Citrus Sinensis ID: 033573

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110------
Protein Sequence
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVICTT
Secondary Structure (PSIPRED)
cccccccccccHHHHHcccccHHHHHcHHHHHHHHccccccHHccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHccccHHHHcccccccccHcccccccHHHHccccccccccccccccHHHHEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHcccEEEEEEEEEEc
Coil and Loop (DISEMBL)
mkvtrgkgavkkdknevvkpvedraAGKRKAVLKASrssnkrtknvksakkdpnkpkrppsaFFVFLEEFRKVYKqehpnvkaVSAVGKAGGEKWKSLTDAIKKEHWMVKFVICTT
Flexible Loop (DISEMBL)
mkvtrgkgavkkdknevvkpvedraagkrkavlkasrssnkrtknvksakkdpnkpkrppSAFFVFLEEFRKVYKqehpnvkavsavgkaggekWKSLTDAIKKEHWMVKFVICTT
Low Complexity Region (SEG)
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVICTT
Disordered region (IsUnstruct)
*************************************************************AFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVIC**
Disordered Region (DISOPRED)
**********************************************************PPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVIC**
Disordered Region (DISEMBL)
**************NEVVKPVED**********************************RPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVICTT
Disordered Region (DISPRO)
*****************************************************NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVICTT
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVICTT
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	116	2.2.26 [Sep-21-2011]
O49595	178	High mobility group B pro	yes	no	0.862	0.561	0.621	4e-26
P40619	144	HMG1/2-like protein OS=Ip	N/A	no	0.525	0.423	0.721	2e-19
P93047	141	High mobility group B pro	no	no	0.543	0.446	0.698	6e-19
P26585	152	HMG1/2-like protein OS=Gl	no	no	0.474	0.361	0.763	1e-18
P40620	149	HMG1/2-like protein OS=Vi	N/A	no	0.431	0.335	0.72	2e-16
O49596	144	High mobility group B pro	no	no	0.491	0.395	0.649	7e-16
Q42344	138	High mobility group B pro	no	no	0.491	0.413	0.631	2e-15
P27347	157	DNA-binding protein MNB1B	N/A	no	0.75	0.554	0.471	2e-15
P40621	161	HMG1/2-like protein OS=Tr	N/A	no	0.448	0.322	0.653	7e-14
O49597	125	High mobility group B pro	no	no	0.560	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 (290), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 64/103 (62%), Positives = 78/103 (75%), Gaps = 3/103 (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  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           SAFFVFLE+FR  +K+E+PNVKAVSAVGKAGG+KWKS++ A K
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEK 100

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 = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/61 (72%), Positives = 51/61 (83%)

Query: 43  TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAI 102
           TK  K A KDPNKPKRPPSAFFVF+E+FRK YK++HPN K+V+ VGKAGG+KWK LT A 
Sbjct: 23  TKKTKKAVKDPNKPKRPPSAFFVFMEDFRKTYKEKHPNNKSVAVVGKAGGDKWKQLTAAE 82

Query: 103 K 103
           K
Sbjct: 83  K 83

Ipomoea nil (taxid: 35883)

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

 Score = 92.8 bits (229), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 51/63 (80%)

Query: 41  KRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
           K  K  K A KDPNKPKRP SAFFVF+E+FR  YK+EHP  K+V+AVGKAGGEKWKSL+D
Sbjct: 20  KPAKGAKGAAKDPNKPKRPSSAFFVFMEDFRVTYKEEHPKNKSVAAVGKAGGEKWKSLSD 79

Query: 101 AIK 103
           + K
Sbjct: 80  SEK 82

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 = 91.3 bits (225), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/55 (76%), Positives = 48/55 (87%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           A KDPNKPKRPPSAFFVF+EEFRKV+ +EHP  KAVSAVGKA G KWK+++DA K
Sbjct: 37  AAKDPNKPKRPPSAFFVFMEEFRKVFNKEHPENKAVSAVGKAAGAKWKTMSDAEK 91

Glycine max (taxid: 3847)

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

 Score = 84.3 bits (207), Expect = 2e-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 = 7e-16,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 49/57 (85%)

Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           K+A KDPNKPKRP SAFFVF+E+FR+ +K+E+P  K+V+ VGKA G+KWKSL+D+ K
Sbjct: 29  KAAAKDPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVGKAAGDKWKSLSDSEK 85

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 = 36/57 (63%), Positives = 45/57 (78%)

Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           K  KKDPN+PKRPPSAFFVFLE+FRK +   +PN K+V+ VGKA G +WK++TD  K
Sbjct: 26  KKTKKDPNQPKRPPSAFFVFLEDFRKEFNLANPNNKSVATVGKAAGARWKAMTDEDK 82

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 = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 17/104 (16%)

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

Query: 60  PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           PSAFFVF+EEFRK +K+++P  K+V+AVGKA G++WKSL+++ K
Sbjct: 45  PSAFFVFMEEFRKEFKEKNPKNKSVAAVGKAAGDRWKSLSESDK 88

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 = 7e-14,   Method: Compositional matrix adjust.
 Identities = 34/52 (65%), Positives = 45/52 (86%)

Query: 52  DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           DPNKPKR PSAFFVF+ EFR+ +KQ++P  K+V+AVGKA GE+WKSL+++ K
Sbjct: 38  DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSESEK 89

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	116
359386154	165	group B HMG-box protein [Citrus sinensis	0.887	0.624	0.990	2e-50
224112525	176	high mobility group family [Populus tric	0.887	0.585	0.757	1e-35
225448398	166	PREDICTED: high mobility group B protein	0.887	0.620	0.786	4e-35
225448400	156	PREDICTED: high mobility group B protein	0.887	0.660	0.786	6e-35
297736623	128	unnamed protein product [Vitis vinifera]	0.879	0.796	0.784	1e-34
118484946	171	unknown [Populus trichocarpa]	0.887	0.602	0.708	1e-33
224098541	179	high mobility group family [Populus tric	0.887	0.575	0.708	1e-33
255571919	190	DNA-binding protein MNB1B, putative [Ric	0.887	0.542	0.737	3e-30
449521910	112	PREDICTED: high mobility group B protein	0.948	0.982	0.639	6e-29
449461783	169	PREDICTED: high mobility group B protein	0.879	0.603	0.689	7e-29

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

 Score =  202 bits (514), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 102/103 (99%), Positives = 102/103 (99%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP
Sbjct: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA K
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEK 103

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 = 1e-35,   Method: Compositional matrix adjust.
 Identities = 78/103 (75%), Positives = 85/103 (82%)

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

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL+ A K
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSAAEK 103

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 = 81/103 (78%), Positives = 88/103 (85%)

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

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL++A K
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSEADK 103

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 =  150 bits (380), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 81/103 (78%), Positives = 88/103 (85%)

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

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL++A K
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSEADK 103

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 =  150 bits (378), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 80/102 (78%), 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  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAI 102
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL++A+
Sbjct: 85  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLSEAV 126

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  147 bits (370), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 73/103 (70%), Positives = 83/103 (80%)

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

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           S+FFVFLEEFRK+YKQEHPN+KAVSAVGKAGGEKWKS++ A K
Sbjct: 61  SSFFVFLEEFRKIYKQEHPNMKAVSAVGKAGGEKWKSMSAAEK 103

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  146 bits (369), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 73/103 (70%), Positives = 83/103 (80%)

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

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           S+FFVFLEEFRK+YKQEHPN+KAVSAVGKAGGEKWKS++ A K
Sbjct: 61  SSFFVFLEEFRKIYKQEHPNMKAVSAVGKAGGEKWKSMSAAEK 103

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 =  135 bits (340), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 76/103 (73%), Positives = 87/103 (84%)

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

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           SAFFVFLE+FRKVYKQEHPNVKAVSAVGKAGGEKWKS+++A K
Sbjct: 61  SAFFVFLEDFRKVYKQEHPNVKAVSAVGKAGGEKWKSMSNAEK 103

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 =  131 bits (329), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 71/111 (63%), Positives = 85/111 (76%), Gaps = 1/111 (0%)

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

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKF 111
           SAFFVFLEEFRK YK+E+PNVKAVSAVGKAGGEKWKSL+ A+    + +K 
Sbjct: 60  SAFFVFLEEFRKEYKRENPNVKAVSAVGKAGGEKWKSLSHAVSIVVYYIKI 110

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 (328), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 71/103 (68%), Positives = 82/103 (79%), 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  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           SAFFVFLEEFRK YK+E+PNVKAVSAVGKAGGEKWKSL+ A K
Sbjct: 60  SAFFVFLEEFRKEYKRENPNVKAVSAVGKAGGEKWKSLSHAEK 102

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	116
TAIR|locus:505006135	144	HMGB2 "high mobility group B2"	0.646	0.520	0.533	1.6e-17
TAIR|locus:2053893	138	HMGB4 "high mobility group B4"	0.655	0.550	0.526	1.1e-16
TAIR|locus:2128003	125	HMGB5 "high mobility group B5"	0.560	0.52	0.492	1.3e-13
TAIR|locus:2154433	241	HMGB6 "high-mobility group box	0.715	0.344	0.461	1.6e-13
RGD|1564407	200	Hmgb3 "high mobility group box	0.508	0.295	0.475	1.5e-10
UNIPROTKB|P40618	202	HMGB3 "High mobility group pro	0.482	0.277	0.491	2.5e-10
UNIPROTKB|F6QYV9	709	SSRP1 "Uncharacterized protein	0.706	0.115	0.415	3.2e-10
UNIPROTKB|F1N927	214	HMGB1 "High mobility group pro	0.836	0.453	0.383	4.1e-10
UNIPROTKB|Q9YH06	215	HMG1 "High mobility group 1 pr	0.836	0.451	0.383	4.1e-10
UNIPROTKB|E1BIF8	194	E1BIF8 "Uncharacterized protei	0.551	0.329	0.439	4.1e-10

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

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 40/75 (53%), Positives = 55/75 (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 KAGGEKWKSLTDAIK 103
             KA G+KWKSL+D+ K
Sbjct:    71 KAAGDKWKSLSDSEK 85

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 = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 40/76 (52%), Positives = 51/76 (67%)

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

Query:    88 GKAGGEKWKSLTDAIK 103
             GKA G +WK++TD  K
Sbjct:    67 GKAAGARWKAMTDEDK 82

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 = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 42/91 (46%), Positives = 52/91 (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 YKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
             +K EH    A  A  K GGEKWKSLT+  KK
Sbjct:   133 FKSEHNGSLAKDAA-KIGGEKWKSLTEEEKK 162

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

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

 Score = 148 (57.2 bits), Expect = 1.5e-10, P = 1.5e-10
 Identities = 29/61 (47%), Positives = 40/61 (65%)

Query:    50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMV 109
             KKDPN PKRPPS FF+F  EFR   K  +P + ++  V K  GE W +L+D+ +K+ +M 
Sbjct:    87 KKDPNAPKRPPSGFFLFCSEFRPKIKSANPGI-SIGDVAKKLGEMWNNLSDS-EKQPYMT 144

Query:   110 K 110
             K
Sbjct:   145 K 145

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

 Score = 146 (56.5 bits), Expect = 2.5e-10, P = 2.5e-10
 Identities = 28/57 (49%), Positives = 37/57 (64%)

Query:    50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
             KKDPN PKRPPSAFF+F  EFR   K  +P + ++  V K  GE W +L+D  K+ +
Sbjct:    87 KKDPNAPKRPPSAFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLSDGEKQPY 142

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

UNIPROTKB|F6QYV9 SSRP1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 156 (60.0 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 37/89 (41%), Positives = 50/89 (56%)

Query:    23 DRAAGKRKAVLKAS----RSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEH 78
             DR   KRK + KA     R S K+   VK  K DPN PKRP SA+ ++L   R+  K +H
Sbjct:   511 DREEKKRKQLKKAKMAKDRKSRKKPLEVKKGK-DPNAPKRPMSAYMLWLNASREKIKSDH 569

Query:    79 PNVKAVSAVGKAGGEKWKSLTDAIKKEHW 107
             P + +V+ + K  GE WK ++   KKE W
Sbjct:   570 PGI-SVTDLSKKAGEIWKGMSKE-KKEEW 596

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 41/107 (38%), Positives = 54/107 (50%)

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

Query:    64 FVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
             F+F  EFR   K EHP + ++  V K  GE W + T A  K+ +  K
Sbjct:   103 FLFCSEFRPKIKGEHPGL-SIGDVAKKLGEMWNN-TAADDKQPYEKK 147

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 41/107 (38%), Positives = 54/107 (50%)

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

Query:    64 FVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
             F+F  EFR   K EHP + ++  V K  GE W + T A  K+ +  K
Sbjct:   103 FLFCSEFRPKIKGEHPGL-SIGDVAKKLGEMWNN-TAADDKQPYEKK 147

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|E1BIF8 E1BIF8 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 29/66 (43%), Positives = 41/66 (62%)

Query:    45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
             + K  KKDPN PKRPPS FF+F  EF    K  +P + ++  V K  GE W +L+D+ KK
Sbjct:    79 SAKGGKKDPNAPKRPPSGFFLFFSEFCSEIKSTNPGI-SIGDVAKKLGEMWNNLSDS-KK 136

Query:   105 EHWMVK 110
             + ++ K
Sbjct:   137 QLYVNK 142

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

Your Input: eugene3.00101840 annotation not avaliable (164 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	116
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-11
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	2e-10
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	3e-10
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	2e-08
smart00398	70	smart00398, HMG, high mobility group	3e-08
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	8e-06
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	1e-04
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	1e-04

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

 Score = 54.2 bits (131), Expect = 3e-11
 Identities = 24/50 (48%), Positives = 33/50 (66%), Gaps = 1/50 (2%)

Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           PKRP SAFF+F +E R   K E+P +K  + + K  GEKWK+L++  KK 
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 = 52.2 bits (126), Expect = 2e-10
 Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           PKRP SA+F+F +E R   K E+P +  V  + K  GE WKSL++  KK+
Sbjct: 1   PKRPLSAYFLFSQEHRAEVKAENPGLS-VGEISKILGEMWKSLSEEEKKK 49

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 = 51.5 bits (124), Expect = 3e-10
 Identities = 24/49 (48%), Positives = 33/49 (67%), Gaps = 1/49 (2%)

Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           PKRP SA+F+F +E R   K+E+P+   V+ V K  GEKWK L++  KK
Sbjct: 1   PKRPLSAYFLFSQEQRPKLKKENPDAS-VTEVTKILGEKWKELSEEEKK 48

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

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

 Score = 49.5 bits (118), Expect = 2e-08
 Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

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

Query: 101 AIKKE 105
             K+ 
Sbjct: 115 EEKEP 119

Length = 211

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

 Score = 46.5 bits (111), Expect = 3e-08
 Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
           KPKRP SAF +F +E R   K E+P++   + + K  GE+WK L++  K  +
Sbjct: 1   KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPY 51

Length = 70

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

 Score = 40.5 bits (95), Expect = 8e-06
 Identities = 20/53 (37%), Positives = 32/53 (60%)

Query: 53  PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           PNKPK   +A+F F++  R   K+E P V  V+   K   EKWK++++  K++
Sbjct: 1   PNKPKAKRNAYFFFVQTMRPELKREGPQVPGVAEFSKLCSEKWKAMSEEEKEK 53

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 = 37.3 bits (87), Expect = 1e-04
 Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           KRP +AF +F +  R+   QE+P  K   A+ K  G++WK+L++  K+ 
Sbjct: 3   KRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQP 50

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 = 37.5 bits (87), Expect = 1e-04
 Identities = 28/72 (38%), Positives = 37/72 (51%), Gaps = 1/72 (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  EKWKSLTDAIKK 104
           E W  L++  K 
Sbjct: 61  EAWNKLSEEEKA 72

Length = 94

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	116
PTZ00199	94	high mobility group protein; Provisional	99.88
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.78
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.77
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.76
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.74
smart00398	70	HMG high mobility group.	99.73
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.71
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.71
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.69
KOG0381	96	consensus HMG box-containing protein [General func	99.66
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.55
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.48
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	99.02
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	98.98
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	98.82
KOG2746	683	consensus HMG-box transcription factor Capicua and	98.61
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.59
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	97.27
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	96.99
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	96.95
COG5648	211	NHP6B Chromatin-associated proteins containing the	95.04
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	94.52
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	94.35
KOG3223	221	consensus Uncharacterized conserved protein [Funct	86.53
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	84.98
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	84.38

>PTZ00199 high mobility group protein; Provisional

Probab=99.88  E-value=2.2e-22  Score=136.09  Aligned_cols=70  Identities=39%  Similarity=0.504  Sum_probs=64.1

Q ss_pred             cccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        43 ~kk~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s--~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+++++..+||+.|+||+|||||||+++|..|..+||++ +  +.+|+++||++|+.||++||.+|+++|...
T Consensus        10 ~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~-~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~d   81 (94)
T PTZ00199         10 VRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPEL-AKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQED   81 (94)
T ss_pred             ccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344556789999999999999999999999999999998 5  899999999999999999999999998763

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

Probab=99.78  E-value=6.6e-19  Score=114.21  Aligned_cols=58  Identities=21%  Similarity=0.325  Sum_probs=55.4

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .|+||+||||||++++|..|+.+||++ ++.+|+++||++|+.|++++|++|+++|...
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~   58 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGL-TNNEISRIIGRMWRSESPEVKAYYKELAEEE   58 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            489999999999999999999999999 9999999999999999999999999998764

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=99.77  E-value=2e-18  Score=107.49  Aligned_cols=57  Identities=42%  Similarity=0.580  Sum_probs=54.7

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        56 PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |++|+|||++|++++|..+..+||++ ++.+|++.||++|+.||+++|.+|.+.|...
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~-~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~   57 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDA-SVTEVTKILGEKWKELSEEEKKKYEEKAEKD   57 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            89999999999999999999999999 9999999999999999999999999988653

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=99.76  E-value=3.5e-18  Score=109.65  Aligned_cols=57  Identities=30%  Similarity=0.449  Sum_probs=54.4

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        56 PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+||+||||+||+++|..++.+||++ ++.+|+++||++|+.||+++|++|.++|...
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~-~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~   58 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLK-ENRAISKILGDRWKALSNEEKQPYYEEAKKL   58 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            47999999999999999999999999 9999999999999999999999999998754

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=99.74  E-value=9.7e-18  Score=105.33  Aligned_cols=57  Identities=32%  Similarity=0.493  Sum_probs=52.9

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        56 PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |+||+|||+|||++++..+..+||++ ++.+|+++||.+|+.||+++|.+|.+.|...
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~-~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~   57 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDL-SNKEISKILAQMWKNLSEEEKAPYKEEAEEE   57 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTS-THHHHHHHHHHHHHCSHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhccc-ccccchhhHHHHHhcCCHHHHHHHHHHHHHH
Confidence            89999999999999999999999999 9999999999999999999999999988754

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=99.73  E-value=1.8e-17  Score=103.57  Aligned_cols=58  Identities=36%  Similarity=0.494  Sum_probs=55.4

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +|++|+|+|++|++++|..+..+||++ ++.+|++.||.+|+.||+++|.+|.+.|...
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~-~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~   58 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDL-SNAEISKKLGERWKLLSEEEKAPYEEKAKKD   58 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            589999999999999999999999999 9999999999999999999999999988754

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

Probab=99.71  E-value=4.7e-17  Score=100.60  Aligned_cols=57  Identities=40%  Similarity=0.563  Sum_probs=54.7

Q ss_pred             CCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        56 PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |++|+|||++|++++|..+..+||++ ++.+|++.||.+|+.|++++|.+|.+.|...
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~-~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~   57 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGL-SVGEISKILGEMWKSLSEEEKKKYEEKAEKD   57 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            79999999999999999999999999 9999999999999999999999999988754

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=99.71  E-value=1.1e-17  Score=127.19  Aligned_cols=68  Identities=41%  Similarity=0.633  Sum_probs=63.8

Q ss_pred             ccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Q 033573           44 KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFV  112 (116)
Q Consensus        44 kk~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~  112 (116)
                      +...++.+|||.|+||+|+||+|++++|+.|+.++|.+ +|.+|++++|++|++|+++|+.+|...+-.
T Consensus        59 k~~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l-~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~  126 (211)
T COG5648          59 KRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKL-TFGEVGKLLSEKWKELTDEEKEPYYKEANS  126 (211)
T ss_pred             HHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHhccHhhhhhHHHHHhh
Confidence            55677789999999999999999999999999999999 999999999999999999999999987753

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

Probab=99.69  E-value=9.5e-17  Score=103.19  Aligned_cols=60  Identities=38%  Similarity=0.520  Sum_probs=52.0

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHh-CCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           53 PNKPKRPPSAFFVFLEEFRKVYKQE-HPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~vk~e-~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |+.|++|+|||+||+.+++..+... ++.. ++.|+++.||+.|+.||++||.+|++.|...
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~-~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~   61 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQ-SFREVMKEISERWKSLSEEEKEPYEERAKED   61 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-S-SHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            7899999999999999999999988 7777 8999999999999999999999999999765

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=99.66  E-value=5.1e-16  Score=103.67  Aligned_cols=62  Identities=42%  Similarity=0.596  Sum_probs=58.2

Q ss_pred             CC--CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhh
Q 033573           52 DP--NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVIC  114 (116)
Q Consensus        52 dp--~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~~  114 (116)
                      ||  +.|+||+|||++|+.++|..++.+||++ ++.+|++++|++|+.|+++++.+|+..+...+
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~-~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k   80 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGL-SVGEVAKALGEMWKNLAEEEKQPYEEKASKLK   80 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            77  4999999999999999999999999999 99999999999999999999999998887654

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.55  E-value=7.4e-15  Score=118.67  Aligned_cols=64  Identities=25%  Similarity=0.405  Sum_probs=58.8

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        49 k~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .......-||||||||+|.+.+|..|..+||.+ ...||++.||.+|+.|+++||.||++.|.-|
T Consensus        56 ~k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~m-HNSEISK~LG~~WK~Lse~EKrPFi~EAeRL  119 (331)
T KOG0527|consen   56 DKTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKM-HNSEISKRLGAEWKLLSEEEKRPFVDEAERL  119 (331)
T ss_pred             CCCCccccCCCcchhhhhhHHHHHHHHHhCcch-hhHHHHHHHHHHHhhcCHhhhccHHHHHHHH
Confidence            345566789999999999999999999999999 9999999999999999999999999988644

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

Probab=99.48  E-value=3.4e-14  Score=119.95  Aligned_cols=63  Identities=38%  Similarity=0.612  Sum_probs=58.9

Q ss_pred             cccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Q 033573           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFV  112 (116)
Q Consensus        45 k~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~  112 (116)
                      +..++.+|||+|||++||||||++..|..|+.+  ++ ++++|++.+|++|+.||.  |.+|+++|++
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi-~~~dv~kk~g~~wk~ms~--k~~we~ka~~  587 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GI-SVGDVAKKAGEKWKQMSA--KEEWEDKAAV  587 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--Cc-hHHHHHHHHhHHHhhhcc--cchhhHHHHH
Confidence            566778999999999999999999999999988  88 999999999999999999  9999999875

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

Probab=99.02  E-value=9.4e-11  Score=98.23  Aligned_cols=63  Identities=24%  Similarity=0.422  Sum_probs=57.1

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ...++.-||||||||+|..|.|..|...+|++ ....|+++||..|+.|+..||+||.+..+.|
T Consensus       320 ~ss~PHIKRPMNAFMVWAkDERRKILqA~PDM-HNSnISKILGSRWKaMSN~eKQPYYEEQaRL  382 (511)
T KOG0528|consen  320 ASSEPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMSNTEKQPYYEEQARL  382 (511)
T ss_pred             CCCCccccCCcchhhcccchhhhhhhhcCccc-cccchhHHhcccccccccccccchHHHHHHH
Confidence            34455779999999999999999999999999 9999999999999999999999999876654

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=98.98  E-value=7e-10  Score=90.07  Aligned_cols=56  Identities=20%  Similarity=0.390  Sum_probs=51.7

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKF  111 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~  111 (116)
                      .-|+|+||||||+.+.|..|..++-.- ...+|.++||.+|..||-+|...|.++|.
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEctlK-eSAaiNqiLGrRWH~LSrEEQAKYyElAr  246 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECTLK-ESAAINQILGRRWHALSREEQAKYYELAR  246 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhhhh-hHHHHHHHHhHHHhhhhHHHHHHHHHHHH
Confidence            568999999999999999999999644 78999999999999999999999999874

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

Probab=98.82  E-value=6.4e-09  Score=84.00  Aligned_cols=62  Identities=23%  Similarity=0.403  Sum_probs=56.6

Q ss_pred             ccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHH
Q 033573           48 SAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK  110 (116)
Q Consensus        48 kk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a  110 (116)
                      ...+.|..|-+|+-+||.|+...|++|+..||++ ...||.++||.+|..|+++||+.|++-.
T Consensus        57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~-kLWeiGK~Ig~mW~dLpd~EK~ey~~EY  118 (410)
T KOG4715|consen   57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPEL-KLWEIGKIIGGMWLDLPDEEKQEYLNEY  118 (410)
T ss_pred             cCCCCCCCCCcccchhhHHhhhhhhhhhccCcch-HHHHHHHHHHHHHhhCcchHHHHHHHHH
Confidence            3456777889999999999999999999999999 8999999999999999999999998654

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

Probab=98.61  E-value=2.8e-08  Score=86.04  Aligned_cols=69  Identities=28%  Similarity=0.422  Sum_probs=62.1

Q ss_pred             cccccCCCCCCCCCCCchhHhHHHHHH--HHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhh
Q 033573           45 NVKSAKKDPNKPKRPPSAFFVFLEEFR--KVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVIC  114 (116)
Q Consensus        45 k~kkk~kdp~~PKRP~say~lF~~e~R--~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~~  114 (116)
                      .+..-++|...-+||||+|++|++.+|  ..+.+.||+. ...-|+++||+.|-.|.+.||+.|.++|..+.
T Consensus       171 grspnkr~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~-DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk  241 (683)
T KOG2746|consen  171 GRSPNKRDKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQ-DNRTISKILGEWWYTLGPNEKQKYHDLAFQVK  241 (683)
T ss_pred             cCCCCcCcchhhhhhhHHHHHHHhhcCCccchhccCccc-cchhHHHHHhhhHhhhCchhhhhHHHHHHHHH
Confidence            334445666788999999999999999  9999999999 89999999999999999999999999998874

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

Probab=97.59  E-value=0.00017  Score=54.17  Aligned_cols=48  Identities=23%  Similarity=0.389  Sum_probs=42.4

Q ss_pred             CchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Q 033573           60 PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFV  112 (116)
Q Consensus        60 ~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~  112 (116)
                      -++|+-|+.++|.    .|.++ +..|+....+..|..|++++|..|..++..
T Consensus        83 nnaYLNFLReFRr----kh~~L-~p~dlI~~AAraW~rLSe~eK~rYrr~~~~  130 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCGL-SPQDLIQRAARAWCRLSEAEKNRYRRMAPS  130 (183)
T ss_pred             chHHHHHHHHHHH----HccCC-CHHHHHHHHHHHHHhCCHHHHHHHHhhcch
Confidence            4679999988876    56799 999999999999999999999999997653

The function of this family is unknown.

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

Probab=97.27  E-value=0.0012  Score=43.71  Aligned_cols=57  Identities=18%  Similarity=0.117  Sum_probs=46.4

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .|..|-++--+|.+.....+...+++- ...+ .+.+...|++|++.+|.+|+.+|++.
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~d-r~K~-~kam~~~W~~me~Kekl~WIkKA~Ed   59 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRND-RKKA-LKAMEAQWSQMEKKEKLKWIKKAAED   59 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTST-HHHH-HHHHHHHHHTTGGGHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHh-HHHH-HHHHHHHHHHhhhhhhhHHHHHHHHH
Confidence            577889999999999999999999987 6666 45999999999999999999999863

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

Probab=96.99  E-value=0.0011  Score=41.11  Aligned_cols=40  Identities=15%  Similarity=0.365  Sum_probs=36.3

Q ss_pred             CchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCH
Q 033573           60 PSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD  100 (116)
Q Consensus        60 ~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~  100 (116)
                      ++.|-+|.+..|+.|...||++ .++.+..+++.+|++-++
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            4678999999999999999999 999999999999987543

; 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=96.95  E-value=0.0023  Score=47.82  Aligned_cols=47  Identities=28%  Similarity=0.496  Sum_probs=41.7

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCC
Q 033573           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT   99 (116)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls   99 (116)
                      .|.+-.|-+|||-.|+.+....|+..||++ +..|.-...+..|...+
T Consensus       118 PPEKRqR~psaYn~f~k~ei~rik~~~p~i-shkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  118 PPEKRQRVPSAYNRFMKEEIQRIKAENPDI-SHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             CccccCCCchhHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHhhhhCc
Confidence            344456779999999999999999999999 99999999999998764

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

Probab=95.04  E-value=0.017  Score=44.56  Aligned_cols=58  Identities=19%  Similarity=0.151  Sum_probs=51.7

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFV  112 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~  112 (116)
                      .+|..|..+|+-|-..+|+.+...+|.. +..++++++|..|.+|++.-+.+|.+.+..
T Consensus       142 ~~~~~~~~~~~e~~~~~r~~~~~~~~~~-~~~e~~k~~~~~w~el~~skK~~~~~~~Kk  199 (211)
T COG5648         142 LPNKAPIGPFIENEPKIRPKVEGPSPDK-ALVEETKIISKAWSELDESKKKKYIDKYKK  199 (211)
T ss_pred             cCCCCCCchhhhccHHhccccCCCCcch-hhhHHhhhhhhhhhhhChhhhhHHHHHHHH
Confidence            3567788888889999999999999998 899999999999999999999999987654

>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=94.52  E-value=0.09  Score=40.20  Aligned_cols=44  Identities=23%  Similarity=0.448  Sum_probs=34.7

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcC
Q 033573           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL   98 (116)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~L   98 (116)
                      ......++||+|+||.|+.=+    ....|+. ...++|..|+..|..=
T Consensus        38 ~~~~~~~kr~lN~Fm~FRsyy----~~~~~~~-~Qk~~S~~l~~lW~~d   81 (201)
T PF04769_consen   38 KRSPEKAKRPLNGFMAFRSYY----SPIFPPL-PQKELSGILTKLWEKD   81 (201)
T ss_pred             cccccccccchhHHHHHHHHH----HhhcCCc-CHHHHHHHHHHHHhCC
Confidence            345557899999999995444    4566788 7899999999999863

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=94.35  E-value=0.066  Score=38.05  Aligned_cols=49  Identities=20%  Similarity=0.299  Sum_probs=41.0

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCH
Q 033573           51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD  100 (116)
Q Consensus        51 kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~  100 (116)
                      .|..+-+|--.||.-|....-+.++.+||+| -.+++-.+|-..|..-++
T Consensus        68 ~drHPErR~KAAy~afeE~~Lp~lK~E~PgL-rlsQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   68 IDRHPERRMKAAYKAFEERRLPELKEENPGL-RLSQYKQMLWKEWQKSPE  116 (122)
T ss_pred             CCCCcchhHHHHHHHHHHHHhHHHHhhCCCc-hHHHHHHHHHHHHhcCCC
Confidence            3443345555789999999999999999999 899999999999987664

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.53  E-value=0.61  Score=35.84  Aligned_cols=58  Identities=24%  Similarity=0.292  Sum_probs=46.8

Q ss_pred             CCC-CCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhhc
Q 033573           54 NKP-KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVICT  115 (116)
Q Consensus        54 ~~P-KRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~~~  115 (116)
                      ..| +|-..||.-|-...-+.++.+||++ ..+++-.+|-.+|..-++.   ||.+.+..+++
T Consensus       162 rHPEkRmrAA~~afEe~~LPrLK~e~P~l-rlsQ~Kqll~Kew~KsPDN---P~Nq~~~a~n~  220 (221)
T KOG3223|consen  162 RHPEKRMRAAFKAFEEARLPRLKKENPGL-RLSQYKQLLKKEWQKSPDN---PFNQAAVAYNT  220 (221)
T ss_pred             cChHHHHHHHHHHHHHhhchhhhhcCCCc-cHHHHHHHHHHHHhhCCCC---hhhHHhhhccC
Confidence            344 4445678899999999999999999 9999999999999988874   77776665543

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=84.98  E-value=1.4  Score=33.19  Aligned_cols=34  Identities=15%  Similarity=0.260  Sum_probs=28.2

Q ss_pred             CCCCHHHHHH-HHHHHhhcCCHHHHHHHHHHHHhhh
Q 033573           80 NVKAVSAVGK-AGGEKWKSLTDAIKKEHWMVKFVIC  114 (116)
Q Consensus        80 ~~~s~~eisK-~lge~Wk~Ls~eEK~~Y~e~a~~~~  114 (116)
                      .. ++..+++ .||..|+.+|+++++.|.+....++
T Consensus        63 ~~-Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l   97 (198)
T TIGR03481        63 AF-DLPAMARLTLGSSWTSLSPEQRRRFIGAFRELS   97 (198)
T ss_pred             hC-CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHH
Confidence            45 7788876 7899999999999999998776543

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

>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional

Probab=84.38  E-value=1.8  Score=32.91  Aligned_cols=34  Identities=24%  Similarity=0.218  Sum_probs=28.7

Q ss_pred             CCCCCHHHHHH-HHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           79 PNVKAVSAVGK-AGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        79 P~~~s~~eisK-~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |.. ++..+++ .||.-|+.+|++++..|.+....+
T Consensus        66 p~~-Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~  100 (211)
T PRK15117         66 PYV-QVKYAGALVLGRYYKDATPAQREAYFAAFREY  100 (211)
T ss_pred             ccC-CHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHH
Confidence            666 7888876 789999999999999999876554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	116
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		4e-07
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		4e-06
1cg7_A	93	Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len		4e-06
1e7j_A	74	Hmg-D Complexed To A Bulge Dna Length = 74		4e-06
2lhj_A	97	Nmr Structure Of The High Mobility Group Protein-Li		5e-06
1qrv_A	73	Crystal Structure Of The Complex Of Hmg-D And Dna L		5e-06
1hma_A	73	The Solution Structure And Dynamics Of The Dna Bind		5e-06
3nm9_A	73	Hmgd(M13a)-Dna Complex Length = 73		9e-06
1hsm_A	79	The Structure Of The Hmg Box And Its Interaction Wi		1e-05
1wxl_A	73	Solution Structure Of The Hmg-Box Domain In The Ssr		2e-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 = 53.5 bits (127), 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 = 25/47 (53%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
          KDPN PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W +
Sbjct: 2  KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNN 47

>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 = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
           N PKRPPS FF+F  EFR   K  +P + ++  V K  GE W +L D+ K+ +
Sbjct: 8   NAPKRPPSGFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLNDSEKQPY 59

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
          N PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W +
Sbjct: 3  NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNN 45

>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 = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 52  DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
           DPN PKR  SA+  F  E R + + E+P++     VGK  GEKWK+LT   K+ +
Sbjct: 17  DPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPY 70

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-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 = 46.2 bits (108), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D   K  W  K
Sbjct: 3   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 55

>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 = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV-KAVSAVGKAGGEKWKSLTDAIKKE 105
           + AKKDPN PKR  S++  F +E R     E+P + K V+A+GK  G  W +L+D  KK 
Sbjct: 14  RKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKP 73
Query: 106 H 106
           +
Sbjct: 74  Y 74

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D   K  W  K
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 54

>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 = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D   K  W  K
Sbjct: 2   DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 54

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
           +KPKRP SA+ ++L   R+  K+E+P +K V+ V K GGE W+++ D   K  W  K
Sbjct: 2   DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 54

>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 = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
          PKRPPSAFF+F  E+R   K EHP + ++  V K  GE W +
Sbjct: 3  PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNN 43

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           PKR  +AF ++L + R+  K+E+P +K V+ + K GGE WK L D  K E
Sbjct: 4   PKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELKDKSKWE 52

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	116
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	1e-15
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	4e-15
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	4e-15
2lhj_A	97	High mobility group protein homolog NHP1; structur	3e-14
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	4e-14
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	5e-14
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	7e-14
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	8e-14
1wgf_A	90	Upstream binding factor 1; transcription factor, D	1e-13
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	2e-12
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	2e-12
1ckt_A	71	High mobility group 1 protein; high-mobility group	7e-11
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	3e-10
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-09
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	4e-10
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-09
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-09
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	1e-09
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	2e-09
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	4e-09
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	8e-09
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	2e-08
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	6e-07
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	8e-07
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	1e-05
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	1e-05
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	3e-05
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	3e-05
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	6e-05
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	1e-04
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	2e-04
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	8e-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 = 65.3 bits (160), Expect = 1e-15
 Identities = 26/54 (48%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           KDPN PKRPPSAFF+F  E+R   K EHP +  +  V K  GE W +     K+
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQ 54

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

 Score = 64.2 bits (157), Expect = 4e-15
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDAIKKE 105
            K DP KP+   S++  F++  R+ +K++HP+     S   K   E+WK+++   K +
Sbjct: 1   GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGK 58

>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 = 64.3 bits (157), Expect = 4e-15
 Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
                + PK P + +  FL E R+  +  HP++     + K  G +W  L  A K+ 
Sbjct: 1   GSSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPAEKQR 56

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

 Score = 62.4 bits (152), Expect = 3e-14
 Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 1/71 (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  KWKSLTDAIKK 104
            W +L+D  KK
Sbjct: 62  AWNALSDEEKK 72

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

 Score = 61.6 bits (150), Expect = 4e-14
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 44  KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDAI 102
            +   AK DP KPK   SA+  F++  R+ +K+++P V    +   K   E+WK+++   
Sbjct: 4   GSSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKE 63

Query: 103 KKE 105
           K +
Sbjct: 64  KSK 66

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

 Score = 61.7 bits (150), Expect = 5e-14
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

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

Query: 100 DAIKK 104
           +  K+
Sbjct: 61  EEQKQ 65

>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 = 61.2 bits (149), Expect = 7e-14
 Identities = 27/67 (40%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

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

Query: 98  LTDAIKK 104
           LT   K+
Sbjct: 62  LTPEEKQ 68

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

 Score = 61.3 bits (149), Expect = 8e-14
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

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

>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 = 60.9 bits (148), Expect = 1e-13
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

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

Query: 98  LTDAIKK 104
           L++  K 
Sbjct: 62  LSEKKKA 68

>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 = 56.9 bits (138), Expect = 2e-12
 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 = 56.5 bits (137), Expect = 2e-12
 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 = 52.8 bits (127), Expect = 7e-11
 Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

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

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 31/94 (32%), Positives = 42/94 (44%), Gaps = 1/94 (1%)

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

Query: 71  RKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           R   K EHP +  +  V K  GE W +     K+
Sbjct: 117 RPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQ 149

>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 = 51.5 bits (123), Expect = 1e-09
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 44  KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDAI 102
            +    K DP KP+   S++  F++  R+ +K++HP+     S   K   E+WK+++   
Sbjct: 4   GSSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKE 63

Query: 103 KKEH 106
           K + 
Sbjct: 64  KGKF 67

>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 = 52.9 bits (127), Expect = 4e-10
 Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           ++ KRP +AF V+  + R+    E+P ++  S + K  G +WK LT+A K 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKW 52

>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 = 51.0 bits (122), Expect = 2e-09
 Identities = 30/86 (34%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

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

Query: 79  PNVKAVSAVGKAGGEKWKSLTDAIKK 104
           P +  +  V K  GE W +     K+
Sbjct: 112 PGLS-IGDVAKKLGEMWNNTAADDKQ 136

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

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 14/57 (24%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           +    + PK+P S++  F +E   ++K ++P+ K  + + +   ++W+ L D+ KK 
Sbjct: 3   SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKI 58

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

 Score = 50.1 bits (120), Expect = 1e-09
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
                +  K+P SA  +F+++ R  +  E+P    +        E WK+L++  K 
Sbjct: 1   GSSGSSGIKKPMSASALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEEEKL 55

>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 = 52.1 bits (124), Expect = 2e-09
 Identities = 16/82 (19%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

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

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

>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 = 4e-09
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 47  KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
             +   PNK KRP +AF +F +++R  Y Q +P  K   A+    G++WK + +  ++
Sbjct: 9   TVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERR 65

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

 Score = 47.7 bits (114), Expect = 8e-09
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 5/50 (10%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           KPKRP SA+ V++ E  +  K + P         K   E WK+L+D+ K+
Sbjct: 2   KPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKE 46

>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 = 2e-08
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 49  AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
                +  +RP +AF +F +  R + +QEHP         K   + W  L    K+
Sbjct: 1   GSSGSSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQ 55

>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 = 43.5 bits (103), Expect = 6e-07
 Identities = 14/70 (20%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

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

Query: 95  WKSLTDAIKK 104
           W+ L ++ K+
Sbjct: 68  WRLLNESEKR 77

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

 Score = 42.2 bits (100), Expect = 8e-07
 Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
             +RP +AF V+ ++ RK   Q++P+    + + K  G+ WK+LT A K+
Sbjct: 2   SIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKR 50

>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 = 39.5 bits (93), Expect = 1e-05
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           ++ KRP +AF V+  + R+    E+P     S + K  G +WK LT+A K 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKW 52

>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 = 39.5 bits (93), Expect = 1e-05
 Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
              ++ +RP +AF V+ ++ RK   Q++P+    + + K  G+ WK+LT A K+
Sbjct: 2   SFTSRIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKR 54

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

 Score = 38.3 bits (90), Expect = 3e-05
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           ++ KRP +AF V+    R+   QE+P     S + K  G +WK L++  K+
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKR 50

>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 = 38.6 bits (89), Expect = 3e-05
 Identities = 12/52 (23%), Positives = 25/52 (48%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
               RP + F ++LEE R     ++P+    + + K G  +++ L+   +K 
Sbjct: 4   GSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKV 55

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

 Score = 37.5 bits (88), Expect = 6e-05
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           KRP +AF V+ +  R+   ++ P+    + + K  G++WK L D+ K 
Sbjct: 4   KRPMNAFMVWSQIERRKIMEQSPD-MHNAEISKRLGKRWKLLKDSDKI 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 = 36.8 bits (86), Expect = 1e-04
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
              KRP +AF V+ ++ R+   Q  P++   S + K  G +WK++T+  K+
Sbjct: 3   PHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQ 52

>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 = 36.8 bits (86), Expect = 2e-04
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           ++ KRP +AF V+  + R+    E+P     S + K  G +WK LT+A K 
Sbjct: 3   DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKW 52

>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 = 34.9 bits (81), Expect = 8e-04
 Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
           K+P +AF ++++E R     E    K  +A+ +  G +W +L+   + 
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQA 50

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	116
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.9
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.88
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.88
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.87
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.87
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.87
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.87
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.86
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.86
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.86
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.85
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.85
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.85
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.85
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.84
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.83
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.83
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.83
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.83
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.83
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.82
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.82
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.82
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.82
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.82
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.81
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.8
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.8
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.79
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.79
2cto_A	93	Novel protein; high mobility group box domain, hel	99.78
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.75
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.75
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.73
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.71
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.71
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.66
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.63
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.61

>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=99.90  E-value=1.4e-23  Score=139.19  Aligned_cols=70  Identities=27%  Similarity=0.453  Sum_probs=65.1

Q ss_pred             cccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        43 ~kk~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .++++++.+||+.|+||+|||||||+++|..|+.+||++ ++.||+++||++|+.|++++|++|+++|...
T Consensus         8 k~k~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~   77 (90)
T 1wgf_A            8 KPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAAL   77 (90)
T ss_dssp             SSCSCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCcCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            345566779999999999999999999999999999999 9999999999999999999999999999764

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

Probab=99.88  E-value=9.9e-23  Score=137.95  Aligned_cols=69  Identities=28%  Similarity=0.440  Sum_probs=63.9

Q ss_pred             ccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           44 KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        44 kk~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+++++.+||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++|++++|++|+++|...
T Consensus         6 ~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~   74 (102)
T 2co9_A            6 SGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQKQVYKKKTEAA   74 (102)
T ss_dssp             CCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHH
Confidence            33456678999999999999999999999999999999 9999999999999999999999999998754

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

Probab=99.88  E-value=1.8e-22  Score=132.50  Aligned_cols=68  Identities=28%  Similarity=0.413  Sum_probs=62.7

Q ss_pred             cccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        45 k~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s--~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++++..+||+.|+||+|||||||+++|..|+.+||++ +  +.||+++||++|++||++||.+|+++|...
T Consensus         5 ~~~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~-~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   74 (86)
T 2eqz_A            5 SSGMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEV-PVNFAEFSKKCSERWKTMSGKEKSKFDEMAKAD   74 (86)
T ss_dssp             CSSCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTS-CCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            3455679999999999999999999999999999998 5  699999999999999999999999998754

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

Probab=99.87  E-value=7.2e-23  Score=138.19  Aligned_cols=66  Identities=29%  Similarity=0.377  Sum_probs=62.5

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        47 kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +++.+||+.|+||+|||||||+++|..|+.+||++ +++||+++||++|++||+++|++|++.|...
T Consensus         2 kkk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~   67 (99)
T 1k99_A            2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQRE   67 (99)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999999 9999999999999999999999999998754

>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=1.8e-22  Score=132.37  Aligned_cols=61  Identities=20%  Similarity=0.247  Sum_probs=58.5

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~vk~e~P~~~s-~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +++.||||+|||||||+++|..|+.+||++ + +.||+++||++|++|+++||++|+++|...
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~-~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDF-SDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTC-CSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-chhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999 8 999999999999999999999999998753

>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=99.87  E-value=3e-22  Score=131.88  Aligned_cols=66  Identities=26%  Similarity=0.465  Sum_probs=62.6

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        47 kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++..+||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++|+++||++|+++|..+
T Consensus         9 ~~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~   74 (87)
T 2e6o_A            9 TVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGK-DNRAISVILGDRWKKMKNEERRMYTLEAKAL   74 (87)
T ss_dssp             SCCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            35678999999999999999999999999999999 9999999999999999999999999998764

>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=99.87  E-value=2.1e-22  Score=129.18  Aligned_cols=63  Identities=41%  Similarity=0.654  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++||+.|+||+|||||||+++|..|..+||++ ++.+|+++||++|+.||+++|.+|++.|...
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   63 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKL   63 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHHSCGGGSHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            47999999999999999999999999999999 9999999999999999999999999998764

>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=99.86  E-value=9.1e-23  Score=135.97  Aligned_cols=68  Identities=38%  Similarity=0.563  Sum_probs=63.6

Q ss_pred             cccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           45 NVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        45 k~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++++..+||+.|+||+|||||||+++|..|..+||++ ++.||+++||++|++||+++|++|+++|...
T Consensus        10 ~~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~   77 (93)
T 1cg7_A           10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQAD   77 (93)
T ss_dssp             CCCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTS-CHHHHTTTHHHHHHTTHHHHHHHHHHHHTTH
T ss_pred             ccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4456678999999999999999999999999999999 9999999999999999999999999998753

>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=99.86  E-value=5.8e-22  Score=126.87  Aligned_cols=61  Identities=30%  Similarity=0.424  Sum_probs=57.2

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ||+.|+||+|||||||+++|..|+.+||++ ++++|+++||++|++||+++|++|+++|...
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   61 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKL   61 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCC-SSSHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHhHHHhCCHHHHHHHHHHHHHH
Confidence            789999999999999999999999999999 9999999999999999999999999998764

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

Probab=99.86  E-value=9.9e-22  Score=130.56  Aligned_cols=63  Identities=24%  Similarity=0.388  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+||+.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|...
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~   64 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDL-PFPEITKMLGAEWSKLQPAEKQRYLDEAEKE   64 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHTCCTTHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            47999999999999999999999999999999 9999999999999999999999999998754

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

Probab=99.85  E-value=8.6e-23  Score=136.89  Aligned_cols=69  Identities=38%  Similarity=0.532  Sum_probs=64.0

Q ss_pred             ccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           44 KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        44 kk~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s--~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +++++..+||+.|+||+|||||||+++|..|..+||++ +  +.+|+++||++|++||+++|++|+++|...
T Consensus        11 ~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~-~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~   81 (97)
T 2lhj_A           11 RRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEI-AKDVAAIGKMIGAAWNALSDEEKKPYERMSDED   81 (97)
T ss_dssp             CCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTS-TTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHH
T ss_pred             cccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            44566779999999999999999999999999999999 8  999999999999999999999999998753

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

Probab=99.85  E-value=3.3e-21  Score=128.02  Aligned_cols=63  Identities=21%  Similarity=0.237  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ..||+.|+||+|||||||+++|..|+.+||++ ++.||+++||++|+.|++++|++|+++|...
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~   64 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPKT-SLEDATLQIEELWKTLSEEEKLKYEEKATKD   64 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCSS-CHHHHHHHHHHHHHSSCHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            36899999999999999999999999999999 9999999999999999999999999998753

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

Probab=99.85  E-value=6.8e-22  Score=128.75  Aligned_cols=63  Identities=27%  Similarity=0.442  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        50 ~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s--~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++||+.|+||+|||||||+++|..|+.+||++ +  +.+|+++||++|++||+++|.+|+++|...
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~-~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   66 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDA-SVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD   66 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTT-CCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            47999999999999999999999999999998 5  599999999999999999999999998754

>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=99.85  E-value=4.9e-21  Score=125.40  Aligned_cols=61  Identities=30%  Similarity=0.423  Sum_probs=58.5

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .|+.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|++|+++|...
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~   61 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKL   61 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Confidence            489999999999999999999999999999 9999999999999999999999999998764

>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=99.84  E-value=4.2e-21  Score=124.71  Aligned_cols=62  Identities=23%  Similarity=0.349  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        51 kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .|++.|+||+|||||||+++|..|+.+||++ ++.+|+++||++|++||+++|++|+++|...
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   64 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRL-DNRGATKILADWWAVLDPKEKQKYTDMAKEY   64 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSS-CTTHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999 9999999999999999999999999998764

>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=99.83  E-value=1e-20  Score=122.81  Aligned_cols=61  Identities=28%  Similarity=0.394  Sum_probs=55.3

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .++.|+||+|||||||+++|..|..+||++ ++++|+++||++|+.|++++|.+|+++|...
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   63 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDL-HNAELSKMLGKSWKALTLAEKRPFVEEAERL   63 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999 9999999999999999999999999998764

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

Probab=99.83  E-value=1.1e-20  Score=119.06  Aligned_cols=59  Identities=29%  Similarity=0.415  Sum_probs=53.3

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +.|+||+|||||||+++|..+..+||++ ++++|+++||++|++||+++|.+|+++|...
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   59 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDL-HNAELSKMLGKSWKALTLAEKRPFVEEAERL   59 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999 9999999999999999999999999998764

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

Probab=99.83  E-value=2.2e-20  Score=127.39  Aligned_cols=64  Identities=22%  Similarity=0.374  Sum_probs=57.3

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        49 k~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ..+|++.|+||+|||||||+++|..|..+||++ ++.+|+++||++|+.|+++||++|+++|...
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~   86 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPHL-HNAELSKTLGKLWRLLNESEKRPFVEEAERL   86 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999 9999999999999999999999999998764

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

Probab=99.83  E-value=1.7e-20  Score=119.50  Aligned_cols=58  Identities=33%  Similarity=0.554  Sum_probs=55.6

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |+.|+||+|||||||+++|..|+.+||++ +++||+++||++|++|  ++|.+|+++|...
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~   58 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGI-KVTEIAKKGGEMWKEL--KDKSKWEDAAAKD   58 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTC-CHHHHHHHHHHHHHTC--TTHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhh--HhhHHHHHHHHHH
Confidence            78999999999999999999999999999 9999999999999999  8999999998764

>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=99.83  E-value=2.4e-20  Score=133.85  Aligned_cols=67  Identities=40%  Similarity=0.630  Sum_probs=62.9

Q ss_pred             ccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        46 ~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +++..+||+.|+||+|||||||+++|..|..+||++ ++++|+++||++|++||+++|++|+++|...
T Consensus        79 ~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~  145 (159)
T 2gzk_A           79 TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKL  145 (159)
T ss_dssp             CGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCC-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccchhhHhhHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999 9999999999999999999999999998764

>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=99.82  E-value=1.4e-20  Score=122.03  Aligned_cols=60  Identities=27%  Similarity=0.442  Sum_probs=56.7

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||++||++|++.|..+
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~   61 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEKQPYYEEQARL   61 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGGHHHHHHHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhhhhhCCHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999 9999999999999999999999999988764

>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=99.82  E-value=1.6e-20  Score=119.74  Aligned_cols=58  Identities=38%  Similarity=0.647  Sum_probs=55.1

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .++||||+|||||||+++|..|+.+||++ +++||+++||++|++|++  |++|+++|...
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~   58 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGI-KVTEVAKRGGELWRAMKD--KSEWEAKAAKA   58 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSC-CHHHHHHHHHHHHHHCSC--CHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCc--hHHHHHHHHHH
Confidence            47899999999999999999999999999 999999999999999998  99999998764

>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=99.82  E-value=2.7e-20  Score=120.25  Aligned_cols=59  Identities=29%  Similarity=0.444  Sum_probs=56.4

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +.|+||+|||||||+++|..|..+||++ ++.+|+++||++|+.||+++|.+|+++|...
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~   59 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRL   59 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999 9999999999999999999999999998764

>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=99.82  E-value=3.5e-20  Score=121.42  Aligned_cols=59  Identities=19%  Similarity=0.336  Sum_probs=56.4

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +.|+||+|||||||+++|..|..+||++ ++++|+++||++|++||+++|++|+++|...
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~   59 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKE   59 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            3699999999999999999999999999 9999999999999999999999999998764

>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=99.82  E-value=2.6e-20  Score=119.73  Aligned_cols=59  Identities=25%  Similarity=0.372  Sum_probs=56.4

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +.|+||+|||||||+++|..|..+||++ ++++|+++||++|++||+++|.+|+++|...
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   59 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDM-HNAEISKRLGKRWKLLKDSDKIPFIQEAERL   59 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999 9999999999999999999999999998764

>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=99.81  E-value=2.3e-20  Score=117.79  Aligned_cols=58  Identities=24%  Similarity=0.405  Sum_probs=54.6

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s--~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +|+||+|||||||+++|..++.+||++ +  +.+|+++||++|++||+++|.+|+++|...
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~-~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   60 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDA-SVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD   60 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTC-CCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCC-CCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            599999999999999999999999998 5  599999999999999999999999998753

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

Probab=99.80  E-value=2.1e-21  Score=129.96  Aligned_cols=62  Identities=11%  Similarity=0.064  Sum_probs=57.6

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA--VSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        47 kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s--~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+..+|||+|+||+|||||||+++|+.|+.+||++ +  +.||+    ++|+.|+++||+||+++|..+
T Consensus        14 ~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~-s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~   77 (90)
T 2yuk_A           14 LKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDW-TTRVKQIA----KLWRKASSQERAPYVQKARDN   77 (90)
T ss_dssp             HHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSH-HHHHHHHH----HHHHHSCHHHHHHHHHHHHHH
T ss_pred             hhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCc-cchHHHHH----HHHHcCCHHHHHHHHHHHHHH
Confidence            34457999999999999999999999999999999 8  99998    999999999999999999865

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

Probab=99.80  E-value=1.4e-19  Score=131.62  Aligned_cols=66  Identities=41%  Similarity=0.639  Sum_probs=62.2

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        47 kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +++.+||+.|+||+|||||||+++|..|..+||++ ++.+|+++||++|+.||+++|++|+++|...
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~  158 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKL  158 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSS-CHHHHHHHHHHHHHHSCGGGHHHHHHHHHHH
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            45568999999999999999999999999999999 9999999999999999999999999998754

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

Probab=99.79  E-value=3.4e-19  Score=129.67  Aligned_cols=67  Identities=27%  Similarity=0.421  Sum_probs=62.1

Q ss_pred             ccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCC--CCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPN--VKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        46 ~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~--~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+...+||+.|+||+|||||||+++|..|..+||+  + ++.||+++||++|++||++||++|+++|...
T Consensus         6 ~k~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   74 (173)
T 2yrq_A            6 SGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASV-NFSEFSKKCSERWKTMSAKEKGKFEDMAKAD   74 (173)
T ss_dssp             CSSSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCC-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            34567899999999999999999999999999999  6 8999999999999999999999999998753

>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=99.79  E-value=2.2e-19  Score=123.00  Aligned_cols=63  Identities=19%  Similarity=0.220  Sum_probs=58.0

Q ss_pred             ccccCCCCCCC-CCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           46 VKSAKKDPNKP-KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        46 ~kkk~kdp~~P-KRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +.++.+||+.| |||+|||||||+++|..|+    ++ ++.||+++||++|+.|+++||++|+++|...
T Consensus         7 ~~kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~-~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~   70 (108)
T 1v64_A            7 GQLKDKFDGRPTKPPPNSYSLYCAELMANMK----DV-PSTERMVLCSQQWKLLSQKEKDAYHKKCDQK   70 (108)
T ss_dssp             CCSSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHh----CC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            45667899999 9999999999999999887    78 9999999999999999999999999998764

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

Probab=99.78  E-value=1.2e-19  Score=121.93  Aligned_cols=62  Identities=16%  Similarity=0.222  Sum_probs=57.8

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHH---HHHhhcCCHHHHHHHHHHHHhh
Q 033573           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAG---GEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        49 k~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~l---ge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ...+++.||||+|||||||+++|..|+.+  ++ ++.||+++|   |++|+.|+++||++|+++|..+
T Consensus         4 ~~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~-~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~   68 (93)
T 2cto_A            4 GSSGMPNRKASRNAYYFFVQEKIPELRRR--GL-PVARVADAIPYCSSDWALLREEEKEKYAEMAREW   68 (93)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHTTHHHHHHH--TC-CCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHc--CC-CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            35789999999999999999999999988  78 899999999   9999999999999999999865

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

Probab=99.75  E-value=1.6e-18  Score=108.53  Aligned_cols=55  Identities=31%  Similarity=0.314  Sum_probs=50.1

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |.||||+|||+|||+++|..++..     ++++|++.||++|++||++||.+|+++|...
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~-----~p~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~   55 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGD-----SPQEKLKTVKENWKNLSDSEKELYIQHAKED   55 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSS-----SHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhc-----CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            589999999999999999999755     4579999999999999999999999998754

>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=99.75  E-value=3.2e-18  Score=114.76  Aligned_cols=59  Identities=15%  Similarity=0.054  Sum_probs=55.6

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .|.|+||+|||+||+++.|..|..+||+  ++++|++.||++|++|+++||++|+++|...
T Consensus         2 ~~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~d   60 (91)
T 1l8y_A            2 GKLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAED   60 (91)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            3689999999999999999999999998  6899999999999999999999999998764

>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=99.73  E-value=8.8e-18  Score=113.70  Aligned_cols=60  Identities=13%  Similarity=0.189  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        51 kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+.++||||+|||||||++++.  ..+++++ ++.||++.||++|+.|+++||++|+++|...
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~-~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~   63 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHL-PLKERMVEIGSRWQRISQSQKEHYKKLAEEQ   63 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4567899999999999999975  3455668 8999999999999999999999999998754

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

Probab=99.71  E-value=7.6e-18  Score=128.82  Aligned_cols=64  Identities=20%  Similarity=0.333  Sum_probs=60.5

Q ss_pred             cCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        49 k~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ...||+.|+||+|||||||+++|..|+.+||++ ++.||+++||++|+.|+++||.+|+++|...
T Consensus        35 s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~   98 (238)
T 3tmm_A           35 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKKKIYQDAYRAE   98 (238)
T ss_dssp             CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999 9999999999999999999999999998753

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

Probab=99.71  E-value=1.1e-17  Score=126.06  Aligned_cols=61  Identities=21%  Similarity=0.352  Sum_probs=58.1

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +|+.|+||+|||||||+++|..|..+||++ +++||+++||++|++||++||.+|+++|...
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~   66 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKKKIYQDAYRAE   66 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHccCHHhhhHHHHHHHHH
Confidence            478999999999999999999999999999 9999999999999999999999999998753

>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=99.66  E-value=2.6e-16  Score=112.70  Aligned_cols=60  Identities=30%  Similarity=0.447  Sum_probs=57.5

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |+.|+||++|||||++++|..|..+||++ ++.||+++||++|++||+++|.+|+++|...
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   61 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKL   61 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSC-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHhhHHHhccHHHHHHHH
Confidence            67899999999999999999999999999 9999999999999999999999999998764

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

Probab=99.63  E-value=4.3e-17  Score=122.92  Aligned_cols=62  Identities=29%  Similarity=0.252  Sum_probs=55.0

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        47 kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++..+||+.|+||+|||||||+++|..|..+     ++.+|+++||++|++|++++|++|+++|...
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~-----~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~  167 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAKGD-----SPQEKLKTVKENWKNLSDSEKELYIQHAKED  167 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSSCS-----SHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhccC-----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4456899999999999999999999988644     5569999999999999999999999998764

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

Probab=99.61  E-value=2.1e-17  Score=126.38  Aligned_cols=62  Identities=29%  Similarity=0.252  Sum_probs=55.0

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        47 kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++..+||+.|+||+|||||||+++|..|..+     ++.+|++.||++|+.|++++|++|+++|..+
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~-----~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~  199 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAKGD-----SPQEKLKTVKENWKNLSDSEKELYIQHAKED  199 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCS-----SHHHHHHHHHHHHHTCCTTTTHHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhcc-----CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4456899999999999999999999888644     4568999999999999999999999998764

---

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	116
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-09
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	6e-09
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-08
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-08
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	3e-08
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-07
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	1e-07
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	3e-07
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	2e-06
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-06
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	5e-05
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	7e-04

>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 = 47.6 bits (113), Expect = 4e-09
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

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

Query: 98  LTDAIKKE 105
           L++  K +
Sbjct: 62  LSEKKKAK 69

>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 = 47.2 bits (112), Expect = 6e-09
 Identities = 27/62 (43%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 44  KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
           K     KKDPN PKR  SA+  F  E R + + E+P++     VGK  GEKWK+LT   K
Sbjct: 9   KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEK 67

Query: 104 KE 105
           + 
Sbjct: 68  QP 69

>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 = 46.4 bits (110), Expect = 1e-08
 Identities = 23/52 (44%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           N PKRPPSAFF+F  E+R   K EHP +  +  V K  GE W +     K+ 
Sbjct: 1   NAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQP 51

>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 = 45.7 bits (108), Expect = 3e-08
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

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

>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 = 45.2 bits (107), Expect = 3e-08
 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

>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 = 43.7 bits (103), Expect = 1e-07
 Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

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

>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 = 43.3 bits (102), Expect = 1e-07
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 1/53 (1%)

Query: 55  KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHW 107
             KRP +AF V+ ++ R+   Q  P++   S + K  G +WK++T+  K+ ++
Sbjct: 2   HIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYY 53

>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 = 42.5 bits (100), Expect = 3e-07
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
           ++ KRP +AF V+    R+   QE+P +   S + K  G +WK L++  K+  
Sbjct: 1   DRVKRPMNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPF 52

>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 = 40.6 bits (95), Expect = 2e-06
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 54  NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
           ++ KRP +AF V+  + R+    E+P ++  S + K  G +WK LT+A K  
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 = 39.9 bits (93), Expect = 4e-06
 Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 3/56 (5%)

Query: 50  KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
                  K P + +  F +E     +  H  +K         G +W+ ++ + K+ 
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 = 37.2 bits (86), Expect = 5e-05
 Identities = 11/52 (21%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 57  KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWM 108
           K+P +AF ++++E R     E    +  +A+ +  G +W +L+   + +++ 
Sbjct: 4   KKPLNAFMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYE 54

>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 = 34.2 bits (78), Expect = 7e-04
 Identities = 11/63 (17%), Positives = 20/63 (31%), Gaps = 5/63 (7%)

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

Query: 103 KKE 105
           K  
Sbjct: 60  KDA 62

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	116
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.85
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.84
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.83
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.83
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.82
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.82
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.79
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.78
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.77
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.67
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.67
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	92.51

>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=99.85  E-value=1.8e-21  Score=128.23  Aligned_cols=70  Identities=39%  Similarity=0.563  Sum_probs=64.4

Q ss_pred             cccccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        43 ~kk~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .++..+..+||+.|+||+|||||||+++|..|+.+||++ ++.+|++.||++|++||+++|.+|++.|...
T Consensus         8 ~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~-~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~   77 (93)
T d1lwma_           8 KKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQAD   77 (93)
T ss_dssp             TSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCC-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            345556778999999999999999999999999999999 9999999999999999999999999998753

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

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

Probab=99.84  E-value=3.7e-21  Score=125.60  Aligned_cols=67  Identities=28%  Similarity=0.472  Sum_probs=62.7

Q ss_pred             ccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        46 ~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ......|++.|+||+|||||||+++|..|..+||++ ++.+|+++||.+|+.|++++|.+|+++|...
T Consensus        11 ~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~-~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~   77 (90)
T d1wgfa_          11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAAL   77 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            344568999999999999999999999999999999 9999999999999999999999999999765

>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=99.83  E-value=2.3e-21  Score=126.87  Aligned_cols=66  Identities=29%  Similarity=0.377  Sum_probs=62.7

Q ss_pred             cccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        47 kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ++..+||+.|+||+||||||++++|..|..+||++ ++.+|++.||+.|+.||+++|.+|.+.|...
T Consensus         2 kk~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~-~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~   67 (91)
T d1k99a_           2 KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQRE   67 (91)
T ss_dssp             CCCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhHhcCCCHHHHHHHHHHHHHH
Confidence            45679999999999999999999999999999999 9999999999999999999999999998764

>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=99.83  E-value=5.8e-21  Score=123.18  Aligned_cols=59  Identities=29%  Similarity=0.444  Sum_probs=56.7

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |.|+||+||||||++++|..|..+||++ ++++|+++||++|++|+++||++|+++|...
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~-~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~   59 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRL   59 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHCcCCHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999 9999999999999999999999999998764

>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=99.82  E-value=1.2e-20  Score=122.49  Aligned_cols=59  Identities=31%  Similarity=0.455  Sum_probs=56.9

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |.|+||+|||||||+++|..|..+||++ ++.+|+++||++|++||+++|.+|+++|...
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~-~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~   61 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKL   61 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999 9999999999999999999999999998764

>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=99.82  E-value=4.4e-21  Score=122.64  Aligned_cols=59  Identities=39%  Similarity=0.630  Sum_probs=56.6

Q ss_pred             CCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        54 ~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      |+||||+|||||||+++|..|+.+||++ ++++|+++||++|+.||+++|.+|++.|...
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~-~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~   59 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKL   59 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTC-CTTTHHHHHHHHHHTSCSTTTHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHhhHHhcCCHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999 9999999999999999999999999998753

>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=99.82  E-value=1e-20  Score=118.84  Aligned_cols=58  Identities=28%  Similarity=0.460  Sum_probs=55.5

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .+|||+|||||||+++|+.|+.+||++ ++++|+++||++|++||+++|++|+++|..+
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   59 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEKQPYYEEQARL   59 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGGHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            468999999999999999999999999 9999999999999999999999999999765

>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=99.79  E-value=1.7e-19  Score=117.27  Aligned_cols=58  Identities=19%  Similarity=0.355  Sum_probs=55.3

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .-+||+||||||++++|..|..+||++ ++++|+++||.+|++||++||++|+++|..+
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~-~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~   59 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKE   59 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            357999999999999999999999999 9999999999999999999999999999765

>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=99.78  E-value=1.8e-19  Score=112.77  Aligned_cols=59  Identities=24%  Similarity=0.391  Sum_probs=54.3

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~-s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      +|+||+|||||||+++|..|+.+||+.. ++++|+++||++|++||+++|++|+++|...
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~   60 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD   60 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence            5999999999999999999999999741 5789999999999999999999999998753

>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=99.77  E-value=2.8e-19  Score=112.77  Aligned_cols=58  Identities=36%  Similarity=0.621  Sum_probs=53.7

Q ss_pred             CCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        53 p~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      .|.|+||+|||||||+++|+.|+.+||++ ++.+|+++||++|++|+  ||++|++.|...
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~-~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~   58 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGI-KVTEVAKRGGELWRAMK--DKSEWEAKAAKA   58 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTC-CHHHHHHHHHHHHHHCS--CCHHHHHHHHHH
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHhcChh--HHHHHHHHHHHH
Confidence            37899999999999999999999999999 99999999999999986  599999988653

>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=99.67  E-value=7.2e-17  Score=108.36  Aligned_cols=63  Identities=17%  Similarity=0.163  Sum_probs=55.5

Q ss_pred             ccccCCCCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        46 ~kkk~kdp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ..+...|+.+|++|+||||||++++|.+    +|++ ++.||+++||++|+.||++||.+|++.|...
T Consensus         8 ~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~-~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~   70 (108)
T d1v64a_           8 QLKDKFDGRPTKPPPNSYSLYCAELMAN----MKDV-PSTERMVLCSQQWKLLSQKEKDAYHKKCDQK   70 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCcHHHHHHHHHHHH----ccCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHH
Confidence            3445578888999999999999998864    6899 9999999999999999999999999998754

>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=99.67  E-value=6.1e-17  Score=107.09  Aligned_cols=59  Identities=12%  Similarity=0.163  Sum_probs=52.5

Q ss_pred             CCCCCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 033573           52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFVI  113 (116)
Q Consensus        52 dp~~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~~  113 (116)
                      ..++||||+|||||||+++|..+...  ++ ++.||++.||++|+.|+++||++|.+.|...
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~--~~-~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~   63 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELN--HL-PLKERMVEIGSRWQRISQSQKEHYKKLAEEQ   63 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTT--TS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhc--CC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            45679999999999999999988644  56 7899999999999999999999999998754

>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=92.51  E-value=0.32  Score=29.51  Aligned_cols=56  Identities=16%  Similarity=0.084  Sum_probs=46.7

Q ss_pred             CCCCCCchhHhHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHHHh
Q 033573           55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVKFV  112 (116)
Q Consensus        55 ~PKRP~say~lF~~e~R~~vk~e~P~~~s~~eisK~lge~Wk~Ls~eEK~~Y~e~a~~  112 (116)
                      .|--|.+|--+|.|.....+...+-+  .-.--.+.+-..|++|...|+.+|+.+|++
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~--DR~KaqkaMeatW~~meKkEki~wikkaae   58 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAE   58 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHh--hHHHHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence            46778899999999999988888755  345566778888999999999999998875