligned_cols=72  Identities=46%  Similarity=0.807  Sum_probs=63.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHh-CCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           35 PNKPKRPASAFFVFMEEFREQYKKD-HPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        35 ~~~PKrP~say~lF~~~~r~~~~~~-~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      |++|++|+|||+||+.+++..++.+ ++. .++.|+++.|+..|++||++||.+|+++|++++++|..+|..|+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~-~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQK-QSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T--SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccC-CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            6789999999999999999999988 665 58999999999999999999999999999999999999999995

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 ....

>smart00398 HMG high mobility group

Probab=99.86  E-value=2.6e-21  Score=116.03  Aligned_cols=70  Identities=49%  Similarity=0.806  Sum_probs=67.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      +|++|+|||++|++++|..+..+||+ +++.+|+++||.+|+.||+++|++|.++|.+++.+|..++..|+
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPD-LSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            58999999999999999999999999 59999999999999999999999999999999999999999884

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

Probab=99.84  E-value=3.3e-21  Score=137.19  Aligned_cols=85  Identities=35%  Similarity=0.736  Sum_probs=81.0

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHH
Q 033714           26 RKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKN  105 (113)
Q Consensus        26 k~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~  105 (113)
                      +..+++.+||+.|+||+||||+|+.++|+++..++|+ +++.+|++++|++|++|+++||++|...|..+.++|..++..
T Consensus        59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~-l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~  137 (211)
T COG5648          59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPK-LTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEE  137 (211)
T ss_pred             HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCC-CChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHh
Confidence            5667889999999999999999999999999999999 599999999999999999999999999999999999999999


Q ss_pred             HHHhhh
Q 033714          106 YNRRQV  111 (113)
Q Consensus       106 y~~~~~  111 (113)
                      |..++.
T Consensus       138 y~~k~~  143 (211)
T COG5648         138 YNKKLP  143 (211)
T ss_pred             hhcccC
Confidence            998764

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

Probab=99.81  E-value=3.1e-19  Score=113.86  Aligned_cols=76  Identities=47%  Similarity=0.788  Sum_probs=72.7

Q ss_pred             CC--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH-HHHHhh
Q 033714           34 DP--NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK-NYNRRQ  110 (113)
Q Consensus        34 d~--~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~-~y~~~~  110 (113)
                      ||  +.|++|++||++|+.+.+..++.+||+ +++.+|++++|++|++|++++|.+|...|..++++|..+|. +|+..+
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~   95 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            66  599999999999999999999999999 69999999999999999999999999999999999999999 998865

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

Probab=99.81  E-value=2.4e-19  Score=106.30  Aligned_cols=65  Identities=51%  Similarity=0.812  Sum_probs=62.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHH
Q 033714           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDM  103 (113)
Q Consensus        38 PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~  103 (113)
                      |++|+|||++|+++.+..+..++|+ .+..+|++.||.+|+.|++++|.+|.+.|..++.+|..++
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            7899999999999999999999999 5999999999999999999999999999999999999875

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

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.79  E-value=9.4e-20  Score=138.69  Aligned_cols=77  Identities=31%  Similarity=0.578  Sum_probs=72.0

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           30 KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        30 k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      .........||||||||+|.+..|.++..++|++ .+.||+|.||.+|+.|+++||.+|+++|++++..|.+++++|+
T Consensus        55 ~~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~m-HNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK  131 (331)
T KOG0527|consen   55 KDKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKM-HNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK  131 (331)
T ss_pred             cCCCCccccCCCcchhhhhhHHHHHHHHHhCcch-hhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc
Confidence            3445567899999999999999999999999995 9999999999999999999999999999999999999999986

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

Probab=99.73  E-value=6.6e-18  Score=133.45  Aligned_cols=79  Identities=46%  Similarity=0.731  Sum_probs=74.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 033714           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK  104 (113)
Q Consensus        25 ~k~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~  104 (113)
                      +.++.|+.+||++||||+||||||++..|..++.+  + .++++|++.+|++|+.||.  |.+|++.|+.++.+|+.+|.
T Consensus       523 ~~k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--g-i~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~  597 (615)
T KOG0526|consen  523 KKKKGKKKKDPNAPKRATSAYMLWLNASRESIKED--G-ISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMK  597 (615)
T ss_pred             cccCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--C-chHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHH
Confidence            44778889999999999999999999999999987  6 4999999999999999999  89999999999999999999


Q ss_pred             HHHH
Q 033714          105 NYNR  108 (113)
Q Consensus       105 ~y~~  108 (113)
                      +|+.
T Consensus       598 ~yk~  601 (615)
T KOG0526|consen  598 EYKN  601 (615)
T ss_pred             hhcC
Confidence            9984

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=99.47  E-value=1e-13  Score=104.97  Aligned_cols=72  Identities=25%  Similarity=0.453  Sum_probs=66.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      ..|+|+||||||++|.|..|..++-- ....+|.++||.+|.+||.||..+|.++|+++++.|.+.+.+|-+.
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEctl-KeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSAR  262 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSAR  262 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhhh-hhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchh
Confidence            67899999999999999999999875 4788999999999999999999999999999999999998888653

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

Probab=99.34  E-value=3.3e-12  Score=96.23  Aligned_cols=78  Identities=26%  Similarity=0.570  Sum_probs=72.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        31 ~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      ..+-|.+|-+|+-+||.|+...+++|+..||+ +...||.++||.||..|+++||+.|.+.++.++..|.+.|..|...
T Consensus        58 ~pkpPkppekpl~pymrySrkvWd~VkA~nPe-~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~s  135 (410)
T KOG4715|consen   58 RPKPPKPPEKPLMPYMRYSRKVWDQVKASNPE-LKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNS  135 (410)
T ss_pred             CCCCCCCCCcccchhhHHhhhhhhhhhccCcc-hHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            34456788899999999999999999999999 6999999999999999999999999999999999999999999764

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

Probab=99.24  E-value=4e-12  Score=99.94  Aligned_cols=72  Identities=25%  Similarity=0.462  Sum_probs=67.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        35 ~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      +...|||+||||+|.++.|..+...+||+ .+..|+++||.+|+.||..||++|.++-..+-..|.+..++|+
T Consensus       323 ~PHIKRPMNAFMVWAkDERRKILqA~PDM-HNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYr  394 (511)
T KOG0528|consen  323 EPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYR  394 (511)
T ss_pred             CccccCCcchhhcccchhhhhhhhcCccc-cccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccc
Confidence            45779999999999999999999999996 8999999999999999999999999999888889998888886

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

Probab=98.83  E-value=3.2e-09  Score=86.45  Aligned_cols=78  Identities=23%  Similarity=0.374  Sum_probs=69.4

Q ss_pred             cCCCCCCCCCCCCCCCCCCCHHHHHHHHHH--HHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHH
Q 033714           24 AGRKSGKAAKDPNKPKRPASAFFVFMEEFR--EQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEK  101 (113)
Q Consensus        24 ~~k~~~k~~~d~~~PKrP~say~lF~~~~r--~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~  101 (113)
                      ....+...+.+....++|||+|++|++.+|  ..+...||+ ..+..|+++||+.|-.|.+.||+.|.++|.+.++.|.+
T Consensus       168 ~kdgrspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn-~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfk  246 (683)
T KOG2746|consen  168 EKDGRSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPN-QDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFK  246 (683)
T ss_pred             ccccCCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCcc-ccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhh
Confidence            334455556666788999999999999999  889999999 69999999999999999999999999999999999987


Q ss_pred             H
Q 033714          102 D  102 (113)
Q Consensus       102 ~  102 (113)
                      +
T Consensus       247 a  247 (683)
T KOG2746|consen  247 A  247 (683)
T ss_pred             h
Confidence            6

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

Probab=98.73  E-value=6.7e-08  Score=59.26  Aligned_cols=72  Identities=19%  Similarity=0.383  Sum_probs=59.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ  110 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  110 (113)
                      -|..|.+|--+|.++....+...++.. ...+ .+.+...|++|++.+|.+|+..|.++..+|+.+|.+|+.-.
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~d-r~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~   74 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRND-RKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAP   74 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTST-HHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHh-HHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            577899999999999999999999983 4444 66999999999999999999999999999999999987643

>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=97.70  E-value=0.00025  Score=49.83  Aligned_cols=49  Identities=29%  Similarity=0.426  Sum_probs=42.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCC
Q 033714           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS   81 (113)
Q Consensus        32 ~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls   81 (113)
                      .+.|.+-.|-+|||..|+++....|+..+|++ +..|+....+..|...+
T Consensus       116 ~kPPEKRqR~psaYn~f~k~ei~rik~~~p~i-shkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  116 NKPPEKRQRVPSAYNRFMKEEIQRIKAENPDI-SHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             cCCccccCCCchhHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHhhhhCc
Confidence            34455556889999999999999999999995 99999999999998765

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

Probab=97.67  E-value=0.00028  Score=49.76  Aligned_cols=48  Identities=29%  Similarity=0.465  Sum_probs=41.9

Q ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHH
Q 033714           42 ASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK   94 (113)
Q Consensus        42 ~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~   94 (113)
                      -+||+-|+.+++..    |.+ ++..|+....+.+|..|++++|..|..++..
T Consensus        83 nnaYLNFLReFRrk----h~~-L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~  130 (183)
T PF06382_consen   83 NNAYLNFLREFRRK----HCG-LSPQDLIQRAARAWCRLSEAEKNRYRRMAPS  130 (183)
T ss_pred             chHHHHHHHHHHHH----ccC-CCHHHHHHHHHHHHHhCCHHHHHHHHhhcch
Confidence            57899999997764    566 6999999999999999999999999987653

The function of this family is unknown.

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

Probab=97.56  E-value=5.7e-05  Score=54.41  Aligned_cols=68  Identities=24%  Similarity=0.353  Sum_probs=62.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK  104 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~  104 (113)
                      .+|..|..+|+-+-...|..+...+|+ ....+++++++..|.+|+++-+.+|.+.+..++..|...++
T Consensus       142 ~~~~~~~~~~~e~~~~~r~~~~~~~~~-~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         142 LPNKAPIGPFIENEPKIRPKVEGPSPD-KALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             cCCCCCCchhhhccHHhccccCCCCcc-hhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            467888899999999999999999998 58999999999999999999999999999999999987764

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

Probab=96.25  E-value=0.0059  Score=35.25  Aligned_cols=40  Identities=20%  Similarity=0.378  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCCh
Q 033714           42 ASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE   82 (113)
Q Consensus        42 ~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~   82 (113)
                      .+.|-+|.+..|+.|...||++ ..+.+...++..|+.-++
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~-~~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKA-PMSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCC-cHHHHHHHHHHHHHHHHh
Confidence            3568899999999999999995 999999999999986543

; 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

>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT)

Probab=94.82  E-value=0.13  Score=37.07  Aligned_cols=57  Identities=19%  Similarity=0.314  Sum_probs=41.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHH
Q 033714           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK   94 (113)
Q Consensus        31 ~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~   94 (113)
                      .......++||+|+||+|..-.-    ...|+ ....+++..|+..|..=+  -|..|.-.|..
T Consensus        37 ~~~~~~~~kr~lN~Fm~FRsyy~----~~~~~-~~Qk~~S~~l~~lW~~dp--~k~~W~l~ak~   93 (201)
T PF04769_consen   37 RKRSPEKAKRPLNGFMAFRSYYS----PIFPP-LPQKELSGILTKLWEKDP--FKNKWSLMAKA   93 (201)
T ss_pred             ccccccccccchhHHHHHHHHHH----hhcCC-cCHHHHHHHHHHHHhCCc--cHhHHHHHhhh
Confidence            33445578999999999987654    44566 478899999999998732  25556655544

MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus

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

Probab=94.24  E-value=0.088  Score=35.18  Aligned_cols=46  Identities=17%  Similarity=0.288  Sum_probs=40.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChh
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA   83 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~   83 (113)
                      +-+|-.-||.-|.....+.++.++|+ +..+++-.+|-.+|...++.
T Consensus        72 PErR~KAAy~afeE~~Lp~lK~E~Pg-LrlsQ~kq~l~K~w~KSPeN  117 (122)
T PF06244_consen   72 PERRMKAAYKAFEERRLPELKEENPG-LRLSQYKQMLWKEWQKSPEN  117 (122)
T ss_pred             cchhHHHHHHHHHHHHhHHHHhhCCC-chHHHHHHHHHHHHhcCCCC
Confidence            34455689999999999999999999 69999999999999887754

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=92.41  E-value=0.41  Score=34.29  Aligned_cols=45  Identities=18%  Similarity=0.438  Sum_probs=38.4

Q ss_pred             CCHHHHHH-HHHhhhcCCChhhhhHHHHHHHH-HHHHHHHHHHHHHH
Q 033714           64 KSVAAVGK-AGGEKWKSMSEADKAPYVAKAEK-RKVEYEKDMKNYNR  108 (113)
Q Consensus        64 ~~~~eisk-~l~~~Wk~ls~~eK~~y~~~a~~-~k~~y~~~~~~y~~  108 (113)
                      .++..|++ .||..|+.+|+++++.|.+.... ....|-..+..|..
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            36777776 68999999999999999999988 67888888888864

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=90.62  E-value=1.9  Score=31.19  Aligned_cols=44  Identities=23%  Similarity=0.363  Sum_probs=36.8

Q ss_pred             CHHHHHH-HHHhhhcCCChhhhhHHHHHHHHH-HHHHHHHHHHHHH
Q 033714           65 SVAAVGK-AGGEKWKSMSEADKAPYVAKAEKR-KVEYEKDMKNYNR  108 (113)
Q Consensus        65 ~~~eisk-~l~~~Wk~ls~~eK~~y~~~a~~~-k~~y~~~~~~y~~  108 (113)
                      ++..+++ .||..|+.+|+++++.|.+..... ..-|-..+..|..
T Consensus        69 Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~  114 (211)
T PRK15117         69 QVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHG  114 (211)
T ss_pred             CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            6777766 689999999999999999988874 5678888888864

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.10  E-value=1.4  Score=31.69  Aligned_cols=51  Identities=24%  Similarity=0.369  Sum_probs=43.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHH
Q 033714           39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE   93 (113)
Q Consensus        39 KrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~   93 (113)
                      +|=.-||.-|-....+.|+.++|+ +..++.-.+|-.+|..-++.   ||.+.+.
T Consensus       166 kRmrAA~~afEe~~LPrLK~e~P~-lrlsQ~Kqll~Kew~KsPDN---P~Nq~~~  216 (221)
T KOG3223|consen  166 KRMRAAFKAFEEARLPRLKKENPG-LRLSQYKQLLKKEWQKSPDN---PFNQAAV  216 (221)
T ss_pred             HHHHHHHHHHHHhhchhhhhcCCC-ccHHHHHHHHHHHHhhCCCC---hhhHHhh
Confidence            455678999999999999999999 69999999999999988876   6665543

>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins

Probab=85.96  E-value=3.2  Score=32.00  Aligned_cols=54  Identities=19%  Similarity=0.201  Sum_probs=44.4

Q ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHH
Q 033714           42 ASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK   96 (113)
Q Consensus        42 ~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k   96 (113)
                      ..|+-+|..-....+....|.+ +..|-....-+.|...|.-+|-.|.++|++-.
T Consensus       229 ~EAlSCFLIpvLrsLar~kPtM-tlEeGl~ra~qEW~~~SnfdRmifyemaekFm  282 (328)
T PF12881_consen  229 AEALSCFLIPVLRSLARLKPTM-TLEEGLWRAVQEWQHTSNFDRMIFYEMAEKFM  282 (328)
T ss_pred             hhhhhhhHHHHHHHHHhcCCCc-cHHHHHHHHHHHhhccccccHHHHHHHHHHHc
Confidence            4566666666666677777884 88999999999999999999999999999753

It is also found in FAM22, which are a family of uncharacterised mammalian proteins.

>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=85.16  E-value=1.5  Score=30.27  Aligned_cols=45  Identities=18%  Similarity=0.372  Sum_probs=32.4

Q ss_pred             CCHHHHHH-HHHhhhcCCChhhhhHHHHHHHHH-HHHHHHHHHHHHH
Q 033714           64 KSVAAVGK-AGGEKWKSMSEADKAPYVAKAEKR-KVEYEKDMKNYNR  108 (113)
Q Consensus        64 ~~~~eisk-~l~~~Wk~ls~~eK~~y~~~a~~~-k~~y~~~~~~y~~  108 (113)
                      .++..|++ .||..|+.||+++++.|.+..... ...|-..+..|..
T Consensus        38 ~D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~   84 (170)
T PF05494_consen   38 FDFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG   84 (170)
T ss_dssp             B-HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred             CCHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            46666665 467899999999999999988774 5667777777653

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	113
1j3c_A	79	Solution Structure Of The C-Terminal Domain Of The		1e-12
1j3d_A	78	Solution Structure Of The C-Terminal Domain Of The		3e-12
2yqi_A	81	Solution Structure Of The Second Hmg-Box Domain Fro		3e-12
1hme_A	77	Structure Of The Hmg Box Motif In The B-Domain Of H		3e-11
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		3e-11
2yrq_A	173	Solution Structure Of The Tandem Hmg Box Domain Fro		5e-11
1nhm_A	81	The Structure Of The Hmg Box And Its Interaction Wi		6e-10
1hsm_A	79	The Structure Of The Hmg Box And Its Interaction Wi		3e-09
1cg7_A	93	Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len		4e-09
1j5n_A	93	Solution Structure Of The Non-Sequence-Specific Hmg		5e-09
2lhj_A	97	Nmr Structure Of The High Mobility Group Protein-Li		1e-08
1e7j_A	74	Hmg-D Complexed To A Bulge Dna Length = 74		1e-07
1qrv_A	73	Crystal Structure Of The Complex Of Hmg-D And Dna L		1e-07
1hma_A	73	The Solution Structure And Dynamics Of The Dna Bind		1e-07
1j3x_A	77	Solution Structure Of The N-Terminal Domain Of The		2e-07
3nm9_A	73	Hmgd(M13a)-Dna Complex Length = 73		2e-07
2ly4_A	83	Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-Bo		2e-06
1wxl_A	73	Solution Structure Of The Hmg-Box Domain In The Ssr		3e-06
4euw_A	106	Crystal Structure Of A Hmg Domain Of Transcription		3e-06
1aab_A	83	Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83		4e-06
4a3n_A	71	Crystal Structure Of Hmg-Box Of Human Sox17 Length		4e-06
3f27_D	83	Structure Of Sox17 Bound To Dna Length = 83		5e-06
2yul_A	82	Solution Structure Of The Hmg Box Of Human Transcri		5e-06
2crj_A	92	Solution Structure Of The Hmg Domain Of Mouse Hmg D		3e-05
1ckt_A	71	Crystal Structure Of Hmg1 Domain A Bound To A Cispl		4e-05
3tq6_A	214	Crystal Structure Of Human Mitochondrial Transcript		5e-05
3u2b_C	79	Structure Of The Sox4 Hmg Domain Bound To Dna Lengt		8e-05
3fgh_A	67	Human Mitochondrial Transcription Factor A Box B Le		1e-04
1o4x_B	88	Ternary Complex Of The Dna Binding Domains Of The O		1e-04
2e6o_A	87	Solution Structure Of The Hmg Box Domain From Human		2e-04
1wgf_A	90	Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1		2e-04
1hrz_A	76	The 3d Structure Of The Human Sry-Dna Complex Solve		3e-04
1j47_A	85	3d Solution Nmr Structure Of The M9i Mutant Of The		3e-04
1j46_A	85	3d Solution Nmr Structure Of The Wild Type Hmg-Box		3e-04
3tmm_A	238	Tfam Imposes A U-Turn On Mitochondrial Dna Length =		3e-04
1k99_A	99	Solution Structure Of The First Hmg Box In Human Up		4e-04
2eqz_A	86	Solution Structure Of The First Hmg-Box Domain From		5e-04

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKRP SAFF+F  E+R + K +HP   S+    K  GE W   S  DK PY  KA 
Sbjct: 5   DPNAPKRPPSAFFLFCSEYRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 63
Query: 94  KRKVEYEKDMKNY 106
           K K +YEKD+  Y
Sbjct: 64  KLKEKYEKDIAAY 76

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKRP SAFF+F  E R + K +HP   S+    K  GE W   S  DK PY  KA 
Sbjct: 4   DPNAPKRPPSAFFLFCSEHRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 62
Query: 94  KRKVEYEKDMKNY 106
           K K +YEKD+  Y
Sbjct: 63  KLKEKYEKDIAAY 75

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/71 (45%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           N PKRP S FF+F  EFR + K  +P   S+  V K  GE W ++++++K PY+ KA K 
Sbjct: 8   NAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKL 66
Query: 96  KVEYEKDMKNY 106
           K +YEKD+ +Y
Sbjct: 67  KEKYEKDVADY 77

>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1 Length = 77

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA 
Sbjct: 3   DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 61
Query: 94  KRKVEYEKDMKNY 106
           K K +YEKD+  Y
Sbjct: 62  KLKEKYEKDIAAY 74

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA 
Sbjct: 85  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 143
Query: 94  KRKVEYEKDMKNY 106
           K K +YEKD+  Y
Sbjct: 144 KLKEKYEKDIAAY 156

>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human High Mobility Group Protein B1 Length = 173

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA 
Sbjct: 98  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 156
Query: 94  KRKVEYEKDMKNY 106
           K K +YEKD+  Y
Sbjct: 157 KLKEKYEKDIAAY 169

>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 81

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 34/71 (47%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           N PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA K 
Sbjct: 3   NAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 61
Query: 96  KVEYEKDMKNY 106
           K +YEKD+  Y
Sbjct: 62  KEKYEKDIAAY 72

>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 79

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
           PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA K K 
Sbjct: 3   PKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61
Query: 98  EYEKDMKNY 106
           +YEKD+  Y
Sbjct: 62  KYEKDIAAY 70

>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK+++  +K PY AKA+
Sbjct: 17  DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 94  KRKVEYEKDMKNYN 107
             K  YE + + YN
Sbjct: 76  ADKKRYESEKELYN 89

>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna Length = 93

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 31/74 (41%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK+++  +K PY AKA+
Sbjct: 17  DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 94  KRKVEYEKDMKNYN 107
             K  YE + + YN
Sbjct: 76  ADKKRYESEKELYN 89

>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A) Length = 97

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 49/79 (62%), Gaps = 1/79 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
           DPN PKR  S++  F +E R +   ++P+  K VAA+GK  G  W ++S+ +K PY   +
Sbjct: 19  DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMS 78
Query: 93  EKRKVEYEKDMKNYNRRQV 111
           ++ +V YE++   Y +R+V
Sbjct: 79  DEDRVRYEREKAEYAQRKV 97

>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna Length = 74

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M   DK+ + AKA K 
Sbjct: 3   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 59
Query: 96  KVEYEKDMKNY 106
           K +Y++ +K +
Sbjct: 60  KDDYDRAVKEF 70

>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna Length = 73

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M   DK+ + AKA K 
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58
Query: 96  KVEYEKDMKNY 106
           K +Y++ +K +
Sbjct: 59  KDDYDRAVKEF 69

>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding Domain Of Hmg-D From Drosophila Melanogaster Length = 73

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M   DK+ + AKA K 
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58
Query: 96  KVEYEKDMKNY 106
           K +Y++ +K +
Sbjct: 59  KDDYDRAVKEF 69

>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2 Length = 77

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKA 92
           DPNKP+   S++  F++  RE++KK HP +  + A   K   E+WK+MS  +K+ +   A
Sbjct: 5   DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMA 64
Query: 93  EKRKVEYEKDMKN 105
           +  K  Y+++MKN
Sbjct: 65  KSDKARYDREMKN 77

>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex Length = 73

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M   DK+ + AKA K 
Sbjct: 2   DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58
Query: 96  KVEYEKDMKNY 106
           K +Y++ +K +
Sbjct: 59  KDDYDRAVKEF 69

>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53 Transactivation Domain Interaction And Is Regulated By The Acidic Tail Length = 83

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
           DP KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS  +K  +   A
Sbjct: 4   DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 93  EKRKVEYEKDMKNY 106
           +  K  YE++MK Y
Sbjct: 64  KADKARYEREMKTY 77

>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1 Subunit Of Fact Length = 73

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
           PKR  +AF +++ + RE  K+++P  K V  + K GGE WK +   DK+ +   A K K 
Sbjct: 4   PKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELK--DKSKWEDAAAKDKQ 60
Query: 98  EYEKDMKNY 106
            Y  +M+NY
Sbjct: 61  RYHDEMRNY 69

>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription Factor Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS AT 2.77 A RESOLUTION Length = 106

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 46/73 (63%), Gaps = 3/73 (4%)
Query: 36  NKP--KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           NKP  KRP +AF V+ +  R +    +P   + A + K  G+ W+ ++E++K P+V +AE
Sbjct: 26  NKPHVKRPMNAFMVWAQAARRKLADQYPHLHN-AELSKTLGKLWRLLNESEKRPFVEEAE 84
Query: 94  KRKVEYEKDMKNY 106
           + +V+++KD  +Y
Sbjct: 85  RLRVQHKKDHPDY 97

>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
           DP KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS  +K  +   A
Sbjct: 4   DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 93  EKRKVEYEKDMKNY 106
           +  K  YE++MK Y
Sbjct: 64  KADKARYEREMKTY 77

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 45/68 (66%), Gaps = 1/68 (1%)
Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           +RP +AF V+ ++ R++  + +P   + A + K  G+ WK+++ A+K P+V +AE+ +V+
Sbjct: 4   RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 99  YEKDMKNY 106
           + +D  NY
Sbjct: 63  HMQDHPNY 70

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           +RP +AF V+ ++ R++  + +P   + A + K  G+ WK+++ A+K P+V +AE+ +V+
Sbjct: 8   RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66
Query: 99  YEKDMKNYNRR 109
           + +D  NY  R
Sbjct: 67  HMQDHPNYKYR 77

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 45/68 (66%), Gaps = 1/68 (1%)
Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           +RP +AF V+ ++ R++  + +P   + A + K  G+ WK+++ A+K P+V +AE+ +V+
Sbjct: 9   RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 67
Query: 99  YEKDMKNY 106
           + +D  NY
Sbjct: 68  HMQDHPNY 75

>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain Protein Hmgx2 Length = 92

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
           PK P + +  F+ E REQ +  HP +     + K  G +W  +  A+K  Y+ +AEK K 
Sbjct: 8   PKAPVTGYVRFLNERREQIRTRHP-DLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQ 66
Query: 98  EYEKDMKNYNR 108
           +Y K++  Y +
Sbjct: 67  QYLKELWAYQQ 77

>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A Cisplatin-modified Dna Duplex Length = 71

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 37  KPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS  +K  +   A+  
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60
Query: 96  KVEYEKDMKNY 106
           K  YE++MK Y
Sbjct: 61  KARYEREMKTY 71

>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription Factor A, Tfam Or Mttfa, Bound To The Light Strand Promoter Lsp Length = 214

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
           KPKRP SA+ V++ E  ++ K D P+ K      K   E WK++S+++K  Y+  A++ +
Sbjct: 114 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDE 168
Query: 97  VEYEKDMKNYNRRQV 111
             Y  +MK++  + +
Sbjct: 169 TRYHNEMKSWEEQMI 183

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           KRP +AF V+ +  R +  +  P   + A + K  G++WK + ++DK P++ +AE+ +++
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPDMHN-AEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62
Query: 99  YEKDMKNYNRR 109
           +  D  +Y  R
Sbjct: 63  HMADYPDYKYR 73

>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B Length = 67

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 5/70 (7%)
Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
           KPKRP SA+ V++ E  ++ K D P+ K      K   E WK++S+++K  Y+  A++ +
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDE 56
Query: 97  VEYEKDMKNY 106
             Y  +MK++
Sbjct: 57  TRYHNEMKSW 66

>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And Sox2 Transcription Factors With A 19mer Oligonucleotide From The Hoxb1 Regulatory Element Length = 88

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 35  PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK 94
           P++ KRP +AF V+    R +  +++PK  + + + K  G +WK +SE +K P++ +A++
Sbjct: 5   PDRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKR 63
Query: 95  RKVEYEKDMKNYNRR 109
            +  + K+  +Y  R
Sbjct: 64  LRALHMKEHPDYKYR 78

>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human Hmg-Box Transcription Factor 1 Length = 87

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
          PNK KRP +AF +F +++R +Y + +P  K   A+    G++WK M   ++  Y  +A
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYP-GKDNRAISVILGDRWKKMKNEERRMYTLEA 71

>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1 Length = 90

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
           KPKRP SA F+F EE R Q +++ P+  S + + +     W  +SE  KA Y A+    K
Sbjct: 20  KPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAALK 78
Query: 97  VEYEK 101
            + E+
Sbjct: 79  AQSER 83

>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr Length = 76

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           KRP +AF V+  + R +   ++P+ ++ + + K  G +WK ++EA+K P+  +A+K +  
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 99  YEKDMKNYNRR 109
           + +   NY  R
Sbjct: 65  HREKYPNYKYR 75

>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           KRP +AF V+  + R +   ++P+ ++ + + K  G +WK ++EA+K P+  +A+K +  
Sbjct: 6   KRPINAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 99  YEKDMKNYNRR 109
           + +   NY  R
Sbjct: 65  HREKYPNYKYR 75

>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           KRP +AF V+  + R +   ++P+ ++ + + K  G +WK ++EA+K P+  +A+K +  
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 99  YEKDMKNYNRR 109
           + +   NY  R
Sbjct: 65  HREKYPNYKYR 75

>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna Length = 238

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 5/75 (6%)
Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
           KPKRP SA+ V++ E  ++ K D P+ K      K   E WK++S+++K  Y+  A++ +
Sbjct: 146 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDE 200
Query: 97  VEYEKDMKNYNRRQV 111
             Y  + K++  + +
Sbjct: 201 TRYHNEXKSWEEQXI 215

>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream Binding Factor Length = 99

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 35  PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK 94
           P+ PK+P + +F F  E R +Y K HP+  ++  + K   +K+K + E  K  Y+   ++
Sbjct: 8   PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNL-DLTKILSKKYKELPEKKKMKYIQDFQR 66
Query: 95  RKVEYEKDMKNY 106
            K E+E+++  +
Sbjct: 67  EKQEFERNLARF 78

>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High Mobility Group Protein B3 Length = 86

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 43  SAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEK 101
           SA+  F++  RE++KK +P+   + A   K   E+WK+MS  +K+ +   A+  KV Y++
Sbjct: 21  SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 102 DMKNYN 107
           +MK+Y 
Sbjct: 81  EMKDYG 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	113
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	3e-23
2lhj_A	97	High mobility group protein homolog NHP1; structur	6e-22
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	4e-21
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	4e-21
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	5e-21
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	1e-20
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	7e-20
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	2e-18
1ckt_A	71	High mobility group 1 protein; high-mobility group	3e-18
1wgf_A	90	Upstream binding factor 1; transcription factor, D	6e-18
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	6e-18
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	6e-18
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	1e-16
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	3e-16
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-11
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	1e-15
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	3e-14
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	3e-13
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	5e-13
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	9e-13
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	2e-09
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	4e-12
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	8e-11
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	2e-08
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	9e-11
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	3e-10
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	2e-09
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	2e-08
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	3e-08
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	5e-08
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	5e-08
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	5e-08
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	1e-07
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	1e-07
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	3e-06
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	5e-06

>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 = 84.6 bits (210), Expect = 3e-23
 Identities = 37/77 (48%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 33  KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
           KDPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKA 60

Query: 93  EKRKVEYEKDMKNYNRR 109
            K K +YEKD+  Y  +
Sbjct: 61  AKLKEKYEKDIAAYRAK 77

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

 Score = 81.7 bits (202), Expect = 6e-22
 Identities = 33/94 (35%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 19  KKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKW 77
                  R+  KA KDPN PKR  S++  F +E R +   ++P+  K VAA+GK  G  W
Sbjct: 4   ASDRTGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAW 63

Query: 78  KSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV 111
            ++S+ +K PY   +++ +V YE++   Y +R+V
Sbjct: 64  NALSDEEKKPYERMSDEDRVRYEREKAEYAQRKV 97

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

 Score = 79.3 bits (196), Expect = 4e-21
 Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 1/84 (1%)

Query: 24  AGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSE 82
           +   SG A  DP KPK   SA+  F++  RE++KK +P+   + A   K   E+WK+MS 
Sbjct: 2   SSGSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSG 61

Query: 83  ADKAPYVAKAEKRKVEYEKDMKNY 106
            +K+ +   A+  KV Y+++MK+Y
Sbjct: 62  KEKSKFDEMAKADKVRYDREMKDY 85

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

 Score = 78.9 bits (195), Expect = 4e-21
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 31  AAKDPNKPKRPASAFFVFMEEFREQYKKDHP-KNKSVAAVGKAGGEKWKSMSEADKAPYV 89
              DP KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS  +K  + 
Sbjct: 1   GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE 60

Query: 90  AKAEKRKVEYEKDMKNYNRRQ 110
             A+  K  YE++MK Y   +
Sbjct: 61  DMAKADKARYEREMKTYIPPK 81

>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 = 79.3 bits (196), Expect = 5e-21
 Identities = 33/89 (37%), Positives = 52/89 (58%), Gaps = 1/89 (1%)

Query: 19  KKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWK 78
             P +  +++ +  KDPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWK 60

Query: 79  SMSEADKAPYVAKAEKRKVEYEKDMKNYN 107
           +++  +K PY AKA+  K  YE + + YN
Sbjct: 61  ALTPEEKQPYEAKAQADKKRYESEKELYN 89

>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 = 78.6 bits (194), Expect = 1e-20
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 31  AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVA 90
            +   + PK P + +  F+ E REQ +  HP +     + K  G +W  +  A+K  Y+ 
Sbjct: 1   GSSGSSGPKAPVTGYVRFLNERREQIRTRHP-DLPFPEITKMLGAEWSKLQPAEKQRYLD 59

Query: 91  KAEKRKVEYEKDMKNYNRRQ 110
           +AEK K +Y K++  Y + +
Sbjct: 60  EAEKEKQQYLKELWAYQQSE 79

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

 Score = 76.7 bits (189), Expect = 7e-20
 Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 22  AKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
           +       K  KDPN+P++P SA+ +F  + +   K  +P N +   V K     W  + 
Sbjct: 2   SSGSSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNP-NATFGEVSKIVASMWDGLG 60

Query: 82  EADKAPYVAKAEKRKVEYEKDMKNYNRRQ 110
           E  K  Y  K E  K EY K +  Y    
Sbjct: 61  EEQKQVYKKKTEAAKKEYLKQLAAYRASL 89

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

 Score = 72.8 bits (179), Expect = 2e-18
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 30  KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYV 89
           K  K P+ PK+P + +F F  E R +Y K HP   S   + K   +K+K + E  K  Y+
Sbjct: 3   KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHP-EMSNLDLTKILSKKYKELPEKKKMKYI 61

Query: 90  AKAEKRKVEYEKDMKNYNRRQ 110
              ++ K E+E+++  +    
Sbjct: 62  QDFQREKQEFERNLARFREDH 82

>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 = 71.6 bits (176), Expect = 3e-18
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           KP+   S++  F++  RE++KK HP    + +   K   E+WK+MS  +K  +   A+  
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 96  KVEYEKDMKNY 106
           K  YE++MK Y
Sbjct: 61  KARYEREMKTY 71

>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 = 71.3 bits (175), Expect = 6e-18
 Identities = 24/88 (27%), Positives = 37/88 (42%), Gaps = 1/88 (1%)

Query: 20  KPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKS 79
             +              KPKRP SA F+F EE R Q +++ P   S + + +     W  
Sbjct: 3   SGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERP-ELSESELTRLLARMWND 61

Query: 80  MSEADKAPYVAKAEKRKVEYEKDMKNYN 107
           +SE  KA Y A+    K + E+     +
Sbjct: 62  LSEKKKAKYKAREAALKAQSERKSGPSS 89

>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 = 70.8 bits (174), Expect = 6e-18
 Identities = 28/72 (38%), Positives = 45/72 (62%), Gaps = 3/72 (4%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           +KPKRP SA+ +++   RE  K+++P    V  V K GGE W++M   DK+ + AKA K 
Sbjct: 2   DKPKRPLSAYALWLNSARESIKRENP-GIKVTEVAKRGGELWRAMK--DKSEWEAKAAKA 58

Query: 96  KVEYEKDMKNYN 107
           K +Y++ +K + 
Sbjct: 59  KDDYDRAVKEFE 70

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

 Score = 70.8 bits (174), Expect = 6e-18
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           + PKR  +AF +++ + RE  K+++P    V  + K GGE WK +   DK+ +   A K 
Sbjct: 2   HMPKRATTAFMLWLNDTRESIKRENP-GIKVTEIAKKGGEMWKELK--DKSKWEDAAAKD 58

Query: 96  KVEYEKDMKNYN 107
           K  Y  +M+NY 
Sbjct: 59  KQRYHDEMRNYK 70

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

 Score = 67.3 bits (165), Expect = 1e-16
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 5/70 (7%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
           KPKRP SA+ V++ E  ++ K D P+        K   E WK++S+++K  Y+  A++ +
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDE 56

Query: 97  VEYEKDMKNY 106
             Y  +MK++
Sbjct: 57  TRYHNEMKSW 66

>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 = 69.3 bits (169), Expect = 3e-16
 Identities = 37/77 (48%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 33  KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
           KDPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA
Sbjct: 97  KDPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKA 155

Query: 93  EKRKVEYEKDMKNYNRR 109
            K K +YEKD+  Y  +
Sbjct: 156 AKLKEKYEKDIAAYRAK 172

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

 Score = 56.2 bits (135), Expect = 2e-11
 Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 1/88 (1%)

Query: 24  AGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSE 82
           +   SG    DP KP+   S++  F++  RE++KK HP    + +   K   E+WK+MS 
Sbjct: 2   SSGSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSA 61

Query: 83  ADKAPYVAKAEKRKVEYEKDMKNYNRRQ 110
            +K  +   A+  K  YE++MK Y   +
Sbjct: 62  KEKGKFEDMAKADKARYEREMKTYIPPK 89

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

 Score = 65.5 bits (160), Expect = 1e-15
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 31  AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVA 90
            +   +  K+P SA  +F+++ R Q+  ++P   S+        E WK++SE +K  Y  
Sbjct: 1   GSSGSSGIKKPMSASALFVQDHRPQFLIENP-KTSLEDATLQIEELWKTLSEEEKLKYEE 59

Query: 91  KAEKRKVEYEKDMKNYNRRQ 110
           KA K    Y   MK    ++
Sbjct: 60  KATKDLERYNSQMKRAIEQE 79

>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 = 63.7 bits (155), Expect = 3e-14
 Identities = 38/99 (38%), Positives = 51/99 (51%), Gaps = 1/99 (1%)

Query: 11  RNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVG 70
           +               ++ K  KDPN PKRP SAFF+F  E+R + K +HP   S+  V 
Sbjct: 62  QAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVA 120

Query: 71  KAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           K  GE W + +  DK PY  KA K K +YEKD+  Y  +
Sbjct: 121 KKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 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 = 61.0 bits (148), Expect = 3e-13
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           ++ KRP +AF V+  + R +   ++P     + + K  G +WK ++EA+K P+  +A+K 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENP-RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 96  KVEYEKDMKNYN 107
           +  + +   NY 
Sbjct: 62  QAMHREKYPNYK 73

>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 = 58.6 bits (142), Expect = 5e-13
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 25  GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAD 84
                 +A  PNK KRP +AF +F +++R +Y + +P  K   A+    G++WK M   +
Sbjct: 5   SSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEE 63

Query: 85  KAPYVAKAEKRKVEYEKD 102
           +  Y  +A+    E ++ 
Sbjct: 64  RRMYTLEAKALAEEQKRL 81

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

 Score = 60.9 bits (147), Expect = 9e-13
 Identities = 12/79 (15%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 30  KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYV 89
            ++   + PK+P S++  F +E    +K  +P +     + +   ++W+ + ++ K  Y 
Sbjct: 2   GSSVLASCPKKPVSSYLRFSKEQLPIFKAQNP-DAKTTELIRRIAQRWRELPDSKKKIYQ 60

Query: 90  AKAEKRKVEYEKDMKNYNR 108
                    Y++++  +  
Sbjct: 61  DAYRAEWQVYKEEISRFKE 79

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

 Score = 51.7 bits (123), Expect = 2e-09
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 5/78 (6%)

Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
              KPKRP SA+ V++ E  ++ K D P+        K   E WK++S+++K  Y+  A+
Sbjct: 111 LLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAK 165

Query: 94  KRKVEYEKDMKNYNRRQV 111
           + +  Y  +MK++  + +
Sbjct: 166 EDETRYHNEMKSWEEQMI 183

>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 = 56.5 bits (137), Expect = 4e-12
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 31  AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVA 90
            +   +  +RP +AF +F +  R   +++HP         K   + W  +   +K  Y  
Sbjct: 1   GSSGSSGARRPMNAFLLFCKRHRSLVRQEHP-RLDNRGATKILADWWAVLDPKEKQKYTD 59

Query: 91  KAEKRKVEYEKDMKNY 106
            A++ K  + K    Y
Sbjct: 60  MAKEYKDAFMKANPGY 75

>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 = 56.0 bits (134), Expect = 8e-11
 Identities = 14/109 (12%), Positives = 39/109 (35%), Gaps = 1/109 (0%)

Query: 5   KSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNK 64
              S        +           G ++   + PK+P S++  F +E    +K  +P + 
Sbjct: 9   HHSSGLVPRGSHMASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNP-DA 67

Query: 65  SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQVIY 113
               + +   ++W+ + ++ K  Y          Y++++  +  +    
Sbjct: 68  KTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPS 116

>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 = 49.1 bits (116), Expect = 2e-08
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 26  RKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADK 85
               K      KPKRP SA+ V++ E  ++ K D P+        K   E WK++S+++K
Sbjct: 135 MTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQE-----KLKTVKENWKNLSDSEK 189

Query: 86  APYVAKAEKRKVEYEKDMKNYNRRQV 111
             Y+  A++ +  Y  +MK++  + +
Sbjct: 190 ELYIQHAKEDETRYHNEMKSWEEQMI 215

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

 Score = 52.6 bits (127), Expect = 9e-11
 Identities = 22/70 (31%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
             +RP +AF V+ ++ R++  + +P +   A + K  G+ WK+++ A+K P+V +AE+ +
Sbjct: 2   SIRRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLAEKRPFVEEAERLR 60

Query: 97  VEYEKDMKNY 106
           V++ +D  NY
Sbjct: 61  VQHMQDHPNY 70

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

 Score = 52.0 bits (125), Expect = 3e-10
 Identities = 24/95 (25%), Positives = 51/95 (53%), Gaps = 1/95 (1%)

Query: 12  NAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGK 71
           +    V+     +     +++K+    KRP +AF V+ +  R +    +P     A + K
Sbjct: 4   HHHHHVDDDDKMSENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPH-LHNAELSK 62

Query: 72  AGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 106
             G+ W+ ++E++K P+V +AE+ +V+++KD  +Y
Sbjct: 63  TLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDY 97

>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 = 49.1 bits (118), Expect = 2e-09
 Identities = 20/71 (28%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           ++ KRP +AF V+  + R +   ++P+    + + K  G +WK ++EA+K P+  +A+K 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 96  KVEYEKDMKNY 106
           +  + +   NY
Sbjct: 62  QAMHREKYPNY 72

>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 = 46.8 bits (112), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 47/75 (62%), Gaps = 1/75 (1%)

Query: 32  AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAK 91
               ++ +RP +AF V+ ++ R++  + +P +   A + K  G+ WK+++ A+K P+V +
Sbjct: 1   GSFTSRIRRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLAEKRPFVEE 59

Query: 92  AEKRKVEYEKDMKNY 106
           AE+ +V++ +D  NY
Sbjct: 60  AERLRVQHMQDHPNY 74

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

 Score = 46.4 bits (111), Expect = 3e-08
 Identities = 20/68 (29%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           KRP +AF V+ +  R +  +  P +   A + K  G++WK + ++DK P++ +AE+ +++
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSP-DMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62

Query: 99  YEKDMKNY 106
           +  D  +Y
Sbjct: 63  HMADYPDY 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 = 45.7 bits (109), Expect = 5e-08
 Identities = 20/71 (28%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           ++ KRP +AF V+  + R +   ++P+    + + K  G +WK ++EA+K P+  +A+K 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 96  KVEYEKDMKNY 106
           +  + +   NY
Sbjct: 62  QAMHREKYPNY 72

>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 = 45.6 bits (109), Expect = 5e-08
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
              KRP +AF V+ ++ R +  +  P +   + + K  G +WK+M+  +K PY  +  + 
Sbjct: 3   PHIKRPMNAFMVWAKDERRKILQAFP-DMHNSNISKILGSRWKAMTNLEKQPYYEEQARL 61

Query: 96  KVEYEKDMKNY 106
             ++ +   +Y
Sbjct: 62  SKQHLEKYPDY 72

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

 Score = 45.6 bits (107), Expect = 5e-08
 Identities = 15/73 (20%), Positives = 30/73 (41%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
               RP + F +++EE R     D+P     A + K G  +++ +S  ++  +  KA+  
Sbjct: 4   GSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE 63

Query: 96  KVEYEKDMKNYNR 108
                 + K    
Sbjct: 64  TASEGTEAKKRKS 76

>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 = 44.9 bits (107), Expect = 1e-07
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           K+P +AF ++M+E R     +    +S AA+ +  G +W ++S  ++A Y   A K +  
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARKERQL 62

Query: 99  YEKDMKNY 106
           + +    +
Sbjct: 63  HMQLYPGW 70

>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 = 44.5 bits (106), Expect = 1e-07
 Identities = 19/71 (26%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           ++ KRP +AF V+    R +  +++P     + + K  G +WK +SE +K P++ +A++ 
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENP-KMHNSEISKRLGAEWKLLSETEKRPFIDEAKRL 59

Query: 96  KVEYEKDMKNY 106
           +  + K+  +Y
Sbjct: 60  RALHMKEHPDY 70

>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 = 41.4 bits (97), Expect = 3e-06
 Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
            K P + +  F +E     +     +  +       G +W+ +S++ K  Y   AE+++ 
Sbjct: 9   KKPPMNGYQKFSQELLSNGEL---NHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQR 65

Query: 98  EYEKDMKNYNRRQ 110
           +Y+  +  + +  
Sbjct: 66  QYKVHLDLWVKSL 78

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

 Score = 41.1 bits (96), Expect = 5e-06
 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 5/88 (5%)

Query: 22  AKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
           +       K   D    K P +++ ++  E     K      + V        ++WK +S
Sbjct: 2   SSGSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERMVLC-----SQQWKLLS 56

Query: 82  EADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           + +K  Y  K +++K +YE ++  +   
Sbjct: 57  QKEKDAYHKKCDQKKKDYEVELLRFLES 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	113
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.96
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.94
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.94
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.94
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.94
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.94
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.94
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.93
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.93
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.93
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.93
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.92
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.92
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.92
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.92
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.92
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.91
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.91
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.91
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.91
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.91
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.91
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.91
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.91
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.9
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.9
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.9
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.9
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.89
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.89
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.88
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.87
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.87
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.85
2cto_A	93	Novel protein; high mobility group box domain, hel	99.84
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.83
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.83
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.83
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.78
2qgu_A	211	Probable signal peptide protein; NESG, RSR89, Q8XV	80.95

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

Probab=99.96  E-value=4e-28  Score=156.39  Aligned_cols=86  Identities=30%  Similarity=0.535  Sum_probs=80.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 033714           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK  104 (113)
Q Consensus        25 ~k~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~  104 (113)
                      ..+++++.+||++|+||+||||||++++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|++++++|..+|+
T Consensus         5 ~~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   83 (102)
T 2co9_A            5 SSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLA   83 (102)
T ss_dssp             CCCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44456777899999999999999999999999999999 59999999999999999999999999999999999999999


Q ss_pred             HHHHhhh
Q 033714          105 NYNRRQV  111 (113)
Q Consensus       105 ~y~~~~~  111 (113)
                      +|+..+.
T Consensus        84 ~Y~~~~~   90 (102)
T 2co9_A           84 AYRASLV   90 (102)
T ss_dssp             HHHHHHT
T ss_pred             HHHhhcc
Confidence            9998764

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

Probab=99.94  E-value=8.5e-27  Score=145.82  Aligned_cols=80  Identities=39%  Similarity=0.660  Sum_probs=74.4

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           28 SGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        28 ~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~-~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      +++..+||++|+||+|||+||++++|..|+.+||+.. ++.||+++||++|++||+++|++|+++|++++++|..+|.+|
T Consensus         6 ~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   85 (86)
T 2eqz_A            6 SGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY   85 (86)
T ss_dssp             SSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4456789999999999999999999999999999942 379999999999999999999999999999999999999999


Q ss_pred             H
Q 033714          107 N  107 (113)
Q Consensus       107 ~  107 (113)
                      +
T Consensus        86 ~   86 (86)
T 2eqz_A           86 G   86 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.94  E-value=3.2e-27  Score=151.49  Aligned_cols=81  Identities=30%  Similarity=0.559  Sum_probs=77.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        29 ~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      +++.+||+.|+||+||||||+++.|..|+.++|+ +++.+|+++||++|++||+++|++|+++|++++++|..+|.+|..
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~   80 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE   80 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGG
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5677899999999999999999999999999999 599999999999999999999999999999999999999999987


Q ss_pred             hh
Q 033714          109 RQ  110 (113)
Q Consensus       109 ~~  110 (113)
                      ..
T Consensus        81 ~~   82 (99)
T 1k99_A           81 DH   82 (99)
T ss_dssp             CC
T ss_pred             HC
Confidence            53

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

Probab=99.94  E-value=2.4e-26  Score=145.49  Aligned_cols=79  Identities=29%  Similarity=0.584  Sum_probs=75.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033714           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV  111 (113)
Q Consensus        32 ~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~  111 (113)
                      .+||++|+||+||||||++++|..|+.+||+ +++.+|+++||++|++||+++|++|+++|++++++|..+|++|+...+
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~   80 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEA   80 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHH
Confidence            4799999999999999999999999999999 599999999999999999999999999999999999999999987653

>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=99.94  E-value=4.5e-27  Score=144.03  Aligned_cols=76  Identities=49%  Similarity=0.819  Sum_probs=73.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        32 ~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      ++||+.|+||+|||+||++++|..++.+||+ +++.+|+++||++|++||+++|++|.++|++++++|..+|++|+.
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4799999999999999999999999999999 599999999999999999999999999999999999999999964

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

Probab=99.94  E-value=2.5e-27  Score=151.28  Aligned_cols=83  Identities=36%  Similarity=0.711  Sum_probs=78.2

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 033714           27 KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK  104 (113)
Q Consensus        27 ~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~--~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~  104 (113)
                      +++++.+||+.|+||+||||||++++|..|+.+||+ ++  +.+|+++||++|++||+++|++|+++|++++++|..+|.
T Consensus        12 ~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~-~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   90 (97)
T 2lhj_A           12 RPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPE-IAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKA   90 (97)
T ss_dssp             CTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTT-STTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677899999999999999999999999999999 48  999999999999999999999999999999999999999


Q ss_pred             HHHHhh
Q 033714          105 NYNRRQ  110 (113)
Q Consensus       105 ~y~~~~  110 (113)
                      +|+.+.
T Consensus        91 ~y~~~~   96 (97)
T 2lhj_A           91 EYAQRK   96 (97)
T ss_dssp             HHHHHH
T ss_pred             HHHhcC
Confidence            999864

>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=99.94  E-value=1.8e-27  Score=150.93  Aligned_cols=83  Identities=39%  Similarity=0.687  Sum_probs=78.6

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           27 KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        27 ~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      ++++..+||+.|+||+|||+||++++|..|..+||+ +++.+|+++||++|++||+++|++|+++|++++++|..+|++|
T Consensus        10 ~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y   88 (93)
T 1cg7_A           10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY   88 (93)
T ss_dssp             CCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTT-SCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHH
T ss_pred             ccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445677899999999999999999999999999999 5999999999999999999999999999999999999999999


Q ss_pred             HHhh
Q 033714          107 NRRQ  110 (113)
Q Consensus       107 ~~~~  110 (113)
                      +.+.
T Consensus        89 ~~~~   92 (93)
T 1cg7_A           89 NATL   92 (93)
T ss_dssp             HHHT
T ss_pred             HHcc
Confidence            9864

>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=99.93  E-value=9.9e-27  Score=145.87  Aligned_cols=77  Identities=29%  Similarity=0.486  Sum_probs=73.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           30 KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        30 k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      +..+||+.|+||+||||||++++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|++++++|..++++|+
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            567899999999999999999999999999999 59999999999999999999999999999999999999998874

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

Probab=99.93  E-value=3.9e-26  Score=144.46  Aligned_cols=78  Identities=29%  Similarity=0.443  Sum_probs=74.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 033714           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ  110 (113)
Q Consensus        32 ~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  110 (113)
                      ..+|++|+||+||||||++++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|++++++|..+|.+|+..+
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~   79 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPK-TSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQE   79 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCS-SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            3578999999999999999999999999999 59999999999999999999999999999999999999999998764

>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=99.93  E-value=9.3e-27  Score=146.87  Aligned_cols=79  Identities=30%  Similarity=0.479  Sum_probs=73.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 033714           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK  104 (113)
Q Consensus        25 ~k~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~  104 (113)
                      +++++++.+||++|+||+||||||++++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|++++++|..+|.
T Consensus         8 k~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A            8 KPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             SSCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             CCCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44556777899999999999999999999999999999 59999999999999999999999999999999999987764

>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=99.93  E-value=2.3e-25  Score=135.36  Aligned_cols=72  Identities=38%  Similarity=0.733  Sum_probs=69.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        35 ~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      .++||||+|||+|||+++|..|+.+||+ +++.+|+++||++|++|++  |++|+++|++++++|..+|++|+++
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~k   72 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPG-IKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSS-CCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3689999999999999999999999999 5999999999999999998  9999999999999999999999875

>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=99.92  E-value=7.7e-26  Score=138.19  Aligned_cols=73  Identities=27%  Similarity=0.520  Sum_probs=69.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        34 d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      ||+.|+||+||||||++++|..|+.+||+ +++.+|+++||++|++||+++|++|.++|++++++|..+|++|+
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   73 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSC-CSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            68999999999999999999999999999 59999999999999999999999999999999999999998875

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

Probab=99.92  E-value=4.4e-26  Score=141.58  Aligned_cols=78  Identities=33%  Similarity=0.607  Sum_probs=72.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        32 ~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~-~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      ++||++|+||+|||+||++++|..|+.+||+.. ++.+|+++||++|++||+++|.+|+++|.+++++|..+|.+|...
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~   80 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP   80 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            479999999999999999999999999999942 259999999999999999999999999999999999999999753

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

Probab=99.92  E-value=3e-25  Score=134.80  Aligned_cols=72  Identities=35%  Similarity=0.714  Sum_probs=69.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        35 ~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      |++|+||+|||+||++++|..|+.+||+ +++.||+++||++|++|  ++|.+|+++|++++++|..+|.+|+.+
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPG-IKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTT-CCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            6899999999999999999999999999 59999999999999999  889999999999999999999999764

>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=99.92  E-value=7e-25  Score=136.79  Aligned_cols=74  Identities=27%  Similarity=0.504  Sum_probs=70.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        34 d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      .|+.|+||+||||||++++|..|..+||+ +++.+|+++||++|++||+++|++|.++|++++++|..+|++|.-
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~   74 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCccccc
Confidence            47899999999999999999999999999 599999999999999999999999999999999999999999863

>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=99.92  E-value=1.4e-24  Score=149.04  Aligned_cols=80  Identities=48%  Similarity=0.791  Sum_probs=76.2

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           28 SGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        28 ~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      ++++.+||+.|+||+|||+|||+++|..|+.+||+ +++.+|+++||++|++||+++|++|+++|++++++|..+|++|+
T Consensus        79 ~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~  157 (159)
T 2gzk_A           79 TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR  157 (159)
T ss_dssp             CGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSC-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccchhhHhhHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34567899999999999999999999999999999 59999999999999999999999999999999999999999998


Q ss_pred             H
Q 033714          108 R  108 (113)
Q Consensus       108 ~  108 (113)
                      +
T Consensus       158 ~  158 (159)
T 2gzk_A          158 A  158 (159)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.91  E-value=5.9e-25  Score=132.55  Aligned_cols=70  Identities=34%  Similarity=0.653  Sum_probs=65.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~-~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      +|+||+|||+||++++|..++.+||+.. ++.+|+++||++|++||+++|.+|.++|++++++|..+|.+|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            5999999999999999999999999942 359999999999999999999999999999999999999876

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

Probab=99.91  E-value=3.7e-25  Score=133.27  Aligned_cols=71  Identities=31%  Similarity=0.597  Sum_probs=63.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      +.|+||+||||||++++|..++.+||+ +++.+|+++||++|++||+++|++|.++|+.++++|..++++|+
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            579999999999999999999999999 59999999999999999999999999999999999999999985

>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=99.91  E-value=3.1e-24  Score=139.57  Aligned_cols=79  Identities=19%  Similarity=0.370  Sum_probs=73.4

Q ss_pred             CCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHH
Q 033714           27 KSGKAAKDPNKP-KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKN  105 (113)
Q Consensus        27 ~~~k~~~d~~~P-KrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~  105 (113)
                      .+.++.+|++.| +||+|||+|||+++|..|+    + +++.||+++||++|++|++++|++|+++|+.++++|..+|.+
T Consensus         6 ~~~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~-~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~   80 (108)
T 1v64_A            6 SGQLKDKFDGRPTKPPPNSYSLYCAELMANMK----D-VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLR   80 (108)
T ss_dssp             SCCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----T-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHh----C-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445677899999 9999999999999999886    5 589999999999999999999999999999999999999999


Q ss_pred             HHHhh
Q 033714          106 YNRRQ  110 (113)
Q Consensus       106 y~~~~  110 (113)
                      |...+
T Consensus        81 Y~~~~   85 (108)
T 1v64_A           81 FLESL   85 (108)
T ss_dssp             HHHHS
T ss_pred             HHhhC
Confidence            99865

>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=99.91  E-value=3.3e-25  Score=137.33  Aligned_cols=75  Identities=21%  Similarity=0.428  Sum_probs=71.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           33 KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        33 ~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      .|++.|+||+||||||++++|..|+.+||+ +++.+|+++||++|++||+++|++|+++|++++++|..+|++|+.
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~   77 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRS   77 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSS-SCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhc
Confidence            578999999999999999999999999999 599999999999999999999999999999999999999988864

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

Probab=99.91  E-value=1.3e-24  Score=140.87  Aligned_cols=76  Identities=30%  Similarity=0.579  Sum_probs=69.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        31 ~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      ..++++.|+||+||||||++++|..|+.++|+ +++.+|+++||++|+.|++++|++|+++|++++++|..+|++|+
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yk   98 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPH-LHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYK   98 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence            35678999999999999999999999999999 59999999999999999999999999999999999999999985

>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=99.91  E-value=1.4e-24  Score=134.58  Aligned_cols=73  Identities=30%  Similarity=0.575  Sum_probs=67.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        34 d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      .++.|+||+||||||++++|..|..+||+ +++.+|+++||++|++|++++|++|.++|++++++|..+|++|+
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   75 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   75 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            46789999999999999999999999999 59999999999999999999999999999999999999999885

>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=99.91  E-value=2e-24  Score=133.08  Aligned_cols=72  Identities=28%  Similarity=0.560  Sum_probs=69.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      +.|+||+||||||++++|..|..+||+ +++.+|+++||++|++||+++|++|.++|++++++|..+|++|+-
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~   72 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKY   72 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCccccc
Confidence            479999999999999999999999999 599999999999999999999999999999999999999999863

>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=99.91  E-value=3.2e-24  Score=134.00  Aligned_cols=71  Identities=24%  Similarity=0.431  Sum_probs=68.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      +.|+||+||||||++++|..|..+||+ +++.+|+++||++|++||+++|++|+++|+.++++|..+|++|.
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS   71 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            469999999999999999999999999 59999999999999999999999999999999999999999986

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

Probab=99.90  E-value=8.2e-24  Score=147.07  Aligned_cols=80  Identities=48%  Similarity=0.796  Sum_probs=76.2

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        29 ~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      +++.+||+.|+||+|||+||++++|..|..+||+ +++.+|+++||++|++||+++|++|+++|++++++|..+|++|+.
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  171 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  171 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4556799999999999999999999999999999 599999999999999999999999999999999999999999986


Q ss_pred             h
Q 033714          109 R  109 (113)
Q Consensus       109 ~  109 (113)
                      +
T Consensus       172 k  172 (173)
T 2yrq_A          172 K  172 (173)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.90  E-value=2.4e-24  Score=133.13  Aligned_cols=73  Identities=23%  Similarity=0.467  Sum_probs=68.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        35 ~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      ++.|+||+||||||++++|..|..+||+ +++.+|+++||++|++||+++|++|.++|++++++|..++++|+-
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky   74 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKY   74 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC--
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            4689999999999999999999999999 599999999999999999999999999999999999999998863

>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=99.90  E-value=2.9e-24  Score=131.92  Aligned_cols=71  Identities=28%  Similarity=0.561  Sum_probs=68.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      |.|+||+||||||++++|..|..++|+ +++.+|+++||++|++||+++|++|.++|++++++|..++++|+
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yk   71 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPD-MHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYK   71 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            579999999999999999999999999 59999999999999999999999999999999999999999885

>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=99.90  E-value=6.6e-24  Score=133.95  Aligned_cols=74  Identities=18%  Similarity=0.311  Sum_probs=71.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV  111 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~  111 (113)
                      +.|+||+|||+||+++.|..+..++|+  ++.+|++.||++|++|++++|++|+++|+.++++|+.+|.+|+.+.+
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~   76 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPA   76 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            689999999999999999999999998  79999999999999999999999999999999999999999987654

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

Probab=99.89  E-value=9.9e-24  Score=126.07  Aligned_cols=66  Identities=33%  Similarity=0.585  Sum_probs=62.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      |.|+||+|||+||++++|..++.+|     +.+|+++||++|++||+++|.+|+++|.+++++|..+|.+|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~-----p~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSS-----HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcC-----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5899999999999999999997654     46999999999999999999999999999999999999988

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

Probab=99.89  E-value=8.9e-23  Score=141.85  Aligned_cols=81  Identities=35%  Similarity=0.622  Sum_probs=75.7

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           28 SGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKN-KSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        28 ~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      .+...+||++|+||+|||+||++++|..|+.+||+. +++.+|+++||++|++||++||++|+++|..++++|..+|.+|
T Consensus         6 ~k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y   85 (173)
T 2yrq_A            6 SGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   85 (173)
T ss_dssp             CSSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            345678999999999999999999999999999994 3899999999999999999999999999999999999999999


Q ss_pred             HH
Q 033714          107 NR  108 (113)
Q Consensus       107 ~~  108 (113)
                      ..
T Consensus        86 ~~   87 (173)
T 2yrq_A           86 IP   87 (173)
T ss_dssp             CC
T ss_pred             hh
Confidence            64

>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=99.88  E-value=1.4e-22  Score=130.28  Aligned_cols=74  Identities=16%  Similarity=0.319  Sum_probs=66.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 033714           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ  110 (113)
Q Consensus        34 d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  110 (113)
                      ...+||||+|||+||+++++.  ..++++ +++.||+++||++|++|+++||++|+++|++++++|..+|.+|...+
T Consensus         5 ~~~~PKrP~say~lF~~e~~~--~p~~~~-~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~   78 (101)
T 1v63_A            5 SSGPKKPPMNGYQKFSQELLS--NGELNH-LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSL   78 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHH--HCTTTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCHHHHHHHHHHh--CCCCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            457899999999999999964  224455 48999999999999999999999999999999999999999999875

>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=99.87  E-value=1.8e-22  Score=125.11  Aligned_cols=61  Identities=25%  Similarity=0.413  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCC-HHHHHHHHHhhhcCCChhhhhHHHHHHHHH
Q 033714           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKS-VAAVGKAGGEKWKSMSEADKAPYVAKAEKR   95 (113)
Q Consensus        34 d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~-~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~   95 (113)
                      +++.|+||+||||||++++|..|+.+||+ ++ +.||+++||++|++|++++|++|+++|..+
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~-~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPD-FSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTT-CCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            68899999999999999999999999999 57 999999999999999999999999999876

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

Probab=99.87  E-value=2.5e-22  Score=146.12  Aligned_cols=78  Identities=15%  Similarity=0.391  Sum_probs=74.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        31 ~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      ...||++|++|+|||+||++++|..|+.+||+ +++.||+++||++|+.|+++||.+|+++|..++++|+.+|..|.+.
T Consensus        35 s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~  112 (238)
T 3tmm_A           35 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQ  112 (238)
T ss_dssp             CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            35689999999999999999999999999999 5999999999999999999999999999999999999999999754

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

Probab=99.85  E-value=1.4e-21  Score=140.33  Aligned_cols=75  Identities=16%  Similarity=0.404  Sum_probs=71.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        34 d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      +|++|+||+|||+||++++|..|+.+||+ +++.||+++||++|+.||+++|.+|+++|..++++|..+|.+|.+.
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~   80 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQ   80 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhccc
Confidence            46799999999999999999999999999 5999999999999999999999999999999999999999999754

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

Probab=99.84  E-value=8e-22  Score=125.08  Aligned_cols=70  Identities=21%  Similarity=0.339  Sum_probs=64.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHH---HhhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 033714           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAG---GEKWKSMSEADKAPYVAKAEKRKVEYEKDMK  104 (113)
Q Consensus        32 ~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l---~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~  104 (113)
                      ..+++.|+||+||||||++++|..|+.+  + +++.||+++|   |++|++|+++||++|+++|+++++.|..++.
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~-~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~   77 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--G-LPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPG   77 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--T-CCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--C-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcccc
Confidence            4578899999999999999999999988  5 5899999999   9999999999999999999999999998763

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

Probab=99.83  E-value=2.7e-22  Score=144.00  Aligned_cols=77  Identities=31%  Similarity=0.497  Sum_probs=70.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        29 ~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      ++..+||+.|+||+|||+|||+++|..+..+     ++.+|+++||++|++|++++|++|+++|++++++|..+|++|++
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~-----~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  180 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAKGD-----SPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  180 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSSCS-----SHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhccC-----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556799999999999999999999988654     45599999999999999999999999999999999999999998


Q ss_pred             hh
Q 033714          109 RQ  110 (113)
Q Consensus       109 ~~  110 (113)
                      ++
T Consensus       181 ~~  182 (214)
T 3tq6_A          181 QM  182 (214)
T ss_dssp             HH
T ss_pred             hC
Confidence            75

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

Probab=99.83  E-value=1.4e-22  Score=127.82  Aligned_cols=69  Identities=20%  Similarity=0.324  Sum_probs=63.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHH
Q 033714           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKD  102 (113)
Q Consensus        29 ~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~--~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~  102 (113)
                      .+..+||+.|+||+|||||||+++|..|+.+||+ ++  +.||+    ++|++|++++|++|+++|++++++|..+
T Consensus        14 ~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~-~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           14 LKWEKEEALGEMATVAPVLYTNINFPNLKEEFPD-WTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             HHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCS-HHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             hhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcC-ccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            3555699999999999999999999999999999 58  88888    9999999999999999999999999753

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

Probab=99.83  E-value=4.5e-22  Score=144.79  Aligned_cols=77  Identities=31%  Similarity=0.497  Sum_probs=70.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        29 ~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      ++..+||+.|+||+|||+|||+++|..++.+     +..+|+++||++|++|++++|++|+++|++++++|+.+|++|++
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~-----~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  212 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAKGD-----SPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  212 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCS-----SHHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhcc-----CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556899999999999999999999888654     45599999999999999999999999999999999999999998


Q ss_pred             hh
Q 033714          109 RQ  110 (113)
Q Consensus       109 ~~  110 (113)
                      ++
T Consensus       213 k~  214 (238)
T 3tmm_A          213 QM  214 (238)
T ss_dssp             HH
T ss_pred             hC
Confidence            75

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

Probab=99.78  E-value=1.9e-19  Score=123.33  Aligned_cols=72  Identities=28%  Similarity=0.541  Sum_probs=69.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 033714           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN  107 (113)
Q Consensus        35 ~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~  107 (113)
                      ++.|+||+||||||+.+.+..|..+||+ +++.||+++||++|++||+++|.+|.++|..++++|..+|.+|.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~   73 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSS-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCS
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccc
Confidence            5789999999999999999999999999 59999999999999999999999999999999999999998885

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

Probab=80.95  E-value=1.3  Score=30.82  Aligned_cols=43  Identities=9%  Similarity=0.134  Sum_probs=33.0

Q ss_pred             CHHHHHHH-HHhhhcCCChhhhhHHHHHHHHH-HHHHHHHHHHHH
Q 033714           65 SVAAVGKA-GGEKWKSMSEADKAPYVAKAEKR-KVEYEKDMKNYN  107 (113)
Q Consensus        65 ~~~eisk~-l~~~Wk~ls~~eK~~y~~~a~~~-k~~y~~~~~~y~  107 (113)
                      ++..+++. ||..|+.+|+++++.|.+..... ...|-..+..|.
T Consensus        73 D~~~~a~~vLG~~wr~at~~Qr~~F~~~F~~~L~~tY~~~l~~y~  117 (211)
T 2qgu_A           73 DFKRTTQIAMGRFWSQATPEQQQQIQDGFKSLLIRTYAGALANVR  117 (211)
T ss_dssp             CHHHHHHHHHGGGTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTCS
T ss_pred             CHHHHHHHHHhHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            55555554 58999999999999999888775 456777777665

---

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	113
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	1e-13
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-13
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	7e-13
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-12
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	4e-12
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	4e-12
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-11
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-11
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	9e-11
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-09
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	5e-09
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-07

>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 = 59.5 bits (144), Expect = 1e-13
 Identities = 33/89 (37%), Positives = 52/89 (58%), Gaps = 1/89 (1%)

Query: 19  KKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWK 78
             P +  +++ +  KDPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWK 60

Query: 79  SMSEADKAPYVAKAEKRKVEYEKDMKNYN 107
           +++  +K PY AKA+  K  YE + + YN
Sbjct: 61  ALTPEEKQPYEAKAQADKKRYESEKELYN 89

>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 = 58.3 bits (141), Expect = 2e-13
 Identities = 34/74 (45%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           N PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA K 
Sbjct: 1   NAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 59

Query: 96  KVEYEKDMKNYNRR 109
           K +YEKD+  Y  +
Sbjct: 60  KEKYEKDIAAYRAK 73

>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 = 56.8 bits (137), Expect = 7e-13
 Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
             KRP +AF V+ ++ R +  +  P +   + + K  G +WK+M+  +K PY  +  +  
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFP-DMHNSNISKILGSRWKAMTNLEKQPYYEEQARLS 60

Query: 97  VEYEKDMKNY 106
            ++ +   +Y
Sbjct: 61  KQHLEKYPDY 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 = 55.6 bits (134), Expect = 2e-12
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           KP+   S++  F++  RE++KK HP    + +   K   E+WK+MS  +K  +   A+  
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 96  KVEYEKDMKNY 106
           K  YE++MK Y
Sbjct: 61  KARYEREMKTY 71

>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 = 54.8 bits (132), Expect = 4e-12
 Identities = 27/72 (37%), Positives = 45/72 (62%), Gaps = 3/72 (4%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           +KPKRP SA+ +++   RE  K+++P    V  V K GGE W++M +  K+ + AKA K 
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENP-GIKVTEVAKRGGELWRAMKD--KSEWEAKAAKA 58

Query: 96  KVEYEKDMKNYN 107
           K +Y++ +K + 
Sbjct: 59  KDDYDRAVKEFE 70

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

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

 Score = 54.8 bits (132), Expect = 4e-12
 Identities = 19/71 (26%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           ++ KRP +AF V+    R +  +++P     + + K  G +WK +SE +K P++ +A++ 
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENP-KMHNSEISKRLGAEWKLLSETEKRPFIDEAKRL 59

Query: 96  KVEYEKDMKNY 106
           +  + K+  +Y
Sbjct: 60  RALHMKEHPDY 70

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

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

 Score = 53.8 bits (129), Expect = 2e-11
 Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 19  KKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWK 78
              +              KPKRP SA F+F EE R Q +++ P   S + + +     W 
Sbjct: 2   SSGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERP-ELSESELTRLLARMWN 60

Query: 79  SMSEADKAPYVAKAEKRKVEYEKDMKNYN 107
            +SE  KA Y A+    K + E+     +
Sbjct: 61  DLSEKKKAKYKAREAALKAQSERKSGPSS 89

>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 = 52.6 bits (126), Expect = 4e-11
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 30  KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYV 89
           K  K P+ PK+P + +F F  E R +Y K HP   S   + K   +K+K + E  K  Y+
Sbjct: 3   KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHP-EMSNLDLTKILSKKYKELPEKKKMKYI 61

Query: 90  AKAEKRKVEYEKDMKNYNRR 109
              ++ K E+E+++  +   
Sbjct: 62  QDFQREKQEFERNLARFRED 81

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

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

 Score = 51.8 bits (124), Expect = 9e-11
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 36  NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
           ++ KRP +AF V+  + R +   ++P     + + K  G +WK ++EA+K P+  +A+K 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENP-RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 96  KVEYEKDMKNYNRR 109
           +  + +   NY  R
Sbjct: 62  QAMHREKYPNYKYR 75

>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 = 48.0 bits (114), Expect = 3e-09
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 32  AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAK 91
           +      K P + +  F +E     + +H   K         G +W+ +S++ K  Y   
Sbjct: 3   SGSSGPKKPPMNGYQKFSQELLSNGELNHLPLKERM---VEIGSRWQRISQSQKEHYKKL 59

Query: 92  AEKRKVEYEKDMKNYNRRQ 110
           AE+++ +Y+  +  + +  
Sbjct: 60  AEEQQRQYKVHLDLWVKSL 78

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

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

 Score = 47.2 bits (112), Expect = 5e-09
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 39  KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
           K+P +AF ++M+E R     +    K  AA+ +  G +W ++S  ++A Y   A K +  
Sbjct: 4   KKPLNAFMLYMKEMRANVVAEST-LKESAAINQILGRRWHALSREEQAKYYELARKERQL 62

Query: 99  YEKDMKNY 106
           + +    +
Sbjct: 63  HMQLYPGW 70

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

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

 Score = 42.6 bits (100), Expect = 4e-07
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 5/88 (5%)

Query: 22  AKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
           +       K   D    K P +++ ++  E     K      +          ++WK +S
Sbjct: 2   SSGSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERM-----VLCSQQWKLLS 56

Query: 82  EADKAPYVAKAEKRKVEYEKDMKNYNRR 109
           + +K  Y  K +++K +YE ++  +   
Sbjct: 57  QKEKDAYHKKCDQKKKDYEVELLRFLES 84

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	113
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.95
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.93
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.92
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.91
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.9
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.9
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.9
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.9
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.88
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.88
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.88
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.87
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	97.76

>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=99.95  E-value=2.1e-27  Score=149.28  Aligned_cols=87  Identities=37%  Similarity=0.663  Sum_probs=80.9

Q ss_pred             cCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHH
Q 033714           24 AGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDM  103 (113)
Q Consensus        24 ~~k~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~  103 (113)
                      .+++..+..+||+.|+||+|||+||+.++|..|+.++|+ +++.+|++.||++|++||+++|.+|+++|++++++|..+|
T Consensus         7 ~~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~   85 (93)
T d1lwma_           7 PKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEK   85 (93)
T ss_dssp             TTSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555677799999999999999999999999999999 5999999999999999999999999999999999999999


Q ss_pred             HHHHHhhh
Q 033714          104 KNYNRRQV  111 (113)
Q Consensus       104 ~~y~~~~~  111 (113)
                      .+|+++|+
T Consensus        86 ~~y~~~l~   93 (93)
T d1lwma_          86 ELYNATLA   93 (93)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHhccC
Confidence            99999875

>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=99.93  E-value=6.4e-26  Score=138.35  Aligned_cols=75  Identities=45%  Similarity=0.771  Sum_probs=71.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQV  111 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~~  111 (113)
                      |.|+||+|||+||++++|..|+.+||+ +++.+|+++||++|++||+++|.+|.++|.+++++|..+|++|+.++.
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~-~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~   75 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGK   75 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTT-CCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence            589999999999999999999999999 599999999999999999999999999999999999999999998753

>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=99.92  E-value=1.7e-25  Score=139.68  Aligned_cols=80  Identities=30%  Similarity=0.561  Sum_probs=76.9

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        29 ~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      ++..+||+.|+||+|||+||++++|..+..+||+ +++.+|++.||++|+.||+++|.+|.++|++++.+|..+|.+|.+
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~-~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~   80 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE   80 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGG
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999999 599999999999999999999999999999999999999999987


Q ss_pred             h
Q 033714          109 R  109 (113)
Q Consensus       109 ~  109 (113)
                      .
T Consensus        81 ~   81 (91)
T d1k99a_          81 D   81 (91)
T ss_dssp             C
T ss_pred             H
Confidence            5

>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=99.91  E-value=5.8e-25  Score=134.61  Aligned_cols=72  Identities=28%  Similarity=0.560  Sum_probs=69.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      +.|+||+||||||++++|..|..+||+ .++.+|+++||++|++||+++|++|+++|..++++|..+|++|+.
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~-~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~   72 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKY   72 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccC
Confidence            478999999999999999999999999 599999999999999999999999999999999999999999863

>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=99.90  E-value=1.7e-24  Score=133.76  Aligned_cols=72  Identities=28%  Similarity=0.533  Sum_probs=69.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      +.|+||+||||||++++|..|..+||+ .++.+|+++||++|++||+++|.+|+++|.+++++|..+|++|+.
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~-~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~   74 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhcc
Confidence            689999999999999999999999999 599999999999999999999999999999999999999999864

>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=99.90  E-value=3e-24  Score=128.35  Aligned_cols=70  Identities=34%  Similarity=0.644  Sum_probs=65.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCC-CCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKN-KSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      +|+||+|||+||++++|..|+.+||+. +++.+|+++||++|++||+++|++|.++|.+++++|..+|++|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            589999999999999999999999973 2678999999999999999999999999999999999999876

>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=99.90  E-value=9.6e-25  Score=130.43  Aligned_cols=69  Identities=25%  Similarity=0.501  Sum_probs=65.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      .++||+||||||+++.|..|+.+||+ .++++|+++||++|++||+++|++|.++|++++++|.+++++|
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            56899999999999999999999999 5999999999999999999999999999999999999888765

>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=99.90  E-value=5.5e-24  Score=127.96  Aligned_cols=71  Identities=39%  Similarity=0.769  Sum_probs=67.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        36 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      ++|+||+||||||++++|..|+.+||+ +++.+|+++||++|++|+  +|++|.++|++++++|..+|++|+.+
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~-~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~   72 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPG-IKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTT-CCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            689999999999999999999999999 599999999999999875  59999999999999999999999875

>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=99.88  E-value=3.8e-23  Score=127.90  Aligned_cols=71  Identities=24%  Similarity=0.439  Sum_probs=67.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR  108 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~  108 (113)
                      ..+||+||||||+++.|..|..+||+ +++++|+++||.+|++||+++|++|.++|++++++|..++++|..
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~-~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~   72 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA   72 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            46899999999999999999999999 599999999999999999999999999999999999999999864

>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=99.88  E-value=4.4e-23  Score=128.34  Aligned_cols=74  Identities=32%  Similarity=0.531  Sum_probs=68.5

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHH
Q 033714           28 SGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKD  102 (113)
Q Consensus        28 ~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~  102 (113)
                      ......|++.|+||+|||+|||+++|..|+.+||+ +++.+|+++|+++|+.|++++|++|.++|.+++++|.++
T Consensus        11 ~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~-~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             ccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34556889999999999999999999999999999 599999999999999999999999999999999888754

>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=99.88  E-value=1.6e-22  Score=129.78  Aligned_cols=79  Identities=18%  Similarity=0.313  Sum_probs=70.9

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 033714           27 KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY  106 (113)
Q Consensus        27 ~~~k~~~d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y  106 (113)
                      ...+...|+.+|++|+|||+||++++|.+    +|+ +++.||+++||++|++||+++|++|.++|.+++++|..+|.+|
T Consensus         7 ~~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~-~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y   81 (108)
T d1v64a_           7 GQLKDKFDGRPTKPPPNSYSLYCAELMAN----MKD-VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRF   81 (108)
T ss_dssp             CCSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCcHHHHHHHHHHHH----ccC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555677888999999999999998865    577 5999999999999999999999999999999999999999999


Q ss_pred             HHhh
Q 033714          107 NRRQ  110 (113)
Q Consensus       107 ~~~~  110 (113)
                      ...+
T Consensus        82 ~~~~   85 (108)
T d1v64a_          82 LESL   85 (108)
T ss_dssp             HHHS
T ss_pred             HhhC
Confidence            8764

>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=99.87  E-value=2.7e-22  Score=127.07  Aligned_cols=74  Identities=18%  Similarity=0.336  Sum_probs=67.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 033714           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ  110 (113)
Q Consensus        34 d~~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~~  110 (113)
                      ..++||||+|||+|||+++|..+...+   +++.||+++||++|++||+++|++|.++|.+++++|..+|.+|...+
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~~---~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~   78 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELNH---LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSL   78 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTT---SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcC---CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            356899999999999999999986554   36899999999999999999999999999999999999999998764

>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=97.76  E-value=0.0001  Score=42.55  Aligned_cols=71  Identities=18%  Similarity=0.321  Sum_probs=61.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q 033714           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR  109 (113)
Q Consensus        37 ~PKrP~say~lF~~~~r~~~~~~~p~~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~~~y~~~  109 (113)
                      -|-.|.+|--+|.+.....+...+-.  +..-..+.+-..|++|...|+.+|+..|.+|..+|+.++-+.+.-
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~--DR~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~~   73 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP   73 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHh--hHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            47788999999999999998888765  466677788899999999999999999999999999998775543