Citrus Sinensis ID: 037983

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-----
Protein Sequence
MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFESLNTYNREVMDPWTLERSHGRWLPFFEILG
Secondary Structure (PSIPRED)
cccccccHHHHHHccccccccHHHHHHHcccccHHHHcccHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHcccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHcccccccccccccHHHccccccccccccccccccccEEEEcccccccccHHccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHccccccHHHHHHHccccEEEEEEEcccccHHHHHHHHHHccccccccccccccccccccccEEEEHHHHHHHcccccHHHHHHHHHHHHHHccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHcccEEEcccccccccEEEEEEEccccccEcEHHcHcHHccccccHEccccccccHHHHcc
Coil and Loop (DISEMBL)
MANQPRTRKRVHAirrapdgsafekcdrcEAMVPIALVDMHECEAKVKNKVKRfkgvcekpklvkqdsysdqtrspFRIFMETFVEtcgsrelidIDQKGFEKWKnmskeerqpyVIKAEMLDAAHRRALLEEvtsmprfmddeadSAMVWkydksydpiysteilkcsnssrfeslntynrevmdpwtlershgrwlpffeilg
Flexible Loop (DISEMBL)
manqprtrkrvhairrapdgsafekcdRCEAMVPIALVDMHECEAKVKNKvkrfkgvcekpklvkqdsysdqtrsPFRIFMETFVETCGSRELIDIDQKGFEKWknmskeerqPYVIKAEMLDAAHRRALLEevtsmprfmddEADSAMVWKYDKSYDPIYSTeilkcsnssrFESLNTYNRevmdpwtlershgrwlpffeiLG
Low Complexity Region (SEG)
MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFESLNTYNREVMDPWTLERSHGRWLPFFEILG
Disordered region (IsUnstruct)
*********************AFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEKPKLV*********RSPFRIFMETFVETCGSRELIDIDQKGFEKWK********PYVIKAEMLDAAHRRALLEEVTSM*RFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFESLNTYNREVMDPWTLERSHGRWLPFFEI**
Disordered Region (DISOPRED)
*********************AFEKCDRCEAMVPIALV***************************************RIFMETF**************KGFEKWKNMSKEERQPYVIKAEMLDAAHRRA*****************************************SSRFESLNTYNREVMDPWTLERSHGRWLPFFEILG
Disordered Region (DISEMBL)
***********HAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFESLNTYNREVMDPWTLERSHGRWLPFFEILG
Disordered Region (DISPRO)
********************SAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFK*****************TRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFESLNTYNREVMDPWTLERSHGRWLPFFEILG
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFESLNTYNREVMDPWTLERSHGRWLPFFEILG
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	205	2.2.26 [Sep-21-2011]
Q8LDF9	241	High mobility group B pro	no	no	0.629	0.535	0.319	2e-11

>sp|Q8LDF9|HMGB7_ARATH High mobility group B protein 7 OS=Arabidopsis thaliana GN=HMGB7 PE=1 SV=1

 Score = 69.3 bits (168), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 79/172 (45%), Gaps = 43/172 (25%)

Query: 2   ANQPRTRKRVHA---------IRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVK 52
           +N P+ RKRV A         +RRA DGSAF  C+ C   V +AL+ MH C    K +V 
Sbjct: 8   SNAPKQRKRVEAETSSNTSTTLRRAKDGSAFALCEGCNKSVAVALISMHNCSLDAKIRVN 67

Query: 53  RFKGVCE--------------------KPKLVKQ-------DSYSDQTRSP---FRIFME 82
               V E                    KPK +K+        S S++ + P   F IFM 
Sbjct: 68  LEAQVVETQAEAKKKPAEKKKTTSDGPKPKRLKKTNDEKKSSSTSNKPKRPLTAFFIFMS 127

Query: 83  TFVETCGSRE----LIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRAL 130
            F +T  S        D  + G EKWK++++EE++ Y+ KA  L A + ++L
Sbjct: 128 DFRKTFKSEHNGSLAKDAAKIGGEKWKSLTEEEKKVYLDKAAELKAEYNKSL 179

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
255559641	209	DNA binding protein, putative [Ricinus c	0.941	0.923	0.512	1e-46
224145922	164	predicted protein [Populus trichocarpa]	0.741	0.926	0.577	1e-44
359486485	267	PREDICTED: uncharacterized protein LOC10	0.863	0.662	0.481	3e-34
147866156	217	hypothetical protein VITISV_041872 [Viti	0.863	0.815	0.475	1e-33
10176745	221	unnamed protein product [Arabidopsis tha	0.765	0.710	0.450	2e-28
145357661	220	HMG-box (high mobility group) DNA-bindin	0.765	0.713	0.450	2e-28
297810645	188	predicted protein [Arabidopsis lyrata su	0.843	0.920	0.433	1e-27
388522281	187	unknown [Lotus japonicus]	0.775	0.850	0.384	2e-18
186520313	168	HMG-box (high mobility group) DNA-bindin	0.658	0.803	0.397	6e-16
145334301	157	HMG-box (high mobility group) DNA-bindin	0.634	0.828	0.404	5e-15

>gi|255559641|ref|XP_002520840.1| DNA binding protein, putative [Ricinus communis] gi|223539971|gb|EEF41549.1| DNA binding protein, putative [Ricinus communis]

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 106/207 (51%), Positives = 136/207 (65%), Gaps = 14/207 (6%)

Query: 1   MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEK 60
           M N PRT KRVHAIRR  DGSAFE CD C  +V IAL DMHECEA+ K  VKRFKGV  K
Sbjct: 1   MGNPPRTGKRVHAIRRGHDGSAFETCDDCGFLVAIALADMHECEAETKRIVKRFKGVIGK 60

Query: 61  PKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAE 120
            K+VKQ+ YSDQ RSPF  FME F  TC + +LI+ID+KGFE W+ MSK+ER+PYV+KAE
Sbjct: 61  HKIVKQN-YSDQPRSPFVTFMEEFRRTCKNGKLIEIDRKGFETWRKMSKQERKPYVVKAE 119

Query: 121 MLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDP-------IYSTEILKCSNSSR 173
            +++A+ ++L++E+  +   +DDEADS MV K+D SY+        +YS +  K      
Sbjct: 120 EVNSAYVKSLIKEI-DVSSEVDDEADSMMVGKFDPSYEDYGHNSSCVYSYDSFK-----E 173

Query: 174 FESLNTYNREVMDPWTLERSHGRWLPF 200
           ++SLNT+         L R   R L  
Sbjct: 174 YQSLNTWKLWFSVAVILTRKKARHLAI 200

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224145922|ref|XP_002325813.1| predicted protein [Populus trichocarpa] gi|222862688|gb|EEF00195.1| predicted protein [Populus trichocarpa]

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 89/154 (57%), Positives = 116/154 (75%), Gaps = 2/154 (1%)

Query: 1   MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEK 60
           M N PRTRKRV  IRRAPDGSAFE C+ C  +V IAL D+HECEA  KN VKRFKG+  K
Sbjct: 1   MGNPPRTRKRVRGIRRAPDGSAFENCNNCGVLVAIALADLHECEAGTKNNVKRFKGLDGK 60

Query: 61  PKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAE 120
             +V+Q S+ DQ RSPFR+FME F++T      IDID+KGFE W+NMSKEERQPY+ +A+
Sbjct: 61  QNVVQQ-SFCDQPRSPFRLFMEDFMKTGKIWNTIDIDRKGFETWRNMSKEERQPYITRAD 119

Query: 121 MLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYD 154
            + +AH ++L++++  M   ++DEADSA+V K+D
Sbjct: 120 EIYSAHVKSLIQDIDHMSE-VNDEADSAIVGKFD 152

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486485|ref|XP_003633450.1| PREDICTED: uncharacterized protein LOC100853686 [Vitis vinifera]

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 89/185 (48%), Positives = 113/185 (61%), Gaps = 8/185 (4%)

Query: 1   MANQPRTRKRVHAI----RRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKG 56
           MAN P TRKRVHAI    RR PDGSAFEKC  C   V IAL DMH+C   +K  VKRFKG
Sbjct: 1   MANPPITRKRVHAIASGFRRGPDGSAFEKCHGCGVSVAIALADMHDC--GLKRDVKRFKG 58

Query: 57  VCEKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYV 116
                 L KQ     + RSPFR+FME F +   +   I +D+ GFE WK MS EER+PY+
Sbjct: 59  QRGVQNLRKQTCLG-EPRSPFRLFMENFRKASKTGNPIHVDRIGFEAWKKMSMEERKPYI 117

Query: 117 IKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFES 176
           I+AE +++ H + LL+E       +DDEADSAMV K+DK Y     +E      S R ++
Sbjct: 118 IQAEKVNSEHLKILLKEEHDRVE-VDDEADSAMVGKFDKFYGFYEDSEDSDSFQSFRSKT 176

Query: 177 LNTYN 181
           + ++N
Sbjct: 177 IESFN 181

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147866156|emb|CAN84129.1| hypothetical protein VITISV_041872 [Vitis vinifera]

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 88/185 (47%), Positives = 112/185 (60%), Gaps = 8/185 (4%)

Query: 1   MANQPRTRKRVHAI----RRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKG 56
           MAN P TRKRVHAI    RR PDGSAFEKC  C   V IAL DMH+C   +   VKRFKG
Sbjct: 1   MANPPITRKRVHAIASGFRRGPDGSAFEKCHGCGVSVAIALADMHDC--GLXRDVKRFKG 58

Query: 57  VCEKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYV 116
                 L KQ     + RSPFR+FME F +   +   I +D+ GFE WK MS EER+PY+
Sbjct: 59  QRGVQNLRKQTCLG-EPRSPFRLFMENFRKASKTGNPIHVDRIGFEAWKKMSMEERKPYI 117

Query: 117 IKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKCSNSSRFES 176
           I+AE +++ H + LL+E       +DDEADSAMV K+DK Y     +E      S R ++
Sbjct: 118 IQAEKVNSEHLKILLKEEHDRVE-VDDEADSAMVGKFDKFYGFYEDSEDSDSFQSFRSKT 176

Query: 177 LNTYN 181
           + ++N
Sbjct: 177 IESFN 181

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|10176745|dbj|BAB09976.1| unnamed protein product [Arabidopsis thaliana]

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 77/171 (45%), Positives = 104/171 (60%), Gaps = 14/171 (8%)

Query: 1   MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVC-- 58
           MA +PRTRKRV A+RRA DGSAF+KC+ C  M+ IAL DMHEC  K + +VKRFK +   
Sbjct: 34  MAIRPRTRKRVQAVRRAADGSAFKKCEECGVMIAIALYDMHECGEK-RREVKRFKYIASG 92

Query: 59  -----EKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQ 113
                 KP      S+ D+ RSPF  F+E F E     +L+D  +  F  WKNMS E+++
Sbjct: 93  NIDNISKP----IGSFEDEPRSPFVFFLEEFRENYNG-DLVDASRICFNVWKNMSAEDQK 147

Query: 114 PYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTE 164
           P+  +A  +D+AH R L EE  ++ +  D+EADS  V +YDK Y+     E
Sbjct: 148 PFNARAMEVDSAHSRKLNEEAKTIYK-ADEEADSKTVGRYDKFYESYVQIE 197

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145357661|ref|NP_196152.2| HMG-box (high mobility group) DNA-binding family protein [Arabidopsis thaliana] gi|61742741|gb|AAX55191.1| hypothetical protein At5g05330 [Arabidopsis thaliana] gi|71905543|gb|AAZ52749.1| hypothetical protein At5g05330 [Arabidopsis thaliana] gi|332003475|gb|AED90858.1| HMG-box (high mobility group) DNA-binding family protein [Arabidopsis thaliana]

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 77/171 (45%), Positives = 104/171 (60%), Gaps = 14/171 (8%)

Query: 1   MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVC-- 58
           MA +PRTRKRV A+RRA DGSAF+KC+ C  M+ IAL DMHEC  K + +VKRFK +   
Sbjct: 33  MAIRPRTRKRVQAVRRAADGSAFKKCEECGVMIAIALYDMHECGEK-RREVKRFKYIASG 91

Query: 59  -----EKPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQ 113
                 KP      S+ D+ RSPF  F+E F E     +L+D  +  F  WKNMS E+++
Sbjct: 92  NIDNISKP----IGSFEDEPRSPFVFFLEEFRENYNG-DLVDASRICFNVWKNMSAEDQK 146

Query: 114 PYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTE 164
           P+  +A  +D+AH R L EE  ++ +  D+EADS  V +YDK Y+     E
Sbjct: 147 PFNARAMEVDSAHSRKLNEEAKTIYK-ADEEADSKTVGRYDKFYESYVQIE 196

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297810645|ref|XP_002873206.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297319043|gb|EFH49465.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  129 bits (323), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 78/180 (43%), Positives = 106/180 (58%), Gaps = 7/180 (3%)

Query: 1   MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEK 60
           MA +PRTRKRV A+RRA DGSAF+KC+ C  M+ I L DMHEC  K + +VKRFK +   
Sbjct: 1   MAIRPRTRKRVQAVRRAADGSAFKKCEECGVMIAIGLFDMHECGEK-RREVKRFKYIASG 59

Query: 61  PKLVKQ---DSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVI 117
             +       S+ D+ RSPF  F+E F E      L+D  +  F  WKNM  E+++P+  
Sbjct: 60  NVINISKPIGSFEDEPRSPFVFFLEDFREKYNGN-LVDASRICFNVWKNMLPEDQKPFNA 118

Query: 118 KAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDP-IYSTEILKCSNSSRFES 176
           +A  +D AH R L EE  S+ +  DDEADS  V +YDK Y+  ++  E     +S  FE+
Sbjct: 119 RAMEVDLAHSRKLNEEAKSIDK-ADDEADSKTVGRYDKFYESYVHYEEEEDYDSSDHFEN 177

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388522281|gb|AFK49202.1| unknown [Lotus japonicus]

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 68/177 (38%), Positives = 93/177 (52%), Gaps = 18/177 (10%)

Query: 1   MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKG---- 56
           M + PR RKRV  + RAPDGSAF+ C+ CE  V +AL D+H CE K+ +K+  FKG    
Sbjct: 1   MVSAPRLRKRVFPLLRAPDGSAFQICELCEVSVAVALADLHHCETKMASKI--FKGKELM 58

Query: 57  ----VCEKPKL-VKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEE 111
               V  +PK  VKQ+   D          E F++   ++  I+ D+ GFEKWK+MSK+ 
Sbjct: 59  QHSPVKVEPKTEVKQEMQDDDPEE------EQFMKDHDNKNYIEADRMGFEKWKSMSKQV 112

Query: 112 RQPYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTEILKC 168
           + PY   A  L   +   LL E   +   + DEADSA   K +K  D   S   +K 
Sbjct: 113 KLPYTFHAFALKNEYVDDLLLEAHQIAE-VSDEADSAYAVKDEKVNDEADSVNAVKV 168

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186520313|ref|NP_001119174.1| HMG-box (high mobility group) DNA-binding family protein [Arabidopsis thaliana] gi|332003477|gb|AED90860.1| HMG-box (high mobility group) DNA-binding family protein [Arabidopsis thaliana]

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 56/141 (39%), Positives = 81/141 (57%), Gaps = 6/141 (4%)

Query: 27  DRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEK--PKLVKQ-DSYSDQTRSPFRIFMET 83
           + C  M+ IAL DMHEC  K + +VKRFK +       + K   S+ D+ RSPF  F+E 
Sbjct: 7   NECGVMIAIALYDMHECGEK-RREVKRFKYIASGNIDNISKPIGSFEDEPRSPFVFFLEE 65

Query: 84  FVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFMDD 143
           F E     +L+D  +  F  WKNMS E+++P+  +A  +D+AH R L EE  ++ +  D+
Sbjct: 66  FRENYNG-DLVDASRICFNVWKNMSAEDQKPFNARAMEVDSAHSRKLNEEAKTIYK-ADE 123

Query: 144 EADSAMVWKYDKSYDPIYSTE 164
           EADS  V +YDK Y+     E
Sbjct: 124 EADSKTVGRYDKFYESYVQIE 144

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145334301|ref|NP_001078532.1| HMG-box (high mobility group) DNA-binding family protein [Arabidopsis thaliana] gi|71905547|gb|AAZ52751.1| hypothetical protein At5g05330 [Arabidopsis thaliana] gi|332003476|gb|AED90859.1| HMG-box (high mobility group) DNA-binding family protein [Arabidopsis thaliana]

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 55/136 (40%), Positives = 79/136 (58%), Gaps = 6/136 (4%)

Query: 32  MVPIALVDMHECEAKVKNKVKRFKGVCEK--PKLVKQ-DSYSDQTRSPFRIFMETFVETC 88
           M+ IAL DMHEC  K + +VKRFK +       + K   S+ D+ RSPF  F+E F E  
Sbjct: 1   MIAIALYDMHECGEK-RREVKRFKYIASGNIDNISKPIGSFEDEPRSPFVFFLEEFRENY 59

Query: 89  GSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFMDDEADSA 148
              +L+D  +  F  WKNMS E+++P+  +A  +D+AH R L EE  ++ +  D+EADS 
Sbjct: 60  NG-DLVDASRICFNVWKNMSAEDQKPFNARAMEVDSAHSRKLNEEAKTIYK-ADEEADSK 117

Query: 149 MVWKYDKSYDPIYSTE 164
            V +YDK Y+     E
Sbjct: 118 TVGRYDKFYESYVQIE 133

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	205
TAIR|locus:2153514	220	AT5G05330 [Arabidopsis thalian	0.785	0.731	0.455	1.6e-31
TAIR|locus:505006631	149	AT5G23405 "AT5G23405" [Arabido	0.492	0.677	0.284	6.1e-05
TAIR|locus:2154433	241	HMGB6 "high-mobility group box	0.360	0.307	0.357	0.00014

TAIR|locus:2153514 AT5G05330 [Arabidopsis thaliana (taxid:3702)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 76/167 (45%), Positives = 104/167 (62%)

Query:     1 MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFKGVCEK 60
             MA +PRTRKRV A+RRA DGSAF+KC+ C  M+ IAL DMHEC  K + +VKRFK +   
Sbjct:    33 MAIRPRTRKRVQAVRRAADGSAFKKCEECGVMIAIALYDMHECGEK-RREVKRFKYIASG 91

Query:    61 --PKLVKQ-DSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVI 117
                 + K   S+ D+ RSPF  F+E F E     +L+D  +  F  WKNMS E+++P+  
Sbjct:    92 NIDNISKPIGSFEDEPRSPFVFFLEEFRENYNG-DLVDASRICFNVWKNMSAEDQKPFNA 150

Query:   118 KAEMLDAAHRRALLEEVTSMPRFMDDEADSAMVWKYDKSYDPIYSTE 164
             +A  +D+AH R L EE  ++ +  D+EADS  V +YDK Y+     E
Sbjct:   151 RAMEVDSAHSRKLNEEAKTIYK-ADEEADSKTVGRYDKFYESYVQIE 196

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:505006631 AT5G23405 "AT5G23405" [Arabidopsis thaliana (taxid:3702)]

 Score = 105 (42.0 bits), Expect = 6.1e-05, P = 6.1e-05
 Identities = 31/109 (28%), Positives = 51/109 (46%)

Query:    19 DGSAFEKCDR--CEAMVPIALVDMHECEAKVKNKV--KRFKGVCEKPKLVKQDSYSDQTR 74
             D S F +C+   C   +P+ LV MH C A     +  + F    +  K       S  + 
Sbjct:     8 DSSIFARCEDVDCNKKIPVELVRMHICYAMFHRTLAARGFGTQTQAKKKPTNKKKSTTSL 67

Query:    75 SPFRIFMETF---VETCGSRELIDIDQK-GFEKWKNMSKEERQPYVIKA 119
             + F +FM  F     T  +  L+    K G+E WK+M+++E++ Y+ KA
Sbjct:    68 TDFAVFMNHFRKSFRTDYNGALVKEGSKIGWEMWKSMTEDEKKDYLDKA 116

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

 Score = 112 (44.5 bits), Expect = 0.00014, P = 0.00014
 Identities = 30/84 (35%), Positives = 42/84 (50%)

Query:     2 ANQPRTRKRVHA---------IRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVK 52
             +N P+ RKRV A         +RRA DGSAF  C+ C   V +AL+ MH C    K +V 
Sbjct:     8 SNAPKQRKRVEAETSSNTSTTLRRAKDGSAFALCEGCNKSVAVALISMHNCSLDAKIRVN 67

Query:    53 RFKGVCE-KPKLVKQDSYSDQTRS 75
                 V E + +  K+ +   +T S
Sbjct:    68 LEAQVVETQAEAKKKPAEKKKTTS 91


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.133   0.406    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      205       205   0.00096  111 3  11 22  0.47    32
                                                     31  0.47    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  602 (64 KB)
  Total size of DFA:  191 KB (2109 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  20.44u 0.07s 20.51t   Elapsed:  00:00:01
  Total cpu time:  20.44u 0.07s 20.51t   Elapsed:  00:00:01
  Start:  Fri May 10 08:13:04 2013   End:  Fri May 10 08:13:05 2013

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_XIX000330 hypothetical protein (164 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	205
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	4e-04
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	0.002

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

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 16/36 (44%), Positives = 24/36 (66%)

Query: 95  DIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRAL 130
           +I +   EKWKN+S+EE++PY  KAE   A + +A 
Sbjct: 30  EISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAY 65

Length = 69

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 74  RSPFRIFM----ETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA 129
            S + +F                + +I +   E WK++S+EE++ Y  KAE     + + 
Sbjct: 5   LSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKE 64

Query: 130 L 130
           +
Sbjct: 65  M 65

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
PTZ00199	94	high mobility group protein; Provisional	99.85
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.75
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.74
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.74
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.72
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.7
smart00398	70	HMG high mobility group.	99.7
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.69
KOG0381	96	consensus HMG box-containing protein [General func	99.67
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.66
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.6
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.55
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	98.85
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	98.61
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.56
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.0
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	97.84
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.53
COG5648	211	NHP6B Chromatin-associated proteins containing the	96.24
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	92.06
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	89.39
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	83.52

>PTZ00199 high mobility group protein; Provisional

Probab=99.85  E-value=1.9e-21  Score=147.37  Aligned_cols=73  Identities=18%  Similarity=0.208  Sum_probs=68.0

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh------hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL------IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP------~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      ++.+||++||||+||||+|++++|..+...||      ++|+++||++|++||++||++|+++|++++++|..+|.+|.
T Consensus        15 k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~   93 (94)
T PTZ00199         15 RKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA   93 (94)
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999876654      68999999999999999999999999999999999999985

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

Probab=99.75  E-value=3.6e-18  Score=122.74  Aligned_cols=67  Identities=21%  Similarity=0.382  Sum_probs=59.5

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCC-----ChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSR-----ELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~-----nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      |++||||+|||++|+++++..++..     +..|+++.+|+.|++||++||.+|+++|++++++|..+|.+|
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~   72 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEW   72 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6799999999999999999987644     458999999999999999999999999999999999999987

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

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

Probab=99.74  E-value=4.8e-18  Score=117.35  Aligned_cols=62  Identities=21%  Similarity=0.280  Sum_probs=58.4

Q ss_pred             CCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHH
Q 037983           70 SDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALL  131 (205)
Q Consensus        70 PKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~  131 (205)
                      ||||+|||++|++++|.+++..+|    .+|++++|++|++||++||++|.+.|++++++|..+|.
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~   66 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK   66 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            899999999999999999987664    89999999999999999999999999999999999873

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.

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

Probab=99.74  E-value=3e-18  Score=124.13  Aligned_cols=65  Identities=17%  Similarity=0.155  Sum_probs=61.0

Q ss_pred             CCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           69 YSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      .||||+||||+|++++|.+++..||    .||++++|++|+.||++||++|.++|++++++|.+++.+|
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Y   69 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDY   69 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            4899999999999999999987766    8999999999999999999999999999999999998776

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=99.72  E-value=1.3e-17  Score=116.34  Aligned_cols=65  Identities=22%  Similarity=0.302  Sum_probs=59.5

Q ss_pred             CCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           70 SDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        70 PKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      ||||+|||++|+++++..++..||    .+|++++|++|++||++||++|.+.|.+++++|.++|..|.
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            899999999999999999987766    79999999999999999999999999999999999999873

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 ....

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

Probab=99.70  E-value=2.2e-17  Score=142.32  Aligned_cols=84  Identities=17%  Similarity=0.200  Sum_probs=77.4

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      ++.+|||+||||+||||+|+++.|.++...+|    .+|++++||+|++||++||+||+..|..++++|..++.+|...+
T Consensus        63 r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~  142 (211)
T COG5648          63 RKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKL  142 (211)
T ss_pred             HHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhccc
Confidence            35679999999999999999999999988877    89999999999999999999999999999999999999999999


Q ss_pred             CCCCChhH
Q 037983          138 PRFMDDEA  145 (205)
Q Consensus       138 p~e~~dea  145 (205)
                      |+.....+
T Consensus       143 ~~~~~~~~  150 (211)
T COG5648         143 PNKAPIGP  150 (211)
T ss_pred             CCCCCCch
Confidence            87755443

>smart00398 HMG high mobility group

Probab=99.70  E-value=4e-17  Score=112.92  Aligned_cols=65  Identities=25%  Similarity=0.307  Sum_probs=60.6

Q ss_pred             CCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           69 YSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      +||||+|||++|++++|..++..+|    .+|++++|++|+.||++||++|.++|++++++|.+++..|
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y   69 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY   69 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5899999999999999999876554    8999999999999999999999999999999999999876

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

Probab=99.69  E-value=2.7e-17  Score=117.92  Aligned_cols=64  Identities=22%  Similarity=0.306  Sum_probs=59.3

Q ss_pred             CCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           70 SDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        70 PKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      .|||+||||+|+++.|.+++..||    .||++++|++|+.||++||++|.++|+.++++|.+++-.|
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y   69 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDY   69 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            589999999999999999887776    7999999999999999999999999999999999986554

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.

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

Probab=99.67  E-value=2.6e-16  Score=117.00  Aligned_cols=72  Identities=25%  Similarity=0.318  Sum_probs=66.9

Q ss_pred             CC--CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHH-HHHhcC
Q 037983           66 QD--SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALL-EEVTSM  137 (205)
Q Consensus        66 Dp--~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~-e~~k~l  137 (205)
                      ||  ++||||+||||+|++++|..++..||    .||++++|++|++|+++||++|+..|..++++|..+|. +|..++
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 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            67  59999999999999999999998887    69999999999999999999999999999999999999 776554

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

Probab=99.66  E-value=2.3e-16  Score=107.92  Aligned_cols=61  Identities=21%  Similarity=0.286  Sum_probs=57.1

Q ss_pred             CCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHH
Q 037983           70 SDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRAL  130 (205)
Q Consensus        70 PKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem  130 (205)
                      ||||+|||++|++++|..++..+|    .+|++++|++|+.||+++|++|.++|.+++..|.+++
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            799999999999999999876654    8999999999999999999999999999999999875

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

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

Probab=99.60  E-value=1.2e-15  Score=145.76  Aligned_cols=74  Identities=22%  Similarity=0.272  Sum_probs=68.9

Q ss_pred             CCCCCCCCCCCCCCCChHHhHHHHhHHHhcCC--ChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           60 KPKLVKQDSYSDQTRSPFRIFMETFVETCGSR--ELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        60 ~~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~--nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      ++|+.||||+|||++||||+|++.-|..+|..  ..+||+|.+|++||.||.  |++|+++|+++|++|+++|.+|..
T Consensus       526 ~~kk~kdpnapkra~sa~m~w~~~~r~~ik~dgi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk~  601 (615)
T KOG0526|consen  526 KGKKKKDPNAPKRATSAYMLWLNASRESIKEDGISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYKN  601 (615)
T ss_pred             CcccCCCCCCCccchhHHHHHHHhhhhhHhhcCchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhcC
Confidence            45778999999999999999999999999866  448999999999999999  999999999999999999999973

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.55  E-value=5.4e-15  Score=134.95  Aligned_cols=71  Identities=20%  Similarity=0.299  Sum_probs=65.5

Q ss_pred             CCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           64 VKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        64 ~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      .+.....||||||||+|.+..|+++..+||    .||||.||.+||.|+++||.||++.|+++++.|.+|-=.|.
T Consensus        57 k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK  131 (331)
T KOG0527|consen   57 KTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK  131 (331)
T ss_pred             CCCccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc
Confidence            346789999999999999999999998888    89999999999999999999999999999999999866553

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=98.85  E-value=3.4e-09  Score=97.84  Aligned_cols=61  Identities=20%  Similarity=0.284  Sum_probs=53.5

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcC----CChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGS----RELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRR  128 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~----~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~k  128 (205)
                      ...|+|+||||+||+++|..+-+    +..++|.++||.+|..||-||..+|.++|..+++-|.+
T Consensus       190 phiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~q  254 (421)
T KOG3248|consen  190 PHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQ  254 (421)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            37889999999999999988742    23389999999999999999999999999999887754

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

Probab=98.61  E-value=9.6e-08  Score=87.85  Aligned_cols=74  Identities=12%  Similarity=0.147  Sum_probs=69.0

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      .+.|-|.+|-+|+-+||.|......+++..||    =||+|++|.+|+.|+++||+-|++.++..|.+|.+.|+.|..
T Consensus        57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~  134 (410)
T KOG4715|consen   57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHN  134 (410)
T ss_pred             cCCCCCCCCCcccchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            35667889999999999999999999999999    499999999999999999999999999999999999998864

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

Probab=98.56  E-value=3.1e-08  Score=94.55  Aligned_cols=63  Identities=19%  Similarity=0.237  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHH
Q 037983           65 KQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHR  127 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~  127 (205)
                      .-++.-||||||||.|.++-|.++-..-|    ..|+|+||-+||.||-.||+||++.-+.+-..|.
T Consensus       321 ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~Hl  387 (511)
T KOG0528|consen  321 SSEPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHL  387 (511)
T ss_pred             CCCccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhh
Confidence            34568899999999999998877754433    7999999999999999999999999999866554

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

Probab=98.00  E-value=5.5e-06  Score=81.79  Aligned_cols=65  Identities=20%  Similarity=0.218  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCChHHhHHHHhH--HH----hcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHH
Q 037983           65 KQDSYSDQTRSPFRIFMETFV--ET----CGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA  129 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~R--k~----~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~ke  129 (205)
                      .+...-.||||||++|++.+|  ..    ++++....|++|+||.|-.|.+.||+.|.|+|.+.|+.|-++
T Consensus       177 r~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  177 RDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             CcchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            455677899999999999998  33    344444789999999999999999999999999999999985

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

Probab=97.84  E-value=3.5e-05  Score=58.39  Aligned_cols=69  Identities=14%  Similarity=0.178  Sum_probs=51.3

Q ss_pred             CCCCCCChHHhHHHHhHHHhcCCCh---hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           69 YSDQTRSPFRIFMETFVETCGSREL---IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~Rk~~K~~nP---~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      .|-.|.||==+|.+.....+-...+   .-.-+.+...|++|++.||-+|+.+|.++..+|+.+|.++..-.
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~K~~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~   74 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRNDRKKALKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAP   74 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            4667888888999887666543322   22356899999999999999999999999999999999886543

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

Probab=97.53  E-value=0.00012  Score=62.55  Aligned_cols=50  Identities=18%  Similarity=0.291  Sum_probs=46.0

Q ss_pred             CChHHhHHHHhHHHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHH
Q 037983           74 RSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLD  123 (205)
Q Consensus        74 ~SAF~lF~~e~Rk~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K  123 (205)
                      -+||+.|+.+||..+.+..|.|+...++..|..||+.||..|..++-...
T Consensus        83 nnaYLNFLReFRrkh~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~~~  132 (183)
T PF06382_consen   83 NNAYLNFLREFRRKHCGLSPQDLIQRAARAWCRLSEAEKNRYRRMAPSVR  132 (183)
T ss_pred             chHHHHHHHHHHHHccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcchhh
Confidence            57999999999999999999999999999999999999999999766443

The function of this family is unknown.

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

Probab=96.24  E-value=0.0047  Score=54.10  Aligned_cols=64  Identities=9%  Similarity=0.102  Sum_probs=56.3

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALL  131 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~  131 (205)
                      .+++.|..+|.-+-+..|.+....++    .+..+++|..|..|++.-|++|++.+..++.+|...+.
T Consensus       142 ~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         142 LPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             cCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            46778888888888888888877777    68999999999999999999999999999999987653

>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=92.06  E-value=0.24  Score=42.18  Aligned_cols=42  Identities=10%  Similarity=0.220  Sum_probs=36.3

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCC
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMS  108 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLS  108 (205)
                      |-+-.|-+|||..||++.-..+|..||    .|..+.+++.|+..+
T Consensus       119 PEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  119 PEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             ccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence            344458899999999999999999988    799999999998754

>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=89.39  E-value=1  Score=39.13  Aligned_cols=55  Identities=7%  Similarity=0.112  Sum_probs=40.7

Q ss_pred             CCCCCCCCCCCChHHhHHHHhHHHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHH
Q 037983           64 VKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAE  120 (205)
Q Consensus        64 ~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~  120 (205)
                      ......+|||.|+||.|+.-+-.-+......++|.+++..|..=+-  |..|.-.|.
T Consensus        38 ~~~~~~~kr~lN~Fm~FRsyy~~~~~~~~Qk~~S~~l~~lW~~dp~--k~~W~l~ak   92 (201)
T PF04769_consen   38 KRSPEKAKRPLNGFMAFRSYYSPIFPPLPQKELSGILTKLWEKDPF--KNKWSLMAK   92 (201)
T ss_pred             cccccccccchhHHHHHHHHHHhhcCCcCHHHHHHHHHHHHhCCcc--HhHHHHHhh
Confidence            3356678999999999999888666665558999999999986433  344444443

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

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=83.52  E-value=1.8  Score=36.95  Aligned_cols=45  Identities=13%  Similarity=0.138  Sum_probs=38.7

Q ss_pred             ChhHHHH-HHHHHhhcCChhhhhhHHHHHHH-HHHHHHHHHHHHHhc
Q 037983           92 ELIDIDQ-KGFEKWKNMSKEERQPYVIKAEM-LDAAHRRALLEEVTS  136 (205)
Q Consensus        92 nP~EIsK-~lGE~WKsLSdeEKkPY~dkA~e-~K~~Y~kem~e~~k~  136 (205)
                      +...+++ .+|..|+.+|++||+-|++.... +...|...+..|..+
T Consensus        65 Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~  111 (198)
T TIGR03481        65 DLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGE  111 (198)
T ss_pred             CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence            3466665 78999999999999999999999 788999999988654

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	205
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	6e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	3e-04

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

 Score = 38.8 bits (91), Expect = 6e-05
 Identities = 10/47 (21%), Positives = 22/47 (46%)

Query: 74  RSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAE 120
           RS + +++    +        +  +   E WKN+S  E++ Y+  A+
Sbjct: 7   RSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAK 53

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.8 bits (97), Expect = 1e-04
 Identities = 36/242 (14%), Positives = 69/242 (28%), Gaps = 71/242 (29%)

Query: 3   NQPRTRKRVHAIRRAP---DGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRFK---G 56
            QP    R++  +R     D   F K +          V   +   K++  +   +    
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDNQVFAKYN----------VSRLQPYLKLRQALLELRPAKN 152

Query: 57  V-------CEKPKLVKQ--DSYSDQTRSPFRIFMETFVETCGSRELID--------IDQK 99
           V         K  +      SY  Q +  F+IF            +++        ID  
Sbjct: 153 VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN 212

Query: 100 GFEKWKNMSKEERQPYVIKAE----MLDAAHRRALLEEVTSMPRFMDDEADSAMVW--KY 153
              +  + S  + + + I+AE    +    +   LL         + +      V   K 
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL--------VLLN------VQNAKA 258

Query: 154 DKSYDPIYSTEILKC------SNSSRFESLN--TYNREVMD--PWTLERSHGRWLPFFEI 203
             +++       L C            + L+  T     +D    TL     + L   + 
Sbjct: 259 WNAFN-------LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL-LLKY 310

Query: 204 LG 205
           L 
Sbjct: 311 LD 312

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 26/83 (31%), Positives = 33/83 (39%), Gaps = 20/83 (24%)

Query: 1  MANQPRTRKRVHAIRRAPDGSAFEKCDRCEAMVPIALVDMHECEAKVKNKVKRF-KG--V 57
          M  +    KR  A RR P+ +    C       P       EC+      V+RF +G  V
Sbjct: 1  MMTRESIDKR--AGRRGPNLNIVLTC-------P-------ECKVYPPKIVERFSEGDVV 44

Query: 58 CEKPKLVKQDSYSDQTRSPFRIF 80
          C    LV  D   D TRS +R F
Sbjct: 45 CALCGLVLSDKLVD-TRSEWRTF 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	205
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.88
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.88
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.88
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.87
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.87
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.86
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.85
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.85
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.84
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.84
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.84
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.84
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.83
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.83
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.82
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.82
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.81
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.81
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.8
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.8
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.8
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.8
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.79
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.79
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.79
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.78
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.78
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.78
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.78
2cto_A	93	Novel protein; high mobility group box domain, hel	99.78
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.77
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.77
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.76
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.76
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.72
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.71
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.71
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.7
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.57

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

Probab=99.88  E-value=4.1e-23  Score=156.31  Aligned_cols=88  Identities=15%  Similarity=0.177  Sum_probs=78.5

Q ss_pred             CCCCCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           59 EKPKLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        59 ~~~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      .+.++.+||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|.+|.
T Consensus         7 ~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~   86 (102)
T 2co9_A            7 GKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYR   86 (102)
T ss_dssp             CSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456789999999999999999999999887666    79999999999999999999999999999999999999999


Q ss_pred             hcCCCCCChhHh
Q 037983          135 TSMPRFMDDEAD  146 (205)
Q Consensus       135 k~lp~e~~deaD  146 (205)
                      .++......|.+
T Consensus        87 ~~~~~~~~~e~~   98 (102)
T 2co9_A           87 ASLVSKSYTDSG   98 (102)
T ss_dssp             HHHTSSCCCCCS
T ss_pred             hhcccccccccc
Confidence            988666555543

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

Probab=99.88  E-value=1.4e-22  Score=141.79  Aligned_cols=67  Identities=15%  Similarity=0.256  Sum_probs=64.5

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      |+||||+|||++|++++|.+++..||.||++++|++|++||++||++|+++|++++++|+++|++|.
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y~   67 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWA   67 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            5899999999999999999999999999999999999999999999999999999999999999873

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

Probab=99.88  E-value=1.5e-22  Score=148.34  Aligned_cols=72  Identities=18%  Similarity=0.240  Sum_probs=67.5

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh------hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL------IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP------~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      +..+||++||||+||||+|++++|.+++..||      .||+++||++|++||++||++|+++|++++++|.++|.+|
T Consensus         8 ~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   85 (86)
T 2eqz_A            8 MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY   85 (86)
T ss_dssp             CSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            45679999999999999999999999976655      7999999999999999999999999999999999999987

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

Probab=99.87  E-value=1.5e-22  Score=152.87  Aligned_cols=77  Identities=16%  Similarity=0.250  Sum_probs=72.5

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      ++.+||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|++|..+-
T Consensus         3 kk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~~   82 (99)
T 1k99_A            3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH   82 (99)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            45689999999999999999999999998877    79999999999999999999999999999999999999998876


Q ss_pred             C
Q 037983          138 P  138 (205)
Q Consensus       138 p  138 (205)
                      |
T Consensus        83 P   83 (99)
T 1k99_A           83 P   83 (99)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.87  E-value=6.8e-22  Score=151.94  Aligned_cols=80  Identities=15%  Similarity=0.208  Sum_probs=75.5

Q ss_pred             CCCCCCCCCCCC-CCCCChHHhHHHHhHHHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           59 EKPKLVKQDSYS-DQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        59 ~~~k~~KDp~aP-KRP~SAF~lF~~e~Rk~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      +.+++.|||++| |||+||||+|++++|.+++..++.||+++||++|++||++||++|+++|++++++|.++|.+|..++
T Consensus         6 ~~~kk~kd~~~P~KrP~say~lF~~e~r~~~k~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~   85 (108)
T 1v64_A            6 SGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESL   85 (108)
T ss_dssp             SCCSSCCTTTSCCCCCSSHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            345678899999 9999999999999999999888899999999999999999999999999999999999999999988


Q ss_pred             C
Q 037983          138 P  138 (205)
Q Consensus       138 p  138 (205)
                      +
T Consensus        86 ~   86 (108)
T 1v64_A           86 P   86 (108)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.86  E-value=3.1e-22  Score=145.32  Aligned_cols=71  Identities=20%  Similarity=0.257  Sum_probs=67.2

Q ss_pred             CCCCCCCCCCChHHhHHHHhHHHhcCCCh------hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           65 KQDSYSDQTRSPFRIFMETFVETCGSREL------IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP------~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      +||++||||+||||+|++++|.+++..||      .||+++||++|++||++||++|+++|++++++|.++|.+|..
T Consensus         3 kdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   79 (83)
T 1aab_A            3 GDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   79 (83)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            69999999999999999999999998876      699999999999999999999999999999999999988743

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

Probab=99.85  E-value=4.1e-22  Score=142.40  Aligned_cols=70  Identities=21%  Similarity=0.314  Sum_probs=66.0

Q ss_pred             CCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           65 KQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      |||++||||+||||+|++++|.+++..||    .+|++++|++|++||++||++|+++|++++++|.++|.+|.
T Consensus         2 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~   75 (77)
T 1hme_A            2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR   75 (77)
T ss_dssp             CCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            69999999999999999999999876665    79999999999999999999999999999999999998774

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

Probab=99.85  E-value=1.8e-21  Score=144.39  Aligned_cols=72  Identities=18%  Similarity=0.179  Sum_probs=68.0

Q ss_pred             CCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhc
Q 037983           65 KQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTS  136 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~  136 (205)
                      +||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|.+|..+
T Consensus         3 kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~   78 (92)
T 2crj_A            3 SGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQS   78 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            69999999999999999999999886666    8999999999999999999999999999999999999999754

>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=99.84  E-value=6.1e-22  Score=147.42  Aligned_cols=77  Identities=21%  Similarity=0.220  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           60 KPKLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        60 ~~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      +.+..+||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|.+|..
T Consensus        11 ~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~~   90 (93)
T 1cg7_A           11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA   90 (93)
T ss_dssp             CCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHHH
T ss_pred             cCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3355789999999999999999999999988776    799999999999999999999999999999999999999976


Q ss_pred             c
Q 037983          136 S  136 (205)
Q Consensus       136 ~  136 (205)
                      +
T Consensus        91 ~   91 (93)
T 1cg7_A           91 T   91 (93)
T ss_dssp             H
T ss_pred             c
Confidence            4

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

Probab=99.84  E-value=1.6e-21  Score=144.65  Aligned_cols=74  Identities=18%  Similarity=0.106  Sum_probs=69.6

Q ss_pred             CCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcCC
Q 037983           65 KQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMP  138 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~lp  138 (205)
                      .+|++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|.+|..+++
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~   80 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQES   80 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            48999999999999999999999986666    899999999999999999999999999999999999999988873

>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=99.84  E-value=4.5e-22  Score=147.33  Aligned_cols=71  Identities=14%  Similarity=0.142  Sum_probs=65.4

Q ss_pred             CCCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHH
Q 037983           61 PKLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALL  131 (205)
Q Consensus        61 ~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~  131 (205)
                      .++.+||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|.
T Consensus        12 ~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A           12 EGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             CCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             CcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356789999999999999999999999987766    79999999999999999999999999999999987764

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

Probab=99.84  E-value=8.1e-22  Score=147.55  Aligned_cols=77  Identities=17%  Similarity=0.171  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCCCCCCChHHhHHHHhHHHhcCCC------hhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           60 KPKLVKQDSYSDQTRSPFRIFMETFVETCGSRE------LIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        60 ~~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~n------P~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      +.++.+||++||||+||||+|++++|.+++..|      ..||+++||++|++||++||++|+++|++++++|.++|.+|
T Consensus        13 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y   92 (97)
T 2lhj_A           13 PRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEY   92 (97)
T ss_dssp             TTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345678999999999999999999999887554      46999999999999999999999999999999999999999


Q ss_pred             Hhc
Q 037983          134 VTS  136 (205)
Q Consensus       134 ~k~  136 (205)
                      ..+
T Consensus        93 ~~~   95 (97)
T 2lhj_A           93 AQR   95 (97)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            764

>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=99.83  E-value=2.6e-21  Score=142.20  Aligned_cols=70  Identities=19%  Similarity=0.259  Sum_probs=64.9

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHH
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALL  131 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~  131 (205)
                      +..+||++||||+||||+|++++|.+++..+|    .||++++|++|++||++||++|+++|++++++|.+++-
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P   83 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNP   83 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            56789999999999999999999999987666    79999999999999999999999999999999988753

>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=99.83  E-value=3.1e-21  Score=137.51  Aligned_cols=68  Identities=16%  Similarity=0.253  Sum_probs=61.9

Q ss_pred             CCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           66 QDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        66 Dp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      ||++||||+||||+|++++|.+++..||    .||++++|++|++||++||++|+++|++++++|.+++.+|
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Y   72 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNY   72 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            6899999999999999999999986665    7999999999999999999999999999999999987655

>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=99.82  E-value=5.7e-21  Score=134.29  Aligned_cols=65  Identities=22%  Similarity=0.279  Sum_probs=60.6

Q ss_pred             CCCCCCChHHhHHHHhHHHhcCCCh------hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           69 YSDQTRSPFRIFMETFVETCGSREL------IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~Rk~~K~~nP------~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      +||||+||||+|++++|.+++..||      .||++++|++|++||++||++|+++|++++++|.++|.+|
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            5999999999999999999876655      8999999999999999999999999999999999999754

>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=99.82  E-value=9.3e-21  Score=143.55  Aligned_cols=70  Identities=17%  Similarity=0.214  Sum_probs=64.4

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCC---ChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSR---ELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~---nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      +.||||+||||+|++++|..++..   +.+||+|+||++|++||++||+||+++|++++++|+++|+.|....
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~   75 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPP   75 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence            689999999999999999998655   4489999999999999999999999999999999999999996643

>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=99.81  E-value=5.3e-20  Score=139.71  Aligned_cols=76  Identities=13%  Similarity=0.113  Sum_probs=67.8

Q ss_pred             CCCCCCCCCChHHhHHHHhHHH--hcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 037983           66 QDSYSDQTRSPFRIFMETFVET--CGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFM  141 (205)
Q Consensus        66 Dp~aPKRP~SAF~lF~~e~Rk~--~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~lp~e~  141 (205)
                      ..++||||+||||+|+++++..  +++.+..||+|+||++|++|+++||+||+++|++++++|.++|..|..+++++.
T Consensus         5 ~~~~PKrP~say~lF~~e~~~~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~~~   82 (101)
T 1v63_A            5 SSGPKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQD   82 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTH
T ss_pred             CCCCCCCCCCHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHHH
Confidence            5679999999999999999863  233455899999999999999999999999999999999999999999996653

>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=99.81  E-value=3.1e-20  Score=132.05  Aligned_cols=67  Identities=16%  Similarity=0.291  Sum_probs=62.7

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      .++||||+||||+|++++|.+++..||    .||++++|++|++||+  |++|+++|++++++|.++|.+|..
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~   71 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHh
Confidence            378999999999999999999987666    8999999999999998  999999999999999999999965

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

Probab=99.80  E-value=1.8e-20  Score=133.31  Aligned_cols=68  Identities=13%  Similarity=0.243  Sum_probs=63.2

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhc
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTS  136 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~  136 (205)
                      |++||||+||||+|++++|.+++..||    .||++++|++|++|  +||++|+++|++++++|.++|.+|..+
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 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            789999999999999999999987766    79999999999999  899999999999999999999988543

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

Probab=99.80  E-value=7.3e-20  Score=146.30  Aligned_cols=74  Identities=22%  Similarity=0.305  Sum_probs=69.2

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      ++.+||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|.+|..
T Consensus        81 k~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A           81 KKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             GGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccccccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45689999999999999999999999987666    899999999999999999999999999999999999999864

>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=99.80  E-value=3.6e-20  Score=135.41  Aligned_cols=69  Identities=16%  Similarity=0.244  Sum_probs=64.4

Q ss_pred             CCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           66 QDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        66 Dp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      .|++||||+||||+|++++|.+++..||    .||++++|++|++||++||++|+++|++++++|..++.+|.
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   73 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            4789999999999999999999876666    79999999999999999999999999999999999988774

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

Probab=99.80  E-value=3.3e-20  Score=129.86  Aligned_cols=66  Identities=15%  Similarity=0.257  Sum_probs=57.6

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      +.||||+||||+|++++|.+++..+|    .+|++++|++|++||++||++|+++|++++++|.+++.+|
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Y   70 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY   70 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC--
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCc
Confidence            46899999999999999999988877    7999999999999999999999999999999999887665

>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=99.79  E-value=1.3e-20  Score=136.42  Aligned_cols=70  Identities=14%  Similarity=0.102  Sum_probs=64.6

Q ss_pred             CCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           65 KQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      .|+++||||+||||+|++++|.+++..||    .+|+++||++|++||++||++|+++|++++++|.++|.+|.
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk   76 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYR   76 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhh
Confidence            48999999999999999999999886665    79999999999999999999999999999999998877663

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

Probab=99.79  E-value=4.8e-20  Score=140.68  Aligned_cols=70  Identities=14%  Similarity=0.290  Sum_probs=62.9

Q ss_pred             CCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           64 VKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        64 ~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      .|++++||||+||||+|++++|.+++..+|    .||++++|++|++||++||++|+++|++++++|.+++..|
T Consensus        24 ~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y   97 (106)
T 4euw_A           24 SKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDY   97 (106)
T ss_dssp             ----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             cCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            569999999999999999999999987766    7999999999999999999999999999999999998876

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

Probab=99.79  E-value=8.6e-20  Score=131.35  Aligned_cols=67  Identities=16%  Similarity=0.273  Sum_probs=63.2

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      +.||||+||||+|++++|.+++..+|    .||+++||++|++||++||++|+++|++++++|..+|.+|.
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK   71 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            47999999999999999999988777    79999999999999999999999999999999999988774

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

Probab=99.78  E-value=8.4e-20  Score=154.36  Aligned_cols=74  Identities=15%  Similarity=0.226  Sum_probs=72.1

Q ss_pred             CCCCCCCCCCCChHHhHHHHhHHHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           64 VKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        64 ~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      .+||++||||+||||+|++++|.+++..+|.||+++||++|++||++||+||+++|++++++|.++|.+|..++
T Consensus       109 ~kdp~~PKrP~say~lF~~e~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~~  182 (214)
T 3tq6_A          109 LTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  182 (214)
T ss_dssp             HHHTTCCCCCCCHHHHHHHHHTTTSSCSSHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccccCcccccchhhhhHHHHHHhhccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999887

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

Probab=99.78  E-value=5.1e-19  Score=143.58  Aligned_cols=75  Identities=21%  Similarity=0.298  Sum_probs=69.2

Q ss_pred             CCCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           61 PKLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        61 ~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      .++.+||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|.++|.+|..
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 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  171 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345679999999999999999999999876655    899999999999999999999999999999999999999864

>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=99.78  E-value=7.6e-20  Score=132.22  Aligned_cols=68  Identities=16%  Similarity=0.246  Sum_probs=60.7

Q ss_pred             CCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           66 QDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        66 Dp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      .++.||||+||||+|++++|..++..+|    .||++++|++|++||++||++|+++|++++++|..++.+|
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Y   74 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY   74 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            4678999999999999999999986666    8999999999999999999999999999999999998776

>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=99.78  E-value=1.7e-19  Score=129.11  Aligned_cols=66  Identities=14%  Similarity=0.246  Sum_probs=62.2

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      +.||||+||||+|++++|.+++..+|    .||++++|++|++||++||++|+++|++++++|.+++.+|
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Y   70 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDY   70 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            47899999999999999999988877    7999999999999999999999999999999999988766

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

Probab=99.78  E-value=4.2e-20  Score=139.82  Aligned_cols=73  Identities=14%  Similarity=0.193  Sum_probs=65.9

Q ss_pred             CCCCCCCCCCChHHhHHHHhHHHhcCC--ChhHHHHHH---HHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           65 KQDSYSDQTRSPFRIFMETFVETCGSR--ELIDIDQKG---FEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        65 KDp~aPKRP~SAF~lF~~e~Rk~~K~~--nP~EIsK~l---GE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      .++++||||+||||+|++++|.+++..  +..||+++|   |++|++|+++||+||+++|++++++|++++....++.
T Consensus         6 ~~~~~PKRP~sAf~lF~~e~R~~ik~e~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~~~~~~~   83 (93)
T 2cto_A            6 SGMPNRKASRNAYYFFVQEKIPELRRRGLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGPSEKQK   83 (93)
T ss_dssp             CCCCCCCSSCCHHHHHHHTTHHHHHHHTCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSSCCCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcccccccccc
Confidence            589999999999999999999998744  458999999   9999999999999999999999999999987655554

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

Probab=99.77  E-value=1.4e-19  Score=155.22  Aligned_cols=74  Identities=15%  Similarity=0.226  Sum_probs=72.1

Q ss_pred             CCCCCCCCCCCChHHhHHHHhHHHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           64 VKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        64 ~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      .+||++||||+||||+|++++|.+++..||.||+++||++|++|+++||+||+++|++++++|+++|.+|..++
T Consensus       141 ~kdp~~PKrP~say~lF~~e~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k~  214 (238)
T 3tmm_A          141 LTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  214 (238)
T ss_dssp             HHHTTCCCCCCCHHHHHHHHHTTTSCCSSHHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcccCCCCCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999887

>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=99.77  E-value=2e-19  Score=129.98  Aligned_cols=67  Identities=16%  Similarity=0.187  Sum_probs=61.4

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      ++.||||+||||+|++++|.+++..+|    .||++++|++|++||++||++|+++|++++++|..++-+|
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Y   72 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   72 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            468999999999999999999987776    7999999999999999999999999999999999876554

>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=99.76  E-value=3e-19  Score=130.50  Aligned_cols=67  Identities=16%  Similarity=0.180  Sum_probs=62.0

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      ..||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|++++++|..++..|.
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS   71 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            36999999999999999999876655    79999999999999999999999999999999999988774

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

Probab=99.76  E-value=1.1e-18  Score=141.65  Aligned_cols=75  Identities=19%  Similarity=0.221  Sum_probs=68.6

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh------hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL------IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP------~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      +..+||++||||+||||+|++++|.+++..||      .||+++||++|++||++||++|+++|++++++|.++|..|..
T Consensus         8 ~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   87 (173)
T 2yrq_A            8 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   87 (173)
T ss_dssp             SSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            34679999999999999999999999875544      799999999999999999999999999999999999999865


Q ss_pred             c
Q 037983          136 S  136 (205)
Q Consensus       136 ~  136 (205)
                      .
T Consensus        88 ~   88 (173)
T 2yrq_A           88 P   88 (173)
T ss_dssp             C
T ss_pred             h
Confidence            4

>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=99.72  E-value=2.2e-18  Score=126.72  Aligned_cols=58  Identities=22%  Similarity=0.314  Sum_probs=53.4

Q ss_pred             CCCCCCCCCChHHhHHHHhHHHhcCCC-----hhHHHHHHHHHhhcCChhhhhhHHHHHHHHH
Q 037983           66 QDSYSDQTRSPFRIFMETFVETCGSRE-----LIDIDQKGFEKWKNMSKEERQPYVIKAEMLD  123 (205)
Q Consensus        66 Dp~aPKRP~SAF~lF~~e~Rk~~K~~n-----P~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K  123 (205)
                      ++++||||+||||+|++++|.+++..|     ..||+|+||++|++||++||+||+++|+.+.
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            689999999999999999999987554     4799999999999999999999999999873

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

Probab=99.71  E-value=3.1e-18  Score=146.77  Aligned_cols=77  Identities=6%  Similarity=0.086  Sum_probs=72.1

Q ss_pred             CCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcCCC
Q 037983           64 VKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPR  139 (205)
Q Consensus        64 ~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~lp~  139 (205)
                      .+||++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|+.++++|+++|..|..++++
T Consensus        36 ~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~~p  115 (238)
T 3tmm_A           36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTP  115 (238)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCH
Confidence            358999999999999999999999987777    8999999999999999999999999999999999999999988865


Q ss_pred             C
Q 037983          140 F  140 (205)
Q Consensus       140 e  140 (205)
                      .
T Consensus       116 ~  116 (238)
T 3tmm_A          116 S  116 (238)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=99.71  E-value=4.1e-19  Score=134.05  Aligned_cols=66  Identities=21%  Similarity=0.236  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCCChHHhHHHHhHHHhcCCChh-H--HHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHH
Q 037983           63 LVKQDSYSDQTRSPFRIFMETFVETCGSRELI-D--IDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA  129 (205)
Q Consensus        63 ~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP~-E--IsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~ke  129 (205)
                      ..||||+||||+||||||++++|.+++.+||. .  ++-+ +++|++|+++||+||+++|++++++|..+
T Consensus        16 ~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eI-se~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           16 WEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQI-AKLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             HHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHH-HHHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             ccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHH-HHHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            45799999999999999999999999999882 1  3333 39999999999999999999999999854

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

Probab=99.70  E-value=8.4e-18  Score=142.11  Aligned_cols=76  Identities=7%  Similarity=0.095  Sum_probs=70.8

Q ss_pred             CCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 037983           66 QDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRFM  141 (205)
Q Consensus        66 Dp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~lp~e~  141 (205)
                      .|++||||+||||+|++++|.+++..||    .||+++||++|++||++||++|+++|+.++++|.++|..|..++++..
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~tp~q   85 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQ   85 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCCHHH
Confidence            5789999999999999999999987776    899999999999999999999999999999999999999998886543

>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=99.57  E-value=1.1e-15  Score=121.93  Aligned_cols=68  Identities=16%  Similarity=0.252  Sum_probs=61.8

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      ++.||||+||||+|+++.|..+...||    .||+++||++|++||++||++|+++|+.++++|..+|..|.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~   73 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCS
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccc
Confidence            678999999999999999887665554    89999999999999999999999999999999999987764

---

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	205
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	6e-04
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	6e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	0.001
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	0.001
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	0.002
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	0.003
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	0.004

>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 = 35.2 bits (81), Expect = 6e-04
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 74  RSPFRIFM----ETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA 129
            S F +F                + D+ +K  E W N + +++QPY  KA  L   + + 
Sbjct: 7   PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 66

Query: 130 L 130
           +
Sbjct: 67  I 67

>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 = 35.7 bits (82), Expect = 6e-04
 Identities = 10/65 (15%), Positives = 26/65 (40%)

Query: 74  RSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE 133
            + + ++    +         +      ++WK +S++E+  Y  K +     +   LL  
Sbjct: 22  PNSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRF 81

Query: 134 VTSMP 138
           + S+P
Sbjct: 82  LESLP 86

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

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

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 10/59 (16%), Positives = 20/59 (33%), Gaps = 4/59 (6%)

Query: 74  RSPFRIFM----ETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRR 128
            S   IF         E        ++ +     W ++S++++  Y  +   L A   R
Sbjct: 25  VSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 83

>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 = 34.4 bits (79), Expect = 0.001
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 4/60 (6%)

Query: 74  RSPFRIFM----ETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA 129
            + F ++        ++        +I +    +WK M+  E+QPY  +   L   H   
Sbjct: 7   MNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 66

>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 = 33.7 bits (77), Expect = 0.002
 Identities = 11/61 (18%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 74  RSPFRIFM----ETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA 129
            + F ++                  +I ++   +WK +++ E+ P+  +A+ L A HR  
Sbjct: 9   MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68

Query: 130 L 130
            
Sbjct: 69  Y 69

>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 = 33.7 bits (77), Expect = 0.003
 Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 74  RSPFRIFM----ETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA 129
            + F ++M       V     +E   I+Q    +W  +S+EE+  Y   A      H + 
Sbjct: 7   LNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQL 66

>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 = 32.8 bits (75), Expect = 0.004
 Identities = 11/61 (18%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 74  RSPFRIFM----ETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA 129
            + F ++         +        +I ++   +WK +S+ E++P++ +A+ L A H + 
Sbjct: 7   MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66

Query: 130 L 130
            
Sbjct: 67  H 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	205
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.84
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.83
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.82
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.82
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.8
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.79
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.78
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.75
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.75
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.7
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	96.73

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

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

Probab=99.84  E-value=1.9e-21  Score=143.37  Aligned_cols=77  Identities=21%  Similarity=0.232  Sum_probs=71.7

Q ss_pred             CCCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhc
Q 037983           61 PKLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTS  136 (205)
Q Consensus        61 ~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~  136 (205)
                      .+..+||++||||+||||+|++++|.+++.++|    .+|++.+|++|++||++||++|+++|++++++|..+|.+|..+
T Consensus        12 ~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~~~   91 (93)
T d1lwma_          12 TRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNAT   91 (93)
T ss_dssp             CSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            356779999999999999999999999986655    8999999999999999999999999999999999999999988


Q ss_pred             C
Q 037983          137 M  137 (205)
Q Consensus       137 l  137 (205)
                      |
T Consensus        92 l   92 (93)
T d1lwma_          92 L   92 (93)
T ss_dssp             H
T ss_pred             c
Confidence            6

>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=99.83  E-value=2.6e-21  Score=138.25  Aligned_cols=73  Identities=19%  Similarity=0.245  Sum_probs=68.3

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRF  140 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~lp~e  140 (205)
                      |+||||+|||++|++++|.+++.+||    .||++++|++|++||++||++|.++|++++++|..+|.+|..+..++
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 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPD   77 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence            79999999999999999999987766    79999999999999999999999999999999999999998887443

>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=99.82  E-value=1.9e-20  Score=141.10  Aligned_cols=80  Identities=14%  Similarity=0.196  Sum_probs=74.7

Q ss_pred             CCCCCCCCCCCCCCCChHHhHHHHhHHHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcCCC
Q 037983           60 KPKLVKQDSYSDQTRSPFRIFMETFVETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPR  139 (205)
Q Consensus        60 ~~k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~lp~  139 (205)
                      +.|...|+.+||+|+||||+|++++|.+++..++.||+++||++|++||++||++|+++|++++++|..+|.+|..+++.
T Consensus         8 ~~k~~~~~~p~K~P~~ay~lF~~~~r~~~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~~~~   87 (108)
T d1v64a_           8 QLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPE   87 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             cccccCCCCCCCCCCcHHHHHHHHHHHHccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            34556688899999999999999999999999999999999999999999999999999999999999999999999853

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

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

Probab=99.82  E-value=1.1e-20  Score=137.98  Aligned_cols=77  Identities=16%  Similarity=0.250  Sum_probs=72.8

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSM  137 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~l  137 (205)
                      ++.|||+.||||+|||++|++++|..++..+|    .+|++++|+.|+.||++||++|+++|++++.+|..+|.+|..+-
T Consensus         3 k~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~~   82 (91)
T d1k99a_           3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH   82 (91)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            46789999999999999999999999988877    79999999999999999999999999999999999999998887


Q ss_pred             C
Q 037983          138 P  138 (205)
Q Consensus       138 p  138 (205)
                      |
T Consensus        83 p   83 (91)
T d1k99a_          83 P   83 (91)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.80  E-value=7.2e-20  Score=135.60  Aligned_cols=75  Identities=13%  Similarity=0.127  Sum_probs=69.8

Q ss_pred             CCCCCCCCCChHHhHHHHhHHHhcCCCh--hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 037983           66 QDSYSDQTRSPFRIFMETFVETCGSREL--IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVTSMPRF  140 (205)
Q Consensus        66 Dp~aPKRP~SAF~lF~~e~Rk~~K~~nP--~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k~lp~e  140 (205)
                      ...+||||+||||+|++++|.+++..++  .||+++||++|++||++||++|.++|++++++|..+|.+|..+++++
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 SSGPKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHH
Confidence            4568999999999999999999887665  89999999999999999999999999999999999999999999765

>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=99.79  E-value=3.6e-20  Score=133.96  Aligned_cols=67  Identities=16%  Similarity=0.273  Sum_probs=63.6

Q ss_pred             CCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHH
Q 037983           68 SYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEV  134 (205)
Q Consensus        68 ~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~  134 (205)
                      +.||||+||||||++++|.+++..||    .||++++|++|++||++||++|.++|++++++|.++|.+|.
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk   71 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK   71 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            57899999999999999999998887    79999999999999999999999999999999999998874

>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=99.79  E-value=2.9e-20  Score=130.09  Aligned_cols=65  Identities=22%  Similarity=0.279  Sum_probs=60.6

Q ss_pred             CCCCCCChHHhHHHHhHHHhcCCCh------hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           69 YSDQTRSPFRIFMETFVETCGSREL------IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~Rk~~K~~nP------~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      .||||+||||+|++++|..++.+||      ++|++++|++|++||++||++|.++|++++++|.++|.+|
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            4899999999999999999987665      6999999999999999999999999999999999998764

>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=99.78  E-value=6.9e-20  Score=133.12  Aligned_cols=69  Identities=16%  Similarity=0.239  Sum_probs=64.5

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      .|.||||+||||||++++|.+++..||    .||++++|++|++||++||++|+++|++++++|..+|.+|..
T Consensus         2 ~~~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~   74 (85)
T d1j46a_           2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhcc
Confidence            368999999999999999999987777    799999999999999999999999999999999999988854

>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=99.76  E-value=1.5e-19  Score=127.07  Aligned_cols=62  Identities=18%  Similarity=0.210  Sum_probs=57.9

Q ss_pred             CCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHH
Q 037983           69 YSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRAL  130 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem  130 (205)
                      .+|||+||||+|++++|.+++..+|    +||++++|++|++||++||++|+++|++++++|.+++
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~   67 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKY   67 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            5689999999999999999988877    8999999999999999999999999999999997653

>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=99.75  E-value=1.5e-19  Score=131.64  Aligned_cols=68  Identities=15%  Similarity=0.182  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHH
Q 037983           62 KLVKQDSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRA  129 (205)
Q Consensus        62 k~~KDp~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~ke  129 (205)
                      ...+|+++||||+||||||++++|.+++..||    .||++++|++|+.|+++||++|+++|++++++|.++
T Consensus        13 ~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          13 GGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             CCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34679999999999999999999999986665    799999999999999999999999999999998754

>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=99.75  E-value=6.8e-19  Score=124.16  Aligned_cols=67  Identities=16%  Similarity=0.296  Sum_probs=62.0

Q ss_pred             CCCCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           67 DSYSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        67 p~aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      .|+||||+||||+|++++|..++.+||    .||+++||++|++|+  ||++|.++|++++++|.++|.+|..
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~   71 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            378999999999999999999998877    799999999999985  5999999999999999999999854

>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=99.70  E-value=3.8e-18  Score=124.01  Aligned_cols=67  Identities=16%  Similarity=0.190  Sum_probs=61.7

Q ss_pred             CCCCCCChHHhHHHHhHHHhcCCCh----hHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHHHh
Q 037983           69 YSDQTRSPFRIFMETFVETCGSREL----IDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEEVT  135 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~Rk~~K~~nP----~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~~k  135 (205)
                      ..|||+||||||+++.|.++...||    ++|+++||++|++||++||++|.++|++++++|.+++.+|..
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~   72 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA   72 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            4689999999999999999987777    899999999999999999999999999999999998877643

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

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

Probab=96.73  E-value=0.0021  Score=45.62  Aligned_cols=64  Identities=17%  Similarity=0.242  Sum_probs=50.6

Q ss_pred             CCCCCCChHHhHHHHhH----HHhcCCChhHHHHHHHHHhhcCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 037983           69 YSDQTRSPFRIFMETFV----ETCGSRELIDIDQKGFEKWKNMSKEERQPYVIKAEMLDAAHRRALLEE  133 (205)
Q Consensus        69 aPKRP~SAF~lF~~e~R----k~~K~~nP~EIsK~lGE~WKsLSdeEKkPY~dkA~e~K~~Y~kem~e~  133 (205)
                      .|--|.+|==+|.+..-    ..+++.. .-..+..-..|++|...||-+|+.+|+++..+|++++.+-
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~DR-~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~em   70 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKNDR-VKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEM   70 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTSTH-HHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhhH-HHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHh
Confidence            46667788888887643    3444433 4456777889999999999999999999999999998765