Citrus Sinensis ID: 033450

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
Protein Sequence
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLLI
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHcHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHccccHHHHHHHHHHHHHHHcHccccccccccccccccccccccccHHHHEHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccHHHHccccccHHHHHHHHHc
Coil and Loop (DISEMBL)
mkvtrgkgavkkdknevvkpvedraAGKRKAVLKASrssnkrtknvksakkdpnkpkrppsaFFVFLEEFRKVYKqehpnvkavsavgkaggekWKSLTDAVSSKISTGSFLNLLGLLI
Flexible Loop (DISEMBL)
mkvtrgkgavkkdknevvkpvedraagkrkavlkasrssnkrtknvksakkdpnkpkrppSAFFVFLEEFRKVYKqehpnvkavsavgkaggekWKSLTDavsskistgsflnllglli
Low Complexity Region (SEG)
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLLI
Disordered region (IsUnstruct)
*************************************************************AFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGL**
Disordered Region (DISOPRED)
**********************************************************PPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS*T***SSKISTGSFLNLLGLLI
Disordered Region (DISEMBL)
**************NEVVKPVED**********************************RPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLLI
Disordered Region (DISPRO)
*****************************************************NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLLI
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	119	2.2.26 [Sep-21-2011]
O49595	178	High mobility group B pro	yes	no	0.823	0.550	0.623	4e-26
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.495	0.409	0.728	1e-19
P93047	141	High mobility group B pro	no	no	0.529	0.446	0.682	6e-19
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.445	0.348	0.773	1e-18
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.420	0.335	0.72	1e-16
O49596	144	High mobility group B pro	no	no	0.462	0.381	0.654	8e-16
Q42344	138	High mobility group B pro	no	no	0.453	0.391	0.648	2e-15
P27347	157	DNA-binding protein MNB1B	N/A	no	0.714	0.541	0.470	4e-15
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.420	0.310	0.66	6e-14
O49597	125	High mobility group B pro	no	no	0.546	0.52	0.492	3e-12

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

 Score =  116 bits (291), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 63/101 (62%), Positives = 77/101 (76%), Gaps = 3/101 (2%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MK  +GK  VK  K E +KPV+DR  GKRKA   A + + + T+  K AKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTK-EALKPVDDRKVGKRKAP--AEKPTKRETRKEKKAKKDPNKPKRAP 57

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           SAFFVFLE+FR  +K+E+PNVKAVSAVGKAGG+KWKS++ 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|P40619|HMGL_IPONI HMG1/2-like protein OS=Ipomoea nil PE=2 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/59 (72%), Positives = 50/59 (84%)

Query: 43  TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           TK  K A KDPNKPKRPPSAFFVF+E+FRK YK++HPN K+V+ VGKAGG+KWK LT A
Sbjct: 23  TKKTKKAVKDPNKPKRPPSAFFVFMEDFRKTYKEKHPNNKSVAVVGKAGGDKWKQLTAA 81

Ipomoea nil (taxid: 35883)

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

 Score = 92.4 bits (228), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 43/63 (68%), Positives = 51/63 (80%)

Query: 39  SNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL 98
           + K  K  K A KDPNKPKRP SAFFVF+E+FR  YK+EHP  K+V+AVGKAGGEKWKSL
Sbjct: 18  TKKPAKGAKGAAKDPNKPKRPSSAFFVFMEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSL 77

Query: 99  TDA 101
           +D+
Sbjct: 78  SDS 80

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/53 (77%), Positives = 47/53 (88%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           A KDPNKPKRPPSAFFVF+EEFRKV+ +EHP  KAVSAVGKA G KWK+++DA
Sbjct: 37  AAKDPNKPKRPPSAFFVFMEEFRKVFNKEHPENKAVSAVGKAAGAKWKTMSDA 89

Glycine max (taxid: 3847)

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

 Score = 85.1 bits (209), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 36/50 (72%), Positives = 46/50 (92%)

Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           KDPNKPKRPPSAFFVF+ +FR+ YK++HPN K+V+AVGKA GE+WKSL++
Sbjct: 40  KDPNKPKRPPSAFFVFMADFREQYKKDHPNNKSVAAVGKACGEEWKSLSE 89

Vicia faba (taxid: 3906)

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

 Score = 82.4 bits (202), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 36/55 (65%), Positives = 48/55 (87%)

Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           K+A KDPNKPKRP SAFFVF+E+FR+ +K+E+P  K+V+ VGKA G+KWKSL+D+
Sbjct: 29  KAAAKDPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDS 83

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/54 (64%), Positives = 44/54 (81%)

Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           K  KKDPN+PKRPPSAFFVFLE+FRK +   +PN K+V+ VGKA G +WK++TD
Sbjct: 26  KKTKKDPNQPKRPPSAFFVFLEDFRKEFNLANPNNKSVATVGKAAGARWKAMTD 79

Binds preferentially double-stranded DNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 48/102 (47%), Positives = 63/102 (61%), Gaps = 17/102 (16%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKS-AKKDPNKPKRP 59
           MK  + KGA K D    VK                S+ + K  K  K  A KDPNKPKR 
Sbjct: 1   MKGAKSKGAAKADAKLAVK----------------SKGAEKPAKGRKGKAGKDPNKPKRA 44

Query: 60  PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           PSAFFVF+EEFRK +K+++P  K+V+AVGKA G++WKSL+++
Sbjct: 45  PSAFFVFMEEFRKEFKEKNPKNKSVAAVGKAAGDRWKSLSES 86

Recognizes an AAGG motif at the MNF1-binding site.

Zea mays (taxid: 4577)

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

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 33/50 (66%), Positives = 44/50 (88%)

Query: 52  DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           DPNKPKR PSAFFVF+ EFR+ +KQ++P  K+V+AVGKA GE+WKSL+++
Sbjct: 38  DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSES 87

Triticum aestivum (taxid: 4565)

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

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/69 (49%), Positives = 49/69 (71%), Gaps = 4/69 (5%)

Query: 36  SRSSNKRTK----NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAG 91
           SRS++ R K     V    KDPN+PK+PPS FFVFL++FRK +   +P+ K+V  VG+A 
Sbjct: 10  SRSTDDRLKVRGNKVGKKTKDPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAA 69

Query: 92  GEKWKSLTD 100
           G+KWK++T+
Sbjct: 70  GKKWKTMTE 78

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	119
359386154	165	group B HMG-box protein [Citrus sinensis	0.848	0.612	1.0	1e-50
224112525	176	high mobility group family [Populus tric	0.848	0.573	0.762	8e-36
225448398	166	PREDICTED: high mobility group B protein	0.848	0.608	0.792	4e-35
297736623	128	unnamed protein product [Vitis vinifera]	0.857	0.796	0.794	6e-35
225448400	156	PREDICTED: high mobility group B protein	0.848	0.647	0.792	6e-35
224098541	179	high mobility group family [Populus tric	0.848	0.564	0.712	7e-34
118484946	171	unknown [Populus trichocarpa]	0.848	0.590	0.712	7e-34
255571919	190	DNA-binding protein MNB1B, putative [Ric	0.873	0.547	0.730	1e-30
449521910	112	PREDICTED: high mobility group B protein	0.857	0.910	0.699	2e-29
449461783	169	PREDICTED: high mobility group B protein	0.840	0.591	0.693	9e-29

>gi|359386154|gb|AEV43366.1| group B HMG-box protein [Citrus sinensis]

 Score =  203 bits (516), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 101/101 (100%), Positives = 101/101 (100%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP
Sbjct: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

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 =  154 bits (388), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 77/101 (76%), Positives = 84/101 (83%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MK+ +GKG  + +K EV+ PVEDR  GKRKA LKA+ SS KR K  K  KKDPNKPKRPP
Sbjct: 1   MKIAKGKGTARTEKKEVLLPVEDRKIGKRKAALKANESSKKRVKKEKITKKDPNKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL+ A
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSAA 101

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448398|ref|XP_002269398.1| PREDICTED: high mobility group B protein 1 isoform 1 [Vitis vinifera] gi|147854340|emb|CAN83423.1| hypothetical protein VITISV_023376 [Vitis vinifera]

 Score =  151 bits (382), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 80/101 (79%), Positives = 87/101 (86%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MKVT+GK A +KDK E +KPVEDR  GKRKA LKA +S+ K  K  K AKKDPNKPKRPP
Sbjct: 1   MKVTKGKAAARKDKKEALKPVEDRRLGKRKAALKADKSTKKLAKKEKLAKKDPNKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL++A
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSEA 101

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736623|emb|CBI25494.3| unnamed protein product [Vitis vinifera]

 Score =  151 bits (381), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 81/102 (79%), Positives = 88/102 (86%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MKVT+GK A +KDK E +KPVEDR  GKRKA LKA +S+ K  K  K AKKDPNKPKRPP
Sbjct: 25  MKVTKGKAAARKDKKEALKPVEDRRLGKRKAALKADKSTKKLAKKEKLAKKDPNKPKRPP 84

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL++AV
Sbjct: 85  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSEAV 126

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448400|ref|XP_002270185.1| PREDICTED: high mobility group B protein 1 isoform 2 [Vitis vinifera]

 Score =  151 bits (381), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 80/101 (79%), Positives = 87/101 (86%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MKVT+GK A +KDK E +KPVEDR  GKRKA LKA +S+ K  K  K AKKDPNKPKRPP
Sbjct: 1   MKVTKGKAAARKDKKEALKPVEDRRLGKRKAALKADKSTKKLAKKEKLAKKDPNKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL++A
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSEA 101

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  147 bits (371), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 72/101 (71%), Positives = 82/101 (81%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MK  +GKGA + +K EV  PVEDR  GKRKA LKA+ SS KR    K  KKDP+KPKRPP
Sbjct: 1   MKTAKGKGAARTEKKEVSLPVEDRKIGKRKAALKATESSKKRAAKEKITKKDPDKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           S+FFVFLEEFRK+YKQEHPN+KAVSAVGKAGGEKWKS++ A
Sbjct: 61  SSFFVFLEEFRKIYKQEHPNMKAVSAVGKAGGEKWKSMSAA 101

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  147 bits (371), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 72/101 (71%), Positives = 82/101 (81%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MK  +GKGA + +K EV  PVEDR  GKRKA LKA+ SS KR    K  KKDP+KPKRPP
Sbjct: 1   MKTAKGKGAARTEKKEVSLPVEDRKIGKRKAALKATESSKKRAAKEKITKKDPDKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           S+FFVFLEEFRK+YKQEHPN+KAVSAVGKAGGEKWKS++ A
Sbjct: 61  SSFFVFLEEFRKIYKQEHPNMKAVSAVGKAGGEKWKSMSAA 101

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255571919|ref|XP_002526902.1| DNA-binding protein MNB1B, putative [Ricinus communis] gi|223533801|gb|EEF35533.1| DNA-binding protein MNB1B, putative [Ricinus communis]

 Score =  136 bits (343), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 76/104 (73%), Positives = 87/104 (83%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MKV +GK   KKD+ EV+KPVEDR  GKR A LK +++S K TK  K AKKDPN+PKRPP
Sbjct: 1   MKVGKGKETAKKDRKEVLKPVEDRKLGKRSAALKPNKNSKKVTKKDKPAKKDPNRPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSS 104
           SAFFVFLE+FRKVYKQEHPNVKAVSAVGKAGGEKWKS+++A  S
Sbjct: 61  SAFFVFLEDFRKVYKQEHPNVKAVSAVGKAGGEKWKSMSNAEKS 104

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 72/103 (69%), Positives = 83/103 (80%), Gaps = 1/103 (0%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MK ++GKG  +  K E +KPV+DR  GKRKAV+KA +   + TK    AKKDPNKPKRPP
Sbjct: 1   MKGSKGKGTSRVSK-EALKPVDDRKVGKRKAVVKADKGIKRPTKKDLKAKKDPNKPKRPP 59

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVS 103
           SAFFVFLEEFRK YK+E+PNVKAVSAVGKAGGEKWKSL+ AVS
Sbjct: 60  SAFFVFLEEFRKEYKRENPNVKAVSAVGKAGGEKWKSLSHAVS 102

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 =  130 bits (327), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 70/101 (69%), Positives = 81/101 (80%), Gaps = 1/101 (0%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MK ++GKG  +  K E +KPV+DR  GKRKAV+KA +   + TK    AKKDPNKPKRPP
Sbjct: 1   MKGSKGKGTSRVSK-EALKPVDDRKVGKRKAVVKADKGIKRPTKKDLKAKKDPNKPKRPP 59

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           SAFFVFLEEFRK YK+E+PNVKAVSAVGKAGGEKWKSL+ A
Sbjct: 60  SAFFVFLEEFRKEYKRENPNVKAVSAVGKAGGEKWKSLSHA 100

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	119
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.613	0.506	0.534	2.5e-17
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.613	0.528	0.534	1.4e-16
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.546	0.52	0.492	1.3e-13
TAIR|locus:2154433	241	HMGB6 "high-mobility group box	0.663	0.327	0.459	7.1e-13
UNIPROTKB|P40618	202	HMGB3 "High mobility group pro	0.420	0.247	0.529	6.6e-10
UNIPROTKB|F1N927	214	HMGB1 "High mobility group pro	0.714	0.397	0.393	6.6e-10
UNIPROTKB|Q9YH06	215	HMG1 "High mobility group 1 pr	0.714	0.395	0.393	6.6e-10
UNIPROTKB|J9NVS3	219	HMGB3 "Uncharacterized protein	0.428	0.232	0.5	1.4e-09
RGD|1564407	200	Hmgb3 "high mobility group box	0.428	0.255	0.5	1.4e-09
UNIPROTKB|E1BIU3	186	LOC532409 "Uncharacterized pro	0.428	0.274	0.5	1.4e-09

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

 Score = 212 (79.7 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 39/73 (53%), Positives = 54/73 (73%)

Query:    29 RKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVG 88
             R + L  ++   K     K+A KDPNKPKRP SAFFVF+E+FR+ +K+E+P  K+V+ VG
Sbjct:    11 RSSKLSVTKKPAKGAGRGKAAAKDPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVG 70

Query:    89 KAGGEKWKSLTDA 101
             KA G+KWKSL+D+
Sbjct:    71 KAAGDKWKSLSDS 83

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 = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 39/73 (53%), Positives = 50/73 (68%)

Query:    28 KRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAV 87
             K +A     R   +  K  K  KKDPN+PKRPPSAFFVFLE+FRK +   +PN K+V+ V
Sbjct:     7 KAEATSTDQRLKTRGRKAGKKTKKDPNQPKRPPSAFFVFLEDFRKEFNLANPNNKSVATV 66

Query:    88 GKAGGEKWKSLTD 100
             GKA G +WK++TD
Sbjct:    67 GKAAGARWKAMTD 79

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 = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 34/69 (49%), Positives = 49/69 (71%)

Query:    36 SRSSNKRTK----NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAG 91
             SRS++ R K     V    KDPN+PK+PPS FFVFL++FRK +   +P+ K+V  VG+A 
Sbjct:    10 SRSTDDRLKVRGNKVGKKTKDPNRPKKPPSPFFVFLDDFRKEFNLANPDNKSVGNVGRAA 69

Query:    92 GEKWKSLTD 100
             G+KWK++T+
Sbjct:    70 GKKWKTMTE 78

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0000785 "chromatin" evidence=TAS

GO:0003682 "chromatin binding" evidence=TAS

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

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

GO:0005737 "cytoplasm" evidence=IDA

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

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

 Score = 170 (64.9 bits), Expect = 7.1e-13, P = 7.1e-13
 Identities = 40/87 (45%), Positives = 50/87 (57%)

Query:    21 VEDRAAGKRKAVLKASRSSN----KRTKNVKSAKKDP---NKPKRPPSAFFVFLEEFRKV 73
             VE +A  K+K   K   +S+    KR K     KK     NKPKRP +AFF+F+ +FRK 
Sbjct:    73 VETQAEAKKKPAEKKKTTSDGPKPKRLKKTNDEKKSSSTSNKPKRPLTAFFIFMSDFRKT 132

Query:    74 YKQEHPNVKAVSAVGKAGGEKWKSLTD 100
             +K EH    A  A  K GGEKWKSLT+
Sbjct:   133 FKSEHNGSLAKDAA-KIGGEKWKSLTE 158

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0003677 "DNA binding" evidence=IDA

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

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

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 27/51 (52%), Positives = 34/51 (66%)

Query:    50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
             KKDPN PKRPPSAFF+F  EFR   K  +P + ++  V K  GE W +L+D
Sbjct:    87 KKDPNAPKRPPSAFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLSD 136

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

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

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 37/94 (39%), Positives = 48/94 (51%)

Query:    12 KDKNEVVKPVEDRAAGKRKAVLKASRSS-NKRTKN-------VKSAKKDPNKPKRPPSAF 63
             K  +E  K +  +  GK + + KA +    K  KN        K   KDPN PKRPPSAF
Sbjct:    43 KKCSERWKTMSSKEKGKFEDMAKADKLRYEKEMKNYVPPKGETKKKFKDPNAPKRPPSAF 102

Query:    64 FVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
             F+F  EFR   K EHP + ++  V K  GE W +
Sbjct:   103 FLFCSEFRPKIKGEHPGL-SIGDVAKKLGEMWNN 135

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

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

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0009986 "cell surface" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

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

GO:0030324 "lung development" evidence=IEA

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

GO:0043005 "neuron projection" evidence=IEA

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

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

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

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

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

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

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

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

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

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

 Score = 142 (55.0 bits), Expect = 6.6e-10, P = 6.6e-10
 Identities = 37/94 (39%), Positives = 48/94 (51%)

Query:    12 KDKNEVVKPVEDRAAGKRKAVLKASRSS-NKRTKN-------VKSAKKDPNKPKRPPSAF 63
             K  +E  K +  +  GK + + KA +    K  KN        K   KDPN PKRPPSAF
Sbjct:    43 KKCSERWKTMSSKEKGKFEDMAKADKLRYEKEMKNYVPPKGETKKKFKDPNAPKRPPSAF 102

Query:    64 FVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
             F+F  EFR   K EHP + ++  V K  GE W +
Sbjct:   103 FLFCSEFRPKIKGEHPGL-SIGDVAKKLGEMWNN 135

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

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

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0009986 "cell surface" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

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

GO:0030324 "lung development" evidence=IEA

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

GO:0043005 "neuron projection" evidence=IEA

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

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

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

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

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

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

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

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

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

UNIPROTKB|J9NVS3 HMGB3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 139 (54.0 bits), Expect = 1.4e-09, P = 1.4e-09
 Identities = 26/52 (50%), Positives = 34/52 (65%)

Query:    50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
             KKDPN PKRPPS FF+F  EFR   K  +P + ++  V K  GE W +L+D+
Sbjct:   105 KKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLSDS 155

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 139 (54.0 bits), Expect = 1.4e-09, P = 1.4e-09
 Identities = 26/52 (50%), Positives = 34/52 (65%)

Query:    50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
             KKDPN PKRPPS FF+F  EFR   K  +P + ++  V K  GE W +L+D+
Sbjct:    87 KKDPNAPKRPPSGFFLFCSEFRPKIKSANPGI-SIGDVAKKLGEMWNNLSDS 137

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

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

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

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

 Score = 139 (54.0 bits), Expect = 1.4e-09, P = 1.4e-09
 Identities = 26/52 (50%), Positives = 34/52 (65%)

Query:    50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
             KKDPN PKRPPS FF+F  EFR   K  +P + ++  V K  GE W +L+D+
Sbjct:    87 KKDPNAPKRPPSGFFLFCSEFRPKIKSANPGI-SIGDVAKKLGEMWNNLSDS 137

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	119
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	2e-11
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	1e-10
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	1e-10
smart00398	70	smart00398, HMG, high mobility group	2e-08
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	4e-08
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	9e-06
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	4e-05
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	8e-05

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

 Score = 54.5 bits (132), Expect = 2e-11
 Identities = 22/50 (44%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSK 105
           PKRP SAFF+F +E R   K E+P +K  + + K  GEKWK+L++     
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKP 49

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 = 52.6 bits (127), Expect = 1e-10
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           PKRP SA+F+F +E R   K E+P +  V  + K  GE WKSL++  
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 = 52.6 bits (127), Expect = 1e-10
 Identities = 22/45 (48%), Positives = 31/45 (68%), Gaps = 1/45 (2%)

Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           PKRP SA+F+F +E R   K+E+P+   V+ V K  GEKWK L++
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|197700 smart00398, HMG, high mobility group

 Score = 46.9 bits (112), Expect = 2e-08
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           KPKRP SAF +F +E R   K E+P++   + + K  GE+WK L++  
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEE 47

Length = 70

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

 Score = 48.7 bits (116), Expect = 4e-08
 Identities = 27/60 (45%), Positives = 37/60 (61%), Gaps = 1/60 (1%)

Query: 41  KRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
            ++K +   KKDPN PKRP SA+F++  E R   ++E+P +     VGK   EKWK LTD
Sbjct: 56  TKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTD 114

Length = 211

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

 Score = 40.1 bits (94), Expect = 9e-06
 Identities = 19/49 (38%), Positives = 29/49 (59%)

Query: 53  PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           PNKPK   +A+F F++  R   K+E P V  V+   K   EKWK++++ 
Sbjct: 1   PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEE 49

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

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

 Score = 38.8 bits (91), Expect = 4e-05
 Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           KRP +AF +F +  R+   QE+P  K   A+ K  G++WK+L++ 
Sbjct: 3   KRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNE 46

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

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

 Score = 38.3 bits (89), Expect = 8e-05
 Identities = 27/69 (39%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 34  KASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV-KAVSAVGKAGG 92
            A +      +  K  KKDPN PKR  SA+  F +E R     E+P + K V+AVGK  G
Sbjct: 1   MAKKQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVG 60

Query: 93  EKWKSLTDA 101
           E W  L++ 
Sbjct: 61  EAWNKLSEE 69

Length = 94

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	119
PTZ00199	94	high mobility group protein; Provisional	99.91
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.83
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.82
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.81
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.79
smart00398	70	HMG high mobility group.	99.79
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.77
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.76
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.74
KOG0381	96	consensus HMG box-containing protein [General func	99.71
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.6
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.59
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	99.17
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	99.04
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.94
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.56
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	97.8
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.46
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	97.08
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.05
COG5648	211	NHP6B Chromatin-associated proteins containing the	96.92
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	94.93
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	93.72
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	84.95
PF05494	170	Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro:	84.82
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	83.49
KOG3223	221	consensus Uncharacterized conserved protein [Funct	82.62

>PTZ00199 high mobility group protein; Provisional

Probab=99.91  E-value=5.4e-24  Score=144.20  Aligned_cols=78  Identities=32%  Similarity=0.464  Sum_probs=70.9

Q ss_pred             ccccccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           41 KRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        41 kk~kk~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +-.+++++..+||+.|+||+||||+||+++|..|..+||++. ++.+|+++||++|++||+++|.+|+++|+.|+.+|.
T Consensus         8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~   86 (94)
T PTZ00199          8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYE   86 (94)
T ss_pred             ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            345555667899999999999999999999999999999982 289999999999999999999999999999999995

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

Probab=99.83  E-value=2.1e-20  Score=121.54  Aligned_cols=63  Identities=19%  Similarity=0.275  Sum_probs=61.0

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .|+||+||||||++++|..|..+||++ ++.+|+++||++|+.||+++|++|.++|+.++.+|+
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~   63 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGL-TNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHA   63 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            489999999999999999999999999 899999999999999999999999999999999885

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=99.82  E-value=4.1e-20  Score=115.46  Aligned_cols=62  Identities=37%  Similarity=0.552  Sum_probs=60.7

Q ss_pred             CCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        56 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |++|+|||++|++++|..+..+||++ ++.+|++.||++|++||+++|++|.+.|..++.+|.
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~-~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~   62 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDA-SVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYE   62 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999 899999999999999999999999999999999995

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=99.81  E-value=8e-20  Score=117.56  Aligned_cols=62  Identities=26%  Similarity=0.315  Sum_probs=60.2

Q ss_pred             CCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        56 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .|||+||||+||+++|..++.+||++ ++.+|+++||++|+.||+++|++|.++|..++.+|+
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~-~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~   63 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLK-ENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHM   63 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999 899999999999999999999999999999999985

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

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

Probab=99.79  E-value=4.8e-19  Score=111.63  Aligned_cols=62  Identities=27%  Similarity=0.468  Sum_probs=58.3

Q ss_pred             CCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        56 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |+||+|||++||++++..+..+||++ ++.+|+++||.+|++||+++|.+|.+.|..++.+|.
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~-~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~   62 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDL-SNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYE   62 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTS-THHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhccc-ccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999 899999999999999999999999999999998884

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=99.79  E-value=7.1e-19  Score=110.28  Aligned_cols=63  Identities=32%  Similarity=0.487  Sum_probs=60.8

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +|++|+|+|++|++++|..+..+||++ ++.+|++.||.+|+.||+++|.+|.+.|..++.+|.
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~-~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~   63 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDL-SNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYE   63 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999 899999999999999999999999999999998884

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

Probab=99.77  E-value=2.3e-18  Score=106.80  Aligned_cols=62  Identities=35%  Similarity=0.537  Sum_probs=60.0

Q ss_pred             CCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        56 PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |++|+|||++|+++.+..+..+||++ ++.+|++.||.+|+.||+++|.+|.+.|..++.+|.
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~-~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~   62 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGL-SVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYE   62 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999 899999999999999999999999999999998884

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

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

Probab=99.76  E-value=8e-19  Score=133.48  Aligned_cols=75  Identities=36%  Similarity=0.535  Sum_probs=71.4

Q ss_pred             ccccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        43 ~kk~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .+...+..+|||.|+||+||||+|++++|+.++.++|.+ +|.+|++++|+.|++|+++|+.+|...|..+..+|.
T Consensus        58 sk~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l-~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq  132 (211)
T COG5648          58 SKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKL-TFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQ  132 (211)
T ss_pred             HHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHH
Confidence            356678889999999999999999999999999999999 899999999999999999999999999999999995

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

Probab=99.74  E-value=9.4e-18  Score=108.14  Aligned_cols=65  Identities=34%  Similarity=0.497  Sum_probs=56.9

Q ss_pred             CCCCCCCCChhHHHHHHHHHHHHHh-CCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           53 PNKPKRPPSAFFVFLEEFRKVYKQE-HPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~ik~e-~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |+.||+|+|||+||+.+++..+... ++.. ++.|+++.||..|++||++||.+|++.|..+..+|-
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~-~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~   66 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQ-SFREVMKEISERWKSLSEEEKEPYEERAKEDKERYE   66 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-S-SHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999988 7777 899999999999999999999999999999999883

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

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

Probab=99.71  E-value=4.8e-17  Score=108.96  Aligned_cols=66  Identities=38%  Similarity=0.530  Sum_probs=63.4

Q ss_pred             CC--CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           52 DP--NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        52 dp--~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ||  +.|++|+|||++|+++.+..++.+||++ ++.+|++++|++|++|+++++++|+..|..+..+|.
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~-~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~   84 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGL-SVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYE   84 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            66  5999999999999999999999999999 899999999999999999999999999999999985

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

Probab=99.60  E-value=1e-15  Score=129.19  Aligned_cols=68  Identities=31%  Similarity=0.557  Sum_probs=64.7

Q ss_pred             ccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhcc
Q 033450           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGL  117 (119)
Q Consensus        45 k~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y  117 (119)
                      +..++.+|||+|||++||||+|++..|..|+.+  +. ++++|++.+|++|+.|+.  |.+|++.|+.|.++|
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi-~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry  592 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GI-SVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRY  592 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--Cc-hHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHH
Confidence            566778999999999999999999999999988  88 899999999999999999  999999999999998

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.59  E-value=2.1e-15  Score=122.12  Aligned_cols=67  Identities=22%  Similarity=0.351  Sum_probs=61.9

Q ss_pred             CCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhc
Q 033450           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLG  116 (119)
Q Consensus        49 ~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~  116 (119)
                      ........||||||||+|++..|..|..+||.+ .+.||||+||..|+.|+++||.+|+++|+...+.
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~m-HNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~  122 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKM-HNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQ  122 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcch-hhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHH
Confidence            445667899999999999999999999999999 9999999999999999999999999999887653

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=99.17  E-value=4.2e-11  Score=97.13  Aligned_cols=60  Identities=20%  Similarity=0.313  Sum_probs=55.5

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhh
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLL  115 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~  115 (119)
                      ..|+|+||||+||.|+|..|..++--. ...+|+++||.+|..||.+|...|.++|.++.+
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEctlK-eSAaiNqiLGrRWH~LSrEEQAKYyElArKerq  250 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECTLK-ESAAINQILGRRWHALSREEQAKYYELARKERQ  250 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhhhh-hHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHH
Confidence            779999999999999999999998755 678999999999999999999999999988764

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

Probab=99.04  E-value=3.4e-10  Score=91.33  Aligned_cols=69  Identities=17%  Similarity=0.332  Sum_probs=64.5

Q ss_pred             cCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhcc
Q 033450           48 SAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGL  117 (119)
Q Consensus        48 k~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y  117 (119)
                      ...+.|.+|-+|+-+||.|+....++|+..||++ -.-||.++||.+|..|+++||+.|+..|+.+++.|
T Consensus        57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~-kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY  125 (410)
T KOG4715|consen   57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPEL-KLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEY  125 (410)
T ss_pred             cCCCCCCCCCcccchhhHHhhhhhhhhhccCcch-HHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHH
Confidence            3446778889999999999999999999999999 79999999999999999999999999999999988

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

Probab=98.94  E-value=3.2e-10  Score=95.16  Aligned_cols=61  Identities=23%  Similarity=0.405  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHH
Q 033450           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGS  110 (119)
Q Consensus        49 ~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A  110 (119)
                      .-..++..||||||||.|.++-|..|...+|++ ....|+++||..|+.||-.||++|.+.-
T Consensus       319 ~~ss~PHIKRPMNAFMVWAkDERRKILqA~PDM-HNSnISKILGSRWKaMSN~eKQPYYEEQ  379 (511)
T KOG0528|consen  319 RASSEPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMSNTEKQPYYEEQ  379 (511)
T ss_pred             cCCCCccccCCcchhhcccchhhhhhhhcCccc-cccchhHHhcccccccccccccchHHHH
Confidence            334556889999999999999999999999999 8999999999999999999999998653

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

Probab=98.56  E-value=4.8e-08  Score=84.79  Aligned_cols=68  Identities=28%  Similarity=0.385  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCChhHHHHHHHH--HHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhcc
Q 033450           49 AKKDPNKPKRPPSAFFVFLEEFR--KVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGL  117 (119)
Q Consensus        49 ~~kdp~~PKRP~say~lF~~e~R--~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y  117 (119)
                      .+.|....++|||+|++|++.+|  ..+...||+. .+.-|+++||+.|-.|.++||+.|.++|.+.....
T Consensus       175 nkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~-DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ah  244 (683)
T KOG2746|consen  175 NKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQ-DNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAH  244 (683)
T ss_pred             CcCcchhhhhhhHHHHHHHhhcCCccchhccCccc-cchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHH
Confidence            34556688999999999999999  8999999999 79999999999999999999999999998876543

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

Probab=97.80  E-value=9.8e-05  Score=48.82  Aligned_cols=61  Identities=16%  Similarity=0.124  Sum_probs=50.7

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhcc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGL  117 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y  117 (119)
                      .|-.|-++--+|.++....+...+++- ...+ .+.+...|++|++.+|.+|+..|..|..+|
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~d-r~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrY   63 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRND-RKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRY   63 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTST-HHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHh-HHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHH
Confidence            477788999999999999999999987 5655 459999999999999999999999988877

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

Probab=97.46  E-value=0.00025  Score=53.31  Aligned_cols=48  Identities=21%  Similarity=0.367  Sum_probs=42.2

Q ss_pred             CChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHH
Q 033450           60 PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFL  112 (119)
Q Consensus        60 ~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~  112 (119)
                      -++|+-|+.+++..    |.+| +..|+....+..|..||+++|..|..++..
T Consensus        83 nnaYLNFLReFRrk----h~~L-~p~dlI~~AAraW~rLSe~eK~rYrr~~~~  130 (183)
T PF06382_consen   83 NNAYLNFLREFRRK----HCGL-SPQDLIQRAARAWCRLSEAEKNRYRRMAPS  130 (183)
T ss_pred             chHHHHHHHHHHHH----ccCC-CHHHHHHHHHHHHHhCCHHHHHHHHhhcch
Confidence            46899999998774    5699 899999999999999999999999987543

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=97.08  E-value=0.00074  Score=41.80  Aligned_cols=40  Identities=15%  Similarity=0.365  Sum_probs=36.2

Q ss_pred             CChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCH
Q 033450           60 PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD  100 (119)
Q Consensus        60 ~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~  100 (119)
                      ++.|-+|.+..|+.+...||++ ..+.|..+++.+|+.-++
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~-~~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKA-PMSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCC-cHHHHHHHHHHHHHHHHh
Confidence            4678899999999999999999 899999999999987543

; 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

>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=97.05  E-value=0.0016  Score=48.67  Aligned_cols=48  Identities=29%  Similarity=0.508  Sum_probs=42.3

Q ss_pred             CCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCC
Q 033450           51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT   99 (119)
Q Consensus        51 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls   99 (119)
                      +.|.+-.|-+|||..|+++.-..|+..+|++ +..|.-...+..|...+
T Consensus       117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~i-shkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPDI-SHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             CCccccCCCchhHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHhhhhCc
Confidence            3444556778999999999999999999999 99999999999998765

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

Probab=96.92  E-value=0.00068  Score=52.16  Aligned_cols=67  Identities=15%  Similarity=0.064  Sum_probs=60.5

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhcccC
Q 033450           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLLI  119 (119)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~i  119 (119)
                      ...+|..|..+|+-+-...|+.+...+|+. +..++++++|..|++|++.-+.+|.+.|..++..|.+
T Consensus       140 ~k~~~~~~~~~~~e~~~~~r~~~~~~~~~~-~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~  206 (211)
T COG5648         140 KKLPNKAPIGPFIENEPKIRPKVEGPSPDK-ALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDS  206 (211)
T ss_pred             cccCCCCCCchhhhccHHhccccCCCCcch-hhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhh
Confidence            344778888889999999999999999998 8899999999999999999999999999999998864

>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=94.93  E-value=0.086  Score=40.36  Aligned_cols=55  Identities=22%  Similarity=0.332  Sum_probs=40.8

Q ss_pred             CCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHH
Q 033450           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGS  110 (119)
Q Consensus        49 ~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A  110 (119)
                      .......++||+|+||.|+.=+-    ...|+. ...++|..|+..|..=+-  +..|.-+|
T Consensus        37 ~~~~~~~~kr~lN~Fm~FRsyy~----~~~~~~-~Qk~~S~~l~~lW~~dp~--k~~W~l~a   91 (201)
T PF04769_consen   37 RKRSPEKAKRPLNGFMAFRSYYS----PIFPPL-PQKELSGILTKLWEKDPF--KNKWSLMA   91 (201)
T ss_pred             ccccccccccchhHHHHHHHHHH----hhcCCc-CHHHHHHHHHHHHhCCcc--HhHHHHHh
Confidence            34455678999999999976554    556788 788999999999987433  45555444

MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus

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

Probab=93.72  E-value=0.098  Score=37.21  Aligned_cols=46  Identities=20%  Similarity=0.295  Sum_probs=39.7

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHH
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA  101 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~  101 (119)
                      +-+|--.||.-|...+-+.++.+||+| -.+++-.+|-..|...|++
T Consensus        72 PErR~KAAy~afeE~~Lp~lK~E~PgL-rlsQ~kq~l~K~w~KSPeN  117 (122)
T PF06244_consen   72 PERRMKAAYKAFEERRLPELKEENPGL-RLSQYKQMLWKEWQKSPEN  117 (122)
T ss_pred             cchhHHHHHHHHHHHHhHHHHhhCCCc-hHHHHHHHHHHHHhcCCCC
Confidence            334445789999999999999999999 8999999999999887753

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=84.95  E-value=1.4  Score=33.24  Aligned_cols=33  Identities=15%  Similarity=0.213  Sum_probs=27.5

Q ss_pred             CCCCHHHHHH-HHHHHhhcCCHHHhHhHHHHHHHH
Q 033450           80 NVKAVSAVGK-AGGEKWKSLTDAVSSKISTGSFLN  113 (119)
Q Consensus        80 ~~~s~~eisk-~lge~Wk~Ls~~EK~~Y~~~A~~~  113 (119)
                      .. ++..|++ .||..|+.+|+++++.|.+.-...
T Consensus        63 ~~-Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~   96 (198)
T TIGR03481        63 AF-DLPAMARLTLGSSWTSLSPEQRRRFIGAFREL   96 (198)
T ss_pred             hC-CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHH
Confidence            45 6788877 789999999999999999876553

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

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

Probab=84.82  E-value=0.8  Score=33.21  Aligned_cols=37  Identities=14%  Similarity=0.234  Sum_probs=27.7

Q ss_pred             CCCCCHHHHHH-HHHHHhhcCCHHHhHhHHHHHHHHhhc
Q 033450           79 PNVKAVSAVGK-AGGEKWKSLTDAVSSKISTGSFLNLLG  116 (119)
Q Consensus        79 P~~~s~~eisk-~lge~Wk~Ls~~EK~~Y~~~A~~~~~~  116 (119)
                      |.. .+..|++ .||..|+.||+++++.|.+.....+.+
T Consensus        36 ~~~-D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~   73 (170)
T PF05494_consen   36 PYF-DFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVR   73 (170)
T ss_dssp             GGB--HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHH
T ss_pred             HhC-CHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHH
Confidence            566 6777877 678899999999999999876655443

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

>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional

Probab=83.49  E-value=2.1  Score=32.64  Aligned_cols=35  Identities=26%  Similarity=0.172  Sum_probs=28.6

Q ss_pred             CCCCCHHHHHH-HHHHHhhcCCHHHhHhHHHHHHHHh
Q 033450           79 PNVKAVSAVGK-AGGEKWKSLTDAVSSKISTGSFLNL  114 (119)
Q Consensus        79 P~~~s~~eisk-~lge~Wk~Ls~~EK~~Y~~~A~~~~  114 (119)
                      |.. ++..+++ .||..|+.+|+++++.|.+.-...+
T Consensus        66 p~~-Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~L  101 (211)
T PRK15117         66 PYV-QVKYAGALVLGRYYKDATPAQREAYFAAFREYL  101 (211)
T ss_pred             ccC-CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHH
Confidence            667 6888877 7899999999999999997754443

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.62  E-value=1.7  Score=33.44  Aligned_cols=44  Identities=27%  Similarity=0.360  Sum_probs=38.5

Q ss_pred             CCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHH
Q 033450           57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA  101 (119)
Q Consensus        57 KRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~  101 (119)
                      +|=..||.-|-...-+.++.+||++ ..++.-.+|-..|..-|++
T Consensus       166 kRmrAA~~afEe~~LPrLK~e~P~l-rlsQ~Kqll~Kew~KsPDN  209 (221)
T KOG3223|consen  166 KRMRAAFKAFEEARLPRLKKENPGL-RLSQYKQLLKKEWQKSPDN  209 (221)
T ss_pred             HHHHHHHHHHHHhhchhhhhcCCCc-cHHHHHHHHHHHHhhCCCC
Confidence            3445678899999999999999999 8999999999999988874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	119
1j3c_A	79	Solution Structure Of The C-Terminal Domain Of The		2e-08
2yrq_A	173	Solution Structure Of The Tandem Hmg Box Domain Fro		3e-08
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		4e-08
1hme_A	77	Structure Of The Hmg Box Motif In The B-Domain Of H		4e-08
1j3d_A	78	Solution Structure Of The C-Terminal Domain Of The		6e-08
2yqi_A	81	Solution Structure Of The Second Hmg-Box Domain Fro		1e-06
1nhm_A	81	The Structure Of The Hmg Box And Its Interaction Wi		2e-06
1j5n_A	93	Solution Structure Of The Non-Sequence-Specific Hmg		5e-06
1cg7_A	93	Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len		5e-06
1e7j_A	74	Hmg-D Complexed To A Bulge Dna Length = 74		6e-06
1qrv_A	73	Crystal Structure Of The Complex Of Hmg-D And Dna L		6e-06
1hma_A	73	The Solution Structure And Dynamics Of The Dna Bind		7e-06
1hsm_A	79	The Structure Of The Hmg Box And Its Interaction Wi		9e-06
2lhj_A	97	Nmr Structure Of The High Mobility Group Protein-Li		1e-05
3nm9_A	73	Hmgd(M13a)-Dna Complex Length = 73		1e-05
1wxl_A	73	Solution Structure Of The Hmg-Box Domain In The Ssr		3e-05

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/46 (54%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
          KKDPN PKRPPSAFF+F  E+R   K EHP + ++    K  GE W
Sbjct: 3  KKDPNAPKRPPSAFFLFCSEYRPKIKSEHPGL-SIGDTAKKLGEMW 47

>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human High Mobility Group Protein B1 Length = 173

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
           KDPN PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W
Sbjct: 97  KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMW 140

>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
           KDPN PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W
Sbjct: 84  KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMW 127

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
          KDPN PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W
Sbjct: 2  KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMW 45

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 25/46 (54%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
          KKDPN PKRPPSAFF+F  E R   K EHP + ++    K  GE W
Sbjct: 2  KKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGL-SIGDTAKKLGEMW 46

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           N PKRPPS FF+F  EFR   K  +P + ++  V K  GE W +L D+
Sbjct: 8   NAPKRPPSGFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLNDS 54

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
          N PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W
Sbjct: 3  NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMW 43

>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna Length = 93

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
          DPN PKR  SA+  F  E R + + E+P++     VGK  GEKWK+LT
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALT 63

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
          DPN PKR  SA+  F  E R + + E+P++     VGK  GEKWK+LT
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALT 63

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D
Sbjct: 3   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 48

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
          PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W
Sbjct: 3  PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMW 41

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV-KAVSAVGKAGGEKWKSLTD 100
           + AKKDPN PKR  S++  F +E R     E+P + K V+A+GK  G  W +L+D
Sbjct: 14  RKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSD 68

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D
Sbjct: 2   DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47

>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1 Subunit Of Fact Length = 73

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           PKR  +AF ++L + R+  K+E+P +K V+ + K GGE WK L D
Sbjct: 4   PKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELKD 47

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	119
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	2e-16
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	6e-16
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	2e-15
2lhj_A	97	High mobility group protein homolog NHP1; structur	2e-15
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	6e-15
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	7e-15
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	1e-14
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	1e-14
1wgf_A	90	Upstream binding factor 1; transcription factor, D	4e-14
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	1e-13
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	2e-13
1ckt_A	71	High mobility group 1 protein; high-mobility group	2e-11
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	3e-11
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-10
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	9e-11
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	4e-10
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	9e-11
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	4e-04
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-10
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	2e-04
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	5e-10
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	4e-09
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	5e-09
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	3e-08
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	8e-07
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	1e-06
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	2e-05
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	3e-05
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	5e-05
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	5e-05
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	1e-04
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
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	7e-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 = 67.3 bits (165), Expect = 2e-16
 Identities = 25/51 (49%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           KDPN PKRPPSAFF+F  E+R   K EHP +  +  V K  GE W +    
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAAD 51

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

 Score = 66.2 bits (162), Expect = 6e-16
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDA 101
            K DP KP+   S++  F++  R+ +K++HP+     S   K   E+WK+++  
Sbjct: 1   GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 54

>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 = 65.1 bits (159), Expect = 2e-15
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
                + PK P + +  FL E R+  +  HP++     + K  G +W  L  A
Sbjct: 1   GSSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPA 52

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

 Score = 65.1 bits (159), Expect = 2e-15
 Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 35  ASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV-KAVSAVGKAGGE 93
           A  S     +  + AKKDPN PKR  S++  F +E R     E+P + K V+A+GK  G 
Sbjct: 2   AGASDRTGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGA 61

Query: 94  KWKSLTDA 101
            W +L+D 
Sbjct: 62  AWNALSDE 69

>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 = 63.9 bits (156), Expect = 6e-15
 Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 38  SSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
           +  +  K     KKDPN PKR  SA+  F  E R + + E+P++     VGK  GEKWK+
Sbjct: 3   TPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKA 61

Query: 98  LTDA 101
           LT  
Sbjct: 62  LTPE 65

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

 Score = 63.5 bits (155), Expect = 7e-15
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 44  KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDA 101
            +   AK DP KPK   SA+  F++  R+ +K+++P V    +   K   E+WK+++  
Sbjct: 4   GSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGK 62

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

 Score = 63.6 bits (155), Expect = 1e-14
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 46  VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           +K  KK P+ PK+P + +F F  E R  Y + HP +     + K   +K+K L + 
Sbjct: 1   MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-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 = 63.6 bits (155), Expect = 1e-14
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 40  NKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
           +  +   K  KKDPN+P++P SA+ +F  + +   K ++PN      V K     W  L 
Sbjct: 2   SSGSSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNAT-FGEVSKIVASMWDGLG 60

Query: 100 DA 101
           + 
Sbjct: 61  EE 62

>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 = 62.0 bits (151), Expect = 4e-14
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 38  SSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
           S +    + +  K    KPKRP SA F+F EE R+  ++E P +   S + +     W  
Sbjct: 3   SGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWND 61

Query: 98  LTDA 101
           L++ 
Sbjct: 62  LSEK 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 = 60.0 bits (146), Expect = 1e-13
 Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D
Sbjct: 2   DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47

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

 Score = 59.6 bits (145), Expect = 2e-13
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           + PKR  +AF ++L + R+  K+E+P +K V+ + K GGE WK L D
Sbjct: 2   HMPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELKD 47

>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 = 54.3 bits (131), Expect = 2e-11
 Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDA 101
           KP+   S++  F++  R+ +K++HP+     S   K   E+WK+++  
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 48

>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 = 56.2 bits (135), Expect = 3e-11
 Identities = 30/91 (32%), Positives = 40/91 (43%), Gaps = 1/91 (1%)

Query: 11  KKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEF 70
           K    +     ED A   +    +  ++        K   KDPN PKRPPSAFF+F  E+
Sbjct: 57  KTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEY 116

Query: 71  RKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           R   K EHP +  +  V K  GE W +    
Sbjct: 117 RPKIKGEHPGLS-IGDVAKKLGEMWNNTAAD 146

>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 = 54.6 bits (131), Expect = 1e-10
 Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 44  KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDA 101
            +    K DP KP+   S++  F++  R+ +K++HP+     S   K   E+WK+++  
Sbjct: 4   GSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAK 62

>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 = 54.9 bits (132), Expect = 9e-11
 Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           ++ KRP +AF V+  + R+    E+P ++  S + K  G +WK LT+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 = 53.3 bits (128), Expect = 4e-10
 Identities = 29/83 (34%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 19  KPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEH 78
            P    A   +    +   +   R    K   KDPN PKRPPSAFF+F  E+R   K EH
Sbjct: 52  WPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEH 111

Query: 79  PNVKAVSAVGKAGGEKWKSLTDA 101
           P +  +  V K  GE W +    
Sbjct: 112 PGLS-IGDVAKKLGEMWNNTAAD 133

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

 Score = 55.5 bits (133), Expect = 9e-11
 Identities = 12/53 (22%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           +    + PK+P S++  F +E   ++K ++P+ K  + + +   ++W+ L D+
Sbjct: 3   SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDS 54

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

 Score = 37.0 bits (85), Expect = 4e-04
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)

Query: 52  DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
              KPKRP SA+ V++ E  +  K + P         K   E WK+L+D+
Sbjct: 111 LLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDS 155

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

 Score = 55.6 bits (133), Expect = 1e-10
 Identities = 14/82 (17%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 24  RAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA 83
            ++G        +  +  +     S+    + PK+P S++  F +E   ++K ++P+ K 
Sbjct: 10  HSSGLVPRGSHMASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK- 68

Query: 84  VSAVGKAGGEKWKSLTDAVSSK 105
            + + +   ++W+ L D+    
Sbjct: 69  TTELIRRIAQRWRELPDSKKKI 90

>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 = 37.9 bits (87), Expect = 2e-04
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)

Query: 52  DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
              KPKRP SA+ V++ E  +  K + P         K   E WK+L+D+
Sbjct: 143 LLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDS 187

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

 Score = 51.3 bits (123), Expect = 5e-10
 Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
                +  K+P SA  +F+++ R  +  E+P    +        E WK+L++ 
Sbjct: 1   GSSGSSGIKKPMSASALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEE 52

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

 Score = 48.4 bits (116), Expect = 4e-09
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 5/47 (10%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           KPKRP SA+ V++ E  +  K + P         K   E WK+L+D+
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDS 43

>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 = 48.6 bits (116), Expect = 5e-09
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
             +   PNK KRP +AF +F +++R  Y Q +P  K   A+    G++WK + + 
Sbjct: 9   TVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNE 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 = 46.4 bits (111), Expect = 3e-08
 Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
                +  +RP +AF +F +  R + +QEHP         K   + W  L    
Sbjct: 1   GSSGSSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKE 53

>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 = 43.1 bits (102), Expect = 8e-07
 Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 35  ASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEK 94
                         + K+    KRP +AF V+ +  R+    ++P+    + + K  G+ 
Sbjct: 9   VDDDDKMSENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPH-LHNAELSKTLGKL 67

Query: 95  WKSLTDAV 102
           W+ L ++ 
Sbjct: 68  WRLLNESE 75

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

 Score = 41.8 bits (99), Expect = 1e-06
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
             +RP +AF V+ ++ RK   Q++P+    + + K  G+ WK+LT A 
Sbjct: 2   SIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAE 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 = 2e-05
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           ++ KRP +AF V+  + R+    E+P     S + K  G +WK LT+A 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAE 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 = 3e-05
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
              ++ +RP +AF V+ ++ RK   Q++P+    + + K  G+ WK+LT A 
Sbjct: 2   SFTSRIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAE 52

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

 Score = 38.2 bits (88), Expect = 5e-05
 Identities = 11/47 (23%), Positives = 23/47 (48%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
               RP + F ++LEE R     ++P+    + + K G  +++ L+ 
Sbjct: 4   GSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLST 50

>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 = 5e-05
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           ++ KRP +AF V+    R+   QE+P     S + K  G +WK L++  
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETE 48

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

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           KRP +AF V+ +  R+   ++ P+    + + K  G++WK L D+ 
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPD-MHNAEISKRLGKRWKLLKDSD 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 = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           ++ KRP +AF V+  + R+    E+P     S + K  G +WK LT+A 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAE 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 = 36.0 bits (84), Expect = 3e-04
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
              KRP +AF V+ ++ R+   Q  P++   S + K  G +WK++T+  
Sbjct: 3   PHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLE 50

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

 Score = 35.3 bits (82), Expect = 7e-04
 Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           K+P +AF ++++E R     E    K  +A+ +  G +W +L+   
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREE 48

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	119
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.92
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.91
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.9
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.9
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.9
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.89
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.89
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.89
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.89
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.88
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.88
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.88
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.87
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.87
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.87
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.86
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.86
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.86
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.86
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.86
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.86
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.86
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.86
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.85
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.85
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.85
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.83
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.83
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.83
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.83
2cto_A	93	Novel protein; high mobility group box domain, hel	99.81
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.8
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.8
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.78
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.76
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.76
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.71
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.7
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.68

>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=99.92  E-value=7.2e-25  Score=145.76  Aligned_cols=75  Identities=25%  Similarity=0.383  Sum_probs=70.8

Q ss_pred             ccccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        43 ~kk~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .+++++..+||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|..+.++|.
T Consensus         8 k~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   82 (90)
T 1wgf_A            8 KPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAALKAQSE   82 (90)
T ss_dssp             SSCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTC
T ss_pred             CCCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            445567778999999999999999999999999999999 899999999999999999999999999999999996

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

Probab=99.91  E-value=5.7e-24  Score=140.09  Aligned_cols=74  Identities=27%  Similarity=0.403  Sum_probs=68.2

Q ss_pred             ccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        45 k~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++++..+||+.|+||+|||||||+++|..|+.+||++. ++.||+++||++|++||+++|++|+++|..++++|.
T Consensus         5 ~~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   79 (86)
T 2eqz_A            5 SSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD   79 (86)
T ss_dssp             CSSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            34566789999999999999999999999999999993 269999999999999999999999999999999984

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

Probab=99.90  E-value=6e-24  Score=144.31  Aligned_cols=74  Identities=26%  Similarity=0.424  Sum_probs=69.5

Q ss_pred             cccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           44 KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        44 kk~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .++++..+||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|..++++|.
T Consensus         6 ~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   79 (102)
T 2co9_A            6 SGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYL   79 (102)
T ss_dssp             CCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHH
Confidence            34456678999999999999999999999999999999 899999999999999999999999999999999985

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

Probab=99.90  E-value=3.9e-24  Score=144.76  Aligned_cols=71  Identities=27%  Similarity=0.367  Sum_probs=67.7

Q ss_pred             ccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        47 kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +++.+||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|..++++|.
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~   72 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFE   72 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            56678999999999999999999999999999999 899999999999999999999999999999999963

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

Probab=99.90  E-value=1e-23  Score=135.77  Aligned_cols=68  Identities=37%  Similarity=0.562  Sum_probs=65.8

Q ss_pred             CCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++||+.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|.+.|..++.+|.
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   68 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE   68 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            47999999999999999999999999999999 899999999999999999999999999999999884

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

Probab=99.89  E-value=2.2e-23  Score=137.62  Aligned_cols=71  Identities=24%  Similarity=0.362  Sum_probs=67.8

Q ss_pred             ccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        47 kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++..+||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|..+.++|.
T Consensus         9 ~~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~   79 (87)
T 2e6o_A            9 TVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGK-DNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQK   79 (87)
T ss_dssp             SCCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            35678999999999999999999999999999999 899999999999999999999999999999999885

>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=99.89  E-value=3.3e-23  Score=133.04  Aligned_cols=66  Identities=26%  Similarity=0.288  Sum_probs=62.5

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|.++|..++++|.
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   66 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHR   66 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCC-SSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999999999 899999999999999999999999999999999884

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

Probab=99.89  E-value=4.6e-24  Score=142.60  Aligned_cols=73  Identities=34%  Similarity=0.535  Sum_probs=69.2

Q ss_pred             ccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        45 k~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++++..+||+.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|+++|..++++|.
T Consensus        10 ~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~   82 (93)
T 1cg7_A           10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYE   82 (93)
T ss_dssp             CCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTS-CHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTT
T ss_pred             ccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            4456678999999999999999999999999999999 899999999999999999999999999999999985

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

Probab=99.89  E-value=5.1e-23  Score=137.14  Aligned_cols=68  Identities=22%  Similarity=0.393  Sum_probs=65.7

Q ss_pred             CCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .+||++|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|..++.+|.
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   69 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDL-PFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYL   69 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            47999999999999999999999999999999 899999999999999999999999999999999884

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

Probab=99.88  E-value=3.6e-24  Score=143.96  Aligned_cols=75  Identities=33%  Similarity=0.489  Sum_probs=70.0

Q ss_pred             ccccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        43 ~kk~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s--~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .+++++..+||+.|+||+|||||||+++|..|..+||++ +  +.+|+++||++|++||+++|++|+++|..++++|.
T Consensus        10 k~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~-~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   86 (97)
T 2lhj_A           10 VRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEI-AKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYE   86 (97)
T ss_dssp             CCCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTS-TTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHH
T ss_pred             ccccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            344566778999999999999999999999999999999 8  99999999999999999999999999999999985

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

Probab=99.88  E-value=2.6e-23  Score=135.84  Aligned_cols=68  Identities=25%  Similarity=0.429  Sum_probs=64.8

Q ss_pred             CCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s--~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++||+.|+||+||||+||+++|..|+.+||++ +  +.+|+++||++|++||+++|++|+++|..++++|.
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~-~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   71 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDA-SVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE   71 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTT-CCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            47999999999999999999999999999998 5  59999999999999999999999999999999984

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

Probab=99.88  E-value=1.7e-22  Score=131.66  Aligned_cols=67  Identities=21%  Similarity=0.332  Sum_probs=65.1

Q ss_pred             CCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        51 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .|++.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|.++|..++++|.
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   69 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRL-DNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFM   69 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSS-CTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999 899999999999999999999999999999999986

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

Probab=99.87  E-value=1.4e-22  Score=134.99  Aligned_cols=67  Identities=21%  Similarity=0.284  Sum_probs=64.8

Q ss_pred             CCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        51 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .+|++||||+||||+||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|..++++|.
T Consensus         3 ~~p~~pKrP~say~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~   69 (92)
T 2cs1_A            3 SGSSGIKKPMSASALFVQDHRPQFLIENPKT-SLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYN   69 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCCSS-CHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999 899999999999999999999999999999999884

>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=99.87  E-value=3.4e-22  Score=131.26  Aligned_cols=66  Identities=26%  Similarity=0.288  Sum_probs=63.7

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .|+.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|.++|..+.++|.
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~   66 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHR   66 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Confidence            488999999999999999999999999999 899999999999999999999999999999999884

>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=99.87  E-value=1.9e-22  Score=132.46  Aligned_cols=62  Identities=18%  Similarity=0.268  Sum_probs=59.7

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhhcCCHHHhHhHHHHHHHHh
Q 033450           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDAVSSKISTGSFLNL  114 (119)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s-~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~  114 (119)
                      +++.||||+|||||||+++|..|+.+||++ + +.||+++||++|++||+++|++|+++|..+.
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~-~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDF-SDEADIIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTC-CSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-chhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            689999999999999999999999999999 8 9999999999999999999999999998774

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

Probab=99.86  E-value=5.5e-22  Score=126.79  Aligned_cols=63  Identities=32%  Similarity=0.559  Sum_probs=61.2

Q ss_pred             CCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |++|+||+||||+||+++|..|+.+||++ ++.||+++||++|++|  ++|++|+++|..++++|.
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~   63 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGI-KVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYH   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTC-CHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999999 8999999999999999  999999999999999985

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

Probab=99.86  E-value=5.9e-22  Score=125.21  Aligned_cols=64  Identities=25%  Similarity=0.359  Sum_probs=58.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.|+||+|||||||+++|..+..+||++ ++.+|+++||++|++||+++|++|+++|..++.+|.
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   64 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDL-HNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHM   64 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999 899999999999999999999999999999999885

>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=99.86  E-value=7.3e-22  Score=128.62  Aligned_cols=66  Identities=24%  Similarity=0.341  Sum_probs=60.4

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .++.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|+++|+.++++|.
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   68 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDL-HNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHM   68 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999 899999999999999999999999999999998884

>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=99.86  E-value=5.8e-22  Score=126.70  Aligned_cols=63  Identities=33%  Similarity=0.562  Sum_probs=60.5

Q ss_pred             CCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .++||||+|||||||+++|+.|+.+||++ ++.||+++||++|++||+  |++|+++|+.++++|.
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~   63 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGI-KVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYD   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSC-CHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999 899999999999999998  9999999999999884

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

Probab=99.86  E-value=6.4e-22  Score=125.34  Aligned_cols=64  Identities=22%  Similarity=0.380  Sum_probs=60.2

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +||||+||||+||+++|..++.+||++. ++.+|+++||++|++||+++|++|.++|..++++|.
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   65 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE   65 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            5999999999999999999999999993 249999999999999999999999999999999984

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

Probab=99.86  E-value=1.3e-21  Score=133.78  Aligned_cols=70  Identities=19%  Similarity=0.298  Sum_probs=62.5

Q ss_pred             cCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           48 SAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        48 k~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ...+|++.|+||+|||||||+++|+.|+.+||++ ++.+|+++||++|++||+++|++|+++|..++++|.
T Consensus        22 ~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   91 (106)
T 4euw_A           22 QSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHL-HNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHK   91 (106)
T ss_dssp             ------CCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999999999 899999999999999999999999999999999884

>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=99.86  E-value=1.4e-21  Score=140.70  Aligned_cols=72  Identities=36%  Similarity=0.545  Sum_probs=68.4

Q ss_pred             cccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        46 ~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +++..+||+.|+||+||||+||+++|..|+.+||++ ++++|+++||++|++||+++|++|+++|..++++|.
T Consensus        79 ~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~  150 (159)
T 2gzk_A           79 TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE  150 (159)
T ss_dssp             CGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCC-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccchhhHhhHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999 899999999999999999999999999999999985

>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=99.86  E-value=1.3e-21  Score=126.72  Aligned_cols=64  Identities=25%  Similarity=0.350  Sum_probs=61.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|.++|..++.+|.
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~   64 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHM   64 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999 899999999999999999999999999999999884

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

Probab=99.85  E-value=1.7e-21  Score=128.10  Aligned_cols=64  Identities=19%  Similarity=0.267  Sum_probs=61.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|.++|..+.++|.
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~   64 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKERQLHM   64 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999999999999999999 899999999999999999999999999999999885

>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=99.85  E-value=1.4e-21  Score=126.06  Aligned_cols=64  Identities=23%  Similarity=0.334  Sum_probs=61.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.|+||+|||||||+++|+.|..+||++ ++.+|+++||++|++||+++|++|+++|+.+.++|.
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   64 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDM-HNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHM   64 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999 899999999999999999999999999999998884

>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=99.85  E-value=1.5e-21  Score=126.87  Aligned_cols=65  Identities=25%  Similarity=0.329  Sum_probs=62.0

Q ss_pred             CCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|.+.|+.+..+|.
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~   66 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHL   66 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999 899999999999999999999999999999998875

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

Probab=99.83  E-value=8.3e-21  Score=138.63  Aligned_cols=71  Identities=37%  Similarity=0.552  Sum_probs=67.8

Q ss_pred             ccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        47 kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++..+||+.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|+++|..++++|.
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~  163 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE  163 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSS-CHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHH
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            45568999999999999999999999999999999 899999999999999999999999999999999985

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

Probab=99.83  E-value=1.5e-20  Score=137.30  Aligned_cols=73  Identities=25%  Similarity=0.408  Sum_probs=68.0

Q ss_pred             ccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCC--CCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPN--VKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        45 k~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~--~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.+...+||+.|+||+|||||||+++|..|..+||+  + ++.+|+++||++|++||++||++|+++|..++++|.
T Consensus         5 ~~k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   79 (173)
T 2yrq_A            5 SSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASV-NFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE   79 (173)
T ss_dssp             SCSSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCC-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTH
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            334567899999999999999999999999999999  6 799999999999999999999999999999999884

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

Probab=99.83  E-value=1.5e-22  Score=135.72  Aligned_cols=68  Identities=15%  Similarity=0.126  Sum_probs=63.3

Q ss_pred             ccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhcccC
Q 033450           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLLI  119 (119)
Q Consensus        47 kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s--~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~i  119 (119)
                      .+..+||++|+||+|||||||+++|+.|+.+||++ +  +.||+    ++|+.|++++|++|+++|+.+++.|.|
T Consensus        14 ~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~-s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~   83 (90)
T 2yuk_A           14 LKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDW-TTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRI   83 (90)
T ss_dssp             HHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSH-HHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCc-cchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            34456999999999999999999999999999999 8  89998    999999999999999999999999864

>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=99.83  E-value=9.5e-21  Score=130.11  Aligned_cols=68  Identities=16%  Similarity=0.206  Sum_probs=63.4

Q ss_pred             cccCCCCCCCC-CCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           46 VKSAKKDPNKP-KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        46 ~kk~~kdp~~P-KRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.++.+||+.| |||+||||+||+++|..|+    ++ ++.||+++||++|++||++||++|+++|..++.+|.
T Consensus         7 ~~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~-~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~   75 (108)
T 1v64_A            7 GQLKDKFDGRPTKPPPNSYSLYCAELMANMK----DV-PSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYE   75 (108)
T ss_dssp             CCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            45667899999 9999999999999999887    78 899999999999999999999999999999999984

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

Probab=99.81  E-value=1.5e-20  Score=126.58  Aligned_cols=66  Identities=15%  Similarity=0.164  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHH---HHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAG---GEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~l---ge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ..+++.||||+|||||||+++|+.|+.+  ++ ++.||+++|   |++|++|+++||++|+++|+.+.+.|.
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~-~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~   73 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--GL-PVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQG   73 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--TC-CCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--CC-CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999988  78 899999999   999999999999999999999999884

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

Probab=99.80  E-value=8.1e-20  Score=114.78  Aligned_cols=60  Identities=27%  Similarity=0.288  Sum_probs=55.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |.||||+||||+||+++|..++..     ++++|+++||++|++||+++|++|+++|..++.+|.
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~-----~p~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~   60 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGD-----SPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYH   60 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSS-----SHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhc-----CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999754     457999999999999999999999999999999884

>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=99.80  E-value=1e-19  Score=122.13  Aligned_cols=63  Identities=13%  Similarity=0.052  Sum_probs=60.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.|+||+|||++|+++.|..+..+||+  ++++|++.||++|++||++||++|+++|+.|+.+|.
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYe   65 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYE   65 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999998  489999999999999999999999999999999883

>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=99.78  E-value=3.8e-19  Score=120.70  Aligned_cols=65  Identities=11%  Similarity=0.140  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        51 kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .+..+||||+|||||||++++.  ..+++++ ++.||+++||++|++|+++||++|+++|+.++++|.
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~-~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~   68 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHL-PLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK   68 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            4567999999999999999975  3355668 899999999999999999999999999999999985

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

Probab=99.76  E-value=4.3e-19  Score=136.10  Aligned_cols=69  Identities=16%  Similarity=0.297  Sum_probs=65.9

Q ss_pred             CCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        49 ~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ...||+.|++|+|||||||+++|..|+.+||++ ++.||+++||++|++|+++||++|+++|..++++|.
T Consensus        35 s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~  103 (238)
T 3tmm_A           35 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK  103 (238)
T ss_dssp             CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            356899999999999999999999999999999 899999999999999999999999999999999884

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

Probab=99.76  E-value=6.2e-19  Score=133.39  Aligned_cols=66  Identities=17%  Similarity=0.313  Sum_probs=63.5

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +|++|++|+||||+||+++|..|..+||++ ++.||+++||++|++||++||++|+++|..++++|.
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~   71 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK   71 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999 899999999999999999999999999999998884

>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=2.3e-17  Score=118.61  Aligned_cols=65  Identities=26%  Similarity=0.308  Sum_probs=62.6

Q ss_pred             CCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |+.|+||+||||+|+++.+..|..+||++ ++.||+++||++|++||+++|++|.++|..+..+|.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   66 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHR   66 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSC-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHH
Confidence            67999999999999999999999999999 899999999999999999999999999999998874

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

Probab=99.70  E-value=1.8e-18  Score=130.79  Aligned_cols=67  Identities=25%  Similarity=0.213  Sum_probs=60.7

Q ss_pred             ccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        47 kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++..+||+.|+||+||||+||+++|..|.    +. +..+|+++||++|++||+++|++|++.|+.++++|.
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k----~~-~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~  172 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAK----GD-SPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYH  172 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSS----CS-SHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhc----cC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            45578999999999999999999998876    44 566999999999999999999999999999999984

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

Probab=99.68  E-value=3.8e-18  Score=130.84  Aligned_cols=67  Identities=25%  Similarity=0.213  Sum_probs=60.6

Q ss_pred             ccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        47 kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++..+||+.|+||+|||||||+++|..|.    +. +..+|++.||++|++|++++|++|+++|+.++++|.
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k----~~-~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~  204 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAK----GD-SPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYH  204 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSC----CS-SHHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHh----cc-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            45578999999999999999999998876    44 566899999999999999999999999999999984

---

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	119
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	4e-10
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-10
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	8e-10
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	9e-10
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-09
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	9e-09
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	8e-08
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	1e-07
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	2e-07
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-06
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	6e-06
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-04

>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 = 50.3 bits (120), Expect = 4e-10
 Identities = 26/58 (44%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 44  KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
           K     KKDPN PKR  SA+  F  E R + + E+P++     VGK  GEKWK+LT  
Sbjct: 9   KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPE 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 = 49.9 bits (119), Expect = 5e-10
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 46  VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSK 105
           +K  KK P+ PK+P + +F F  E R  Y + HP +     + K   +K+K L +    K
Sbjct: 1   MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMK 59

>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 = 49.6 bits (118), Expect = 8e-10
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 38  SSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
           S +    + +  K    KPKRP SA F+F EE R+  ++E P +   S + +     W  
Sbjct: 3   SGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWND 61

Query: 98  LTDA 101
           L++ 
Sbjct: 62  LSEK 65

>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 = 49.0 bits (117), Expect = 9e-10
 Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 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 = 48.3 bits (115), Expect = 2e-09
 Identities = 22/47 (46%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           N PKRPPSAFF+F  E+R   K EHP +  +  V K  GE W +   
Sbjct: 1   NAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAA 46

>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 = 46.4 bits (110), Expect = 9e-09
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDAVSSK 105
           KP+   S++  F++  R+ +K++HP+     S   K   E+WK+++     K
Sbjct: 1   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGK 52

>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 = 44.0 bits (104), Expect = 8e-08
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           ++ KRP +AF V+    R+   QE+P +   S + K  G +WK L++  
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETE 48

>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 = 43.7 bits (103), Expect = 1e-07
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSK 105
             KRP +AF V+ ++ R+   Q  P++   S + K  G +WK++T+     
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQP 51

>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 = 43.3 bits (102), Expect = 2e-07
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSK 105
           ++ KRP +AF V+  + R+    E+P ++  S + K  G +WK LT+A    
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWP 53

>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 = 41.0 bits (96), Expect = 2e-06
 Identities = 8/56 (14%), Positives = 18/56 (32%), Gaps = 3/56 (5%)

Query: 50  KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSK 105
                  K P + +  F +E     +  H  +K         G +W+ ++ +    
Sbjct: 3   SGSSGPKKPPMNGYQKFSQELLSNGELNHLPLKERM---VEIGSRWQRISQSQKEH 55

>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 = 39.5 bits (92), Expect = 6e-06
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSK 105
           K+P +AF ++++E R     E    +  +A+ +  G +W +L+    +K
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAK 51

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108

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

 Score = 35.7 bits (82), Expect = 2e-04
 Identities = 10/63 (15%), Positives = 19/63 (30%), Gaps = 5/63 (7%)

Query: 43  TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAV 102
           +      K D    K PP+++ ++  E     K                 ++WK L+   
Sbjct: 5   SSGQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPST-----ERMVLCSQQWKLLSQKE 59

Query: 103 SSK 105
              
Sbjct: 60  KDA 62

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	119
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.88
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.87
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.87
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.86
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.85
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.83
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.82
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.82
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.75
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.75
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	96.36

>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=99.88  E-value=7.2e-23  Score=135.40  Aligned_cols=75  Identities=35%  Similarity=0.536  Sum_probs=70.0

Q ss_pred             ccccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        43 ~kk~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .++.++..+||+.|++|+|||||||+++|..|+.+||++ ++.+|++.||++|++||+++|.+|.+.|..++.+|.
T Consensus         8 ~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~-~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~   82 (93)
T d1lwma_           8 KKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYE   82 (93)
T ss_dssp             TSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCC-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            445556778999999999999999999999999999999 899999999999999999999999999999999985

>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=99.87  E-value=2.3e-22  Score=131.78  Aligned_cols=73  Identities=26%  Similarity=0.396  Sum_probs=68.6

Q ss_pred             ccccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        45 k~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ..+....|++.|+||+|||||||+++|..|..+||++ ++.+|+++||.+|+.|++++|++|.++|..++.+|.
T Consensus        10 ~~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~-~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~   82 (90)
T d1wgfa_          10 SQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAALKAQSE   82 (90)
T ss_dssp             CSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTC
T ss_pred             CccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            3345568999999999999999999999999999999 899999999999999999999999999999999985

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

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

Probab=99.87  E-value=1e-22  Score=133.76  Aligned_cols=71  Identities=27%  Similarity=0.367  Sum_probs=68.0

Q ss_pred             ccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        47 kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ++..+||+.|+||+||||+||+++|..|..+||++ ++.+|++.||+.|+.||+++|.+|.+.|+.++.+|.
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~-~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~   72 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFE   72 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHH
Confidence            46779999999999999999999999999999999 899999999999999999999999999999999883

>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=99.86  E-value=1.1e-22  Score=130.51  Aligned_cols=64  Identities=34%  Similarity=0.534  Sum_probs=62.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |+||||+||||+||+++|..|+.+||++ ++.+|+++||++|++||+++|.+|.+.|..++.+|.
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~-~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~   64 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE   64 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTC-CTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999 899999999999999999999999999999999985

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

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

Probab=99.86  E-value=4.3e-22  Score=128.79  Aligned_cols=64  Identities=25%  Similarity=0.350  Sum_probs=61.8

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      +.|+||+||||||++++|..|..+||++ ++.+|+++||++|++||+++|++|+++|+.+.++|.
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~-~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~   64 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHM   64 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999 899999999999999999999999999999999884

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=8.4e-22  Score=128.37  Aligned_cols=64  Identities=27%  Similarity=0.313  Sum_probs=62.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      |.||||+|||||||+++|..|..+||++ ++.||+++||.+|++||+++|++|+++|..+..+|.
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~-~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~   66 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHR   66 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999 899999999999999999999999999999999884

>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=99.85  E-value=6.5e-22  Score=124.69  Aligned_cols=63  Identities=25%  Similarity=0.342  Sum_probs=60.8

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .+|||+||||+||+++|+.|+.+||++ ++++|+++||++|++||+++|++|.++|+.+..+|+
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~   64 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHL   64 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            568999999999999999999999999 899999999999999999999999999999999885

>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=99.83  E-value=3.6e-21  Score=120.96  Aligned_cols=64  Identities=22%  Similarity=0.380  Sum_probs=60.0

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~-s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .||||+||||+||+++|+.|+.+||+.. ++.+|+++||++|++||+++|++|.++|..++.+|.
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~   65 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE   65 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence            5999999999999999999999999741 578999999999999999999999999999999985

>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=99.82  E-value=6.6e-21  Score=120.67  Aligned_cols=63  Identities=32%  Similarity=0.543  Sum_probs=59.5

Q ss_pred             CCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      .|.||||+|||||||+++|+.|+.+||++ ++.+|+++||++|++|+  +|++|++.|+.++++|.
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~-~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~   63 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGI-KVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYD   63 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTC-CHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHH
Confidence            37899999999999999999999999999 89999999999999986  59999999999999984

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

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

Probab=99.82  E-value=1.3e-20  Score=122.94  Aligned_cols=63  Identities=19%  Similarity=0.283  Sum_probs=60.3

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ..+||+||||||++++|..|..+||++ ++++|+++||.+|++||++||++|.++|..+.++|+
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~-~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~   64 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKERQLHM   64 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999 899999999999999999999999999999998874

>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=99.75  E-value=1.2e-18  Score=115.79  Aligned_cols=64  Identities=9%  Similarity=0.106  Sum_probs=58.0

Q ss_pred             CCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ..++||||+|||||||+++|..+..  +++ ++.||++.||++|++||++||++|.++|..++.+|.
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~--~~~-~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~   68 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGEL--NHL-PLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK   68 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTT--TTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHh--cCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            4568999999999999999998764  456 689999999999999999999999999999999984

>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=99.75  E-value=1.7e-18  Score=116.79  Aligned_cols=68  Identities=15%  Similarity=0.153  Sum_probs=61.3

Q ss_pred             cccCCCCCCCCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhccc
Q 033450           46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGLL  118 (119)
Q Consensus        46 ~kk~~kdp~~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y~  118 (119)
                      ..+...|+.+|++|+|||||||+++|.+    +|++ ++.||+++||.+|++||+++|++|.++|..++.+|.
T Consensus         8 ~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~-~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~   75 (108)
T d1v64a_           8 QLKDKFDGRPTKPPPNSYSLYCAELMAN----MKDV-PSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYE   75 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCcHHHHHHHHHHHH----ccCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHH
Confidence            3455578888999999999999998864    6899 899999999999999999999999999999999985

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

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

Probab=96.36  E-value=0.0081  Score=36.93  Aligned_cols=61  Identities=13%  Similarity=0.050  Sum_probs=52.8

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHhHhHHHHHHHHhhcc
Q 033450           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAVSSKISTGSFLNLLGL  117 (119)
Q Consensus        55 ~PKRP~say~lF~~e~R~~ik~e~P~~~s~~eisk~lge~Wk~Ls~~EK~~Y~~~A~~~~~~Y  117 (119)
                      .|-.|.+|--+|.+.....+...+-+-  -.-..+.+...|++|...|+.+|...|+.|..+|
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~D--R~KaqkaMeatW~~meKkEki~wikkaaedqkry   63 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKND--RVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRY   63 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTST--HHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhh--HHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHH
Confidence            466788899999999999998887664  4566778889999999999999999999999888