Citrus Sinensis ID: 044275

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
Protein Sequence
MKGPRVVAVAQKKPHADMLKARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEVQSGKSSSSEINDEAEQEFSSQVSSYFMGFYCFSSRN
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHcHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHHHHHHHHHHccHHHHHHcccccccccccccccHHHEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHEEEccccc
Coil and Loop (DISEMBL)
MKGPRVVAVAQKKPHADMLKARKaenkpkkekagkkkdsnapkrplsaYFIFMEDFRKsfkesfpdnksvaamgkaggqkwksmseaeKAPYVQKALNKKAEYELALEAYKKQLndngagvsedswkstsevqsgksssseiNDEAEQEFSSQVSSYFMGFYCFSSRN
Flexible Loop (DISEMBL)
mkgprvvavaqkkphadmlkarkaenkpkkekagkkkdsnapkrplsAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLndngagvsedswkstsevqsgksssseiNDEAEQEFSSQVSSYFMGFYCFSSRN
Low Complexity Region (SEG)
MKGPRVVAVAQKKPHADMLkarkaenkpkkekagkkkDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKstsevqsgkssssEINDEAEQEFSSQVSSYFMGFYCFSSRN
Disordered region (IsUnstruct)
***********************************************AYFIFMEDFR**************************************************************************************************SYFMGFYCF****
Disordered Region (DISOPRED)
********************************************PLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELAL************************************************SYFMGFYCFSSRN
Disordered Region (DISEMBL)
*****************MLKARKA*****************PKRPLSAYFIFMEDFRKSFKESFPDNKSV***************EAEKAPYVQKALNKKAEYELALEAYKKQLND***********************************SQVSSYFMGFYCFSSRN
Disordered Region (DISPRO)
**********************************KKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL********************************EQEFSSQVSSYFMGFYCFSS**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKGPRVVAVAQKKPHADMLKARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYxxxxxxxxxxxxxxxxxxxxxLNDNGAGVSEDSWKSTSEVQSGKSSSSEINDEAEQEFSSQVSSYFMGFYCFSSRN
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	168	2.2.26 [Sep-21-2011]
P93047	141	High mobility group B pro	yes	no	0.625	0.744	0.594	3e-26
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.559	0.630	0.604	1e-24
O49596	144	High mobility group B pro	no	no	0.565	0.659	0.593	4e-24
O49595	178	High mobility group B pro	no	no	0.583	0.550	0.544	1e-23
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.702	0.819	0.457	7e-23
Q42344	138	High mobility group B pro	no	no	0.708	0.862	0.471	4e-21
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.5	0.552	0.559	1e-20
P27347	157	DNA-binding protein MNB1B	N/A	no	0.654	0.700	0.530	5e-20
O49597	125	High mobility group B pro	no	no	0.553	0.744	0.468	2e-19
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.446	0.465	0.6	4e-18

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

 Score =  117 bits (293), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 63/106 (59%), Positives = 78/106 (73%), Gaps = 1/106 (0%)

Query: 27  KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
           KP K   G  KD N PKRP SA+F+FMEDFR ++KE  P NKSVAA+GKAGG+KWKS+S+
Sbjct: 20  KPAKGAKGAAKDPNKPKRPSSAFFVFMEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSD 79

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEV 132
           +EKAPYV KA  +K EYE  ++AY K+L + G    E+S KS SEV
Sbjct: 80  SEKAPYVAKADKRKVEYEKNMKAYNKKL-EEGPKEDEESDKSVSEV 124

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

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

 Score =  112 bits (280), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 58/96 (60%), Positives = 72/96 (75%), Gaps = 2/96 (2%)

Query: 37  KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
           KD N PKRP SA+F+FM DFR+ +K+  P+NKSVAA+GKA G++WKS+SE EKAPYV +A
Sbjct: 40  KDPNKPKRPPSAFFVFMADFREQYKKDHPNNKSVAAVGKACGEEWKSLSEEEKAPYVDRA 99

Query: 97  LNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEV 132
           L KK EYE+ L+AY K+L   G    E S KS SEV
Sbjct: 100 LKKKEEYEITLQAYNKKL--EGKDDEEGSDKSKSEV 133

Vicia faba (taxid: 3906)

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

 Score =  110 bits (275), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 57/96 (59%), Positives = 72/96 (75%), Gaps = 1/96 (1%)

Query: 37  KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
           KD N PKRP SA+F+FMEDFR++FK+  P NKSVA +GKA G KWKS+S++EKAPYV KA
Sbjct: 33  KDPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKAPYVAKA 92

Query: 97  LNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEV 132
             +K EYE  ++AY K+L + G    E+S KS SEV
Sbjct: 93  EKRKVEYEKNIKAYNKKL-EEGPKEDEESDKSVSEV 127

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  108 bits (271), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/112 (54%), Positives = 77/112 (68%), Gaps = 14/112 (12%)

Query: 36  KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQK 95
           KKD N PKR  SA+F+F+EDFR +FK+  P+ K+V+A+GKAGGQKWKSMS+AEKAPY +K
Sbjct: 47  KKDPNKPKRAPSAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEK 106

Query: 96  ALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEVQSGKSSSSEINDEAE 147
           A  +KAEYE  ++AY K L + G+  SE              S SEINDE E
Sbjct: 107 AAKRKAEYEKQMDAYNKNL-EEGSDESE-------------KSRSEINDEDE 144

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

 Score =  106 bits (265), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 65/142 (45%), Positives = 82/142 (57%), Gaps = 24/142 (16%)

Query: 9   VAQKKPHADMLKARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNK 68
           +A KK  AD  K +KA            KD N PKRP SA+F+FMEDFRK++KE  P+NK
Sbjct: 14  LAVKKQAADTKKTKKAV-----------KDPNKPKRPPSAFFVFMEDFRKTYKEKHPNNK 62

Query: 69  SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAY-KKQLNDNGAGVSEDSWK 127
           SVA +GKAGG KWK ++ AEKAP++ KA  +K EYE  L+AY KKQ          D   
Sbjct: 63  SVAVVGKAGGDKWKQLTAAEKAPFISKAEKRKQEYEKNLQAYNKKQAAGAAEEEESD--- 119

Query: 128 STSEVQSGKSSSSEINDEAEQE 149
                     S SE+ND+ E +
Sbjct: 120 ---------KSRSEVNDDDEDQ 132

Ipomoea nil (taxid: 35883)

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

 Score =  100 bits (249), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 77/121 (63%), Gaps = 2/121 (1%)

Query: 27  KPKKEKAGKK--KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSM 84
           K +  KAGKK  KD N PKRP SA+F+F+EDFRK F  + P+NKSVA +GKA G +WK+M
Sbjct: 18  KTRGRKAGKKTKKDPNQPKRPPSAFFVFLEDFRKEFNLANPNNKSVATVGKAAGARWKAM 77

Query: 85  SEAEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEVQSGKSSSSEIND 144
           ++ +KAPYV KA ++K EY   ++ Y  +L        +DS KS SEV    S     +D
Sbjct: 78  TDEDKAPYVAKAESRKTEYIKNVQQYNLKLASGTNREEDDSDKSKSEVDEAVSEEEAEDD 137

Query: 145 E 145
           +
Sbjct: 138 D 138

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 99.4 bits (246), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/84 (55%), Positives = 62/84 (73%)

Query: 37  KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
           KD N PKRP SA+F+FME+FRK F +  P+NK+V+A+GKA G KWK+MS+AEKAPYV K+
Sbjct: 39  KDPNKPKRPPSAFFVFMEEFRKVFNKEHPENKAVSAVGKAAGAKWKTMSDAEKAPYVAKS 98

Query: 97  LNKKAEYELALEAYKKQLNDNGAG 120
             +K EYE  + AY K+  +   G
Sbjct: 99  EKRKVEYEKNMRAYNKKQAEGPTG 122

Glycine max (taxid: 3847)

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

 Score = 97.1 bits (240), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 60/113 (53%), Positives = 72/113 (63%), Gaps = 3/113 (2%)

Query: 1   MKGPRVVAVAQKKPHADMLKARKAENKPKKEKAGKK-KDSNAPKRPLSAYFIFMEDFRKS 59
           MKG +    A  K  A +    K   KP K + GK  KD N PKR  SA+F+FME+FRK 
Sbjct: 1   MKGAKSKGAA--KADAKLAVKSKGAEKPAKGRKGKAGKDPNKPKRAPSAFFVFMEEFRKE 58

Query: 60  FKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK 112
           FKE  P NKSVAA+GKA G +WKS+SE++KAPYV KA   K EY  A+ AY K
Sbjct: 59  FKEKNPKNKSVAAVGKAAGDRWKSLSESDKAPYVAKANKLKLEYNKAIAAYNK 111

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

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

 Score = 95.1 bits (235), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/94 (46%), Positives = 65/94 (69%), Gaps = 1/94 (1%)

Query: 32  KAGKK-KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKA 90
           K GKK KD N PK+P S +F+F++DFRK F  + PDNKSV  +G+A G+KWK+M+E E+A
Sbjct: 23  KVGKKTKDPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTEEERA 82

Query: 91  PYVQKALNKKAEYELALEAYKKQLNDNGAGVSED 124
           P+V K+ +KK EY + ++ Y  +L +      +D
Sbjct: 83  PFVAKSQSKKTEYAVTMQQYNMELANGNKTTGDD 116

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 90.9 bits (224), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/75 (60%), Positives = 56/75 (74%)

Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D N PKR  SA+F+FM +FR+ FK+  P NKSVAA+GKA G++WKS+SE+EKAPYV KA 
Sbjct: 38  DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSESEKAPYVAKAN 97

Query: 98  NKKAEYELALEAYKK 112
             K EY  A+ AY K
Sbjct: 98  KLKGEYNKAIAAYNK 112

Triticum aestivum (taxid: 4565)

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	168
255566393	155	DNA-binding protein MNB1B, putative [Ric	0.672	0.729	0.638	2e-35
449468356	142	PREDICTED: HMG1/2-like protein-like [Cuc	0.827	0.978	0.542	2e-33
145323962	140	high mobility group B3 protein [Arabidop	0.690	0.828	0.535	1e-24
18394900	141	high mobility group B3 protein [Arabidop	0.625	0.744	0.594	2e-24
8886929	662	F2D10.18 [Arabidopsis thaliana]	0.625	0.158	0.594	3e-24
297845042	141	hypothetical protein ARALYDRAFT_472304 [	0.690	0.822	0.511	4e-24
309243128	139	high mobility group box 3 protein [Gossy	0.553	0.669	0.6	1e-23
224081483	144	high mobility group family [Populus tric	0.559	0.652	0.618	1e-23
116778852	157	unknown [Picea sitchensis] gi|116782574|	0.619	0.662	0.566	2e-23
118484838	144	unknown [Populus trichocarpa]	0.559	0.652	0.608	3e-23

>gi|255566393|ref|XP_002524182.1| DNA-binding protein MNB1B, putative [Ricinus communis] gi|223536551|gb|EEF38197.1| DNA-binding protein MNB1B, putative [Ricinus communis]

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 76/119 (63%), Positives = 98/119 (82%), Gaps = 6/119 (5%)

Query: 1   MKGPRVVAVAQKKPHADMLKARKAENKPKKEKAGKKK------DSNAPKRPLSAYFIFME 54
           MKGPR   +AQKKP + +LKARKAE+KP KE+A  +K      D++APKRP SA+FIFM+
Sbjct: 1   MKGPRNAVIAQKKPSSKVLKARKAESKPGKEEASSRKKKNVSKDTDAPKRPASAFFIFMD 60

Query: 55  DFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ 113
           +FRK FKE +PDNK+V+A+GKAGG+KWKS+SE +KAPY++KAL +KAEYE  LEAYK+Q
Sbjct: 61  EFRKYFKEKYPDNKAVSAVGKAGGEKWKSLSETDKAPYLEKALKRKAEYEKVLEAYKQQ 119

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468356|ref|XP_004151887.1| PREDICTED: HMG1/2-like protein-like [Cucumis sativus] gi|449517965|ref|XP_004166014.1| PREDICTED: HMG1/2-like protein-like [Cucumis sativus]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 83/153 (54%), Positives = 101/153 (66%), Gaps = 14/153 (9%)

Query: 1   MKGPRVVAVAQKKPHADMLKARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSF 60
           M+  R   V  KKP+   LK RKAE K  K    KKKD NAPKRP + +F+FME+FRK++
Sbjct: 1   MRALRNAVVTHKKPNPQKLKQRKAEMKSTK---SKKKDQNAPKRPATTFFVFMEEFRKTY 57

Query: 61  KESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLN-DNGA 119
           KE FPD K+   +GK GG+KWKSMS+AEKAPY +KAL +KAEYE+ALEAYK  LN     
Sbjct: 58  KEQFPDAKAGPVVGKVGGEKWKSMSDAEKAPYAEKALKRKAEYEIALEAYKNNLNCPQNH 117

Query: 120 GVSEDSWKSTSEVQSGKSSSSEINDEAEQEFSS 152
            +  +S KSTSEV          ND+ EQE SS
Sbjct: 118 RMPTESQKSTSEV----------NDDTEQEASS 140

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 68/127 (53%), Positives = 85/127 (66%), Gaps = 11/127 (8%)

Query: 27  KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
           KP K   G  KD N PKRP SA+F+FMEDFR ++KE  P NKSVAA+GKAGG+KWKS+S+
Sbjct: 20  KPAKGAKGAAKDPNKPKRPSSAFFVFMEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSD 79

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEVQSGKSSSSEINDEA 146
           +EKAPYV KA  +K EYE  ++AY K+L + G    E+S KS SEV          NDE 
Sbjct: 80  SEKAPYVAKADKRKVEYEKNMKAYNKKL-EEGPKEDEESDKSVSEV----------NDED 128

Query: 147 EQEFSSQ 153
           + E  S+
Sbjct: 129 DAEDGSE 135

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 63/106 (59%), Positives = 78/106 (73%), Gaps = 1/106 (0%)

Query: 27  KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
           KP K   G  KD N PKRP SA+F+FMEDFR ++KE  P NKSVAA+GKAGG+KWKS+S+
Sbjct: 20  KPAKGAKGAAKDPNKPKRPSSAFFVFMEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSD 79

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEV 132
           +EKAPYV KA  +K EYE  ++AY K+L + G    E+S KS SEV
Sbjct: 80  SEKAPYVAKADKRKVEYEKNMKAYNKKL-EEGPKEDEESDKSVSEV 124

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 63/106 (59%), Positives = 78/106 (73%), Gaps = 1/106 (0%)

Query: 27  KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
           KP K   G  KD N PKRP SA+F+FMEDFR ++KE  P NKSVAA+GKAGG+KWKS+S+
Sbjct: 541 KPAKGAKGAAKDPNKPKRPSSAFFVFMEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSD 600

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEV 132
           +EKAPYV KA  +K EYE  ++AY K+L + G    E+S KS SEV
Sbjct: 601 SEKAPYVAKADKRKVEYEKNMKAYNKKL-EEGPKEDEESDKSVSEV 645

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 65/127 (51%), Positives = 85/127 (66%), Gaps = 11/127 (8%)

Query: 27  KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
           KP K   G  KD N PKRP SA+F+FMEDFR+++K+  P NKSVAA+GKAGG+KWKS+S+
Sbjct: 22  KPAKGGKGAAKDPNKPKRPSSAFFVFMEDFRETYKKEHPKNKSVAAVGKAGGEKWKSLSD 81

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEVQSGKSSSSEINDEA 146
           +EKAPYV KA  +K EYE  ++AY K+L +   G  ED        +    S SE+NDE 
Sbjct: 82  SEKAPYVAKADKRKVEYEKNMKAYNKKLEE---GPKED--------EESDKSVSEVNDED 130

Query: 147 EQEFSSQ 153
           + E  S+
Sbjct: 131 DAEDGSE 137

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|309243128|gb|ADD74180.2| high mobility group box 3 protein [Gossypium hirsutum]

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/95 (60%), Positives = 75/95 (78%), Gaps = 2/95 (2%)

Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D N PKRP SA+F+FME+FRK +KE+ PDN+SV+A+GKAGG+KWKSM++AEKAPYVQKA 
Sbjct: 34  DPNKPKRPASAFFVFMEEFRKQYKEANPDNRSVSAVGKAGGEKWKSMTDAEKAPYVQKAE 93

Query: 98  NKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEV 132
            +K+EY   ++AY  +L   G G  ++S KS SEV
Sbjct: 94  KRKSEYNKKMQAYNLKL--AGGGNDDESDKSKSEV 126

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224081483|ref|XP_002306429.1| high mobility group family [Populus trichocarpa] gi|222855878|gb|EEE93425.1| high mobility group family [Populus trichocarpa]

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 60/97 (61%), Positives = 71/97 (73%), Gaps = 3/97 (3%)

Query: 37  KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
           KD N PKRP SA+F+FMEDFRK +KES P+NKSVAA+GKAGG KWKS+SEAEKAPY  KA
Sbjct: 34  KDPNKPKRPASAFFVFMEDFRKQYKESHPNNKSVAAVGKAGGDKWKSLSEAEKAPYAAKA 93

Query: 97  LNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEVQ 133
             +K EY   + AY K+L     G  ++S KS SEV 
Sbjct: 94  EKRKFEYNKDMAAYNKRL---AGGNDDESDKSKSEVN 127

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116778852|gb|ABK21026.1| unknown [Picea sitchensis] gi|116782574|gb|ABK22556.1| unknown [Picea sitchensis] gi|116782678|gb|ABK22606.1| unknown [Picea sitchensis] gi|116782786|gb|ABK22657.1| unknown [Picea sitchensis] gi|116782898|gb|ABK22712.1| unknown [Picea sitchensis] gi|116791878|gb|ABK26144.1| unknown [Picea sitchensis] gi|148907501|gb|ABR16881.1| unknown [Picea sitchensis] gi|224284566|gb|ACN40016.1| unknown [Picea sitchensis] gi|224285212|gb|ACN40332.1| unknown [Picea sitchensis] gi|224286734|gb|ACN41070.1| unknown [Picea sitchensis]

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 60/106 (56%), Positives = 76/106 (71%), Gaps = 2/106 (1%)

Query: 29  KKEKAGKK--KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
           ++EK G+K  KD N PKRP SA+F+FMEDFRK++KE  P+ KSV+ +GKAGG KWKSMSE
Sbjct: 37  RQEKKGRKAAKDPNKPKRPASAFFVFMEDFRKTYKEKNPNVKSVSVVGKAGGDKWKSMSE 96

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEV 132
           A+KAPYV KA  +K EYE  + AY  +        +E+S KS SEV
Sbjct: 97  ADKAPYVAKAGKRKTEYEKNMAAYNNKQTSTAGDSAEESDKSKSEV 142

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118484838|gb|ABK94286.1| unknown [Populus trichocarpa]

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 59/97 (60%), Positives = 71/97 (73%), Gaps = 3/97 (3%)

Query: 37  KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
           KD N PKRP SA+F+FMEDFRK +KES P+NKSVAA+GKAGG KWKS+SEAEKAP+  KA
Sbjct: 34  KDPNKPKRPASAFFVFMEDFRKQYKESHPNNKSVAAVGKAGGDKWKSLSEAEKAPFAAKA 93

Query: 97  LNKKAEYELALEAYKKQLNDNGAGVSEDSWKSTSEVQ 133
             +K EY   + AY K+L     G  ++S KS SEV 
Sbjct: 94  EKRKFEYNKDMAAYNKRL---AGGNDDESDKSKSEVN 127

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	168
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.625	0.729	0.5	8.7e-24
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.511	0.623	0.505	5.1e-19
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.517	0.696	0.448	5.1e-19
TAIR|locus:2154433	241	HMGB6 "high-mobility group box	0.613	0.427	0.428	3.3e-15
UNIPROTKB|Q32L31	200	HMGB3 "High mobility group pro	0.660	0.555	0.336	3.1e-12
ZFIN|ZDB-GENE-030131-341	205	hmgb1a "high-mobility group bo	0.660	0.541	0.339	3.9e-12
UNIPROTKB|F1RQ19	202	LOC100517745 "Uncharacterized	0.660	0.549	0.327	6.4e-12
UNIPROTKB|E1BIU3	186	LOC532409 "Uncharacterized pro	0.482	0.435	0.390	8.2e-12
MGI|MGI:1098219	200	Hmgb3 "high mobility group box	0.660	0.555	0.345	1e-11
RGD|1564407	200	Hmgb3 "high mobility group box	0.660	0.555	0.336	1e-11

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

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 58/116 (50%), Positives = 76/116 (65%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D N PKRP SA+F+FMEDFR++FK+  P NKSVA +GKA G KWKS+S++EKAPYV KA 
Sbjct:    34 DPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAE 93

Query:    98 NKKAEYELALEAYKKQLNDNGAGVSEDSWKXXXXXXXXXXXXXEINDEAEQEFSSQ 153
              +K EYE  ++AY K+L + G    E+S K             E+NDE + E  S+
Sbjct:    94 KRKVEYEKNIKAYNKKLEE-GPKEDEESDKSVS----------EVNDEDDAEDGSE 138

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 = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 44/87 (50%), Positives = 61/87 (70%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D N PKRP SA+F+F+EDFRK F  + P+NKSVA +GKA G +WK+M++ +KAPYV KA 
Sbjct:    31 DPNQPKRPPSAFFVFLEDFRKEFNLANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAE 90

Query:    98 NKKAEYELALEAYKKQLNDNGAGVSED 124
             ++K EY   ++ Y  +L  +G    ED
Sbjct:    91 SRKTEYIKNVQQYNLKLA-SGTNREED 116

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 = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 39/87 (44%), Positives = 60/87 (68%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D N PK+P S +F+F++DFRK F  + PDNKSV  +G+A G+KWK+M+E E+AP+V K+ 
Sbjct:    30 DPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTEEERAPFVAKSQ 89

Query:    98 NKKAEYELALEAYKKQLNDNGAGVSED 124
             +KK EY + ++ Y  +L +      +D
Sbjct:    90 SKKTEYAVTMQQYNMELANGNKTTGDD 116

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 = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 48/112 (42%), Positives = 62/112 (55%)

Query:    39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAA-MGKAGGQKWKSMSEAEKAPYVQKAL 97
             SN PKRPL+A+FIFM DFRK+FK     N S+A    K GG+KWKS++E EK  Y+ KA 
Sbjct:   112 SNKPKRPLTAFFIFMSDFRKTFKSEH--NGSLAKDAAKIGGEKWKSLTEEEKKVYLDKAA 169

Query:    98 NKKAEYELALEAYKKQLNDNGAGVSEDSWKXXXXXXXXXXXXXEINDEAEQE 149
               KAEY  +LE+     ND      ED  K             + +DE E++
Sbjct:   170 ELKAEYNKSLES-----NDADEE-EEDEEKQSDDVDDAEEKQVDDDDEVEEK 215

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

 Score = 164 (62.8 bits), Expect = 3.1e-12, P = 3.1e-12
 Identities = 38/113 (33%), Positives = 58/113 (51%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D NAPKRP S +F+F  +FR   K + P   S+  + K  G+ W ++S++EK PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSANP-GISIGDVAKKLGEMWNNLSDSEKQPYINKAA 147

Query:    98 NKKAEYELALEAYKKQLNDNGA-GVSEDSWKXXXXXXXXXXXXXEINDEAEQE 149
               K +YE  +  YK +   +GA G ++ + K             E  +E E E
Sbjct:   148 KLKEKYEKDVADYKSKGKFDGAKGAAKVARKKVEEEDEEDEEEEEEEEEEEDE 200

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

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

GO:0006310 "DNA recombination" evidence=IDA

GO:0005694 "chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 38/112 (33%), Positives = 52/112 (46%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D NAPKRP SA+FIF  +FR   KE  P   S+  + K  G+ W  +S  EK PY +KA 
Sbjct:    90 DPNAPKRPPSAFFIFCSEFRPKVKEETP-GLSIGDVAKRLGEMWNKISSEEKQPYEKKAA 148

Query:    98 NKKAEYELALEAYKKQLNDNGAGVSEDSWKXXXXXXXXXXXXXEINDEAEQE 149
               K +YE  + AY+ +    G      S               E  D+ ++E
Sbjct:   149 KLKEKYEKDIAAYRSKGKVGGGAAKAPSKPDKANDEDEDDDEEEDEDDDDEE 200

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

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 37/113 (32%), Positives = 59/113 (52%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D NAPKRP S +F+F  +FR   K + P   S+  + K  G+ W ++S++EK PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLSDSEKQPYINKAA 147

Query:    98 NKKAEYELALEAYKKQLNDNGA-GVSEDSWKXXXXXXXXXXXXXEINDEAEQE 149
               K +YE  +  YK +   +GA G ++ + K             +  +E E+E
Sbjct:   148 KLKEKYEKDVADYKSKGKFDGAKGPAKVARKKVEEDDEDEDDDDDDEEEEEEE 200

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E1BIU3 LOC532409 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 32/82 (39%), Positives = 48/82 (58%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D NAPKRP S +F+F  +FR   K + P   S+  + K  G+ W ++S++EK PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSANP-GISIGDVAKKLGEMWNNLSDSEKQPYINKAA 147

Query:    98 NKKAEYELALEAYKKQLNDNGA 119
               K +YE  +  YK +   +GA
Sbjct:   148 KLKEKYEKDVADYKSKGKFDGA 169

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 39/113 (34%), Positives = 57/113 (50%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D NAPKRP S +F+F  +FR   K + P   S+  + K  G+ W ++S+ EK PYV KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLSDNEKQPYVTKAA 147

Query:    98 NKKAEYELALEAYKKQLNDNGA-GVSEDSWKXXXXXXXXXXXXXEINDEAEQE 149
               K +YE  +  YK +   +GA G ++ + K             E  +E E E
Sbjct:   148 KLKEKYEKDVADYKSKGKFDGAKGPAKVARKKVEEEEEEEEEEEEEEEEEEDE 200

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005694 "chromosome" evidence=IEA

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

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

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

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 38/113 (33%), Positives = 58/113 (51%)

Query:    38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
             D NAPKRP S +F+F  +FR   K + P   S+  + K  G+ W ++S++EK PY+ KA 
Sbjct:    89 DPNAPKRPPSGFFLFCSEFRPKIKSANP-GISIGDVAKKLGEMWNNLSDSEKQPYMTKAA 147

Query:    98 NKKAEYELALEAYKKQLNDNGA-GVSEDSWKXXXXXXXXXXXXXEINDEAEQE 149
               K +YE  +  YK +   +GA G ++ + K             E  +E E E
Sbjct:   148 KLKEKYEKDVADYKSKGKFDGAKGPAKVARKKVEEEEEEEEEEEEEEEEEEDE 200

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P93047	HMGB3_ARATH	No assigned EC number	0.5943	0.625	0.7446	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	168
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	5e-17
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	7e-15
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	4e-14
smart00398	70	smart00398, HMG, high mobility group	9e-13
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	1e-10
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	2e-10
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	3e-07
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	1e-05

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

 Score = 70.7 bits (174), Expect = 5e-17
 Identities = 35/70 (50%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
           PKRPLSA+F+F ++ R   K   P  K  A + K  G+KWK++SE EK PY +KA  +KA
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKPYEEKAEKEKA 59

Query: 102 EYELALEAYK 111
            YE A  AYK
Sbjct: 60  RYEKAYPAYK 69

Length = 69

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

 Score = 65.0 bits (159), Expect = 7e-15
 Identities = 31/67 (46%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
           PKRPLSAYF+F ++ R   K+  PD  SV  + K  G+KWK +SE EK  Y +KA   K 
Sbjct: 1   PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKE 59

Query: 102 EYELALE 108
            YE  ++
Sbjct: 60  RYEKEMK 66

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

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

 Score = 63.0 bits (154), Expect = 4e-14
 Identities = 30/67 (44%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
           PKRPLSAYF+F ++ R   K   P   SV  + K  G+ WKS+SE EK  Y +KA   K 
Sbjct: 1   PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKE 59

Query: 102 EYELALE 108
            YE  + 
Sbjct: 60  RYEKEMP 66

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

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

 Score = 59.6 bits (145), Expect = 9e-13
 Identities = 30/71 (42%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 41  APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
            PKRP+SA+ +F ++ R   K   PD    A + K  G++WK +SE EKAPY +KA   K
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDK 59

Query: 101 AEYELALEAYK 111
             YE  +  YK
Sbjct: 60  ERYEEEMPEYK 70

Length = 70

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

 Score = 54.9 bits (132), Expect = 1e-10
 Identities = 40/94 (42%), Positives = 50/94 (53%), Gaps = 1/94 (1%)

Query: 20  KARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGG 78
            A+K      ++   KKKD NAPKR LSAY  F ++ R       P+  K VAA+GK  G
Sbjct: 1   MAKKQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVG 60

Query: 79  QKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK 112
           + W  +SE EKAPY +KA   K  YE     Y K
Sbjct: 61  EAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Length = 94

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

 Score = 56.8 bits (137), Expect = 2e-10
 Identities = 37/106 (34%), Positives = 59/106 (55%), Gaps = 2/106 (1%)

Query: 9   VAQKKPHADMLKARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNK 68
           V  +KP   +L   + + K K+    KKKD N PKRPLSAYF++  + R   ++  P   
Sbjct: 39  VELEKPLQQLLTKPRKKTKSKRLVR-KKKDPNGPKRPLSAYFLYSAENRDEIRKENPK-L 96

Query: 69  SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL 114
           +   +GK   +KWK +++ EK PY ++A + +  Y+   E Y K+L
Sbjct: 97  TFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKL 142

Length = 211

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

 Score = 45.4 bits (108), Expect = 3e-07
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 4/68 (5%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           KRP++A+ +F +  R+   + +P  K   A+ K  G +WK++S  EK PY ++A   K  
Sbjct: 3   KRPMNAFMLFSKRHRRKVLQEYP-LKENRAISKILGDRWKALSNEEKQPYYEEA---KKL 58

Query: 103 YELALEAY 110
            EL ++ Y
Sbjct: 59  KELHMKLY 66

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|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898)

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 26/64 (40%), Positives = 32/64 (50%)

Query: 40  NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
           N PK   +AYF F++  R   K   P    VA   K   +KWK+MSE EK  Y +KA   
Sbjct: 2   NKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKARED 61

Query: 100 KAEY 103
           K  Y
Sbjct: 62  KKRY 65

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	168
PTZ00199	94	high mobility group protein; Provisional	99.91
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.82
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.81
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.8
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.79
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.79
smart00398	70	HMG high mobility group.	99.78
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.78
KOG0381	96	consensus HMG box-containing protein [General func	99.75
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.72
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.66
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.65
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	99.51
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	99.34
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	99.08
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.36
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.31
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.15
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.1
COG5648	211	NHP6B Chromatin-associated proteins containing the	96.71
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	94.65
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	92.9
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	91.67
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	85.58
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	80.69

>PTZ00199 high mobility group protein; Provisional

Probab=99.91  E-value=3.1e-24  Score=153.45  Aligned_cols=85  Identities=42%  Similarity=0.640  Sum_probs=77.4

Q ss_pred             CcchhcccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHH
Q 044275           27 KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYEL  105 (168)
Q Consensus        27 ~~kk~~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~-~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~k  105 (168)
                      ..+++++++.+||+.||||+|||+|||.++|..|..+||+.. .+.+|+++||++|+.||+++|.+|+++|..++.+|..
T Consensus         8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~   87 (94)
T PTZ00199          8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEK   87 (94)
T ss_pred             ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence            334455677899999999999999999999999999999942 3899999999999999999999999999999999999


Q ss_pred             HHHHHH
Q 044275          106 ALEAYK  111 (168)
Q Consensus       106 e~~~y~  111 (168)
                      +|.+|+
T Consensus        88 e~~~Y~   93 (94)
T PTZ00199         88 EKAEYA   93 (94)
T ss_pred             HHHHHh
Confidence            999995

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

Probab=99.82  E-value=3.1e-20  Score=127.65  Aligned_cols=73  Identities=23%  Similarity=0.327  Sum_probs=70.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      .||||+||||||+++.|..|+.+||+ .++.+|+++||.+|+.|++++|++|..+|+.++++|..++++|+...
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p   73 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPG-LTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTP   73 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccC
Confidence            48999999999999999999999999 69999999999999999999999999999999999999999998753

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.

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

Probab=99.81  E-value=1.8e-19  Score=120.30  Aligned_cols=69  Identities=42%  Similarity=0.694  Sum_probs=65.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        42 PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      ||||+|||+|||.+++..++.+||+ .++.+|+++||.+|+.|++++|.+|..+|..++.+|..++..|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~-~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPD-LSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTT-STHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcc-cccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            8999999999999999999999999 69999999999999999999999999999999999999999995

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 ....

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

Probab=99.80  E-value=1.9e-19  Score=122.34  Aligned_cols=69  Identities=32%  Similarity=0.558  Sum_probs=67.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        42 PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      .|||+|||+|||++.|..++.+||+ +++.+|+++||++|+.|++++|++|.++|..++++|.++++.|+
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            5899999999999999999999999 79999999999999999999999999999999999999999986

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.

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

Probab=99.79  E-value=5e-19  Score=117.02  Aligned_cols=65  Identities=48%  Similarity=0.779  Sum_probs=63.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHH
Q 044275           42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELAL  107 (168)
Q Consensus        42 PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~  107 (168)
                      ||||+|||++|++++|..++..||+ +++.+|++.||.+|+.||+++|.+|..+|..++.+|..+|
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999999999 7999999999999999999999999999999999999886

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

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

Probab=99.79  E-value=6.5e-19  Score=119.94  Aligned_cols=72  Identities=39%  Similarity=0.657  Sum_probs=63.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHh-CCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           39 SNAPKRPLSAYFIFMEDFRKSFKES-FPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        39 p~~PKRP~sAy~lF~~e~r~~vk~~-~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      |++||||+|||+||+.+.+..++.. ++. ..+.++++.|+..|++||+++|.+|+.+|..++.+|..++..|+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~-~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQK-QSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T--SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccC-CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            7899999999999999999999888 665 68999999999999999999999999999999999999999995

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

>smart00398 HMG high mobility group

Probab=99.78  E-value=9.1e-19  Score=116.45  Aligned_cols=70  Identities=44%  Similarity=0.741  Sum_probs=67.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      +||||+|||+||++++|..+..+||+ .++.+|+++||.+|+.|++++|.+|..+|..++.+|..++..|+
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPD-LSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            58999999999999999999999999 69999999999999999999999999999999999999999884

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

Probab=99.78  E-value=3.4e-19  Score=142.41  Aligned_cols=87  Identities=37%  Similarity=0.687  Sum_probs=82.9

Q ss_pred             hhcccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHH
Q 044275           30 KEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEA  109 (168)
Q Consensus        30 k~~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~  109 (168)
                      +..+++.+|||.||||+||||+|+.++|..+...+|. +++.+|+++||++|++|++++|++|...|..++.+|+.++..
T Consensus        59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~-l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~  137 (211)
T COG5648          59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPK-LTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEE  137 (211)
T ss_pred             HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCC-CChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHh
Confidence            3457788999999999999999999999999999999 799999999999999999999999999999999999999999


Q ss_pred             HHhhcCCC
Q 044275          110 YKKQLNDN  117 (168)
Q Consensus       110 y~~k~~~~  117 (168)
                      |..+++..
T Consensus       138 y~~k~~~~  145 (211)
T COG5648         138 YNKKLPNK  145 (211)
T ss_pred             hhcccCCC
Confidence            99998875

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

Probab=99.75  E-value=1.6e-17  Score=117.94  Aligned_cols=76  Identities=46%  Similarity=0.750  Sum_probs=72.5

Q ss_pred             CC--CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH-HHHhhc
Q 044275           38 DS--NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALE-AYKKQL  114 (168)
Q Consensus        38 dp--~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~-~y~~k~  114 (168)
                      +|  +.||||++||++|+.++|..++.+||+ +++.+|+++||++|++|++++|.+|+..|..++.+|..+|. .|+..+
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~   95 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            66  599999999999999999999999999 79999999999999999999999999999999999999999 888764

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

Probab=99.72  E-value=3.1e-17  Score=107.84  Aligned_cols=65  Identities=46%  Similarity=0.744  Sum_probs=62.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHH
Q 044275           42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELAL  107 (168)
Q Consensus        42 PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~  107 (168)
                      ||||+|||+||++++|..++..||+ .++.+|++.||.+|+.|++++|.+|..+|..++.+|..++
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            7999999999999999999999999 6999999999999999999999999999999999998775

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

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.66  E-value=9.2e-17  Score=137.43  Aligned_cols=82  Identities=26%  Similarity=0.464  Sum_probs=76.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           35 KKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        35 ~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      .+......||||||||+|++..|.+|..++|. ..+.||+|.||.+|+.|+++||.+|++.|++++..|++++.+|+.+-
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~-mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYRP  134 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPK-MHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYRP  134 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcc-hhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCccccc
Confidence            45566788999999999999999999999999 69999999999999999999999999999999999999999999886


Q ss_pred             CCC
Q 044275          115 NDN  117 (168)
Q Consensus       115 ~~~  117 (168)
                      ...
T Consensus       135 RRK  137 (331)
T KOG0527|consen  135 RRK  137 (331)
T ss_pred             ccc
Confidence            553

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

Probab=99.65  E-value=3.4e-16  Score=138.93  Aligned_cols=77  Identities=44%  Similarity=0.678  Sum_probs=73.2

Q ss_pred             hcccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 044275           31 EKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAY  110 (168)
Q Consensus        31 ~~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y  110 (168)
                      ++.|+++|||+||||+||||||++..|..|+.+  + .++++|++.+|++|+.|+.  |.+|+++|+.++++|+.+|.+|
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--g-i~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~y  599 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--G-ISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEY  599 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--C-chHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhh
Confidence            567888999999999999999999999999987  5 7999999999999999999  9999999999999999999999


Q ss_pred             Hh
Q 044275          111 KK  112 (168)
Q Consensus       111 ~~  112 (168)
                      +.
T Consensus       600 k~  601 (615)
T KOG0526|consen  600 KN  601 (615)
T ss_pred             cC
Confidence            93

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

Probab=99.51  E-value=2.7e-14  Score=120.31  Aligned_cols=131  Identities=22%  Similarity=0.381  Sum_probs=103.9

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 044275           34 GKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ  113 (168)
Q Consensus        34 k~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k  113 (168)
                      ...+.|.+|-+|+-+||.|++..+.+|+..||+ +.+.+|.++||.+|..|++++|..|...++..+..|.+.|.+|...
T Consensus        57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe-~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~s  135 (410)
T KOG4715|consen   57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPE-LKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNS  135 (410)
T ss_pred             cCCCCCCCCCcccchhhHHhhhhhhhhhccCcc-hHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            455678889999999999999999999999999 7999999999999999999999999999999999999999999775


Q ss_pred             cCCC------CC---CCCcccccccccccCCCCCCcccchhhhhhhccccccceeeeeecc
Q 044275          114 LNDN------GA---GVSEDSWKSTSEVQSGKSSSSEINDEAEQEFSSQVSSYFMGFYCFS  165 (168)
Q Consensus       114 ~~~~------~~---~~~e~s~kskse~~~~d~~~de~eddded~~~~~~~~~~~~~~~~~  165 (168)
                      ....      ..   +-+..+....|-.+-..---+....+|+|+.++++|-.|+++++|-
T Consensus       136 p~y~ayinaKsra~a~le~~sr~~~sr~~~ge~~~~IQPaeDeDD~ddg~stkhla~arf~  196 (410)
T KOG4715|consen  136 PAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDEDDYDDGFSTKHLATARFQ  196 (410)
T ss_pred             chHHHHhhhhhhhhhhhccccccccchhhcCCcceecccccCccccccccchhhhhhhhhh
Confidence            4321      11   1233343444443333333445555677778889999999999984

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=99.34  E-value=1.2e-12  Score=111.33  Aligned_cols=78  Identities=22%  Similarity=0.377  Sum_probs=72.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDNGA  119 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~~~~  119 (168)
                      ..|+|+||||||++|.|..|..++-- +...+|.++||++|..||.+|.++|.++|.++++-|...+..|.++...+++
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEctl-KeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYgKK  268 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKK  268 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhhh-hhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhh
Confidence            56899999999999999999999976 6889999999999999999999999999999999999999999998888644

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

Probab=99.08  E-value=4.7e-11  Score=105.45  Aligned_cols=81  Identities=25%  Similarity=0.456  Sum_probs=73.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcC
Q 044275           36 KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLN  115 (168)
Q Consensus        36 ~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~  115 (168)
                      ...+..-||||||||+|.++.|-+|...+|++ .+.+|+++||.+|+.|+..||++|++.-.++-..|...++.|+.+-.
T Consensus       320 ~ss~PHIKRPMNAFMVWAkDERRKILqA~PDM-HNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPR  398 (511)
T KOG0528|consen  320 ASSEPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPR  398 (511)
T ss_pred             CCCCccccCCcchhhcccchhhhhhhhcCccc-cccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCC
Confidence            33444569999999999999999999999995 89999999999999999999999999999999999999999998876


Q ss_pred             CC
Q 044275          116 DN  117 (168)
Q Consensus       116 ~~  117 (168)
                      +.
T Consensus       399 PK  400 (511)
T KOG0528|consen  399 PK  400 (511)
T ss_pred             CC
Confidence            64

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

Probab=98.36  E-value=3e-06  Score=58.27  Aligned_cols=74  Identities=24%  Similarity=0.389  Sum_probs=61.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      .|..|.+|-.||.+.....+.+.++. ....+ .+.+...|.+|++.+|-+|..+|.++..+|+.+|.+|+.-...
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~-dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~   76 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRN-DRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPAD   76 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTS-THHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhH-hHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            47788899999999999999999998 45555 5589999999999999999999999999999999999987665

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

Probab=98.31  E-value=5.2e-07  Score=82.78  Aligned_cols=72  Identities=25%  Similarity=0.433  Sum_probs=65.5

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHH--HHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHH
Q 044275           34 GKKKDSNAPKRPLSAYFIFMEDFR--KSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELA  106 (168)
Q Consensus        34 k~~kdp~~PKRP~sAy~lF~~e~r--~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke  106 (168)
                      ..+.+...-+||||||+||++.+|  ..+...||+ ..+..|+++||+.|-.|-+.||+.|.++|.+.+..|.+.
T Consensus       174 pnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn-~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  174 PNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPN-QDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             CCcCcchhhhhhhHHHHHHHhhcCCccchhccCcc-ccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            344555667899999999999999  889999999 799999999999999999999999999999999999876

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

Probab=97.15  E-value=0.0018  Score=51.26  Aligned_cols=49  Identities=29%  Similarity=0.434  Sum_probs=42.9

Q ss_pred             CCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHH
Q 044275           46 LSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK   99 (168)
Q Consensus        46 ~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~   99 (168)
                      -+||+-|+.++|.    .|.+ +...++....+..|..|++.+|..|..++...
T Consensus        83 nnaYLNFLReFRr----kh~~-L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~~  131 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCG-LSPQDLIQRAARAWCRLSEAEKNRYRRMAPSV  131 (183)
T ss_pred             chHHHHHHHHHHH----HccC-CCHHHHHHHHHHHHHhCCHHHHHHHHhhcchh
Confidence            4789999999987    4667 79999999999999999999999999876544

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=97.10  E-value=0.0012  Score=52.12  Aligned_cols=48  Identities=27%  Similarity=0.338  Sum_probs=42.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCC
Q 044275           37 KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMS   85 (168)
Q Consensus        37 kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls   85 (168)
                      +.|.+-.|-+|||..|+++.-..|+..+|+ ++..|.....+..|...+
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            334445677899999999999999999999 699999999999998765

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

Probab=96.71  E-value=0.0013  Score=53.31  Aligned_cols=69  Identities=22%  Similarity=0.360  Sum_probs=61.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 044275           39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALE  108 (168)
Q Consensus        39 p~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~  108 (168)
                      ..+|+.|..+|.-+-.+.|+.+...+|+ .+..+++++++..|.+|++.-|.+|...+.+++..|...++
T Consensus       141 k~~~~~~~~~~~e~~~~~r~~~~~~~~~-~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         141 KLPNKAPIGPFIENEPKIRPKVEGPSPD-KALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             ccCCCCCCchhhhccHHhccccCCCCcc-hhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            4467888888999999999999999999 69999999999999999999999999999999888876553

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

Probab=94.65  E-value=0.05  Score=35.20  Aligned_cols=38  Identities=16%  Similarity=0.344  Sum_probs=34.5

Q ss_pred             CHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCC
Q 044275           47 SAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMS   85 (168)
Q Consensus        47 sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls   85 (168)
                      +.|-+|.+-.|+.|...||+ ..+..+...++..|++-+
T Consensus        14 t~yK~Fsq~vRP~l~~~NPk-~~~sKl~~l~~AKwrEF~   51 (55)
T PF08073_consen   14 TNYKAFSQHVRPLLAKANPK-APMSKLMMLLQAKWREFQ   51 (55)
T ss_pred             HHHHHHHHHHHHHHHHHCCC-CcHHHHHHHHHHHHHHHH
Confidence            56889999999999999999 699999999999998644

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

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

Probab=92.90  E-value=0.32  Score=39.32  Aligned_cols=56  Identities=20%  Similarity=0.356  Sum_probs=40.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHH
Q 044275           35 KKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL   97 (168)
Q Consensus        35 ~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~   97 (168)
                      ++..+..++||+|+||+|..=+-    .-.|+ ....+++..|+..|..=+-  |..|.-+|.
T Consensus        37 ~~~~~~~~kr~lN~Fm~FRsyy~----~~~~~-~~Qk~~S~~l~~lW~~dp~--k~~W~l~ak   92 (201)
T PF04769_consen   37 RKRSPEKAKRPLNGFMAFRSYYS----PIFPP-LPQKELSGILTKLWEKDPF--KNKWSLMAK   92 (201)
T ss_pred             ccccccccccchhHHHHHHHHHH----hhcCC-cCHHHHHHHHHHHHhCCcc--HhHHHHHhh
Confidence            44556678999999999987666    34455 5678999999999997443  445554443

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=91.67  E-value=0.27  Score=36.83  Aligned_cols=50  Identities=22%  Similarity=0.281  Sum_probs=42.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChh
Q 044275           37 KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEA   87 (168)
Q Consensus        37 kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~   87 (168)
                      .|..|-+|-.-||.-|.....+.++.++|+ +-.+++-..|-..|..-|+.
T Consensus        68 ~drHPErR~KAAy~afeE~~Lp~lK~E~Pg-LrlsQ~kq~l~K~w~KSPeN  117 (122)
T PF06244_consen   68 IDRHPERRMKAAYKAFEERRLPELKEENPG-LRLSQYKQMLWKEWQKSPEN  117 (122)
T ss_pred             CCCCcchhHHHHHHHHHHHHhHHHHhhCCC-chHHHHHHHHHHHHhcCCCC
Confidence            344444555689999999999999999999 79999999999999887753

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=85.58  E-value=2  Score=34.46  Aligned_cols=46  Identities=20%  Similarity=0.418  Sum_probs=39.3

Q ss_pred             ccHHHHHH-HHHhhhcCCChhhhhHHHHHHHH-HHHHHHHHHHHHHhh
Q 044275           68 KSVAAMGK-AGGQKWKSMSEAEKAPYVQKALN-KKAEYELALEAYKKQ  113 (168)
Q Consensus        68 ~~~~ev~k-~lg~~Wk~ls~~eK~~Y~~~A~~-~k~~y~ke~~~y~~k  113 (168)
                      ..+..|++ .||..|+.+++++|+.|...... ....|-..+..|...
T Consensus        64 ~Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~  111 (198)
T TIGR03481        64 FDLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGE  111 (198)
T ss_pred             CCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence            46777776 78999999999999999998887 778899999998764

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

>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional

Probab=80.69  E-value=8.2  Score=31.17  Aligned_cols=46  Identities=26%  Similarity=0.345  Sum_probs=38.0

Q ss_pred             ccHHHHHH-HHHhhhcCCChhhhhHHHHHHHH-HHHHHHHHHHHHHhh
Q 044275           68 KSVAAMGK-AGGQKWKSMSEAEKAPYVQKALN-KKAEYELALEAYKKQ  113 (168)
Q Consensus        68 ~~~~ev~k-~lg~~Wk~ls~~eK~~Y~~~A~~-~k~~y~ke~~~y~~k  113 (168)
                      ..+..+++ .||..|+.+++++|..|...... ...-|-..+..|...
T Consensus        68 ~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q  115 (211)
T PRK15117         68 VQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQ  115 (211)
T ss_pred             CCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence            36777765 78999999999999999987766 567899999999764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	168
2yqi_A	81	Solution Structure Of The Second Hmg-Box Domain Fro		9e-09
1j3c_A	79	Solution Structure Of The C-Terminal Domain Of The		3e-08
1j3d_A	78	Solution Structure Of The C-Terminal Domain Of The		6e-08
1cg7_A	93	Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len		8e-08
1j5n_A	93	Solution Structure Of The Non-Sequence-Specific Hmg		8e-08
1hme_A	77	Structure Of The Hmg Box Motif In The B-Domain Of H		3e-06
2yrq_A	173	Solution Structure Of The Tandem Hmg Box Domain Fro		4e-06
1nhm_A	81	The Structure Of The Hmg Box And Its Interaction Wi		4e-06
2lhj_A	97	Nmr Structure Of The High Mobility Group Protein-Li		4e-06
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		4e-06
1qrv_A	73	Crystal Structure Of The Complex Of Hmg-D And Dna L		1e-05
1e7j_A	74	Hmg-D Complexed To A Bulge Dna Length = 74		1e-05
3nm9_A	73	Hmgd(M13a)-Dna Complex Length = 73		3e-05
1hma_A	73	The Solution Structure And Dynamics Of The Dna Bind		4e-05
1hsm_A	79	The Structure Of The Hmg Box And Its Interaction Wi		6e-05
4a3n_A	71	Crystal Structure Of Hmg-Box Of Human Sox17 Length		1e-04
2yul_A	82	Solution Structure Of The Hmg Box Of Human Transcri		1e-04
1i11_A	81	Solution Structure Of The Dna Binding Domain, Sox-5		1e-04
3f27_D	83	Structure Of Sox17 Bound To Dna Length = 83		2e-04
1wgf_A	90	Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1		9e-04

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 40  NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
           NAPKRP S +F+F  +FR   K + P   S+  + K  G+ W +++++EK PY+ KA   
Sbjct: 8   NAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKL 66
Query: 100 KAEYELALEAYK 111
           K +YE  +  YK
Sbjct: 67  KEKYEKDVADYK 78

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D NAPKRP SA+F+F  ++R   K   P   S+    K  G+ W   S  +K PY QKA 
Sbjct: 5   DPNAPKRPPSAFFLFCSEYRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 63
Query: 98  NKKAEYELALEAYK 111
             K +YE  + AY+
Sbjct: 64  KLKEKYEKDIAAYR 77

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D NAPKRP SA+F+F  + R   K   P   S+    K  G+ W   S  +K PY QKA 
Sbjct: 4   DPNAPKRPPSAFFLFCSEHRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 62
Query: 98  NKKAEYELALEAYK 111
             K +YE  + AY+
Sbjct: 63  KLKEKYEKDIAAYR 76

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D NAPKR LSAY  F  + R   +   PD  +   +GK  G+KWK+++  EK PY  KA 
Sbjct: 17  DPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 98  NKKAEYELALEAYKKQL 114
             K  YE   E Y   L
Sbjct: 76  ADKKRYESEKELYNATL 92

>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 = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D NAPKR LSAY  F  + R   +   PD  +   +GK  G+KWK+++  EK PY  KA 
Sbjct: 17  DPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 98  NKKAEYELALEAYKKQL 114
             K  YE   E Y   L
Sbjct: 76  ADKKRYESEKELYNATL 92

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D NAPKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA 
Sbjct: 3   DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 61
Query: 98  NKKAEYELALEAYK 111
             K +YE  + AY+
Sbjct: 62  KLKEKYEKDIAAYR 75

>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 = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D NAPKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA 
Sbjct: 98  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 156
Query: 98  NKKAEYELALEAYK 111
             K +YE  + AY+
Sbjct: 157 KLKEKYEKDIAAYR 170

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           SNAPKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA  
Sbjct: 2   SNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 60
Query: 99  KKAEYELALEAYK 111
            K +YE  + AY+
Sbjct: 61  LKEKYEKDIAAYR 73

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
           D NAPKR LS+Y  F ++ R       P+  K VAA+GK  G  W ++S+ EK PY + +
Sbjct: 19  DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMS 78
Query: 97  LNKKAEYE 104
              +  YE
Sbjct: 79  DEDRVRYE 86

>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 = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 38  DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKAL 97
           D NAPKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA 
Sbjct: 85  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 143
Query: 98  NKKAEYELALEAYK 111
             K +YE  + AY+
Sbjct: 144 KLKEKYEKDIAAYR 157

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S+ PKRPLSAY +++   R+S K   P  K V  + K GG+ W++M   +K+ +  KA  
Sbjct: 1   SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAK 57
Query: 99  KKAEYELALEAY 110
            K +Y+ A++ +
Sbjct: 58  AKDDYDRAVKEF 69

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S+ PKRPLSAY +++   R+S K   P  K V  + K GG+ W++M   +K+ +  KA  
Sbjct: 2   SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAK 58
Query: 99  KKAEYELALEAY 110
            K +Y+ A++ +
Sbjct: 59  AKDDYDRAVKEF 70

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S+ PKRPLSAY +++   R+S K   P  K V  + K GG+ W++M   +K+ +  KA  
Sbjct: 1   SDKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAK 57
Query: 99  KKAEYELALEAY 110
            K +Y+ A++ +
Sbjct: 58  AKDDYDRAVKEF 69

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
           PKRPLSAY +++   R+S K   P  K V  + K GG+ W++M   +K+ +  KA   K 
Sbjct: 4   PKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKD 60
Query: 102 EYELALEAY 110
           +Y+ A++ +
Sbjct: 61  DYDRAVKEF 69

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 41  APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
           APKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA   K
Sbjct: 2   APKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLK 60
Query: 101 AEYELALEAYK 111
            +YE  + AY+
Sbjct: 61  EKYEKDIAAYR 71

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           +RP++A+ ++ +D RK   +  PD  + A + K  G+ WK+++ AEK P+V++A   + +
Sbjct: 4   RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 103 Y 103
           +
Sbjct: 63  H 63

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S+  +RP++A+ ++ +D RK   +  PD  + A + K  G+ WK+++ AEK P+V++A  
Sbjct: 5   SSGIRRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAER 63
Query: 99  KKAEY 103
            + ++
Sbjct: 64  LRVQH 68

>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg Box From Mouse Length = 81

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQ 94
          KRP++A+ ++ +D R+   ++FPD  + + + K  G +WK+M+  EK PY +
Sbjct: 6  KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYE 56

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           +RP++A+ ++ +D RK   +  PD  + A + K  G+ WK+++ AEK P+V++A   + +
Sbjct: 8   RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66
Query: 103 Y 103
           +
Sbjct: 67  H 67

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S  PKRP+SA FIF E+ R+  +E  P+  S + + +   + W  +SE +KA Y  +   
Sbjct: 18  SEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAA 76
Query: 99  KKAEYE 104
            KA+ E
Sbjct: 77  LKAQSE 82

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	168
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	4e-24
2lhj_A	97	High mobility group protein homolog NHP1; structur	8e-23
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	1e-22
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	6e-22
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	2e-21
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	2e-21
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	5e-20
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	7e-20
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	1e-18
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	2e-18
1wgf_A	90	Upstream binding factor 1; transcription factor, D	4e-18
1ckt_A	71	High mobility group 1 protein; high-mobility group	5e-17
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	6e-17
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-12
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	3e-16
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	9e-15
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	7e-14
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	5e-10
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	7e-13
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	9e-13
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-12
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	6e-10
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	2e-11
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	6e-10
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	2e-09
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	2e-09
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	4e-09
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	2e-08
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	2e-08
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	9e-08
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	9e-08
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	1e-07
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	3e-07
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	3e-07
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	7e-07
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	8e-07

>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 = 88.9 bits (221), Expect = 4e-24
 Identities = 38/92 (41%), Positives = 47/92 (51%), Gaps = 1/92 (1%)

Query: 23  KAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWK 82
               +PKK    KKKD NAPKR LSAY  F  + R   +   PD  +   +GK  G+KWK
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWK 60

Query: 83  SMSEAEKAPYVQKALNKKAEYELALEAYKKQL 114
           +++  EK PY  KA   K  YE   E Y   L
Sbjct: 61  ALTPEEKQPYEAKAQADKKRYESEKELYNATL 92

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

 Score = 85.9 bits (213), Expect = 8e-23
 Identities = 31/94 (32%), Positives = 47/94 (50%), Gaps = 1/94 (1%)

Query: 21  ARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPD-NKSVAAMGKAGGQ 79
           A  ++    +     KKD NAPKR LS+Y  F ++ R       P+  K VAA+GK  G 
Sbjct: 2   AGASDRTGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGA 61

Query: 80  KWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ 113
            W ++S+ EK PY + +   +  YE     Y ++
Sbjct: 62  AWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR 95

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

 Score = 84.6 bits (210), Expect = 1e-22
 Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 37  KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
           KD NAPKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKA 60

Query: 97  LNKKAEYELALEAYKKQ 113
              K +YE  + AY+ +
Sbjct: 61  AKLKEKYEKDIAAYRAK 77

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

 Score = 83.6 bits (207), Expect = 6e-22
 Identities = 31/100 (31%), Positives = 44/100 (44%), Gaps = 1/100 (1%)

Query: 26  NKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMS 85
           +     K  KKKD N P++P+SAY +F  D + + K   P N +   + K     W  + 
Sbjct: 2   SSGSSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNP-NATFGEVSKIVASMWDGLG 60

Query: 86  EAEKAPYVQKALNKKAEYELALEAYKKQLNDNGAGVSEDS 125
           E +K  Y +K    K EY   L AY+  L       S  S
Sbjct: 61  EEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSYTDSGPS 100

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

 Score = 82.4 bits (204), Expect = 2e-21
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 36  KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQ 94
           K D   P+  +S+Y  F++  R+  K+  PD   + +   K   ++WK+MS  EK  +  
Sbjct: 2   KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFED 61

Query: 95  KALNKKAEYELALEAYKKQ 113
            A   KA YE  ++ Y   
Sbjct: 62  MAKADKARYEREMKTYIPP 80

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

 Score = 82.0 bits (203), Expect = 2e-21
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 29  KKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEA 87
                  K D   PK  +SAY  F++  R+  K+  P+   + A   K   ++WK+MS  
Sbjct: 3   SGSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGK 62

Query: 88  EKAPYVQKALNKKAEYELALEAY 110
           EK+ + + A   K  Y+  ++ Y
Sbjct: 63  EKSKFDEMAKADKVRYDREMKDY 85

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92

 Score = 78.6 bits (194), Expect = 5e-20
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 36  KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQK 95
              S+ PK P++ Y  F+ + R+  +   PD      + K  G +W  +  AEK  Y+ +
Sbjct: 2   SSGSSGPKAPVTGYVRFLNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYLDE 60

Query: 96  ALNKKAEYELALEAYKKQ 113
           A  +K +Y   L AY++ 
Sbjct: 61  AEKEKQQYLKELWAYQQS 78

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

 Score = 78.6 bits (194), Expect = 7e-20
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 35  KKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQ 94
            KK  + PK+PL+ YF F  + R  + +  P+  S   + K   +K+K + E +K  Y+Q
Sbjct: 4   LKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQ 62

Query: 95  KALNKKAEYELALEAYKKQLND 116
               +K E+E  L  +++   D
Sbjct: 63  DFQREKQEFERNLARFREDHPD 84

>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 = 74.2 bits (183), Expect = 1e-18
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 3/75 (4%)

Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S+ PKRPLSAY +++   R+S K   P    V  + K GG+ W++M   +K+ +  KA  
Sbjct: 1   SDKPKRPLSAYALWLNSARESIKRENPG-IKVTEVAKRGGELWRAMK--DKSEWEAKAAK 57

Query: 99  KKAEYELALEAYKKQ 113
            K +Y+ A++ ++  
Sbjct: 58  AKDDYDRAVKEFEAN 72

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

 Score = 73.8 bits (182), Expect = 2e-18
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S+ PKR  +A+ +++ D R+S K   P    V  + K GG+ WK +   +K+ +   A  
Sbjct: 1   SHMPKRATTAFMLWLNDTRESIKRENPG-IKVTEIAKKGGEMWKELK--DKSKWEDAAAK 57

Query: 99  KKAEYELALEAYKKQ 113
            K  Y   +  YK +
Sbjct: 58  DKQRYHDEMRNYKPE 72

>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 = 73.6 bits (181), Expect = 4e-18
 Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 24  AENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKS 83
           + +  K  + G K  S  PKRP+SA FIF E+ R+  +E  P+  S + + +   + W  
Sbjct: 3   SGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWND 61

Query: 84  MSEAEKAPYVQKALNKKAEYELALEAYK 111
           +SE +KA Y  +    KA+ E       
Sbjct: 62  LSEKKKAKYKAREAALKAQSERKSGPSS 89

>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 = 70.1 bits (172), Expect = 5e-17
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
           P+  +S+Y  F++  R+  K+  PD   + +   K   ++WK+MS  EK  +   A   K
Sbjct: 2   PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK 61

Query: 101 AEYELALEAY 110
           A YE  ++ Y
Sbjct: 62  ARYEREMKTY 71

>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 = 73.1 bits (179), Expect = 6e-17
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 40  NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
           NAPKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA   
Sbjct: 100 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 158

Query: 100 KAEYELALEAYKKQ 113
           K +YE  + AY+ +
Sbjct: 159 KEKYEKDIAAYRAK 172

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

 Score = 61.5 bits (149), Expect = 1e-12
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 29  KKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEA 87
                  K D   P+  +S+Y  F++  R+  K+  PD   + +   K   ++WK+MS  
Sbjct: 3   SGSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 62

Query: 88  EKAPYVQKALNKKAEY 103
           EK  +   A   KA Y
Sbjct: 63  EKGKFEDMAKADKARY 78

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

 Score = 69.0 bits (169), Expect = 3e-16
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 36  KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQK 95
              S+  K+P+SA  +F++D R  F    P   S+        + WK++SE EK  Y +K
Sbjct: 2   SSGSSGIKKPMSASALFVQDHRPQFLIENPK-TSLEDATLQIEELWKTLSEEEKLKYEEK 60

Query: 96  ALNKKAEYELALEAYKKQ 113
           A      Y   ++   +Q
Sbjct: 61  ATKDLERYNSQMKRAIEQ 78

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

 Score = 64.2 bits (157), Expect = 9e-15
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
           PKRP SAY +++ +  +  K   P  K      K   + WK++S++EK  Y+Q A   + 
Sbjct: 3   PKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDET 57

Query: 102 EYELALEAY 110
            Y   ++++
Sbjct: 58  RYHNEMKSW 66

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

 Score = 65.5 bits (159), Expect = 7e-14
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 1/94 (1%)

Query: 34  GKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYV 93
           G    ++ PK+P+S+Y  F ++    FK   PD      + +   Q+W+ + +++K  Y 
Sbjct: 2   GSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQ 60

Query: 94  QKALNKKAEYELALEAYKKQLNDNGAGVSEDSWK 127
                +   Y+  +  +K+QL  +     E    
Sbjct: 61  DAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIM 94

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

 Score = 55.1 bits (132), Expect = 5e-10
 Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 5/108 (4%)

Query: 11  QKKPHADMLKARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSV 70
            +    +     K   +    K  +      PKRP SAY +++ +  +  K   P  K  
Sbjct: 84  SQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKL- 142

Query: 71  AAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDNG 118
               K   + WK++S++EK  Y+Q A   +  Y   ++++++Q+ + G
Sbjct: 143 ----KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVG 186

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

 Score = 61.8 bits (150), Expect = 7e-13
 Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 9/112 (8%)

Query: 10  AQKKPHADMLKARKAE--------NKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFK 61
           A+K P     +  +A            K E   K KD NAPKRP SA+F+F  ++R   K
Sbjct: 49  AEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIK 108

Query: 62  ESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ 113
              P   S+  + K  G+ W + +  +K PY +KA   K +YE  + AY+ +
Sbjct: 109 GEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 159

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

 Score = 61.4 bits (149), Expect = 9e-13
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 40  NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
           +  KRP++A+ ++  D R+      P     + + K  G +WK ++EAEK P+ Q+A   
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 100 KAEYELALEAYKKQ 113
           +A +      YK +
Sbjct: 62  QAMHREKYPNYKYR 75

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

 Score = 62.9 bits (152), Expect = 1e-12
 Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 1/98 (1%)

Query: 20  KARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQ 79
                    +  +      ++ PK+P+S+Y  F ++    FK   PD      + +   Q
Sbjct: 20  HMASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQ 78

Query: 80  KWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDN 117
           +W+ + +++K  Y      +   Y+  +  +K+QL  +
Sbjct: 79  RWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPS 116

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

 Score = 55.2 bits (132), Expect = 6e-10
 Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 5/119 (4%)

Query: 1   MKGPRVVAVAQKKPHADMLKARKAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSF 60
           +   +      +    +     K   +    K  +      PKRP SAY +++ +  +  
Sbjct: 106 ISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEA 165

Query: 61  KESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDNGA 119
           K   P  K      K   + WK++S++EK  Y+Q A   +  Y   ++++++Q+ + G 
Sbjct: 166 KGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGR 219

>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 = 56.3 bits (136), Expect = 2e-11
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 26 NKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMS 85
          +             N  KRP++A+ +F + +R  + + +P  K   A+    G +WK M 
Sbjct: 2  SSGSSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMK 60

Query: 86 EAEKAPYVQKA 96
            E+  Y  +A
Sbjct: 61 NEERRMYTLEA 71

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

 Score = 52.7 bits (126), Expect = 6e-10
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 28  PKKEKAGKKKDSNAPKRP-LSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
                  K K    P +P  ++Y ++  +   + K     +           Q+WK +S+
Sbjct: 3   SGSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMK-----DVPSTERMVLCSQQWKLLSQ 57

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQL 114
            EK  Y +K   KK +YE+ L  + + L
Sbjct: 58  KEKDAYHKKCDQKKKDYEVELLRFLESL 85

>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 = 50.7 bits (122), Expect = 2e-09
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 37  KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
             S+  +RP++A+ +F +  R   ++  P         K     W  +   EK  Y   A
Sbjct: 3   SGSSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQKYTDMA 61

Query: 97  LNKKAEYELALEAYK 111
              K  +  A   Y+
Sbjct: 62  KEYKDAFMKANPGYR 76

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

 Score = 50.3 bits (121), Expect = 2e-09
 Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKA 101
            +RP++A+ ++ +D RK   +  PD    A + K  G+ WK+++ AEK P+V++A   + 
Sbjct: 3   IRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 61

Query: 102 E 102
           +
Sbjct: 62  Q 62

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

 Score = 50.7 bits (121), Expect = 4e-09
 Identities = 16/79 (20%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 38  DSNAP-KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
            S+ P K P++ Y  F ++   + + +   +  +       G +W+ +S+++K  Y + A
Sbjct: 4   GSSGPKKPPMNGYQKFSQELLSNGELN---HLPLKERMVEIGSRWQRISQSQKEHYKKLA 60

Query: 97  LNKKAEYELALEAYKKQLN 115
             ++ +Y++ L+ + K L+
Sbjct: 61  EEQQRQYKVHLDLWVKSLS 79

>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 = 47.9 bits (115), Expect = 2e-08
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           KRP++A+ ++  D R+      P     + + K  G +WK ++EAEK P+ Q+A   +A 
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64

>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 = 48.5 bits (116), Expect = 2e-08
 Identities = 17/74 (22%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 29  KKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAE 88
           +       K+    KRP++A+ ++ +  R+   + +P     A + K  G+ W+ ++E+E
Sbjct: 17  ENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPH-LHNAELSKTLGKLWRLLNESE 75

Query: 89  KAPYVQKALNKKAE 102
           K P+V++A   + +
Sbjct: 76  KRPFVEEAERLRVQ 89

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

 Score = 46.4 bits (111), Expect = 9e-08
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           KRP++A+ ++  D R+      P     + + K  G +WK ++EAEK P+ Q+A   +A 
Sbjct: 6   KRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64

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

 Score = 46.4 bits (111), Expect = 9e-08
 Identities = 17/62 (27%), Positives = 37/62 (59%), Gaps = 5/62 (8%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPD--NKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
           KRP++A+ ++ +  R+   E  PD  N  ++   K  G++WK + +++K P++Q+A   +
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPDMHNAEIS---KRLGKRWKLLKDSDKIPFIQEAERLR 60

Query: 101 AE 102
            +
Sbjct: 61  LK 62

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 16/74 (21%), Positives = 33/74 (44%)

Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S +  RP + + +++E+ R +     PD    A + K G  +++ +S  E+  +  KA  
Sbjct: 3   SGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKG 62

Query: 99  KKAEYELALEAYKK 112
           + A      +  K 
Sbjct: 63  ETASEGTEAKKRKS 76

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

 Score = 44.9 bits (107), Expect = 3e-07
 Identities = 18/54 (33%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 43 KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKA 96
          KRP++A+ ++ +D R+   ++FPD    + + K  G +WK+M+  EK PY ++ 
Sbjct: 6  KRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQ 58

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

 Score = 44.9 bits (107), Expect = 3e-07
 Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           K+PL+A+ ++M++ R +        +S AA+ +  G++W ++S  E+A Y + A  ++  
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARKERQL 62

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

 Score = 44.1 bits (105), Expect = 7e-07
 Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 5/62 (8%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPD--NKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
           +RP++A+ ++ +D RK   +  PD  N  ++   K  G+ WK+++ AEK P+V++A   +
Sbjct: 8   RRPMNAFMVWAKDERKRLAQQNPDLHNAELS---KMLGKSWKALTLAEKRPFVEEAERLR 64

Query: 101 AE 102
            +
Sbjct: 65  VQ 66

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

 Score = 43.7 bits (104), Expect = 8e-07
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPD--NKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
           KRP++A+ ++    R+   +  P   N  ++   K  G +WK +SE EK P++ +A   +
Sbjct: 4   KRPMNAFMVWSRGQRRKMAQENPKMHNSEIS---KRLGAEWKLLSETEKRPFIDEAKRLR 60

Query: 101 AE 102
           A 
Sbjct: 61  AL 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	168
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.92
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.91
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.91
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.9
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.9
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.9
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.9
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.9
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.89
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.89
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.88
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.88
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.88
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.87
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.87
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.86
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.86
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.86
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.86
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.86
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.85
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.85
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.85
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.85
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.85
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.85
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.84
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.84
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.84
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.82
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.82
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.8
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.79
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.78
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.77
2cto_A	93	Novel protein; high mobility group box domain, hel	99.77
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.76
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.76
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.68

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

Probab=99.92  E-value=5.7e-25  Score=157.99  Aligned_cols=86  Identities=31%  Similarity=0.532  Sum_probs=81.3

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      +++.+||++||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|..++++|..+|..|+.
T Consensus         9 kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   87 (102)
T 2co9_A            9 KKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA   87 (102)
T ss_dssp             CSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5567899999999999999999999999999999 799999999999999999999999999999999999999999999


Q ss_pred             hcCCCCC
Q 044275          113 QLNDNGA  119 (168)
Q Consensus       113 k~~~~~~  119 (168)
                      ++.....
T Consensus        88 ~~~~~~~   94 (102)
T 2co9_A           88 SLVSKSY   94 (102)
T ss_dssp             HHTSSCC
T ss_pred             hcccccc
Confidence            9877433

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

Probab=99.91  E-value=3.2e-24  Score=149.42  Aligned_cols=79  Identities=29%  Similarity=0.505  Sum_probs=73.9

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~-~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      ++.++||++||||+|||||||+++|..|+.+||+.. ++.+|+++||++|++|++++|.+|+++|..++++|..+|..|+
T Consensus         7 ~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A            7 GMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             SCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            456799999999999999999999999999999932 3799999999999999999999999999999999999999994

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

Probab=99.91  E-value=1.6e-24  Score=155.02  Aligned_cols=83  Identities=29%  Similarity=0.506  Sum_probs=79.3

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      +++.+||++||||+|||||||+++|..|+.+||+ +++.+|+++||++|++||+++|++|+++|+.++++|..+|.+|..
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~   80 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE   80 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGG
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999999 799999999999999999999999999999999999999999999


Q ss_pred             hcCC
Q 044275          113 QLND  116 (168)
Q Consensus       113 k~~~  116 (168)
                      +.+.
T Consensus        81 ~~P~   84 (99)
T 1k99_A           81 DHPD   84 (99)
T ss_dssp             CCCC
T ss_pred             HCCC
Confidence            8654

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

Probab=99.90  E-value=4.6e-25  Score=156.97  Aligned_cols=85  Identities=34%  Similarity=0.579  Sum_probs=79.4

Q ss_pred             chhcccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCcc--HHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHH
Q 044275           29 KKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKS--VAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELA  106 (168)
Q Consensus        29 kk~~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~--~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke  106 (168)
                      +++++++.+||++||||+|||||||+++|..|+.+||+ ++  +.+|+++||++|++|++++|++|+++|..++.+|..+
T Consensus        10 k~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~-~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e   88 (97)
T 2lhj_A           10 VRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPE-IAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYERE   88 (97)
T ss_dssp             CCCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTT-STTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            33456778999999999999999999999999999999 68  9999999999999999999999999999999999999


Q ss_pred             HHHHHhhc
Q 044275          107 LEAYKKQL  114 (168)
Q Consensus       107 ~~~y~~k~  114 (168)
                      |..|+.+.
T Consensus        89 ~~~y~~~~   96 (97)
T 2lhj_A           89 KAEYAQRK   96 (97)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhcC
Confidence            99998764

>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=99.90  E-value=6.5e-25  Score=155.19  Aligned_cols=83  Identities=42%  Similarity=0.674  Sum_probs=78.7

Q ss_pred             hcccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 044275           31 EKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAY  110 (168)
Q Consensus        31 ~~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y  110 (168)
                      +++++.+||+.||||+|||||||+++|..|+.+||+ +++.+|+++||++|++||+++|.+|+++|..++++|..+|..|
T Consensus        10 ~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y   88 (93)
T 1cg7_A           10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY   88 (93)
T ss_dssp             CCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTT-SCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHH
T ss_pred             ccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346678999999999999999999999999999999 7999999999999999999999999999999999999999999


Q ss_pred             Hhhc
Q 044275          111 KKQL  114 (168)
Q Consensus       111 ~~k~  114 (168)
                      +.++
T Consensus        89 ~~~~   92 (93)
T 1cg7_A           89 NATL   92 (93)
T ss_dssp             HHHT
T ss_pred             HHcc
Confidence            9864

>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=99.90  E-value=3.9e-24  Score=145.68  Aligned_cols=76  Identities=38%  Similarity=0.704  Sum_probs=73.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           36 KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        36 ~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      ++||++||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.||+++|.+|+++|+.++.+|..+|..|+.
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4799999999999999999999999999999 799999999999999999999999999999999999999999975

>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=99.90  E-value=1.1e-24  Score=153.13  Aligned_cols=79  Identities=33%  Similarity=0.506  Sum_probs=73.1

Q ss_pred             hhcccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHH
Q 044275           30 KEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEA  109 (168)
Q Consensus        30 k~~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~  109 (168)
                      ++++++.+||++||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|+.++++|..+|..
T Consensus         9 ~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~   87 (90)
T 1wgf_A            9 PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGP   87 (90)
T ss_dssp             SCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSS
T ss_pred             CCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3446778999999999999999999999999999999 799999999999999999999999999999999999876543

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

Probab=99.90  E-value=2.8e-23  Score=146.44  Aligned_cols=79  Identities=28%  Similarity=0.527  Sum_probs=75.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcC
Q 044275           36 KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLN  115 (168)
Q Consensus        36 ~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~  115 (168)
                      .+||++||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|..++++|..+|..|+.+..
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~   80 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEA   80 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHH
Confidence            4799999999999999999999999999999 799999999999999999999999999999999999999999998644

>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=99.89  E-value=8.8e-24  Score=147.57  Aligned_cols=77  Identities=23%  Similarity=0.416  Sum_probs=73.9

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           34 GKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        34 k~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      +..+||+.||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|+.++++|..++++|+
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            357899999999999999999999999999999 79999999999999999999999999999999999999998885

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

Probab=99.89  E-value=5.8e-23  Score=144.76  Aligned_cols=80  Identities=28%  Similarity=0.383  Sum_probs=76.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           37 KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        37 kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      .+|++||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.|++++|++|+++|+.++++|..+|..|+.++..
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~~   81 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPK-TSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQ   81 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCS-SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            579999999999999999999999999999 7999999999999999999999999999999999999999999998765


Q ss_pred             C
Q 044275          117 N  117 (168)
Q Consensus       117 ~  117 (168)
                      .
T Consensus        82 ~   82 (92)
T 2cs1_A           82 M   82 (92)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.88  E-value=7.6e-23  Score=138.24  Aligned_cols=72  Identities=35%  Similarity=0.686  Sum_probs=69.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 044275           39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ  113 (168)
Q Consensus        39 p~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k  113 (168)
                      .++||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++  |++|+++|..++++|..+|++|+++
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~k   72 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPG-IKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSS-CCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4789999999999999999999999999 7999999999999999998  9999999999999999999999875

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

Probab=99.88  E-value=1.5e-23  Score=144.88  Aligned_cols=77  Identities=31%  Similarity=0.560  Sum_probs=73.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCcc--HHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 044275           36 KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKS--VAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ  113 (168)
Q Consensus        36 ~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~--~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k  113 (168)
                      ++||++||||+|||||||+++|..|+.+||+ ++  +.+|+++||++|++|++++|.+|+++|..++++|..+|..|+..
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~-~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~   80 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPD-ASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP   80 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTT-TCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4799999999999999999999999999999 54  59999999999999999999999999999999999999999765

>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=99.88  E-value=4.2e-23  Score=140.21  Aligned_cols=74  Identities=28%  Similarity=0.446  Sum_probs=70.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        38 dp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      ||+.||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.|++++|++|.++|..++++|..++++|+.
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky   74 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSC-CSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence            68999999999999999999999999999 799999999999999999999999999999999999999999874

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

Probab=99.87  E-value=2.1e-22  Score=136.02  Aligned_cols=72  Identities=31%  Similarity=0.618  Sum_probs=69.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 044275           39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ  113 (168)
Q Consensus        39 p~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k  113 (168)
                      |++||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|  ++|.+|+++|..++++|..+|..|+.+
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPG-IKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTT-CCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            7899999999999999999999999999 79999999999999999  899999999999999999999999764

>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=99.87  E-value=7.3e-22  Score=151.19  Aligned_cols=80  Identities=38%  Similarity=0.682  Sum_probs=76.3

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      +++.+||+.||||+|||+|||+++|..|+.+||+ +++.+|+++||++|++|++++|++|+.+|..++.+|..+|.+|+.
T Consensus        80 kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A           80 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             GGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSC-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccccccccccccccchhhHhhHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4567899999999999999999999999999999 799999999999999999999999999999999999999999986


Q ss_pred             h
Q 044275          113 Q  113 (168)
Q Consensus       113 k  113 (168)
                      +
T Consensus       159 ~  159 (159)
T 2gzk_A          159 K  159 (159)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.86  E-value=5.5e-22  Score=137.75  Aligned_cols=78  Identities=27%  Similarity=0.420  Sum_probs=74.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        38 dp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      .|+.||||+|||||||+++|..|+.+||+ +++.+|+++||++|++||+++|++|.++|+.++++|..++++|+.+...
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~prr   78 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRR   78 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccCCCC
Confidence            48999999999999999999999999999 7999999999999999999999999999999999999999999876543

>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=99.86  E-value=5.1e-22  Score=133.06  Aligned_cols=70  Identities=30%  Similarity=0.596  Sum_probs=65.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAY  110 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~~-~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y  110 (168)
                      +||||+|||+|||+++|..++.+||+.. ++.+|+++||++|++|++++|.+|+++|..++++|..+|..|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            5999999999999999999999999932 369999999999999999999999999999999999999876

>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=99.86  E-value=1.5e-22  Score=139.57  Aligned_cols=77  Identities=21%  Similarity=0.369  Sum_probs=73.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           37 KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        37 kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      .+|++||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++++|++|+++|..++++|..++.+|+.+.
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~p   79 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSGP   79 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSS-SCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCCT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcCC
Confidence            578999999999999999999999999999 79999999999999999999999999999999999999999998754

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

Probab=99.86  E-value=6.9e-22  Score=142.91  Aligned_cols=81  Identities=25%  Similarity=0.486  Sum_probs=70.8

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      ....++|+.||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.|++++|++|+++|..++++|..++++|+.
T Consensus        21 ~~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky   99 (106)
T 4euw_A           21 FQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPH-LHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKY   99 (106)
T ss_dssp             -------CCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             hhccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCc
Confidence            4457889999999999999999999999999999 799999999999999999999999999999999999999999987


Q ss_pred             hc
Q 044275          113 QL  114 (168)
Q Consensus       113 k~  114 (168)
                      +.
T Consensus       100 ~P  101 (106)
T 4euw_A          100 QP  101 (106)
T ss_dssp             --
T ss_pred             CC
Confidence            54

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

Probab=99.86  E-value=3.6e-22  Score=133.52  Aligned_cols=71  Identities=30%  Similarity=0.539  Sum_probs=63.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      +.||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.||+++|.+|+++|..++.+|..++++|+
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            579999999999999999999999999 79999999999999999999999999999999999999999885

>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=99.85  E-value=1.5e-21  Score=141.72  Aligned_cols=79  Identities=28%  Similarity=0.431  Sum_probs=73.8

Q ss_pred             ccCCCCCCCC-CCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           33 AGKKKDSNAP-KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        33 kk~~kdp~~P-KRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      .++.+||+.| |||+|||+|||+++|..|+    + +++.+|+++||++|+.|++++|++|+++|+.++.+|..+|..|.
T Consensus         8 ~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~-~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~   82 (108)
T 1v64_A            8 QLKDKFDGRPTKPPPNSYSLYCAELMANMK----D-VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFL   82 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----T-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHHHh----C-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467899999 9999999999999999886    5 69999999999999999999999999999999999999999999


Q ss_pred             hhcCC
Q 044275          112 KQLND  116 (168)
Q Consensus       112 ~k~~~  116 (168)
                      .++.+
T Consensus        83 ~~~~~   87 (108)
T 1v64_A           83 ESLPE   87 (108)
T ss_dssp             HHSCH
T ss_pred             hhCCH
Confidence            98765

>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=99.85  E-value=2.5e-21  Score=134.56  Aligned_cols=77  Identities=22%  Similarity=0.374  Sum_probs=72.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDN  117 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~~  117 (168)
                      +.||||+|||||||+++|..|..+||+ +++.+|+++||++|++||+++|++|+++|+.++++|..+++.|+.+....
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~~   77 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG   77 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCCC
Confidence            469999999999999999999999999 79999999999999999999999999999999999999999998775543

>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=99.85  E-value=1.6e-21  Score=133.67  Aligned_cols=75  Identities=25%  Similarity=0.453  Sum_probs=71.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcC
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLN  115 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~  115 (168)
                      +.||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.||+++|++|+++|..++++|..++++|+.+..
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~   75 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPR   75 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccCCC
Confidence            479999999999999999999999999 799999999999999999999999999999999999999999987643

>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=99.85  E-value=9e-22  Score=135.68  Aligned_cols=76  Identities=28%  Similarity=0.472  Sum_probs=69.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        38 dp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      .++.||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.|++++|.+|.++|+.++++|..++++|+.+.
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~P   78 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRP   78 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCC
Confidence            46789999999999999999999999999 79999999999999999999999999999999999999999998653

>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=99.85  E-value=2.1e-21  Score=137.05  Aligned_cols=75  Identities=21%  Similarity=0.325  Sum_probs=72.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      +.||||+|||+||++++|..++.+||+  ++.+|++.||++|++|++.+|++|+.+|..++.+|+++|.+|+.+...
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~~   77 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAA   77 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            689999999999999999999999998  799999999999999999999999999999999999999999987665

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

Probab=99.85  E-value=3.6e-21  Score=149.42  Aligned_cols=80  Identities=38%  Similarity=0.682  Sum_probs=76.4

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      +++.+||+.||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++++|++|+.+|..++.+|..+|.+|+.
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  171 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  171 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4456799999999999999999999999999999 799999999999999999999999999999999999999999987


Q ss_pred             h
Q 044275          113 Q  113 (168)
Q Consensus       113 k  113 (168)
                      +
T Consensus       172 k  172 (173)
T 2yrq_A          172 K  172 (173)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.84  E-value=2e-21  Score=132.70  Aligned_cols=74  Identities=26%  Similarity=0.471  Sum_probs=70.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      +.||||+|||||||+++|..|+.+||+ +++.+|+++||++|+.|++++|++|.++|+.++++|..++++|+...
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~P   74 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPD-MHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRP   74 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCC
Confidence            579999999999999999999999999 79999999999999999999999999999999999999999998654

>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=99.84  E-value=2e-21  Score=133.62  Aligned_cols=75  Identities=28%  Similarity=0.513  Sum_probs=68.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        39 p~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      ++.||||+|||||||+++|..|+.+||+ +++.+|+++||++|++|++++|++|.++|+.++.+|..++++|+.+.
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p   76 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKP   76 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC----
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeecc
Confidence            5789999999999999999999999999 79999999999999999999999999999999999999999998653

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

Probab=99.84  E-value=2.8e-21  Score=128.34  Aligned_cols=66  Identities=29%  Similarity=0.523  Sum_probs=62.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAY  110 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y  110 (168)
                      |+||||+|||+|||+++|..++..||     .+|+++||++|+.||+++|.+|+++|..++.+|.++|.+|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999987554     5999999999999999999999999999999999999988

>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=99.82  E-value=3.9e-20  Score=132.69  Aligned_cols=78  Identities=19%  Similarity=0.392  Sum_probs=70.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           37 KDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        37 kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      ....+||||+|||||||++++.  ...+++ +++.+|+++||++|+.|++++|++|+++|..++++|.++|..|..++.+
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~-~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~   80 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNH-LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSP   80 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            4567899999999999999975  234555 5899999999999999999999999999999999999999999999877


Q ss_pred             C
Q 044275          117 N  117 (168)
Q Consensus       117 ~  117 (168)
                      .
T Consensus        81 ~   81 (101)
T 1v63_A           81 Q   81 (101)
T ss_dssp             T
T ss_pred             H
Confidence            4

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

Probab=99.82  E-value=2.3e-20  Score=144.91  Aligned_cols=82  Identities=28%  Similarity=0.498  Sum_probs=77.0

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-ccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHH
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDN-KSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYK  111 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~-~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~  111 (168)
                      ++.++||++||||+|||+|||+++|..|+.+||+. +++.+|+++||++|+.|++++|++|+++|..++.+|..+|..|.
T Consensus         7 k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~   86 (173)
T 2yrq_A            7 GMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYI   86 (173)
T ss_dssp             SSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            45678999999999999999999999999999994 38999999999999999999999999999999999999999998


Q ss_pred             hhc
Q 044275          112 KQL  114 (168)
Q Consensus       112 ~k~  114 (168)
                      ...
T Consensus        87 ~~~   89 (173)
T 2yrq_A           87 PPK   89 (173)
T ss_dssp             CCC
T ss_pred             hhh
Confidence            754

>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=99.80  E-value=4.1e-20  Score=127.82  Aligned_cols=61  Identities=25%  Similarity=0.402  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCcc-HHHHHHHHHhhhcCCChhhhhHHHHHHHHH
Q 044275           38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKS-VAAMGKAGGQKWKSMSEAEKAPYVQKALNK   99 (168)
Q Consensus        38 dp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~-~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~   99 (168)
                      +++.||||+|||||||+++|..|+.+||+ ++ +.+|+++||++|+.|++++|++|+++|..+
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~-~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPD-FSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTT-CCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999 67 999999999999999999999999999886

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

Probab=99.79  E-value=1.1e-19  Score=148.13  Aligned_cols=82  Identities=22%  Similarity=0.419  Sum_probs=76.9

Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 044275           34 GKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ  113 (168)
Q Consensus        34 k~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k  113 (168)
                      ....+|++||||+|||+|||+++|..|+.+||+ .++.+|+++||++|+.|++++|.+|+++|..++++|..+|..|...
T Consensus        34 ~s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~  112 (238)
T 3tmm_A           34 SSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQ  112 (238)
T ss_dssp             -CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            346789999999999999999999999999999 6999999999999999999999999999999999999999999876


Q ss_pred             cCC
Q 044275          114 LND  116 (168)
Q Consensus       114 ~~~  116 (168)
                      +.+
T Consensus       113 ~~p  115 (238)
T 3tmm_A          113 LTP  115 (238)
T ss_dssp             CCH
T ss_pred             CCH
Confidence            654

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

Probab=99.78  E-value=1.3e-20  Score=132.75  Aligned_cols=69  Identities=28%  Similarity=0.428  Sum_probs=63.7

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCcc--HHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHH
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKS--VAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELA  106 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~--~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke  106 (168)
                      .+..+||++||||+|||||||+++|..|+.+||+ ++  +.+|+    ++|+.|++++|++|+.+|+.++++|..+
T Consensus        14 ~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~-~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           14 LKWEKEEALGEMATVAPVLYTNINFPNLKEEFPD-WTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             HHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCS-HHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             hhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcC-ccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            4456799999999999999999999999999999 78  88887    9999999999999999999999999753

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

Probab=99.77  E-value=4.3e-19  Score=142.54  Aligned_cols=78  Identities=23%  Similarity=0.445  Sum_probs=74.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        38 dp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      .|++||||+|||+|||+++|..|+.+||+ .++.+|+++||++|+.||+++|.+|+++|..++++|..+|..|...+.+
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~tp   83 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPD-AKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTP   83 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCCH
Confidence            47899999999999999999999999999 6999999999999999999999999999999999999999999877654

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

Probab=99.77  E-value=1.4e-19  Score=128.21  Aligned_cols=69  Identities=20%  Similarity=0.290  Sum_probs=64.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHH---HhhhcCCChhhhhHHHHHHHHHHHHHHHHH
Q 044275           36 KKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAG---GQKWKSMSEAEKAPYVQKALNKKAEYELAL  107 (168)
Q Consensus        36 ~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~l---g~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~  107 (168)
                      ..+++.||||+|||||||+++|..|+.+  + +++.+|+++|   |++|+.|++++|++|+++|.+++++|.+++
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~-~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--G-LPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--T-CCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--C-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            4678999999999999999999999988  5 6899999999   999999999999999999999999998875

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

Probab=99.76  E-value=6e-20  Score=147.54  Aligned_cols=80  Identities=25%  Similarity=0.420  Sum_probs=72.7

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      ++..+||+.||||+|||||||+++|..|+..||     .+|+++||++|++|++++|++|+.+|..++++|..+|.+|+.
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  180 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  180 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSSCSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhccCCH-----HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445689999999999999999999998876554     499999999999999999999999999999999999999999


Q ss_pred             hcCCC
Q 044275          113 QLNDN  117 (168)
Q Consensus       113 k~~~~  117 (168)
                      ++...
T Consensus       181 ~~~~~  185 (214)
T 3tq6_A          181 QMIEV  185 (214)
T ss_dssp             HHHHT
T ss_pred             hCccc
Confidence            98553

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

Probab=99.76  E-value=7.9e-20  Score=148.96  Aligned_cols=81  Identities=26%  Similarity=0.442  Sum_probs=73.2

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      ++..+||++||||+|||||||+++|..|+..||     .+|+++||++|++|++++|++|+.+|+.++++|+++|.+|+.
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  212 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  212 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSSH-----HHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhccCH-----HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445689999999999999999999998876554     489999999999999999999999999999999999999999


Q ss_pred             hcCCCC
Q 044275          113 QLNDNG  118 (168)
Q Consensus       113 k~~~~~  118 (168)
                      ++....
T Consensus       213 k~~~~~  218 (238)
T 3tmm_A          213 QMIEVG  218 (238)
T ss_dssp             HHHHTT
T ss_pred             hCcccc
Confidence            975543

>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=99.68  E-value=5.9e-17  Score=123.78  Aligned_cols=74  Identities=28%  Similarity=0.466  Sum_probs=71.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhh
Q 044275           39 SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQ  113 (168)
Q Consensus        39 p~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k  113 (168)
                      |+.||||+||||||+.+.|..|..+||+ +++.+|+++||++|+.|++++|.+|+++|..++.+|..++..|...
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~   75 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSS-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccc
Confidence            6789999999999999999999999999 7999999999999999999999999999999999999999999754

---

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	168
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	5e-18
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-15
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-14
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	4e-13
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	7e-13
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-12
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-12
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	7e-12
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	9e-12
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	4e-11
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	1e-10
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	8e-10

>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 = 72.2 bits (177), Expect = 5e-18
 Identities = 38/88 (43%), Positives = 47/88 (53%), Gaps = 1/88 (1%)

Query: 27  KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
           +PKK    KKKD NAPKR LSAY  F  + R   +   PD  +   +GK  G+KWK+++ 
Sbjct: 6   EPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTP 64

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQL 114
            EK PY  KA   K  YE   E Y   L
Sbjct: 65  EEKQPYEAKAQADKKRYESEKELYNATL 92

>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 = 66.0 bits (161), Expect = 1e-15
 Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 40  NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
           NAPKRP SA+F+F  ++R   K   P   S+  + K  G+ W + +  +K PY +KA   
Sbjct: 1   NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 59

Query: 100 KAEYELALEAYKKQLNDNGA 119
           K +YE  + AY+ +   + A
Sbjct: 60  KEKYEKDIAAYRAKGKPDAA 79

>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 = 62.3 bits (151), Expect = 5e-14
 Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 35  KKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQ 94
            KK  + PK+PL+ YF F  + R  + +  P+  S   + K   +K+K + E +K  Y+Q
Sbjct: 4   LKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQ 62

Query: 95  KALNKKAEYELALEAYKKQ 113
               +K E+E  L  +++ 
Sbjct: 63  DFQREKQEFERNLARFRED 81

>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 = 59.0 bits (143), Expect = 4e-13
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 3/75 (4%)

Query: 39  SNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALN 98
           S+ PKRPLSAY +++   R+S K   P  K V  + K GG+ W++M   +K+ +  KA  
Sbjct: 1   SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAK 57

Query: 99  KKAEYELALEAYKKQ 113
            K +Y+ A++ ++  
Sbjct: 58  AKDDYDRAVKEFEAN 72

>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 = 58.7 bits (142), Expect = 7e-13
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 40  NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
           +  KRP++A+ ++    R+   +  P     + + K  G +WK +SE EK P++ +A   
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENP-KMHNSEISKRLGAEWKLLSETEKRPFIDEAKRL 59

Query: 100 KAEYELALEAYKKQ 113
           +A +      YK +
Sbjct: 60  RALHMKEHPDYKYR 73

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

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

 Score = 58.0 bits (140), Expect = 2e-12
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 23  KAENKPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWK 82
            + +  K  + G K  S  PKRP+SA FIF E+ R+  +E  P+  S + + +   + W 
Sbjct: 2   SSGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWN 60

Query: 83  SMSEAEKAPYVQKALNKKAEYE 104
            +SE +KA Y  +    KA+ E
Sbjct: 61  DLSEKKKAKYKAREAALKAQSE 82

>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 = 57.2 bits (138), Expect = 2e-12
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 42  PKRPLSAYFIFMEDFRKSFKESFPDNK-SVAAMGKAGGQKWKSMSEAEKAPYVQKALNKK 100
           P+  +S+Y  F++  R+  K+  PD   + +   K   ++WK+MS  EK  +   A   K
Sbjct: 2   PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK 61

Query: 101 AEYELALEAY 110
           A YE  ++ Y
Sbjct: 62  ARYEREMKTY 71

>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 = 56.8 bits (137), Expect = 7e-12
 Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 34  GKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYV 93
           G    S   K P++ Y  F ++   + + +    K         G +W+ +S+++K  Y 
Sbjct: 1   GSSGSSGPKKPPMNGYQKFSQELLSNGELNHLPLKERM---VEIGSRWQRISQSQKEHYK 57

Query: 94  QKALNKKAEYELALEAYKKQL 114
           + A  ++ +Y++ L+ + K L
Sbjct: 58  KLAEEQQRQYKVHLDLWVKSL 78

>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 = 56.0 bits (135), Expect = 9e-12
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 40  NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNK 99
           +  KRP++A+ ++  D R+      P  ++   + K  G +WK ++EAEK P+ Q+A   
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMRNSE-ISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 100 KAEYELALEAYKKQ 113
           +A +      YK +
Sbjct: 62  QAMHREKYPNYKYR 75

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

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

 Score = 54.1 bits (130), Expect = 4e-11
 Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           K+PL+A+ ++M++ R +        +S A   +  G++W ++S  E+A Y + A  ++  
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKESAAIN-QILGRRWHALSREEQAKYYELARKERQL 62

Query: 103 YELALEAYKKQLN 115
           +      +  + N
Sbjct: 63  HMQLYPGWSARDN 75

>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 = 52.5 bits (126), Expect = 1e-10
 Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 43  KRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAE 102
           KRP++A+ ++ +D R+   ++FPD    + + K  G +WK+M+  EK PY ++      +
Sbjct: 4   KRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQ 62

Query: 103 YE 104
           + 
Sbjct: 63  HL 64

>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 = 51.5 bits (123), Expect = 8e-10
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 27  KPKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSE 86
                +   K D    K P ++Y ++  +   + K+                Q+WK +S+
Sbjct: 3   SGSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKD-----VPSTERMVLCSQQWKLLSQ 57

Query: 87  AEKAPYVQKALNKKAEYELALEAYKKQLND 116
            EK  Y +K   KK +YE+ L  + + L +
Sbjct: 58  KEKDAYHKKCDQKKKDYEVELLRFLESLPE 87

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	168
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.91
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.89
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.88
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.85
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.85
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.84
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.83
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.82
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.81
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.79
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	97.06

>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=99.91  E-value=2.1e-24  Score=151.07  Aligned_cols=87  Identities=44%  Similarity=0.695  Sum_probs=80.8

Q ss_pred             cchhcccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHH
Q 044275           28 PKKEKAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELAL  107 (168)
Q Consensus        28 ~kk~~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~  107 (168)
                      .+++++++.++|++||||+|||+|||.++|..|+.+||+ .++.+|++.||.+|++||+++|.+|+.+|..++.+|..+|
T Consensus         7 ~~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~   85 (93)
T d1lwma_           7 PKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEK   85 (93)
T ss_dssp             TTSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            344456677899999999999999999999999999999 7999999999999999999999999999999999999999


Q ss_pred             HHHHhhcC
Q 044275          108 EAYKKQLN  115 (168)
Q Consensus       108 ~~y~~k~~  115 (168)
                      ..|+.+++
T Consensus        86 ~~y~~~l~   93 (93)
T d1lwma_          86 ELYNATLA   93 (93)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHhccC
Confidence            99998763

>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=99.89  E-value=2.4e-23  Score=141.29  Aligned_cols=77  Identities=35%  Similarity=0.670  Sum_probs=74.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDN  117 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~~  117 (168)
                      |+||||+|||+|||.++|..|+.+||+ +++.+|+++||.+|+.||+++|.+|+.+|..++.+|..+|.+|+.++.++
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~-~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~~~   77 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPD   77 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTT-CCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence            689999999999999999999999999 79999999999999999999999999999999999999999999987763

>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=99.88  E-value=4.7e-23  Score=143.21  Aligned_cols=83  Identities=29%  Similarity=0.506  Sum_probs=79.7

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      +++++||+.||||+|||+|||+++|..|..+||+ +++.+|+++||.+|+.||+++|.+|..+|..++.+|..+|..|..
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~-~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~   80 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE   80 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGG
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999999 799999999999999999999999999999999999999999999


Q ss_pred             hcCC
Q 044275          113 QLND  116 (168)
Q Consensus       113 k~~~  116 (168)
                      +...
T Consensus        81 ~~pe   84 (91)
T d1k99a_          81 DHPD   84 (91)
T ss_dssp             CCCC
T ss_pred             HCcc
Confidence            8765

>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=99.86  E-value=3.1e-22  Score=136.49  Aligned_cols=74  Identities=26%  Similarity=0.458  Sum_probs=70.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      +.||||+||||||++++|..|+.+||+ .++.+|+++||.+|++|++++|.+|+.+|..++++|..++++|+.+.
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~-~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p   74 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRP   74 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCC
Confidence            579999999999999999999999999 79999999999999999999999999999999999999999997653

>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=99.85  E-value=1.1e-21  Score=134.90  Aligned_cols=74  Identities=28%  Similarity=0.455  Sum_probs=71.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      +.||||+|||||||+++|..|+.+||+ .++.+|+++||.+|++|++++|.+|+++|..++.+|..++++|+.+.
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~-~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p   76 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCC
Confidence            689999999999999999999999999 69999999999999999999999999999999999999999998754

>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=99.85  E-value=1.6e-21  Score=130.48  Aligned_cols=72  Identities=33%  Similarity=0.673  Sum_probs=68.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 044275           40 NAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQL  114 (168)
Q Consensus        40 ~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~  114 (168)
                      ++||||+|||||||.++|..|+.+||+ .++.+|+++||.+|++|+  +|++|+.+|+.++.+|..+|..|+.++
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~-~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~g   73 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPG-IKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEANG   73 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTT-CCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            789999999999999999999999999 799999999999999886  599999999999999999999998763

>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=99.84  E-value=9.4e-22  Score=130.69  Aligned_cols=69  Identities=28%  Similarity=0.549  Sum_probs=65.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAY  110 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y  110 (168)
                      .+|||+|||||||++.|..|+.+||+ .++.+|+++||.+|++|++++|++|+++|+.++.+|.+++++|
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            46899999999999999999999999 7999999999999999999999999999999999998877665

>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=99.84  E-value=3.3e-21  Score=127.97  Aligned_cols=70  Identities=30%  Similarity=0.588  Sum_probs=66.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCC-ccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHH
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDN-KSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAY  110 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~-~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y  110 (168)
                      +||||+|||||||.++|..|+.+||+. ..+.+|+++||.+|+.||+++|++|.++|..++.+|..+|.+|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            599999999999999999999999972 3578999999999999999999999999999999999999876

>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=99.83  E-value=4.1e-21  Score=133.00  Aligned_cols=74  Identities=35%  Similarity=0.554  Sum_probs=68.6

Q ss_pred             cccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHH
Q 044275           32 KAGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELA  106 (168)
Q Consensus        32 ~kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke  106 (168)
                      .+...++|+.||||+|||+|||+++|..|+.+||+ .++.+|+++|+.+|+.|++++|.+|+.+|..++.+|.++
T Consensus        11 ~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~-~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             ccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            35567899999999999999999999999999999 799999999999999999999999999999998888643

>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=99.82  E-value=1.9e-20  Score=128.95  Aligned_cols=74  Identities=23%  Similarity=0.400  Sum_probs=70.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           42 PKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        42 PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      .|||+||||||+++.|..|..+||+ +++.+|+++||.+|++||+++|++|.++|..++++|..++++|+.....
T Consensus         3 ikRP~naf~lF~~~~r~~~~~~~P~-~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~   76 (86)
T d2lefa_           3 IKKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY   76 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSST
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCC
Confidence            5799999999999999999999999 7999999999999999999999999999999999999999999766444

>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=99.81  E-value=6.6e-20  Score=130.99  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=72.5

Q ss_pred             ccCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 044275           33 AGKKKDSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKK  112 (168)
Q Consensus        33 kk~~kdp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~  112 (168)
                      .+...++.+||+|+|||||||+++|.+    +|+ +++.+|+++||.+|++||+++|++|+.+|..++.+|..+|.+|..
T Consensus         9 ~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~-~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~   83 (108)
T d1v64a_           9 LKDKFDGRPTKPPPNSYSLYCAELMAN----MKD-VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             SSCCTTTSCCCCCSSHHHHHHHHHHHH----CTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCCCCcHHHHHHHHHHHH----ccC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            456688889999999999999999864    577 799999999999999999999999999999999999999999998


Q ss_pred             hcCC
Q 044275          113 QLND  116 (168)
Q Consensus       113 k~~~  116 (168)
                      ++.+
T Consensus        84 ~~~~   87 (108)
T d1v64a_          84 SLPE   87 (108)
T ss_dssp             HSCH
T ss_pred             hCCH
Confidence            8765

>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=99.79  E-value=1.1e-19  Score=128.09  Aligned_cols=77  Identities=19%  Similarity=0.372  Sum_probs=70.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 044275           38 DSNAPKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLNDN  117 (168)
Q Consensus        38 dp~~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~~  117 (168)
                      ..++||||+|||||||.++|..++..|   +++.+|+++||++|+.|++++|++|.++|..++.+|..+|..|...+.+.
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~~---~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~~   81 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELNH---LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTT---SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcC---CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHH
Confidence            457899999999999999999986554   47899999999999999999999999999999999999999999988763

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

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

Probab=97.06  E-value=0.0019  Score=41.52  Aligned_cols=74  Identities=22%  Similarity=0.326  Sum_probs=61.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 044275           41 APKRPLSAYFIFMEDFRKSFKESFPDNKSVAAMGKAGGQKWKSMSEAEKAPYVQKALNKKAEYELALEAYKKQLND  116 (168)
Q Consensus        41 ~PKRP~sAy~lF~~e~r~~vk~~~p~~~~~~ev~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~y~ke~~~y~~k~~~  116 (168)
                      -|--|.+|-.+|-+..-..+...+-+  .-.-..+.+-..|++|...+|.+|..+|.++..+|+.++-+.+.-...
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~--DR~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~~~a~   76 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAA   76 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHh--hHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence            46677799999999999998888766  445556677788999999999999999999999999999887765443