Citrus Sinensis ID: 034575

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90
Protein Sequence
MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVLV
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHHcccccccHccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccHccEEEEEc
Coil and Loop (DISEMBL)
mkggksksdtrnaklsvnkkpakagrksgkaakdpnkpkrpasAFFVFMEEFREQykkdhpknksVAAVGKAGGEKWKSMSEAVSGLVLV
Flexible Loop (DISEMBL)
mkggksksdtrnaklsvnkkpakagrksgkaakdpnkpkrpASAFFVFMEEFREqykkdhpknksvaavgkaggekwksmseavsglvlv
Low Complexity Region (SEG)
MKGGKSKSDTRNAKLSVNkkpakagrksgkaakDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVLV
Disordered region (IsUnstruct)
********************************************FFVFME****************************************
Disordered Region (DISOPRED)
*****************************************ASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA**GLVLV
Disordered Region (DISEMBL)
***************************************RPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVLV
Disordered Region (DISPRO)
************************************KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVLV
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVLV
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	90	2.2.26 [Sep-21-2011]
P93047	141	High mobility group B pro	no	no	0.888	0.567	0.734	2e-27
O49596	144	High mobility group B pro	no	no	0.922	0.576	0.710	3e-27
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.911	0.550	0.685	6e-23
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.922	0.546	0.662	2e-22
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.9	0.562	0.662	1e-21
P27347	157	DNA-binding protein MNB1B	N/A	no	0.9	0.515	0.659	3e-20
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.922	0.515	0.643	5e-17
Q42344	138	High mobility group B pro	no	no	0.866	0.565	0.518	2e-16
O49595	178	High mobility group B pro	no	no	0.644	0.325	0.689	8e-16
O49597	125	High mobility group B pro	no	no	0.644	0.464	0.551	1e-13

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

 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 61/83 (73%), Positives = 72/83 (86%), Gaps = 3/83 (3%)

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

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          PKNKSVAAVGKAGGEKWKS+S++
Sbjct: 58 PKNKSVAAVGKAGGEKWKSLSDS 80

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 =  120 bits (300), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 59/83 (71%), Positives = 72/83 (86%)

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

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          PKNKSVA VGKA G+KWKS+S++
Sbjct: 61 PKNKSVATVGKAAGDKWKSLSDS 83

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  105 bits (263), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 61/89 (68%), Positives = 69/89 (77%), Gaps = 7/89 (7%)

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

Query: 54 EQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          EQYKKDHP NKSVAAVGKA GE+WKS+SE
Sbjct: 61 EQYKKDHPNNKSVAAVGKACGEEWKSLSE 89

Vicia faba (taxid: 3906)

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

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 59/89 (66%), Positives = 72/89 (80%), Gaps = 6/89 (6%)

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

Query: 55 QYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
           + K+HP+NK+V+AVGKA G KWK+MS+A
Sbjct: 61 VFNKEHPENKAVSAVGKAAGAKWKTMSDA 89

Glycine max (taxid: 3847)

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

 Score =  102 bits (253), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 55/83 (66%), Positives = 66/83 (79%), Gaps = 2/83 (2%)

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 PKNKSVAAVGKAGGEKWKSMSEA 83
          P NKSVA VGKAGG+KWK ++ A
Sbjct: 59 PNNKSVAVVGKAGGDKWKQLTAA 81

Ipomoea nil (taxid: 35883)

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

 Score = 97.1 bits (240), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 58/88 (65%), Positives = 71/88 (80%), Gaps = 7/88 (7%)

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

Query: 56 YKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          +K+ +PKNKSVAAVGKA G++WKS+SE+
Sbjct: 59 FKEKNPKNKSVAAVGKAAGDRWKSLSES 86

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

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

 Score = 86.3 bits (212), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 56/87 (64%), Positives = 67/87 (77%), Gaps = 4/87 (4%)

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

Query: 57 KKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          K+ +PKNKSVAAVGKA GE+WKS+SE+
Sbjct: 61 KQKNPKNKSVAAVGKAAGERWKSLSES 87

Triticum aestivum (taxid: 4565)

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

 Score = 84.7 bits (208), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 43/83 (51%), Positives = 61/83 (73%), Gaps = 5/83 (6%)

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

Query: 60 HPKNKSVAAVGKAGGEKWKSMSE 82
          +P NKSVA VGKA G +WK+M++
Sbjct: 57 NPNNKSVATVGKAAGARWKAMTD 79

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 82.4 bits (202), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 49/58 (84%)

Query: 26 RKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          RK  KA KDPNKPKR  SAFFVF+E+FR  +KK++P  K+V+AVGKAGG+KWKSMS+A
Sbjct: 41 RKEKKAKKDPNKPKRAPSAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQA 98

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 = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 45/58 (77%)

Query: 25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          G K GK  KDPN+PK+P S FFVF+++FR+++   +P NKSV  VG+A G+KWK+M+E
Sbjct: 21 GNKVGKKTKDPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTE 78

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	90
308569654	146	high mobility group box 2 protein [Gossy	0.922	0.568	0.880	2e-32
224083306	160	high mobility group family [Populus tric	0.922	0.518	0.820	4e-32
297845042	141	hypothetical protein ARALYDRAFT_472304 [	0.888	0.567	0.807	2e-29
312282031	141	unnamed protein product [Thellungiella h	0.888	0.567	0.783	1e-28
312281681	144	unnamed protein product [Thellungiella h	0.922	0.576	0.771	2e-28
255539248	145	DNA-binding protein MNB1B, putative [Ric	0.922	0.572	0.855	2e-28
304651500	146	high mobility group protein [Hevea brasi	0.922	0.568	0.892	2e-28
118488125	151	unknown [Populus trichocarpa]	0.922	0.549	0.75	9e-27
357640485	145	high mobility group B2 protein [Brassica	0.922	0.572	0.795	2e-26
308569660	142	high mobility group box 1 protein [Gossy	0.888	0.563	0.879	3e-26

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

 Score =  142 bits (359), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 74/84 (88%), Positives = 80/84 (95%), Gaps = 1/84 (1%)

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

Query: 60 HPKNKSVAAVGKAGGEKWKSMSEA 83
          HPKNKSVAAVGKAGG+KWKS+SEA
Sbjct: 61 HPKNKSVAAVGKAGGDKWKSLSEA 84

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 =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 73/89 (82%), Positives = 80/89 (89%), Gaps = 6/89 (6%)

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

Query: 55 QYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          QYK++HPKNKSVAAVGKAGG+KWKS+SEA
Sbjct: 61 QYKREHPKNKSVAAVGKAGGDKWKSLSEA 89

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 =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 67/83 (80%), Positives = 76/83 (91%), Gaps = 3/83 (3%)

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

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          PKNKSVAAVGKAGGEKWKS+S++
Sbjct: 60 PKNKSVAAVGKAGGEKWKSLSDS 82

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  130 bits (326), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 65/83 (78%), Positives = 75/83 (90%), Gaps = 3/83 (3%)

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

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          P NKSVAAVGKAGG+KWKS+S++
Sbjct: 58 PNNKSVAAVGKAGGQKWKSLSDS 80

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 64/83 (77%), Positives = 75/83 (90%)

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

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          PKNKSVAAVGKA G+KWKS+S+A
Sbjct: 61 PKNKSVAAVGKAAGDKWKSLSDA 83

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

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 =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 71/83 (85%), Positives = 80/83 (96%)

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

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          PKNKSVAAVGKAGG++WKSMSE+
Sbjct: 61 PKNKSVAAVGKAGGDRWKSMSES 83

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 75/84 (89%), Positives = 81/84 (96%), Gaps = 1/84 (1%)

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

Query: 60 HPKNKSVAAVGKAGGEKWKSMSEA 83
          HPKNKSVAAVGKAGG+KWKS+SEA
Sbjct: 61 HPKNKSVAAVGKAGGDKWKSLSEA 84

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  124 bits (310), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 66/88 (75%), Positives = 73/88 (82%), Gaps = 5/88 (5%)

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

Query: 56 YKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          YKK+HPKNKSVAAVGKAGG+KWKS+S A
Sbjct: 61 YKKEHPKNKSVAAVGKAGGDKWKSLSAA 88

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357640485|gb|AET87126.1| high mobility group B2 protein [Brassica napus]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 66/83 (79%), Positives = 75/83 (90%)

Query: 1  MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
          MKGGKSK++TR++KLSV KKPAKA   S  AAKDPNKPKRPASAFFVFME+FR+ YKKDH
Sbjct: 1  MKGGKSKTETRSSKLSVAKKPAKAAGGSKAAAKDPNKPKRPASAFFVFMEDFRQTYKKDH 60

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          P NKSVAAVGKAGGEKWKS+S++
Sbjct: 61 PNNKSVAAVGKAGGEKWKSLSDS 83

Source: Brassica napus

Species: Brassica napus

Genus: Brassica

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  122 bits (305), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 73/83 (87%), Positives = 79/83 (95%), Gaps = 3/83 (3%)

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

Query: 61 PKNKSVAAVGKAGGEKWKSMSEA 83
          PKNKSVAAVGKAGG+KWKS+SEA
Sbjct: 58 PKNKSVAAVGKAGGDKWKSLSEA 80

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	90
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.922	0.576	0.614	1.1e-23
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.877	0.572	0.439	1.1e-14
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.544	0.392	0.551	2.4e-12
TAIR|locus:2154433	241	HMGB6 "high-mobility group box	0.5	0.186	0.562	9.5e-10
UNIPROTKB|P40618	202	HMGB3 "High mobility group pro	0.533	0.237	0.489	1.2e-07
UNIPROTKB|F1N927	214	HMGB1 "High mobility group pro	0.5	0.210	0.521	1.3e-07
UNIPROTKB|Q9YH06	215	HMG1 "High mobility group 1 pr	0.5	0.209	0.521	1.3e-07
ZFIN|ZDB-GENE-030131-341	205	hmgb1a "high-mobility group bo	0.522	0.229	0.5	1.3e-07
UNIPROTKB|Q5T7C4	158	HMGB1 "High mobility group pro	0.5	0.284	0.5	1.8e-07
UNIPROTKB|Q5T7C6	162	HMGB1 "High mobility group pro	0.5	0.277	0.5	1.8e-07

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

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 51/83 (61%), Positives = 63/83 (75%)

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

Query:    61 PKNKSVAAVGKAGGEKWKSMSEA 83
             PKNKSVA VGKA G+KWKS+S++
Sbjct:    61 PKNKSVATVGKAAGDKWKSLSDS 83

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 = 187 (70.9 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 36/82 (43%), Positives = 52/82 (63%)

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

Query:    61 PKNKSVAAVGKAGGEKWKSMSE 82
             P NKSVA VGKA G +WK+M++
Sbjct:    58 PNNKSVATVGKAAGARWKAMTD 79

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 = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 27/49 (55%), Positives = 40/49 (81%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
             DPN+PK+P S FFVF+++FR+++   +P NKSV  VG+A G+KWK+M+E
Sbjct:    30 DPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTE 78

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

TAIR|locus:2154433 HMGB6 "high-mobility group box 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 9.5e-10, P = 9.5e-10
 Identities = 27/48 (56%), Positives = 36/48 (75%)

Query:    36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAA-VGKAGGEKWKSMSE 82
             NKPKRP +AFF+FM +FR+ +K +H  N S+A    K GGEKWKS++E
Sbjct:   113 NKPKRPLTAFFIFMSDFRKTFKSEH--NGSLAKDAAKIGGEKWKSLTE 158

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0003677 "DNA binding" evidence=IDA

GO:0006261 "DNA-dependent DNA replication" evidence=RCA

UNIPROTKB|P40618 HMGB3 "High mobility group protein B3" [Gallus gallus (taxid:9031)]

 Score = 121 (47.7 bits), Expect = 1.2e-07, P = 1.2e-07
 Identities = 24/49 (48%), Positives = 31/49 (63%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
             DPN PKRP SAFF+F  EFR + K  +P   S+  V K  GE W ++S+
Sbjct:    89 DPNAPKRPPSAFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLSD 136

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

UNIPROTKB|F1N927 HMGB1 "High mobility group protein B1" [Gallus gallus (taxid:9031)]

 Score = 122 (48.0 bits), Expect = 1.3e-07, P = 1.3e-07
 Identities = 24/46 (52%), Positives = 29/46 (63%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKS 79
             DPN PKRP SAFF+F  EFR + K +HP   S+  V K  GE W +
Sbjct:    91 DPNAPKRPPSAFFLFCSEFRPKIKGEHP-GLSIGDVAKKLGEMWNN 135

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

GO:0002437 "inflammatory response to antigenic stimulus" evidence=IEA

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006288 "base-excision repair, DNA ligation" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0010858 "calcium-dependent protein kinase regulator activity" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0017055 "negative regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0030295 "protein kinase activator activity" evidence=IEA

GO:0030324 "lung development" evidence=IEA

GO:0033151 "V(D)J recombination" evidence=IEA

GO:0043005 "neuron projection" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0045639 "positive regulation of myeloid cell differentiation" evidence=IEA

GO:0045819 "positive regulation of glycogen catabolic process" evidence=IEA

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

GO:0051384 "response to glucocorticoid stimulus" evidence=IEA

GO:0070491 "repressing transcription factor binding" evidence=IEA

GO:2000426 "negative regulation of apoptotic cell clearance" evidence=IEA

UNIPROTKB|Q9YH06 HMG1 "High mobility group 1 protein" [Gallus gallus (taxid:9031)]

 Score = 122 (48.0 bits), Expect = 1.3e-07, P = 1.3e-07
 Identities = 24/46 (52%), Positives = 29/46 (63%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKS 79
             DPN PKRP SAFF+F  EFR + K +HP   S+  V K  GE W +
Sbjct:    91 DPNAPKRPPSAFFLFCSEFRPKIKGEHP-GLSIGDVAKKLGEMWNN 135

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

GO:0002437 "inflammatory response to antigenic stimulus" evidence=IEA

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006288 "base-excision repair, DNA ligation" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0010858 "calcium-dependent protein kinase regulator activity" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0017055 "negative regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0030295 "protein kinase activator activity" evidence=IEA

GO:0030324 "lung development" evidence=IEA

GO:0033151 "V(D)J recombination" evidence=IEA

GO:0043005 "neuron projection" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0045639 "positive regulation of myeloid cell differentiation" evidence=IEA

GO:0045819 "positive regulation of glycogen catabolic process" evidence=IEA

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

GO:0051384 "response to glucocorticoid stimulus" evidence=IEA

GO:0070491 "repressing transcription factor binding" evidence=IEA

GO:2000426 "negative regulation of apoptotic cell clearance" evidence=IEA

ZFIN|ZDB-GENE-030131-341 hmgb1a "high-mobility group box 1a" [Danio rerio (taxid:7955)]

 Score = 121 (47.7 bits), Expect = 1.3e-07, P = 1.3e-07
 Identities = 24/48 (50%), Positives = 30/48 (62%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
             DPN PKRP SAFF+F  EFR + K++ P   S+  V K  GE W  +S
Sbjct:    90 DPNAPKRPPSAFFIFCSEFRPKVKEETP-GLSIGDVAKRLGEMWNKIS 136

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0009409 "response to cold" evidence=IDA

GO:0030900 "forebrain development" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|Q5T7C4 HMGB1 "High mobility group protein B1" [Homo sapiens (taxid:9606)]

 Score = 119 (46.9 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 23/46 (50%), Positives = 29/46 (63%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKS 79
             DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W +
Sbjct:    91 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNN 135

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q5T7C6 HMGB1 "High mobility group protein B1" [Homo sapiens (taxid:9606)]

 Score = 119 (46.9 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 23/46 (50%), Positives = 29/46 (63%)

Query:    34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKS 79
             DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W +
Sbjct:    91 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNN 135

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Fail to connect to STRING server

---

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	90
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	9e-11
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-10
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	4e-10
smart00398	70	smart00398, HMG, high mobility group	1e-07
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	2e-06
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	8e-06
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	6e-05
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	6e-05

>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 = 51.9 bits (125), Expect = 9e-11
 Identities = 24/45 (53%), Positives = 32/45 (71%), Gaps = 1/45 (2%)

Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          PKRP SA+F+F +E R + KK++P + SV  V K  GEKWK +SE
Sbjct: 1  PKRPLSAYFLFSQEQRPKLKKENP-DASVTEVTKILGEKWKELSE 44

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

 Score = 51.1 bits (123), Expect = 3e-10
 Identities = 23/47 (48%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
          PKRP SAFF+F +E R + K ++P  K  A + K  GEKWK++SE  
Sbjct: 1  PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEE 46

Length = 69

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

 Score = 50.3 bits (121), Expect = 4e-10
 Identities = 22/47 (46%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
          PKRP SA+F+F +E R + K ++P   SV  + K  GE WKS+SE  
Sbjct: 1  PKRPLSAYFLFSQEHRAEVKAENP-GLSVGEISKILGEMWKSLSEEE 46

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

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

 Score = 44.2 bits (105), Expect = 1e-07
 Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
          KPKRP SAF +F +E R + K ++P     A + K  GE+WK +SE  
Sbjct: 1  KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEE 47

Length = 70

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

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

Query: 74  GEKWKSMSE 82
            EKWK +++
Sbjct: 106 SEKWKELTD 114

Length = 211

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

 Score = 39.7 bits (93), Expect = 8e-06
 Identities = 21/49 (42%), Positives = 30/49 (61%)

Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          PNKPK   +A+F F++  R + K++ P+   VA   K   EKWK+MSE 
Sbjct: 1  PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEE 49

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 = 37.3 bits (87), Expect = 6e-05
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KRP +AF +F +  R +  +++P  K   A+ K  G++WK++S  
Sbjct: 3  KRPMNAFMLFSKRHRRKVLQEYP-LKENRAISKILGDRWKALSNE 46

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

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

 Score = 37.9 bits (88), Expect = 6e-05
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (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 EA 83
          E 
Sbjct: 68 EE 69

Length = 94

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	90
PTZ00199	94	high mobility group protein; Provisional	99.87
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.76
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.74
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.73
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.71
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.7
smart00398	70	HMG high mobility group.	99.7
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.68
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.64
KOG0381	96	consensus HMG box-containing protein [General func	99.59
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.59
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.37
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	99.06
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	99.0
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.98
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.32
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.54
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.36
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	96.97
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	96.59
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	95.68
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	94.84
COG5648	211	NHP6B Chromatin-associated proteins containing the	94.34
KOG3223	221	consensus Uncharacterized conserved protein [Funct	84.92

>PTZ00199 high mobility group protein; Provisional

Probab=99.87  E-value=3.2e-22  Score=125.75  Aligned_cols=66  Identities=39%  Similarity=0.578  Sum_probs=60.3

Q ss_pred             ccccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCChhhhcccc
Q 034575           23 KAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        23 ~~~k~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~--~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ..++++++..+||+.|+||+||||+|++++|..|..+||+ ++  +++|+++||++|+.||++||.+|+
T Consensus         8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~-~~~~~~evsk~ige~Wk~ls~eeK~~y~   75 (94)
T PTZ00199          8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPE-LAKDVAAVGKMVGEAWNKLSEEEKAPYE   75 (94)
T ss_pred             ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcC-CcccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            3456666778999999999999999999999999999999 65  899999999999999999999996

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

Probab=99.76  E-value=1.5e-18  Score=104.88  Aligned_cols=52  Identities=25%  Similarity=0.445  Sum_probs=50.3

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +|+||+||||||+++.|..+..+||+ +++.||+++||++|++|++++|++|+
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~~g~~Wk~ls~eeK~~y~   52 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPG-LTNNEISRIIGRMWRSESPEVKAYYK   52 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHH
Confidence            48999999999999999999999999 99999999999999999999999985

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.

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

Probab=99.74  E-value=4.1e-18  Score=99.07  Aligned_cols=51  Identities=47%  Similarity=0.716  Sum_probs=49.8

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        38 PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |++|+|||++|++++|..+..+||+ +++.+|++.||++|++||++||.+|+
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~   51 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYE   51 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            8999999999999999999999999 99999999999999999999999985

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

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

Probab=99.73  E-value=7.3e-18  Score=100.78  Aligned_cols=51  Identities=29%  Similarity=0.514  Sum_probs=49.4

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        38 PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .|||+||||+|++++|..++.+||+ +++.||++.||++|+.||+++|++|+
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~-~~~~eisk~l~~~Wk~ls~~eK~~y~   52 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQPYY   52 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            5899999999999999999999999 99999999999999999999999985

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.

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

Probab=99.71  E-value=6.1e-18  Score=119.03  Aligned_cols=63  Identities=37%  Similarity=0.673  Sum_probs=59.9

Q ss_pred             cccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           26 RKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        26 k~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +...++.+|||.||||+|+||+|++++|+.++.++|+ +++++|++++|++|++|+++||++|.
T Consensus        59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~-l~~~e~~k~~~e~WK~Ltd~eke~y~  121 (211)
T COG5648          59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPK-LTFGEVGKLLSEKWKELTDEEKEPYY  121 (211)
T ss_pred             HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCC-CChHHHHHHHHHHHHhccHhhhhhHH
Confidence            4567788999999999999999999999999999999 99999999999999999999999985

>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=99.70  E-value=2e-17  Score=96.95  Aligned_cols=51  Identities=33%  Similarity=0.570  Sum_probs=47.7

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        38 PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |+||+|||++|+++++..+..+||+ ++..+|+++|+++|++|+++||.+|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~-~~~~~i~~~~~~~W~~l~~~eK~~y~   51 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPD-LSNKEISKILAQMWKNLSEEEKAPYK   51 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTT-STHHHHHHHHHHHHHCSHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcc-cccccchhhHHHHHhcCCHHHHHHHH
Confidence            8999999999999999999999999 99999999999999999999999985

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

>smart00398 HMG high mobility group

Probab=99.70  E-value=4.3e-17  Score=95.17  Aligned_cols=52  Identities=42%  Similarity=0.643  Sum_probs=50.3

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +|++|+|+|++|+++++..+..+||+ +++.+|++.||.+|+.|++++|.+|+
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~ek~~y~   52 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPD-LSNAEISKKLGERWKLLSEEEKAPYE   52 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            58999999999999999999999999 99999999999999999999999985

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

Probab=99.68  E-value=9.1e-17  Score=92.81  Aligned_cols=51  Identities=43%  Similarity=0.675  Sum_probs=49.6

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        38 PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |++|+|||++|+++.+..+..+||+ +++.+|++.|+.+|+.|++++|.+|.
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~   51 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYE   51 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            7899999999999999999999999 99999999999999999999999985

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

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

Probab=99.64  E-value=3.5e-16  Score=93.70  Aligned_cols=54  Identities=43%  Similarity=0.644  Sum_probs=46.6

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHh-CCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           35 PNKPKRPASAFFVFMEEFREQYKKD-HPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        35 p~~PKrP~say~lf~~~~r~~~~~~-~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |+.||+|+|||+||+.+++..+..+ ++. .++.|+++.|++.|++||++||.+|+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~-~~~~e~~k~~~~~Wk~Ls~~EK~~Y~   55 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQK-QSFREVMKEISERWKSLSEEEKEPYE   55 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T--SSHHHHHHHHHHHHHHS-HHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccC-CCHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            6789999999999999999999988 666 89999999999999999999999996

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 ....

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

Probab=99.59  E-value=4.3e-15  Score=92.43  Aligned_cols=55  Identities=45%  Similarity=0.699  Sum_probs=52.5

Q ss_pred             CC--CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           34 DP--NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        34 dp--~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ||  +.|++|++||++|+.+.+..+..+||+ +++.+|++++|++|++|+++++.+|+
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~   73 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYE   73 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            66  499999999999999999999999999 99999999999999999999999884

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.59  E-value=1.4e-15  Score=113.66  Aligned_cols=58  Identities=28%  Similarity=0.476  Sum_probs=54.2

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        31 ~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ......+.||||||||+|+++.|.++..+||. +++.||++.||.+|+.|+++||.+|+
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~-mHNSEISK~LG~~WK~Lse~EKrPFi  113 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPK-MHNSEISKRLGAEWKLLSEEEKRPFV  113 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcc-hhhHHHHHHHHHHHhhcCHhhhccHH
Confidence            34455689999999999999999999999999 99999999999999999999999997

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

Probab=99.37  E-value=5.4e-13  Score=104.36  Aligned_cols=60  Identities=45%  Similarity=0.679  Sum_probs=54.3

Q ss_pred             ccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        25 ~k~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++++.++.+|||+|||++||||+|++..|..++.+  + .+++||++.+|++|+.|++  |.+|+
T Consensus       523 ~~k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--g-i~~~dv~kk~g~~wk~ms~--k~~we  582 (615)
T KOG0526|consen  523 KKKKGKKKKDPNAPKRATSAYMLWLNASRESIKED--G-ISVGDVAKKAGEKWKQMSA--KEEWE  582 (615)
T ss_pred             cccCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--C-chHHHHHHHHhHHHhhhcc--cchhh
Confidence            34677888999999999999999999999999987  6 8999999999999999998  66665

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=99.06  E-value=1.2e-10  Score=87.51  Aligned_cols=51  Identities=25%  Similarity=0.496  Sum_probs=48.3

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLV   88 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Y   88 (90)
                      ..|+|+||||+|+.|.|..|.+++.- ....+|.++||++|++||.||..+|
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEctl-KeSAaiNqiLGrRWH~LSrEEQAKY  241 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECTL-KESAAINQILGRRWHALSREEQAKY  241 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhhh-hhHHHHHHHHhHHHhhhhHHHHHHH
Confidence            68999999999999999999999987 7899999999999999999998877

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

Probab=99.00  E-value=2.9e-10  Score=84.86  Aligned_cols=58  Identities=21%  Similarity=0.443  Sum_probs=53.8

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        31 ~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ..+.|.+|.+|+.+||.|+..+|++|++.||+ +...||.++||.+|..|+++||+.|+
T Consensus        58 ~pkpPkppekpl~pymrySrkvWd~VkA~nPe-~kLWeiGK~Ig~mW~dLpd~EK~ey~  115 (410)
T KOG4715|consen   58 RPKPPKPPEKPLMPYMRYSRKVWDQVKASNPE-LKLWEIGKIIGGMWLDLPDEEKQEYL  115 (410)
T ss_pred             CCCCCCCCCcccchhhHHhhhhhhhhhccCcc-hHHHHHHHHHHHHHhhCcchHHHHHH
Confidence            34467788999999999999999999999999 99999999999999999999999885

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

Probab=98.98  E-value=1.5e-10  Score=89.74  Aligned_cols=59  Identities=25%  Similarity=0.403  Sum_probs=54.4

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhccc
Q 034575           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLV   88 (90)
Q Consensus        29 kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Y   88 (90)
                      +.....+++.||||||||+|..|.|-.+-..+|+ +....|+++||.+|+.|+..||++|
T Consensus       317 rg~~ss~PHIKRPMNAFMVWAkDERRKILqA~PD-MHNSnISKILGSRWKaMSN~eKQPY  375 (511)
T KOG0528|consen  317 RGRASSEPHIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMSNTEKQPY  375 (511)
T ss_pred             cCcCCCCccccCCcchhhcccchhhhhhhhcCcc-ccccchhHHhcccccccccccccch
Confidence            4455566789999999999999999999999999 9999999999999999999999998

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

Probab=98.32  E-value=2e-07  Score=74.81  Aligned_cols=59  Identities=22%  Similarity=0.436  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHH--HHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           30 KAAKDPNKPKRPASAFFVFMEEFR--EQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        30 k~~~dp~~PKrP~say~lf~~~~r--~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .-.+|..+..+|||+|++|++.++  ..+...||+ ..+..|+++||+.|-.|-+.||+.|-
T Consensus       174 pnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn-~DNrtIskiLgewWytL~~~Ekq~yh  234 (683)
T KOG2746|consen  174 PNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPN-QDNRTISKILGEWWYTLGPNEKQKYH  234 (683)
T ss_pred             CCcCcchhhhhhhHHHHHHHhhcCCccchhccCcc-ccchhHHHHHhhhHhhhCchhhhhHH
Confidence            344556688999999999999999  899999999 99999999999999999999999984

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

Probab=97.54  E-value=0.00013  Score=50.81  Aligned_cols=43  Identities=26%  Similarity=0.376  Sum_probs=38.0

Q ss_pred             CChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           42 ASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        42 ~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      -++|+-|+.+++.    .|.+ ++..|+....+..|..|+++||..|+
T Consensus        83 nnaYLNFLReFRr----kh~~-L~p~dlI~~AAraW~rLSe~eK~rYr  125 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCG-LSPQDLIQRAARAWCRLSEAEKNRYR  125 (183)
T ss_pred             chHHHHHHHHHHH----HccC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            4679999999876    4566 89999999999999999999999985

The function of this family is unknown.

>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=97.36  E-value=0.00061  Score=47.16  Aligned_cols=48  Identities=29%  Similarity=0.441  Sum_probs=42.1

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 034575           33 KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS   81 (90)
Q Consensus        33 ~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls   81 (90)
                      +.|.+-.|-+|||-.|+.+....++++||+ +++.|.-...+..|...+
T Consensus       117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~-ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPD-ISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             CCccccCCCchhHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHhhhhCc
Confidence            334455677899999999999999999999 999999999999998765

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

Probab=96.97  E-value=0.0012  Score=37.84  Aligned_cols=40  Identities=20%  Similarity=0.377  Sum_probs=35.9

Q ss_pred             CChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCh
Q 034575           42 ASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE   82 (90)
Q Consensus        42 ~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~   82 (90)
                      ++.|=+|.+..|+.+...||+ +..+.+..+++.+|++-++
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk-~~~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPK-APMSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCC-CcHHHHHHHHHHHHHHHHh
Confidence            356889999999999999999 9999999999999987544

; 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

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

Probab=96.59  E-value=0.0045  Score=37.98  Aligned_cols=51  Identities=18%  Similarity=0.216  Sum_probs=40.0

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .|..|.+|--+|.+.....+-+.+++ -...+ .+.+...|.+|++.+|.+|+
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~-dr~K~-~kam~~~W~~me~Kekl~WI   53 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRN-DRKKA-LKAMEAQWSQMEKKEKLKWI   53 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTS-THHHH-HHHHHHHHHTTGGGHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhH-hHHHH-HHHHHHHHHHhhhhhhhHHH
Confidence            57888999999999999999999998 45555 45899999999999998875

>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=95.68  E-value=0.039  Score=39.12  Aligned_cols=45  Identities=20%  Similarity=0.383  Sum_probs=35.2

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 034575           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSM   80 (90)
Q Consensus        31 ~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~l   80 (90)
                      .......++||+|+||.|+.-+-    ...|+ ....+++..|+..|..=
T Consensus        37 ~~~~~~~~kr~lN~Fm~FRsyy~----~~~~~-~~Qk~~S~~l~~lW~~d   81 (201)
T PF04769_consen   37 RKRSPEKAKRPLNGFMAFRSYYS----PIFPP-LPQKELSGILTKLWEKD   81 (201)
T ss_pred             ccccccccccchhHHHHHHHHHH----hhcCC-cCHHHHHHHHHHHHhCC
Confidence            33445578999999999965554    56677 78899999999999763

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=94.84  E-value=0.053  Score=35.72  Aligned_cols=46  Identities=20%  Similarity=0.345  Sum_probs=40.1

Q ss_pred             CCC-CCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChh
Q 034575           37 KPK-RPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA   83 (90)
Q Consensus        37 ~PK-rP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~   83 (90)
                      +|- |-.-||.-|....-+.++.+||+ +-.+++-.+|-..|..-|++
T Consensus        71 HPErR~KAAy~afeE~~Lp~lK~E~Pg-LrlsQ~kq~l~K~w~KSPeN  117 (122)
T PF06244_consen   71 HPERRMKAAYKAFEERRLPELKEENPG-LRLSQYKQMLWKEWQKSPEN  117 (122)
T ss_pred             CcchhHHHHHHHHHHHHhHHHHhhCCC-chHHHHHHHHHHHHhcCCCC
Confidence            454 44578999999999999999999 99999999999999887764

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

Probab=94.34  E-value=0.016  Score=41.38  Aligned_cols=53  Identities=17%  Similarity=0.265  Sum_probs=47.5

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .++..|.-+|+-+-..++..+...+|+ .+..+++++++..|.+|+++-+.+|+
T Consensus       142 ~~~~~~~~~~~e~~~~~r~~~~~~~~~-~~~~e~~k~~~~~w~el~~skK~~~~  194 (211)
T COG5648         142 LPNKAPIGPFIENEPKIRPKVEGPSPD-KALVEETKIISKAWSELDESKKKKYI  194 (211)
T ss_pred             cCCCCCCchhhhccHHhccccCCCCcc-hhhhHHhhhhhhhhhhhChhhhhHHH
Confidence            357788888999999999999999998 88999999999999999999988875

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.92  E-value=1.6  Score=31.18  Aligned_cols=47  Identities=23%  Similarity=0.386  Sum_probs=40.1

Q ss_pred             CCC-CCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChh
Q 034575           36 NKP-KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA   83 (90)
Q Consensus        36 ~~P-KrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~   83 (90)
                      .+| +|-.-+|.-|-....+.++.+||+ +..+++-.+|-.+|..-|+.
T Consensus       162 rHPEkRmrAA~~afEe~~LPrLK~e~P~-lrlsQ~Kqll~Kew~KsPDN  209 (221)
T KOG3223|consen  162 RHPEKRMRAAFKAFEEARLPRLKKENPG-LRLSQYKQLLKKEWQKSPDN  209 (221)
T ss_pred             cChHHHHHHHHHHHHHhhchhhhhcCCC-ccHHHHHHHHHHHHhhCCCC
Confidence            455 455667999999999999999999 99999999999999887754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	90
1hme_A	77	Structure Of The Hmg Box Motif In The B-Domain Of H		1e-06
1j3c_A	79	Solution Structure Of The C-Terminal Domain Of The		2e-06
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		2e-06
2yrq_A	173	Solution Structure Of The Tandem Hmg Box Domain Fro		2e-06
1j3d_A	78	Solution Structure Of The C-Terminal Domain Of The		6e-06
1nhm_A	81	The Structure Of The Hmg Box And Its Interaction Wi		3e-05
1e7j_A	74	Hmg-D Complexed To A Bulge Dna Length = 74		8e-05
1qrv_A	73	Crystal Structure Of The Complex Of Hmg-D And Dna L		8e-05
2yqi_A	81	Solution Structure Of The Second Hmg-Box Domain Fro		8e-05
1hma_A	73	The Solution Structure And Dynamics Of The Dna Bind		9e-05
1hsm_A	79	The Structure Of The Hmg Box And Its Interaction Wi		1e-04
3nm9_A	73	Hmgd(M13a)-Dna Complex Length = 73		2e-04
1j3x_A	77	Solution Structure Of The N-Terminal Domain Of The		2e-04
1j5n_A	93	Solution Structure Of The Non-Sequence-Specific Hmg		3e-04
1cg7_A	93	Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len		3e-04
2e6o_A	87	Solution Structure Of The Hmg Box Domain From Human		7e-04

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +
Sbjct: 3  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTA 49

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKRP SAFF+F  E+R + K +HP   S+    K  GE W   S
Sbjct: 5  DPNAPKRPPSAFFLFCSEYRPKIKSEHP-GLSIGDTAKKLGEMWSEQS 51

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKW 77
           DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W
Sbjct: 85  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMW 127

>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 = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKW 77
           DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W
Sbjct: 98  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMW 140

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKRP SAFF+F  E R + K +HP   S+    K  GE W   S
Sbjct: 4  DPNAPKRPPSAFFLFCSEHRPKIKSEHP-GLSIGDTAKKLGEMWSEQS 50

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          N PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +
Sbjct: 3  NAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTA 47

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 3  DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 48

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          N PKRP S FF+F  EFR + K  +P   S+  V K  GE W +++++
Sbjct: 8  NAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDS 54

>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 = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +
Sbjct: 3  PKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTA 45

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMS 81
          DPNKP+   S++  F++  RE++KK HP +  + A   K   E+WK+MS
Sbjct: 5  DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMS 53

>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 = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK+++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALT 63

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK+++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALT 63

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSM 80
          PNK KRP +AF +F +++R +Y + +P  K   A+    G++WK M
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYP-GKDNRAISVILGDRWKKM 59

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	90
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	5e-15
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	1e-14
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	2e-14
2lhj_A	97	High mobility group protein homolog NHP1; structur	3e-14
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	7e-14
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-13
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	4e-13
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	9e-13
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	3e-12
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	4e-12
1wgf_A	90	Upstream binding factor 1; transcription factor, D	1e-11
1ckt_A	71	High mobility group 1 protein; high-mobility group	5e-11
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	5e-10
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	5e-09
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-09
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	7e-04
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	3e-09
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	8e-09
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	1e-08
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	1e-08
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-06
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	4e-08
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	4e-07
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	5e-06
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	1e-05
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	2e-04
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	5e-04
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	8e-04

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Length = 77

 Score = 62.7 bits (153), Expect = 5e-15
 Identities = 24/51 (47%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 33 KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KDPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  
Sbjct: 2  KDPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAAD 51

>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 = 62.0 bits (151), Expect = 1e-14
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

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

Query: 79 SMSEA 83
          +++  
Sbjct: 61 ALTPE 65

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

 Score = 61.2 bits (149), Expect = 2e-14
 Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 1/61 (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 A 83
           
Sbjct: 62 K 62

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

 Score = 61.3 bits (149), Expect = 3e-14
 Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 1/66 (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 KSMSEA 83
           ++S+ 
Sbjct: 64 NALSDE 69

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

 Score = 60.0 bits (146), Expect = 7e-14
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHP-KNKSVAAVGKAGGEKWKSMSEA 83
             DP KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS  
Sbjct: 1  GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 54

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

 Score = 58.6 bits (142), Expect = 3e-13
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

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

Query: 82 EA 83
          E 
Sbjct: 61 EE 62

>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 = 58.2 bits (141), Expect = 4e-13
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
           +   + PK P + +  F+ E REQ +  HP +     + K  G +W  +  A
Sbjct: 1  GSSGSSGPKAPVTGYVRFLNERREQIRTRHP-DLPFPEITKMLGAEWSKLQPA 52

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

 Score = 57.4 bits (139), Expect = 9e-13
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 30 KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          K  K P+ PK+P + +F F  E R +Y K HP   S   + K   +K+K + E 
Sbjct: 3  KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHP-EMSNLDLTKILSKKYKELPEK 55

>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 = 55.4 bits (134), Expect = 3e-12
 Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P    V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYALWLNSARESIKRENP-GIKVTEVAKRGGELWRAMKD 47

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

 Score = 55.0 bits (133), Expect = 4e-12
 Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          + PKR  +AF +++ + RE  K+++P    V  + K GGE WK + +
Sbjct: 2  HMPKRATTAFMLWLNDTRESIKRENP-GIKVTEIAKKGGEMWKELKD 47

>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 = 54.3 bits (131), Expect = 1e-11
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

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

Query: 80 MSEA 83
          +SE 
Sbjct: 62 LSEK 65

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

 Score = 52.4 bits (126), Expect = 5e-11
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEA 83
          KP+   S++  F++  RE++KK HP    + +   K   E+WK+MS  
Sbjct: 1  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 48

>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 = 51.9 bits (124), Expect = 5e-10
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

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

Query: 83 A 83
           
Sbjct: 62 K 62

>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 = 49.2 bits (117), Expect = 5e-09
 Identities = 24/51 (47%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 33  KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
           KDPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  
Sbjct: 97  KDPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAAD 146

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

 Score = 51.3 bits (122), Expect = 1e-09
 Identities = 9/54 (16%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 30 KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
           ++   + PK+P S++  F +E    +K  +P +     + +   ++W+ + ++
Sbjct: 2  GSSVLASCPKKPVSSYLRFSKEQLPIFKAQNP-DAKTTELIRRIAQRWRELPDS 54

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

 Score = 35.5 bits (81), Expect = 7e-04
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 5/50 (10%)

Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
              KPKRP SA+ V++ E  ++ K D P+        K   E WK++S++
Sbjct: 111 LLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDS 155

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

 Score = 47.7 bits (114), Expect = 3e-09
 Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 5/47 (10%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KPKRP SA+ V++ E  ++ K D P+        K   E WK++S++
Sbjct: 2  KPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDS 43

>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 = 49.4 bits (117), Expect = 8e-09
 Identities = 11/79 (13%), Positives = 30/79 (37%), Gaps = 1/79 (1%)

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

Query: 65 SVAAVGKAGGEKWKSMSEA 83
              + +   ++W+ + ++
Sbjct: 68 KTTELIRRIAQRWRELPDS 86

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

 Score = 47.0 bits (112), Expect = 1e-08
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
           +   +  K+P SA  +F+++ R Q+  ++P   S+        E WK++SE 
Sbjct: 1  GSSGSSGIKKPMSASALFVQDHRPQFLIENP-KTSLEDATLQIEELWKTLSEE 52

>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 = 48.3 bits (115), Expect = 1e-08
 Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          ++ KRP +AF V+  + R +   ++P     + + K  G +WK ++EA
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENP-RMRNSEISKQLGYQWKMLTEA 49

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

 Score = 42.1 bits (99), Expect = 2e-06
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

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

Query: 71  KAGGEKWKSMSEA 83
           K  GE W + +  
Sbjct: 121 KKLGEMWNNTAAD 133

>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 = 45.5 bits (108), Expect = 4e-08
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
                +A  PNK KRP +AF +F +++R +Y + +P  K   A+    G++WK M   
Sbjct: 5  SSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNE 62

>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 = 42.6 bits (101), Expect = 4e-07
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
           +   +  +RP +AF +F +  R   +++HP         K   + W  +    
Sbjct: 1  GSSGSSGARRPMNAFLLFCKRHRSLVRQEHP-RLDNRGATKILADWWAVLDPKE 53

>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 = 40.1 bits (94), Expect = 5e-06
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

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

Query: 72 AGGEKWKSMSEAV 84
            G+ W+ ++E+ 
Sbjct: 63 TLGKLWRLLNESE 75

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

 Score = 38.3 bits (90), Expect = 1e-05
 Identities = 13/48 (27%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
            +RP +AF V+ ++ R++  + +P +   A + K  G+ WK+++ A 
Sbjct: 2  SIRRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLAE 48

>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 = 35.6 bits (83), Expect = 2e-04
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
          ++ KRP +AF V+  + R +   ++P     + + K  G +WK ++EA 
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENP-RMRNSEISKQLGYQWKMLTEAE 50

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

 Score = 34.5 bits (80), Expect = 5e-04
 Identities = 13/53 (24%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
              ++ +RP +AF V+ ++ R++  + +P +   A + K  G+ WK+++ A 
Sbjct: 1  GSFTSRIRRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLAE 52

>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 = 34.0 bits (77), Expect = 8e-04
 Identities = 12/46 (26%), Positives = 22/46 (47%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
              RP + F +++EE R     D+P     A + K G  +++ +S
Sbjct: 4  GSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLS 49

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	90
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.89
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.88
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.87
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.86
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.86
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.85
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.85
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.85
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.85
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.84
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.84
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.83
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.82
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.82
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.82
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.8
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.8
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.8
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.8
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.8
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.8
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.79
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.79
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.79
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.79
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.79
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.77
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.77
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.76
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.75
2cto_A	93	Novel protein; high mobility group box domain, hel	99.73
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.72
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.69
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.68
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.68
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.68
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.61
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.58
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.56

>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=99.89  E-value=2.6e-23  Score=128.35  Aligned_cols=64  Identities=28%  Similarity=0.446  Sum_probs=59.9

Q ss_pred             ccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        25 ~k~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++++++.+||+.|+||+|||||||+++|..|..+||+ +++.||+++||++|++|+++||++|+
T Consensus         8 k~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~   71 (90)
T 1wgf_A            8 KPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYK   71 (90)
T ss_dssp             SSCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            44556677899999999999999999999999999999 99999999999999999999999996

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

Probab=99.88  E-value=1.2e-22  Score=127.98  Aligned_cols=64  Identities=25%  Similarity=0.493  Sum_probs=59.3

Q ss_pred             ccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        25 ~k~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ..+++++.+||+.|+||+||||||++++|..|..+||+ +++.||+++||++|++|+++||++|+
T Consensus         5 ~~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~   68 (102)
T 2co9_A            5 SSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYK   68 (102)
T ss_dssp             CCCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHH
Confidence            34445677899999999999999999999999999999 99999999999999999999999995

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

Probab=99.87  E-value=4.4e-22  Score=121.71  Aligned_cols=62  Identities=37%  Similarity=0.543  Sum_probs=57.2

Q ss_pred             ccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCChhhhcccc
Q 034575           27 KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        27 ~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~--~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++++..+||+.|+||+||||+|++++|..+..+||+ ++  +.||+++||++|++|+++||.+|+
T Consensus         5 ~~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~-~~~~~~eisk~lg~~Wk~ls~~eK~~y~   68 (86)
T 2eqz_A            5 SSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPE-VPVNFAEFSKKCSERWKTMSGKEKSKFD   68 (86)
T ss_dssp             CSSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTT-SCCCHHHHHHHHHHHHHSSCHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCCcHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            344567899999999999999999999999999999 75  799999999999999999999996

>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=99.86  E-value=4.1e-22  Score=122.21  Aligned_cols=59  Identities=32%  Similarity=0.585  Sum_probs=56.7

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           30 KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        30 k~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +..+||+.|+||+||||||++++|..+..+||+ +++.||+++||++|++|+++||++|+
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~   68 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMYT   68 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHH
Confidence            467899999999999999999999999999999 99999999999999999999999996

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

Probab=99.86  E-value=2e-22  Score=126.53  Aligned_cols=60  Identities=32%  Similarity=0.478  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        29 kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++.+||+.|+||+|||||||+++|..+..+||+ +++.||+++||++|++||++||++|+
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~   61 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYI   61 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            4567899999999999999999999999999999 99999999999999999999999996

>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=99.85  E-value=8e-22  Score=120.21  Aligned_cols=55  Identities=24%  Similarity=0.347  Sum_probs=53.3

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCChhhhcccc
Q 034575           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKS-VAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        34 dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~-~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++.||||+|||||||+++|..|..+||+ ++ ++||+++||++|++|+++||++|+
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~-~~~~~eisK~lge~Wk~ls~eeK~~y~   57 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPD-FSDEADIIKEGMIRFRVLSTEERKVWA   57 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTT-CCSHHHHHHHHHHHHSSSCHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CchhHHHHHHHHHHHHcCCHHHHHHHH
Confidence            68899999999999999999999999999 87 999999999999999999999996

>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=99.85  E-value=9.5e-22  Score=117.61  Aligned_cols=57  Identities=42%  Similarity=0.692  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        32 ~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .+||+.|+||+||||+|++++|..+..+||+ +++.+|+++||++|++||++||.+|+
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~   57 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYE   57 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHSCGGGSHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            3799999999999999999999999999999 99999999999999999999999986

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

Probab=99.85  E-value=2.4e-22  Score=125.39  Aligned_cols=63  Identities=37%  Similarity=0.599  Sum_probs=59.0

Q ss_pred             cccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCChhhhcccc
Q 034575           26 RKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        26 k~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~--~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++++..+||+.|+||+||||||++++|..+..+||+ ++  +.||+++||++|++|+++||++|+
T Consensus        11 ~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~-~~~~~~eisk~lg~~Wk~ls~eeK~~Y~   75 (97)
T 2lhj_A           11 RRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPE-IAKDVAAIGKMIGAAWNALSDEEKKPYE   75 (97)
T ss_dssp             CCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTT-STTCSSHHHHHHHHTSSSSCSTTTSSSS
T ss_pred             cccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCccHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            3446677899999999999999999999999999999 88  999999999999999999999996

>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=99.85  E-value=1.7e-22  Score=125.41  Aligned_cols=62  Identities=34%  Similarity=0.601  Sum_probs=58.6

Q ss_pred             ccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           27 KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        27 ~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++++..+||+.|+||+||||||++++|..+..+||+ +++.||+++||++|++||++||.+|+
T Consensus        10 ~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~   71 (93)
T 1cg7_A           10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYE   71 (93)
T ss_dssp             CCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTT-SCHHHHTTTHHHHHHTTHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            455677899999999999999999999999999999 99999999999999999999999995

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

Probab=99.84  E-value=2.7e-21  Score=119.57  Aligned_cols=57  Identities=26%  Similarity=0.506  Sum_probs=55.2

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        32 ~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .+||++|+||+||||+|++++|..|..+||+ +++.+|+++||++|++|+++||++|+
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~Y~   58 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYL   58 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHTCCTTHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            4799999999999999999999999999999 99999999999999999999999995

>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=99.84  E-value=1.9e-21  Score=116.00  Aligned_cols=55  Identities=25%  Similarity=0.458  Sum_probs=51.9

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        34 dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ||+.|+||+||||||++++|..+..+||+ +++.||+++||++|++||++||++|+
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~   55 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFF   55 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSC-CSSSHHHHHHHHHHHTCCHHHHHHHH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHhHHHhCCHHHHHHHH
Confidence            68999999999999999999999999999 99999999999999999999999985

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

Probab=99.83  E-value=9.5e-21  Score=117.14  Aligned_cols=57  Identities=26%  Similarity=0.355  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        32 ~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ..+|++||||+||||+|++++|..|+.+||+ +++.||+++||++|++|+++||++|+
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~   58 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPK-TSLEDATLQIEELWKTLSEEEKLKYE   58 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCS-SCHHHHHHHHHHHHHSSCHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            3689999999999999999999999999999 99999999999999999999999995

>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=99.82  E-value=1.9e-20  Score=114.22  Aligned_cols=55  Identities=25%  Similarity=0.457  Sum_probs=53.1

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        34 dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .|+.|+||+||||+||+++|..|..+||+ +++.||+++||++|++||++||.+|+
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~   55 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFF   55 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHCCHHHHHHHH
Confidence            47899999999999999999999999999 99999999999999999999999985

>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=99.82  E-value=1.3e-20  Score=114.08  Aligned_cols=56  Identities=18%  Similarity=0.375  Sum_probs=54.2

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           33 KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        33 ~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .|++.|+||+||||||++++|..+..+||+ +++.+|+++||++|++||++||++|+
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~   58 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQKYT   58 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSS-SCTTHHHHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHH
Confidence            578999999999999999999999999999 99999999999999999999999985

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

Probab=99.82  E-value=3.1e-21  Score=117.06  Aligned_cols=57  Identities=35%  Similarity=0.592  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCChhhhcccc
Q 034575           32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        32 ~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~--~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .+||+.|+||+||||+||+++|..+..+||+ ++  +.||+++||++|++|+++||.+|+
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~-~~~~~~eisk~lg~~Wk~ls~~eK~~y~   60 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPD-ASVNFSEFSKKCSERWKTMSAKEKGKFE   60 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTT-TCCCSSSSHHHHHHHHTTSCTTHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCCcHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            4799999999999999999999999999999 75  599999999999999999999995

>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=99.80  E-value=4e-20  Score=111.89  Aligned_cols=55  Identities=24%  Similarity=0.444  Sum_probs=50.1

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        34 dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .++.|+||+|||||||+++|..+..+||+ +++.||+++||++|++|+++||.+|+
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~   57 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFV   57 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            46789999999999999999999999999 99999999999999999999999986

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

Probab=99.80  E-value=6.5e-20  Score=116.26  Aligned_cols=58  Identities=24%  Similarity=0.438  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        31 ~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ..+|++.|+||+|||||||+++|..+..+||+ +++.||+++||++|++|+++||++|+
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~   80 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPH-LHNAELSKTLGKLWRLLNESEKRPFV   80 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            45788999999999999999999999999999 99999999999999999999999996

>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=99.80  E-value=7.3e-20  Score=122.18  Aligned_cols=61  Identities=41%  Similarity=0.664  Sum_probs=57.7

Q ss_pred             cCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           28 SGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        28 ~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++..+||+.|+||+||||+||+++|..+..+||+ ++++||+++||++|++|+++||++|+
T Consensus        79 ~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~  139 (159)
T 2gzk_A           79 TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYE  139 (159)
T ss_dssp             CGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSC-CCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             ccccccccccccccccccchhhHhhHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            34567899999999999999999999999999999 99999999999999999999999996

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

Probab=99.80  E-value=4e-20  Score=108.62  Aligned_cols=53  Identities=25%  Similarity=0.469  Sum_probs=48.1

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +.|+||+||||+|++++|..+..+||+ +++.+|+++||++|++||++||.+|+
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~   53 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFV   53 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            469999999999999999999999999 99999999999999999999999986

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

Probab=99.80  E-value=8.4e-20  Score=108.41  Aligned_cols=52  Identities=31%  Similarity=0.620  Sum_probs=50.0

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        35 p~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |++|+||+||||+|++++|..+..+||+ +++.||+++||++|++|  +||.+|+
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~l--~eK~~y~   52 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPG-IKVTEIAKKGGEMWKEL--KDKSKWE   52 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTT-CCHHHHHHHHHHHHHTC--TTHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhh--HhhHHHH
Confidence            7899999999999999999999999999 99999999999999999  8898885

>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=99.80  E-value=6.8e-20  Score=110.62  Aligned_cols=54  Identities=24%  Similarity=0.429  Sum_probs=51.4

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        35 p~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++.|+||+||||||++++|..+..+||+ +++.||+++||++|++|+++||.+|+
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~   55 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYY   55 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHhhhhhCCHHHHHHHH
Confidence            4689999999999999999999999999 99999999999999999999999985

>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=99.79  E-value=8.6e-20  Score=109.85  Aligned_cols=53  Identities=28%  Similarity=0.527  Sum_probs=51.2

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +.|+||+||||+|++++|..+..+||+ +++.||+++||++|++||++||.+|+
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~   53 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFI   53 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            479999999999999999999999999 99999999999999999999999995

>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=99.79  E-value=1.4e-19  Score=110.48  Aligned_cols=53  Identities=25%  Similarity=0.466  Sum_probs=51.0

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ..|+||+||||||++++|..+..+||+ ++++||+++||++|++||++||++|+
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~   53 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYY   53 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            369999999999999999999999999 99999999999999999999999995

>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=99.79  E-value=9.6e-20  Score=109.18  Aligned_cols=53  Identities=25%  Similarity=0.419  Sum_probs=51.2

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +.|+||+||||||++++|..+..+||+ +++.||+++||++|++|+++||.+|+
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~   53 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPD-MHNAEISKRLGKRWKLLKDSDKIPFI   53 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            479999999999999999999999999 99999999999999999999999986

>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=99.79  E-value=1e-19  Score=108.00  Aligned_cols=52  Identities=37%  Similarity=0.685  Sum_probs=49.3

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        35 p~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .++||||+||||+||+++|..+..+||+ +++.||+++||++|++|++  |++|+
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~--K~~y~   52 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPG-IKVTEVAKRGGELWRAMKD--KSEWE   52 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSS-CCHHHHHHHHHHHHHHCSC--CHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCc--hHHHH
Confidence            3689999999999999999999999999 9999999999999999997  88885

>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=99.79  E-value=9.4e-20  Score=107.27  Aligned_cols=52  Identities=35%  Similarity=0.588  Sum_probs=49.4

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~--~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +||||+||||+|++++|..+..+||+ ++  +.||+++||++|++|+++||.+|+
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~-~~~~~~eisk~lg~~Wk~ls~~eK~~y~   54 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPD-ASVNFSEFSKKCSERWKTMSAKEKGKFE   54 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTT-CCCCHHHHHHHHHHHHHTCCTTTSHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCC-CCCcHHHHHHHHHHHHhhCCHHHHHHHH
Confidence            59999999999999999999999999 75  599999999999999999999985

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

Probab=99.77  E-value=3.7e-19  Score=120.36  Aligned_cols=60  Identities=42%  Similarity=0.667  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        29 kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++.+||+.|+||+|||||||+++|..+..+||+ +++.||+++||++|++|+++||++|+
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~  152 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYE  152 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCGGGHHHHH
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            4556799999999999999999999999999999 99999999999999999999999995

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

Probab=99.77  E-value=8.6e-19  Score=118.57  Aligned_cols=63  Identities=33%  Similarity=0.574  Sum_probs=57.7

Q ss_pred             ccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           27 KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKN-KSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        27 ~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~-~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++....||+.|+||+||||||++++|..|..+||+. +++.||+++||++|++|+++||++|+
T Consensus         5 ~~k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~   68 (173)
T 2yrq_A            5 SSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE   68 (173)
T ss_dssp             SCSSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            3445678999999999999999999999999999994 38999999999999999999999985

>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=99.76  E-value=6e-19  Score=112.34  Aligned_cols=58  Identities=16%  Similarity=0.239  Sum_probs=53.2

Q ss_pred             ccCCCCCCCCCC-CCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           27 KSGKAAKDPNKP-KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        27 ~~kk~~~dp~~P-KrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .+.++.+|++.| |||+||||+||+++|..+.    + +++.||+++||++|++|+++||++|+
T Consensus         6 ~~~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~-~~~~eisk~lg~~Wk~Ls~~eK~~Y~   64 (108)
T 1v64_A            6 SGQLKDKFDGRPTKPPPNSYSLYCAELMANMK----D-VPSTERMVLCSQQWKLLSQKEKDAYH   64 (108)
T ss_dssp             SCCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----T-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHh----C-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            445667899999 9999999999999999887    6 89999999999999999999999996

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

Probab=99.75  E-value=9.4e-21  Score=117.77  Aligned_cols=55  Identities=15%  Similarity=0.192  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHhcCChhhhcccc
Q 034575           30 KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        30 k~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~--~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +..+||++|+||+|||||||+++|..|+.+||+ ++  ++||+    ++|++|+++||++|+
T Consensus        15 k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~-~s~~~~eIs----e~Wk~ls~eeK~pY~   71 (90)
T 2yuk_A           15 KWEKEEALGEMATVAPVLYTNINFPNLKEEFPD-WTTRVKQIA----KLWRKASSQERAPYV   71 (90)
T ss_dssp             HHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCS-HHHHHHHHH----HHHHHSCHHHHHHHH
T ss_pred             hccCCCCCCCCCccHHHHHHHHhHHHHHHHCcC-ccchHHHHH----HHHHcCCHHHHHHHH
Confidence            445699999999999999999999999999999 98  99998    999999999999996

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

Probab=99.73  E-value=8.6e-19  Score=109.40  Aligned_cols=56  Identities=18%  Similarity=0.273  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHH---HHHHhcCChhhhcccc
Q 034575           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAG---GEKWKSMSEAVSGLVL   89 (90)
Q Consensus        31 ~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l---~~~W~~ls~~eK~~Ye   89 (90)
                      ...+++.||||+|||||||+++|..++.+  + +++.||++.|   |++|++|+++||++|+
T Consensus         4 ~~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~-~~~~eisK~l~~cGe~Wk~ls~eEK~pYe   62 (93)
T 2cto_A            4 GSSGMPNRKASRNAYYFFVQEKIPELRRR--G-LPVARVADAIPYCSSDWALLREEEKEKYA   62 (93)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHTTHHHHHHH--T-CCCSSHHHHTGGGHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHc--C-CCHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            35678999999999999999999999988  6 8999999999   9999999999999996

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

Probab=99.72  E-value=1.8e-18  Score=100.98  Aligned_cols=49  Identities=37%  Similarity=0.566  Sum_probs=45.0

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |.||||+|||++|++++|..+..+||     +||++.||++|++||++||.+|+
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~   49 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYI   49 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHH
Confidence            57999999999999999999986555     59999999999999999999996

>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=99.69  E-value=1.8e-17  Score=103.13  Aligned_cols=52  Identities=15%  Similarity=0.199  Sum_probs=50.4

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +.|+||+|||++|+++.|..+..++|+  +++||++.||++|++|+++||++|+
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye   54 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWI   54 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            689999999999999999999999998  8999999999999999999999996

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

Probab=99.68  E-value=1.1e-17  Score=118.65  Aligned_cols=58  Identities=16%  Similarity=0.389  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           31 AAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        31 ~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ...||+.|++|+||||||++++|..|..+||+ +++.||+++||++|++|+++||.+|+
T Consensus        35 s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~   92 (238)
T 3tmm_A           35 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQ   92 (238)
T ss_dssp             CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            35689999999999999999999999999999 99999999999999999999999996

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

Probab=99.68  E-value=2.1e-17  Score=115.69  Aligned_cols=55  Identities=16%  Similarity=0.407  Sum_probs=53.0

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        34 dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +|++|+||+|||||||+++|..+..+||+ +++.||+++||++|++||++||.+|+
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~   60 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQ   60 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHccCHHhhhHHH
Confidence            47899999999999999999999999999 99999999999999999999999996

>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=99.68  E-value=4.9e-17  Score=102.32  Aligned_cols=54  Identities=13%  Similarity=0.216  Sum_probs=47.3

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           33 KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        33 ~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .+..+||||+|||||||++++.  ..++++ +++.||++.||++|++|+++||++|+
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~-~~~~eisK~lge~Wk~ls~~eK~~Y~   57 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNH-LPLKERMVEIGSRWQRISQSQKEHYK   57 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTT-SCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            3567899999999999999975  345566 78999999999999999999999996

>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=99.61  E-value=7.2e-16  Score=102.71  Aligned_cols=54  Identities=26%  Similarity=0.484  Sum_probs=52.1

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        35 p~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++.|+||++|||+|+++.+..|..+||+ +++.||+++||++|++||++||.+|+
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~-~~~~eisk~lg~~Wk~ls~~eK~~y~   55 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFF   55 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSS-CCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHhhHHHhccHH
Confidence            6789999999999999999999999999 99999999999999999999999985

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

Probab=99.58  E-value=2.7e-17  Score=115.12  Aligned_cols=56  Identities=34%  Similarity=0.464  Sum_probs=49.8

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        29 kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++..+||+.|+||+||||+||+++|..+..++|     .+|++.||++|++|+++||++|+
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~Y~  161 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYI  161 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSSCSSH-----HHHHHHHHHHHHTCCHHHHHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhccCCH-----HHHHHHHHHHHHcCCHHHHHHHH
Confidence            445679999999999999999999998865444     48999999999999999999996

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

Probab=99.56  E-value=4.9e-17  Score=115.35  Aligned_cols=56  Identities=34%  Similarity=0.464  Sum_probs=49.9

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        29 kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++..+||+.|+||+|||||||+++|..+..+||     .+|++.||++|++|+++||++|+
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~Y~  193 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYI  193 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSSH-----HHHHHHHHHHHHTCCTTTTHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhccCH-----HHHHHHHHHHHHhCCHHHHHHHH
Confidence            445689999999999999999999998875554     48999999999999999999996

---

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	90
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	4e-09
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	2e-08
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	7e-08
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-07
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-07
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	7e-07
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	7e-07
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	9e-07
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	4e-06
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	7e-05
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-04
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	0.004

>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 = 46.8 bits (111), Expect = 4e-09
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

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

Query: 79 SMSEA 83
          +++  
Sbjct: 61 ALTPE 65

>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 = 44.4 bits (105), Expect = 2e-08
 Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P    V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYMLWLNSARESIKRENP-GIKVTEVAKRGGELWRAMKD 47

>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 = 43.3 bits (102), Expect = 7e-08
 Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          N PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + + 
Sbjct: 1  NAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAA 46

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

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

 Score = 43.4 bits (102), Expect = 1e-07
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 30 KAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          K  K P+ PK+P + +F F  E R +Y K HP   S   + K   +K+K + E 
Sbjct: 3  KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHP-EMSNLDLTKILSKKYKELPEK 55

>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 = 41.8 bits (98), Expect = 3e-07
 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSE 82
          KP+   S++  F++  RE++KK HP    + +   K   E+WK+MS 
Sbjct: 1  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSA 47

>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 = 40.9 bits (96), Expect = 7e-07
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
          ++ KRP +AF V+    R +  +++P     + + K  G +WK +SE  
Sbjct: 1  DRVKRPMNAFMVWSRGQRRKMAQENP-KMHNSEISKRLGAEWKLLSETE 48

>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 = 41.1 bits (96), Expect = 7e-07
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

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

Query: 79 SMSEA 83
           +SE 
Sbjct: 61 DLSEK 65

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

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

 Score = 40.2 bits (94), Expect = 9e-07
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
            KRP +AF V+ ++ R +  +  P +   + + K  G +WK+M+  
Sbjct: 2  HIKRPMNAFMVWAKDERRKILQAFP-DMHNSNISKILGSRWKAMTNL 47

>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 = 39.0 bits (91), Expect = 4e-06
 Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          ++ KRP +AF V+  + R +   ++P     + + K  G +WK ++E
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENP-RMRNSEISKQLGYQWKMLTE 48

>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 = 35.6 bits (82), Expect = 7e-05
 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAV 84
          K+P +AF ++M+E R     +    K  AA+ +  G +W ++S   
Sbjct: 4  KKPLNAFMLYMKEMRANVVAEST-LKESAAINQILGRRWHALSREE 48

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

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

 Score = 34.5 bits (79), Expect = 3e-04
 Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 3/51 (5%)

Query: 32 AKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +      K P + +  F +E     + +H   K         G +W+ +S+
Sbjct: 3  SGSSGPKKPPMNGYQKFSQELLSNGELNHLPLKERM---VEIGSRWQRISQ 50

>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 = 31.8 bits (72), Expect = 0.004
 Identities = 9/62 (14%), Positives = 20/62 (32%), Gaps = 5/62 (8%)

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

Query: 82 EA 83
          + 
Sbjct: 57 QK 58

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	90
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.84
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.82
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.82
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.8
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.8
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.75
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.74
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.73
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.67
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.62
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	89.03

>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=99.84  E-value=2.7e-21  Score=118.57  Aligned_cols=64  Identities=33%  Similarity=0.591  Sum_probs=59.1

Q ss_pred             ccccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        25 ~k~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +++..+..+||+.|+||+||||||++++|..+..+||+ +++.+|++.||++|++||++||.+|+
T Consensus         8 ~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~   71 (93)
T d1lwma_           8 KKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYE   71 (93)
T ss_dssp             TSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             CCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            34455567799999999999999999999999999999 99999999999999999999999995

>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=99.82  E-value=8e-21  Score=115.47  Aligned_cols=61  Identities=30%  Similarity=0.479  Sum_probs=57.2

Q ss_pred             cCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           28 SGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        28 ~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .+....|++.|+||+|||||||+++|..+..+||+ +++.||+++|+++|++|+++||.+|+
T Consensus        11 ~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~-~~~~ei~k~l~~~W~~Ls~~eK~~Y~   71 (90)
T d1wgfa_          11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYK   71 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            34456789999999999999999999999999999 99999999999999999999999995

>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=99.82  E-value=4.6e-21  Score=116.76  Aligned_cols=60  Identities=32%  Similarity=0.478  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           29 GKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        29 kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++..+||+.|+||+|||+||++++|..+..+||+ +++.+|++.||++|+.||++||.+|+
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~-~~~~ev~k~l~~~W~~ls~~eK~~y~   61 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYI   61 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHH
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHhHhcCCCHHHHHHHH
Confidence            4577899999999999999999999999999999 99999999999999999999999985

>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=99.80  E-value=8.9e-21  Score=112.91  Aligned_cols=53  Identities=40%  Similarity=0.661  Sum_probs=51.5

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |+||||+||||+|++++|..|..+||+ +++.||+++||++|++||++||.+|+
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~-~~~~ei~k~~~~~W~~ls~~eK~~y~   53 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYE   53 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTT-CCTTTHHHHHHHHHHTSCSTTTHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHhhHHhcCCHHHHHHHH
Confidence            689999999999999999999999999 99999999999999999999999985

>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=99.80  E-value=2.1e-20  Score=112.13  Aligned_cols=53  Identities=28%  Similarity=0.527  Sum_probs=51.2

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +.|+||+||||||++++|..|..+||+ +++.||+++||++|++|+++||.+|+
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~-~~~~eisk~~g~~W~~l~~eeK~~y~   53 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFI   53 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHCcCCHHHHHHHH
Confidence            579999999999999999999999999 99999999999999999999999985

>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=99.80  E-value=3.4e-20  Score=112.00  Aligned_cols=53  Identities=26%  Similarity=0.495  Sum_probs=51.6

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |.||||+||||||++++|..+..+||+ +++.||+++||++|++||++||.+|+
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~-~~~~eisk~ig~~W~~L~~eeK~~y~   55 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFF   55 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            689999999999999999999999999 99999999999999999999999985

>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=99.79  E-value=4.3e-20  Score=107.97  Aligned_cols=52  Identities=25%  Similarity=0.448  Sum_probs=50.2

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ++|||+||||+||+++|..|..+||+ +++++|+++||++|++|+++||.+|+
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~   53 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYY   53 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            57899999999999999999999999 99999999999999999999999985

>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=99.75  E-value=6.2e-19  Score=106.57  Aligned_cols=52  Identities=25%  Similarity=0.489  Sum_probs=50.1

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      +.+||+||||||++++|..|..+||+ +++++|+++||.+|++||++||.+|+
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~-~~~~~Isk~lg~~Wk~ls~~eK~~y~   53 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYY   53 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            56899999999999999999999999 99999999999999999999999985

>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=99.74  E-value=9.9e-19  Score=101.91  Aligned_cols=53  Identities=32%  Similarity=0.559  Sum_probs=49.1

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKN-KSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~-~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .||||+||||+|++++|..+..+||+. +++++|+++||++|++||++||.+|+
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~   54 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE   54 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            599999999999999999999999972 45889999999999999999999985

>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=99.73  E-value=1.2e-18  Score=102.23  Aligned_cols=51  Identities=37%  Similarity=0.685  Sum_probs=47.5

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        36 ~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      |.||||+||||+|++++|..|+.+||+ +++.||+++||++|++|+  ||++|+
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~-~~~~eisk~l~~~Wk~~~--eK~~y~   52 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPG-IKVTEVAKRGGELWRAMK--DKSEWE   52 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTT-CCHHHHHHHHHHHHHHCS--CCHHHH
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHhcChh--HHHHHH
Confidence            689999999999999999999999999 999999999999999886  477774

>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=99.67  E-value=3.9e-17  Score=102.01  Aligned_cols=58  Identities=14%  Similarity=0.161  Sum_probs=51.0

Q ss_pred             ccCCCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           27 KSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        27 ~~kk~~~dp~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ...+...|+.+|++|+||||||++++|.+    +|+ +++.||+++||++|++|+++||++|+
T Consensus         7 ~~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~-~~~~e~~k~ig~~W~~Ls~~eK~~Y~   64 (108)
T d1v64a_           7 GQLKDKFDGRPTKPPPNSYSLYCAELMAN----MKD-VPSTERMVLCSQQWKLLSQKEKDAYH   64 (108)
T ss_dssp             CCSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTT-SCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCcHHHHHHHHHHHH----ccC-CCHHHHHHHHHHHHccCCHHHHHHHH
Confidence            34455678888999999999999998864    578 89999999999999999999999995

>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=99.62  E-value=1.4e-16  Score=98.07  Aligned_cols=52  Identities=13%  Similarity=0.198  Sum_probs=46.7

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        35 p~~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      ..+||||+||||+||+++|..+..  ++ +++.||++.||++|++|+++||++|+
T Consensus         6 ~~p~KrP~~ay~~F~~e~r~~~~~--~~-~~~~ei~k~~g~~Wk~ls~~eK~~Y~   57 (101)
T d1v63a_           6 SGPKKPPMNGYQKFSQELLSNGEL--NH-LPLKERMVEIGSRWQRISQSQKEHYK   57 (101)
T ss_dssp             CSSCCCCSSSHHHHHHHHHHHCTT--TT-SCHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHh--cC-CCHHHHHHHHHHHHhhCCHHHHHHHH
Confidence            457899999999999999998764  45 67899999999999999999999995

>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=89.03  E-value=0.45  Score=26.63  Aligned_cols=51  Identities=16%  Similarity=0.197  Sum_probs=41.5

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCChhhhcccc
Q 034575           37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL   89 (90)
Q Consensus        37 ~PKrP~say~lf~~~~r~~~~~~~P~~~~~~eisk~l~~~W~~ls~~eK~~Ye   89 (90)
                      .|.-|.+|--+|.+.....+-+.+-+  .-.--.+.+-..|++|...|+.+|+
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~--DR~KaqkaMeatW~~meKkEki~wi   53 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWI   53 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHh--hHHHHHHHHHHHHHhhhhhhhhHHH
Confidence            47778899999999999988887776  4445566778889999999998875