Citrus Sinensis ID: 032101

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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-------
Protein Sequence
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNLVPFFNSVDAFGSLLCV
Secondary Structure (PSIPRED)
cccccccccccccHHccccccHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHccHHHHccHHHHHHHcHHHHHHHHHHccccccccccccccccccccccccEEEEEcHHHcHHHHHcccccccHHHHHHHHHHHHHHccHHHccHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHcccEEcc
Coil and Loop (DISEMBL)
mkgakgkgaarvsqealkpndrkvgkRKAATAkldsgskrqgkrekkakkdpnkpkrppsaFFVFLEEFRKTFkkenpnvtaVSAVgkaaggkwksmspaekapyesKAEKLKSEYGKkmnaynkkqvtnlvpffnsvdafgsllcv
Flexible Loop (DISEMBL)
mkgakgkgaarvsqealkpndrkvgkrkaatakldsgskrqgkrekkakkdpnkpkrppsAFFVFLEEFRKTfkkenpnvtavsavgkaaggkwksmspaekapyesKAEKLKSEYGKKMNAYNKKQVTNLVPFFNSVDAFGSLLCV
Low Complexity Region (SEG)
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSkrqgkrekkakkdpnkpkrppSAFFVFLEEFRKTFKKENPNvtavsavgkaaggkwkSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNLVPFFNSVDAFGSLLCV
Disordered region (IsUnstruct)
************************************************************AFFVFLEEFRKTFK************************************************YNKKQVTNLVPFFNSVDAFGSLLC*
Disordered Region (DISOPRED)
**********************************************************PSAFFVFLEEFRKTFKK*NPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM*********************GSLLCV
Disordered Region (DISEMBL)
********************************************************RPPSAFFVFLEEFRKTFKKENPNVTAVSAVG*************************KSEYGKKMNAYNKKQVTNLVPFFNSVDAFGSLLCV
Disordered Region (DISPRO)
*************************K**AATAKLDSGSKRQ********KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNLVPFFNSVDAFGSLLCV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNLVPFFNSVDAFGSLLCV
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	147	2.2.26 [Sep-21-2011]
O49595	178	High mobility group B pro	yes	no	0.829	0.685	0.714	1e-39
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.557	0.539	0.756	2e-27
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.578	0.590	0.670	5e-26
P27347	157	DNA-binding protein MNB1B	N/A	no	0.782	0.732	0.534	6e-25
O49596	144	High mobility group B pro	no	no	0.564	0.576	0.698	7e-25
Q42344	138	High mobility group B pro	no	no	0.721	0.768	0.484	6e-24
P93047	141	High mobility group B pro	no	no	0.619	0.645	0.626	4e-23
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.727	0.664	0.530	1e-21
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.523	0.516	0.623	7e-21
O49597	125	High mobility group B pro	no	no	0.612	0.72	0.488	2e-18

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

 Score =  161 bits (408), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/126 (71%), Positives = 102/126 (80%), Gaps = 4/126 (3%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGK   + ++EALKP +DRKVGKRKA   K    +KR+ ++EKKAKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTKEALKPVDDRKVGKRKAPAEKP---TKRETRKEKKAKKDPNKPKRAP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS AEKAPYE KA K K+EY K+
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKQ 117

Query: 120 MNAYNK 125
           M+AYNK
Sbjct: 118 MDAYNK 123

Binds preferentially double-stranded DNA. Modulates general plant growth and stress tolerance. Confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 62/82 (75%), Positives = 67/82 (81%)

Query: 47  KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYE 106
           KA KDPNKPKRPPSAFFVF+EEFRK F KE+P   AVSAVGKAAG KWK+MS AEKAPY 
Sbjct: 36  KAAKDPNKPKRPPSAFFVFMEEFRKVFNKEHPENKAVSAVGKAAGAKWKTMSDAEKAPYV 95

Query: 107 SKAEKLKSEYGKKMNAYNKKQV 128
           +K+EK K EY K M AYNKKQ 
Sbjct: 96  AKSEKRKVEYEKNMRAYNKKQA 117

Glycine max (taxid: 3847)

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

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 57/85 (67%), Positives = 70/85 (82%)

Query: 43  KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEK 102
           K+ KKA KDPNKPKRPPSAFFVF+E+FRKT+K+++PN  +V+ VGKA G KWK ++ AEK
Sbjct: 24  KKTKKAVKDPNKPKRPPSAFFVFMEDFRKTYKEKHPNNKSVAVVGKAGGDKWKQLTAAEK 83

Query: 103 APYESKAEKLKSEYGKKMNAYNKKQ 127
           AP+ SKAEK K EY K + AYNKKQ
Sbjct: 84  APFISKAEKRKQEYEKNLQAYNKKQ 108

Ipomoea nil (taxid: 35883)

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

 Score =  112 bits (281), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 69/129 (53%), Positives = 85/129 (65%), Gaps = 14/129 (10%)

Query: 1   MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPS 60
           MKGAK KGAA+         D K+  +     K   G      R+ KA KDPNKPKR PS
Sbjct: 1   MKGAKSKGAAKA--------DAKLAVKSKGAEKPAKG------RKGKAGKDPNKPKRAPS 46

Query: 61  AFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM 120
           AFFVF+EEFRK FK++NP   +V+AVGKAAG +WKS+S ++KAPY +KA KLK EY K +
Sbjct: 47  AFFVFMEEFRKEFKEKNPKNKSVAAVGKAAGDRWKSLSESDKAPYVAKANKLKLEYNKAI 106

Query: 121 NAYNKKQVT 129
            AYNK + T
Sbjct: 107 AAYNKGEST 115

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

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

 Score =  112 bits (280), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 58/83 (69%), Positives = 67/83 (80%)

Query: 44  REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKA 103
           R K A KDPNKPKRP SAFFVF+E+FR+TFKKENP   +V+ VGKAAG KWKS+S +EKA
Sbjct: 27  RGKAAAKDPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKA 86

Query: 104 PYESKAEKLKSEYGKKMNAYNKK 126
           PY +KAEK K EY K + AYNKK
Sbjct: 87  PYVAKAEKRKVEYEKNIKAYNKK 109

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  109 bits (272), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 61/126 (48%), Positives = 75/126 (59%), Gaps = 20/126 (15%)

Query: 1   MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPS 60
           MKG + K  A  + + LK   RK GK                    K KKDPN+PKRPPS
Sbjct: 1   MKGGESKAEATSTDQRLKTRGRKAGK--------------------KTKKDPNQPKRPPS 40

Query: 61  AFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM 120
           AFFVFLE+FRK F   NPN  +V+ VGKAAG +WK+M+  +KAPY +KAE  K+EY K +
Sbjct: 41  AFFVFLEDFRKEFNLANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNV 100

Query: 121 NAYNKK 126
             YN K
Sbjct: 101 QQYNLK 106

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  106 bits (265), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 57/91 (62%), Positives = 70/91 (76%)

Query: 36  SGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWK 95
           S +K+  K  K A KDPNKPKRP SAFFVF+E+FR T+K+E+P   +V+AVGKA G KWK
Sbjct: 16  SVTKKPAKGAKGAAKDPNKPKRPSSAFFVFMEDFRVTYKEEHPKNKSVAAVGKAGGEKWK 75

Query: 96  SMSPAEKAPYESKAEKLKSEYGKKMNAYNKK 126
           S+S +EKAPY +KA+K K EY K M AYNKK
Sbjct: 76  SLSDSEKAPYVAKADKRKVEYEKNMKAYNKK 106

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  102 bits (253), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 69/130 (53%), Positives = 83/130 (63%), Gaps = 23/130 (17%)

Query: 1   MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGK-----REKKAKKDPNKP 55
           MKGAK KGAA+                  A AKL   SK   K     ++ KA KDPNKP
Sbjct: 1   MKGAKSKGAAK------------------ADAKLAVKSKGAEKPAAKGKKGKAGKDPNKP 42

Query: 56  KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSE 115
           KR PSAFFVF+ EFR+ FK++NP   +V+AVGKAAG +WKS+S +EKAPY +KA KLK E
Sbjct: 43  KRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSESEKAPYVAKANKLKGE 102

Query: 116 YGKKMNAYNK 125
           Y K + AYNK
Sbjct: 103 YNKAIAAYNK 112

Triticum aestivum (taxid: 4565)

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

 Score = 99.4 bits (246), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 48/77 (62%), Positives = 60/77 (77%)

Query: 50  KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKA 109
           KDPNKPKRPPSAFFVF+ +FR+ +KK++PN  +V+AVGKA G +WKS+S  EKAPY  +A
Sbjct: 40  KDPNKPKRPPSAFFVFMADFREQYKKDHPNNKSVAAVGKACGEEWKSLSEEEKAPYVDRA 99

Query: 110 EKLKSEYGKKMNAYNKK 126
            K K EY   + AYNKK
Sbjct: 100 LKKKEEYEITLQAYNKK 116

Vicia faba (taxid: 3906)

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

 Score = 91.3 bits (225), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 61/90 (67%)

Query: 35  DSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKW 94
           D   K +G +  K  KDPN+PK+PPS FFVFL++FRK F   NP+  +V  VG+AAG KW
Sbjct: 14  DDRLKVRGNKVGKKTKDPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKW 73

Query: 95  KSMSPAEKAPYESKAEKLKSEYGKKMNAYN 124
           K+M+  E+AP+ +K++  K+EY   M  YN
Sbjct: 74  KTMTEEERAPFVAKSQSKKTEYAVTMQQYN 103

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

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	147
449461783	169	PREDICTED: high mobility group B protein	0.877	0.763	0.717	5e-41
255574381	171	DNA-binding protein MNB1B, putative [Ric	0.857	0.736	0.781	3e-40
297819892	185	hypothetical protein ARALYDRAFT_323737 [	0.829	0.659	0.714	1e-38
312281849	185	unnamed protein product [Thellungiella h	0.829	0.659	0.706	3e-38
42572635	185	high mobility group protein B1 [Arabidop	0.829	0.659	0.714	4e-38
334185909	161	high mobility group protein B1 [Arabidop	0.829	0.757	0.714	5e-38
15231065	178	high mobility group protein B1 [Arabidop	0.829	0.685	0.714	7e-38
224112525	176	high mobility group family [Populus tric	0.857	0.715	0.697	6e-37
224098541	179	high mobility group family [Populus tric	0.870	0.715	0.664	3e-36
118484946	171	unknown [Populus trichocarpa]	0.870	0.748	0.664	4e-36

>gi|449461783|ref|XP_004148621.1| PREDICTED: high mobility group B protein 1-like [Cucumis sativus]

 Score =  172 bits (435), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 94/131 (71%), Positives = 108/131 (82%), Gaps = 2/131 (1%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MKG+KGKG +RVS+EALKP +DRKVGKRKA   K D G KR  K++ KAKKDPNKPKRPP
Sbjct: 1   MKGSKGKGTSRVSKEALKPVDDRKVGKRKAVV-KADKGIKRPTKKDLKAKKDPNKPKRPP 59

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLEEFRK +K+ENPNV AVSAVGKA G KWKS+S AEKAPYE+KA K K+EY K 
Sbjct: 60  SAFFVFLEEFRKEYKRENPNVKAVSAVGKAGGEKWKSLSHAEKAPYEAKAAKRKAEYEKL 119

Query: 120 MNAYNKKQVTN 130
           M AY+ K+V +
Sbjct: 120 MRAYDSKKVAS 130

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574381|ref|XP_002528104.1| DNA-binding protein MNB1B, putative [Ricinus communis] gi|223532493|gb|EEF34283.1| DNA-binding protein MNB1B, putative [Ricinus communis]

 Score =  169 bits (428), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 100/128 (78%), Positives = 111/128 (86%), Gaps = 2/128 (1%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK +KG GAA+ S++ALKP +DRKVGKRKAA A +D  SK + KREKKAKKDPNKPKRPP
Sbjct: 1   MKNSKGTGAAKASKDALKPADDRKVGKRKAAAA-VDRSSKLKAKREKKAKKDPNKPKRPP 59

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLEEFRKTFKKENP+VT+V+AVGKA G KWKSMS AEKAPYE+KA K K EYGK 
Sbjct: 60  SAFFVFLEEFRKTFKKENPSVTSVAAVGKAGGAKWKSMSSAEKAPYEAKAAKKKDEYGKL 119

Query: 120 MNAYNKKQ 127
           MNAYNKKQ
Sbjct: 120 MNAYNKKQ 127

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297819892|ref|XP_002877829.1| hypothetical protein ARALYDRAFT_323737 [Arabidopsis lyrata subsp. lyrata] gi|297323667|gb|EFH54088.1| hypothetical protein ARALYDRAFT_323737 [Arabidopsis lyrata subsp. lyrata]

 Score =  164 bits (414), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 90/126 (71%), Positives = 102/126 (80%), Gaps = 4/126 (3%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGK   + ++EALKP +DRKVGKRKA   K    +KR+ ++EKKAKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTKEALKPVDDRKVGKRKAPAEK---ATKRETRKEKKAKKDPNKPKRAP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS AEKAPYE KA K K+EY K+
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKQ 117

Query: 120 MNAYNK 125
           M+AYNK
Sbjct: 118 MDAYNK 123

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312281849|dbj|BAJ33790.1| unnamed protein product [Thellungiella halophila]

 Score =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 89/126 (70%), Positives = 102/126 (80%), Gaps = 4/126 (3%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGK   + ++E LKP +DRKVGKRKA  AK    +KR+ ++EK+AKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTKETLKPVDDRKVGKRKAPAAK---ATKRETRKEKRAKKDPNKPKRAP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLE+FR+TFKKENPNV AVSAVGKA G KWKSMS AEKAPYE KA K K+EY K 
Sbjct: 58  SAFFVFLEDFRQTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKL 117

Query: 120 MNAYNK 125
           M+AYNK
Sbjct: 118 MDAYNK 123

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42572635|ref|NP_974413.1| high mobility group protein B1 [Arabidopsis thaliana] gi|222423104|dbj|BAH19531.1| AT3G51880 [Arabidopsis thaliana] gi|332645335|gb|AEE78856.1| high mobility group protein B1 [Arabidopsis thaliana]

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 90/126 (71%), Positives = 102/126 (80%), Gaps = 4/126 (3%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGK   + ++EALKP +DRKVGKRKA   K    +KR+ ++EKKAKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTKEALKPVDDRKVGKRKAPAEK---PTKRETRKEKKAKKDPNKPKRAP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS AEKAPYE KA K K+EY K+
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKQ 117

Query: 120 MNAYNK 125
           M+AYNK
Sbjct: 118 MDAYNK 123

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185909|ref|NP_001190062.1| high mobility group protein B1 [Arabidopsis thaliana] gi|332645337|gb|AEE78858.1| high mobility group protein B1 [Arabidopsis thaliana]

 Score =  162 bits (409), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 90/126 (71%), Positives = 102/126 (80%), Gaps = 4/126 (3%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGK   + ++EALKP +DRKVGKRKA   K    +KR+ ++EKKAKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTKEALKPVDDRKVGKRKAPAEK---PTKRETRKEKKAKKDPNKPKRAP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS AEKAPYE KA K K+EY K+
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKQ 117

Query: 120 MNAYNK 125
           M+AYNK
Sbjct: 118 MDAYNK 123

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231065|ref|NP_190756.1| high mobility group protein B1 [Arabidopsis thaliana] gi|145332807|ref|NP_001078269.1| high mobility group protein B1 [Arabidopsis thaliana] gi|75274976|sp|O49595.1|HMGB1_ARATH RecName: Full=High mobility group B protein 1; AltName: Full=High mobility group protein A; Short=AtHMGalpha; Short=HMG alpha; AltName: Full=Nucleosome/chromatin assembly factor group D 01; Short=Nucleosome/chromatin assembly factor group D 1 gi|2832357|emb|CAA74400.1| HMG protein [Arabidopsis thaliana] gi|3068715|gb|AAC14415.1| unknown [Arabidopsis thaliana] gi|15912191|gb|AAL08229.1| At3g51880/ORF13 [Arabidopsis thaliana] gi|21360557|gb|AAM47475.1| At3g51880/ORF13 [Arabidopsis thaliana] gi|332645334|gb|AEE78855.1| high mobility group protein B1 [Arabidopsis thaliana] gi|332645336|gb|AEE78857.1| high mobility group protein B1 [Arabidopsis thaliana]

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 90/126 (71%), Positives = 102/126 (80%), Gaps = 4/126 (3%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGK   + ++EALKP +DRKVGKRKA   K    +KR+ ++EKKAKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTKEALKPVDDRKVGKRKAPAEKP---TKRETRKEKKAKKDPNKPKRAP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS AEKAPYE KA K K+EY K+
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKQ 117

Query: 120 MNAYNK 125
           M+AYNK
Sbjct: 118 MDAYNK 123

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112525|ref|XP_002316220.1| high mobility group family [Populus trichocarpa] gi|222865260|gb|EEF02391.1| high mobility group family [Populus trichocarpa]

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 90/129 (69%), Positives = 102/129 (79%), Gaps = 3/129 (2%)

Query: 1   MKGAKGKGAARVSQ-EALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRP 58
           MK AKGKG AR  + E L P  DRK+GKRKAA  K +  SK++ K+EK  KKDPNKPKRP
Sbjct: 1   MKIAKGKGTARTEKKEVLLPVEDRKIGKRKAAL-KANESSKKRVKKEKITKKDPNKPKRP 59

Query: 59  PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK 118
           PSAFFVFLEEFRK +K+E+PNV AVSAVGKA G KWKS+S AEKAPYE+KA K KS+Y K
Sbjct: 60  PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSAAEKAPYEAKAAKRKSDYEK 119

Query: 119 KMNAYNKKQ 127
            M AYNKKQ
Sbjct: 120 LMTAYNKKQ 128

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224098541|ref|XP_002311212.1| high mobility group family [Populus trichocarpa] gi|222851032|gb|EEE88579.1| high mobility group family [Populus trichocarpa]

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 87/131 (66%), Positives = 101/131 (77%), Gaps = 3/131 (2%)

Query: 1   MKGAKGKGAARVSQE--ALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRP 58
           MK AKGKGAAR  ++  +L   DRK+GKRKAA    +S  KR  K EK  KKDP+KPKRP
Sbjct: 1   MKTAKGKGAARTEKKEVSLPVEDRKIGKRKAALKATESSKKRAAK-EKITKKDPDKPKRP 59

Query: 59  PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK 118
           PS+FFVFLEEFRK +K+E+PN+ AVSAVGKA G KWKSMS AEKAPYE+KA   KS+YGK
Sbjct: 60  PSSFFVFLEEFRKIYKQEHPNMKAVSAVGKAGGEKWKSMSAAEKAPYEAKAAIKKSDYGK 119

Query: 119 KMNAYNKKQVT 129
            M AY+KKQ T
Sbjct: 120 LMTAYSKKQET 130

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118484946|gb|ABK94338.1| unknown [Populus trichocarpa]

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 87/131 (66%), Positives = 101/131 (77%), Gaps = 3/131 (2%)

Query: 1   MKGAKGKGAARVSQE--ALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRP 58
           MK AKGKGAAR  ++  +L   DRK+GKRKAA    +S  KR  K EK  KKDP+KPKRP
Sbjct: 1   MKTAKGKGAARTEKKEVSLPVEDRKIGKRKAALKATESSKKRAAK-EKITKKDPDKPKRP 59

Query: 59  PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK 118
           PS+FFVFLEEFRK +K+E+PN+ AVSAVGKA G KWKSMS AEKAPYE+KA   KS+YGK
Sbjct: 60  PSSFFVFLEEFRKIYKQEHPNMKAVSAVGKAGGEKWKSMSAAEKAPYEAKAAIKKSDYGK 119

Query: 119 KMNAYNKKQVT 129
            M AY+KKQ T
Sbjct: 120 LMTAYSKKQET 130

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	147
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.455	0.465	0.537	4.8e-17
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.455	0.485	0.447	2.4e-14
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.442	0.52	0.353	1.4e-09
ZFIN|ZDB-GENE-030131-341	205	hmgb1a "high-mobility group bo	0.448	0.321	0.402	9.2e-07
RGD|1559962	209	RGD1559962 "similar to High mo	0.448	0.315	0.388	6.4e-06
TAIR|locus:2154433	241	HMGB6 "high-mobility group box	0.421	0.257	0.365	9.6e-06
UNIPROTKB|P40618	202	HMGB3 "High mobility group pro	0.448	0.326	0.373	9.8e-06
UNIPROTKB|F1MF42	196	LOC618297 "Uncharacterized pro	0.448	0.336	0.373	1.5e-05
UNIPROTKB|P40673	209	HMGB2 "High mobility group pro	0.448	0.315	0.373	1.9e-05
UNIPROTKB|P26583	209	HMGB2 "High mobility group pro	0.448	0.315	0.373	1.9e-05

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

 Score = 178 (67.7 bits), Expect = 4.8e-17, Sum P(2) = 4.8e-17
 Identities = 36/67 (53%), Positives = 43/67 (64%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFFVF+E+FR+TFKKENP                 S+S +EKAPY +KAEK K EY K 
Sbjct:    43 SAFFVFMEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKN 102

Query:   120 MNAYNKK 126
             + AYNKK
Sbjct:   103 IKAYNKK 109

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0000785 "chromatin" evidence=TAS

GO:0003682 "chromatin binding" evidence=TAS

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

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

GO:0006096 "glycolysis" evidence=RCA

GO:0006833 "water transport" evidence=RCA

GO:0006972 "hyperosmotic response" evidence=RCA

GO:0007030 "Golgi organization" evidence=RCA

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

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

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

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

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

 Score = 143 (55.4 bits), Expect = 2.4e-14, Sum P(2) = 2.4e-14
 Identities = 30/67 (44%), Positives = 37/67 (55%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFFVFLE+FRK F   NPN                +M+  +KAPY +KAE  K+EY K 
Sbjct:    40 SAFFVFLEDFRKEFNLANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKN 99

Query:   120 MNAYNKK 126
             +  YN K
Sbjct:   100 VQQYNLK 106

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0000785 "chromatin" evidence=TAS

GO:0003682 "chromatin binding" evidence=TAS

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

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

GO:0005737 "cytoplasm" evidence=IDA

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

GO:0006342 "chromatin silencing" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0008283 "cell proliferation" evidence=RCA

GO:0016572 "histone phosphorylation" evidence=RCA

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

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

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

 Score = 114 (45.2 bits), Expect = 1.4e-09, Sum P(2) = 1.4e-09
 Identities = 23/65 (35%), Positives = 34/65 (52%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             S FFVFL++FRK F   NP+                +M+  E+AP+ +K++  K+EY   
Sbjct:    39 SPFFVFLDDFRKEFNLANPDNKSVGNVGRAAGKKWKTMTEEERAPFVAKSQSKKTEYAVT 98

Query:   120 MNAYN 124
             M  YN
Sbjct:    99 MQQYN 103

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0000785 "chromatin" evidence=TAS

GO:0003682 "chromatin binding" evidence=TAS

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

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

GO:0005737 "cytoplasm" evidence=IDA

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

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

 Score = 114 (45.2 bits), Expect = 9.2e-07, P = 9.2e-07
 Identities = 27/67 (40%), Positives = 32/67 (47%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  EFR   K+E P                  +S  EK PYE KA KLK +Y K 
Sbjct:    99 SAFFIFCSEFRPKVKEETPGLSIGDVAKRLGEMWN-KISSEEKQPYEKKAAKLKEKYEKD 157

Query:   120 MNAYNKK 126
             + AY  K
Sbjct:   158 IAAYRSK 164

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0009409 "response to cold" evidence=IDA

GO:0030900 "forebrain development" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

RGD|1559962 RGD1559962 "similar to High mobility group protein 2 (HMG-2)" [Rattus norvegicus (taxid:10116)]

 Score = 107 (42.7 bits), Expect = 6.4e-06, P = 6.4e-06
 Identities = 26/67 (38%), Positives = 30/67 (44%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  E R   K E+P                   S  +K PYE KA KLK EY K 
Sbjct:   100 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWS-EQSAKDKQPYEQKAAKLKEEYEKD 158

Query:   120 MNAYNKK 126
             + AY  K
Sbjct:   159 IAAYRAK 165

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 107 (42.7 bits), Expect = 9.6e-06, P = 9.6e-06
 Identities = 23/63 (36%), Positives = 34/63 (53%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             +AFF+F+ +FRKTFK E+ N                S++  EK  Y  KA +LK+EY K 
Sbjct:   120 TAFFIFMSDFRKTFKSEH-NGSLAKDAAKIGGEKWKSLTEEEKKVYLDKAAELKAEYNKS 178

Query:   120 MNA 122
             + +
Sbjct:   179 LES 181

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0003677 "DNA binding" evidence=IDA

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

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

 Score = 105 (42.0 bits), Expect = 9.8e-06, P = 9.8e-06
 Identities = 25/67 (37%), Positives = 31/67 (46%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  EFR   K  NP                 ++S  EK PY +KA KLK +Y K 
Sbjct:    98 SAFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWN-NLSDGEKQPYNNKAAKLKEKYEKD 156

Query:   120 MNAYNKK 126
             +  Y  K
Sbjct:   157 VADYKSK 163

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

UNIPROTKB|F1MF42 LOC618297 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 103 (41.3 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 25/67 (37%), Positives = 30/67 (44%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  E R   K E+P                   S  +K PYE KA KLK +Y K 
Sbjct:    89 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWS-EQSAKDKQPYEQKAAKLKEKYEKD 147

Query:   120 MNAYNKK 126
             + AY  K
Sbjct:   148 IAAYRAK 154

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P40673 HMGB2 "High mobility group protein B2" [Bos taurus (taxid:9913)]

 Score = 103 (41.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 25/67 (37%), Positives = 30/67 (44%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  E R   K E+P                   S  +K PYE KA KLK +Y K 
Sbjct:   100 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWS-EQSAKDKQPYEQKAAKLKEKYEKD 158

Query:   120 MNAYNKK 126
             + AY  K
Sbjct:   159 IAAYRAK 165

GO:0048471 "perinuclear region of cytoplasm" evidence=ISS

GO:0000793 "condensed chromosome" evidence=ISS

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

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

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

GO:0005737 "cytoplasm" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0003684 "damaged DNA binding" evidence=IDA

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

GO:0006338 "chromatin remodeling" evidence=NAS

GO:0042393 "histone binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0006265 "DNA topological change" evidence=IDA

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

GO:0006310 "DNA recombination" evidence=IDA

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

GO:0060326 "cell chemotaxis" evidence=IEA

GO:0050786 "RAGE receptor binding" evidence=IEA

GO:0048545 "response to steroid hormone stimulus" evidence=IEA

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

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0045654 "positive regulation of megakaryocyte differentiation" evidence=IEA

GO:0045648 "positive regulation of erythrocyte differentiation" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

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

GO:0043234 "protein complex" evidence=IEA

GO:0042056 "chemoattractant activity" evidence=IEA

GO:0032075 "positive regulation of nuclease activity" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0007289 "spermatid nucleus differentiation" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

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

GO:0001938 "positive regulation of endothelial cell proliferation" evidence=IEA

UNIPROTKB|P26583 HMGB2 "High mobility group protein B2" [Homo sapiens (taxid:9606)]

 Score = 103 (41.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 25/67 (37%), Positives = 30/67 (44%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  E R   K E+P                   S  +K PYE KA KLK +Y K 
Sbjct:   100 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWS-EQSAKDKQPYEQKAAKLKEKYEKD 158

Query:   120 MNAYNKK 126
             + AY  K
Sbjct:   159 IAAYRAK 165

GO:0007289 "spermatid nucleus differentiation" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0048545 "response to steroid hormone stimulus" evidence=IEA

GO:0048015 "phosphatidylinositol-mediated signaling" evidence=NAS

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0048471 "perinuclear region of cytoplasm" evidence=IDA

GO:0006325 "chromatin organization" evidence=NAS

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

GO:0006334 "nucleosome assembly" evidence=NAS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0000793 "condensed chromosome" evidence=IDA

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

GO:0001938 "positive regulation of endothelial cell proliferation" evidence=IDA

GO:0042056 "chemoattractant activity" evidence=IDA

GO:0060326 "cell chemotaxis" evidence=IDA

GO:0050786 "RAGE receptor binding" evidence=IGI

GO:0003684 "damaged DNA binding" evidence=IDA

GO:0043234 "protein complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0003677 "DNA binding" evidence=IMP

GO:0005615 "extracellular space" evidence=IDA

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEP

GO:0051103 "DNA ligation involved in DNA repair" evidence=ISS

GO:0006265 "DNA topological change" evidence=ISS

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

GO:0003697 "single-stranded DNA binding" evidence=ISS

GO:0032075 "positive regulation of nuclease activity" evidence=IDA

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

GO:0044212 "transcription regulatory region DNA binding" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

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

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

GO:0045648 "positive regulation of erythrocyte differentiation" evidence=IMP

GO:0045654 "positive regulation of megakaryocyte differentiation" evidence=IMP

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006309 "apoptotic DNA fragmentation" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0006921 "cellular component disassembly involved in execution phase of apoptosis" evidence=TAS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0050918 "positive chemotaxis" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O49595	HMGB1_ARATH	No assigned EC number	0.7142	0.8299	0.6853	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh1_pm.C_scaffold_5001281 annotation not avaliable (185 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	147
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	2e-18
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	1e-16
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	9e-16
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	2e-14
smart00398	70	smart00398, HMG, high mobility group	1e-13
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	1e-11
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	3e-11
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	5e-08
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	2e-07

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

 Score = 73.8 bits (182), Expect = 2e-18
 Identities = 35/70 (50%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 55  PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKS 114
           PKRP SAFF+F +E R   K ENP +   + + K  G KWK++S  EK PYE KAEK K+
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKPYEEKAEKEKA 59

Query: 115 EYGKKMNAYN 124
            Y K   AY 
Sbjct: 60  RYEKAYPAYK 69

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 = 69.2 bits (170), Expect = 1e-16
 Identities = 33/66 (50%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 55  PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKS 114
           PKRP SA+F+F +E R   K ENP ++ V  + K  G  WKS+S  EK  YE KAEK K 
Sbjct: 1   PKRPLSAYFLFSQEHRAEVKAENPGLS-VGEISKILGEMWKSLSEEEKKKYEEKAEKDKE 59

Query: 115 EYGKKM 120
            Y K+M
Sbjct: 60  RYEKEM 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

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

 Score = 66.9 bits (164), Expect = 9e-16
 Identities = 35/66 (53%), Positives = 43/66 (65%), Gaps = 1/66 (1%)

Query: 55  PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKS 114
           PKRP SA+F+F +E R   KKENP+ + V+ V K  G KWK +S  EK  YE KAEK K 
Sbjct: 1   PKRPLSAYFLFSQEQRPKLKKENPDAS-VTEVTKILGEKWKELSEEEKKKYEEKAEKDKE 59

Query: 115 EYGKKM 120
            Y K+M
Sbjct: 60  RYEKEM 65

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

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

 Score = 66.8 bits (163), Expect = 2e-14
 Identities = 38/89 (42%), Positives = 51/89 (57%), Gaps = 1/89 (1%)

Query: 38  SKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSM 97
            K + KR  + KKDPN PKRP SA+F++  E R   +KENP +T    VGK    KWK +
Sbjct: 54  KKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKEL 112

Query: 98  SPAEKAPYESKAEKLKSEYGKKMNAYNKK 126
           +  EK PY  +A   +  Y ++   YNKK
Sbjct: 113 TDEEKEPYYKEANSDRERYQREKEEYNKK 141

Length = 211

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

 Score = 61.2 bits (149), Expect = 1e-13
 Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK 113
           KPKRP SAF +F +E R   K ENP+++  + + K  G +WK +S  EKAPYE KA+K K
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDK 59

Query: 114 SEYGKKMNAYN 124
             Y ++M  Y 
Sbjct: 60  ERYEEEMPEYK 70

Length = 70

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

 Score = 57.2 bits (138), Expect = 1e-11
 Identities = 39/91 (42%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 36  SGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTA-VSAVGKAAGGKW 94
              K   ++ K+ KKDPN PKR  SA+  F +E R     ENP +   V+AVGK  G  W
Sbjct: 4   KQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAW 63

Query: 95  KSMSPAEKAPYESKAEKLKSEYGKKMNAYNK 125
             +S  EKAPYE KA++ K  Y K+   Y K
Sbjct: 64  NKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Length = 94

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

 Score = 55.1 bits (133), Expect = 3e-11
 Identities = 29/69 (42%), Positives = 39/69 (56%)

Query: 52  PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEK 111
           PNKPK   +A+F F++  R   K+E P V  V+   K    KWK+MS  EK  YE KA +
Sbjct: 1   PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKARE 60

Query: 112 LKSEYGKKM 120
            K  Y ++M
Sbjct: 61  DKKRYDREM 69

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

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

 Score = 46.9 bits (112), Expect = 5e-08
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 56  KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSE 115
           KRP +AF +F +  R+   +E P      A+ K  G +WK++S  EK PY  +A+KLK  
Sbjct: 3   KRPMNAFMLFSKRHRRKVLQEYPLKEN-RAISKILGDRWKALSNEEKQPYYEEAKKLKEL 61

Query: 116 YGKK 119
           + K 
Sbjct: 62  HMKL 65

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

>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK 113
           K  RP +AF ++ ++     K ENP +T  + + +  G  W+S SP  KA Y+  AE+ K
Sbjct: 1   KIPRPRNAFILYRQDKHAQLKTENPGLTN-NEISRIIGRMWRSESPEVKAYYKELAEEEK 59

Query: 114 SEYGKK 119
             + ++
Sbjct: 60  ERHARE 65

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. Length = 77

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	147
PTZ00199	94	high mobility group protein; Provisional	99.93
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.84
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.83
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.83
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.82
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.82
smart00398	70	HMG high mobility group.	99.81
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.8
KOG0381	96	consensus HMG box-containing protein [General func	99.77
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.75
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.71
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.7
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	99.35
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	99.32
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	99.14
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.61
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.25
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.2
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.18
COG5648	211	NHP6B Chromatin-associated proteins containing the	97.1
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	95.21
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	93.11
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	90.52
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	89.76
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	89.33

>PTZ00199 high mobility group protein; Provisional

Probab=99.93  E-value=2.4e-25  Score=155.28  Aligned_cols=86  Identities=44%  Similarity=0.699  Sum_probs=79.9

Q ss_pred             ccccccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHH
Q 032101           39 KRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYG  117 (147)
Q Consensus        39 kk~~kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~  117 (147)
                      ++.+++++++.+||+.|+||+||||+|++++|..|..+||+++ ++++|+++||++|++||+++|.+|++.|..++++|.
T Consensus         7 ~~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~   86 (94)
T PTZ00199          7 KVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYE   86 (94)
T ss_pred             CccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            4445667778899999999999999999999999999999985 479999999999999999999999999999999999


Q ss_pred             HHHHHHh
Q 032101          118 KKMNAYN  124 (147)
Q Consensus       118 k~~~~Y~  124 (147)
                      .+|.+|+
T Consensus        87 ~e~~~Y~   93 (94)
T PTZ00199         87 KEKAEYA   93 (94)
T ss_pred             HHHHHHh
Confidence            9999996

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

Probab=99.84  E-value=6.4e-21  Score=127.80  Aligned_cols=72  Identities=31%  Similarity=0.517  Sum_probs=69.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      .|+||+||||||+++.|..|+.+||+++ +.+|+++||++|++||+++|++|.++|..++++|..++++|...
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   72 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLT-NNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYT   72 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCccc
Confidence            4899999999999999999999999997 79999999999999999999999999999999999999999875

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=99.83  E-value=2.9e-20  Score=121.08  Aligned_cols=69  Identities=43%  Similarity=0.797  Sum_probs=65.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHh
Q 032101           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (147)
Q Consensus        55 PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~  124 (147)
                      |+||+|||++|+.+++..++.+||+++ +.+|+++||++|++||+++|.+|.+.|..++.+|..++.+|+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~-~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLS-NKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTST-HHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccc-cccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            899999999999999999999999998 799999999999999999999999999999999999999995

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

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

Probab=99.83  E-value=2.6e-20  Score=123.41  Aligned_cols=70  Identities=36%  Similarity=0.527  Sum_probs=67.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        55 PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      .+||+||||+|++++|..++.+||+++ +.+|+++||++|+.||+++|++|.+.|..++++|..++++|+.
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~~-~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~y   71 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLKE-NRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKW   71 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            589999999999999999999999997 7999999999999999999999999999999999999999963

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

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

Probab=99.82  E-value=1e-19  Score=117.38  Aligned_cols=65  Identities=54%  Similarity=0.836  Sum_probs=63.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHH
Q 032101           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM  120 (147)
Q Consensus        55 PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~  120 (147)
                      |++|+|||++|++++|..+..+||+++ +.+|++.||++|++||+++|.+|.+.|..++.+|..+|
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~-~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDAS-VTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            899999999999999999999999997 89999999999999999999999999999999999887

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.

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

Probab=99.82  E-value=5e-20  Score=143.59  Aligned_cols=89  Identities=42%  Similarity=0.689  Sum_probs=84.5

Q ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHH
Q 032101           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA  122 (147)
Q Consensus        43 kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~  122 (147)
                      +...+.++|||.|+||+||||+|+.++|.+|..++|.++ |.+|++.+|++|++|++++|.+|...|..++++|..++..
T Consensus        59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~-~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~  137 (211)
T COG5648          59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEE  137 (211)
T ss_pred             HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCC-hHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHh
Confidence            566778899999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             HhhhCCCCCC
Q 032101          123 YNKKQVTNLV  132 (147)
Q Consensus       123 Y~~~~~~~~~  132 (147)
                      |+.+..+...
T Consensus       138 y~~k~~~~~~  147 (211)
T COG5648         138 YNKKLPNKAP  147 (211)
T ss_pred             hhcccCCCCC
Confidence            9999887753

>smart00398 HMG high mobility group

Probab=99.81  E-value=1.8e-19  Score=116.81  Aligned_cols=70  Identities=47%  Similarity=0.793  Sum_probs=67.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHh
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~  124 (147)
                      +|++|+|+|++|++++|..+..+||+++ +.+|++.||++|+.||+++|.+|.+.|..++.+|..++..|.
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~-~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            5899999999999999999999999997 899999999999999999999999999999999999999984

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

Probab=99.80  E-value=2.3e-19  Score=119.15  Aligned_cols=72  Identities=43%  Similarity=0.785  Sum_probs=63.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHh-CCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHh
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKE-NPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e-~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~  124 (147)
                      |+.||+|+|||+||+.+++..++.+ ++... +.++++.|++.|++||++||.+|.++|..++.+|..+|..|+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~-~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQS-FREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SS-HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCC-HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            6899999999999999999999988 66665 899999999999999999999999999999999999999995

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

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

Probab=99.77  E-value=3.6e-18  Score=118.24  Aligned_cols=76  Identities=49%  Similarity=0.831  Sum_probs=72.3

Q ss_pred             CC--CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHH-HHhhhC
Q 032101           51 DP--NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN-AYNKKQ  127 (147)
Q Consensus        51 dp--~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~-~Y~~~~  127 (147)
                      ||  +.|+||+|||++|+.+.|..++.+||+++ +.+|++++|++|++|++++|.+|...+..++++|..+|. .|+...
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 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLS-VGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            66  59999999999999999999999999987 899999999999999999999999999999999999999 998754

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

Probab=99.75  E-value=9.6e-18  Score=107.52  Aligned_cols=65  Identities=51%  Similarity=0.807  Sum_probs=62.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHH
Q 032101           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM  120 (147)
Q Consensus        55 PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~  120 (147)
                      |+||+|||++|+++.|..+..+||+++ +.+|++.||++|+.|++++|.+|.+.|..++.+|..++
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~-~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLS-VGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            799999999999999999999999997 79999999999999999999999999999999999875

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

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.71  E-value=1.3e-17  Score=139.03  Aligned_cols=79  Identities=32%  Similarity=0.590  Sum_probs=74.3

Q ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 032101           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (147)
Q Consensus        48 ~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~  127 (147)
                      .+......||||||||+|.+..|.+|.++||.+.| .||+++||.+|+.|+++||.+|+++|++++..|.++..+|+.+-
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHN-SEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYRP  134 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHN-SEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYRP  134 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcchhh-HHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCccccc
Confidence            44556789999999999999999999999999997 89999999999999999999999999999999999999998763

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

Probab=99.70  E-value=3e-17  Score=142.08  Aligned_cols=78  Identities=41%  Similarity=0.708  Sum_probs=73.6

Q ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 032101           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (147)
Q Consensus        44 k~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y  123 (147)
                      ++.++.+|||+|||++||||+|++..|..|+.+  +++ +++|++.+|++|+.||.  |.+|++.|+.++++|+.+|.+|
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~-~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~y  599 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GIS-VGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEY  599 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--Cch-HHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhh
Confidence            667788999999999999999999999999987  887 99999999999999999  9999999999999999999999


Q ss_pred             hhh
Q 032101          124 NKK  126 (147)
Q Consensus       124 ~~~  126 (147)
                      +.-
T Consensus       600 k~g  602 (615)
T KOG0526|consen  600 KNG  602 (615)
T ss_pred             cCC
Confidence            943

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

Probab=99.35  E-value=2.2e-12  Score=106.25  Aligned_cols=78  Identities=28%  Similarity=0.558  Sum_probs=73.9

Q ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        48 ~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      ..+.|.+|-+|+-.||.|+..++++|+..||++. +.+|+++||.||..|+++||..|...++.++.+|++.|.+|+..
T Consensus        58 ~pkpPkppekpl~pymrySrkvWd~VkA~nPe~k-LWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~s  135 (410)
T KOG4715|consen   58 RPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELK-LWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNS  135 (410)
T ss_pred             CCCCCCCCCcccchhhHHhhhhhhhhhccCcchH-HHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            4457889999999999999999999999999998 99999999999999999999999999999999999999999764

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=99.32  E-value=2.3e-12  Score=106.96  Aligned_cols=71  Identities=23%  Similarity=0.416  Sum_probs=65.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      ..|+|+||||+|++++|..|..++. ++...+|.++||.+|++||-||.+.|+++|+++++.+......|-+
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEct-lKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSA  261 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECT-LKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA  261 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcch
Confidence            6799999999999999999999996 4446899999999999999999999999999999999988877744

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

Probab=99.14  E-value=1.4e-11  Score=106.11  Aligned_cols=80  Identities=29%  Similarity=0.474  Sum_probs=73.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 032101           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVT  129 (147)
Q Consensus        50 kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~  129 (147)
                      ..++..||||||||+|.++.|..|.+.+|++.| ..|+++||.+|+.||..||++|++.-.++-..|.+..+.|+.+-.+
T Consensus       321 ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHN-SnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPRP  399 (511)
T KOG0528|consen  321 SSEPHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPRP  399 (511)
T ss_pred             CCCccccCCcchhhcccchhhhhhhhcCccccc-cchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCCC
Confidence            334577999999999999999999999999997 6999999999999999999999999999999999999999987655


Q ss_pred             C
Q 032101          130 N  130 (147)
Q Consensus       130 ~  130 (147)
                      .
T Consensus       400 K  400 (511)
T KOG0528|consen  400 K  400 (511)
T ss_pred             C
Confidence            4

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

Probab=98.61  E-value=4.1e-08  Score=87.60  Aligned_cols=76  Identities=26%  Similarity=0.453  Sum_probs=69.7

Q ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHH--HHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHH
Q 032101           43 KREKKAKKDPNKPKRPPSAFFVFLEEFR--KTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK  119 (147)
Q Consensus        43 kk~kk~~kdp~~PKRP~sAy~lF~~e~r--~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~  119 (147)
                      ..+-..+.|....+||||+|++|++.+|  ..+.+.||+..| ..|+++||+.|-.|.+.||+.|.++|.+.++.|.++
T Consensus       170 dgrspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DN-rtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  170 DGRSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDN-RTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             ccCCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccc-hhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            4455566777789999999999999999  899999999997 899999999999999999999999999999999886

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

Probab=98.25  E-value=7.4e-06  Score=55.11  Aligned_cols=74  Identities=19%  Similarity=0.274  Sum_probs=61.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVT  129 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~  129 (147)
                      .|..|-++--+|.+.....+...+++.. ..+ .+.+...|++|++.+|.+|+..|.++..+|+.+|.+|+.-...
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr-~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~   76 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRNDR-KKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPAD   76 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTSTH-HHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHhH-HHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            5778889999999999999999999885 344 5699999999999999999999999999999999999876443

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

Probab=97.20  E-value=0.0007  Score=52.20  Aligned_cols=49  Identities=29%  Similarity=0.480  Sum_probs=42.8

Q ss_pred             CCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHH
Q 032101           59 PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL  112 (147)
Q Consensus        59 ~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~  112 (147)
                      -+||+-|+.++|..    |.+++ ..|+....+..|..||+++|..|..++...
T Consensus        83 nnaYLNFLReFRrk----h~~L~-p~dlI~~AAraW~rLSe~eK~rYrr~~~~~  131 (183)
T PF06382_consen   83 NNAYLNFLREFRRK----HCGLS-PQDLIQRAARAWCRLSEAEKNRYRRMAPSV  131 (183)
T ss_pred             chHHHHHHHHHHHH----ccCCC-HHHHHHHHHHHHHhCCHHHHHHHHhhcchh
Confidence            47899999998875    57897 789999999999999999999999876543

The function of this family is unknown.

>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]

Probab=97.18  E-value=0.00097  Score=51.23  Aligned_cols=49  Identities=33%  Similarity=0.542  Sum_probs=42.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCC
Q 032101           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS   98 (147)
Q Consensus        49 ~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls   98 (147)
                      .+.|.+-.|-+|||..|+++.-.+|+..||+++ ..|.-...+..|...+
T Consensus       116 ~kPPEKRqR~psaYn~f~k~ei~rik~~~p~is-hkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  116 NKPPEKRQRVPSAYNRFMKEEIQRIKAENPDIS-HKEAFSAAAKNWAHFP  164 (170)
T ss_pred             cCCccccCCCchhHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHhhhhCc
Confidence            344555567789999999999999999999998 7999999999998765

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

Probab=97.10  E-value=0.00041  Score=54.74  Aligned_cols=69  Identities=22%  Similarity=0.312  Sum_probs=62.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHH
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN  121 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~  121 (147)
                      ..++..|...|+-+-..+|..+...+|... ..++++++|..|.+|++.-|..|.+.+..++..|...+.
T Consensus       141 k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~-~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         141 KLPNKAPIGPFIENEPKIRPKVEGPSPDKA-LVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             ccCCCCCCchhhhccHHhccccCCCCcchh-hhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            457788888999999999999999999886 789999999999999999999999999999999987654

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

Probab=95.21  E-value=0.031  Score=35.32  Aligned_cols=39  Identities=21%  Similarity=0.422  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCCh
Q 032101           60 SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP   99 (147)
Q Consensus        60 sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~   99 (147)
                      +.|-+|.+-.|..|...||++. ++.|..+++.+|+..++
T Consensus        14 t~yK~Fsq~vRP~l~~~NPk~~-~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   14 TNYKAFSQHVRPLLAKANPKAP-MSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCc-HHHHHHHHHHHHHHHHh
Confidence            5688999999999999999997 89999999999987554

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

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

Probab=93.11  E-value=0.15  Score=37.16  Aligned_cols=50  Identities=22%  Similarity=0.324  Sum_probs=41.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChh
Q 032101           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA  100 (147)
Q Consensus        50 kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~e  100 (147)
                      -|..|-+|---||.-|....-..|+.+||++. .+++-.+|-..|..-++.
T Consensus        68 ~drHPErR~KAAy~afeE~~Lp~lK~E~PgLr-lsQ~kq~l~K~w~KSPeN  117 (122)
T PF06244_consen   68 IDRHPERRMKAAYKAFEERRLPELKEENPGLR-LSQYKQMLWKEWQKSPEN  117 (122)
T ss_pred             CCCCcchhHHHHHHHHHHHHhHHHHhhCCCch-HHHHHHHHHHHHhcCCCC
Confidence            34434455557899999999999999999998 899999999999876653

>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=90.52  E-value=0.87  Score=35.90  Aligned_cols=53  Identities=21%  Similarity=0.353  Sum_probs=38.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHH
Q 032101           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKA  109 (147)
Q Consensus        50 kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A  109 (147)
                      .....++||.|+||.|..=.-.    -.|+.. ..+++..|+..|..=+.  |..|.-.|
T Consensus        39 ~~~~~~kr~lN~Fm~FRsyy~~----~~~~~~-Qk~~S~~l~~lW~~dp~--k~~W~l~a   91 (201)
T PF04769_consen   39 RSPEKAKRPLNGFMAFRSYYSP----IFPPLP-QKELSGILTKLWEKDPF--KNKWSLMA   91 (201)
T ss_pred             ccccccccchhHHHHHHHHHHh----hcCCcC-HHHHHHHHHHHHhCCcc--HhHHHHHh
Confidence            3455789999999999766553    346776 68999999999986332  45555444

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=89.76  E-value=0.91  Score=35.43  Aligned_cols=44  Identities=18%  Similarity=0.511  Sum_probs=38.7

Q ss_pred             HHHHHH-HHHHHhcCCChhhhhhHHHHHHH-HHHHHHHHHHHHhhh
Q 032101           83 VSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNKK  126 (147)
Q Consensus        83 ~~eisk-~lge~Wk~Ls~eeK~~Y~~~A~~-~k~~y~k~~~~Y~~~  126 (147)
                      |..|++ .||..|+.+|+++++.|.+.... ....|-..+..|...
T Consensus        66 f~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~  111 (198)
T TIGR03481        66 LPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGE  111 (198)
T ss_pred             HHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence            778876 68999999999999999998888 778899999999763

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

>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional

Probab=89.33  E-value=1.1  Score=35.36  Aligned_cols=48  Identities=29%  Similarity=0.562  Sum_probs=40.3

Q ss_pred             CCCCcHHHHHH-HHHHHhcCCChhhhhhHHHHHHH-HHHHHHHHHHHHhhh
Q 032101           78 PNVTAVSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNKK  126 (147)
Q Consensus        78 P~~~~~~eisk-~lge~Wk~Ls~eeK~~Y~~~A~~-~k~~y~k~~~~Y~~~  126 (147)
                      |... |..+++ .||..|+++|++++..|.+.... ....|-..+..|...
T Consensus        66 p~~D-f~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q  115 (211)
T PRK15117         66 PYVQ-VKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQ  115 (211)
T ss_pred             ccCC-HHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence            5564 778875 68999999999999999987777 667899999999764

---

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	147
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	9e-26
2lhj_A	97	High mobility group protein homolog NHP1; structur	2e-25
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	2e-24
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	2e-23
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	4e-23
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	5e-23
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	8e-23
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	9e-23
1wgf_A	90	Upstream binding factor 1; transcription factor, D	1e-20
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	2e-20
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	3e-20
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	4e-19
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-14
1ckt_A	71	High mobility group 1 protein; high-mobility group	1e-18
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-17
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	4e-17
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	9e-17
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	2e-12
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	5e-16
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	5e-16
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-14
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	3e-11
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	3e-14
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	6e-14
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	9e-14
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	1e-12
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	4e-12
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	8e-12
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	2e-11
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	2e-11
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	6e-11
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	1e-10
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	2e-10
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	4e-10
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	3e-09
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	3e-09

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

 Score = 91.9 bits (229), Expect = 9e-26
 Identities = 37/77 (48%), Positives = 48/77 (62%), Gaps = 1/77 (1%)

Query: 50  KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKA 109
           KDPN PKRPPSAFF+F  E+R   K E+P ++ +  V K  G  W + +  +K PYE KA
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKA 60

Query: 110 EKLKSEYGKKMNAYNKK 126
            KLK +Y K + AY  K
Sbjct: 61  AKLKEKYEKDIAAYRAK 77

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

 Score = 92.1 bits (229), Expect = 2e-25
 Identities = 33/94 (35%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 36  SGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTA-VSAVGKAAGGKW 94
           +  +   +R +KAKKDPN PKR  S++  F +E R     ENP +   V+A+GK  G  W
Sbjct: 4   ASDRTGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAW 63

Query: 95  KSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQV 128
            ++S  EK PYE  +++ +  Y ++   Y +++V
Sbjct: 64  NALSDEEKKPYERMSDEDRVRYEREKAEYAQRKV 97

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93

 Score = 88.9 bits (221), Expect = 2e-24
 Identities = 38/89 (42%), Positives = 50/89 (56%), Gaps = 1/89 (1%)

Query: 39  KRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
           +   KR  + KKDPN PKR  SA+  F  E R   + ENP++T    VGK  G KWK+++
Sbjct: 5   REPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALT 63

Query: 99  PAEKAPYESKAEKLKSEYGKKMNAYNKKQ 127
           P EK PYE+KA+  K  Y  +   YN   
Sbjct: 64  PEEKQPYEAKAQADKKRYESEKELYNATL 92

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

 Score = 86.2 bits (214), Expect = 2e-23
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYE 106
            K DP KP+   S++  F++  R+  KK++P+ +   S   K    +WK+MS  EK  +E
Sbjct: 1   GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE 60

Query: 107 SKAEKLKSEYGKKMNAYNKKQ 127
             A+  K+ Y ++M  Y   +
Sbjct: 61  DMAKADKARYEREMKTYIPPK 81

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

 Score = 86.3 bits (214), Expect = 4e-23
 Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 1/89 (1%)

Query: 39  KRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
                 +KK KKDPN+P++P SA+ +F  + +   K +NPN T    V K     W  + 
Sbjct: 2   SSGSSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNAT-FGEVSKIVASMWDGLG 60

Query: 99  PAEKAPYESKAEKLKSEYGKKMNAYNKKQ 127
             +K  Y+ K E  K EY K++ AY    
Sbjct: 61  EEQKQVYKKKTEAAKKEYLKQLAAYRASL 89

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

 Score = 85.5 bits (212), Expect = 5e-23
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYES 107
                + PK P + +  FL E R+  +  +P++     + K  G +W  + PAEK  Y  
Sbjct: 1   GSSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPAEKQRYLD 59

Query: 108 KAEKLKSEYGKKMNAYNKKQ 127
           +AEK K +Y K++ AY + +
Sbjct: 60  EAEKEKQQYLKELWAYQQSE 79

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

 Score = 84.7 bits (210), Expect = 8e-23
 Identities = 28/83 (33%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 42  GKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTA-VSAVGKAAGGKWKSMSPA 100
                 AK DP KPK   SA+  F++  R+  KK+NP V    +   K    +WK+MS  
Sbjct: 3   SGSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGK 62

Query: 101 EKAPYESKAEKLKSEYGKKMNAY 123
           EK+ ++  A+  K  Y ++M  Y
Sbjct: 63  EKSKFDEMAKADKVRYDREMKDY 85

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

 Score = 85.2 bits (211), Expect = 9e-23
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 46  KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPY 105
           KK KK P+ PK+P + +F F  E R  + K +P ++    + K    K+K +   +K  Y
Sbjct: 2   KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMKY 60

Query: 106 ESKAEKLKSEYGKKMNAYNKKQ 127
               ++ K E+ + +  + +  
Sbjct: 61  IQDFQREKQEFERNLARFREDH 82

>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 90

 Score = 79.3 bits (196), Expect = 1e-20
 Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 1/89 (1%)

Query: 36  SGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWK 95
           S        ++  K    KPKRP SA F+F EE R+  ++E P ++  S + +     W 
Sbjct: 2   SSGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWN 60

Query: 96  SMSPAEKAPYESKAEKLKSEYGKKMNAYN 124
            +S  +KA Y+++   LK++  +K    +
Sbjct: 61  DLSEKKKAKYKAREAALKAQSERKSGPSS 89

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

 Score = 78.5 bits (194), Expect = 2e-20
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 3/74 (4%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           +KPKRP SA+ ++L   R++ K+ENP +  V+ V K  G  W++M   +K+ +E+KA K 
Sbjct: 2   DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58

Query: 113 KSEYGKKMNAYNKK 126
           K +Y + +  +   
Sbjct: 59  KDDYDRAVKEFEAN 72

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

 Score = 77.7 bits (192), Expect = 3e-20
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           + PKR  +AF ++L + R++ K+ENP +  V+ + K  G  WK +   +K+ +E  A K 
Sbjct: 2   HMPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELK--DKSKWEDAAAKD 58

Query: 113 KSEYGKKMNAYNKK 126
           K  Y  +M  Y  +
Sbjct: 59  KQRYHDEMRNYKPE 72

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

 Score = 77.7 bits (191), Expect = 4e-19
 Identities = 42/114 (36%), Positives = 56/114 (49%), Gaps = 1/114 (0%)

Query: 13  SQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKT 72
           S +     +      KA   +            KK  KDPN PKRPPSAFF+F  E+R  
Sbjct: 60  SAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPK 119

Query: 73  FKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK 126
            K E+P ++ +  V K  G  W + +  +K PYE KA KLK +Y K + AY  K
Sbjct: 120 IKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 172

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

 Score = 65.8 bits (160), Expect = 2e-14
 Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 42  GKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTA-VSAVGKAAGGKWKSMSPA 100
                  K DP KP+   S++  F++  R+  KK++P+ +   S   K    +WK+MS  
Sbjct: 3   SGSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 62

Query: 101 EKAPYESKAEKLKSEYGKKMNAYNKKQ 127
           EK  +E  A+  K+ Y ++M  Y   +
Sbjct: 63  EKGKFEDMAKADKARYEREMKTYIPPK 89

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

 Score = 74.0 bits (182), Expect = 1e-18
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           KP+   S++  F++  R+  KK++P+ +   S   K    +WK+MS  EK  +E  A+  
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 113 KSEYGKKMNAY 123
           K+ Y ++M  Y
Sbjct: 61  KARYEREMKTY 71

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

 Score = 71.3 bits (175), Expect = 2e-17
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYES 107
                +  K+P SA  +F+++ R  F  ENP  + +          WK++S  EK  YE 
Sbjct: 1   GSSGSSGIKKPMSASALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEEEKLKYEE 59

Query: 108 KAEKLKSEYGKKMNAYNKKQ 127
           KA K    Y  +M    +++
Sbjct: 60  KATKDLERYNSQMKRAIEQE 79

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

 Score = 69.6 bits (171), Expect = 4e-17
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK 113
           KPKRP SA+ V++ E  +  K ++P         K     WK++S +EK  Y   A++ +
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDE 56

Query: 114 SEYGKKMNAY 123
           + Y  +M ++
Sbjct: 57  TRYHNEMKSW 66

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

 Score = 72.5 bits (177), Expect = 9e-17
 Identities = 14/81 (17%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 47  KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYE 106
            +    + PK+P S++  F +E    FK +NP+    + + +    +W+ +  ++K  Y+
Sbjct: 2   GSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQ 60

Query: 107 SKAEKLKSEYGKKMNAYNKKQ 127
                    Y ++++ + ++ 
Sbjct: 61  DAYRAEWQVYKEEISRFKEQL 81

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

 Score = 61.3 bits (148), Expect = 2e-12
 Identities = 27/127 (21%), Positives = 50/127 (39%), Gaps = 5/127 (3%)

Query: 2   KGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSA 61
                    +      K               +D   KR+   +KK      KPKRP SA
Sbjct: 62  AYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSA 121

Query: 62  FFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN 121
           + V++ E  +  K ++P         K     WK++S +EK  Y   A++ ++ Y  +M 
Sbjct: 122 YNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMK 176

Query: 122 AYNKKQV 128
           ++ ++ +
Sbjct: 177 SWEEQMI 183

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

 Score = 69.5 bits (170), Expect = 5e-16
 Identities = 43/109 (39%), Positives = 59/109 (54%), Gaps = 1/109 (0%)

Query: 18  KPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKEN 77
            P  ++  K +A   +     K +    KK  KDPN PKRPPSAFF+F  E+R   K E+
Sbjct: 52  WPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEH 111

Query: 78  PNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK 126
           P ++ +  V K  G  W + +  +K PYE KA KLK +Y K + AY  K
Sbjct: 112 PGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 159

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

 Score = 69.5 bits (170), Expect = 5e-16
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ AEK P+  +A+KL
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 113 KSEYGKKMNAYNKKQVTN 130
           ++ + +K   Y  ++   
Sbjct: 62  QAMHREKYPNYKYRKGET 79

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

 Score = 67.6 bits (164), Expect = 1e-14
 Identities = 16/109 (14%), Positives = 45/109 (41%), Gaps = 1/109 (0%)

Query: 28  KAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVG 87
               + + S +  Q      +    + PK+P S++  F +E    FK +NP+    + + 
Sbjct: 15  VPRGSHMASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELI 73

Query: 88  KAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNLVPFFN 136
           +    +W+ +  ++K  Y+         Y ++++ + ++   + +    
Sbjct: 74  RRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLE 122

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

 Score = 58.3 bits (140), Expect = 3e-11
 Identities = 24/89 (26%), Positives = 45/89 (50%), Gaps = 5/89 (5%)

Query: 40  RQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP 99
           R+   +KK      KPKRP SA+ V++ E  +  K ++P         K     WK++S 
Sbjct: 132 RKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSD 186

Query: 100 AEKAPYESKAEKLKSEYGKKMNAYNKKQV 128
           +EK  Y   A++ ++ Y  +M ++ ++ +
Sbjct: 187 SEKELYIQHAKEDETRYHNEMKSWEEQMI 215

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

 Score = 63.6 bits (155), Expect = 3e-14
 Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 34  LDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGK 93
           +D   K       ++ K+    KRP +AF V+ +  R+    + P++   + + K  G  
Sbjct: 9   VDDDDKMSENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLH-NAELSKTLGKL 67

Query: 94  WKSMSPAEKAPYESKAEKLKSE 115
           W+ ++ +EK P+  +AE+L+ +
Sbjct: 68  WRLLNESEKRPFVEEAERLRVQ 89

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

 Score = 62.0 bits (151), Expect = 6e-14
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 42  GKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAE 101
                 +   PNK KRP +AF +F +++R  + +  P      A+    G +WK M   E
Sbjct: 5   SSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKD-NRAISVILGDRWKKMKNEE 63

Query: 102 KAPYESKAEKLKSEYGKK 119
           +  Y  +A+ L  E  + 
Sbjct: 64  RRMYTLEAKALAEEQKRL 81

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

 Score = 61.5 bits (150), Expect = 9e-14
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYES 107
                +  +RP +AF +F +  R   ++E+P +       K     W  + P EK  Y  
Sbjct: 1   GSSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLD-NRGATKILADWWAVLDPKEKQKYTD 59

Query: 108 KAEKLKSEYGKK 119
            A++ K  + K 
Sbjct: 60  MAKEYKDAFMKA 71

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

 Score = 58.4 bits (142), Expect = 1e-12
 Identities = 20/66 (30%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK 113
             +RP +AF V+ ++ RK   ++NP++   + + K  G  WK+++ AEK P+  +AE+L+
Sbjct: 2   SIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLR 60

Query: 114 SEYGKK 119
            ++ + 
Sbjct: 61  VQHMQD 66

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

 Score = 57.2 bits (139), Expect = 4e-12
 Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ AEK P+  +A+KL
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 113 KSEYGKK 119
           ++ + +K
Sbjct: 62  QAMHREK 68

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

 Score = 56.4 bits (137), Expect = 8e-12
 Identities = 20/70 (28%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 50  KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKA 109
              ++ +RP +AF V+ ++ RK   ++NP++   + + K  G  WK+++ AEK P+  +A
Sbjct: 2   SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEA 60

Query: 110 EKLKSEYGKK 119
           E+L+ ++ + 
Sbjct: 61  ERLRVQHMQD 70

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

 Score = 55.3 bits (134), Expect = 2e-11
 Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 56  KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSE 115
           KRP +AF V+ +  R+   +++P++   + + K  G +WK +  ++K P+  +AE+L+ +
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPDMH-NAEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62

Query: 116 YGKK 119
           +   
Sbjct: 63  HMAD 66

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

 Score = 55.3 bits (134), Expect = 2e-11
 Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           ++ KRP +AF V+    R+   +ENP +   S + K  G +WK +S  EK P+  +A++L
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRL 59

Query: 113 KSE 115
           ++ 
Sbjct: 60  RAL 62

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

 Score = 54.1 bits (131), Expect = 6e-11
 Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ AEK P+  +A+KL
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 113 KSEYGKK 119
           ++ + +K
Sbjct: 62  QAMHREK 68

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

 Score = 53.7 bits (130), Expect = 1e-10
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
              KRP +AF V+ ++ R+   +  P++   S + K  G +WK+M+  EK PY  +  +L
Sbjct: 3   PHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYEEQARL 61

Query: 113 KSEYGKK 119
             ++ +K
Sbjct: 62  SKQHLEK 68

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

 Score = 53.0 bits (128), Expect = 2e-10
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 56  KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSE 115
           K+P +AF ++++E R     E+    + +A+ +  G +W ++S  E+A Y   A K +  
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARKERQL 62

Query: 116 YGKK 119
           + + 
Sbjct: 63  HMQL 66

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

 Score = 52.7 bits (126), Expect = 4e-10
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 41  QGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
               + K K D    K PP+++ ++  E     K                  +WK +S  
Sbjct: 4   GSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERM-----VLCSQQWKLLSQK 58

Query: 101 EKAPYESKAEKLKSEYGKKMNAYNKK 126
           EK  Y  K ++ K +Y  ++  + + 
Sbjct: 59  EKDAYHKKCDQKKKDYEVELLRFLES 84

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

 Score = 50.3 bits (120), Expect = 3e-09
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 55  PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKS 114
            K P + +  F +E     +  +  +          G +W+ +S ++K  Y+  AE+ + 
Sbjct: 9   KKPPMNGYQKFSQELLSNGELNHLPLKERM---VEIGSRWQRISQSQKEHYKKLAEEQQR 65

Query: 115 EYGKKMNAYNKKQ 127
           +Y   ++ + K  
Sbjct: 66  QYKVHLDLWVKSL 78

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

 Score = 49.8 bits (118), Expect = 3e-09
 Identities = 15/73 (20%), Positives = 33/73 (45%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
               RP + F ++LEE R     +NP+ +  + + K    +++ +S  E+  + +KA+  
Sbjct: 4   GSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE 63

Query: 113 KSEYGKKMNAYNK 125
            +  G +      
Sbjct: 64  TASEGTEAKKRKS 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	147
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.93
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.93
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.92
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.92
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.92
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.91
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.91
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.91
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.91
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.91
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.9
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.9
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.9
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.89
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.89
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.89
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.88
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.88
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.88
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.87
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.87
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.87
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.87
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.87
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.87
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.87
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.86
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.86
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.85
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.85
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.84
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.84
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.81
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.8
2cto_A	93	Novel protein; high mobility group box domain, hel	99.8
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.78
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.78
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.77
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.72

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

Probab=99.93  E-value=1.3e-25  Score=157.36  Aligned_cols=88  Identities=35%  Similarity=0.616  Sum_probs=82.2

Q ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHH
Q 032101           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA  122 (147)
Q Consensus        43 kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~  122 (147)
                      .+++++++||+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++|++++|++|.++|..++++|..+|.+
T Consensus         6 ~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~   84 (102)
T 2co9_A            6 SGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNAT-FGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAA   84 (102)
T ss_dssp             CCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSC-HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344567799999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             HhhhCCCCC
Q 032101          123 YNKKQVTNL  131 (147)
Q Consensus       123 Y~~~~~~~~  131 (147)
                      |+.+.....
T Consensus        85 Y~~~~~~~~   93 (102)
T 2co9_A           85 YRASLVSKS   93 (102)
T ss_dssp             HHHHHTSSC
T ss_pred             HHhhccccc
Confidence            999877654

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

Probab=99.93  E-value=1.7e-25  Score=152.03  Aligned_cols=81  Identities=35%  Similarity=0.586  Sum_probs=75.9

Q ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHH
Q 032101           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA  122 (147)
Q Consensus        44 k~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~  122 (147)
                      +.++.++||++|+||+||||+|++++|..|+.+||+++ +|.+|+++||++|++||+++|.+|++.|..++++|..+|.+
T Consensus         5 ~~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~   84 (86)
T 2eqz_A            5 SSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKD   84 (86)
T ss_dssp             CSSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456799999999999999999999999999999997 37999999999999999999999999999999999999999


Q ss_pred             Hh
Q 032101          123 YN  124 (147)
Q Consensus       123 Y~  124 (147)
                      |+
T Consensus        85 Y~   86 (86)
T 2eqz_A           85 YG   86 (86)
T ss_dssp             HC
T ss_pred             cC
Confidence            94

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

Probab=99.92  E-value=2.9e-25  Score=154.96  Aligned_cols=83  Identities=25%  Similarity=0.482  Sum_probs=78.4

Q ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        46 kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      +++++||++|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|++|.+.|..++++|..+|.+|..
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~   80 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE   80 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSC-SHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGG
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999998 6999999999999999999999999999999999999999998


Q ss_pred             hCCC
Q 032101          126 KQVT  129 (147)
Q Consensus       126 ~~~~  129 (147)
                      ....
T Consensus        81 ~~P~   84 (99)
T 1k99_A           81 DHPD   84 (99)
T ss_dssp             CCCC
T ss_pred             HCCC
Confidence            7543

>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=99.92  E-value=4.4e-25  Score=146.66  Aligned_cols=76  Identities=47%  Similarity=0.873  Sum_probs=73.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        49 ~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      ++||+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..+|.+|+.
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCC-HHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999999999999997 8999999999999999999999999999999999999999975

>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=99.92  E-value=9e-26  Score=155.64  Aligned_cols=84  Identities=45%  Similarity=0.776  Sum_probs=79.3

Q ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHH
Q 032101           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA  122 (147)
Q Consensus        43 kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~  122 (147)
                      ++.++..+||+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..+|.+
T Consensus         9 ~~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~   87 (93)
T 1cg7_A            9 KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKEL   87 (93)
T ss_dssp             CCCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSC-HHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHH
T ss_pred             cccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355667799999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             HhhhC
Q 032101          123 YNKKQ  127 (147)
Q Consensus       123 Y~~~~  127 (147)
                      |+.++
T Consensus        88 Y~~~~   92 (93)
T 1cg7_A           88 YNATL   92 (93)
T ss_dssp             HHHHT
T ss_pred             HHHcc
Confidence            99864

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

Probab=99.91  E-value=1.5e-25  Score=155.46  Aligned_cols=88  Identities=36%  Similarity=0.679  Sum_probs=80.3

Q ss_pred             cccccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHH
Q 032101           40 RQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK  118 (147)
Q Consensus        40 k~~kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k  118 (147)
                      ..+++.++..+||+.|+||+||||||++++|..|+.+||+++ ++.+|+++||++|++||+++|.+|++.|..++++|..
T Consensus         8 ~~k~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~   87 (97)
T 2lhj_A            8 TGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYER   87 (97)
T ss_dssp             SSCCCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHH
T ss_pred             ccccccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            334556778899999999999999999999999999999985 1489999999999999999999999999999999999


Q ss_pred             HHHHHhhhC
Q 032101          119 KMNAYNKKQ  127 (147)
Q Consensus       119 ~~~~Y~~~~  127 (147)
                      +|.+|+.+.
T Consensus        88 e~~~y~~~~   96 (97)
T 2lhj_A           88 EKAEYAQRK   96 (97)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhcC
Confidence            999998763

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

Probab=99.91  E-value=3e-24  Score=147.64  Aligned_cols=77  Identities=31%  Similarity=0.606  Sum_probs=74.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        49 ~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      .+||++|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|++|.++|..++++|..+|.+|+.+
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~   78 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQS   78 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCC-HHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            479999999999999999999999999999997 89999999999999999999999999999999999999999875

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

Probab=99.91  E-value=5.3e-25  Score=148.44  Aligned_cols=79  Identities=32%  Similarity=0.583  Sum_probs=74.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 032101           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (147)
Q Consensus        49 ~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~  127 (147)
                      ++||++|+||+||||+|++++|..|+.+||+++ +|.+|+++||++|++||+++|.+|.++|..++++|..+|.+|+...
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~   81 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK   81 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            579999999999999999999999999999986 2589999999999999999999999999999999999999998753

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

Probab=99.91  E-value=4.2e-24  Score=146.88  Aligned_cols=79  Identities=28%  Similarity=0.412  Sum_probs=75.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 032101           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVT  129 (147)
Q Consensus        50 kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~  129 (147)
                      .||++|+||+||||+|++++|..|+.+||+++ +.+|+++||++|++|++++|.+|.++|..++++|..+|.+|+.+...
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~~   81 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQ   81 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSC-HHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            68999999999999999999999999999998 89999999999999999999999999999999999999999987543

>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=99.91  E-value=3.6e-25  Score=151.76  Aligned_cols=79  Identities=30%  Similarity=0.560  Sum_probs=73.4

Q ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHH
Q 032101           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA  122 (147)
Q Consensus        43 kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~  122 (147)
                      ++.+++.+||+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++|++++|++|+++|..++++|..+|..
T Consensus         9 ~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~   87 (90)
T 1wgf_A            9 PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGP   87 (90)
T ss_dssp             SCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSS
T ss_pred             CCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455677799999999999999999999999999999997 8999999999999999999999999999999999876643

>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=99.90  E-value=3.1e-24  Score=146.13  Aligned_cols=79  Identities=27%  Similarity=0.441  Sum_probs=74.9

Q ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHh
Q 032101           45 EKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (147)
Q Consensus        45 ~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~  124 (147)
                      .++..+||+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++|++++|++|+++|..++++|..++++|+
T Consensus         8 ~~~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A            8 GTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKD-NRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             SSCCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            3357789999999999999999999999999999997 799999999999999999999999999999999999999885

>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=99.90  E-value=1.1e-23  Score=138.87  Aligned_cols=72  Identities=36%  Similarity=0.732  Sum_probs=69.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      +++||||+||||||++++|..|+.+||+++ +.+|+++||++|++|++  |++|++.|..++++|..+|++|+.+
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~k   72 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCC-HHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999999999998 89999999999999998  9999999999999999999999875

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

Probab=99.90  E-value=4.7e-24  Score=141.34  Aligned_cols=75  Identities=32%  Similarity=0.530  Sum_probs=70.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        51 dp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      ||+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|++|.++|..++++|..++.+|+.+
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~   75 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCS-SSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCCC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence            7899999999999999999999999999998 69999999999999999999999999999999999999999753

>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=99.89  E-value=3.3e-23  Score=135.43  Aligned_cols=70  Identities=31%  Similarity=0.607  Sum_probs=67.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y  123 (147)
                      .||||+||||+|++++|..|+.+||+++ +|.+|+++||++|++||+++|.+|.+.|..++++|..+|.+|
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            5999999999999999999999999997 379999999999999999999999999999999999999887

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

Probab=99.89  E-value=2.9e-23  Score=136.85  Aligned_cols=72  Identities=33%  Similarity=0.693  Sum_probs=69.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      |++|+||+||||+|++++|..|+.+||+++ +.+|+++||++|++|  ++|.+|.+.|..++++|..+|.+|+.+
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 SHMPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCC-HHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            789999999999999999999999999997 899999999999999  899999999999999999999999864

>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=99.89  E-value=5.1e-23  Score=139.44  Aligned_cols=76  Identities=32%  Similarity=0.521  Sum_probs=72.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 032101           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (147)
Q Consensus        51 dp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~  127 (147)
                      .|+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..++.+|..+.
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   76 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccCC
Confidence            4789999999999999999999999999997 799999999999999999999999999999999999999998764

>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=99.88  E-value=1.5e-22  Score=151.01  Aligned_cols=79  Identities=48%  Similarity=0.865  Sum_probs=75.8

Q ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        46 kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      ++..+||+.|+||+||||+|++++|..|+.+||+++ +.+|+++||++|++||+++|++|.+.|..++++|..+|.+|+.
T Consensus        80 kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~-~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A           80 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             GGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccccccccccccccchhhHhhHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            456789999999999999999999999999999997 8999999999999999999999999999999999999999986

>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=99.88  E-value=1.6e-23  Score=140.84  Aligned_cols=76  Identities=24%  Similarity=0.464  Sum_probs=73.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        50 kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      .|++.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|++|.++|..++++|..+|.+|+.+
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~   78 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLD-NRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSG   78 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSC-TTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcC
Confidence            58999999999999999999999999999997 69999999999999999999999999999999999999999865

>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=99.88  E-value=1.9e-22  Score=138.99  Aligned_cols=78  Identities=17%  Similarity=0.204  Sum_probs=73.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNL  131 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~~~  131 (147)
                      .|.|+||+|||+||++++|..++.+||+ . +.+|++.||++|++|++++|++|++.|..++++|+++|.+|+.+....+
T Consensus         2 ~~kPKrP~SAy~lf~~~~r~~~k~~~p~-~-~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~~~~   79 (91)
T 1l8y_A            2 GKLPESPKRAEEIWQQSVIGDYLARFKN-D-RVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATN   79 (91)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHHTTS-T-HHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGSSS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCC-C-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc
Confidence            3689999999999999999999999999 4 8999999999999999999999999999999999999999998876533

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

Probab=99.87  E-value=1.4e-22  Score=142.80  Aligned_cols=78  Identities=26%  Similarity=0.517  Sum_probs=70.6

Q ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        48 ~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      ..+|++.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++|++++|++|.++|..++++|..++++|+.+
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~  100 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLH-NAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQ  100 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC-
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcC
Confidence            4578999999999999999999999999999997 89999999999999999999999999999999999999999865

>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=99.87  E-value=1.5e-22  Score=135.36  Aligned_cols=74  Identities=31%  Similarity=0.565  Sum_probs=70.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~  127 (147)
                      +.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..+|.+|+.+.
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   74 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRP   74 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccCC
Confidence            47999999999999999999999999997 799999999999999999999999999999999999999998653

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

Probab=99.87  E-value=7.9e-23  Score=133.39  Aligned_cols=71  Identities=30%  Similarity=0.581  Sum_probs=63.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHh
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~  124 (147)
                      +.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..++++|+
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            46899999999999999999999999998 799999999999999999999999999999999999999885

>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=99.87  E-value=1.3e-22  Score=136.38  Aligned_cols=75  Identities=28%  Similarity=0.547  Sum_probs=69.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        51 dp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      .++.|+||+||||||++++|..|..+||+++ +.+|+++||++|++|++++|.+|.+.|..++++|..++++|+.+
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~   77 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYR   77 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeC
Confidence            4678999999999999999999999999998 79999999999999999999999999999999999999999865

>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=1.1e-22  Score=144.07  Aligned_cols=81  Identities=21%  Similarity=0.387  Sum_probs=74.1

Q ss_pred             cccCCCCCCC-CCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHh
Q 032101           46 KKAKKDPNKP-KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (147)
Q Consensus        46 kk~~kdp~~P-KRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~  124 (147)
                      .++.+|++.| |||+||||+|++++|..|+    +++ +.+|+++||++|++|++++|.+|.++|..++++|..+|.+|.
T Consensus         8 ~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~~-~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~   82 (108)
T 1v64_A            8 QLKDKFDGRPTKPPPNSYSLYCAELMANMK----DVP-STERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFL   82 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456899999 9999999999999999986    676 899999999999999999999999999999999999999999


Q ss_pred             hhCCCCC
Q 032101          125 KKQVTNL  131 (147)
Q Consensus       125 ~~~~~~~  131 (147)
                      ..+.+..
T Consensus        83 ~~~~~~~   89 (108)
T 1v64_A           83 ESLPEEE   89 (108)
T ss_dssp             HHSCHHH
T ss_pred             hhCCHHH
Confidence            9876543

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

Probab=99.87  E-value=5.6e-22  Score=149.93  Aligned_cols=80  Identities=49%  Similarity=0.868  Sum_probs=76.3

Q ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        46 kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      ++..+||+.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|++|.++|..++++|..+|.+|+.
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 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  171 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSC-HHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            445679999999999999999999999999999997 8999999999999999999999999999999999999999987


Q ss_pred             h
Q 032101          126 K  126 (147)
Q Consensus       126 ~  126 (147)
                      +
T Consensus       172 k  172 (173)
T 2yrq_A          172 K  172 (173)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.87  E-value=4.1e-22  Score=135.15  Aligned_cols=74  Identities=22%  Similarity=0.389  Sum_probs=70.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~  127 (147)
                      ..|+||+||||||++++|..|..+||+++ +.+|+++||++|++||+++|++|.+.|..++++|..++++|..+.
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   74 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARD   74 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCC
Confidence            36999999999999999999999999997 799999999999999999999999999999999999999998653

>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=99.86  E-value=3.6e-22  Score=132.98  Aligned_cols=73  Identities=25%  Similarity=0.499  Sum_probs=70.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      +.|+||+||||||++++|..|..+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..++++|+.+
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~   73 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMH-NAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYR   73 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeC
Confidence            57999999999999999999999999998 79999999999999999999999999999999999999999865

>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=99.86  E-value=3.3e-22  Score=134.12  Aligned_cols=74  Identities=30%  Similarity=0.522  Sum_probs=68.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      ++.|+||+||||||++++|..|+.+||+++ +.+|+++||++|++||+++|++|.+.|..++++|..++++|..+
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   75 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYK   75 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCC-HHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC---
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeec
Confidence            578999999999999999999999999998 79999999999999999999999999999999999999999865

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

Probab=99.85  E-value=1.2e-21  Score=126.90  Aligned_cols=66  Identities=32%  Similarity=0.536  Sum_probs=62.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y  123 (147)
                      |.||||+|||++|++++|..++.+||     .+|+++||++|++||+++|.+|.+.|..++++|..+|.+|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            58999999999999999999987664     6999999999999999999999999999999999999998

>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=99.85  E-value=7.2e-21  Score=133.14  Aligned_cols=79  Identities=18%  Similarity=0.315  Sum_probs=69.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 032101           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVT  129 (147)
Q Consensus        50 kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~  129 (147)
                      ...++||||+||||||+++++.  ..++++++ +.||+++||++|++|++++|++|+++|..++++|..+|.+|...+.+
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~~-~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~   80 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHLP-LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSP   80 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            3567999999999999999964  23445575 89999999999999999999999999999999999999999998876


Q ss_pred             CC
Q 032101          130 NL  131 (147)
Q Consensus       130 ~~  131 (147)
                      ..
T Consensus        81 ~~   82 (101)
T 1v63_A           81 QD   82 (101)
T ss_dssp             TH
T ss_pred             HH
Confidence            64

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

Probab=99.84  E-value=4.3e-21  Score=145.08  Aligned_cols=82  Identities=30%  Similarity=0.557  Sum_probs=76.0

Q ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 032101           45 EKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (147)
Q Consensus        45 ~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y  123 (147)
                      .+..++||++|+||+||||||++++|..|+.+||+++ ++.+|+++||++|++||+++|.+|.+.|..++++|..+|.+|
T Consensus         6 ~k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y   85 (173)
T 2yrq_A            6 SGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   85 (173)
T ss_dssp             CSSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            3456789999999999999999999999999999941 389999999999999999999999999999999999999999


Q ss_pred             hhh
Q 032101          124 NKK  126 (147)
Q Consensus       124 ~~~  126 (147)
                      ...
T Consensus        86 ~~~   88 (173)
T 2yrq_A           86 IPP   88 (173)
T ss_dssp             CCC
T ss_pred             hhh
Confidence            764

>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=99.84  E-value=3.1e-21  Score=130.21  Aligned_cols=63  Identities=22%  Similarity=0.378  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHH
Q 032101           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL  112 (147)
Q Consensus        50 kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~  112 (147)
                      .+++.||||+||||||++++|..|+.+||+++++.+|+++||++|++|++++|++|+++|..+
T Consensus         1 ~~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            1 GSSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            378999999999999999999999999999964799999999999999999999999999887

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

Probab=99.81  E-value=3.2e-20  Score=147.30  Aligned_cols=80  Identities=18%  Similarity=0.390  Sum_probs=75.9

Q ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 032101           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (147)
Q Consensus        48 ~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~  127 (147)
                      ...||++|+||+|||+||++++|..|+.+||+++ +.+|+++||++|++|++++|.+|++.|..++++|+.+|..|...+
T Consensus        35 s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~  113 (238)
T 3tmm_A           35 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQL  113 (238)
T ss_dssp             CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4578999999999999999999999999999998 899999999999999999999999999999999999999997655


Q ss_pred             C
Q 032101          128 V  128 (147)
Q Consensus       128 ~  128 (147)
                      .
T Consensus       114 ~  114 (238)
T 3tmm_A          114 T  114 (238)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.80  E-value=6.6e-20  Score=143.43  Aligned_cols=77  Identities=18%  Similarity=0.407  Sum_probs=73.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 032101           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQV  128 (147)
Q Consensus        51 dp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~  128 (147)
                      +|++|+||+|||++|++++|..|+.+||+++ +.+|+++||++|++||+++|.+|++.|..++++|..+|..|...+.
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~t   82 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLT   82 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCC
Confidence            4789999999999999999999999999998 8999999999999999999999999999999999999999986554

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

Probab=99.80  E-value=2.6e-20  Score=128.87  Aligned_cols=70  Identities=20%  Similarity=0.391  Sum_probs=65.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHH---HHHhcCCChhhhhhHHHHHHHHHHHHHHHHH
Q 032101           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAA---GGKWKSMSPAEKAPYESKAEKLKSEYGKKMN  121 (147)
Q Consensus        49 ~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l---ge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~  121 (147)
                      ..+++.||||+||||||++++|.+|+.+  +++ +.||+++|   |++|++|++++|++|+++|.++++.|++++.
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~~-~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~   77 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--GLP-VARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPG   77 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--TCC-CSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--CCC-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcccc
Confidence            4678999999999999999999999988  676 68999999   9999999999999999999999999998863

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

Probab=99.78  E-value=7.6e-21  Score=130.77  Aligned_cols=69  Identities=23%  Similarity=0.292  Sum_probs=62.3

Q ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHH
Q 032101           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK  118 (147)
Q Consensus        46 kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k  118 (147)
                      .+..+|||+|+||+|||||||+++|..|+.+||+++ .+.+|+    ++|++|++++|++|+++|+.++++|..
T Consensus        14 ~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~   83 (90)
T 2yuk_A           14 LKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRI   83 (90)
T ss_dssp             HHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            455679999999999999999999999999999994 046776    999999999999999999999999875

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

Probab=99.78  E-value=3e-20  Score=145.39  Aligned_cols=78  Identities=28%  Similarity=0.430  Sum_probs=71.3

Q ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        46 kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      ++..+||+.|+||+||||+||+++|..|+.+|     ..+|+++||++|++|++++|++|.+.|..++++|..+|.+|+.
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~-----p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  180 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  180 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSSCSS-----HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhccCC-----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34568999999999999999999999987655     4599999999999999999999999999999999999999999


Q ss_pred             hCC
Q 032101          126 KQV  128 (147)
Q Consensus       126 ~~~  128 (147)
                      +..
T Consensus       181 ~~~  183 (214)
T 3tq6_A          181 QMI  183 (214)
T ss_dssp             HHH
T ss_pred             hCc
Confidence            853

>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=3.3e-20  Score=147.18  Aligned_cols=78  Identities=29%  Similarity=0.470  Sum_probs=71.4

Q ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        46 kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      ++..+||+.|+||+|||||||+++|..|+.+||     .+|+++||++|++|++++|++|+++|..++++|+.+|.+|+.
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  212 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  212 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSSH-----HHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhccCH-----HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445689999999999999999999999876554     589999999999999999999999999999999999999999


Q ss_pred             hCC
Q 032101          126 KQV  128 (147)
Q Consensus       126 ~~~  128 (147)
                      +..
T Consensus       213 k~~  215 (238)
T 3tmm_A          213 QMI  215 (238)
T ss_dssp             HHH
T ss_pred             hCc
Confidence            853

>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=99.72  E-value=1e-17  Score=124.72  Aligned_cols=74  Identities=32%  Similarity=0.550  Sum_probs=70.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      ++.|+||+||||+|+.+.|..|..+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..+|..|...
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~   75 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccc
Confidence            678999999999999999999999999997 89999999999999999999999999999999999999999653

---

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	147
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	4e-18
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-16
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	9e-16
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-15
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	7e-15
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	1e-14
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-14
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	4e-14
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	1e-13
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-12
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	8e-12
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-10

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93

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

 Score = 72.2 bits (177), Expect = 4e-18
 Identities = 38/88 (43%), Positives = 50/88 (56%), Gaps = 1/88 (1%)

Query: 39  KRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
           +   KR  + KKDPN PKR  SA+  F  E R   + ENP++T    VGK  G KWK+++
Sbjct: 5   REPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALT 63

Query: 99  PAEKAPYESKAEKLKSEYGKKMNAYNKK 126
           P EK PYE+KA+  K  Y  +   YN  
Sbjct: 64  PEEKQPYEAKAQADKKRYESEKELYNAT 91

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

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

 Score = 66.5 bits (162), Expect = 5e-16
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 46  KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPY 105
           KK KK P+ PK+P + +F F  E R  + K +P ++    + K    K+K +   +K  Y
Sbjct: 2   KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMKY 60

Query: 106 ESKAEKLKSEYGKKMNAYNKK 126
               ++ K E+ + +  + + 
Sbjct: 61  IQDFQREKQEFERNLARFRED 81

>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 = 65.6 bits (160), Expect = 9e-16
 Identities = 34/74 (45%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           N PKRPPSAFF+F  E+R   K E+P ++ +  V K  G  W + +  +K PYE KA KL
Sbjct: 1   NAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKL 59

Query: 113 KSEYGKKMNAYNKK 126
           K +Y K + AY  K
Sbjct: 60  KEKYEKDIAAYRAK 73

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

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

 Score = 64.2 bits (156), Expect = 3e-15
 Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 1/89 (1%)

Query: 36  SGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWK 95
           S        ++  K    KPKRP SA F+F EE R+  ++E P ++  S + +     W 
Sbjct: 2   SSGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWN 60

Query: 96  SMSPAEKAPYESKAEKLKSEYGKKMNAYN 124
            +S  +KA Y+++   LK++  +K    +
Sbjct: 61  DLSEKKKAKYKAREAALKAQSERKSGPSS 89

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73

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

 Score = 62.9 bits (153), Expect = 7e-15
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 3/74 (4%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           +KPKRP SA+ ++L   R++ K+ENP +  V+ V K  G  W++M   +K+ +E+KA K 
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58

Query: 113 KSEYGKKMNAYNKK 126
           K +Y + +  +   
Sbjct: 59  KDDYDRAVKEFEAN 72

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

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

 Score = 62.9 bits (153), Expect = 1e-14
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           ++ KRP +AF V+    R+   +ENP +   S + K  G +WK +S  EK P+  +A++L
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRL 59

Query: 113 KSEYGKKMNAYNKK 126
           ++ + K+   Y  +
Sbjct: 60  RALHMKEHPDYKYR 73

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

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

 Score = 62.6 bits (152), Expect = 1e-14
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTA-VSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           KP+   S++  F++  R+  KK++P+ +   S   K    +WK+MS  EK  +E  A+  
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 113 KSEYGKKMNAY 123
           K+ Y ++M  Y
Sbjct: 61  KARYEREMKTY 71

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

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

 Score = 61.0 bits (148), Expect = 4e-14
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK 113
             KRP +AF V+ ++ R+   +  P++   S + K  G +WK+M+  EK PY  +  +L 
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQARLS 60

Query: 114 SEYGKKMNAY 123
            ++ +K   Y
Sbjct: 61  KQHLEKYPDY 70

>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 = 60.2 bits (146), Expect = 1e-13
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL 112
           ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ AEK P+  +A+KL
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 113 KSEYGKKMNAYNKK 126
           ++ + +K   Y  +
Sbjct: 62  QAMHREKYPNYKYR 75

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

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

 Score = 56.4 bits (136), Expect = 4e-12
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 49  KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESK 108
                  K P + +  F +E     +  +  +          G +W+ +S ++K  Y+  
Sbjct: 3   SGSSGPKKPPMNGYQKFSQELLSNGELNHLPLKERM---VEIGSRWQRISQSQKEHYKKL 59

Query: 109 AEKLKSEYGKKMNAYNKKQ 127
           AE+ + +Y   ++ + K  
Sbjct: 60  AEEQQRQYKVHLDLWVKSL 78

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

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

 Score = 55.6 bits (134), Expect = 8e-12
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 56  KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSE 115
           K+P +AF ++++E R     E+      +A+ +  G +W ++S  E+A Y   A K +  
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQL 62

Query: 116 YGKKMNAYNKK 126
           + +    ++ +
Sbjct: 63  HMQLYPGWSAR 73

>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 = 53.0 bits (127), Expect = 1e-10
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 41  QGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
               + K K D    K PP+++ ++  E     K                  +WK +S  
Sbjct: 4   GSSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPST-----ERMVLCSQQWKLLSQK 58

Query: 101 EKAPYESKAEKLKSEYGKKMNAYNKK 126
           EK  Y  K ++ K +Y  ++  + + 
Sbjct: 59  EKDAYHKKCDQKKKDYEVELLRFLES 84

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	147
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.92
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.91
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.9
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.88
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.87
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.86
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.84
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.84
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.82
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.82
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	96.67

>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=99.92  E-value=9.8e-25  Score=148.93  Aligned_cols=85  Identities=45%  Similarity=0.763  Sum_probs=79.8

Q ss_pred             cccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHH
Q 032101           42 GKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN  121 (147)
Q Consensus        42 ~kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~  121 (147)
                      +++..+..+||+.|+||+|||+||+.++|..|+.+||+++ +.+|++.||++|++||+++|.+|.+.|..++++|..+|.
T Consensus         8 ~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~-~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~   86 (93)
T d1lwma_           8 KKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKE   86 (93)
T ss_dssp             TSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCc-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455667789999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             HHhhhC
Q 032101          122 AYNKKQ  127 (147)
Q Consensus       122 ~Y~~~~  127 (147)
                      +|+.++
T Consensus        87 ~y~~~l   92 (93)
T d1lwma_          87 LYNATL   92 (93)
T ss_dssp             HHHHHH
T ss_pred             HHHhcc
Confidence            999874

>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=99.91  E-value=9e-25  Score=144.76  Aligned_cols=78  Identities=44%  Similarity=0.806  Sum_probs=75.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCCCC
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTNL  131 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~~~  131 (147)
                      |+||||+||||+|+.++|..|+.+||+++ +.+|+++||++|++||+++|.+|.+.|..++++|..+|.+|+.++.+++
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~-~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~~~a   78 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDA   78 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCC-TTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCC
Confidence            68999999999999999999999999997 7999999999999999999999999999999999999999999987765

>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=99.90  E-value=8.2e-24  Score=143.40  Aligned_cols=84  Identities=25%  Similarity=0.464  Sum_probs=79.7

Q ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhh
Q 032101           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (147)
Q Consensus        46 kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~  125 (147)
                      ++.++||+.|+||+|||+||++++|..|..+||+++ +.+|++.||++|+.||+++|.+|.+.|..++.+|..+|.+|..
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~-~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~   80 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE   80 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSC-SHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGG
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999998 7999999999999999999999999999999999999999998


Q ss_pred             hCCCC
Q 032101          126 KQVTN  130 (147)
Q Consensus       126 ~~~~~  130 (147)
                      ...+.
T Consensus        81 ~~pe~   85 (91)
T d1k99a_          81 DHPDL   85 (91)
T ss_dssp             CCCCC
T ss_pred             HCccc
Confidence            86654

>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=99.88  E-value=3.8e-23  Score=137.67  Aligned_cols=73  Identities=32%  Similarity=0.574  Sum_probs=70.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      +.|+||+||||||++++|.+|+.+||+++ +.+|+++||++|++|++++|.+|+++|..++++|..+|++|+..
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~-~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~   73 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR   73 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCC
Confidence            57999999999999999999999999997 89999999999999999999999999999999999999999765

>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=99.88  E-value=8.5e-23  Score=137.14  Aligned_cols=75  Identities=32%  Similarity=0.534  Sum_probs=71.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 032101           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQV  128 (147)
Q Consensus        53 ~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~  128 (147)
                      |.|+||+||||||++++|..|..+||+++ +.+|+++||++|++||+++|.+|++.|..++.+|..+|++|+.+..
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~~-~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p~   77 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPR   77 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCCC
Confidence            68999999999999999999999999998 8999999999999999999999999999999999999999987643

>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=99.87  E-value=1.6e-22  Score=132.04  Aligned_cols=73  Identities=36%  Similarity=0.750  Sum_probs=68.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 032101           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (147)
Q Consensus        52 p~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~  127 (147)
                      .|.||||+||||||+.++|..|+.+||+++ +.+|+++||++|++|+  +|++|.+.|..++++|..+|.+|+.++
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~~-~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~g   73 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEANG   73 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTCC-HHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            378999999999999999999999999997 8999999999999885  599999999999999999999998763

>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=99.86  E-value=3.8e-22  Score=129.32  Aligned_cols=70  Identities=31%  Similarity=0.607  Sum_probs=66.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y  123 (147)
                      .||||+||||+|+.++|..|+.+||+.. ++.+|+++||++|++||+++|.+|.++|..++++|..+|.+|
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            4899999999999999999999999743 368999999999999999999999999999999999999887

>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=99.86  E-value=1.7e-22  Score=131.08  Aligned_cols=69  Identities=30%  Similarity=0.553  Sum_probs=65.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y  123 (147)
                      .+|||+||||||++++|..|..+||+++ +++|+++||++|++||+++|++|.+.|+.++++|.+++++|
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCC-HHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            4689999999999999999999999998 79999999999999999999999999999999999887765

>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=99.84  E-value=3.6e-21  Score=129.34  Aligned_cols=76  Identities=21%  Similarity=0.372  Sum_probs=70.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCCC
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTN  130 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~~  130 (147)
                      ..+||+||||||++++|..|..+||+++ +.+|+++||++|++||+++|++|.++|..++++|..++++|.......
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~-~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~~   77 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG   77 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCCC
Confidence            4689999999999999999999999997 799999999999999999999999999999999999999998664443

>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=99.84  E-value=1.9e-21  Score=131.26  Aligned_cols=76  Identities=32%  Similarity=0.585  Sum_probs=69.5

Q ss_pred             ccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHH
Q 032101           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK  119 (147)
Q Consensus        43 kk~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~  119 (147)
                      ......+.|++.|+||+||||||++++|.+|+.+||+++ +.+|+++||++|++|++++|.+|.++|..++++|.++
T Consensus         9 ~~~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~-~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_           9 PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             SCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            344556789999999999999999999999999999997 8999999999999999999999999999998887643

>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=1.7e-20  Score=130.76  Aligned_cols=81  Identities=21%  Similarity=0.347  Sum_probs=73.0

Q ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 032101           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (147)
Q Consensus        44 k~kk~~kdp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y  123 (147)
                      ...+.+.|+.+|++|+||||||++++|.+    +|+++ +.+|+++||++|++||+++|++|.++|..++.+|..+|.+|
T Consensus         7 ~~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~~-~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y   81 (108)
T d1v64a_           7 GQLKDKFDGRPTKPPPNSYSLYCAELMAN----MKDVP-STERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRF   81 (108)
T ss_dssp             CCSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCcHHHHHHHHHHHH----ccCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44556688899999999999999999875    57886 79999999999999999999999999999999999999999


Q ss_pred             hhhCCC
Q 032101          124 NKKQVT  129 (147)
Q Consensus       124 ~~~~~~  129 (147)
                      ..++.+
T Consensus        82 ~~~~~~   87 (108)
T d1v64a_          82 LESLPE   87 (108)
T ss_dssp             HHHSCH
T ss_pred             HhhCCH
Confidence            987654

>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=99.82  E-value=2.5e-20  Score=128.05  Aligned_cols=77  Identities=17%  Similarity=0.327  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhhCCCC
Q 032101           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQVTN  130 (147)
Q Consensus        51 dp~~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~~~~~  130 (147)
                      ..++||||+||||||++++|..+...|  ++ +.+|+++||++|++||+++|++|.++|..++++|..+|.+|.....+.
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~~--~~-~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~~   81 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELNH--LP-LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTT--SC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcC--CC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHH
Confidence            356899999999999999999987655  44 789999999999999999999999999999999999999999887654

>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=96.67  E-value=0.0089  Score=37.40  Aligned_cols=71  Identities=18%  Similarity=0.224  Sum_probs=59.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhcCCChhhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 032101           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (147)
Q Consensus        54 ~PKRP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~lge~Wk~Ls~eeK~~Y~~~A~~~k~~y~k~~~~Y~~~  126 (147)
                      .|--|-+|--+|-+.+-..+...+-+-  -.-..+.+...|++|...|+.+|...|.++..+|+.++-+-+.-
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~D--R~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~~   73 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKND--RVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP   73 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTST--HHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhh--HHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            466778899999998888888777554  24667778889999999999999999999999999988776543