Citrus Sinensis ID: 034117

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100---
Protein Sequence
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVSI
Secondary Structure (PSIPRED)
ccccccccccHHHHHHcccccHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHccccHHccccccccHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
mkgakgkgaarvsqealkpndrkvgkRKAATAkldsgskrqgkrekkakkdpnkpkrppsaFFVFLEEFRKTFkkenpnvtaVSAVgkaaggkwksmspavsi
Flexible Loop (DISEMBL)
mkgakgkgaarvsqealkpndrkvgkrkaatakldsgskrqgkrekkakkdpnkpkrppsAFFVFLEEFRKTfkkenpnvtavsavgkaaggkwksmspavsi
Low Complexity Region (SEG)
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSkrqgkrekkakkdpnkpkrppSAFFVFLEEFRKTFKKENPNvtavsavgkaaggkwkSMSPAVSI
Disordered region (IsUnstruct)
************************************************************AFFVFLEEFRKTFK*****************************
Disordered Region (DISOPRED)
**********************************************************PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSM******
Disordered Region (DISEMBL)
********************************************************RPPSAFFVFLEEFRKTFKKENPNVTAVSAVG****************
Disordered Region (DISPRO)
***************************************************PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKGAKGKGAARVSQEALKPNDRKVGKRKAATAKLDSGSKRQGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVSI
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	103	2.2.26 [Sep-21-2011]
O49595	178	High mobility group B pro	yes	no	0.941	0.544	0.712	9e-30
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.524	0.355	0.796	1e-17
Q42344	138	High mobility group B pro	no	no	0.757	0.565	0.479	6e-17
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.563	0.402	0.655	3e-16
P27347	157	DNA-binding protein MNB1B	N/A	no	0.776	0.509	0.539	3e-16
O49596	144	High mobility group B pro	no	no	0.533	0.381	0.727	5e-16
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.475	0.328	0.673	2e-14
P93047	141	High mobility group B pro	no	no	0.611	0.446	0.619	3e-14
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.776	0.496	0.504	5e-13
O49597	125	High mobility group B pro	no	no	0.621	0.512	0.531	2e-12

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

 Score =  128 bits (322), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 72/101 (71%), Positives = 81/101 (80%), Gaps = 4/101 (3%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS A
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQA 98

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

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

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 43/54 (79%), Positives = 46/54 (85%)

Query: 47  KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           KA KDPNKPKRPPSAFFVF+EEFRK F KE+P   AVSAVGKAAG KWK+MS A
Sbjct: 36  KAAKDPNKPKRPPSAFFVFMEEFRKVFNKEHPENKAVSAVGKAAGAKWKTMSDA 89

Glycine max (taxid: 3847)

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

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 47/98 (47%), Positives = 57/98 (58%), Gaps = 20/98 (20%)

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

Query: 61 AFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          AFFVFLE+FRK F   NPN  +V+ VGKAAG +WK+M+
Sbjct: 41 AFFVFLEDFRKEFNLANPNNKSVATVGKAAGARWKAMT 78

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 38/58 (65%), Positives = 49/58 (84%)

Query: 43  KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           K+ KKA KDPNKPKRPPSAFFVF+E+FRKT+K+++PN  +V+ VGKA G KWK ++ A
Sbjct: 24  KKTKKAVKDPNKPKRPPSAFFVFMEDFRKTYKEKHPNNKSVAVVGKAGGDKWKQLTAA 81

Ipomoea nil (taxid: 35883)

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

 Score = 83.6 bits (205), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 55/102 (53%), Positives = 64/102 (62%), Gaps = 22/102 (21%)

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

Query: 57 RPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          R PSAFFVF+EEFRK FK++NP   +V+AVGKAAG +WKS+S
Sbjct: 43 RAPSAFFVFMEEFRKEFKEKNPKNKSVAAVGKAAGDRWKSLS 84

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

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

 Score = 83.2 bits (204), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 40/55 (72%), Positives = 46/55 (83%)

Query: 44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          R K A KDPNKPKRP SAFFVF+E+FR+TFKKENP   +V+ VGKAAG KWKS+S
Sbjct: 27 RGKAAAKDPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVGKAAGDKWKSLS 81

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 33/49 (67%), Positives = 43/49 (87%)

Query: 50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          KDPNKPKRPPSAFFVF+ +FR+ +KK++PN  +V+AVGKA G +WKS+S
Sbjct: 40 KDPNKPKRPPSAFFVFMADFREQYKKDHPNNKSVAAVGKACGEEWKSLS 88

Vicia faba (taxid: 3906)

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

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 39/63 (61%), Positives = 49/63 (77%)

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 SMS 98
          S+S
Sbjct: 76 SLS 78

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 72.8 bits (177), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 63/103 (61%), Gaps = 23/103 (22%)

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

Query: 56 KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          KR PSAFFVF+ EFR+ FK++NP   +V+AVGKAAG +WKS+S
Sbjct: 43 KRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLS 85

Triticum aestivum (taxid: 4565)

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

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/64 (53%), Positives = 45/64 (70%)

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 KSMS 98
          K+M+
Sbjct: 74 KTMT 77

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	103
449521910	112	PREDICTED: high mobility group B protein	0.990	0.910	0.759	4e-33
449461783	169	PREDICTED: high mobility group B protein	0.961	0.585	0.752	7e-32
312281849	185	unnamed protein product [Thellungiella h	0.941	0.524	0.702	8e-29
297819892	185	hypothetical protein ARALYDRAFT_323737 [	0.941	0.524	0.712	1e-28
42572635	185	high mobility group protein B1 [Arabidop	0.941	0.524	0.712	2e-28
255574381	171	DNA-binding protein MNB1B, putative [Ric	0.961	0.578	0.772	3e-28
15231065	178	high mobility group protein B1 [Arabidop	0.941	0.544	0.712	4e-28
334185909	161	high mobility group protein B1 [Arabidop	0.941	0.602	0.712	4e-28
224112525	176	high mobility group family [Populus tric	0.961	0.562	0.686	7e-27
224098541	179	high mobility group family [Populus tric	0.961	0.553	0.656	4e-26

>gi|449521910|ref|XP_004167972.1| PREDICTED: high mobility group B protein 1-like [Cucumis sativus]

 Score =  145 bits (365), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 79/104 (75%), Positives = 88/104 (84%), Gaps = 2/104 (1%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVSI 103
           SAFFVFLEEFRK +K+ENPNV AVSAVGKA G KWKS+S AVSI
Sbjct: 60  SAFFVFLEEFRKEYKRENPNVKAVSAVGKAGGEKWKSLSHAVSI 103

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  140 bits (354), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 76/101 (75%), Positives = 85/101 (84%), Gaps = 2/101 (1%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLEEFRK +K+ENPNV AVSAVGKA G KWKS+S A
Sbjct: 60  SAFFVFLEEFRKEYKRENPNVKAVSAVGKAGGEKWKSLSHA 100

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  130 bits (328), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 71/101 (70%), Positives = 82/101 (81%), Gaps = 4/101 (3%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLE+FR+TFKKENPNV AVSAVGKA G KWKSMS A
Sbjct: 58  SAFFVFLEDFRQTFKKENPNVKAVSAVGKAGGQKWKSMSQA 98

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

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 =  130 bits (327), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 72/101 (71%), Positives = 81/101 (80%), Gaps = 4/101 (3%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS A
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQA 98

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 =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 72/101 (71%), Positives = 81/101 (80%), Gaps = 4/101 (3%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS A
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQA 98

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  129 bits (323), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 78/101 (77%), Positives = 88/101 (87%), Gaps = 2/101 (1%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLEEFRKTFKKENP+VT+V+AVGKA G KWKSMS A
Sbjct: 60  SAFFVFLEEFRKTFKKENPSVTSVAAVGKAGGAKWKSMSSA 100

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 72/101 (71%), Positives = 81/101 (80%), Gaps = 4/101 (3%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS A
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQA 98

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 72/101 (71%), Positives = 81/101 (80%), Gaps = 4/101 (3%)

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

Query: 60  SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           SAFFVFLE+FR TFKKENPNV AVSAVGKA G KWKSMS A
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQA 98

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  124 bits (311), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 70/102 (68%), Positives = 80/102 (78%), Gaps = 3/102 (2%)

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

Query: 59  PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           PSAFFVFLEEFRK +K+E+PNV AVSAVGKA G KWKS+S A
Sbjct: 60  PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSAA 101

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  121 bits (304), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 67/102 (65%), Positives = 78/102 (76%), Gaps = 3/102 (2%)

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

Query: 59  PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           PS+FFVFLEEFRK +K+E+PN+ AVSAVGKA G KWKSMS A
Sbjct: 60  PSSFFVFLEEFRKIYKQEHPNMKAVSAVGKAGGEKWKSMSAA 101

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	103
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.184	0.131	0.842	6.1e-08
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.194	0.144	0.75	1.2e-07
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.194	0.16	0.6	0.00017

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

 Score = 90 (36.7 bits), Expect = 6.1e-08, Sum P(2) = 6.1e-08
 Identities = 16/19 (84%), Positives = 19/19 (100%)

Query:    60 SAFFVFLEEFRKTFKKENP 78
             SAFFVF+E+FR+TFKKENP
Sbjct:    43 SAFFVFMEDFRETFKKENP 61

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 = 78 (32.5 bits), Expect = 1.2e-07, Sum P(2) = 1.2e-07
 Identities = 15/20 (75%), Positives = 16/20 (80%)

Query:    60 SAFFVFLEEFRKTFKKENPN 79
             SAFFVFLE+FRK F   NPN
Sbjct:    40 SAFFVFLEDFRKEFNLANPN 59

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 = 65 (27.9 bits), Expect = 0.00017, Sum P(2) = 0.00017
 Identities = 12/20 (60%), Positives = 15/20 (75%)

Query:    60 SAFFVFLEEFRKTFKKENPN 79
             S FFVFL++FRK F   NP+
Sbjct:    39 SPFFVFLDDFRKEFNLANPD 58

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

---

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	0.7128	0.9417	0.5449	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	103
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	9e-10
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	8e-09
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	3e-08
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	2e-07
smart00398	70	smart00398, HMG, high mobility group	1e-06
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	2e-05
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	1e-04
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	0.004

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

 Score = 49.9 bits (120), Expect = 9e-10
 Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 55  PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           PKRP SAFF+F +E R   K ENP +   + + K  G KWK++S   
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEE 46

Length = 69

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

 Score = 47.6 bits (114), Expect = 8e-09
 Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 55  PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           PKRP SA+F+F +E R   K ENP ++ V  + K  G  WKS+S   
Sbjct: 1   PKRPLSAYFLFSQEHRAEVKAENPGLS-VGEISKILGEMWKSLSEEE 46

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

>gnl|CDD|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 = 46.1 bits (110), Expect = 3e-08
 Identities = 23/45 (51%), Positives = 30/45 (66%), Gaps = 1/45 (2%)

Query: 55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP 99
          PKRP SA+F+F +E R   KKENP+ + V+ V K  G KWK +S 
Sbjct: 1  PKRPLSAYFLFSQEQRPKLKKENPDAS-VTEVTKILGEKWKELSE 44

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

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

 Score = 46.8 bits (111), Expect = 2e-07
 Identities = 28/62 (45%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

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

Query: 98  SP 99
           + 
Sbjct: 113 TD 114

Length = 211

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

 Score = 41.9 bits (99), Expect = 1e-06
 Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           KPKRP SAF +F +E R   K ENP+++  + + K  G +WK +S   
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEE 47

Length = 70

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

 Score = 39.0 bits (91), Expect = 2e-05
 Identities = 20/49 (40%), Positives = 27/49 (55%)

Query: 52  PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           PNKPK   +A+F F++  R   K+E P V  V+   K    KWK+MS  
Sbjct: 1   PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEE 49

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

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

 Score = 37.1 bits (86), Expect = 1e-04
 Identities = 26/66 (39%), Positives = 34/66 (51%), Gaps = 1/66 (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  KSMSPA 100
             +S  
Sbjct: 64  NKLSEE 69

Length = 94

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

 Score = 33.0 bits (76), Expect = 0.004
 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           K  RP +AF ++ ++     K ENP +T  + + +  G  W+S SP V
Sbjct: 1   KIPRPRNAFILYRQDKHAQLKTENPGLTN-NEISRIIGRMWRSESPEV 47

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11. Length = 77

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	103
PTZ00199	94	high mobility group protein; Provisional	99.8
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.65
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.63
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.62
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.59
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.58
smart00398	70	HMG high mobility group.	99.57
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.55
KOG0381	96	consensus HMG box-containing protein [General func	99.47
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.46
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.44
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.28
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.71
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	98.66
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	98.4
KOG2746	683	consensus HMG-box transcription factor Capicua and	97.69
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.22
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	96.22
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	95.92
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	95.04
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	92.98
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	92.82
COG5648	211	NHP6B Chromatin-associated proteins containing the	87.99

>PTZ00199 high mobility group protein; Provisional

Probab=99.80  E-value=1e-19  Score=120.86  Aligned_cols=62  Identities=40%  Similarity=0.670  Sum_probs=55.4

Q ss_pred             ccccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhhCCCcccc
Q 034117           41 QGKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        41 ~~~k~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .+++++++.+|||.|+||+||||+|++++|..|..+||++. ++.+|+++||++|+.||++||
T Consensus         9 ~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK   71 (94)
T PTZ00199          9 LVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEK   71 (94)
T ss_pred             cccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHH
Confidence            34455667789999999999999999999999999999983 389999999999999999886

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

Probab=99.65  E-value=1.7e-16  Score=101.04  Aligned_cols=48  Identities=31%  Similarity=0.623  Sum_probs=45.9

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .|+||+||||||+++.|..|..+||++ ++.||+++||++|+.|+++||
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~~g~~Wk~ls~eeK   48 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGL-TNNEISRIIGRMWRSESPEVK   48 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHH
Confidence            489999999999999999999999999 699999999999999999986

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

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

Probab=99.63  E-value=4.9e-16  Score=94.81  Aligned_cols=47  Identities=49%  Similarity=0.820  Sum_probs=45.5

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        55 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |+||+|+|++|++++|..+..+||++ ++.+|++.||++|++||++||
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~-~~~~i~~~~~~~W~~ls~~eK   47 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDA-SVTEVTKILGEKWKELSEEEK   47 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            89999999999999999999999999 699999999999999999986

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

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

Probab=99.62  E-value=7.4e-16  Score=97.06  Aligned_cols=47  Identities=32%  Similarity=0.551  Sum_probs=45.0

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        55 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .|||+||||+|++++|..++.+||++ ++.||+++||++|+.|+++||
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~-~~~eisk~l~~~Wk~ls~~eK   48 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLK-ENRAISKILGDRWKALSNEEK   48 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHH
Confidence            58999999999999999999999999 599999999999999999886

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

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

Probab=99.59  E-value=1.1e-15  Score=114.49  Aligned_cols=59  Identities=44%  Similarity=0.755  Sum_probs=54.6

Q ss_pred             ccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        43 ~k~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +...++.+|||.||||+|+||+|++++|.++..++|.+ +|.+|++.+|++|++|+++||
T Consensus        59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l-~~~e~~k~~~e~WK~Ltd~ek  117 (211)
T COG5648          59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKL-TFGEVGKLLSEKWKELTDEEK  117 (211)
T ss_pred             HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHhccHhhh
Confidence            34556678999999999999999999999999999999 599999999999999999986

>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=99.58  E-value=1.8e-15  Score=93.17  Aligned_cols=47  Identities=38%  Similarity=0.738  Sum_probs=43.4

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        55 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |+||+|||++|+++++..++.+||++ ++.+|++.||++|++|+++||
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~-~~~~i~~~~~~~W~~l~~~eK   47 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDL-SNKEISKILAQMWKNLSEEEK   47 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTS-THHHHHHHHHHHHHCSHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhccc-ccccchhhHHHHHhcCCHHHH
Confidence            89999999999999999999999999 599999999999999999986

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

>smart00398 HMG high mobility group

Probab=99.57  E-value=4.6e-15  Score=90.77  Aligned_cols=48  Identities=42%  Similarity=0.728  Sum_probs=45.9

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .|+||+|+|++|++++|..+..+||++ ++.+|++.||++|+.|++++|
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~-~~~~i~~~~~~~W~~l~~~ek   48 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDL-SNAEISKKLGERWKLLSEEEK   48 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHcCCHHHH
Confidence            589999999999999999999999999 599999999999999999986

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

Probab=99.55  E-value=8.9e-15  Score=88.56  Aligned_cols=47  Identities=45%  Similarity=0.780  Sum_probs=45.2

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           55 PKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        55 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |+||+|+||+|++++|..+..+||++ ++.+|++.||++|+.|++++|
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~-~~~~i~~~~~~~W~~l~~~~k   47 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGL-SVGEISKILGEMWKSLSEEEK   47 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            79999999999999999999999999 599999999999999999986

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

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

Probab=99.47  E-value=1e-13  Score=90.76  Aligned_cols=51  Identities=47%  Similarity=0.806  Sum_probs=48.4

Q ss_pred             CC--CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           51 DP--NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        51 dp--~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |+  +.|+||++||++|++++|..++.+||++ ++.||++++|++|++|+++++
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~-~~~~v~k~~g~~W~~l~~~~k   69 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGL-SVGEVAKALGEMWKNLAEEEK   69 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCCHHHH
Confidence            66  5999999999999999999999999998 699999999999999999886

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

Probab=99.46  E-value=8e-14  Score=87.97  Aligned_cols=50  Identities=42%  Similarity=0.735  Sum_probs=42.2

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHh-CCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKE-NPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e-~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |+.||||+|||+||+.+++..+..+ ++.. ++.|+++.|++.|++||++||
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~-~~~e~~k~~~~~Wk~Ls~~EK   51 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQ-SFREVMKEISERWKSLSEEEK   51 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-S-SHHHHHHHHHHHHHHS-HHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCC-CHHHHHHHHHHHHHhcCHHHH
Confidence            6899999999999999999999988 6767 599999999999999999986

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 ....

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.44  E-value=1e-13  Score=110.16  Aligned_cols=55  Identities=31%  Similarity=0.549  Sum_probs=50.7

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCccccC
Q 034117           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVSI  103 (103)
Q Consensus        48 k~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER~  103 (103)
                      .....+..||||||||+|.+.+|.+|..+||.++ +.||||.||.+|+.|+++||.
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mH-NSEISK~LG~~WK~Lse~EKr  110 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMH-NSEISKRLGAEWKLLSEEEKR  110 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcchh-hHHHHHHHHHHHhhcCHhhhc
Confidence            3356779999999999999999999999999995 999999999999999999973

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

Probab=99.28  E-value=3.1e-12  Score=106.60  Aligned_cols=55  Identities=44%  Similarity=0.765  Sum_probs=50.1

Q ss_pred             cccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCccc
Q 034117           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV  101 (103)
Q Consensus        44 k~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eE  101 (103)
                      ++.++.+|||+|||++||||+|.+..|..|+.+  +. +++||++.+|++|+.|+..+
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi-~~~dv~kk~g~~wk~ms~k~  579 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GI-SVGDVAKKAGEKWKQMSAKE  579 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--Cc-hHHHHHHHHhHHHhhhcccc
Confidence            455667899999999999999999999999987  88 69999999999999999854

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

Probab=98.71  E-value=5.3e-09  Score=86.52  Aligned_cols=55  Identities=27%  Similarity=0.474  Sum_probs=49.5

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCccccC
Q 034117           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVSI  103 (103)
Q Consensus        48 k~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER~  103 (103)
                      ....++..||||||||+|.+|.|..|...+|+++ +..|+++||-+|+.|+..|++
T Consensus       319 ~~ss~PHIKRPMNAFMVWAkDERRKILqA~PDMH-NSnISKILGSRWKaMSN~eKQ  373 (511)
T KOG0528|consen  319 RASSEPHIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMSNTEKQ  373 (511)
T ss_pred             cCCCCccccCCcchhhcccchhhhhhhhcCcccc-ccchhHHhccccccccccccc
Confidence            3455678999999999999999999999999996 999999999999999988763

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=98.66  E-value=2e-08  Score=80.58  Aligned_cols=48  Identities=23%  Similarity=0.479  Sum_probs=43.9

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ..|+|+||||+|++|.|..|.+|+.-- ...+|.++||.+|..||.||.
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEctlK-eSAaiNqiLGrRWH~LSrEEQ  238 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECTLK-ESAAINQILGRRWHALSREEQ  238 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhhhh-hHHHHHHHHhHHHhhhhHHHH
Confidence            789999999999999999999999744 588999999999999998874

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

Probab=98.40  E-value=2.6e-07  Score=73.75  Aligned_cols=54  Identities=22%  Similarity=0.527  Sum_probs=49.9

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           48 AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        48 k~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ..+.|..|-+|+-+||.|+...|.++++.||++. .-||.++||.+|..|+++|+
T Consensus        58 ~pkpPkppekpl~pymrySrkvWd~VkA~nPe~k-LWeiGK~Ig~mW~dLpd~EK  111 (410)
T KOG4715|consen   58 RPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELK-LWEIGKIIGGMWLDLPDEEK  111 (410)
T ss_pred             CCCCCCCCCcccchhhHHhhhhhhhhhccCcchH-HHHHHHHHHHHHhhCcchHH
Confidence            3456778999999999999999999999999996 99999999999999999986

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

Probab=97.69  E-value=1.7e-05  Score=68.01  Aligned_cols=54  Identities=26%  Similarity=0.535  Sum_probs=48.6

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHH--HHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           48 AKKDPNKPKRPPSAFFVFLEEFR--KTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        48 k~kdp~~PKRP~say~lF~~e~R--~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      -+.+.....||||+|++|++.+|  ..+.+.||+. .+.-|+++|||.|-.|-++|+
T Consensus       175 nkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~-DNrtIskiLgewWytL~~~Ek  230 (683)
T KOG2746|consen  175 NKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQ-DNRTISKILGEWWYTLGPNEK  230 (683)
T ss_pred             CcCcchhhhhhhHHHHHHHhhcCCccchhccCccc-cchhHHHHHhhhHhhhCchhh
Confidence            33566689999999999999999  9999999999 599999999999999988886

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

Probab=97.22  E-value=0.00086  Score=49.33  Aligned_cols=49  Identities=33%  Similarity=0.527  Sum_probs=43.2

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCc
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP   99 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~   99 (103)
                      +-|.+..|-+|||..|+++.-+.|++.+|++ +..|.-...+..|...+.
T Consensus       117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~i-shkeaFs~aAknW~h~ph  165 (170)
T PF04690_consen  117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPDI-SHKEAFSAAAKNWAHFPH  165 (170)
T ss_pred             CCccccCCCchhHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHhhhhCcc
Confidence            4456666888999999999999999999999 699999999999988753

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

Probab=96.22  E-value=0.006  Score=45.31  Aligned_cols=39  Identities=26%  Similarity=0.448  Sum_probs=34.5

Q ss_pred             CchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           59 PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        59 ~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      -++|+-|+.++|..    |.+| +..|+....+..|..|+++||
T Consensus        83 nnaYLNFLReFRrk----h~~L-~p~dlI~~AAraW~rLSe~eK  121 (183)
T PF06382_consen   83 NNAYLNFLREFRRK----HCGL-SPQDLIQRAARAWCRLSEAEK  121 (183)
T ss_pred             chHHHHHHHHHHHH----ccCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            36799999999884    5789 599999999999999999886

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=95.92  E-value=0.011  Score=36.19  Aligned_cols=40  Identities=20%  Similarity=0.392  Sum_probs=35.5

Q ss_pred             CchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCc
Q 034117           59 PSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP   99 (103)
Q Consensus        59 ~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~   99 (103)
                      ++.|=+|.+..|+.|...||++. ...|...++.+|++-++
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~~-~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKAP-MSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCc-HHHHHHHHHHHHHHHHh
Confidence            46788999999999999999995 99999999999987543

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

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

Probab=95.04  E-value=0.046  Score=35.83  Aligned_cols=48  Identities=19%  Similarity=0.252  Sum_probs=37.4

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCccccC
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVSI  103 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER~  103 (103)
                      .|..|-++--+|.+.....+...|++. ...+ .+.+...|.+|++.+||
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~d-r~K~-~kam~~~W~~me~Kekl   50 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRND-RKKA-LKAMEAQWSQMEKKEKL   50 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTST-HHHH-HHHHHHHHHTTGGGHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHh-HHHH-HHHHHHHHHHhhhhhhh
Confidence            466788999999999999999999988 4656 45899999999998875

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

Probab=92.98  E-value=0.2  Score=35.04  Aligned_cols=46  Identities=24%  Similarity=0.385  Sum_probs=39.7

Q ss_pred             CCCCCC-chhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcc
Q 034117           54 KPKRPP-SAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA  100 (103)
Q Consensus        54 ~PKRP~-say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~e  100 (103)
                      +|-|.+ -||.-|....-+.|+.+||+|. .+.+-.+|-..|..-+++
T Consensus        71 HPErR~KAAy~afeE~~Lp~lK~E~PgLr-lsQ~kq~l~K~w~KSPeN  117 (122)
T PF06244_consen   71 HPERRMKAAYKAFEERRLPELKEENPGLR-LSQYKQMLWKEWQKSPEN  117 (122)
T ss_pred             CcchhHHHHHHHHHHHHhHHHHhhCCCch-HHHHHHHHHHHHhcCCCC
Confidence            455555 6899999999999999999996 999999999999887653

>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=92.82  E-value=0.26  Score=37.08  Aligned_cols=42  Identities=21%  Similarity=0.452  Sum_probs=33.8

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhC
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKS   96 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~   96 (103)
                      .....++||+|+||.|+.=+-    ...|+.+ ..++|..|+..|..
T Consensus        39 ~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~-Qk~~S~~l~~lW~~   80 (201)
T PF04769_consen   39 RSPEKAKRPLNGFMAFRSYYS----PIFPPLP-QKELSGILTKLWEK   80 (201)
T ss_pred             ccccccccchhHHHHHHHHHH----hhcCCcC-HHHHHHHHHHHHhC
Confidence            455678999999999987665    3457774 88999999999975

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

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

Probab=87.99  E-value=0.22  Score=37.90  Aligned_cols=49  Identities=16%  Similarity=0.257  Sum_probs=42.5

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcc
Q 034117           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA  100 (103)
Q Consensus        51 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~e  100 (103)
                      ..-+++.|..+|+-|..+.|+.+...+|.. +..+++++++..|.+|+++
T Consensus       140 ~k~~~~~~~~~~~e~~~~~r~~~~~~~~~~-~~~e~~k~~~~~w~el~~s  188 (211)
T COG5648         140 KKLPNKAPIGPFIENEPKIRPKVEGPSPDK-ALVEETKIISKAWSELDES  188 (211)
T ss_pred             cccCCCCCCchhhhccHHhccccCCCCcch-hhhHHhhhhhhhhhhhChh
Confidence            344677888889999999999999889888 5889999999999999875

---

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	103
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	7e-14
2lhj_A	97	High mobility group protein homolog NHP1; structur	1e-13
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	3e-13
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	3e-13
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	5e-13
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	3e-12
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-12
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	7e-12
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-11
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	5e-11
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	8e-11
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	4e-10
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	3e-08
1ckt_A	71	High mobility group 1 protein; high-mobility group	2e-09
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	5e-09
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	1e-08
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	7e-06
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	6e-08
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	6e-08
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	1e-07
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-07
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	4e-07
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	6e-07
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	6e-06
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	1e-05
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	2e-05
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	4e-05
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	9e-05
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	2e-04
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	3e-04

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

 Score = 60.3 bits (147), Expect = 7e-14
 Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 50  KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           KDPN PKRPPSAFF+F  E+R   K E+P ++ +  V K  G  W + +  
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAAD 51

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

 Score = 60.1 bits (146), Expect = 1e-13
 Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 1/66 (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  KSMSPA 100
            ++S  
Sbjct: 64  NALSDE 69

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

 Score = 58.9 bits (143), Expect = 3e-13
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

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

>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 = 59.3 bits (144), Expect = 3e-13
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

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

Query: 99  PA 100
           P 
Sbjct: 64  PE 65

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

 Score = 58.1 bits (141), Expect = 5e-13
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPA 100
            K DP KP+   S++  F++  R+  KK++P+ +   S   K    +WK+MS  
Sbjct: 1   GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 54

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

 Score = 56.7 bits (137), Expect = 3e-12
 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 46  KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           KK KK P+ PK+P + +F F  E R  + K +P ++    + K    K+K +   
Sbjct: 2   KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEK 55

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

 Score = 56.7 bits (137), Expect = 3e-12
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

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

Query: 99  PA 100
             
Sbjct: 61  EE 62

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

 Score = 55.5 bits (134), Expect = 7e-12
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
                + PK P + +  FL E R+  +  +P++     + K  G +W  + PA
Sbjct: 1   GSSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPA 52

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

 Score = 54.7 bits (132), Expect = 2e-11
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

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

Query: 96  SMSPA 100
            +S  
Sbjct: 61  DLSEK 65

>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 = 52.7 bits (127), Expect = 5e-11
 Identities = 19/46 (41%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          +KPKRP SA+ ++L   R++ K+ENP +  V+ V K  G  W++M 
Sbjct: 2  DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK 46

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

 Score = 52.3 bits (126), Expect = 8e-11
 Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          + PKR  +AF ++L + R++ K+ENP +  V+ + K  G  WK + 
Sbjct: 2  HMPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELK 46

>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 = 52.7 bits (126), Expect = 4e-10
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

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

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

 Score = 47.7 bits (113), Expect = 3e-08
 Identities = 28/88 (31%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

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

Query: 73  FKKENPNVTAVSAVGKAAGGKWKSMSPA 100
            K E+P ++ +  V K  G  W + +  
Sbjct: 120 IKGEHPGLS-IGDVAKKLGEMWNNTAAD 146

>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 = 48.9 bits (117), Expect = 2e-09
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPA 100
           KP+   S++  F++  R+  KK++P+ +   S   K    +WK+MS  
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 48

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

 Score = 50.5 bits (120), Expect = 5e-09
 Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 47  KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
            +    + PK+P S++  F +E    FK +NP+    + + +    +W+ +  +
Sbjct: 2   GSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDS 54

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

 Score = 48.3 bits (115), Expect = 1e-08
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ A
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEA 49

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

 Score = 41.4 bits (97), Expect = 7e-06
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

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

Query: 78  PNVTAVSAVGKAAGGKWKSMSPA 100
           P ++ +  V K  G  W + +  
Sbjct: 112 PGLS-IGDVAKKLGEMWNNTAAD 133

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

 Score = 45.0 bits (107), Expect = 6e-08
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 5/47 (10%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           KPKRP SA+ V++ E  +  K ++P         K     WK++S +
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDS 43

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

 Score = 47.5 bits (112), Expect = 6e-08
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

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

Query: 88  KAAGGKWKSMSPA 100
           +    +W+ +  +
Sbjct: 74  RRIAQRWRELPDS 86

>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 = 45.1 bits (107), Expect = 1e-07
 Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

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

Query: 94  WKSMSPAV 101
           W+ ++ + 
Sbjct: 68  WRLLNESE 75

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

 Score = 44.0 bits (104), Expect = 2e-07
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
                +  K+P SA  +F+++ R  F  ENP  + +          WK++S  
Sbjct: 1   GSSGSSGIKKPMSASALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEE 52

>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 = 43.2 bits (102), Expect = 4e-07
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 42  GKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
                 +   PNK KRP +AF +F +++R  + +  P      A+    G +WK M   
Sbjct: 5   SSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKD-NRAISVILGDRWKKMKNE 62

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

 Score = 42.6 bits (101), Expect = 6e-07
 Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 48  AKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
                +  +RP +AF +F +  R   ++E+P +       K     W  + P  
Sbjct: 1   GSSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLD-NRGATKILADWWAVLDPKE 53

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

 Score = 39.5 bits (93), Expect = 6e-06
 Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
             +RP +AF V+ ++ RK   ++NP++   + + K  G  WK+++ A 
Sbjct: 2   SIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAE 48

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

 Score = 38.7 bits (91), Expect = 1e-05
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ A 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAE 50

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

 Score = 38.7 bits (91), Expect = 2e-05
 Identities = 14/52 (26%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 50  KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
              ++ +RP +AF V+ ++ RK   ++NP++   + + K  G  WK+++ A 
Sbjct: 2   SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAE 52

>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 = 37.9 bits (89), Expect = 4e-05
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           ++ KRP +AF V+    R+   +ENP +   S + K  G +WK +S   
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETE 48

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

 Score = 36.8 bits (86), Expect = 9e-05
 Identities = 12/46 (26%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 56  KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           KRP +AF V+ +  R+   +++P++   + + K  G +WK +  + 
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPDMH-NAEISKRLGKRWKLLKDSD 48

>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 = 36.4 bits (85), Expect = 2e-04
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ A 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAE 50

>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 = 35.6 bits (83), Expect = 3e-04
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
              KRP +AF V+ ++ R+   +  P++   S + K  G +WK+M+   
Sbjct: 3   PHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLE 50

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	103
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.83
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.81
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.8
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.8
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.79
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.79
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.79
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.79
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.78
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.77
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.77
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.75
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.75
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.74
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.74
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.73
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.72
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.72
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.72
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.71
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.71
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.71
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.71
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.71
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.7
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.7
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.68
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.66
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.63
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.63
2cto_A	93	Novel protein; high mobility group box domain, hel	99.6
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.59
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.58
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.56
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.56
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.52
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.48
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.43
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.42

>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=99.83  E-value=7.5e-21  Score=123.70  Aligned_cols=58  Identities=31%  Similarity=0.575  Sum_probs=54.1

Q ss_pred             cccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        44 k~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +.+++.+||+.|+||+|||||||+++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus        10 k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~-~~~eisk~lg~~Wk~ls~eeK   67 (90)
T 1wgf_A           10 SQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKK   67 (90)
T ss_dssp             CSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            4456678999999999999999999999999999999 699999999999999999886

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

Probab=99.81  E-value=1.2e-20  Score=124.16  Aligned_cols=60  Identities=43%  Similarity=0.730  Sum_probs=55.5

Q ss_pred             cccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCc--HHHHHHHHHHHhhCCCcccc
Q 034117           42 GKREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTA--VSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        42 ~~k~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s--~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++++++..+||+.|+||+||||||++++|..|+.+||++ +  +.||+++||++|++|+++||
T Consensus        10 k~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~-~~~~~eisk~lg~~Wk~ls~eeK   71 (97)
T 2lhj_A           10 VRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEI-AKDVAAIGKMIGAAWNALSDEEK   71 (97)
T ss_dssp             CCCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTS-TTCSSHHHHHHHHTSSSSCSTTT
T ss_pred             ccccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CccHHHHHHHHHHHHHhCCHHHH
Confidence            345566778999999999999999999999999999999 7  99999999999999999987

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

Probab=99.80  E-value=6e-20  Score=121.97  Aligned_cols=57  Identities=33%  Similarity=0.659  Sum_probs=53.2

Q ss_pred             ccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           45 EKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        45 ~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++++.+||+.|+||+||||||++++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus         8 ~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~-~~~eisk~lg~~Wk~ls~eeK   64 (102)
T 2co9_A            8 KKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQK   64 (102)
T ss_dssp             SCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHccCCHHHH
Confidence            345668999999999999999999999999999999 599999999999999999986

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

Probab=99.80  E-value=3.4e-20  Score=122.80  Aligned_cols=56  Identities=30%  Similarity=0.515  Sum_probs=52.7

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +++.+||+.||||+|||||||+++|..|+.+||++ ++.||+++||++|++||++||
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~-~~~eisk~lg~~Wk~ls~eeK   57 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKK   57 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            44568999999999999999999999999999999 699999999999999999986

>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=99.79  E-value=8.7e-20  Score=117.57  Aligned_cols=52  Identities=21%  Similarity=0.367  Sum_probs=49.7

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCc-HHHHHHHHHHHhhCCCcccc
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTA-VSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s-~~eisK~lge~Wk~Ls~eER  102 (103)
                      .++|.||||+|||||||+++|..|+.+||++ + +.||+++||++|++|+++||
T Consensus         1 ~~~~~PKRP~say~lF~~e~R~~ik~~~P~~-~~~~eisK~lge~Wk~ls~eeK   53 (81)
T 2d7l_A            1 GSSGSSGRPKTGFQMWLEENRSNILSDNPDF-SDEADIIKEGMIRFRVLSTEER   53 (81)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHHHHHCTTC-CSHHHHHHHHHHHHSSSCHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-chhHHHHHHHHHHHHcCCHHHH
Confidence            3789999999999999999999999999999 7 99999999999999999886

>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=99.79  E-value=1.1e-19  Score=114.24  Aligned_cols=53  Identities=43%  Similarity=0.822  Sum_probs=50.8

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        49 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++||+.|+||+||||||++++|..|+.+||++ ++.||+++||++|++||++||
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK   53 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDK   53 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHHSCGGGS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            36999999999999999999999999999999 699999999999999999987

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

Probab=99.79  E-value=1e-19  Score=117.16  Aligned_cols=57  Identities=37%  Similarity=0.585  Sum_probs=52.0

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++..+||+.||||+||||||++++|..|+.+||++. ++.||+++||++|++|+++||
T Consensus         7 ~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK   64 (86)
T 2eqz_A            7 GMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEK   64 (86)
T ss_dssp             SCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHH
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHH
Confidence            345689999999999999999999999999999984 269999999999999999986

>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=99.79  E-value=1.6e-20  Score=122.78  Aligned_cols=58  Identities=43%  Similarity=0.799  Sum_probs=54.0

Q ss_pred             cccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           44 REKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        44 k~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++++..+||+.|+||+||||||++++|..|..+||++ ++.||+++||++|++||++||
T Consensus        10 ~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK   67 (93)
T 1cg7_A           10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEK   67 (93)
T ss_dssp             CCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTS-CHHHHTTTHHHHHHTTHHHHH
T ss_pred             ccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            4456678999999999999999999999999999999 699999999999999999886

>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=99.78  E-value=1.7e-19  Score=116.44  Aligned_cols=55  Identities=29%  Similarity=0.555  Sum_probs=52.0

Q ss_pred             ccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        47 kk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +..+||+.|+||+||||||++++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK   64 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGK-DNRAISVILGDRWKKMKNEER   64 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHH
Confidence            4567999999999999999999999999999999 599999999999999999986

>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=99.77  E-value=2.3e-19  Score=112.60  Aligned_cols=51  Identities=31%  Similarity=0.540  Sum_probs=47.5

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        51 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ||+.|+||+||||||++++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK   51 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEK   51 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCC-SSSHHHHHHHHHHHTCCHHHH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHhHHHhCCHHHH
Confidence            689999999999999999999999999999 599999999999999999986

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

Probab=99.77  E-value=4.2e-19  Score=115.70  Aligned_cols=52  Identities=25%  Similarity=0.608  Sum_probs=50.3

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +||+.||||+||||||++++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus         3 kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK   54 (92)
T 2crj_A            3 SGSSGPKAPVTGYVRFLNERREQIRTRHPDL-PFPEITKMLGAEWSKLQPAEK   54 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHTCCTTHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHH
Confidence            6999999999999999999999999999999 599999999999999999986

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

Probab=99.75  E-value=3.3e-19  Score=113.81  Aligned_cols=54  Identities=31%  Similarity=0.593  Sum_probs=50.1

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhhCCCcccc
Q 034117           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        49 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++||+.||||+|||||||+++|..|+.+||++. ++.||+++||++|++|+++||
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK   56 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK   56 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHH
Confidence            379999999999999999999999999999984 259999999999999999986

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

Probab=99.75  E-value=1.7e-18  Score=112.81  Aligned_cols=52  Identities=25%  Similarity=0.402  Sum_probs=49.9

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .++++||||+||||+|++++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK   54 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKT-SLEDATLQIEELWKTLSEEEK   54 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSS-CHHHHHHHHHHHHHSSCHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHH
Confidence            5899999999999999999999999999999 599999999999999999986

>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=99.74  E-value=2e-18  Score=110.89  Aligned_cols=51  Identities=31%  Similarity=0.539  Sum_probs=48.8

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        51 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .||.|+||+||||||++++|..|..+||++ ++.||+++||++|++||++||
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK   51 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEK   51 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHCCHHHH
Confidence            479999999999999999999999999999 699999999999999999986

>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=99.74  E-value=1.8e-18  Score=110.10  Aligned_cols=52  Identities=21%  Similarity=0.471  Sum_probs=49.8

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .|++.|+||+||||||++++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK   54 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRL-DNRGATKILADWWAVLDPKEK   54 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSS-CTTHHHHHHHHHHHTCCHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHH
Confidence            5889999999999999999999999999999 599999999999999999886

>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=99.73  E-value=5.9e-18  Score=107.53  Aligned_cols=50  Identities=28%  Similarity=0.522  Sum_probs=47.3

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++.|+||+||||||++++|..|..+||++ ++.||+++||++|++|+++||
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK   51 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEK   51 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGG
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhhhhhCCHHHH
Confidence            57899999999999999999999999999 599999999999999999986

>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=99.72  E-value=7.3e-18  Score=105.37  Aligned_cols=47  Identities=40%  Similarity=0.793  Sum_probs=45.1

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCc
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP   99 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~   99 (103)
                      .|+||||+|||||||+++|..|+.+||++ ++.||+++||++|++|++
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~   47 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGI-KVTEVAKRGGELWRAMKD   47 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSC-CHHHHHHHHHHHHHHCSC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCc
Confidence            47899999999999999999999999999 699999999999999987

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

Probab=99.72  E-value=8.6e-18  Score=105.04  Aligned_cols=45  Identities=36%  Similarity=0.803  Sum_probs=43.9

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCC
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSM   97 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~L   97 (103)
                      ||.||||+||||+|++++|..|+.+||++ ++.||+++||++|++|
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~l   45 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGI-KVTEIAKKGGEMWKEL   45 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTC-CHHHHHHHHHHHHHTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhh
Confidence            78999999999999999999999999999 6999999999999999

>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=99.72  E-value=5.2e-18  Score=107.96  Aligned_cols=51  Identities=27%  Similarity=0.544  Sum_probs=45.7

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        51 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .++.|+||+||||||++++|..|..+||++ ++.||+++||++|++|+++||
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK   53 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDL-HNAELSKMLGKSWKALTLAEK   53 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHH
Confidence            467899999999999999999999999999 599999999999999999986

>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=99.71  E-value=1.1e-17  Score=103.56  Aligned_cols=49  Identities=29%  Similarity=0.564  Sum_probs=45.7

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhhCCCcccc
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +||||+||||+|++++|..++.+||++. ++.||+++||++|++|+++||
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK   50 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK   50 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTS
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHH
Confidence            5999999999999999999999999984 259999999999999999986

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

Probab=99.71  E-value=8.8e-18  Score=112.36  Aligned_cols=53  Identities=23%  Similarity=0.486  Sum_probs=47.6

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        49 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .++++.|+||+|||||||+++|..|+.+||++ ++.||+++||++|++|+++||
T Consensus        24 ~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~-~~~eisk~lg~~Wk~ls~eeK   76 (106)
T 4euw_A           24 SKNKPHVKRPMNAFMVWAQAARRKLADQYPHL-HNAELSKTLGKLWRLLNESEK   76 (106)
T ss_dssp             ----CCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHH
T ss_pred             cCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHH
Confidence            46899999999999999999999999999999 699999999999999999986

>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=99.71  E-value=9.3e-18  Score=117.86  Aligned_cols=56  Identities=45%  Similarity=0.814  Sum_probs=52.6

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++..+||+.||||+|||||||+++|..|+.+||++ +++||+++||++|++|+++||
T Consensus        80 kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK  135 (159)
T 2gzk_A           80 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDK  135 (159)
T ss_dssp             GGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCC-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             cccccccccccccccccchhhHhhHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            44568999999999999999999999999999999 699999999999999999886

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

Probab=99.71  E-value=5.3e-18  Score=104.63  Aligned_cols=49  Identities=29%  Similarity=0.575  Sum_probs=43.7

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        53 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +.||||+||||||++++|..+..+||++ ++.||+++||++|++||++||
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK   49 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDL-HNAELSKMLGKSWKALTLAEK   49 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHH
Confidence            4799999999999999999999999999 599999999999999999986

>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=99.71  E-value=9.8e-18  Score=106.13  Aligned_cols=49  Identities=33%  Similarity=0.603  Sum_probs=46.8

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        53 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +.|+||+||||||++++|..|..+||++ ++.||+++||++|++||++||
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK   49 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEK   49 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            5799999999999999999999999999 599999999999999999986

>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=99.70  E-value=1.8e-17  Score=106.48  Aligned_cols=49  Identities=22%  Similarity=0.476  Sum_probs=46.6

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        53 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ..|+||+||||||++++|..|..+||++ ++.||+++||++|++||++||
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK   49 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQ   49 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHH
Confidence            3699999999999999999999999999 699999999999999999986

>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=99.70  E-value=1.2e-17  Score=105.20  Aligned_cols=49  Identities=24%  Similarity=0.495  Sum_probs=46.8

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        53 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +.||||+||||||++++|..|..+||++ ++.||+++||++|++|+++||
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK   49 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDM-HNAEISKRLGKRWKLLKDSDK   49 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            5799999999999999999999999999 599999999999999999986

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

Probab=99.68  E-value=4.3e-17  Score=116.13  Aligned_cols=55  Identities=44%  Similarity=0.809  Sum_probs=51.9

Q ss_pred             ccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        47 kk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++.+||+.|+||+|||||||+++|..|..+||++ ++.||+++||++|++|+++|+
T Consensus        94 k~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK  148 (173)
T 2yrq_A           94 KKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDK  148 (173)
T ss_dssp             CSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSS-CHHHHHHHHHHHHHHSCGGGH
T ss_pred             ccccCCccccCcccHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            4557999999999999999999999999999999 599999999999999999986

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

Probab=99.66  E-value=7.6e-17  Score=114.83  Aligned_cols=55  Identities=33%  Similarity=0.600  Sum_probs=51.4

Q ss_pred             ccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCC--CCcHHHHHHHHHHHhhCCCcccc
Q 034117           47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPN--VTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        47 kk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~--~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ...+||+.|+||+||||||++++|..|+.+||+  + ++.||+++||++|++|+++|+
T Consensus         8 ~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~-~~~eisk~lg~~Wk~ls~~eK   64 (173)
T 2yrq_A            8 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASV-NFSEFSKKCSERWKTMSAKEK   64 (173)
T ss_dssp             SSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCC-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            455799999999999999999999999999999  5 599999999999999999886

>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=99.63  E-value=1.2e-16  Score=107.34  Aligned_cols=52  Identities=21%  Similarity=0.395  Sum_probs=47.3

Q ss_pred             cccCCCCCCC-CCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKP-KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~P-KRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .++.+|++.| |||+|||||||+++|..|+    ++ ++.||++.||++|++|+++||
T Consensus         8 ~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~-~~~eisk~lg~~Wk~Ls~~eK   60 (108)
T 1v64_A            8 QLKDKFDGRPTKPPPNSYSLYCAELMANMK----DV-PSTERMVLCSQQWKLLSQKEK   60 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CC-CHHHHHHHHHHHHHhCCHHHH
Confidence            3456799999 9999999999999999887    78 599999999999999999986

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

Probab=99.63  E-value=5.8e-18  Score=111.51  Aligned_cols=52  Identities=17%  Similarity=0.195  Sum_probs=47.7

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCc--HHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTA--VSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s--~~eisK~lge~Wk~Ls~eER  102 (103)
                      .+..+|||+||||+|||||||+++|..|+.+||++ +  +.||+    ++|++|+++||
T Consensus        14 ~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~-s~~~~eIs----e~Wk~ls~eeK   67 (90)
T 2yuk_A           14 LKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDW-TTRVKQIA----KLWRKASSQER   67 (90)
T ss_dssp             HHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSH-HHHHHHHH----HHHHHSCHHHH
T ss_pred             hhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCc-cchHHHHH----HHHHcCCHHHH
Confidence            34456999999999999999999999999999999 8  89998    99999999886

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

Probab=99.60  E-value=1.9e-16  Score=104.56  Aligned_cols=50  Identities=16%  Similarity=0.359  Sum_probs=47.0

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHH---HHHhhCCCcccc
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAA---GGKWKSMSPAVS  102 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~l---ge~Wk~Ls~eER  102 (103)
                      .++|.||||+||||||++++|.+|+.+  ++ ++.||+++|   |++|++|+++||
T Consensus         6 ~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~-~~~eisK~l~~cGe~Wk~ls~eEK   58 (93)
T 2cto_A            6 SGMPNRKASRNAYYFFVQEKIPELRRR--GL-PVARVADAIPYCSSDWALLREEEK   58 (93)
T ss_dssp             CCCCCCCSSCCHHHHHHHTTHHHHHHH--TC-CCSSHHHHTGGGHHHHHHSCHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHc--CC-CHHHHHHHHHHHHHHHHcCCHHHH
Confidence            588999999999999999999999988  78 599999999   999999999886

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

Probab=99.59  E-value=5.2e-16  Score=95.31  Aligned_cols=45  Identities=31%  Similarity=0.458  Sum_probs=41.0

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        53 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |.||||+||||+|++++|..++.+|     ++||++.||++|++||++||
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~-----p~ei~k~lg~~Wk~ls~~eK   45 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEK   45 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSS-----HHHHHHHHHHHHHTCCHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcC-----HHHHHHHHHHHHhhCCHHHH
Confidence            6899999999999999999997554     46999999999999999986

>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=99.58  E-value=2e-15  Score=99.60  Aligned_cols=49  Identities=16%  Similarity=0.168  Sum_probs=46.3

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .|.|+||+|||+||++++|..++.+||+ . +.||++.||++|++|+++|+
T Consensus         2 ~~kPKrP~SAy~lf~~~~r~~~k~~~p~-~-~~evsK~lGe~Wk~ls~~eK   50 (91)
T 1l8y_A            2 GKLPESPKRAEEIWQQSVIGDYLARFKN-D-RVKALKAMEMTWNNMEKKEK   50 (91)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHHTTS-T-HHHHHHHHHHHHHTTGGGHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCC-C-HHHHHHHHHHHHhcCCHHHH
Confidence            3789999999999999999999999998 4 99999999999999999886

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

Probab=99.56  E-value=9.6e-16  Score=114.84  Aligned_cols=53  Identities=21%  Similarity=0.444  Sum_probs=50.6

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        49 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ..||+.||||+|||||||+++|..|+.+||++ ++.||+++||++|++|+++|+
T Consensus        36 ~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK   88 (238)
T 3tmm_A           36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKK   88 (238)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            46899999999999999999999999999999 599999999999999999886

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

Probab=99.56  E-value=1.4e-15  Score=112.36  Aligned_cols=51  Identities=22%  Similarity=0.472  Sum_probs=48.7

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        51 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +|+.|+||+|||||||+++|..|+.+||++ ++.||+++||++|++|+++|+
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK   56 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKK   56 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHccCHHhh
Confidence            578999999999999999999999999999 699999999999999999886

>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=99.52  E-value=8.2e-15  Score=97.27  Aligned_cols=50  Identities=16%  Similarity=0.300  Sum_probs=42.8

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           50 KDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        50 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ...++||||+|||||||++++.  ..+++++ ++.||++.||++|++|+++||
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~-~~~eisK~lge~Wk~ls~~eK   53 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHL-PLKERMVEIGSRWQRISQSQK   53 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTS-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            3567899999999999999975  3345667 599999999999999999986

>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=99.48  E-value=3.7e-14  Score=99.39  Aligned_cols=50  Identities=32%  Similarity=0.570  Sum_probs=47.8

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++.|+||+++||+|+++.|..|..+||++ ++.||+++||++|++|+++|+
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~-~~~eisk~lg~~Wk~ls~~eK   51 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEK   51 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSC-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHhhHHHh
Confidence            67999999999999999999999999999 599999999999999999886

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

Probab=99.43  E-value=3.4e-15  Score=110.31  Aligned_cols=52  Identities=31%  Similarity=0.385  Sum_probs=45.4

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++..+|||.|+||+||||+||+++|..|..+|     +.||++.||++|++|+++||
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~-----p~ei~k~lg~~Wk~ls~~eK  157 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEK  157 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSSCSS-----HHHHHHHHHHHHHTCCHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhccCC-----HHHHHHHHHHHHHcCCHHHH
Confidence            44567999999999999999999999886433     56999999999999999886

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

Probab=99.42  E-value=6e-15  Score=110.52  Aligned_cols=52  Identities=31%  Similarity=0.385  Sum_probs=45.6

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++..+|++.||||+|||||||+++|..|+.+|     ..||++.||++|++|+++||
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~-----p~ei~k~lg~~Wk~ls~~eK  189 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEK  189 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSS-----HHHHHHHHHHHHHTCCTTTT
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhccC-----HHHHHHHHHHHHHhCCHHHH
Confidence            34567999999999999999999999886443     56999999999999999986

---

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	103
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	6e-09
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-07
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	3e-07
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	9e-07
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-06
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-06
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	3e-06
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	4e-06
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	2e-05
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	2e-04
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	0.001

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

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

 Score = 46.8 bits (111), Expect = 6e-09
 Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

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

Query: 99  PA 100
           P 
Sbjct: 64  PE 65

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

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

 Score = 43.0 bits (101), Expect = 2e-07
 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 46  KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
           KK KK P+ PK+P + +F F  E R  + K +P ++    + K    K+K +   
Sbjct: 2   KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEK 55

>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 = 42.1 bits (99), Expect = 3e-07
 Identities = 19/46 (41%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMS 98
          +KPKRP SA+ ++L   R++ K+ENP +  V+ V K  G  W++M 
Sbjct: 2  DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK 46

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

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

 Score = 41.1 bits (96), Expect = 9e-07
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

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

Query: 96  SMSPA 100
            +S  
Sbjct: 61  DLSEK 65

>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 = 40.2 bits (94), Expect = 1e-06
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 54 KPKRPPSAFFVFLEEFRKTFKKENPNVTA-VSAVGKAAGGKWKSMSP 99
          KP+   S++  F++  R+  KK++P+ +   S   K    +WK+MS 
Sbjct: 1  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSA 47

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

 Score = 40.2 bits (94), Expect = 2e-06
 Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP 99
          N PKRPPSAFF+F  E+R   K E+P ++ +  V K  G  W + + 
Sbjct: 1  NAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAA 46

>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 = 39.4 bits (92), Expect = 3e-06
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 54  KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPA 100
             KRP +AF V+ ++ R+   +  P++   S + K  G +WK+M+  
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNL 47

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

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

 Score = 39.4 bits (92), Expect = 4e-06
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 53  NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           ++ KRP +AF V+    R+   +ENP +   S + K  G +WK +S   
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETE 48

>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 = 37.5 bits (87), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP 99
          ++ KRP +AF V+  + R+    ENP +   S + K  G +WK ++ 
Sbjct: 3  DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTE 48

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

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

 Score = 34.8 bits (80), Expect = 2e-04
 Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 56  KRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV 101
           K+P +AF ++++E R     E+      +A+ +  G +W ++S   
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREE 48

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

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

 Score = 33.3 bits (76), Expect = 0.001
 Identities = 7/51 (13%), Positives = 16/51 (31%), Gaps = 3/51 (5%)

Query: 49 KKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSP 99
                 K P + +  F +E     +  +  +          G +W+ +S 
Sbjct: 3  SGSSGPKKPPMNGYQKFSQELLSNGELNHLPLKERM---VEIGSRWQRISQ 50

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	103
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.77
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.74
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.74
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.73
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.7
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.66
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.65
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.48
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.45

>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=99.77  E-value=3.5e-19  Score=115.05  Aligned_cols=59  Identities=44%  Similarity=0.804  Sum_probs=54.4

Q ss_pred             ccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           43 KREKKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        43 ~k~kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++..+..+||+.||||+||||||++++|..|+.+||++ ++.+|++.||++|++||++||
T Consensus         9 k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~-~~~ei~k~l~~~W~~ls~~eK   67 (93)
T d1lwma_           9 KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEK   67 (93)
T ss_dssp             SCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHTSCHHHH
T ss_pred             CccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCC-cHHHHHHHHHHHHHhCCHHHH
Confidence            45555668999999999999999999999999999999 699999999999999999986

>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=99.74  E-value=5.9e-19  Score=113.08  Aligned_cols=56  Identities=30%  Similarity=0.515  Sum_probs=52.7

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ++..+||+.|+||+|+||||++++|..|..+||++ ++.+|++.||++|+.||++||
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~-~~~ev~k~l~~~W~~ls~~eK   57 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKK   57 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTH
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhHhcCCCHHHH
Confidence            34668999999999999999999999999999999 699999999999999999986

>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=99.74  E-value=8.2e-19  Score=109.94  Aligned_cols=49  Identities=41%  Similarity=0.807  Sum_probs=47.5

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        53 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |+||||+||||+|++++|..|+.+||++ ++.||+++||++|++||++||
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~-~~~ei~k~~~~~W~~ls~~eK   49 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDK   49 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTC-CTTTHHHHHHHHHHTSCSTTT
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHhhHHhcCCHHHH
Confidence            7899999999999999999999999999 699999999999999999987

>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=99.73  E-value=1.6e-18  Score=110.87  Aligned_cols=56  Identities=32%  Similarity=0.587  Sum_probs=52.1

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           46 KKAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        46 kkk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .....|++.|+||+|+|||||+++|.+|+.+||++ ++.||+++||++|+.|+++||
T Consensus        12 ~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~-~~~ei~k~l~~~W~~Ls~~eK   67 (90)
T d1wgfa_          12 EGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKK   67 (90)
T ss_dssp             CCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             cCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            34457999999999999999999999999999999 599999999999999999986

>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=99.72  E-value=2.1e-18  Score=109.16  Aligned_cols=49  Identities=33%  Similarity=0.603  Sum_probs=47.1

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           53 NKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        53 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      |.|+||+||||||++++|.+|..+||++ ++.||+++||++|++|+++||
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~-~~~eisk~~g~~W~~l~~eeK   49 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEK   49 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHCcCCHHHH
Confidence            5799999999999999999999999999 699999999999999999986

>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=99.72  E-value=3.6e-18  Score=108.71  Aligned_cols=50  Identities=32%  Similarity=0.570  Sum_probs=47.7

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .|.||||+||||||++++|.+|..+||++ ++.||+++||++|++|+++||
T Consensus         2 ~~~iKRP~nay~lF~~~~r~~i~~~~p~~-~~~eisk~ig~~W~~L~~eeK   51 (85)
T d1j46a_           2 QDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEK   51 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHhcCCHHHH
Confidence            37899999999999999999999999999 599999999999999999986

>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=99.70  E-value=7.8e-18  Score=103.69  Aligned_cols=48  Identities=29%  Similarity=0.547  Sum_probs=46.0

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .+|||+|||||||+++|..|+.+||++ +++||+++||++|++|+++||
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~-~~~eisk~lg~~Wk~ls~~eK   49 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEK   49 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGG
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhCCHHHH
Confidence            578999999999999999999999999 599999999999999999987

>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=99.70  E-value=6.5e-18  Score=104.57  Aligned_cols=49  Identities=39%  Similarity=0.778  Sum_probs=45.6

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCccc
Q 034117           52 PNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAV  101 (103)
Q Consensus        52 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eE  101 (103)
                      .|.||||+||||||++++|..|+.+||++ ++.||+++||++|++|++.+
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~-~~~eisk~l~~~Wk~~~eK~   49 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGI-KVTEVAKRGGELWRAMKDKS   49 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTC-CHHHHHHHHHHHHHHCSCCH
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHhcChhHHH
Confidence            37899999999999999999999999999 69999999999999987644

>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=99.66  E-value=8.4e-17  Score=98.64  Aligned_cols=49  Identities=29%  Similarity=0.564  Sum_probs=45.0

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCC-cHHHHHHHHHHHhhCCCcccc
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVT-AVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisK~lge~Wk~Ls~eER  102 (103)
                      .||||+||||+|++++|..|+.+||+.. ++.+|+++||++|++||++||
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK   50 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK   50 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTS
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHH
Confidence            5999999999999999999999999742 378999999999999999987

>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=99.65  E-value=6.7e-17  Score=102.91  Aligned_cols=48  Identities=23%  Similarity=0.501  Sum_probs=45.8

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           54 KPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        54 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ..+||+||||||+++.|..|..+||++ ++++|+++||++|++||++||
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~-~~~~Isk~lg~~Wk~ls~~eK   49 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQ   49 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHH
Confidence            468999999999999999999999999 699999999999999999986

>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=99.48  E-value=8e-15  Score=94.89  Aligned_cols=49  Identities=14%  Similarity=0.286  Sum_probs=43.4

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           51 DPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        51 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      ...+||||+|+|||||+++|..+..+  ++ ++.||++.||++|++|+++||
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~--~~-~~~ei~k~~g~~Wk~ls~~eK   53 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELN--HL-PLKERMVEIGSRWQRISQSQK   53 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTT--TS-CHHHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhc--CC-CHHHHHHHHHHHHhhCCHHHH
Confidence            45679999999999999999998654  45 588999999999999999986

>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=99.45  E-value=3.8e-14  Score=93.04  Aligned_cols=51  Identities=22%  Similarity=0.337  Sum_probs=45.0

Q ss_pred             ccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhhCCCcccc
Q 034117           47 KAKKDPNKPKRPPSAFFVFLEEFRKTFKKENPNVTAVSAVGKAAGGKWKSMSPAVS  102 (103)
Q Consensus        47 kk~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisK~lge~Wk~Ls~eER  102 (103)
                      +...|+.+||+|+||||||++++|.+    +|++ ++.||++.||++|++|+++||
T Consensus        10 k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~-~~~e~~k~ig~~W~~Ls~~eK   60 (108)
T d1v64a_          10 KDKFDGRPTKPPPNSYSLYCAELMAN----MKDV-PSTERMVLCSQQWKLLSQKEK   60 (108)
T ss_dssp             SCCTTTSCCCCCSSHHHHHHHHHHHH----CTTS-CHHHHHHHHHHHHHHSCHHHH
T ss_pred             cccCCCCCCCCCCcHHHHHHHHHHHH----ccCC-CHHHHHHHHHHHHccCCHHHH
Confidence            34468888999999999999999864    6889 699999999999999999986