Citrus Sinensis ID: 030283

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180
Protein Sequence
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEASGEEEHQLEPEPEPEQDEDEEVEEDEDDEEDDDD
Secondary Structure (PSIPRED)
ccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccHHHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHcccccccccccccccHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHccHHHcccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEEEcHHHcHHHHHcccccccHHHHHHHHHHHHHHccHHHccHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHccccccccccHHHcccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mkgakgkgaarvsqealkpndrkvgkRKAATAkldsgskrqgkrekkakkdpnkpkrppsaFFVFLEEFRKTFkkenpnvtaVSAVgkaaggkwksmspaekapyesKAEKLKSEYGKKMnaynkkqdgdeasdksksevndedeasgeeehqlepepepeqdedeeveededdeedddd
Flexible Loop (DISEMBL)
mkgakgkgaarvsqealkpndrkvgkrkaatakldsgskrqgkrekkakkdpnkpkrppsAFFVFLEEFRKTfkkenpnvtavsavgkaaggkwksmspaekapyeskAEKLKSEYGKKMnaynkkqdgdeasdkskseVNDEdeasgeeehqlepepepeqdedeeveededdeedddd
Low Complexity Region (SEG)
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSkrqgkrekkakkdpnkpkrppSAFFVFLEEFRKTFKKENPNvtavsavgkaaggkwkSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEASGeeehqlepepepeqdedeeveededdeedddd
Disordered region (IsUnstruct)
************************************************************AFFVFLEEFRKTFK**********************************************************************************************************
Disordered Region (DISOPRED)
*********************************************************PPSAFFVFLEEFRKTFK**NPN*TAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK*************************************************************
Disordered Region (DISEMBL)
********************************************************RPPSAFFVFLEEFRKTFKKENPNVTAVSAVG*************************KSEYGKKMNAYNK*******************************************************
Disordered Region (DISPRO)
*************************K**AATAKLDSGSKR*********KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK******************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEASGEEEHQLEPEPEPEQDEDEEVEEDEDDEEDDDD
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	180	2.2.26 [Sep-21-2011]
O49595	178	High mobility group B pro	yes	no	0.805	0.814	0.693	5e-46
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.572	0.715	0.644	5e-30
O49596	144	High mobility group B pro	no	no	0.544	0.680	0.676	2e-27
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.45	0.532	0.765	3e-27
Q42344	138	High mobility group B pro	no	no	0.711	0.927	0.480	9e-27
P93047	141	High mobility group B pro	no	no	0.588	0.751	0.618	7e-26
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.511	0.617	0.621	1e-24
P27347	157	DNA-binding protein MNB1B	N/A	no	0.594	0.681	0.550	2e-24
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.594	0.664	0.523	7e-22
O49597	125	High mobility group B pro	no	no	0.5	0.72	0.488	1e-18

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

 Score =  183 bits (465), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 104/150 (69%), Positives = 122/150 (81%), Gaps = 5/150 (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 MNAYNKK-QDGDEASDKSKSEVNDEDEASG 148
           M+AYNK  ++G + S+KS+SE+NDEDEASG
Sbjct: 118 MDAYNKNLEEGSDESEKSRSEINDEDEASG 147

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

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

 Score =  130 bits (327), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 69/107 (64%), Positives = 85/107 (79%), Gaps = 4/107 (3%)

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

Query: 103 APYESKAEKLKSEYGKKMNAYNKKQ----DGDEASDKSKSEVNDEDE 145
           AP+ SKAEK K EY K + AYNKKQ      +E SDKS+SEVND+DE
Sbjct: 84  APFISKAEKRKQEYEKNLQAYNKKQAAGAAEEEESDKSRSEVNDDDE 130

Ipomoea nil (taxid: 35883)

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

 Score =  121 bits (304), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 69/102 (67%), Positives = 80/102 (78%), Gaps = 4/102 (3%)

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

Query: 104 PYESKAEKLKSEYGKKMNAYNKK-QDG---DEASDKSKSEVN 141
           PY +KAEK K EY K + AYNKK ++G   DE SDKS SEVN
Sbjct: 87  PYVAKAEKRKVEYEKNIKAYNKKLEEGPKEDEESDKSVSEVN 128

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  121 bits (303), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 62/81 (76%), Positives = 67/81 (82%)

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

Query: 107 SKAEKLKSEYGKKMNAYNKKQ 127
           +K+EK K EY K M AYNKKQ
Sbjct: 96  AKSEKRKVEYEKNMRAYNKKQ 116

Glycine max (taxid: 3847)

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

 Score =  119 bits (299), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 75/156 (48%), Positives = 91/156 (58%), Gaps = 28/156 (17%)

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 NAYNKKQDG-----DEASDKSKSEVNDEDEASGEEE 151
             YN K        ++ SDKSKSEV   DEA  EEE
Sbjct: 101 QQYNLKLASGTNREEDDSDKSKSEV---DEAVSEEE 133

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 =  116 bits (291), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 68/110 (61%), Positives = 83/110 (75%), Gaps = 4/110 (3%)

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-QDG---DEASDKSKSEVN 141
           S+S +EKAPY +KA+K K EY K M AYNKK ++G   DE SDKS SEVN
Sbjct: 76  SLSDSEKAPYVAKADKRKVEYEKNMKAYNKKLEEGPKEDEESDKSVSEVN 125

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  112 bits (281), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 59/95 (62%), Positives = 73/95 (76%), Gaps = 3/95 (3%)

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

Query: 110 EKLKSEYGKKMNAYNKKQDG---DEASDKSKSEVN 141
            K K EY   + AYNKK +G   +E SDKSKSEVN
Sbjct: 100 LKKKEEYEITLQAYNKKLEGKDDEEGSDKSKSEVN 134

Vicia faba (taxid: 3906)

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

 Score =  111 bits (278), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 71/129 (55%), Positives = 84/129 (65%), Gaps = 22/129 (17%)

Query: 1   MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGK----REKKAKKDPNKPK 56
           MKGAK KGAA+                  A AKL   SK   K    R+ KA KDPNKPK
Sbjct: 1   MKGAKSKGAAK------------------ADAKLAVKSKGAEKPAKGRKGKAGKDPNKPK 42

Query: 57  RPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEY 116
           R PSAFFVF+EEFRK FK++NP   +V+AVGKAAG +WKS+S ++KAPY +KA KLK EY
Sbjct: 43  RAPSAFFVFMEEFRKEFKEKNPKNKSVAAVGKAAGDRWKSLSESDKAPYVAKANKLKLEY 102

Query: 117 GKKMNAYNK 125
            K + AYNK
Sbjct: 103 NKAIAAYNK 111

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

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

 Score =  103 bits (256), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 68/130 (52%), Positives = 82/130 (63%), Gaps = 23/130 (17%)

Query: 1   MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSK-----RQGKREKKAKKDPNKP 55
           MKGAK KGAA+                  A AKL   SK         ++ 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|O49597|HMGB5_ARATH High mobility group B protein 5 OS=Arabidopsis thaliana GN=HMGB5 PE=2 SV=1

 Score = 92.8 bits (229), Expect = 1e-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	180
255574381	171	DNA-binding protein MNB1B, putative [Ric	0.8	0.842	0.754	1e-46
449461783	169	PREDICTED: high mobility group B protein	0.811	0.863	0.710	2e-46
297819892	185	hypothetical protein ARALYDRAFT_323737 [	0.811	0.789	0.701	1e-45
42572635	185	high mobility group protein B1 [Arabidop	0.811	0.789	0.695	3e-45
15231065	178	high mobility group protein B1 [Arabidop	0.805	0.814	0.693	2e-44
312281849	185	unnamed protein product [Thellungiella h	0.766	0.745	0.678	5e-41
334185909	161	high mobility group protein B1 [Arabidop	0.766	0.857	0.678	2e-40
351725417	169	uncharacterized protein LOC100305961 [Gl	0.805	0.857	0.710	9e-40
224112525	176	high mobility group family [Populus tric	0.794	0.812	0.632	3e-39
407971018	166	uncharacterized protein LOC100499704 [Gl	0.766	0.831	0.724	6e-39

>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 =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 114/151 (75%), Positives = 128/151 (84%), Gaps = 7/151 (4%)

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-----DGDEASDKSKSEVNDEDE 145
           MNAYNKKQ     DG+E SD+SKSEVNDED+
Sbjct: 120 MNAYNKKQESTADDGEEESDRSKSEVNDEDD 150

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  190 bits (482), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 108/152 (71%), Positives = 123/152 (80%), Gaps = 6/152 (3%)

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 MNAYNKKQDG----DEASDKSKSEVNDEDEAS 147
           M AY+ K+      DE S++SKSEVNDEDEAS
Sbjct: 120 MRAYDSKKVASAADDEESERSKSEVNDEDEAS 151

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  187 bits (476), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 106/151 (70%), Positives = 123/151 (81%), Gaps = 5/151 (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 MNAYNKK-QDGDEASDKSKSEVNDEDEASGE 149
           M+AYNK  ++G + S+KS+SEVNDEDEASGE
Sbjct: 118 MDAYNKNMEEGSDESEKSRSEVNDEDEASGE 148

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

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 =  186 bits (472), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 105/151 (69%), Positives = 123/151 (81%), Gaps = 5/151 (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 MNAYNKK-QDGDEASDKSKSEVNDEDEASGE 149
           M+AYNK  ++G + S+KS+SE+NDEDEASGE
Sbjct: 118 MDAYNKNLEEGSDESEKSRSEINDEDEASGE 148

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 =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 104/150 (69%), Positives = 122/150 (81%), Gaps = 5/150 (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 MNAYNKK-QDGDEASDKSKSEVNDEDEASG 148
           M+AYNK  ++G + S+KS+SE+NDEDEASG
Sbjct: 118 MDAYNKNLEEGSDESEKSRSEINDEDEASG 147

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  172 bits (436), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 97/143 (67%), Positives = 115/143 (80%), Gaps = 5/143 (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 MNAYNKK-QDGDEASDKSKSEVN 141
           M+AYNK  ++G + S+KS+SEVN
Sbjct: 118 MDAYNKNMEEGSDESEKSRSEVN 140

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

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 =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 97/143 (67%), Positives = 115/143 (80%), Gaps = 5/143 (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 MNAYNKK-QDGDEASDKSKSEVN 141
           M+AYNK  ++G + S+KS+SE+N
Sbjct: 118 MDAYNKNLEEGSDESEKSRSEIN 140

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725417|ref|NP_001235556.1| uncharacterized protein LOC100305961 [Glycine max] gi|255627113|gb|ACU13901.1| unknown [Glycine max]

 Score =  168 bits (425), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 108/152 (71%), Positives = 119/152 (78%), Gaps = 7/152 (4%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGKGAAR S+E+LKP +DRKVGKRKA+     S   R  K+EKKAKKDPNKPKRPP
Sbjct: 1   MKTAKGKGAARPSKESLKPVDDRKVGKRKASGKPEKS---RAPKKEKKAKKDPNKPKRPP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAF VFLEEFRKTFK ENP V AVS VGKA G KWKS+S AEKAPYE+KA K K+EY K 
Sbjct: 58  SAFLVFLEEFRKTFKAENPLVKAVSVVGKAGGEKWKSLSSAEKAPYEAKAAKRKAEYEKL 117

Query: 120 MNAYNKKQDG---DEASDKSKSEVNDEDEASG 148
           + AY KKQ     D+ SDKSKSEVNDED+ASG
Sbjct: 118 IKAYEKKQASSADDDESDKSKSEVNDEDDASG 149

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 100/158 (63%), Positives = 114/158 (72%), Gaps = 15/158 (9%)

Query: 1   MKGAKGKGAARV-SQEALKP-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------------DGDEASDKSKSEVNDED 144
            M AYNKKQ            D  E S KSKSEVN ++
Sbjct: 120 LMTAYNKKQDTDDGDDDDNDDDNIEQSHKSKSEVNGQN 157

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|407971018|ref|NP_001238631.1| uncharacterized protein LOC100499704 [Glycine max] gi|255625939|gb|ACU13314.1| unknown [Glycine max]

 Score =  165 bits (418), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 105/145 (72%), Positives = 114/145 (78%), Gaps = 7/145 (4%)

Query: 1   MKGAKGKGAARVSQEALKP-NDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPP 59
           MK AKGKGAAR S+E+LKP +DRKVGKRKA+      G     K+EKKAKKDPNKPKRPP
Sbjct: 1   MKNAKGKGAARASKESLKPVDDRKVGKRKASG---KPGRSSAPKKEKKAKKDPNKPKRPP 57

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK 119
           SAFFVFLEEFRKTFK ENPNV AVS VGKA G KWKS+S AEKAPYESKA K K+EY K 
Sbjct: 58  SAFFVFLEEFRKTFKAENPNVKAVSVVGKAGGEKWKSLSSAEKAPYESKAAKRKAEYEKL 117

Query: 120 MNAYNKKQDG---DEASDKSKSEVN 141
           + AY+KKQ     DE SDKSKSEVN
Sbjct: 118 IKAYDKKQASSADDEESDKSKSEVN 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	180
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.483	0.604	0.560	5.4e-23
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.483	0.630	0.442	4.8e-17
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.472	0.68	0.321	2.1e-10
ZFIN|ZDB-GENE-030131-341	205	hmgb1a "high-mobility group bo	0.472	0.414	0.404	4.7e-09
TAIR|locus:2154433	241	HMGB6 "high-mobility group box	0.466	0.348	0.337	1.1e-08
ZFIN|ZDB-GENE-050417-290	198	hmgb3b "high-mobility group bo	0.472	0.429	0.348	2.6e-08
RGD|1559962	209	RGD1559962 "similar to High mo	0.472	0.406	0.361	1.1e-07
UNIPROTKB|P40618	202	HMGB3 "High mobility group pro	0.472	0.420	0.355	1.2e-07
UNIPROTKB|F1N927	214	HMGB1 "High mobility group pro	0.472	0.397	0.368	2.2e-07
UNIPROTKB|Q9YH06	215	HMG1 "High mobility group 1 pr	0.472	0.395	0.368	2.2e-07

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

 Score = 235 (87.8 bits), Expect = 5.4e-23, Sum P(2) = 5.4e-23
 Identities = 51/91 (56%), Positives = 61/91 (67%)

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

Query:   120 MNAYNKK-QDG---DEASDKSKSEVNDEDEA 146
             + AYNKK ++G   DE SDKS SEVNDED+A
Sbjct:   103 IKAYNKKLEEGPKEDEESDKSVSEVNDEDDA 133

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 = 169 (64.5 bits), Expect = 4.8e-17, Sum P(2) = 4.8e-17
 Identities = 42/95 (44%), Positives = 54/95 (56%)

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

Query:   120 MNAYNKK-QDG----DEASDKSKSEVND---EDEA 146
             +  YN K   G    ++ SDKSKSEV++   E+EA
Sbjct:   100 VQQYNLKLASGTNREEDDSDKSKSEVDEAVSEEEA 134

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 = 122 (48.0 bits), Expect = 2.1e-10, Sum P(2) = 2.1e-10
 Identities = 28/87 (32%), Positives = 45/87 (51%)

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

Query:   120 MNAYNKK-QDGDEAS-DKSKSEVNDED 144
             M  YN +  +G++ + D  K E   +D
Sbjct:    99 MQQYNMELANGNKTTGDDEKQEKAADD 125

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 = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 36/89 (40%), Positives = 42/89 (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 MNAYNKKQD--GDEASDKSKSE-VNDEDE 145
             + AY  K    G  A   SK +  NDEDE
Sbjct:   158 IAAYRSKGKVGGGAAKAPSKPDKANDEDE 186

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

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

 Score = 133 (51.9 bits), Expect = 1.1e-08, P = 1.1e-08
 Identities = 29/86 (33%), Positives = 46/86 (53%)

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

Query:   120 MNAYNKKQDGDEASDKSKSEVNDEDE 145
             + + N   + +E  +K   +V+D +E
Sbjct:   179 LES-NDADEEEEDEEKQSDDVDDAEE 203

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

ZFIN|ZDB-GENE-050417-290 hmgb3b "high-mobility group box 3b" [Danio rerio (taxid:7955)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 30/86 (34%), Positives = 45/86 (52%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             S FF+F  E R   K +NP+                ++S +EK P+ S A+KLK +Y K 
Sbjct:    99 SGFFLFCAEQRPIIKAQNPSLGIGDVAKKLGGMWN-NLSDSEKQPFLSNADKLKDKYQKD 157

Query:   120 MNAYNKKQDGDEASDKSKSEVNDEDE 145
             M  Y KK  G  +S KS+ + +D+D+
Sbjct:   158 MAFYRKKGSGGSSSAKSEPKDDDDDD 183

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

 Score = 122 (48.0 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 34/94 (36%), Positives = 40/94 (42%)

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 MNAYN--------KKQDGDEASDKSKSEVNDEDE 145
             + AY         KK  G     K K+E  DE+E
Sbjct:   159 IAAYRAKGKSEVGKKGPGRPTGSKKKNEPEDEEE 192

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 121 (47.7 bits), Expect = 1.2e-07, P = 1.2e-07
 Identities = 32/90 (35%), Positives = 44/90 (48%)

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

Query:   120 MNAYNKKQ--DGDE--ASDKSKSEVNDEDE 145
             +  Y  K   DG +  A+  ++ +V +EDE
Sbjct:   157 VADYKSKGKFDGAKGAATKAARKKVEEEDE 186

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

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

 Score = 120 (47.3 bits), Expect = 2.2e-07, P = 2.2e-07
 Identities = 35/95 (36%), Positives = 42/95 (44%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  EFR   K E+P                 + +  +K PYE KA KLK +Y K 
Sbjct:   100 SAFFLFCSEFRPKIKGEHPGLSIGDVAKKLGEMWNNTAAD-DKQPYEKKAAKLKEKYEKD 158

Query:   120 MNAYNKKQDGD---------EASDKSKSEVNDEDE 145
             + AY  K   D         E S K K E  DEDE
Sbjct:   159 IAAYRAKGKVDAGKKVVAKAEKSKKKKEEEEDEDE 193

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

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

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0009986 "cell surface" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

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

GO:0030324 "lung development" evidence=IEA

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

GO:0043005 "neuron projection" evidence=IEA

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

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

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

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

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

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

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

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

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

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

 Score = 120 (47.3 bits), Expect = 2.2e-07, P = 2.2e-07
 Identities = 35/95 (36%), Positives = 42/95 (44%)

Query:    60 SAFFVFLEEFRKTFKKENPNXXXXXXXXXXXXXXXXSMSPAEKAPYESKAEKLKSEYGKK 119
             SAFF+F  EFR   K E+P                 + +  +K PYE KA KLK +Y K 
Sbjct:   100 SAFFLFCSEFRPKIKGEHPGLSIGDVAKKLGEMWNNTAAD-DKQPYEKKAAKLKEKYEKD 158

Query:   120 MNAYNKKQDGD---------EASDKSKSEVNDEDE 145
             + AY  K   D         E S K K E  DEDE
Sbjct:   159 IAAYRAKGKVDAGKKVVAKAEKSKKKKEEEEDEDE 193

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

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

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0009986 "cell surface" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

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

GO:0030324 "lung development" evidence=IEA

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

GO:0043005 "neuron projection" evidence=IEA

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

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

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

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

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

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

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

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

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

---

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	0.6933	0.8055	0.8146	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	180
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-16
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	3e-14
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	5e-13
smart00398	70	smart00398, HMG, high mobility group	3e-11
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	1e-10
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	3e-09
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	8e-09
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	2e-07
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	1e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	5e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	8e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.001
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.001
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.002
pfam09184	285	pfam09184, PPP4R2, PPP4R2	0.002

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

 Score = 69.2 bits (170), Expect = 3e-16
 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 = 63.8 bits (156), Expect = 3e-14
 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 = 60.7 bits (148), Expect = 5e-13
 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|197700 smart00398, HMG, high mobility group

 Score = 56.2 bits (136), Expect = 3e-11
 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|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

 Score = 57.6 bits (139), Expect = 1e-10
 Identities = 38/100 (38%), Positives = 51/100 (51%), Gaps = 1/100 (1%)

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

Query: 98  SPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSK 137
           +  EK PY  +A   +  Y ++   YNKK           
Sbjct: 113 TDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAPIGPFI 152

Length = 211

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

 Score = 51.4 bits (123), Expect = 3e-09
 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 = 49.7 bits (119), Expect = 8e-09
 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 = 46.1 bits (110), Expect = 2e-07
 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 = 43.8 bits (104), Expect = 1e-06
 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

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 25/84 (29%), Positives = 51/84 (60%), Gaps = 2/84 (2%)

Query: 98  SPAEKAPYESKA-EKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEASGEEEHQLEP 156
           +  E A  E++  +KL++E  ++M    +  + +E S +S  +++DE E   ++   L  
Sbjct: 259 TEEELAKEEAERLKKLEAERLRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLG- 317

Query: 157 EPEPEQDEDEEVEEDEDDEEDDDD 180
           + E +++E+E+  +DED+E+DDDD
Sbjct: 318 QGEEDEEEEEDGVDDEDEEDDDDD 341

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 38.9 bits (91), Expect = 8e-04
 Identities = 32/183 (17%), Positives = 60/183 (32%), Gaps = 10/183 (5%)

Query: 5    KGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFV 64
            K K   +   +    +       +    K    S ++ K +K      ++     S+  +
Sbjct: 1206 KRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDL 1265

Query: 65   FLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN 124
              E   K   K    V               +      +P + K +K        +    
Sbjct: 1266 SKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKK 1325

Query: 125  KKQDGDEASDKSKSEVNDEDEASGEEEHQLEPEP-------EPEQDEDEEVEEDEDDEED 177
            K +       KSK+ V     AS  +  +L   P         E D+D EV++ ED++++
Sbjct: 1326 KSEKKTARKKKSKTRVKQ---ASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDSEDEDDE 1382

Query: 178  DDD 180
            DD+
Sbjct: 1383 DDE 1385

Length = 1388

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 22/174 (12%), Positives = 50/174 (28%)

Query: 7   KGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFL 66
           K AA+   +     +      ++     +   +         K   +  +          
Sbjct: 22  KLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKT 81

Query: 67  EEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK 126
                  K                  K  ++   +   Y    + L        +  +  
Sbjct: 82  AAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDD 141

Query: 127 QDGDEASDKSKSEVNDEDEASGEEEHQLEPEPEPEQDEDEEVEEDEDDEEDDDD 180
            D D+  D    E +DED+   + + + E + E ++ E    ++D   +EDD +
Sbjct: 142 LDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSE 195

Length = 509

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 1/94 (1%)

Query: 88  KAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEAS 147
             A G+    S  E         K ++E   ++ A  K +   E   ++K   +  +  +
Sbjct: 653 TEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEA 712

Query: 148 GEEEHQLEPEPEPEQDEDE-EVEEDEDDEEDDDD 180
            E EH+ E E E  +DE E E  E+ ++ ED+ +
Sbjct: 713 EEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGE 746

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 29/177 (16%), Positives = 64/177 (36%), Gaps = 8/177 (4%)

Query: 12  VSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEF-- 69
            ++E  K   +K+  +  +   +     ++    KK   +         +  V   +   
Sbjct: 11  AAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDAT 70

Query: 70  -----RKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEK-APYESKAEKLKSEYGKKMNAY 123
                +K  K       A +   K    +  S   AEK    +   +    +    +N  
Sbjct: 71  ESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQA 130

Query: 124 NKKQDGDEASDKSKSEVNDEDEASGEEEHQLEPEPEPEQDEDEEVEEDEDDEEDDDD 180
           +   D D+  D    +++D+D+   ++E   + + + E +E +E +E E   +DDD 
Sbjct: 131 DDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDF 187

Length = 509

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 19/75 (25%), Positives = 41/75 (54%)

Query: 105 YESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEASGEEEHQLEPEPEPEQDE 164
            + K + L+  Y K+ +     QD        K++ +D++E   ++   +E +   E +E
Sbjct: 211 SQDKNKSLEEYYEKESSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEE 270

Query: 165 DEEVEEDEDDEEDDD 179
           +EE EE+E++E++D+
Sbjct: 271 EEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	180
PTZ00199	94	high mobility group protein; Provisional	99.91
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.82
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.81
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.8
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.78
smart00398	70	HMG high mobility group.	99.78
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.77
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.77
KOG0381	96	consensus HMG box-containing protein [General func	99.72
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.71
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.67
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.6
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	99.31
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	99.26
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	99.1
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.56
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.16
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	96.8
COG5648	211	NHP6B Chromatin-associated proteins containing the	96.71
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	96.33
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	95.41
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	94.52
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	92.93
KOG3223	221	consensus Uncharacterized conserved protein [Funct	92.56
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	86.63
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	82.58
PF05494	170	Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro:	80.09

>PTZ00199 high mobility group protein; Provisional

Probab=99.91  E-value=7.3e-24  Score=153.09  Aligned_cols=85  Identities=44%  Similarity=0.694  Sum_probs=78.6

Q ss_pred             cccccccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHH
Q 030283           40 RQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK  118 (180)
Q Consensus        40 kk~kk~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~  118 (180)
                      +.+++++++.+||++|+||+|||||||+++|..|..+||++. ++.+|+++||++|+.||+++|.+|+.+|..++.+|..
T Consensus         8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~   87 (94)
T PTZ00199          8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEK   87 (94)
T ss_pred             ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence            444555667899999999999999999999999999999985 4889999999999999999999999999999999999


Q ss_pred             HHHHHh
Q 030283          119 KMNAYN  124 (180)
Q Consensus       119 e~~~y~  124 (180)
                      +|.+|.
T Consensus        88 e~~~Y~   93 (94)
T PTZ00199         88 EKAEYA   93 (94)
T ss_pred             HHHHHh
Confidence            999996

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

Probab=99.82  E-value=2.4e-20  Score=129.55  Aligned_cols=73  Identities=30%  Similarity=0.509  Sum_probs=70.2

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~  127 (180)
                      +|+||+|||||||+++|..|+.+||+++ +.+|+++||.+|+.|++++|.+|..+|..++.+|..+|+.|+...
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p   73 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLT-NNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTP   73 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccC
Confidence            5899999999999999999999999997 899999999999999999999999999999999999999998754

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

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

Probab=99.81  E-value=9.2e-20  Score=125.15  Aligned_cols=71  Identities=35%  Similarity=0.522  Sum_probs=68.2

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      +.|||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+++.|+.
T Consensus         1 ~iKrP~naf~~F~~~~r~~~~~~~p~~~-~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~y   71 (72)
T cd01388           1 HIKRPMNAFMLFSKRHRRKVLQEYPLKE-NRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKW   71 (72)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            4689999999999999999999999997 8999999999999999999999999999999999999999964

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

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

Probab=99.80  E-value=2.3e-19  Score=121.11  Aligned_cols=69  Identities=43%  Similarity=0.797  Sum_probs=65.6

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (180)
Q Consensus        55 PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~  124 (180)
                      |+||+|||+|||.+++..|+.+||+++ +.+|+++||++|+.|++++|.+|...|..++.+|..+|..|+
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 899999999999999999999999999999999999999995

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

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

Probab=99.78  E-value=8.7e-19  Score=117.15  Aligned_cols=65  Identities=54%  Similarity=0.836  Sum_probs=63.4

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHH
Q 030283           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM  120 (180)
Q Consensus        55 PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~  120 (180)
                      |++|+|||+||++++|..++..||+++ +.+|++.||.+|+.||+++|.+|...|..++.+|..+|
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.

>smart00398 HMG high mobility group

Probab=99.78  E-value=1.2e-18  Score=117.20  Aligned_cols=70  Identities=47%  Similarity=0.793  Sum_probs=67.8

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~  124 (180)
                      +|++|+|||+||++++|..+..+||+++ +.+|+++||.+|+.|++++|.+|..+|..++.+|..+|..|+
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

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

Probab=99.77  E-value=8.6e-19  Score=141.41  Aligned_cols=87  Identities=43%  Similarity=0.719  Sum_probs=81.9

Q ss_pred             ccccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHH
Q 030283           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA  122 (180)
Q Consensus        43 kk~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~  122 (180)
                      +..+++.++||.|+||+||||||+..+|..|...+|.++ |.+|+++||++|++|++++|++|...|..++.+|..++..
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            455677899999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             HhhhCCCC
Q 030283          123 YNKKQDGD  130 (180)
Q Consensus       123 y~~~~~~~  130 (180)
                      |..++...
T Consensus       138 y~~k~~~~  145 (211)
T COG5648         138 YNKKLPNK  145 (211)
T ss_pred             hhcccCCC
Confidence            99988533

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

Probab=99.77  E-value=1.4e-18  Score=119.50  Aligned_cols=72  Identities=43%  Similarity=0.785  Sum_probs=63.3

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHh-CCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283           52 PNKPKRPPSAFFVFLEEFRKTFKKE-NPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (180)
Q Consensus        52 p~~PKrP~sAy~lF~~e~r~~ik~e-~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~  124 (180)
                      |++||+|+|||+||+.+++..++.. ++.+. +.+|++.|+.+|+.||+++|.+|..+|..++.+|..+|..|+
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            7899999999999999999999988 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=99.72  E-value=5.1e-17  Score=116.70  Aligned_cols=76  Identities=49%  Similarity=0.831  Sum_probs=72.2

Q ss_pred             CC--CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHH-HHhhhC
Q 030283           51 DP--NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN-AYNKKQ  127 (180)
Q Consensus        51 dp--~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~-~y~~~~  127 (180)
                      +|  +.|++|+|||++||.+.|..++.+||+++ +.+|+++||++|++|++++|.+|...|..++.+|..+|. .|+..+
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            56  59999999999999999999999999987 999999999999999999999999999999999999999 988754

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

Probab=99.71  E-value=5.4e-17  Score=107.89  Aligned_cols=65  Identities=51%  Similarity=0.807  Sum_probs=62.7

Q ss_pred             CCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHH
Q 030283           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKM  120 (180)
Q Consensus        55 PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~  120 (180)
                      |++|+|||+||++++|..++..||+++ +.+|++.||.+|+.|++++|.+|...|...+.+|...+
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            899999999999999999999999997 89999999999999999999999999999999999875

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=99.67  E-value=6.9e-17  Score=139.68  Aligned_cols=87  Identities=30%  Similarity=0.540  Sum_probs=79.1

Q ss_pred             ccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        47 k~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      .......+.||||||||||++..|..|..+||.+. -.||++.||.+|+.|++++|.+|++.|++++..|.++++.|+.+
T Consensus        55 ~~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mH-NSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYR  133 (331)
T KOG0527|consen   55 KDKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMH-NSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYR  133 (331)
T ss_pred             cCCCCccccCCCcchhhhhhHHHHHHHHHhCcchh-hHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccc
Confidence            34566789999999999999999999999999997 58999999999999999999999999999999999999999998


Q ss_pred             CCCCcccc
Q 030283          127 QDGDEASD  134 (180)
Q Consensus       127 ~~~~~~s~  134 (180)
                      -.......
T Consensus       134 PRRKkk~~  141 (331)
T KOG0527|consen  134 PRRKKKKR  141 (331)
T ss_pred             cccccccc
Confidence            87554433

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

Probab=99.60  E-value=9.1e-16  Score=137.62  Aligned_cols=77  Identities=42%  Similarity=0.722  Sum_probs=72.3

Q ss_pred             cccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        44 k~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      +..++.+|||+||||+||||||++..|..|+..  +++ +++|++.+|++|+.|+.  |.+|...|+.++++|+.+|.+|
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            445678999999999999999999999999987  887 99999999999999999  9999999999999999999999


Q ss_pred             hh
Q 030283          124 NK  125 (180)
Q Consensus       124 ~~  125 (180)
                      +.
T Consensus       600 k~  601 (615)
T KOG0526|consen  600 KN  601 (615)
T ss_pred             cC
Confidence            94

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=99.31  E-value=2.4e-12  Score=110.41  Aligned_cols=75  Identities=21%  Similarity=0.386  Sum_probs=68.8

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      ...|+|+||||||+++.|..|..++--.. -..|+++||++|..||.++..+|+++|.++++.|...+..|-++..
T Consensus       190 phiKKPLNAFmlyMKEmRa~vvaEctlKe-SAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdN  264 (421)
T KOG3248|consen  190 PHIKKPLNAFMLYMKEMRAKVVAECTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDN  264 (421)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhhhh-HHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhh
Confidence            37899999999999999999999986443 5789999999999999999999999999999999999999988764

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

Probab=99.26  E-value=1.5e-11  Score=104.84  Aligned_cols=81  Identities=27%  Similarity=0.536  Sum_probs=76.2

Q ss_pred             ccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        47 k~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      ...+.|.+|-+|+-+||.|++..+.+|+..||.+. +++|.++||.+|..|++.+|..|...++..+..|.+.|.+|+..
T Consensus        57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~k-LWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~s  135 (410)
T KOG4715|consen   57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELK-LWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNS  135 (410)
T ss_pred             cCCCCCCCCCcccchhhHHhhhhhhhhhccCcchH-HHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            44567888999999999999999999999999998 99999999999999999999999999999999999999999987


Q ss_pred             CC
Q 030283          127 QD  128 (180)
Q Consensus       127 ~~  128 (180)
                      ..
T Consensus       136 p~  137 (410)
T KOG4715|consen  136 PA  137 (410)
T ss_pred             ch
Confidence            63

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

Probab=99.10  E-value=3.3e-11  Score=107.46  Aligned_cols=81  Identities=28%  Similarity=0.475  Sum_probs=72.8

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      +.....+++.||||||||+|.++.|..|...+|++.| ..|+++||.+|+.|+-.+|++|++.-..+-..|...++.|+.
T Consensus       317 rg~~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMHN-SnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrY  395 (511)
T KOG0528|consen  317 RGRASSEPHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRY  395 (511)
T ss_pred             cCcCCCCccccCCcchhhcccchhhhhhhhcCccccc-cchhHHhcccccccccccccchHHHHHHHHHhhhccCccccc
Confidence            3445556788999999999999999999999999985 679999999999999999999999888888899999999998


Q ss_pred             hC
Q 030283          126 KQ  127 (180)
Q Consensus       126 ~~  127 (180)
                      +.
T Consensus       396 kP  397 (511)
T KOG0528|consen  396 KP  397 (511)
T ss_pred             CC
Confidence            66

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

Probab=98.56  E-value=6.1e-08  Score=89.67  Aligned_cols=74  Identities=27%  Similarity=0.468  Sum_probs=67.3

Q ss_pred             ccccCCCCCCCCCCCChHHHHHHHHH--HHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHH
Q 030283           45 EKKAKKDPNKPKRPPSAFFVFLEEFR--KTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK  119 (180)
Q Consensus        45 ~kk~~kdp~~PKrP~sAy~lF~~e~r--~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e  119 (180)
                      +-..+.+..+.++|||||+||++.+|  ..+.+.||+..| .-|++|||+.|-.|-+.+|..|.++|.+.+..|.++
T Consensus       172 rspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DN-rtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  172 RSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDN-RTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             CCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccccc-hhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            33456667788999999999999999  899999999985 779999999999999999999999999999999886

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

Probab=98.16  E-value=1.3e-05  Score=55.61  Aligned_cols=75  Identities=19%  Similarity=0.268  Sum_probs=61.3

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCCC
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGD  130 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~~  130 (180)
                      .|..|.+|-.||.+..+..+...|+.-. ... -+.+...|++|+..+|-+|...|.++..+|+..|.+|+......
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr-~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~~   77 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRNDR-KKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPADA   77 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTSTH-HHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHhH-HHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            5788999999999999999998998875 444 45889999999999999999999999999999999998876543

>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=96.80  E-value=0.0028  Score=50.43  Aligned_cols=48  Identities=33%  Similarity=0.548  Sum_probs=41.7

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCC
Q 030283           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS   98 (180)
Q Consensus        50 kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls   98 (180)
                      +.|.+-.|-+|||..|+++....|+..||+++ ..|+....+..|...+
T Consensus       117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~is-hkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPDIS-HKEAFSAAAKNWAHFP  164 (170)
T ss_pred             CCccccCCCchhHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHhhhhCc
Confidence            33444557789999999999999999999998 8999999999998765

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

Probab=96.71  E-value=0.0013  Score=53.82  Aligned_cols=70  Identities=21%  Similarity=0.310  Sum_probs=61.8

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHH
Q 030283           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN  121 (180)
Q Consensus        51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~  121 (180)
                      -..+|..|.-+|+-|....|+.+...+|... ..+++++++..|.+|++.-|.+|.+.+.+.+..|...|+
T Consensus       140 ~k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~-~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         140 KKLPNKAPIGPFIENEPKIRPKVEGPSPDKA-LVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             cccCCCCCCchhhhccHHhccccCCCCcchh-hhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            3456788888888888999999888888886 889999999999999999999999999999999987664

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

Probab=96.33  E-value=0.011  Score=47.29  Aligned_cols=50  Identities=28%  Similarity=0.496  Sum_probs=43.3

Q ss_pred             CChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHH
Q 030283           59 PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLK  113 (180)
Q Consensus        59 ~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k  113 (180)
                      -+||+-|+.++|.    .|.++. ..++....+..|..|++.+|..|..++....
T Consensus        83 nnaYLNFLReFRr----kh~~L~-p~dlI~~AAraW~rLSe~eK~rYrr~~~~~~  132 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCGLS-PQDLIQRAARAWCRLSEAEKNRYRRMAPSVR  132 (183)
T ss_pred             chHHHHHHHHHHH----HccCCC-HHHHHHHHHHHHHhCCHHHHHHHHhhcchhh
Confidence            5799999999875    668897 8899999999999999999999998766443

The function of this family is unknown.

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

Probab=95.41  E-value=0.015  Score=37.91  Aligned_cols=39  Identities=21%  Similarity=0.422  Sum_probs=34.9

Q ss_pred             ChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCc
Q 030283           60 SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP   99 (180)
Q Consensus        60 sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~   99 (180)
                      +.|-+|++-.|+.|...||++. +..|..+|+..|+..+.
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 89999999999987543

; 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=94.52  E-value=0.053  Score=41.00  Aligned_cols=48  Identities=23%  Similarity=0.379  Sum_probs=41.5

Q ss_pred             CCCCCCC-CChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCch
Q 030283           52 PNKPKRP-PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA  100 (180)
Q Consensus        52 p~~PKrP-~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~e  100 (180)
                      ..+|-|. .-||.-|+....+.|+.+||++. ++++..+|-..|...|++
T Consensus        69 drHPErR~KAAy~afeE~~Lp~lK~E~PgLr-lsQ~kq~l~K~w~KSPeN  117 (122)
T PF06244_consen   69 DRHPERRMKAAYKAFEERRLPELKEENPGLR-LSQYKQMLWKEWQKSPEN  117 (122)
T ss_pred             CCCcchhHHHHHHHHHHHHhHHHHhhCCCch-HHHHHHHHHHHHhcCCCC
Confidence            4456444 47899999999999999999998 999999999999988765

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

Probab=92.93  E-value=0.31  Score=39.84  Aligned_cols=56  Identities=21%  Similarity=0.357  Sum_probs=39.9

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHH
Q 030283           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEK  111 (180)
Q Consensus        49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~  111 (180)
                      ......++||+|+||+|+.=+-    .-.|+.. ...++..|+..|..=+  -|..|.-+|..
T Consensus        38 ~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~-Qk~~S~~l~~lW~~dp--~k~~W~l~ak~   93 (201)
T PF04769_consen   38 KRSPEKAKRPLNGFMAFRSYYS----PIFPPLP-QKELSGILTKLWEKDP--FKNKWSLMAKA   93 (201)
T ss_pred             cccccccccchhHHHHHHHHHH----hhcCCcC-HHHHHHHHHHHHhCCc--cHhHHHHHhhh
Confidence            3345578999999999977665    3346665 6789999999998632  25556655543

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

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.56  E-value=0.099  Score=42.42  Aligned_cols=54  Identities=30%  Similarity=0.463  Sum_probs=46.2

Q ss_pred             CCC-CCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHH
Q 030283           53 NKP-KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAE  110 (180)
Q Consensus        53 ~~P-KrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~  110 (180)
                      .+| +|=.-||.-|-....+.|+.+||++. +.++-.+|-.+|..-|+.   ||.+++.
T Consensus       162 rHPEkRmrAA~~afEe~~LPrLK~e~P~lr-lsQ~Kqll~Kew~KsPDN---P~Nq~~~  216 (221)
T KOG3223|consen  162 RHPEKRMRAAFKAFEEARLPRLKKENPGLR-LSQYKQLLKKEWQKSPDN---PFNQAAV  216 (221)
T ss_pred             cChHHHHHHHHHHHHHhhchhhhhcCCCcc-HHHHHHHHHHHHhhCCCC---hhhHHhh
Confidence            566 45557899999999999999999998 899999999999999887   7777653

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=86.63  E-value=1.5  Score=35.61  Aligned_cols=45  Identities=18%  Similarity=0.511  Sum_probs=39.0

Q ss_pred             HHHHHH-HHHhhhcCCCchhhhhHHHHHHH-HHHHHHHHHHHHhhhC
Q 030283           83 VSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        83 ~~eisk-~l~e~Wk~Ls~eeK~~Y~~~A~~-~k~~y~~e~~~y~~~~  127 (180)
                      |..|++ .||..|+.++++++..|...... ....|-..+..|....
T Consensus        66 f~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~~  112 (198)
T TIGR03481        66 LPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGER  112 (198)
T ss_pred             HHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCce
Confidence            667776 78999999999999999998888 7788999999997643

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=82.58  E-value=3  Score=34.06  Aligned_cols=49  Identities=29%  Similarity=0.551  Sum_probs=40.2

Q ss_pred             CCCccHHHHHH-HHHhhhcCCCchhhhhHHHHHHH-HHHHHHHHHHHHhhhC
Q 030283           78 PNVTAVSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        78 P~~~~~~eisk-~l~e~Wk~Ls~eeK~~Y~~~A~~-~k~~y~~e~~~y~~~~  127 (180)
                      |... |..|++ .||..|+.++++++..|...... +...|-..+..|....
T Consensus        66 p~~D-f~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q~  116 (211)
T PRK15117         66 PYVQ-VKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQT  116 (211)
T ss_pred             ccCC-HHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCce
Confidence            4554 777776 68999999999999999987766 6678999999997653

>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []

Probab=80.09  E-value=3.4  Score=32.17  Aligned_cols=47  Identities=21%  Similarity=0.548  Sum_probs=35.5

Q ss_pred             CCCccHHHHHH-HHHhhhcCCCchhhhhHHHHHHH-HHHHHHHHHHHHhh
Q 030283           78 PNVTAVSAVGK-AAGGKWKSMSPAEKAPYESKAEK-LKSEYGKKMNAYNK  125 (180)
Q Consensus        78 P~~~~~~eisk-~l~e~Wk~Ls~eeK~~Y~~~A~~-~k~~y~~e~~~y~~  125 (180)
                      |.+. |..|++ .||..|+.|+++++..|...... ....|-..+..|..
T Consensus        36 ~~~D-~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~   84 (170)
T PF05494_consen   36 PYFD-FERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG   84 (170)
T ss_dssp             GGB--HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred             HhCC-HHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            4443 667766 58899999999999999987766 56778889998875

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

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	180
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	7e-23
2lhj_A	97	High mobility group protein homolog NHP1; structur	1e-22
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	1e-21
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-21
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	1e-20
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	3e-20
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	3e-20
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	2e-19
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	2e-18
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	4e-18
1wgf_A	90	Upstream binding factor 1; transcription factor, D	5e-18
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	9e-17
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-12
1ckt_A	71	High mobility group 1 protein; high-mobility group	4e-16
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-15
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	2e-14
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	5e-14
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	5e-14
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	6e-13
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	6e-13
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	9e-13
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-09
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	1e-12
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	1e-11
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	4e-11
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	4e-11
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	5e-11
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-08
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	7e-11
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	1e-10
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	2e-10
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	5e-10
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	1e-09
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	6e-07
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	8e-07
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	3e-05

>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 = 85.8 bits (213), Expect = 7e-23
 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 = 85.5 bits (212), Expect = 1e-22
 Identities = 32/93 (34%), Positives = 53/93 (56%), Gaps = 1/93 (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  KSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ 127
            ++S  EK PYE  +++ +  Y ++   Y +++
Sbjct: 64  NALSDEEKKPYERMSDEDRVRYEREKAEYAQRK 96

>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 = 83.5 bits (207), Expect = 1e-21
 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

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

 Score = 82.5 bits (204), Expect = 3e-21
 Identities = 32/100 (32%), Positives = 47/100 (47%), Gaps = 1/100 (1%)

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

Query: 99  PAEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKS 138
             +K  Y+ K E  K EY K++ AY         +D   S
Sbjct: 61  EEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSYTDSGPS 100

>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 = 80.9 bits (200), Expect = 1e-20
 Identities = 25/91 (27%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

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

Query: 108 KAEKLKSEYGKKMNAYNKKQDGDEASDKSKS 138
           +AEK K +Y K++ AY + +     ++   S
Sbjct: 60  EAEKEKQQYLKELWAYQQSEAYKVCTESGPS 90

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

 Score = 79.3 bits (196), Expect = 3e-20
 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 1/82 (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 SKAEKLKSEYGKKMNAYNKKQD 128
             A+  K+ Y ++M  Y   + 
Sbjct: 61  DMAKADKARYEREMKTYIPPKG 82

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

 Score = 79.3 bits (196), Expect = 3e-20
 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 = 77.8 bits (192), Expect = 2e-19
 Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 1/97 (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 ESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVND 142
               ++ K E+ + +  + +       + K     + 
Sbjct: 61  IQDFQREKQEFERNLARFREDHPDLIQNAKKLEHHHH 97

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

 Score = 74.2 bits (183), Expect = 2e-18
 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 = 73.5 bits (181), Expect = 4e-18
 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

>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 = 74.0 bits (182), Expect = 5e-18
 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

>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 = 72.7 bits (178), Expect = 9e-17
 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 = 61.5 bits (149), Expect = 2e-12
 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 = 68.2 bits (167), Expect = 4e-16
 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 = 67.1 bits (164), Expect = 2e-15
 Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

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

Query: 108 KAEKLKSEYGKKMNAYNKKQDGDEASDKSKS 138
           KA K    Y  +M    +++      D   S
Sbjct: 60  KATKDLERYNSQMKRAIEQESQMSLKDSGPS 90

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

 Score = 63.8 bits (156), Expect = 2e-14
 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

>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 = 65.3 bits (159), Expect = 5e-14
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (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 KSEYGKKMNAYNKKQD 128
           ++ + +K   Y  ++ 
Sbjct: 62  QAMHREKYPNYKYRKG 77

>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 = 65.3 bits (159), Expect = 5e-14
 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

>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 = 60.9 bits (148), Expect = 6e-13
 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

>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 = 60.3 bits (147), Expect = 6e-13
 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

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

 Score = 62.8 bits (152), Expect = 9e-13
 Identities = 15/116 (12%), Positives = 46/116 (39%), Gaps = 1/116 (0%)

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

Query: 107 SKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEASGEEEHQLEPEPEPEQ 162
                    Y ++++ + ++    +     K  ++   +     + +        +
Sbjct: 61  DAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPK 116

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

 Score = 54.8 bits (131), Expect = 1e-09
 Identities = 31/152 (20%), Positives = 57/152 (37%), Gaps = 5/152 (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 AYNKKQDGDEASDKSKSEVNDEDEASGEEEHQ 153
           ++ ++       D  +  +  + +   EE  Q
Sbjct: 177 SWEEQMIEVGRKDLLRRTIKKQRKYGAEECLQ 208

>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 = 59.7 bits (145), Expect = 1e-12
 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

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

 Score = 56.4 bits (137), Expect = 1e-11
 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 = 55.2 bits (134), Expect = 4e-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

>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 = 55.7 bits (135), Expect = 4e-11
 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

>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 = 5e-11
 Identities = 17/134 (12%), Positives = 50/134 (37%), Gaps = 1/134 (0%)

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

Query: 88  KAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEAS 147
           +    +W+ +  ++K  Y+         Y ++++ + ++    +     K  ++   +  
Sbjct: 74  RRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRK 133

Query: 148 GEEEHQLEPEPEPE 161
              + +        
Sbjct: 134 AMTKKKELTLLGKP 147

>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 = 51.8 bits (123), Expect = 1e-08
 Identities = 27/111 (24%), Positives = 51/111 (45%), Gaps = 5/111 (4%)

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

Query: 100 AEKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSEVNDEDEASGEE 150
           +EK  Y   A++ ++ Y  +M ++ ++       D  +  +  + +   EE
Sbjct: 187 SEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKKQRKYGAEE 237

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

 Score = 54.9 bits (133), Expect = 7e-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 = 54.1 bits (131), Expect = 1e-10
 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 = 53.4 bits (129), Expect = 2e-10
 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 = 52.6 bits (127), Expect = 5e-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 = 51.8 bits (125), Expect = 1e-09
 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

>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 = 44.9 bits (106), Expect = 6e-07
 Identities = 13/77 (16%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

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

Query: 115 EYGKKMNAYNKKQDGDE 131
           +Y   ++ + K     +
Sbjct: 66  QYKVHLDLWVKSLSPQD 82

>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 = 45.0 bits (106), Expect = 8e-07
 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

>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 = 40.2 bits (93), Expect = 3e-05
 Identities = 15/76 (19%), Positives = 33/76 (43%)

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

Query: 113 KSEYGKKMNAYNKKQD 128
            +  G +         
Sbjct: 64  TASEGTEAKKRKSGPS 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	180
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.91
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.91
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.9
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.9
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.89
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.89
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.89
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.89
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.88
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.88
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.88
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.88
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.88
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.87
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.87
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.86
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.86
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.85
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.85
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.85
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.85
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.85
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.85
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.84
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.84
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.84
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.84
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.83
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.83
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.81
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.81
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.81
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.77
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.76
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.76
2cto_A	93	Novel protein; high mobility group box domain, hel	99.75
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.75
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.74
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.68

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

Probab=99.91  E-value=2.3e-24  Score=156.49  Aligned_cols=85  Identities=35%  Similarity=0.620  Sum_probs=80.2

Q ss_pred             ccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283           45 EKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (180)
Q Consensus        45 ~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~  124 (180)
                      ++++.+||++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|++|++++|.+|.++|..++++|..+|..|+
T Consensus         8 ~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~   86 (102)
T 2co9_A            8 KKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNAT-FGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYR   86 (102)
T ss_dssp             SCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSC-HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999999999997 899999999999999999999999999999999999999999


Q ss_pred             hhCCCC
Q 030283          125 KKQDGD  130 (180)
Q Consensus       125 ~~~~~~  130 (180)
                      .++...
T Consensus        87 ~~~~~~   92 (102)
T 2co9_A           87 ASLVSK   92 (102)
T ss_dssp             HHHTSS
T ss_pred             hhcccc
Confidence            988644

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

Probab=99.91  E-value=3.3e-24  Score=150.95  Aligned_cols=80  Identities=35%  Similarity=0.594  Sum_probs=75.4

Q ss_pred             ccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           45 EKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        45 ~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      +++..+||++|+||+|||||||+++|..|+.+||+++ +|.+|+++||++|+.|++++|.+|.++|..++++|..+|..|
T Consensus         6 ~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   85 (86)
T 2eqz_A            6 SGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY   85 (86)
T ss_dssp             SSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3456789999999999999999999999999999997 379999999999999999999999999999999999999999


Q ss_pred             h
Q 030283          124 N  124 (180)
Q Consensus       124 ~  124 (180)
                      +
T Consensus        86 ~   86 (86)
T 2eqz_A           86 G   86 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.90  E-value=6.6e-24  Score=153.44  Aligned_cols=82  Identities=26%  Similarity=0.492  Sum_probs=78.4

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      +++.+||++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.||+++|.+|.++|..++++|..+|..|..
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            456789999999999999999999999999999997 8999999999999999999999999999999999999999998


Q ss_pred             hCC
Q 030283          126 KQD  128 (180)
Q Consensus       126 ~~~  128 (180)
                      ...
T Consensus        81 ~~P   83 (99)
T 1k99_A           81 DHP   83 (99)
T ss_dssp             CCC
T ss_pred             HCC
Confidence            765

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

Probab=99.90  E-value=7.3e-24  Score=145.90  Aligned_cols=76  Identities=47%  Similarity=0.873  Sum_probs=73.5

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      ++||++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.||+++|.+|.++|..++.+|..+|+.|+.
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

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

Probab=99.89  E-value=4e-24  Score=153.75  Aligned_cols=84  Identities=38%  Similarity=0.723  Sum_probs=78.1

Q ss_pred             ccccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHH
Q 030283           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMN  121 (180)
Q Consensus        43 kk~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~  121 (180)
                      ++++++.+||++|+||+|||||||+++|..|+.+||+++ ++.+|+++||++|+.|++++|.+|.++|..++.+|..+|.
T Consensus        11 ~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   90 (97)
T 2lhj_A           11 RRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKA   90 (97)
T ss_dssp             CCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344567889999999999999999999999999999985 3689999999999999999999999999999999999999


Q ss_pred             HHhhh
Q 030283          122 AYNKK  126 (180)
Q Consensus       122 ~y~~~  126 (180)
                      .|+.+
T Consensus        91 ~y~~~   95 (97)
T 2lhj_A           91 EYAQR   95 (97)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            99875

>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=99.89  E-value=1.8e-24  Score=154.58  Aligned_cols=83  Identities=45%  Similarity=0.773  Sum_probs=78.3

Q ss_pred             cccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        44 k~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      +++++.+||++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|++|++++|.+|.++|..++.+|..+|..|
T Consensus        10 ~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y   88 (93)
T 1cg7_A           10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY   88 (93)
T ss_dssp             CCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSC-HHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHH
T ss_pred             ccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566789999999999999999999999999999997 99999999999999999999999999999999999999999


Q ss_pred             hhhC
Q 030283          124 NKKQ  127 (180)
Q Consensus       124 ~~~~  127 (180)
                      ..+.
T Consensus        89 ~~~~   92 (93)
T 1cg7_A           89 NATL   92 (93)
T ss_dssp             HHHT
T ss_pred             HHcc
Confidence            8764

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

Probab=99.89  E-value=3.5e-23  Score=147.48  Aligned_cols=78  Identities=31%  Similarity=0.606  Sum_probs=75.4

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~  127 (180)
                      .+||++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|+.|+...
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~   79 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSE   79 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCC-HHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccH
Confidence            579999999999999999999999999999997 899999999999999999999999999999999999999998865

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

Probab=99.89  E-value=8.3e-24  Score=147.79  Aligned_cols=78  Identities=32%  Similarity=0.584  Sum_probs=74.1

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      ++||++|+||+|||||||+++|..|+.+||+++ +|.+|+++||++|+.|++++|.+|.++|..++++|..+|..|...
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~   80 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP   80 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            579999999999999999999999999999986 368999999999999999999999999999999999999999765

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

Probab=99.88  E-value=6.4e-23  Score=146.14  Aligned_cols=80  Identities=28%  Similarity=0.409  Sum_probs=76.3

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      ..+|++||||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++++|..+|..|..++.
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~   80 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQES   80 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSC-HHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            357999999999999999999999999999997 8999999999999999999999999999999999999999998875


Q ss_pred             C
Q 030283          129 G  129 (180)
Q Consensus       129 ~  129 (180)
                      .
T Consensus        81 ~   81 (92)
T 2cs1_A           81 Q   81 (92)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=99.88  E-value=1e-22  Score=139.02  Aligned_cols=72  Identities=36%  Similarity=0.732  Sum_probs=69.3

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        52 p~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      .++||||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++  |.+|.++|..++++|..+|+.|+++
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

>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=99.88  E-value=5.6e-24  Score=151.14  Aligned_cols=79  Identities=30%  Similarity=0.560  Sum_probs=72.7

Q ss_pred             ccccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHH
Q 030283           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNA  122 (180)
Q Consensus        43 kk~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~  122 (180)
                      ++++++.+||++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++++|..+|..
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            344566789999999999999999999999999999997 9999999999999999999999999999999999877643

>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=99.88  E-value=3.3e-23  Score=146.22  Aligned_cols=78  Identities=27%  Similarity=0.450  Sum_probs=74.5

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~  124 (180)
                      ++..++|++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++++|..+++.|+
T Consensus         9 ~~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A            9 TVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKD-NRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             SCCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            356789999999999999999999999999999997 899999999999999999999999999999999999999886

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

Probab=99.88  E-value=4.8e-23  Score=141.43  Aligned_cols=75  Identities=32%  Similarity=0.530  Sum_probs=70.6

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      ||++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|+.|+.+
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            6899999999999999999999999999997 89999999999999999999999999999999999999999753

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

Probab=99.87  E-value=2e-22  Score=137.61  Aligned_cols=72  Identities=33%  Similarity=0.693  Sum_probs=69.5

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        52 p~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      |++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|  ++|.+|.++|..++.+|..+|..|+.+
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  889999999999999999999999864

>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=99.87  E-value=4e-22  Score=135.00  Aligned_cols=70  Identities=31%  Similarity=0.607  Sum_probs=67.1

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      +||||+|||||||+++|..|+.+||+++ +|.+|+++||++|++|++++|.+|.++|..++.+|..+|..|
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 369999999999999999999999999999999999999877

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

Probab=99.86  E-value=5.6e-22  Score=139.22  Aligned_cols=78  Identities=31%  Similarity=0.503  Sum_probs=74.4

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 030283           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDG  129 (180)
Q Consensus        51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~  129 (180)
                      .|++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++++|..+|+.|+.+...
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~prr   78 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRR   78 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccCCCC
Confidence            3799999999999999999999999999997 89999999999999999999999999999999999999999987653

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

Probab=99.86  E-value=2.3e-22  Score=140.15  Aligned_cols=78  Identities=23%  Similarity=0.452  Sum_probs=74.1

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~  127 (180)
                      ..++++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|+.|+.+.
T Consensus         2 ~~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~p   79 (82)
T 1wz6_A            2 SSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLD-NRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSGP   79 (82)
T ss_dssp             CSSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSC-TTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCCT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcCC
Confidence            357899999999999999999999999999997 899999999999999999999999999999999999999998754

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

Probab=99.85  E-value=3.5e-22  Score=135.05  Aligned_cols=71  Identities=30%  Similarity=0.581  Sum_probs=63.2

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~  124 (180)
                      |.|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.||+++|.+|.++|..++.+|..+|+.|+
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            57999999999999999999999999998 899999999999999999999999999999999999999885

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

Probab=99.85  E-value=9.6e-22  Score=143.68  Aligned_cols=81  Identities=25%  Similarity=0.502  Sum_probs=70.9

Q ss_pred             ccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        47 k~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      ...+++++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++++|..+|+.|+.+
T Consensus        22 ~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~  100 (106)
T 4euw_A           22 QSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLH-NAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQ  100 (106)
T ss_dssp             ------CCCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC-
T ss_pred             hccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcC
Confidence            44678999999999999999999999999999997 89999999999999999999999999999999999999999876


Q ss_pred             CC
Q 030283          127 QD  128 (180)
Q Consensus       127 ~~  128 (180)
                      ..
T Consensus       101 Pr  102 (106)
T 4euw_A          101 PR  102 (106)
T ss_dssp             --
T ss_pred             CC
Confidence            54

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

Probab=99.85  E-value=1.2e-21  Score=135.69  Aligned_cols=75  Identities=31%  Similarity=0.556  Sum_probs=71.9

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      ++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.||+++|.+|.++|..++.+|..+|+.|+....
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~   75 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPR   75 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccCCC
Confidence            57999999999999999999999999997 8999999999999999999999999999999999999999987654

>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=99.85  E-value=2.3e-21  Score=150.22  Aligned_cols=79  Identities=48%  Similarity=0.865  Sum_probs=75.7

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      +++.++|++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|++|++++|.+|..+|..++.+|..+|.+|++
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            345789999999999999999999999999999997 9999999999999999999999999999999999999999985

>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A

Probab=99.85  E-value=8.4e-22  Score=137.33  Aligned_cols=77  Identities=27%  Similarity=0.531  Sum_probs=70.3

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      .++.|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|+.|+.+..
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~P~   79 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRPR   79 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCCc
Confidence            4678999999999999999999999999998 8999999999999999999999999999999999999999987643

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

Probab=99.85  E-value=2.4e-21  Score=136.15  Aligned_cols=76  Identities=21%  Similarity=0.371  Sum_probs=72.3

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDG  129 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~  129 (180)
                      +.|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.||+++|.+|.++|..++++|..+|+.|..+...
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~   76 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY   76 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSST
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCC
Confidence            47999999999999999999999999997 89999999999999999999999999999999999999999977653

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1

Probab=99.84  E-value=1.3e-21  Score=135.16  Aligned_cols=75  Identities=24%  Similarity=0.484  Sum_probs=71.7

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      |+|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++++|..+|+.|+.+..
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~Pr   75 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMH-NAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRPR   75 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCCC
Confidence            68999999999999999999999999997 8999999999999999999999999999999999999999987643

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

Probab=99.84  E-value=1.9e-21  Score=135.16  Aligned_cols=75  Identities=29%  Similarity=0.514  Sum_probs=68.7

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        52 p~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~  127 (180)
                      +++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|+.|+.+.
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p   76 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKP   76 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCC-HHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC----
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeecc
Confidence            578999999999999999999999999997 899999999999999999999999999999999999999998754

>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=99.84  E-value=4.1e-21  Score=140.92  Aligned_cols=78  Identities=22%  Similarity=0.415  Sum_probs=72.8

Q ss_pred             cccCCCCCCC-CCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHh
Q 030283           46 KKAKKDPNKP-KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYN  124 (180)
Q Consensus        46 kk~~kdp~~P-KrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~  124 (180)
                      .++.++|++| |||+|||||||+++|..|+    +++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|..|.
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            3557899999 9999999999999999886    675 899999999999999999999999999999999999999999


Q ss_pred             hhCC
Q 030283          125 KKQD  128 (180)
Q Consensus       125 ~~~~  128 (180)
                      ..+.
T Consensus        83 ~~~~   86 (108)
T 1v64_A           83 ESLP   86 (108)
T ss_dssp             HHSC
T ss_pred             hhCC
Confidence            9875

>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=8.1e-21  Score=149.18  Aligned_cols=80  Identities=49%  Similarity=0.868  Sum_probs=76.1

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      +++.++|++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|++|++++|.+|..+|..++.+|..+|..|+.
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            345679999999999999999999999999999997 9999999999999999999999999999999999999999987


Q ss_pred             h
Q 030283          126 K  126 (180)
Q Consensus       126 ~  126 (180)
                      +
T Consensus       172 k  172 (173)
T 2yrq_A          172 K  172 (173)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.83  E-value=1.5e-20  Score=133.90  Aligned_cols=76  Identities=17%  Similarity=0.218  Sum_probs=71.9

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 030283           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDG  129 (180)
Q Consensus        52 p~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~  129 (180)
                      .+.|+||+|||+||++++|..++..||+ . +.+|++.||++|+.|++.+|.+|+.+|..++.+|..+|..|+.....
T Consensus         2 ~~kPKrP~SAy~lf~~~~r~~~k~~~p~-~-~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~~   77 (91)
T 1l8y_A            2 GKLPESPKRAEEIWQQSVIGDYLARFKN-D-RVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAA   77 (91)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHHTTS-T-HHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCC-C-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            3689999999999999999999999999 4 89999999999999999999999999999999999999999887653

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

Probab=99.83  E-value=8.3e-21  Score=127.41  Aligned_cols=66  Identities=30%  Similarity=0.488  Sum_probs=62.4

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      |+||||+|||+|||+++|..|+..|     +.+|+++||++|+.||+++|.+|.++|..++.+|..+|..|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~-----p~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSS-----HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcC-----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6899999999999999999997665     46899999999999999999999999999999999999998

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

Probab=99.81  E-value=5.1e-20  Score=144.62  Aligned_cols=84  Identities=30%  Similarity=0.550  Sum_probs=77.2

Q ss_pred             ccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           45 EKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        45 ~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      .++.++||++|+||+|||||||+++|..|+.+||+++ ++.+|+++||++|+.|++++|.+|.++|..++.+|..+|..|
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            3456789999999999999999999999999999952 489999999999999999999999999999999999999999


Q ss_pred             hhhCC
Q 030283          124 NKKQD  128 (180)
Q Consensus       124 ~~~~~  128 (180)
                      .....
T Consensus        86 ~~~~~   90 (173)
T 2yrq_A           86 IPPKG   90 (173)
T ss_dssp             CCCCC
T ss_pred             hhhhh
Confidence            87543

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

Probab=99.81  E-value=1e-19  Score=131.93  Aligned_cols=77  Identities=18%  Similarity=0.345  Sum_probs=68.3

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCCC
Q 030283           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGD  130 (180)
Q Consensus        51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~~  130 (180)
                      ..++||||+|||||||++++.  ...+++++ +.+|+++||++|+.|++++|.+|.++|..++++|..+|..|...+...
T Consensus         5 ~~~~PKrP~say~lF~~e~~~--~p~~~~~~-~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~~   81 (101)
T 1v63_A            5 SSGPKKPPMNGYQKFSQELLS--NGELNHLP-LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHH--HCTTTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHh--CCCCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHH
Confidence            467899999999999999964  23345565 899999999999999999999999999999999999999999988644

>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=99.81  E-value=5.2e-20  Score=128.60  Aligned_cols=63  Identities=22%  Similarity=0.378  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHH
Q 030283           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKL  112 (180)
Q Consensus        50 kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~  112 (180)
                      .++++||||+|||||||+++|..|+.+||+++++.+|+++||++|+.|++++|.+|+++|..+
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            368999999999999999999999999999954899999999999999999999999999886

>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=4.3e-19  Score=146.30  Aligned_cols=80  Identities=18%  Similarity=0.390  Sum_probs=76.1

Q ss_pred             cCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        48 ~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~  127 (180)
                      ...+|++||||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|+++|..++++|..+|..|...+
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            3568999999999999999999999999999998 999999999999999999999999999999999999999998766


Q ss_pred             C
Q 030283          128 D  128 (180)
Q Consensus       128 ~  128 (180)
                      .
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=99.76  E-value=7.2e-19  Score=142.88  Aligned_cols=77  Identities=18%  Similarity=0.407  Sum_probs=73.7

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      .|++|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++++|..+|..|...+.
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            3789999999999999999999999999998 9999999999999999999999999999999999999999987664

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

Probab=99.76  E-value=6.4e-20  Score=149.11  Aligned_cols=87  Identities=26%  Similarity=0.352  Sum_probs=75.4

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      ++..++|++|+||+|||||||+++|..|+..|     +.+|+++||++|++|++++|.+|..+|..++.+|..+|.+|..
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            34567999999999999999999999886544     5589999999999999999999999999999999999999999


Q ss_pred             hCCCCccccccc
Q 030283          126 KQDGDEASDKSK  137 (180)
Q Consensus       126 ~~~~~~~s~~~~  137 (180)
                      ++......+.+.
T Consensus       181 ~~~~~~~~dlvr  192 (214)
T 3tq6_A          181 QMIEVGRKDLLR  192 (214)
T ss_dssp             HHHHTTBGGGSC
T ss_pred             hCcccccccccc
Confidence            986544444433

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

Probab=99.75  E-value=4.4e-19  Score=126.95  Aligned_cols=70  Identities=20%  Similarity=0.391  Sum_probs=64.8

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHH---HhhhcCCCchhhhhHHHHHHHHHHHHHHHHH
Q 030283           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAA---GGKWKSMSPAEKAPYESKAEKLKSEYGKKMN  121 (180)
Q Consensus        49 ~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l---~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~  121 (180)
                      -..+++||||+|||||||+++|..|+.+  +++ +.+|+++|   |++|+.|++++|.+|+++|..++++|.+++.
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  675 78999999   9999999999999999999999999998763

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

Probab=99.75  E-value=1.2e-19  Score=149.70  Aligned_cols=86  Identities=27%  Similarity=0.346  Sum_probs=74.9

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      ++..++|++|+||+|||||||+++|..|+..|     +.+|+++||++|++|++++|.+|..+|..++++|..+|.+|+.
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 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  212 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSS-----HHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhccC-----HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567999999999999999999998886554     4589999999999999999999999999999999999999999


Q ss_pred             hCCCCcccccc
Q 030283          126 KQDGDEASDKS  136 (180)
Q Consensus       126 ~~~~~~~s~~~  136 (180)
                      ++........+
T Consensus       213 k~~~~~~~dlv  223 (238)
T 3tmm_A          213 QMIEVGRKDLL  223 (238)
T ss_dssp             HHHHTTCGGGS
T ss_pred             hCccccccchh
Confidence            98644444333

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

Probab=99.74  E-value=9.7e-20  Score=129.57  Aligned_cols=69  Identities=23%  Similarity=0.292  Sum_probs=61.8

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHH
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGK  118 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~  118 (180)
                      .+..+|||+|+||+|||||||+++|..|+.+||+++ .+.+|+    ++|+.|++++|.+|+.+|..++++|..
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            345679999999999999999999999999999984 145665    999999999999999999999999875

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

Probab=99.68  E-value=4.5e-17  Score=125.91  Aligned_cols=75  Identities=32%  Similarity=0.549  Sum_probs=71.7

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhC
Q 030283           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQ  127 (180)
Q Consensus        52 p~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~  127 (180)
                      |++|+||+||||||++..|..|+.+||+++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|..|....
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~k   76 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRK   76 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCCC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhcccccc
Confidence            689999999999999999999999999997 899999999999999999999999999999999999999997653

---

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	180
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	1e-16
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	4e-14
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-13
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	3e-13
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-12
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	2e-12
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	4e-12
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	6e-12
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	6e-12
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	2e-10
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-09
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-07

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

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

 Score = 69.2 bits (169), Expect = 1e-16
 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

>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 = 62.2 bits (151), Expect = 4e-14
 Identities = 36/80 (45%), Positives = 47/80 (58%), Gaps = 1/80 (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 KSEYGKKMNAYNKKQDGDEA 132
           K +Y K + AY  K   D A
Sbjct: 60  KEKYEKDIAAYRAKGKPDAA 79

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

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

 Score = 60.7 bits (147), Expect = 2e-13
 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

>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 = 59.8 bits (145), Expect = 3e-13
 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

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

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

 Score = 58.4 bits (141), Expect = 1e-12
 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 = 57.5 bits (139), Expect = 2e-12
 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

>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 = 56.8 bits (137), Expect = 4e-12
 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 = 56.4 bits (136), Expect = 6e-12
 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 = 56.8 bits (137), Expect = 6e-12
 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

>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 = 52.9 bits (127), Expect = 2e-10
 Identities = 16/84 (19%), Positives = 41/84 (48%), Gaps = 1/84 (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 YGKKMNAYNKKQDGDEASDKSKSE 139
           + +    ++ + +  +   + + +
Sbjct: 63  HMQLYPGWSARDNYGKKKKRKREK 86

>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 = 50.7 bits (121), Expect = 2e-09
 Identities = 13/87 (14%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

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

Query: 109 AEKLKSEYGKKMNAYNKKQDGDEASDK 135
           AE+ + +Y   ++ + K     + +  
Sbjct: 60  AEEQQRQYKVHLDLWVKSLSPQDRAAY 86

>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 = 45.7 bits (108), Expect = 1e-07
 Identities = 19/99 (19%), Positives = 35/99 (35%), Gaps = 5/99 (5%)

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

Query: 101 EKAPYESKAEKLKSEYGKKMNAYNKKQDGDEASDKSKSE 139
           EK  Y  K ++ K +Y  ++  + +    +E       E
Sbjct: 59  EKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEE 97

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	180
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.9
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.88
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.87
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.86
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.85
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.84
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.83
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.81
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.78
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.78
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	96.4

>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=99.90  E-value=8.7e-24  Score=149.43  Aligned_cols=83  Identities=45%  Similarity=0.773  Sum_probs=78.3

Q ss_pred             cccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        44 k~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      +.++..++|++|+||+|||||||+++|..|+.+||+++ +.+|++.||.+|++||+++|.+|.++|..++.+|..+|..|
T Consensus        10 ~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~-~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y   88 (93)
T d1lwma_          10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY   88 (93)
T ss_dssp             CCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCc-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44456779999999999999999999999999999997 89999999999999999999999999999999999999999


Q ss_pred             hhhC
Q 030283          124 NKKQ  127 (180)
Q Consensus       124 ~~~~  127 (180)
                      +.++
T Consensus        89 ~~~l   92 (93)
T d1lwma_          89 NATL   92 (93)
T ss_dssp             HHHH
T ss_pred             Hhcc
Confidence            9875

>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=99.88  E-value=5.1e-23  Score=141.12  Aligned_cols=75  Identities=45%  Similarity=0.843  Sum_probs=72.6

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      |+||||+|||||||+++|..|+.+||+++ +.+|+++||.+|+.||+++|.+|..+|..++.+|..+|..|+.+..
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~-~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~   75 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGK   75 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCC-TTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence            78999999999999999999999999997 8999999999999999999999999999999999999999998764

>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=99.87  E-value=1.8e-22  Score=141.71  Aligned_cols=83  Identities=25%  Similarity=0.487  Sum_probs=79.0

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      ++.+++|+.|+||+|||||||+++|..|+.+||+++ +.+|+++||++|+.||+++|.+|.++|..++.+|..+|..|..
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            467889999999999999999999999999999997 8999999999999999999999999999999999999999998


Q ss_pred             hCCC
Q 030283          126 KQDG  129 (180)
Q Consensus       126 ~~~~  129 (180)
                      ....
T Consensus        81 ~~pe   84 (91)
T d1k99a_          81 DHPD   84 (91)
T ss_dssp             CCCC
T ss_pred             HCcc
Confidence            8653

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

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

Probab=99.86  E-value=2.1e-22  Score=138.79  Aligned_cols=75  Identities=31%  Similarity=0.556  Sum_probs=71.7

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      +.|+||+|||||||+++|..|+.+||+++ +.+|+++||.+|++|++++|.+|..+|..++++|..+|+.|+....
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~-~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p~   75 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPR   75 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCCC
Confidence            57999999999999999999999999997 8999999999999999999999999999999999999999987653

>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=99.86  E-value=5e-22  Score=138.14  Aligned_cols=75  Identities=32%  Similarity=0.541  Sum_probs=72.2

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        53 ~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      |+||||+|||||||+++|..|+.+||+++ +.+|+++||.+|++|++++|.+|+++|..++.+|..+|+.|+.+..
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            78999999999999999999999999997 9999999999999999999999999999999999999999987653

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

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

Probab=99.85  E-value=1.5e-21  Score=131.94  Aligned_cols=72  Identities=36%  Similarity=0.765  Sum_probs=68.1

Q ss_pred             CCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q 030283           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKK  126 (180)
Q Consensus        52 p~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~  126 (180)
                      .|+||||+|||||||+++|..|+.+||+++ +.+|+++||.+|+.|+  +|.+|..+|..++.+|..+|..|+.+
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~~-~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~   72 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTCC-HHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            378999999999999999999999999997 8999999999999886  49999999999999999999999875

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

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

Probab=99.84  E-value=1.7e-21  Score=130.76  Aligned_cols=70  Identities=31%  Similarity=0.607  Sum_probs=66.2

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~-~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      .||||+|||||||+++|..|+.+||+.. ++.+|+++||.+|+.||+++|.+|.++|..++.+|..+|..|
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            5999999999999999999999999754 478999999999999999999999999999999999999877

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

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

Probab=99.84  E-value=6.2e-22  Score=132.92  Aligned_cols=69  Identities=30%  Similarity=0.553  Sum_probs=65.9

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHH
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAY  123 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y  123 (180)
                      ++|||+|||||||+++|..|+.+||+++ +.+|+++||++|++|++++|.+|.++|..++.+|..++++|
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            5799999999999999999999999998 89999999999999999999999999999999999887765

>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=99.83  E-value=7.5e-21  Score=132.35  Aligned_cols=75  Identities=21%  Similarity=0.386  Sum_probs=71.2

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCC
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDG  129 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~  129 (180)
                      +.+||+|||||||+++|..|..+||+++ +.+|+++||.+|++||+++|.+|.++|..++++|..+++.|+.....
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~-~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~   76 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY   76 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSST
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCC
Confidence            6799999999999999999999999997 89999999999999999999999999999999999999999876543

>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=99.81  E-value=1e-20  Score=132.35  Aligned_cols=75  Identities=32%  Similarity=0.595  Sum_probs=68.9

Q ss_pred             cccccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHH
Q 030283           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKK  119 (180)
Q Consensus        44 k~kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e  119 (180)
                      ..+....+++.|+||+|||||||+++|..|+.+||++. +.+|+++|+.+|+.|++++|.+|.++|..++.+|..+
T Consensus        10 ~~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~-~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          10 SQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             CSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34456789999999999999999999999999999997 8999999999999999999999999999998887643

>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=99.78  E-value=1.5e-19  Score=128.80  Aligned_cols=77  Identities=17%  Similarity=0.327  Sum_probs=69.6

Q ss_pred             CCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCCCC
Q 030283           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQDGD  130 (180)
Q Consensus        51 dp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~~~  130 (180)
                      ..++||||+|||||||+++|..++..|  ++ +.+|+++||++|+.|++++|.+|.++|..++.+|..+|..|...+...
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            456889999999999999999986555  44 789999999999999999999999999999999999999999987543

>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=99.78  E-value=3.4e-19  Score=128.66  Aligned_cols=78  Identities=22%  Similarity=0.363  Sum_probs=70.9

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhh
Q 030283           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNK  125 (180)
Q Consensus        46 kk~~kdp~~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~  125 (180)
                      ++.+.++.+||+|+|||||||+++|..    +|+++ +.+|+++||.+|+.|++++|.+|..+|..++.+|..+|..|..
T Consensus         9 ~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~~-~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~   83 (108)
T d1v64a_           9 LKDKFDGRPTKPPPNSYSLYCAELMAN----MKDVP-STERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             SSCCTTTSCCCCCSSHHHHHHHHHHHH----CTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCCCCcHHHHHHHHHHHH----ccCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345577888899999999999998864    57886 8999999999999999999999999999999999999999998


Q ss_pred             hCC
Q 030283          126 KQD  128 (180)
Q Consensus       126 ~~~  128 (180)
                      ++.
T Consensus        84 ~~~   86 (108)
T d1v64a_          84 SLP   86 (108)
T ss_dssp             HSC
T ss_pred             hCC
Confidence            875

>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=96.40  E-value=0.013  Score=37.73  Aligned_cols=73  Identities=18%  Similarity=0.216  Sum_probs=58.9

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHhhhcCCCchhhhhHHHHHHHHHHHHHHHHHHHhhhCC
Q 030283           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAEKAPYESKAEKLKSEYGKKMNAYNKKQD  128 (180)
Q Consensus        54 ~PKrP~sAy~lF~~e~r~~ik~e~P~~~~~~eisk~l~e~Wk~Ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~~  128 (180)
                      .|-.|.+|-.+|.+.....+...+-+-  ..-..+.+-..|++|...++-+|...|.++..+|+.++-+-+.-..
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~D--R~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~~~a   75 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKND--RVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPA   75 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTST--HHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhh--HHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence            577889999999999988887766443  2345566777899999999999999999999999998876655443