Citrus Sinensis ID: 034697

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80------
Protein Sequence
MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYRSTTGTGN
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccc
Coil and Loop (DISEMBL)
masntmtssrssgsswtvKQNKQFETALAfydkdtpdrwdnvakavsgktvEDVKKHYELLVKDIndieagryphpnyrsttgtgn
Flexible Loop (DISEMBL)
masntmtssrssgsswtvkqNKQFETALAfydkdtpdrWDNVAkavsgktvedvkKHYELLVKdindieagryphpnyrsttgtgn
Low Complexity Region (SEG)
MAsntmtssrssgsswtVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYRSTTGTGN
Disordered region (IsUnstruct)
***********************FETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAG***************
Disordered Region (DISOPRED)
********************NKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPH***********
Disordered Region (DISEMBL)
******************KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY********
Disordered Region (DISPRO)
***************WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYR*******
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYRSTTGTGN
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	86	2.2.26 [Sep-21-2011]
Q58FS3	93	Transcription factor RADI	N/A	no	0.906	0.838	0.653	2e-25
Q6NNN0	81	Protein RADIALIS-like 3 O	yes	no	0.755	0.802	0.723	6e-25
Q1A173	97	Protein RADIALIS-like 6 O	no	no	0.883	0.783	0.675	2e-24
F4JVB8	100	Protein RADIALIS-like 1 O	no	no	0.825	0.71	0.676	1e-23
Q9SIJ5	101	Protein RADIALIS-like 2 O	no	no	0.825	0.702	0.647	5e-22
Q1G3C4	77	Protein RADIALIS-like 4 O	no	no	0.732	0.818	0.650	2e-21
Q8GW75	100	Protein RADIALIS-like 5 O	no	no	0.732	0.63	0.603	4e-17
Q8S9H7	307	Transcription factor DIVA	N/A	no	0.883	0.247	0.467	6e-14
Q4R8H2	621	DnaJ homolog subfamily C	N/A	no	0.825	0.114	0.355	3e-06
Q99543	621	DnaJ homolog subfamily C	no	no	0.825	0.114	0.355	3e-06

>sp|Q58FS3|RAD_ANTMA Transcription factor RADIALIS OS=Antirrhinum majus GN=RAD PE=1 SV=1

 Score =  114 bits (285), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 51/78 (65%), Positives = 62/78 (79%)

Query: 6  MTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65
          M S+R SG  W+ K+NK FE ALA YDKDTPDRW NVA+AV G+T E+VKKHYE+LV+DI
Sbjct: 1  MASTRGSGRPWSAKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDI 60

Query: 66 NDIEAGRYPHPNYRSTTG 83
            IE+G+ P PNYR+T G
Sbjct: 61 KYIESGKVPFPNYRTTGG 78

Involved in the dorsovental asymmetry of flowers. Promotes dorsal identity.
Antirrhinum majus (taxid: 4151)

>sp|Q6NNN0|RADL3_ARATH Protein RADIALIS-like 3 OS=Arabidopsis thaliana GN=RL3 PE=2 SV=1

 Score =  112 bits (280), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 47/65 (72%), Positives = 58/65 (89%)

Query: 16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPH 75
          WT K+NK FE ALA YD+DTPDRW NVA+AV GK+ E+V++HYELL++D+NDIE+GRYPH
Sbjct: 12 WTRKENKLFERALATYDQDTPDRWHNVARAVGGKSAEEVRRHYELLIRDVNDIESGRYPH 71

Query: 76 PNYRS 80
          PNYRS
Sbjct: 72 PNYRS 76

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q1A173|RADL6_ARATH Protein RADIALIS-like 6 OS=Arabidopsis thaliana GN=RL6 PE=2 SV=1

 Score =  111 bits (277), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 54/80 (67%), Positives = 63/80 (78%), Gaps = 4/80 (5%)

Query: 1  MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          MASN    SRSS S WT  QNK FE ALA YDKDTPDRW NVAKAV GKTVE+VK+HY++
Sbjct: 1  MASN----SRSSISPWTFSQNKMFERALAVYDKDTPDRWHNVAKAVGGKTVEEVKRHYDI 56

Query: 61 LVKDINDIEAGRYPHPNYRS 80
          LV+D+ +IE GR P PNY++
Sbjct: 57 LVEDLINIETGRVPLPNYKT 76

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|F4JVB8|RADL1_ARATH Protein RADIALIS-like 1 OS=Arabidopsis thaliana GN=RL1 PE=2 SV=1

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 48/71 (67%), Positives = 55/71 (77%)

Query: 16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPH 75
          WT KQNK FE ALA YD+DTP+RW NVAK V GKT E+VK+HYELLV+DIN IE G  P 
Sbjct: 14 WTAKQNKAFEQALATYDQDTPNRWQNVAKVVGGKTTEEVKRHYELLVQDINSIENGHVPF 73

Query: 76 PNYRSTTGTGN 86
          PNYR++ G  N
Sbjct: 74 PNYRTSGGCTN 84

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIJ5|RADL2_ARATH Protein RADIALIS-like 2 OS=Arabidopsis thaliana GN=RL2 PE=2 SV=1

 Score =  102 bits (255), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 46/71 (64%), Positives = 55/71 (77%)

Query: 16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPH 75
          WTVKQNK FE ALA YD+DTPDRW NVA+AV GKT E+ K+ Y+LLV+DI  IE G  P 
Sbjct: 14 WTVKQNKAFERALAVYDQDTPDRWHNVARAVGGKTPEEAKRQYDLLVRDIESIENGHVPF 73

Query: 76 PNYRSTTGTGN 86
          P+Y++TTG  N
Sbjct: 74 PDYKTTTGNSN 84

Probable transcription factor. Required for female gametophyte development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q1G3C4|RADL4_ARATH Protein RADIALIS-like 4 OS=Arabidopsis thaliana GN=RL4 PE=2 SV=1

 Score =  101 bits (251), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 41/63 (65%), Positives = 55/63 (87%)

Query: 19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
          +++KQFE ALA +DKDTPDRW  +A+AV GK+ E+VK+HYELL++D+NDIE+GRYP P Y
Sbjct: 14 REDKQFEMALAKFDKDTPDRWQKIARAVGGKSTEEVKRHYELLLRDVNDIESGRYPQPRY 73

Query: 79 RST 81
          R+T
Sbjct: 74 RNT 76

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GW75|RADL5_ARATH Protein RADIALIS-like 5 OS=Arabidopsis thaliana GN=RL5 PE=3 SV=1

 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 48/63 (76%)

Query: 19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
          KQNK FE ALA YDKDTPDRW NVAKAV  K+ E+VK+HY++LV+D+ +IE    P P Y
Sbjct: 15 KQNKMFERALAVYDKDTPDRWQNVAKAVGSKSAEEVKRHYDILVEDLMNIEQDLVPLPKY 74

Query: 79 RST 81
          ++ 
Sbjct: 75 KTV 77

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8S9H7|DIV_ANTMA Transcription factor DIVARICATA OS=Antirrhinum majus GN=DIVARICATA PE=2 SV=1

 Score = 76.3 bits (186), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 53/77 (68%), Gaps = 1/77 (1%)

Query: 6  MTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65
          +  SRS+ + WT  +NK FE ALA +D++TP+RW+ VA+ V GKTV DV + Y+ L  D+
Sbjct: 17 LEESRST-TRWTAAENKAFENALAVFDENTPNRWERVAERVPGKTVGDVMRQYKELEDDV 75

Query: 66 NDIEAGRYPHPNYRSTT 82
          + IEAG  P P Y +++
Sbjct: 76 SSIEAGFVPVPGYSTSS 92

Involved in the dorsovental asymmetry of flowers. Promotes ventral identity.

Antirrhinum majus (taxid: 4151)

>sp|Q4R8H2|DNJC2_MACFA DnaJ homolog subfamily C member 2 OS=Macaca fascicularis GN=DNAJC2 PE=2 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 2   ASNTMTSSRSSG-----SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKK 56
           A N   S R  G     + WT ++ K  E AL  Y  +TP+RW+ +A+AV G+T +D  K
Sbjct: 535 ADNAAPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKKDCMK 594

Query: 57  HYELLVKDINDIEAGR 72
            Y+ LV+ +   +A +
Sbjct: 595 RYKELVEMVKAKKAAQ 610

Acts both as a chaperone in the cytosol and as a chromatin regulator in the nucleus. When cytosolic, acts as a molecular chaperone: component of the ribosome-associated complex (RAC), a complex involved in folding or maintaining nascent polypeptides in a folding-competent state. In the RAC complex, stimulates the ATPase activity of the ribosome-associated pool of Hsp70-type chaperones HSPA14 that bind to the nascent polypeptide chain. When nuclear, mediates the switching from polycomb-repressed genes to an active state: specifically recruited at histone H2A ubiquitinated at 'Lys-119' (H2AK119ub), and promotes the displacement of the polycomb PRC1 complex from chromatin, thereby facilitating transcription activation. Specifically binds DNA sequence 5'-GTCAAGC-3'.

Macaca fascicularis (taxid: 9541)

>sp|Q99543|DNJC2_HUMAN DnaJ homolog subfamily C member 2 OS=Homo sapiens GN=DNAJC2 PE=1 SV=4

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 2   ASNTMTSSRSSG-----SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKK 56
           A N   S R  G     + WT ++ K  E AL  Y  +TP+RW+ +A+AV G+T +D  K
Sbjct: 535 ADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKKDCMK 594

Query: 57  HYELLVKDINDIEAGR 72
            Y+ LV+ +   +A +
Sbjct: 595 RYKELVEMVKAKKAAQ 610

Acts both as a chaperone in the cytosol and as a chromatin regulator in the nucleus. When cytosolic, acts as a molecular chaperone: component of the ribosome-associated complex (RAC), a complex involved in folding or maintaining nascent polypeptides in a folding-competent state. In the RAC complex, stimulates the ATPase activity of the ribosome-associated pool of Hsp70-type chaperones HSPA14 that bind to the nascent polypeptide chain. When nuclear, mediates the switching from polycomb-repressed genes to an active state: specifically recruited at histone H2A ubiquitinated at 'Lys-119' (H2AK119ub), and promotes the displacement of the polycomb PRC1 complex from chromatin, thereby facilitating transcription activation. Specifically binds DNA sequence 5'-GTCAAGC-3'.

Homo sapiens (taxid: 9606)

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	86
225430734	79	PREDICTED: dnaJ homolog subfamily C memb	0.918	1.0	0.708	2e-27
224133822	85	predicted protein [Populus trichocarpa]	0.941	0.952	0.679	4e-27
297735143	74	unnamed protein product [Vitis vinifera]	0.860	1.0	0.702	7e-25
75320414	93	RecName: Full=Transcription factor RADIA	0.906	0.838	0.653	9e-24
224097018	78	predicted protein [Populus trichocarpa]	0.906	1.0	0.627	1e-23
356538793	92	PREDICTED: dnaJ homolog subfamily C memb	1.0	0.934	0.581	2e-23
297802294	81	At4g36570 [Arabidopsis lyrata subsp. lyr	0.755	0.802	0.723	3e-23
110931770	100	MYB transcription factor MYB164 [Glycine	0.895	0.77	0.636	3e-23
15222161	126	RAD-like 6 protein [Arabidopsis thaliana	0.883	0.603	0.675	4e-23
356553883	98	PREDICTED: dnaJ homolog subfamily C memb	0.872	0.765	0.64	4e-23

>gi|225430734|ref|XP_002266235.1| PREDICTED: dnaJ homolog subfamily C member 1-like [Vitis vinifera]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 56/79 (70%), Positives = 68/79 (86%)

Query: 1  MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          MASN+MTSSR+SGSSWT KQNK FE ALA YDKDTPDRW N+AKAV GK+ E+VK+HYE+
Sbjct: 1  MASNSMTSSRTSGSSWTPKQNKLFEKALAKYDKDTPDRWQNIAKAVGGKSAEEVKRHYEI 60

Query: 61 LVKDINDIEAGRYPHPNYR 79
          L++D+  IE+G+ P PNYR
Sbjct: 61 LIEDVKHIESGKVPFPNYR 79

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133822|ref|XP_002327689.1| predicted protein [Populus trichocarpa] gi|222836774|gb|EEE75167.1| predicted protein [Populus trichocarpa]

 Score =  125 bits (314), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 55/81 (67%), Positives = 68/81 (83%)

Query: 1  MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          MASN++ SSR+  SSWT KQNK FE ALA YDKDTPDRW NVAKAV GK+ E+V++HYE+
Sbjct: 1  MASNSLNSSRNCSSSWTPKQNKLFEKALALYDKDTPDRWHNVAKAVGGKSAEEVERHYEI 60

Query: 61 LVKDINDIEAGRYPHPNYRST 81
          L+KD+ +IE+GR P PNYRS+
Sbjct: 61 LIKDVREIESGRVPFPNYRSS 81

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735143|emb|CBI17505.3| unnamed protein product [Vitis vinifera]

 Score =  117 bits (294), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 52/74 (70%), Positives = 63/74 (85%)

Query: 6  MTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65
          MTSSR+SGSSWT KQNK FE ALA YDKDTPDRW N+AKAV GK+ E+VK+HYE+L++D+
Sbjct: 1  MTSSRTSGSSWTPKQNKLFEKALAKYDKDTPDRWQNIAKAVGGKSAEEVKRHYEILIEDV 60

Query: 66 NDIEAGRYPHPNYR 79
            IE+G+ P PNYR
Sbjct: 61 KHIESGKVPFPNYR 74

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|75320414|sp|Q58FS3.1|RAD_ANTMA RecName: Full=Transcription factor RADIALIS gi|118137433|pdb|2CJJ|A Chain A, Crystal Structure Of The Myb Domain Of The Rad Transcription Factor From Antirrhinum Majus gi|61652985|gb|AAX48042.1| RADIALIS [Antirrhinum majus]

 Score =  114 bits (285), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 51/78 (65%), Positives = 62/78 (79%)

Query: 6  MTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65
          M S+R SG  W+ K+NK FE ALA YDKDTPDRW NVA+AV G+T E+VKKHYE+LV+DI
Sbjct: 1  MASTRGSGRPWSAKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDI 60

Query: 66 NDIEAGRYPHPNYRSTTG 83
            IE+G+ P PNYR+T G
Sbjct: 61 KYIESGKVPFPNYRTTGG 78

Source: Antirrhinum majus

Species: Antirrhinum majus

Genus: Antirrhinum

Family: Plantaginaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224097018|ref|XP_002310812.1| predicted protein [Populus trichocarpa] gi|222853715|gb|EEE91262.1| predicted protein [Populus trichocarpa]

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 54/86 (62%), Positives = 67/86 (77%), Gaps = 8/86 (9%)

Query: 1  MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          M+SN++TS       WT KQNK FE ALA +DKDTPDRW NVAKAV GK+ E+VK+HYE+
Sbjct: 1  MSSNSLTS-------WTPKQNKLFEKALALHDKDTPDRWHNVAKAVGGKSAEEVKRHYEI 53

Query: 61 LVKDINDIEAGRYPHPNYRSTTGTGN 86
          L+KD+ +IE+GR P PNYRS +G GN
Sbjct: 54 LIKDVREIESGRVPFPNYRS-SGNGN 78

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538793|ref|XP_003537885.1| PREDICTED: dnaJ homolog subfamily C member 2-like [Glycine max]

 Score =  112 bits (280), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/86 (58%), Positives = 68/86 (79%)

Query: 1  MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          MAS++++  ++S SSWT KQNK FE ALA YDKDTP+RW NVAKAV GK+ ++VK+HYE+
Sbjct: 1  MASSSLSKQKASDSSWTPKQNKLFEKALAKYDKDTPERWQNVAKAVGGKSADEVKRHYEI 60

Query: 61 LVKDINDIEAGRYPHPNYRSTTGTGN 86
          L++D+  IE+GR P P Y+ST  + N
Sbjct: 61 LLEDLRHIESGRVPLPKYKSTGSSTN 86

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297802294|ref|XP_002869031.1| At4g36570 [Arabidopsis lyrata subsp. lyrata] gi|75324337|sp|Q6NNN0.1|RADL3_ARATH RecName: Full=Protein RADIALIS-like 3; Short=AtRL3; Short=Protein RAD-like 3 gi|38566494|gb|AAR24137.1| At4g36570 [Arabidopsis thaliana] gi|40823588|gb|AAR92291.1| At4g36570 [Arabidopsis thaliana] gi|297314867|gb|EFH45290.1| At4g36570 [Arabidopsis lyrata subsp. lyrata]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 47/65 (72%), Positives = 58/65 (89%)

Query: 16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPH 75
          WT K+NK FE ALA YD+DTPDRW NVA+AV GK+ E+V++HYELL++D+NDIE+GRYPH
Sbjct: 12 WTRKENKLFERALATYDQDTPDRWHNVARAVGGKSAEEVRRHYELLIRDVNDIESGRYPH 71

Query: 76 PNYRS 80
          PNYRS
Sbjct: 72 PNYRS 76

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|110931770|gb|ABH02884.1| MYB transcription factor MYB164 [Glycine max]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 60/77 (77%)

Query: 9  SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDI 68
          S +S S+WT KQNK+FE ALA YD+DTPDRW N+A+AV GKTVE+VK+HYE+LV D+  I
Sbjct: 3  SMASSSAWTTKQNKKFENALAIYDRDTPDRWQNLARAVGGKTVEEVKRHYEMLVDDLKQI 62

Query: 69 EAGRYPHPNYRSTTGTG 85
          E G  P PNYR+   TG
Sbjct: 63 EEGHVPLPNYRNAAATG 79

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15222161|ref|NP_177661.1| RAD-like 6 protein [Arabidopsis thaliana] gi|10092271|gb|AAG12684.1|AC025814_8 myb-related protein; 20671-21051 [Arabidopsis thaliana] gi|41618978|gb|AAS09995.1| MYB transcription factor [Arabidopsis thaliana] gi|109946537|gb|ABG48447.1| At1g75250 [Arabidopsis thaliana] gi|332197572|gb|AEE35693.1| RAD-like 6 protein [Arabidopsis thaliana]

 Score =  112 bits (279), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 54/80 (67%), Positives = 63/80 (78%), Gaps = 4/80 (5%)

Query: 1  MASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          MASN    SRSS S WT  QNK FE ALA YDKDTPDRW NVAKAV GKTVE+VK+HY++
Sbjct: 1  MASN----SRSSISPWTFSQNKMFERALAVYDKDTPDRWHNVAKAVGGKTVEEVKRHYDI 56

Query: 61 LVKDINDIEAGRYPHPNYRS 80
          LV+D+ +IE GR P PNY++
Sbjct: 57 LVEDLINIETGRVPLPNYKT 76

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356553883|ref|XP_003545280.1| PREDICTED: dnaJ homolog subfamily C member 2-like [Glycine max]

 Score =  111 bits (278), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/75 (64%), Positives = 59/75 (78%)

Query: 11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEA 70
          +S S+WT KQNK+FE ALA YD+DTPDRW N+A+AV GKTVE+VK+HYE+LV D+  IE 
Sbjct: 2  ASSSAWTTKQNKKFENALAIYDRDTPDRWQNLARAVGGKTVEEVKRHYEMLVDDLKQIEE 61

Query: 71 GRYPHPNYRSTTGTG 85
          G  P PNYR+   TG
Sbjct: 62 GHVPLPNYRNAAATG 76

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	86
TAIR|locus:2115260	81	RL3 "RAD-like 3" [Arabidopsis	0.720	0.765	0.725	4.8e-23
TAIR|locus:4010713631	77	RL4 "RAD-like 4" [Arabidopsis	0.732	0.818	0.650	4.9e-21
TAIR|locus:2136283	100	RL1 "RAD-like 1" [Arabidopsis	0.790	0.68	0.676	4.9e-21
UNIPROTKB|Q58FS3	93	RAD "Transcription factor RADI	0.755	0.698	0.692	6.3e-21
TAIR|locus:2049374	101	MEE3 "MATERNAL EFFECT EMBRYO A	0.802	0.683	0.637	2.1e-20
TAIR|locus:2025182	97	RL6 "RAD-like 6" [Arabidopsis	0.709	0.628	0.704	3.5e-20
TAIR|locus:2016417	100	RL5 "RAD-like 5" [Arabidopsis	0.779	0.67	0.588	2.5e-17
TAIR|locus:2042872	298	AT2G38090 [Arabidopsis thalian	0.767	0.221	0.590	4.7e-16
TAIR|locus:2166459	277	AT5G05790 [Arabidopsis thalian	0.779	0.241	0.537	1.8e-14
TAIR|locus:2074723	263	AT3G11280 [Arabidopsis thalian	0.697	0.228	0.566	1.6e-13

TAIR|locus:2115260 RL3 "RAD-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 45/62 (72%), Positives = 56/62 (90%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             K+NK FE ALA YD+DTPDRW NVA+AV GK+ E+V++HYELL++D+NDIE+GRYPHPNY
Sbjct:    15 KENKLFERALATYDQDTPDRWHNVARAVGGKSAEEVRRHYELLIRDVNDIESGRYPHPNY 74

Query:    79 RS 80
             RS
Sbjct:    75 RS 76

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

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

TAIR|locus:4010713631 RL4 "RAD-like 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 41/63 (65%), Positives = 55/63 (87%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             +++KQFE ALA +DKDTPDRW  +A+AV GK+ E+VK+HYELL++D+NDIE+GRYP P Y
Sbjct:    14 REDKQFEMALAKFDKDTPDRWQKIARAVGGKSTEEVKRHYELLLRDVNDIESGRYPQPRY 73

Query:    79 RST 81
             R+T
Sbjct:    74 RNT 76

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2136283 RL1 "RAD-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/68 (67%), Positives = 53/68 (77%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             KQNK FE ALA YD+DTP+RW NVAK V GKT E+VK+HYELLV+DIN IE G  P PNY
Sbjct:    17 KQNKAFEQALATYDQDTPNRWQNVAKVVGGKTTEEVKRHYELLVQDINSIENGHVPFPNY 76

Query:    79 RSTTGTGN 86
             R++ G  N
Sbjct:    77 RTSGGCTN 84

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

UNIPROTKB|Q58FS3 RAD "Transcription factor RADIALIS" [Antirrhinum majus (taxid:4151)]

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 45/65 (69%), Positives = 54/65 (83%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             K+NK FE ALA YDKDTPDRW NVA+AV G+T E+VKKHYE+LV+DI  IE+G+ P PNY
Sbjct:    14 KENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDIKYIESGKVPFPNY 73

Query:    79 RSTTG 83
             R+T G
Sbjct:    74 RTTGG 78

GO:0009908 "flower development" evidence=IMP

GO:0048262 "determination of dorsal/ventral asymmetry" evidence=IMP

TAIR|locus:2049374 MEE3 "MATERNAL EFFECT EMBRYO ARREST 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 44/69 (63%), Positives = 53/69 (76%)

Query:    18 VKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPN 77
             VKQNK FE ALA YD+DTPDRW NVA+AV GKT E+ K+ Y+LLV+DI  IE G  P P+
Sbjct:    16 VKQNKAFERALAVYDQDTPDRWHNVARAVGGKTPEEAKRQYDLLVRDIESIENGHVPFPD 75

Query:    78 YRSTTGTGN 86
             Y++TTG  N
Sbjct:    76 YKTTTGNSN 84

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

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

GO:0005634 "nucleus" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP

GO:0009630 "gravitropism" evidence=IMP

GO:0010114 "response to red light" evidence=IMP

TAIR|locus:2025182 RL6 "RAD-like 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 43/61 (70%), Positives = 52/61 (85%)

Query:    20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYR 79
             QNK FE ALA YDKDTPDRW NVAKAV GKTVE+VK+HY++LV+D+ +IE GR P PNY+
Sbjct:    16 QNKMFERALAVYDKDTPDRWHNVAKAVGGKTVEEVKRHYDILVEDLINIETGRVPLPNYK 75

Query:    80 S 80
             +
Sbjct:    76 T 76

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0009507 "chloroplast" evidence=ISM

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

TAIR|locus:2016417 RL5 "RAD-like 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 212 (79.7 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 40/68 (58%), Positives = 50/68 (73%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             KQNK FE ALA YDKDTPDRW NVAKAV  K+ E+VK+HY++LV+D+ +IE    P P Y
Sbjct:    15 KQNKMFERALAVYDKDTPDRWQNVAKAVGSKSAEEVKRHYDILVEDLMNIEQDLVPLPKY 74

Query:    79 RSTTGTGN 86
             + T   G+
Sbjct:    75 K-TVDVGS 81

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

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

TAIR|locus:2042872 AT2G38090 [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 39/66 (59%), Positives = 47/66 (71%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             ++NK+FE ALAFYDKDTPDRW  VA  + GKTV DV K Y  L +D++DIEAG  P P Y
Sbjct:    32 EENKKFENALAFYDKDTPDRWSRVAAMLPGKTVGDVIKQYRELEEDVSDIEAGLIPIPGY 91

Query:    79 RSTTGT 84
              S + T
Sbjct:    92 ASDSFT 97

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

TAIR|locus:2166459 AT5G05790 [Arabidopsis thaliana (taxid:3702)]

 Score = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 36/67 (53%), Positives = 44/67 (65%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             ++NK+FE ALA Y  DTPDRW  VA  + GKT+ DV + Y  L +D+ DIEAG  P P Y
Sbjct:    34 EENKKFERALAVYADDTPDRWFKVAAMIPGKTISDVMRQYSKLEEDLFDIEAGLVPIPGY 93

Query:    79 RSTTGTG 85
             RS T  G
Sbjct:    94 RSVTPCG 100

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

TAIR|locus:2074723 AT3G11280 [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 34/60 (56%), Positives = 41/60 (68%)

Query:    19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY 78
             ++NK FE ALA Y +D+PDRW  VA  + GKTV DV K Y  L +D+ DIEAGR P P Y
Sbjct:    36 EENKMFERALAIYAEDSPDRWFKVASMIPGKTVFDVMKQYSKLEEDVFDIEAGRVPIPGY 95

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0009751 "response to salicylic acid stimulus" evidence=IEP

GO:0009739 "response to gibberellin stimulus" evidence=IEP

GO:0019344 "cysteine biosynthetic process" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6NNN0	RADL3_ARATH	No assigned EC number	0.7230	0.7558	0.8024	yes	no
Q58FS3	RAD_ANTMA	No assigned EC number	0.6538	0.9069	0.8387	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.57.329.1 hypothetical protein (74 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	86
smart00717	49	smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIII	2e-05
cd00167	45	cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-	3e-05
pfam00249	47	pfam00249, Myb_DNA-binding, Myb-like DNA-binding d	0.004

>gnl|CDD|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

 Score = 37.6 bits (88), Expect = 2e-05
 Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK 63
             WT ++++     +  Y K+    W+ +AK + G+T E  ++ +  L+K
Sbjct: 1  KGEWTEEEDELLIELVKKYGKN---NWEKIAKELPGRTAEQCRERWRNLLK 48

Length = 49

>gnl|CDD|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains

 Score = 37.2 bits (87), Expect = 3e-05
 Identities = 11/48 (22%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62
           WT ++++    A+  Y K+    W+ +AK + G+T +  ++ +  L+
Sbjct: 1  PWTEEEDELLLEAVKKYGKN---NWEKIAKELPGRTPKQCRERWRNLL 45

Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA. Length = 45

>gnl|CDD|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain

 Score = 31.7 bits (73), Expect = 0.004
 Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 3/44 (6%)

Query: 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHY 58
           WT ++++    A+  +       W  +AK + G+T    K  +
Sbjct: 3  PWTPEEDELLIEAVKKHGNG---NWSKIAKHLPGRTDNQCKNRW 43

This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family. Length = 47

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	86
PF00249	48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	99.62
smart00717	49	SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-bindi	99.43
cd00167	45	SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding do	99.38
PF13921	60	Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB:	99.26
PLN03212	249	Transcription repressor MYB5; Provisional	99.12
PLN03212	249	Transcription repressor MYB5; Provisional	99.11
KOG0048	238	consensus Transcription factor, Myb superfamily [T	99.0
PLN03091	459	hypothetical protein; Provisional	98.99
PLN03091	459	hypothetical protein; Provisional	98.98
KOG0048	238	consensus Transcription factor, Myb superfamily [T	98.92
KOG0457	438	consensus Histone acetyltransferase complex SAGA/A	98.82
TIGR01557	57	myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c	98.63
COG5259	531	RSC8 RSC chromatin remodeling complex subunit RSC8	98.55
KOG0049	939	consensus Transcription factor, Myb superfamily [T	98.42
KOG1279	506	consensus Chromatin remodeling factor subunit and	98.34
COG5114	432	Histone acetyltransferase complex SAGA/ADA, subuni	98.14
KOG0724	335	consensus Zuotin and related molecular chaperones	98.09
PF13837	90	Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain;	97.97
KOG4167	907	consensus Predicted DNA-binding protein, contains	97.91
KOG0050	617	consensus mRNA splicing protein CDC5 (Myb superfam	97.6
PF13873	78	Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain	97.54
KOG0050	617	consensus mRNA splicing protein CDC5 (Myb superfam	97.41
COG5147	512	REB1 Myb superfamily proteins, including transcrip	97.3
KOG0049	939	consensus Transcription factor, Myb superfamily [T	97.24
KOG0051	607	consensus RNA polymerase I termination factor, Myb	97.19
PF09111	118	SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain	97.18
PF12776	96	Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain;	96.94
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.91
KOG0051	607	consensus RNA polymerase I termination factor, Myb	96.53
KOG4282	345	consensus Transcription factor GT-2 and related pr	96.4
PF08914	65	Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR0150	95.9
KOG4468	782	consensus Polycomb-group transcriptional regulator	95.83
COG5147	512	REB1 Myb superfamily proteins, including transcrip	95.81
COG5118	507	BDP1 Transcription initiation factor TFIIIB, Bdp1	95.77
PRK13923	170	putative spore coat protein regulator protein YlbO	95.53
KOG1194	534	consensus Predicted DNA-binding protein, contains	95.32
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	95.25
smart00595	89	MADF subfamily of SANT domain.	95.12
KOG4329	445	consensus DNA-binding protein [General function pr	94.78
KOG3841	455	consensus TEF-1 and related transcription factor,	94.43
PF11035	344	SnAPC_2_like: Small nuclear RNA activating complex	94.35
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	93.57
PF10545	85	MADF_DNA_bdg: Alcohol dehydrogenase transcription	93.12
KOG2656	445	consensus DNA methyltransferase 1-associated prote	91.89
smart00426	68	TEA TEA domain.	91.32
PF04504	98	DUF573: Protein of unknown function, DUF573; Inter	91.18
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	90.05
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	89.93
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	89.48
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	88.57
PF13325	199	MCRS_N: N-terminal region of micro-spherule protei	87.47
PRK11169	164	leucine-responsive transcriptional regulator; Prov	87.42
KOG3554	693	consensus Histone deacetylase complex, MTA1 compon	87.35
PF13325	199	MCRS_N: N-terminal region of micro-spherule protei	86.01
PF01285	431	TEA: TEA/ATTS domain family; InterPro: IPR000818 T	84.37
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	83.76
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	83.33
KOG1194	534	consensus Predicted DNA-binding protein, contains	81.77
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	80.85

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins

Probab=99.62  E-value=1.1e-15  Score=87.12  Aligned_cols=45  Identities=29%  Similarity=0.686  Sum_probs=40.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELL   61 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L   61 (86)
                      ..||.+|+.+|.++|.+|+.+   +|..||..|| |||..||+.||..+
T Consensus         2 ~~Wt~eE~~~l~~~v~~~g~~---~W~~Ia~~~~~~Rt~~qc~~~~~~~   47 (48)
T PF00249_consen    2 GPWTEEEDEKLLEAVKKYGKD---NWKKIAKRMPGGRTAKQCRSRYQNL   47 (48)
T ss_dssp             -SS-HHHHHHHHHHHHHSTTT---HHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCc---HHHHHHHHcCCCCCHHHHHHHHHhh
Confidence            589999999999999999854   7999999999 99999999999876

These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....

>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

Probab=99.43  E-value=5e-13  Score=73.31  Aligned_cols=46  Identities=24%  Similarity=0.632  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ..||.+|+.+|+.++.+|+.   .+|..||..||+||..+|+.||..+.
T Consensus         2 ~~Wt~~E~~~l~~~~~~~g~---~~w~~Ia~~~~~rt~~~~~~~~~~~~   47 (49)
T smart00717        2 GEWTEEEDELLIELVKKYGK---NNWEKIAKELPGRTAEQCRERWNNLL   47 (49)
T ss_pred             CCCCHHHHHHHHHHHHHHCc---CCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence            58999999999999999973   47999999999999999999998764

>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains

Probab=99.38  E-value=2e-12  Score=70.02  Aligned_cols=44  Identities=25%  Similarity=0.635  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      .||.+|++.|..++.+|+.   .+|..||+.||+||..||+.||..+
T Consensus         1 ~Wt~eE~~~l~~~~~~~g~---~~w~~Ia~~~~~rs~~~~~~~~~~~   44 (45)
T cd00167           1 PWTEEEDELLLEAVKKYGK---NNWEKIAKELPGRTPKQCRERWRNL   44 (45)
T ss_pred             CCCHHHHHHHHHHHHHHCc---CCHHHHHhHcCCCCHHHHHHHHHHh
Confidence            5999999999999999973   4799999999999999999999875

Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.

>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A

Probab=99.26  E-value=1.4e-11  Score=72.34  Aligned_cols=41  Identities=15%  Similarity=0.494  Sum_probs=35.9

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           16 WTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        16 WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      ||.+||.+|..++.+|+    ..|..||+.||.||..+|+.||..
T Consensus         1 WT~eEd~~L~~~~~~~g----~~W~~Ia~~l~~Rt~~~~~~r~~~   41 (60)
T PF13921_consen    1 WTKEEDELLLELVKKYG----NDWKKIAEHLGNRTPKQCRNRWRN   41 (60)
T ss_dssp             S-HHHHHHHHHHHHHHT----S-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHC----cCHHHHHHHHCcCCHHHHHHHHHH
Confidence            99999999999999995    379999999977999999999998

...

>PLN03212 Transcription repressor MYB5; Provisional

Probab=99.12  E-value=9.3e-11  Score=87.51  Aligned_cols=47  Identities=13%  Similarity=0.304  Sum_probs=42.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELL   61 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L   61 (86)
                      ....||+|||++|.+++.+|+.   .+|..||+.++ |||.+||++||..+
T Consensus        24 KRg~WT~EEDe~L~~lV~kyG~---~nW~~IAk~~g~gRT~KQCReRW~N~   71 (249)
T PLN03212         24 KRGPWTVEEDEILVSFIKKEGE---GRWRSLPKRAGLLRCGKSCRLRWMNY   71 (249)
T ss_pred             cCCCCCHHHHHHHHHHHHHhCc---ccHHHHHHhhhcCCCcchHHHHHHHh
Confidence            4678999999999999999974   48999999994 89999999999764

>PLN03212 Transcription repressor MYB5; Provisional

Probab=99.11  E-value=2e-10  Score=85.79  Aligned_cols=51  Identities=14%  Similarity=0.296  Sum_probs=45.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv   65 (86)
                      -..++||.|||.+|.+++..|+    .+|..||+.|||||..+|++||..+....
T Consensus        76 I~kgpWT~EED~lLlel~~~~G----nKWs~IAk~LpGRTDnqIKNRWns~LrK~  126 (249)
T PLN03212         76 VKRGGITSDEEDLILRLHRLLG----NRWSLIAGRIPGRTDNEIKNYWNTHLRKK  126 (249)
T ss_pred             cccCCCChHHHHHHHHHHHhcc----ccHHHHHhhcCCCCHHHHHHHHHHHHhHH
Confidence            4568999999999999999985    58999999999999999999998766554

>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]

Probab=99.00  E-value=1.2e-09  Score=79.90  Aligned_cols=46  Identities=20%  Similarity=0.417  Sum_probs=42.2

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      ..+.||+|||.++.++.+.++    +||..||++|||||+.+|++||...
T Consensus        61 krg~fT~eEe~~Ii~lH~~~G----NrWs~IA~~LPGRTDNeIKN~Wnt~  106 (238)
T KOG0048|consen   61 KRGNFSDEEEDLIIKLHALLG----NRWSLIAGRLPGRTDNEVKNHWNTH  106 (238)
T ss_pred             cCCCCCHHHHHHHHHHHHHHC----cHHHHHHhhCCCcCHHHHHHHHHHH
Confidence            467999999999999999985    6899999999999999999999754

>PLN03091 hypothetical protein; Provisional

Probab=98.99  E-value=1.4e-09  Score=86.67  Aligned_cols=49  Identities=16%  Similarity=0.407  Sum_probs=44.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      ..++||.|||++|.+++..|+    .+|.+||+.|||||..+|++||..++..
T Consensus        66 kKgpWT~EED~lLLeL~k~~G----nKWskIAk~LPGRTDnqIKNRWnslLKK  114 (459)
T PLN03091         66 KRGTFSQQEENLIIELHAVLG----NRWSQIAAQLPGRTDNEIKNLWNSCLKK  114 (459)
T ss_pred             cCCCCCHHHHHHHHHHHHHhC----cchHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence            467999999999999999986    4899999999999999999999976654

>PLN03091 hypothetical protein; Provisional

Probab=98.98  E-value=5.3e-10  Score=89.05  Aligned_cols=47  Identities=11%  Similarity=0.323  Sum_probs=41.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELL   61 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L   61 (86)
                      ....||.|||++|..+|.+|+.   ..|..||+.++ |||.+||++||.++
T Consensus        13 rKg~WTpEEDe~L~~~V~kyG~---~nWs~IAk~~g~gRT~KQCRERW~Ny   60 (459)
T PLN03091         13 RKGLWSPEEDEKLLRHITKYGH---GCWSSVPKQAGLQRCGKSCRLRWINY   60 (459)
T ss_pred             cCCCCCHHHHHHHHHHHHHhCc---CCHHHHhhhhccCcCcchHhHHHHhc
Confidence            3568999999999999999975   48999999986 89999999999863

>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]

Probab=98.92  E-value=5.9e-10  Score=81.60  Aligned_cols=51  Identities=12%  Similarity=0.244  Sum_probs=45.9

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHH-HHHHHHh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYE-LLVKDIN   66 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~-~L~~dv~   66 (86)
                      .++||.|||.+|...|.+|+++   +|..||+.+| ||+.++|+.||. +|..+|+
T Consensus         9 kGpWt~EED~~L~~~V~~~G~~---~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik   61 (238)
T KOG0048|consen    9 KGPWTQEEDLTQIRSIKSFGKH---NGTALPKLAGLRRCGKSCRLRWTNYLRPDLK   61 (238)
T ss_pred             CCCCChHHHHHHHHHHHHhCCC---CcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence            5899999999999999999764   8999999999 999999999996 4666665

>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]

Probab=98.82  E-value=9.8e-09  Score=81.51  Aligned_cols=51  Identities=27%  Similarity=0.414  Sum_probs=45.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      |..-....||.+|+.+|.+|+..|+-|   +|+.||.+||.||.++|++||.+.
T Consensus        67 s~~i~~~~WtadEEilLLea~~t~G~G---NW~dIA~hIGtKtkeeck~hy~k~  117 (438)
T KOG0457|consen   67 SFPILDPSWTADEEILLLEAAETYGFG---NWQDIADHIGTKTKEECKEHYLKH  117 (438)
T ss_pred             CCCCCCCCCChHHHHHHHHHHHHhCCC---cHHHHHHHHcccchHHHHHHHHHH
Confidence            344467889999999999999999865   899999999999999999999864

>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class

Probab=98.63  E-value=1.2e-07  Score=56.53  Aligned_cols=48  Identities=17%  Similarity=0.293  Sum_probs=41.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchH---HHHHHHcC-CC-CHHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRW---DNVAKAVS-GK-TVEDVKKHYELLVK   63 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW---~~IA~~vp-gR-T~~qc~~ry~~L~~   63 (86)
                      .-.||.||...|..||..|+.+   .|   .+|++.|. .+ |..||+.|++++..
T Consensus         3 r~~WT~eeh~~Fl~ai~~~G~g---~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~   55 (57)
T TIGR01557         3 RVVWTEDLHDRFLQAVQKLGGP---DWATPKRILELMVVDGLTRDQVASHLQKYRL   55 (57)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCC---cccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence            3579999999999999999754   69   99999986 35 99999999987653

This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.

>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]

Probab=98.55  E-value=7.3e-08  Score=77.56  Aligned_cols=45  Identities=29%  Similarity=0.539  Sum_probs=41.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      ...||.+|..+|.++|..|+    +.|.+||.+|+.||++||+.||.+|
T Consensus       279 dk~WS~qE~~LLLEGIe~yg----DdW~kVA~HVgtKt~EqCIl~FL~L  323 (531)
T COG5259         279 DKNWSRQELLLLLEGIEMYG----DDWDKVARHVGTKTKEQCILHFLQL  323 (531)
T ss_pred             cccccHHHHHHHHHHHHHhh----hhHHHHHHHhCCCCHHHHHHHHHcC
Confidence            35899999999999999996    5699999999999999999999875

>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]

Probab=98.42  E-value=5e-07  Score=75.56  Aligned_cols=52  Identities=17%  Similarity=0.413  Sum_probs=45.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      +-+.+.||.+||..|..|+.+|+.   ..|-+|-+.|||||..||+.||.+.+..
T Consensus       357 sikhg~wt~~ED~~L~~AV~~Yg~---kdw~k~R~~vPnRSdsQcR~RY~nvL~~  408 (939)
T KOG0049|consen  357 SVKHGRWTDQEDVLLVCAVSRYGA---KDWAKVRQAVPNRSDSQCRERYTNVLNR  408 (939)
T ss_pred             cccCCCCCCHHHHHHHHHHHHhCc---cchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence            345689999999999999999974   4899999999999999999999876544

>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]

Probab=98.34  E-value=8.9e-07  Score=71.75  Aligned_cols=49  Identities=27%  Similarity=0.484  Sum_probs=44.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697            9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus         9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      ..+....||.+|.-+|.++|..|+    +.|.+||.+|++||.+||..||.+|
T Consensus       249 ~~~~~~~WT~qE~lLLLE~ie~y~----ddW~kVa~hVg~ks~eqCI~kFL~L  297 (506)
T KOG1279|consen  249 GESARPNWTEQETLLLLEAIEMYG----DDWNKVADHVGTKSQEQCILKFLRL  297 (506)
T ss_pred             cccCCCCccHHHHHHHHHHHHHhc----ccHHHHHhccCCCCHHHHHHHHHhc
Confidence            456678999999999999999996    4699999999999999999999886

>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]

Probab=98.14  E-value=6.2e-06  Score=64.53  Aligned_cols=48  Identities=17%  Similarity=0.446  Sum_probs=43.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ....|+.+|+-+|.+++...+.|   +|+.||.+||.|+.++|+.||.+..
T Consensus        62 ~~e~WgadEEllli~~~~TlGlG---NW~dIadyiGsr~kee~k~HylK~y  109 (432)
T COG5114          62 GEEGWGADEELLLIECLDTLGLG---NWEDIADYIGSRAKEEIKSHYLKMY  109 (432)
T ss_pred             cCCCcCchHHHHHHHHHHhcCCC---cHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            56789999999999999999865   8999999999999999999998754

>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]

Probab=98.09  E-value=6.6e-06  Score=62.19  Aligned_cols=68  Identities=44%  Similarity=0.677  Sum_probs=63.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCC----CCchHHHHHHHcCC-CCHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCC
Q 034697           14 SSWTVKQNKQFETALAFYDKD----TPDRWDNVAKAVSG-KTVEDVKKHYELLVKDINDIEAGRYPHPNYRST   81 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~----~~~rW~~IA~~vpg-RT~~qc~~ry~~L~~dv~~ie~g~v~~P~y~~~   81 (86)
                      ..|+.++.+.|++|+..|...    .+++|.+++..||+ .+..+.+.+|..++.++..++++.+++|.|...
T Consensus        32 ~~~~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~  104 (335)
T KOG0724|consen   32 SLWTEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKS  104 (335)
T ss_pred             hhhHHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCcc
Confidence            569999999999999999753    68999999999999 999999999999999999999999999999763

>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A

Probab=97.97  E-value=1.9e-05  Score=48.74  Aligned_cols=57  Identities=19%  Similarity=0.414  Sum_probs=41.3

Q ss_pred             CCCCHHHHHHHHHHHHh------cC--CC-CC-chHHHHHHHcC----CCCHHHHHHHHHHHHHHHhhhhc
Q 034697           14 SSWTVKQNKQFETALAF------YD--KD-TP-DRWDNVAKAVS----GKTVEDVKKHYELLVKDINDIEA   70 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~------~~--~~-~~-~rW~~IA~~vp----gRT~~qc~~ry~~L~~dv~~ie~   70 (86)
                      ..||.+|-..|+.++..      |.  .. .. .-|..||..|.    .||+.||+.+|+.|..+-+.+..
T Consensus         2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~   72 (90)
T PF13837_consen    2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKD   72 (90)
T ss_dssp             -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSS
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            57999999999998777      21  12 22 37999999984    49999999999999999887654

>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]

Probab=97.91  E-value=2.5e-05  Score=66.04  Aligned_cols=44  Identities=36%  Similarity=0.476  Sum_probs=40.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE   59 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~   59 (86)
                      ++..||..|-++|.+||-.|.++    +..|+++|+|||+.||.+.|.
T Consensus       618 gSd~WTp~E~~lF~kA~y~~~KD----F~~v~km~~~KtVaqCVeyYY  661 (907)
T KOG4167|consen  618 GSDKWTPLERKLFNKALYTYSKD----FIFVQKMVKSKTVAQCVEYYY  661 (907)
T ss_pred             CcccccHHHHHHHHHHHHHhccc----HHHHHHHhccccHHHHHHHHH
Confidence            57799999999999999999764    999999999999999999875

>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]

Probab=97.60  E-value=8.9e-05  Score=60.79  Aligned_cols=52  Identities=23%  Similarity=0.498  Sum_probs=44.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH-HHHHhh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL-VKDIND   67 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L-~~dv~~   67 (86)
                      .+.|+..||.+|..++.+|+.+   .|.+||+.++-+|+.||+.||.+. -+.|+.
T Consensus         7 ggvwrntEdeilkaav~kyg~n---qws~i~sll~~kt~rqC~~rw~e~ldp~i~~   59 (617)
T KOG0050|consen    7 GGVWRNTEDEVLKAAVMKYGKN---QWSRIASLLNRKTARQCKARWEEWLDPAIKK   59 (617)
T ss_pred             cceecccHHHHHHHHHHHcchH---HHHHHHHHHhhcchhHHHHHHHHHhCHHHhh
Confidence            4689999999999999999864   899999999999999999999764 344443

>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain

Probab=97.54  E-value=0.00036  Score=42.49  Aligned_cols=54  Identities=9%  Similarity=0.302  Sum_probs=45.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCC---C----------CCchHHHHHHHc----C-CCCHHHHHHHHHHHHHHHhh
Q 034697           14 SSWTVKQNKQFETALAFYDK---D----------TPDRWDNVAKAV----S-GKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~---~----------~~~rW~~IA~~v----p-gRT~~qc~~ry~~L~~dv~~   67 (86)
                      ..||.+|..+|.+.|.+|+.   +          ...-|+.|+..|    | .||..||+..|..+...++.
T Consensus         3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk   74 (78)
T PF13873_consen    3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK   74 (78)
T ss_pred             CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            47999999999999999851   1          346799999988    2 49999999999999888764

>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]

Probab=97.41  E-value=0.00021  Score=58.63  Aligned_cols=53  Identities=13%  Similarity=0.373  Sum_probs=45.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhh
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIE   69 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie   69 (86)
                      ....|+.+||..|..+...+|    ..|.-||..| |||..||.+||..|+.......
T Consensus        58 ~~tews~eederlLhlakl~p----~qwrtIa~i~-gr~~~qc~eRy~~ll~~~~s~~  110 (617)
T KOG0050|consen   58 KKTEWSREEDERLLHLAKLEP----TQWRTIADIM-GRTSQQCLERYNNLLDVYVSYH  110 (617)
T ss_pred             hhhhhhhhHHHHHHHHHHhcC----CccchHHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence            346899999999999988875    4799999999 7999999999999887655433

>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]

Probab=97.30  E-value=0.00037  Score=56.84  Aligned_cols=52  Identities=13%  Similarity=0.338  Sum_probs=46.2

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      ....|+.+|+..|..+-.+++    .+|.-||..+||||..+|.++|..+..+...
T Consensus        71 k~~~~~~eed~~li~l~~~~~----~~wstia~~~d~rt~~~~~ery~~~~~~~~s  122 (512)
T COG5147          71 KKKNWSEEEDEQLIDLDKELG----TQWSTIADYKDRRTAQQCVERYVNTLEDLSS  122 (512)
T ss_pred             ccccccHHHHHHHHHHHHhcC----chhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence            457899999999999988875    4699999999999999999999988777665

>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]

Probab=97.24  E-value=0.00058  Score=57.69  Aligned_cols=45  Identities=22%  Similarity=0.478  Sum_probs=39.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKH   57 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~r   57 (86)
                      +.....||-.||..|..+|.+|+.+   .|.+||..+|.||.+|...|
T Consensus       409 s~K~~rW~l~edeqL~~~V~~YG~g---~WakcA~~Lp~~t~~q~~rr  453 (939)
T KOG0049|consen  409 SAKVERWTLVEDEQLLYAVKVYGKG---NWAKCAMLLPKKTSRQLRRR  453 (939)
T ss_pred             hhccCceeecchHHHHHHHHHHccc---hHHHHHHHccccchhHHHHH
Confidence            3456889999999999999999876   89999999999999775544

>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]

Probab=97.19  E-value=0.0006  Score=56.59  Aligned_cols=47  Identities=19%  Similarity=0.502  Sum_probs=41.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK   63 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~   63 (86)
                      ..+.||++|++.|-..+.+++    ..|..|++.| ||.+..|+.||..++.
T Consensus       383 ~rg~wt~ee~eeL~~l~~~~g----~~W~~Ig~~l-gr~P~~crd~wr~~~~  429 (607)
T KOG0051|consen  383 KRGKWTPEEEEELKKLVVEHG----NDWKEIGKAL-GRMPMDCRDRWRQYVK  429 (607)
T ss_pred             ccCCCCcchHHHHHHHHHHhc----ccHHHHHHHH-ccCcHHHHHHHHHhhc
Confidence            567999999999999999975    5799999999 7999999999987653

>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices

Probab=97.18  E-value=0.002  Score=43.39  Aligned_cols=57  Identities=14%  Similarity=0.387  Sum_probs=47.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc------------CCCCHHHHHHHHHHHHHHHh
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV------------SGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v------------pgRT~~qc~~ry~~L~~dv~   66 (86)
                      +.+...+|.+||..|.-.+.+|+-+.++.|++|-..+            -.||+.++..|...|+.-|.
T Consensus        46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~  114 (118)
T PF09111_consen   46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIE  114 (118)
T ss_dssp             TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHH
Confidence            5667899999999999999999987788999999876            57999999999998887665

It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.

>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains

Probab=96.94  E-value=0.0035  Score=39.01  Aligned_cols=54  Identities=22%  Similarity=0.344  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHHHhcC-------CC--CCchHHHHHHHcC-----CCCHHHHHHHHHHHHHHHhhh
Q 034697           15 SWTVKQNKQFETALAFYD-------KD--TPDRWDNVAKAVS-----GKTVEDVKKHYELLVKDINDI   68 (86)
Q Consensus        15 ~WT~eEdk~Le~al~~~~-------~~--~~~rW~~IA~~vp-----gRT~~qc~~ry~~L~~dv~~i   68 (86)
                      .||.++++.|.+++...-       .+  ++..|..|++.|-     ..|..||++||..|..+-+.+
T Consensus         1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~   68 (96)
T PF12776_consen    1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIW   68 (96)
T ss_pred             CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHH
Confidence            599999999999876651       11  3457999999883     378999999999887766554

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=96.91  E-value=0.0011  Score=47.08  Aligned_cols=50  Identities=12%  Similarity=0.289  Sum_probs=41.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCC---CCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKD---TPDRWDNVAKAVSGKTVEDVKKHYELLVK   63 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~---~~~rW~~IA~~vpgRT~~qc~~ry~~L~~   63 (86)
                      .+.||.|||.+|-+.|.+|-..   .-.-++.|+..+ +||.-.|-=||+.++.
T Consensus         4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VR   56 (161)
T TIGR02894         4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVR   56 (161)
T ss_pred             ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHH
Confidence            3589999999999999888422   246799999999 7999999999987654

In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.

>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]

Probab=96.53  E-value=0.005  Score=51.24  Aligned_cols=52  Identities=8%  Similarity=0.266  Sum_probs=42.5

Q ss_pred             CCCCCCCHHHHHHHHHHHH-------hc------------CCC---CCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALA-------FY------------DKD---TPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~-------~~------------~~~---~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ...+.||.||+..|.+++.       +|            |.+   .+-.|..|++.+++|+..||+.+|.+|+
T Consensus       434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~  507 (607)
T KOG0051|consen  434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLT  507 (607)
T ss_pred             cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHH
Confidence            4678999999999999984       33            111   3457999999999999999999998875

>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]

Probab=96.40  E-value=0.014  Score=44.41  Aligned_cols=59  Identities=19%  Similarity=0.291  Sum_probs=46.1

Q ss_pred             CCCCHHHHHHHHHHHHhcC------CCCCchHHHHHHHcC----CCCHHHHHHHHHHHHHHHhhhhcCC
Q 034697           14 SSWTVKQNKQFETALAFYD------KDTPDRWDNVAKAVS----GKTVEDVKKHYELLVKDINDIEAGR   72 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~------~~~~~rW~~IA~~vp----gRT~~qc~~ry~~L~~dv~~ie~g~   72 (86)
                      ..|+.+|=..|+.+.....      .....-|+.||..+.    -||..||+.+|..|....+....+.
T Consensus        55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~  123 (345)
T KOG4282|consen   55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKK  123 (345)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence            7899999999999855432      123567999999553    2999999999999988888766553

>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif

Probab=95.90  E-value=0.021  Score=34.76  Aligned_cols=49  Identities=8%  Similarity=0.168  Sum_probs=33.9

Q ss_pred             CCCCCHHHHHHHHHHHHhcCC-----CCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDK-----DTPDRWDNVAKAVS-GKTVEDVKKHYELL   61 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~-----~~~~rW~~IA~~vp-gRT~~qc~~ry~~L   61 (86)
                      ..++|.+||.+|...|..+..     ..+.=|..+++.-| ..|-+.-++||.+-
T Consensus         2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~   56 (65)
T PF08914_consen    2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKH   56 (65)
T ss_dssp             -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            457999999999999976631     24678999999999 89999999999653

The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.

>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]

Probab=95.83  E-value=0.023  Score=47.86  Aligned_cols=54  Identities=30%  Similarity=0.487  Sum_probs=44.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHH----------HHHcCCCCHHHHHHHHHHHHHHHhhhhc
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNV----------AKAVSGKTVEDVKKHYELLVKDINDIEA   70 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~I----------A~~vpgRT~~qc~~ry~~L~~dv~~ie~   70 (86)
                      ...||..|...|-.||.+|+++    +++|          -..+.-||..||+.+|.+++..+.+-..
T Consensus        88 ktaWt~~E~~~Ffdal~~~GKd----Fe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~F  151 (782)
T KOG4468|consen   88 KTAWTHQEEESFFDALRQVGKD----FEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLLF  151 (782)
T ss_pred             ccccchhhHHHHHHHHHHhccc----HHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhhc
Confidence            3579999999999999999864    8888          4445569999999999988877766543

>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]

Probab=95.81  E-value=0.0055  Score=50.15  Aligned_cols=45  Identities=18%  Similarity=0.468  Sum_probs=40.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      .+.|+..||..|..++..|+   ++.|.+||+.++-++.+||+.||..
T Consensus        20 ~gsw~~~EDe~l~~~vk~l~---~nnws~vas~~~~~~~kq~~~rw~~   64 (512)
T COG5147          20 GGSWKRTEDEDLKALVKKLG---PNNWSKVASLLISSTGKQSSNRWNN   64 (512)
T ss_pred             CCCCCCcchhHHHHHHhhcc---cccHHHHHHHhcccccccccchhhh
Confidence            35899999999999999986   4579999999998999999999854

>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]

Probab=95.77  E-value=0.024  Score=45.58  Aligned_cols=45  Identities=13%  Similarity=0.364  Sum_probs=41.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      ....||.+|-..|-+||..++-    .+..||..+|.|..+||+..|.+
T Consensus       364 ~~~~Ws~~e~ekFYKALs~wGt----dF~LIs~lfP~R~RkqIKaKfi~  408 (507)
T COG5118         364 GALRWSKKEIEKFYKALSIWGT----DFSLISSLFPNRERKQIKAKFIK  408 (507)
T ss_pred             CCCcccHHHHHHHHHHHHHhcc----hHHHHHHhcCchhHHHHHHHHHH
Confidence            4578999999999999999974    59999999999999999999975

>PRK13923 putative spore coat protein regulator protein YlbO; Provisional

Probab=95.53  E-value=0.022  Score=40.72  Aligned_cols=48  Identities=10%  Similarity=0.237  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCC---CchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDT---PDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~---~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      ...||.|+|.+|.+.+..|....   -.-.+.++..+ +||.-+|--||+.+
T Consensus         5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~   55 (170)
T PRK13923          5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSV   55 (170)
T ss_pred             hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHH
Confidence            35899999999999988886432   35577888889 69999999999654

>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]

Probab=95.32  E-value=0.056  Score=44.19  Aligned_cols=44  Identities=20%  Similarity=0.476  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      ...||.||--+|++|...|++    ++.+|-++||.||...++..|..
T Consensus       187 ~d~WT~Ed~vlFe~aF~~~GK----~F~kIrq~LP~rsLaSlvqyYy~  230 (534)
T KOG1194|consen  187 PDEWTAEDIVLFEQAFQFFGK----DFHKIRQALPHRSLASLVQYYYS  230 (534)
T ss_pred             cccchHHHHHHHHHHHHHhcc----cHHHHHHHccCccHHHHHHHHHH
Confidence            357999999999999999975    69999999999999999988764

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=95.25  E-value=0.052  Score=47.68  Aligned_cols=45  Identities=24%  Similarity=0.414  Sum_probs=39.2

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE   59 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~   59 (86)
                      +=..||..+=..|..|..+|+.+   ..+.||..|.|||.+||+..++
T Consensus       823 gf~~w~~~~f~~f~~~~~~~gr~---~~~~i~~~~~~k~~~ev~~y~~  867 (1033)
T PLN03142        823 GFSTWSRRDFNAFIRACEKYGRN---DIKSIASEMEGKTEEEVERYAK  867 (1033)
T ss_pred             CcCcccHHHHHHHHHHHHHhCHh---HHHHHHHHhcCCCHHHHHHHHH
Confidence            34579999999999999999864   7999999999999999986443

>smart00595 MADF subfamily of SANT domain

Probab=95.12  E-value=0.043  Score=33.67  Aligned_cols=27  Identities=26%  Similarity=0.583  Sum_probs=22.9

Q ss_pred             chHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           37 DRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        37 ~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      .-|..||..|+ .|+++|+.+|+.|...
T Consensus        28 ~aW~~Ia~~l~-~~~~~~~~kw~~LR~~   54 (89)
T smart00595       28 KAWEEIAEELG-LSVEECKKRWKNLRDR   54 (89)
T ss_pred             HHHHHHHHHHC-cCHHHHHHHHHHHHHH
Confidence            46999999995 5999999999987533

>KOG4329 consensus DNA-binding protein [General function prediction only]

Probab=94.78  E-value=0.064  Score=42.92  Aligned_cols=47  Identities=28%  Similarity=0.432  Sum_probs=39.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE   59 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~   59 (86)
                      ......||++|=+.|++.|..|+++   +-..=|..|+.||+-+|...|.
T Consensus       274 rd~l~~wsEeEcr~FEegl~~yGKD---F~lIr~nkvrtRsvgElVeyYY  320 (445)
T KOG4329|consen  274 RDDLSGWSEEECRNFEEGLELYGKD---FHLIRANKVRTRSVGELVEYYY  320 (445)
T ss_pred             ccccccCCHHHHHHHHHHHHHhccc---HHHHHhcccccchHHHHHHHHH
Confidence            3456789999999999999999875   4444477899999999998765

>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]

Probab=94.43  E-value=0.21  Score=40.10  Aligned_cols=59  Identities=24%  Similarity=0.454  Sum_probs=45.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCC------------CchHHHHHHHcC-----CCCHHHHHHHHHHHHH-HHhhhhc
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDT------------PDRWDNVAKAVS-----GKTVEDVKKHYELLVK-DINDIEA   70 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~------------~~rW~~IA~~vp-----gRT~~qc~~ry~~L~~-dv~~ie~   70 (86)
                      +.+.|+++=++.|.+||+.||+..            -+|=+.||.++.     .||.+||-.|-+.|.. .++.|.+
T Consensus        75 aegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~reiq~  151 (455)
T KOG3841|consen   75 AEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQA  151 (455)
T ss_pred             cccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHh
Confidence            567899999999999999998541            368899999984     4899999999887643 3334444

>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like

Probab=94.35  E-value=0.24  Score=38.86  Aligned_cols=55  Identities=13%  Similarity=0.312  Sum_probs=43.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      +...||..|.+.|.++|..........-..|++.|+||+..||++..+.|...|.
T Consensus        20 gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rva   74 (344)
T PF11035_consen   20 GPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVA   74 (344)
T ss_pred             CcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHH
Confidence            3468999999999999886533233456679999999999999998877765554

SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=93.57  E-value=0.37  Score=26.65  Aligned_cols=39  Identities=13%  Similarity=0.226  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        20 Edk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      =|..|..+|..-+.   .-|..||+.+ |-|...|..|.+.|.
T Consensus         4 ~D~~Il~~Lq~d~r---~s~~~la~~l-glS~~~v~~Ri~rL~   42 (42)
T PF13404_consen    4 LDRKILRLLQEDGR---RSYAELAEEL-GLSESTVRRRIRRLE   42 (42)
T ss_dssp             HHHHHHHHHHH-TT---S-HHHHHHHH-TS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCC---ccHHHHHHHH-CcCHHHHHHHHHHhC
Confidence            36677788777643   5799999999 699999999998873

...

>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats

Probab=93.12  E-value=0.18  Score=29.93  Aligned_cols=30  Identities=23%  Similarity=0.529  Sum_probs=24.7

Q ss_pred             chHHHHHHHcCC-CCHHHHHHHHHHHHHHHh
Q 034697           37 DRWDNVAKAVSG-KTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        37 ~rW~~IA~~vpg-RT~~qc~~ry~~L~~dv~   66 (86)
                      .-|..||..++. -++++|+.+|..|....+
T Consensus        27 ~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~   57 (85)
T PF10545_consen   27 EAWQEIARELGKEFSVDDCKKRWKNLRDRYR   57 (85)
T ss_pred             HHHHHHHHHHccchhHHHHHHHHHHHHHHHH
Confidence            569999999974 689999999998765443

The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.

>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]

Probab=91.89  E-value=0.13  Score=41.40  Aligned_cols=51  Identities=22%  Similarity=0.360  Sum_probs=41.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH-----cCC-CCHHHHHHHHHHHHHHHhhh
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKA-----VSG-KTVEDVKKHYELLVKDINDI   68 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~-----vpg-RT~~qc~~ry~~L~~dv~~i   68 (86)
                      +.||.+|-.-|-+....|..    ||--||..     .+. ||+++.++||......+.+.
T Consensus       131 n~WskeETD~LF~lck~fDL----Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kA  187 (445)
T KOG2656|consen  131 NSWSKEETDYLFDLCKRFDL----RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKA  187 (445)
T ss_pred             ccccHHHHHHHHHHHHhcCe----eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHc
Confidence            68999999999999999864    67777766     676 99999999998876666543

>smart00426 TEA TEA domain

Probab=91.32  E-value=0.4  Score=29.68  Aligned_cols=23  Identities=26%  Similarity=0.524  Sum_probs=20.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCC
Q 034697           12 SGSSWTVKQNKQFETALAFYDKD   34 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~   34 (86)
                      +...|..+=+..|++||..|++.
T Consensus         2 g~~vWp~~lE~Af~~aL~~~~~~   24 (68)
T smart00426        2 AEGVWSPDIEQAFQEALAIYPPC   24 (68)
T ss_pred             CCCcCcHHHHHHHHHHHHHcCcc
Confidence            45689999999999999999854

>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins

Probab=91.18  E-value=0.89  Score=29.37  Aligned_cols=54  Identities=9%  Similarity=0.119  Sum_probs=36.1

Q ss_pred             CCCCCHHHHHHHHHHHHhcCC--C--CCchHHHHHH----HcC-CCCHHHHHHHHHHHHHHHh
Q 034697           13 GSSWTVKQNKQFETALAFYDK--D--TPDRWDNVAK----AVS-GKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~--~--~~~rW~~IA~----~vp-gRT~~qc~~ry~~L~~dv~   66 (86)
                      ...||++++-.|.++|..|-.  |  ....|..+-.    .+. .=|..|+.+..+.|.....
T Consensus         4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~   66 (98)
T PF04504_consen    4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYR   66 (98)
T ss_pred             cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence            357999999999999999931  1  1234544444    443 2488898888777655544

>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator

Probab=90.05  E-value=0.53  Score=33.06  Aligned_cols=42  Identities=19%  Similarity=0.209  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      .||.|+...|.++..+     +-.=.+||..|||.|-..|+-+...|
T Consensus         2 ~Wtde~~~~L~~lw~~-----G~SasqIA~~lg~vsRnAViGk~hRl   43 (162)
T PF07750_consen    2 SWTDERVERLRKLWAE-----GLSASQIARQLGGVSRNAVIGKAHRL   43 (162)
T ss_pred             CCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCcchhhhhhhhhcc
Confidence            5999999988888654     34578999999989999999887765

These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=89.93  E-value=2.1  Score=23.57  Aligned_cols=44  Identities=9%  Similarity=0.225  Sum_probs=32.2

Q ss_pred             CHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           17 TVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        17 T~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      +++|.++|....  |   .+..+..||..+ |-|...|+.+....+..++
T Consensus         6 ~~~er~vi~~~y--~---~~~t~~eIa~~l-g~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    6 PPREREVIRLRY--F---EGLTLEEIAERL-GISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             -HHHHHHHHHHH--T---ST-SHHHHHHHH-TSCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHh--c---CCCCHHHHHHHH-CCcHHHHHHHHHHHHHHhc
Confidence            456666665554  2   235799999999 6999999999888777765

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=89.48  E-value=1.4  Score=29.93  Aligned_cols=42  Identities=14%  Similarity=0.194  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        19 eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      +-|..|..+|.+-+.   -.|..||+.+ |-|...|..|++.|.+.
T Consensus         9 ~~D~~Il~~Lq~d~R---~s~~eiA~~l-glS~~tV~~Ri~rL~~~   50 (153)
T PRK11179          9 NLDRGILEALMENAR---TPYAELAKQF-GVSPGTIHVRVEKMKQA   50 (153)
T ss_pred             HHHHHHHHHHHHcCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            467788888888653   4799999999 79999999999998754

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=88.57  E-value=2  Score=38.07  Aligned_cols=53  Identities=13%  Similarity=0.322  Sum_probs=44.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc------------CCCCHHHHHHHHHHHHHHHh
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV------------SGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v------------pgRT~~qc~~ry~~L~~dv~   66 (86)
                      .....+|.+||..|.-.+.+|+-+   +|++|-..+            ..||+.++..|...|+.-|.
T Consensus       924 ~~~~~~~~~~d~~~~~~~~~~g~~---~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~  988 (1033)
T PLN03142        924 NKGKLYNEECDRFMLCMVHKLGYG---NWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIE  988 (1033)
T ss_pred             CCCCcCCHHHHHHHHHHHHHhccc---hHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHH
Confidence            456689999999999999999754   699997665            57999999999998876664

>PF13325 MCRS_N: N-terminal region of micro-spherule protein

Probab=87.47  E-value=3.4  Score=30.23  Aligned_cols=55  Identities=9%  Similarity=0.225  Sum_probs=40.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc-----CCCCHHHHHHHHHHHHHH
Q 034697            9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV-----SGKTVEDVKKHYELLVKD   64 (86)
Q Consensus         9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v-----pgRT~~qc~~ry~~L~~d   64 (86)
                      +..+...||.+|+.+|........+ ....+++|=..=     ++||+++...||..+..-
T Consensus        69 ~iq~kalfS~~EE~lL~~v~s~~~p-~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy  128 (199)
T PF13325_consen   69 AIQSKALFSKEEEQLLGTVASSSQP-SLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQY  128 (199)
T ss_pred             cccccCCCCHHHHHHHHhhhhccCC-cHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHh
Confidence            4456789999999999997655533 346788775433     589999999999965433

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=87.42  E-value=1.9  Score=29.60  Aligned_cols=42  Identities=12%  Similarity=0.088  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        19 eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      +-|..+..+|.+-+.   -.|..||+.+ |-|...|..|+++|.+.
T Consensus        14 ~~D~~IL~~Lq~d~R---~s~~eiA~~l-glS~~tv~~Ri~rL~~~   55 (164)
T PRK11169         14 RIDRNILNELQKDGR---ISNVELSKRV-GLSPTPCLERVRRLERQ   55 (164)
T ss_pred             HHHHHHHHHhccCCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            446677778777543   4799999999 79999999999998754

>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]

Probab=87.35  E-value=0.8  Score=38.06  Aligned_cols=43  Identities=23%  Similarity=0.485  Sum_probs=35.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHH-HHHcCCCCHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNV-AKAVSGKTVEDVKKHYE   59 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~I-A~~vpgRT~~qc~~ry~   59 (86)
                      ...||..|--+||+||.+|+++    +..| +.++|=||...+.+.|.
T Consensus       285 mEEWSasEanLFEeALeKyGKD----FndIrqdfLPWKSl~sIveyYY  328 (693)
T KOG3554|consen  285 MEEWSASEANLFEEALEKYGKD----FNDIRQDFLPWKSLTSIVEYYY  328 (693)
T ss_pred             hhhccchhhHHHHHHHHHhccc----HHHHHHhhcchHHHHHHHHHHH
Confidence            4679999999999999999875    4455 66788899999988764

>PF13325 MCRS_N: N-terminal region of micro-spherule protein

Probab=86.01  E-value=1.8  Score=31.73  Aligned_cols=43  Identities=14%  Similarity=0.297  Sum_probs=37.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC---CCCHHHHHHHHHHHH
Q 034697           15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS---GKTVEDVKKHYELLV   62 (86)
Q Consensus        15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp---gRT~~qc~~ry~~L~   62 (86)
                      .|++.+|-+|..|+.+-     ..-+.|+..|+   .-|..++.+||..|.
T Consensus         1 rW~~~DDl~Li~av~~~-----~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll   46 (199)
T PF13325_consen    1 RWKPEDDLLLINAVEQT-----NDLESVHLGVKFSCKFTLQEIEERWYALL   46 (199)
T ss_pred             CCCchhhHHHHHHHHHh-----cCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence            59999999999999983     46888988886   479999999999864

>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids

Probab=84.37  E-value=2  Score=34.65  Aligned_cols=50  Identities=22%  Similarity=0.381  Sum_probs=34.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCC----------CchHHHHHHHcC-----CCCHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDT----------PDRWDNVAKAVS-----GKTVEDVKKHYELL   61 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~----------~~rW~~IA~~vp-----gRT~~qc~~ry~~L   61 (86)
                      +...|+.+=+..|++||+.||+..          -.|=+-||.+|-     .||.+||-.|.+.|
T Consensus        48 ~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl  112 (431)
T PF01285_consen   48 GEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL  112 (431)
T ss_dssp             GS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence            467899999999999999998652          234456777772     39999999999988

The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=83.76  E-value=3.6  Score=28.15  Aligned_cols=36  Identities=17%  Similarity=0.377  Sum_probs=28.6

Q ss_pred             hcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           30 FYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        30 ~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      .|......-|..||..+ ..+..+|+..+....++|.
T Consensus        93 ry~~r~~~TW~~IA~~l-~i~erta~r~~~~fK~~i~  128 (130)
T PF05263_consen   93 RYDRRSRRTWYQIAQKL-HISERTARRWRDRFKNDIY  128 (130)
T ss_pred             HHcccccchHHHHHHHh-CccHHHHHHHHHHHHHHhc
Confidence            34443456899999999 5999999998888887765

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF00046 Homeobox: Homeobox domain not present here

Probab=83.33  E-value=5.9  Score=22.01  Aligned_cols=50  Identities=20%  Similarity=0.229  Sum_probs=40.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK   63 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~   63 (86)
                      ...+|.++...|+......+--....-+.||..+ |-|..+|..=|.+-..
T Consensus         4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nrR~   53 (57)
T PF00046_consen    4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNRRR   53 (57)
T ss_dssp             SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHhHH
Confidence            3568999999999998876544567899999999 7999999887765443

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]

Probab=81.77  E-value=0.87  Score=37.44  Aligned_cols=47  Identities=26%  Similarity=0.376  Sum_probs=35.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv   65 (86)
                      -.||++|-.    ++.-|+- -...++.||..++.+|+.|++.+|..-..-|
T Consensus       471 ~~wSp~e~s----~ircf~~-y~~~fe~ia~l~~tktp~Q~~~fy~~n~k~i  517 (534)
T KOG1194|consen  471 YGWSPEEKS----AIRCFHW-YKDNFELIAELMATKTPEQIKKFYMDNEKLI  517 (534)
T ss_pred             CCCCCcccc----cccCchh-hccchHHHHHHhcCCCHHHHHHHhcCchhhh
Confidence            469999988    4444432 3467999999999999999999997644433

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=80.85  E-value=7.1  Score=24.32  Aligned_cols=42  Identities=17%  Similarity=0.192  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           19 KQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        19 eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      +.|..+..+|.+.+.   -.+..||+.+ |-+...|..|.+.|.+.
T Consensus         3 ~~D~~il~~L~~~~~---~~~~~la~~l-~~s~~tv~~~l~~L~~~   44 (108)
T smart00344        3 EIDRKILEELQKDAR---ISLAELAKKV-GLSPSTVHNRVKRLEEE   44 (108)
T ss_pred             HHHHHHHHHHHHhCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            456777788887653   4699999999 79999999999998764

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	86
2cjj_A	93	Crystal Structure Of The Myb Domain Of The Rad Tran		7e-22
4eef_G	74	Crystal Structure Of The Designed Inhibitor Protein		3e-09
2m2e_A	73	Solution Nmr Structure Of The Sant Domain Of Human		4e-05
2cqr_A	73	Solution Structure Of Rsgi Ruh-043, A Myb Dna-Bindi		3e-04

>pdb|2CJJ|A Chain A, Crystal Structure Of The Myb Domain Of The Rad Transcription Factor From Antirrhinum Majus Length = 93

Iteration: 1
 Score = 98.6 bits (244), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 45/66 (68%), Positives = 54/66 (81%)
Query: 18 VKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPN 77
           K+NK FE ALA YDKDTPDRW NVA+AV G+T E+VKKHYE+LV+DI  IE+G+ P PN
Sbjct: 13 AKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDIKYIESGKVPFPN 72
Query: 78 YRSTTG 83
          YR+T G
Sbjct: 73 YRTTGG 78

>pdb|4EEF|G Chain G, Crystal Structure Of The Designed Inhibitor Protein F-Hb80.4 In Complex With The 1918 Influenza Virus Hemagglutinin. Length = 74

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 32/41 (78%)
Query: 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          +N  FE AL+F +KDTPDRW  VA+ V G+T E+VKKHYEL
Sbjct: 27 ENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEEVKKHYEL 67

>pdb|2M2E|A Chain A, Solution Nmr Structure Of The Sant Domain Of Human Dnajc2, Northeast Structural Genomics Consortium Target Hr8254a Length = 73

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 32/53 (60%)
Query: 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGR 72
          + K  E AL  Y  +TP+RW  +A+AV G+T +D  K Y+ LV+ +   +A +
Sbjct: 10 EQKLLEQALKTYPVNTPERWKKIAEAVPGRTKKDCMKRYKELVEMVKAKKAAQ 62

>pdb|2CQR|A Chain A, Solution Structure Of Rsgi Ruh-043, A Myb Dna-Binding Domain In Human Cdna Length = 73

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 24/43 (55%)
Query: 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62
          Q K  E AL  Y + + D WD +A+ V  K+ ED    Y+LLV
Sbjct: 25 QQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLLV 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	86
2cjj_A	93	Radialis; plant development, DNA-binding protein,	1e-37
4eef_G	74	F-HB80.4, designed hemagglutinin binding protein;	1e-28
2cqr_A	73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	2e-23
2cqq_A	72	RSGI RUH-037, DNAJ homolog subfamily C member 1; m	4e-08
2yum_A	75	ZZZ3 protein, zinc finger ZZ-type-containing prote	4e-06
2ltp_A	89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	4e-06
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	6e-06
2yus_A	79	SWI/SNF-related matrix-associated actin- dependent	1e-05
2eqr_A	61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	2e-05
2cu7_A	72	KIAA1915 protein; nuclear protein, SANT domain, DN	6e-05
4a69_C	94	Nuclear receptor corepressor 2; transcription, hyd	8e-05
2iw5_B	235	Protein corest, REST corepressor 1; oxidoreductase	4e-04

>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription FA DNA-binding, nuclear protein, floral asymmetry; 1.9A {Antirrhinum majus} SCOP: a.4.1.3 Length = 93

 Score =  120 bits (302), Expect = 1e-37
 Identities = 51/81 (62%), Positives = 62/81 (76%)

Query: 6  MTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65
          M S+R SG  W+ K+NK FE ALA YDKDTPDRW NVA+AV G+T E+VKKHYE+LV+DI
Sbjct: 1  MASTRGSGRPWSAKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDI 60

Query: 66 NDIEAGRYPHPNYRSTTGTGN 86
            IE+G+ P PNYR+T G   
Sbjct: 61 KYIESGKVPFPNYRTTGGNMK 81

>4eef_G F-HB80.4, designed hemagglutinin binding protein; immunoglobulin, fusion of virus membrane with membrane, membrane fusion, sialic acid, virion; HET: NAG BMA; 2.70A {Artificial gene} Length = 74

 Score = 96.9 bits (241), Expect = 1e-28
 Identities = 32/64 (50%), Positives = 41/64 (64%)

Query: 3  SNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62
           + M S+R SG  W   +N  FE AL+F +KDTPDRW  VA+ V G+T E+VKKHYEL  
Sbjct: 10 GSHMASTRGSGRPWKFSENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEEVKKHYELEH 69

Query: 63 KDIN 66
             +
Sbjct: 70 HHHH 73

>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Length = 73

 Score = 83.8 bits (207), Expect = 2e-23
 Identities = 23/65 (35%), Positives = 32/65 (49%)

Query: 2  ASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61
           S     +RS+   WT  Q K  E AL  Y + + D WD +A+ V  K+ ED    Y+LL
Sbjct: 7  GSLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLL 66

Query: 62 VKDIN 66
          V   +
Sbjct: 67 VSGPS 71

>2cqq_A RSGI RUH-037, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Length = 72

 Score = 44.7 bits (105), Expect = 4e-08
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 8  SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND 67
          S  S    WT +   Q   ++  +   TP RW+ +A  + G++V DV    + L   +  
Sbjct: 3  SGSSGAPEWTEEDLSQLTRSMVKFPGGTPGRWEKIAHEL-GRSVTDVTTKAKQLKDSVTC 61

Query: 68 IEA 70
             
Sbjct: 62 SPG 64

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 39.6 bits (92), Expect = 4e-06
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 7  TSSRSSGSSWTVKQNKQFETALAFYDKDTPD--RWDNVAKAVSGKTVEDVKKHY 58
          +S  S    WTV++ K+ E  L  Y  +  +  RW  +A  +  +T + V    
Sbjct: 2  SSGSSGNQLWTVEEQKKLEQLLIKYPPEEVESRRWQKIADELGNRTAKQVASQV 55

>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens} Length = 89

 Score = 39.9 bits (93), Expect = 4e-06
 Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 4/59 (6%)

Query: 8  SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66
                  WT ++    +  L  + ++    W  +A+ V  KTV   K  Y    K  N
Sbjct: 11 RENLYFQGWTEEEMGTAKKGLLEHGRN----WSAIARMVGSKTVSQCKNFYFNYKKRQN 65

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 40.7 bits (94), Expect = 6e-06
 Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 9/36 (25%)

Query: 19 KQN-KQFETALAFYDKDT-PDRWDNVAKAVSGKTVE 52
          KQ  K+ + +L  Y  D+ P      A A+   T+E
Sbjct: 19 KQALKKLQASLKLYADDSAP------ALAIKA-TME 47

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens} Length = 79

 Score = 38.7 bits (90), Expect = 1e-05
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 7  TSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHY 58
          +   S+G  WT ++      AL  Y  D    W+ V++ V  +T ++   H+
Sbjct: 12 SKGASAGREWTEQETLLLLEALEMYKDD----WNKVSEHVGSRTQDECILHF 59

>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 61

 Score = 37.8 bits (88), Expect = 2e-05
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 4/57 (7%)

Query: 2  ASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHY 58
           S+  +  R   + WT  + + F+     + K+    +  +A  +  K+V D   +Y
Sbjct: 1  GSSGSSGDRQFMNVWTDHEKEIFKDKFIQHPKN----FGLIASYLERKSVPDCVLYY 53

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Length = 72

 Score = 36.7 bits (85), Expect = 6e-05
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 7  TSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHY 58
          + S      WT+++ + FE  LA + +     W  ++K +  +TV  VK + 
Sbjct: 3  SGSSGYSVKWTIEEKELFEQGLAKFGRR----WTKISKLIGSRTVLQVKSYA 50

>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A Length = 94

 Score = 36.8 bits (85), Expect = 8e-05
 Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHY 58
          R   + W+ ++ + F      + K+    +  +A  +  KTV +   +Y
Sbjct: 40 RQVMNMWSEQEKETFREKFMQHPKN----FGLIASFLERKTVAECVLYY 84

>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B* Length = 235

 Score = 35.9 bits (81), Expect = 4e-04
 Identities = 10/60 (16%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 7   TSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66
              +   + WT ++      A+  Y +D    +  ++  +  K+V  VK  +    +  N
Sbjct: 127 EVIQKCNARWTTEEQLLAVQAIRKYGRD----FQAISDVIGNKSVVQVKNFFVNYRRRFN 182

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	86
2cjj_A	93	Radialis; plant development, DNA-binding protein,	99.96
2cqq_A	72	RSGI RUH-037, DNAJ homolog subfamily C member 1; m	99.93
2cqr_A	73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	99.85
4eef_G	74	F-HB80.4, designed hemagglutinin binding protein;	99.84
1wgx_A	73	KIAA1903 protein; MYB DNA-binding domain, human cD	99.83
2yum_A	75	ZZZ3 protein, zinc finger ZZ-type-containing prote	99.73
1x41_A	60	Transcriptional adaptor 2-like, isoform B; transcr	99.69
2yus_A	79	SWI/SNF-related matrix-associated actin- dependent	99.69
2din_A	66	Cell division cycle 5-like protein; MYB_DNA-bindin	99.65
1guu_A	52	C-MYB, MYB proto-oncogene protein; transcription,	99.65
2d9a_A	60	B-MYB, MYB-related protein B; DNA binding, structu	99.64
2elk_A	58	SPCC24B10.08C protein; hypothetical protein, struc	99.64
2cu7_A	72	KIAA1915 protein; nuclear protein, SANT domain, DN	99.63
3sjm_A	64	Telomeric repeat-binding factor 2; human telomeric	99.62
1gvd_A	52	MYB proto-oncogene protein; transcription, transcr	99.61
2dim_A	70	Cell division cycle 5-like protein; MYB_DNA-bindin	99.58
1w0t_A	53	Telomeric repeat binding factor 1; telomere, DNA-b	99.58
1ity_A	69	TRF1; helix-turn-helix, telomeres, DNA binding, MY	99.54
2k9n_A	107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	99.48
2eqr_A	61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	99.46
2llk_A	73	Cyclin-D-binding MYB-like transcription factor 1;	99.45
2ltp_A	89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	99.16
1gv2_A	105	C-MYB, MYB proto-oncogene protein; transcription,	99.43
3osg_A	126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	99.43
2k9n_A	107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	99.43
1gv2_A	105	C-MYB, MYB proto-oncogene protein; transcription,	99.42
1h8a_C	128	AMV V-MYB, MYB transforming protein; transcription	99.4
3osg_A	126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	99.37
1h8a_C	128	AMV V-MYB, MYB transforming protein; transcription	99.35
3zqc_A	131	MYB3; transcription-DNA complex, DNA-binding prote	99.34
2ckx_A	83	NGTRF1, telomere binding protein TBP1; nuclear pro	99.33
3zqc_A	131	MYB3; transcription-DNA complex, DNA-binding prote	99.32
1h89_C	159	C-MYB, MYB proto-oncogene protein; transcription/D	99.26
1h89_C	159	C-MYB, MYB proto-oncogene protein; transcription/D	99.26
2aje_A	105	Telomere repeat-binding protein; DNA-binding, Trp,	99.18
2iw5_B	235	Protein corest, REST corepressor 1; oxidoreductase	99.17
2yqk_A	63	Arginine-glutamic acid dipeptide repeats protein;	99.14
2roh_A	122	RTBP1, telomere binding protein-1; plant, nucleus,	99.14
2crg_A	70	Metastasis associated protein MTA3; transcription	99.12
2juh_A	121	Telomere binding protein TBP1; helix, nucleus, nuc	99.11
1x58_A	62	Hypothetical protein 4930532D21RIK; MUS musculus a	99.09
1ign_A	246	Protein (RAP1); RAP1,yeast,telomeres,homoeodomain,	99.09
4a69_C	94	Nuclear receptor corepressor 2; transcription, hyd	98.97
2xag_B	482	REST corepressor 1; amine oxidase, chromatin regul	98.72
1ug2_A	95	2610100B20RIK gene product; hypothetical protein,	98.66
3hm5_A	93	DNA methyltransferase 1-associated protein 1; DNA	98.62
1fex_A	59	TRF2-interacting telomeric RAP1 protein; helix tur	98.54
2lr8_A	70	CAsp8-associated protein 2; structural genomics, n	97.82
1ofc_X	304	ISWI protein; nuclear protein, chromatin remodelin	98.26
2ebi_A	86	DNA binding protein GT-1; DNA-binding domain, phos	98.05
4iej_A	93	DNA methyltransferase 1-associated protein 1; DNA	97.93
1irz_A	64	ARR10-B; helix-turn-helix, DNA binding protein; NM	97.79
2xag_B	482	REST corepressor 1; amine oxidase, chromatin regul	97.65
4b4c_A	211	Chromodomain-helicase-DNA-binding protein 1; chrom	97.19
1ign_A	246	Protein (RAP1); RAP1,yeast,telomeres,homoeodomain,	97.03
1ofc_X	304	ISWI protein; nuclear protein, chromatin remodelin	96.88
2y9y_A	374	Imitation switch protein 1 (DEL_ATPase); transcrip	95.99
2y9y_A	374	Imitation switch protein 1 (DEL_ATPase); transcrip	95.73
4b4c_A	211	Chromodomain-helicase-DNA-binding protein 1; chrom	94.44
2xb0_X	270	Chromo domain-containing protein 1; hydrolase, DNA	92.62
2hzd_A	82	Transcriptional enhancer factor TEF-1; DNA-binding	89.57
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	86.19
2xb0_X	270	Chromo domain-containing protein 1; hydrolase, DNA	85.96
2cxy_A	125	BAF250B subunit, HBAF250B; DNA-binding domain, str	85.19
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	81.32

>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription FA DNA-binding, nuclear protein, floral asymmetry; 1.9A {Antirrhinum majus} SCOP: a.4.1.3

Probab=99.96  E-value=3.7e-29  Score=161.39  Aligned_cols=77  Identities=65%  Similarity=1.100  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCC
Q 034697            6 MTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYRSTT   82 (86)
Q Consensus         6 ~~~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g~v~~P~y~~~~   82 (86)
                      |+||.++...||.|||++|++||++|+.+.++||.+||++|||||++||++||+.|++||+.||+|.||+|.|..+|
T Consensus         1 ~~~~~~~~~~WT~eEd~~L~~al~~~~~~~~~rW~~IA~~vpGRT~~q~k~ry~~l~~dv~~iesg~vp~P~y~~~~   77 (93)
T 2cjj_A            1 MASTRGSGRPWSAKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDIKYIESGKVPFPNYRTTG   77 (93)
T ss_dssp             -------CCSCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHSTTCCHHHHHHHHHHHHHHHHHHHHSSCCC-------
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCC
Confidence            77888888999999999999999999988889999999999999999999999999999999999999999998765

>2cqq_A RSGI RUH-037, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=99.93  E-value=3.3e-26  Score=141.48  Aligned_cols=70  Identities=24%  Similarity=0.495  Sum_probs=64.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcCCCCCCCCC
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNYR   79 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g~v~~P~y~   79 (86)
                      +|+++...||.||+++|++||++||.++++||++||++| |||++||++||+.|++++ .|++|+||+|+|.
T Consensus         3 ~~~~~~~~WT~eE~k~fe~al~~~p~~t~~RW~~IA~~l-gRt~~eV~~~y~~L~~d~-~~~~G~vp~P~~~   72 (72)
T 2cqq_A            3 SGSSGAPEWTEEDLSQLTRSMVKFPGGTPGRWEKIAHEL-GRSVTDVTTKAKQLKDSV-TCSPGMVSGPSSG   72 (72)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHH-TSCHHHHHHHHHHHHHSC-CCCSCCCSCSCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCCcHHHHHHHHh-CCCHHHHHHHHHHHHHhc-CccCCCCCCCCCC
Confidence            455567799999999999999999999999999999999 899999999999999996 6899999999983

>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=99.85  E-value=1.6e-21  Score=120.74  Aligned_cols=62  Identities=35%  Similarity=0.598  Sum_probs=55.7

Q ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697            5 TMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus         5 ~~~~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      +..-+.++...||.+||++|+.||.+|+++.++||.+||++|||||++||++||+.|++|+.
T Consensus        10 ~~~~~~~~~~~WT~eEd~~L~~al~~~g~~~~~rW~~IA~~vpGRT~~qcr~Ry~~L~~d~~   71 (73)
T 2cqr_A           10 RKERARSAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLLVSGPS   71 (73)
T ss_dssp             CCCTTTCSSCCCCHHHHHHHHHHHHHSCSSSHHHHHHHGGGCSSSCHHHHHHHHHHHHSSCC
T ss_pred             cccccccCCCCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHccc
Confidence            34445667789999999999999999998778999999999999999999999999998864

>4eef_G F-HB80.4, designed hemagglutinin binding protein; immunoglobulin, fusion of virus membrane with membrane, membrane fusion, sialic acid, virion; HET: NAG BMA; 2.70A {Artificial gene}

Probab=99.84  E-value=1e-22  Score=126.64  Aligned_cols=56  Identities=55%  Similarity=0.956  Sum_probs=44.2

Q ss_pred             CcCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697            4 NTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE   59 (86)
Q Consensus         4 ~~~~~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~   59 (86)
                      .+|.||+.+...||.+|+++||+||++||+++++||++||++|||||++||+.||.
T Consensus        11 ~~m~s~~~ss~~WT~eE~K~FE~ALa~yp~~tpdRWekIA~~VpGKT~eEVk~hY~   66 (74)
T 4eef_G           11 SHMASTRGSGRPWKFSENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEEVKKHYE   66 (74)
T ss_dssp             -----------CCCTTHHHHHHHHTSSSCSSCCSSSTTTGGGSCSSCHHHHHGGGC
T ss_pred             ceeccCCCCCCCCCHHHHHHHHHHHHHCCCCCCcHHHHHHHHcCCCCHHHHHHHHH
Confidence            57999998999999999999999999999999999999999999999999999996

>1wgx_A KIAA1903 protein; MYB DNA-binding domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=99.83  E-value=5.7e-21  Score=118.58  Aligned_cols=57  Identities=25%  Similarity=0.436  Sum_probs=51.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      .+....||.+|+++|++||+.|+.++++||++||++|||||++||+.||..|.++..
T Consensus         5 ~~~~~~WT~eE~k~fe~ALa~~~~~tp~rWe~IA~~V~gKT~eE~~~hY~~l~~~~~   61 (73)
T 1wgx_A            5 SSGDKEWNEKELQKLHCAFASLPKHKPGFWSEVAAAVGSRSPEECQRKYMENPRGKG   61 (73)
T ss_dssp             CCSSSCCCHHHHHHHHHHHHHSCSSSSSHHHHHHHHTTTSCHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCccHHHHHHHHcCCCCHHHHHHHHHHHHhccc
Confidence            344568999999999999999999999999999999999999999999999855543

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.7e-17  Score=101.46  Aligned_cols=66  Identities=24%  Similarity=0.484  Sum_probs=53.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCC--CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcCCCCCCCC
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDT--PDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPNY   78 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~--~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g~v~~P~y   78 (86)
                      ......||.|||++|+++|.+|+.+.  +.+|.+||++|||||..||++||.+++..+  +..| +++|.+
T Consensus         5 ~~~~~~WT~eEd~~L~~~v~~~g~~~~~~~~W~~IA~~~~~Rt~~qcr~r~~~~l~~~--~k~g-~~~pg~   72 (75)
T 2yum_A            5 SSGNQLWTVEEQKKLEQLLIKYPPEEVESRRWQKIADELGNRTAKQVASQVQKYFIKL--TKAG-IPVSGP   72 (75)
T ss_dssp             CCCSSCCCHHHHHHHHHHHHHSCCCSCHHHHHHHHHHHHSSSCHHHHHHHHHHHHGGG--STTC-SCCCCS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCHHHHHHHHHHHHHHH--HhcC-CCCCCC
Confidence            44567999999999999999998643  279999999999999999999997766553  3455 467765

>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.69  E-value=5.8e-17  Score=95.82  Aligned_cols=52  Identities=29%  Similarity=0.454  Sum_probs=45.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      +.+.....||.|||++|++++.+|+.   .+|.+||+.|||||..||++||..++
T Consensus         3 s~~~~~~~WT~eED~~L~~~v~~~G~---~~W~~Ia~~~~~Rt~~qcr~r~~~~l   54 (60)
T 1x41_A            3 SGSSGDPSWTAQEEMALLEAVMDCGF---GNWQDVANQMCTKTKEECEKHYMKYF   54 (60)
T ss_dssp             CCCCCCSSSCHHHHHHHHHHHHHTCT---TCHHHHHHHHTTSCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCc---CcHHHHHHHhCCCCHHHHHHHHHHHc
Confidence            33456789999999999999999974   48999999999999999999998764

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens}

Probab=99.69  E-value=9.5e-18  Score=104.83  Aligned_cols=61  Identities=25%  Similarity=0.470  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH-HHHHhhhhcCC
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL-VKDINDIEAGR   72 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L-~~dv~~ie~g~   72 (86)
                      ........||.|||++|++||.+|+    ++|.+||++|||||..||+.||..+ ++|+..++++-
T Consensus        13 ~~~~~~~~WT~eEd~~Ll~~v~~~G----~~W~~IA~~v~~RT~~qcr~r~~~~~i~d~~~~~~~~   74 (79)
T 2yus_A           13 KGASAGREWTEQETLLLLEALEMYK----DDWNKVSEHVGSRTQDECILHFLRLPIEDPYLENSDS   74 (79)
T ss_dssp             CSSCCSCCCCHHHHHHHHHHHHHSS----SCHHHHHHHHSSCCHHHHHHHHTTSCCCCSSCCCCCC
T ss_pred             cccccCCCcCHHHHHHHHHHHHHhC----CCHHHHHHHcCCCCHHHHHHHHHHhcccccccccCCC
Confidence            3445578999999999999999997    4899999999999999999999987 78877776653

>2din_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.9e-16  Score=93.48  Aligned_cols=57  Identities=18%  Similarity=0.506  Sum_probs=51.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcC
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAG   71 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g   71 (86)
                      ......||.|||++|..++..|+    .+|.+||+ ++|||..||++||..++.....+++|
T Consensus         6 ~~~k~~WT~eED~~L~~~~~~~g----~~W~~Ia~-~~gRt~~qcr~Rw~~~l~~~~~~~~~   62 (66)
T 2din_A            6 SGKKTEWSREEEEKLLHLAKLMP----TQWRTIAP-IIGRTAAQCLEHYEFLLDKAAQRDSG   62 (66)
T ss_dssp             SSSCCCCCHHHHHHHHHHHHHCT----TCHHHHHH-HHSSCHHHHHHHHHHHHHHHHHSSSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcC----CCHHHHhc-ccCcCHHHHHHHHHHHhChHhcCCCC
Confidence            34567999999999999999986    38999999 88999999999999999998888876

>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A

Probab=99.65  E-value=3.9e-16  Score=89.38  Aligned_cols=47  Identities=13%  Similarity=0.410  Sum_probs=43.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      .+.||.|||.+|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus         3 ~~~Wt~eED~~L~~~v~~~G~---~~W~~Ia~~~~~Rt~~qcr~Rw~~~L   49 (52)
T 1guu_A            3 KTRWTREEDEKLKKLVEQNGT---DDWKVIANYLPNRTDVQCQHRWQKVL   49 (52)
T ss_dssp             CCCCCHHHHHHHHHHHHHHCS---SCHHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhCC---CCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence            568999999999999999974   37999999999999999999998865

>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=4.3e-16  Score=91.65  Aligned_cols=52  Identities=15%  Similarity=0.373  Sum_probs=45.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      +.......||.|||++|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus         3 ~p~~~k~~Wt~eED~~L~~~v~~~G~---~~W~~Ia~~~~~Rt~~qcr~Rw~~~l   54 (60)
T 2d9a_A            3 SGSSGKVKWTHEEDEQLRALVRQFGQ---QDWKFLASHFPNRTDQQCQYRWLRVL   54 (60)
T ss_dssp             SCCCCCSCCCHHHHHHHHHHHHHTCT---TCHHHHHHHCSSSCHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHhCC---CCHHHHHHHccCCCHHHHHHHHHHHc
Confidence            34456789999999999999999963   47999999999999999999998754

>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe}

Probab=99.64  E-value=4.9e-16  Score=91.46  Aligned_cols=46  Identities=20%  Similarity=0.400  Sum_probs=42.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELL   61 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L   61 (86)
                      ...||.+||++|.+++.+|+.   .+|..||+.|| |||+.||++||..+
T Consensus         9 ~~~WT~eED~~L~~~v~~~G~---~~W~~IA~~~~~~Rt~~qcr~r~~~~   55 (58)
T 2elk_A            9 DENWGADEELLLIDACETLGL---GNWADIADYVGNARTKEECRDHYLKT   55 (58)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTT---TCHHHHHHHHCSSCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHCc---CCHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            568999999999999999974   48999999999 99999999999875

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3

Probab=99.63  E-value=8.3e-16  Score=93.60  Aligned_cols=54  Identities=28%  Similarity=0.519  Sum_probs=47.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697            9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus         9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      .......||.|||.+|+.++.+|+.    +|..||++|||||..||++||..++....
T Consensus         5 p~~~~~~WT~eEd~~l~~~~~~~G~----~W~~Ia~~~~~Rt~~q~k~r~~~~l~~~~   58 (72)
T 2cu7_A            5 SSGYSVKWTIEEKELFEQGLAKFGR----RWTKISKLIGSRTVLQVKSYARQYFKNKV   58 (72)
T ss_dssp             CSSCCCCCCHHHHHHHHHHHHHTCS----CHHHHHHHHSSSCHHHHHHHHHHHHHHHS
T ss_pred             CCcCCCCCCHHHHHHHHHHHHHHCc----CHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            3446789999999999999999964    89999999999999999999998876644

>3sjm_A Telomeric repeat-binding factor 2; human telomeric repeat binding protein 2, telomere, telomeri homeodomain proteins amino acid sequence; HET: DNA; 1.35A {Homo sapiens} PDB: 1xg1_A 1vfc_A 1vf9_A 1w0u_A

Probab=99.62  E-value=1.4e-15  Score=91.46  Aligned_cols=55  Identities=18%  Similarity=0.458  Sum_probs=44.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC--CCCHHHHHHHHHHHHH
Q 034697            6 MTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS--GKTVEDVKKHYELLVK   63 (86)
Q Consensus         6 ~~~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp--gRT~~qc~~ry~~L~~   63 (86)
                      |++..+....||+|||++|..+|.+|+.+   +|..||+.+|  |||..||++||..|..
T Consensus         4 ~~~~~~kk~~WT~eED~~L~~~V~~~G~~---~W~~Ia~~~~~~~Rt~~qcr~Rw~nl~k   60 (64)
T 3sjm_A            4 MTTNITKKQKWTVEESEWVKAGVQKYGEG---NWAAISKNYPFVNRTAVMIKDRWRTMKR   60 (64)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHHCTT---CHHHHHHHSCCSSCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCC---chHHHHhhcCCCCCCHHHHHHHHHHHhc
Confidence            45555667899999999999999999743   7999999987  9999999999998753

>1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} SCOP: a.4.1.3 PDB: 1gv5_A 1mbg_A 1mbh_A

Probab=99.61  E-value=7e-16  Score=88.42  Aligned_cols=47  Identities=17%  Similarity=0.480  Sum_probs=42.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      .+.||.|||.+|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus         3 k~~Wt~eED~~L~~~v~~~G~---~~W~~Ia~~~~~Rt~~qcr~Rw~~~L   49 (52)
T 1gvd_A            3 KGPWTKEEDQRLIKLVQKYGP---KRWSVIAKHLKGRIGKQCRERWHNHL   49 (52)
T ss_dssp             CCSCCHHHHHHHHHHHHHHCT---TCHHHHHTTSTTCCHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHHCc---ChHHHHHHHcCCCCHHHHHHHHHHHc
Confidence            568999999999999999974   37999999999999999999998753

>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=3.4e-15  Score=90.25  Aligned_cols=50  Identities=18%  Similarity=0.469  Sum_probs=44.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ......||.|||++|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus         6 ~~k~~~Wt~eED~~L~~~v~~~G~---~~W~~Ia~~l~~Rt~~qcr~Rw~~~L   55 (70)
T 2dim_A            6 SGKGGVWRNTEDEILKAAVMKYGK---NQWSRIASLLHRKSAKQCKARWYEWL   55 (70)
T ss_dssp             CSTTCCCCHHHHHHHHHHHHHTCS---SCHHHHHHHSTTCCHHHHHHHHHHTS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCc---CCHHHHHHHhcCCCHHHHHHHHHHHc
Confidence            335679999999999999999973   48999999999999999999998754

>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A

Probab=99.58  E-value=5e-15  Score=85.33  Aligned_cols=47  Identities=13%  Similarity=0.391  Sum_probs=43.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC--CCCHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS--GKTVEDVKKHYELLV   62 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp--gRT~~qc~~ry~~L~   62 (86)
                      ...||+|||.+|..++.+|+.   .+|..||+.||  |||..||++||..++
T Consensus         2 r~~WT~eEd~~L~~~v~~~G~---~~W~~Ia~~~~~~~Rt~~qcr~Rw~~~~   50 (53)
T 1w0t_A            2 RQAWLWEEDKNLRSGVRKYGE---GNWSKILLHYKFNNRTSVMLKDRWRTMK   50 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHHCT---TCHHHHHHHSCCSSCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHCc---CCHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence            468999999999999999974   48999999999  999999999999875

>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A

Probab=99.54  E-value=2.5e-14  Score=86.26  Aligned_cols=51  Identities=14%  Similarity=0.377  Sum_probs=45.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC--CCCHHHHHHHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS--GKTVEDVKKHYELLVK   63 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp--gRT~~qc~~ry~~L~~   63 (86)
                      ......||.|||.+|..++.+|+.   .+|..||+.||  |||..||++||..++.
T Consensus         7 ~~~r~~WT~eED~~L~~~v~~~G~---~~W~~Ia~~~~~~~Rt~~qcr~Rw~~~l~   59 (69)
T 1ity_A            7 ARKRQAWLWEEDKNLRSGVRKYGE---GNWSKILLHYKFNNRTSVMLKDRWRTMKK   59 (69)
T ss_dssp             SSSCCCCCHHHHHHHHHHHHHHCS---SCHHHHHHHSCCSSCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCC---CcHHHHHHHcCcCCCCHHHHHHHHHHHcC
Confidence            345679999999999999999974   48999999999  9999999999987654

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A

Probab=99.48  E-value=1.2e-13  Score=89.01  Aligned_cols=53  Identities=9%  Similarity=0.448  Sum_probs=47.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      ...++||.|||.+|..++.+|+    .+|..||+.|||||..||++||..|...+..
T Consensus        51 i~~~~WT~eEd~~L~~~~~~~G----~~W~~Ia~~l~gRt~~~~k~rw~~l~r~~~~  103 (107)
T 2k9n_A           51 LRTDPWSPEEDMLLDQKYAEYG----PKWNKISKFLKNRSDNNIRNRWMMIARHRAK  103 (107)
T ss_dssp             CTTCCCCHHHHHHHHHHHHHTC----SCHHHHHHHHSSSCHHHHHHHHHHHHHHHHS
T ss_pred             ccccccCHHHHHHHHHHHHHhC----cCHHHHHHHCCCCCHHHHHHHHHHHHhhHHH
Confidence            3567999999999999999996    3799999999999999999999998877654

>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=2.8e-13  Score=80.35  Aligned_cols=45  Identities=22%  Similarity=0.278  Sum_probs=41.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      ....||++|+++|++++.+||+    +|.+||..|||||+.||+.+|..
T Consensus        11 ~~~~WT~eE~~~F~~~~~~~gk----~w~~Ia~~l~~rt~~~~v~~Yy~   55 (61)
T 2eqr_A           11 FMNVWTDHEKEIFKDKFIQHPK----NFGLIASYLERKSVPDCVLYYYL   55 (61)
T ss_dssp             CCCSCCHHHHHHHHHHHHHSTT----CHHHHHHHCTTSCHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHhCC----CHHHHHHHcCCCCHHHHHHHHHH
Confidence            5689999999999999999974    69999999999999999999864

>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle, SGC, structural genomics consortium, NESG, NOR structural genomics consortium; NMR {Homo sapiens}

Probab=99.45  E-value=1.1e-13  Score=85.43  Aligned_cols=51  Identities=16%  Similarity=0.337  Sum_probs=44.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697            9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus         9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      .....++||+|||++|.+++.+|+.    +|..||+.| |||..||++||..|..+
T Consensus        19 P~i~k~~wT~EED~~L~~l~~~~G~----kW~~IA~~l-gRt~~q~knRw~~L~~~   69 (73)
T 2llk_A           19 DRNHVGKYTPEEIEKLKELRIKHGN----DWATIGAAL-GRSASSVKDRCRLMKDT   69 (73)
T ss_dssp             CCCCCCSSCHHHHHHHHHHHHHHSS----CHHHHHHHH-TSCHHHHHHHHHHCSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCC----CHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence            3456789999999999999999963    599999999 99999999999977543

>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens}

Probab=99.16  E-value=9.1e-15  Score=92.61  Aligned_cols=54  Identities=22%  Similarity=0.284  Sum_probs=46.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv   65 (86)
                      +.....+.||.|||.+|..++.+|+.    +|..||.+|||||..||++||..++..+
T Consensus        11 ~p~~~~~~WT~eEd~~l~~~~~~~G~----~W~~IA~~l~gRt~~q~k~r~~~~lrk~   64 (89)
T 2ltp_A           11 RENLYFQGWTEEEMGTAKKGLLEHGR----NWSAIARMVGSKTVSQCKNFYFNYKKRQ   64 (89)
Confidence            33445789999999999999999963    7999999999999999999998765543

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A

Probab=99.43  E-value=2.1e-13  Score=87.17  Aligned_cols=49  Identities=24%  Similarity=0.529  Sum_probs=44.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVK   63 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~   63 (86)
                      ...++||.|||.+|..++.+|+    .+|..||++|||||..||++||..++.
T Consensus        54 ~~~~~Wt~eEd~~L~~~~~~~G----~~W~~Ia~~l~gRt~~~~k~rw~~~~~  102 (105)
T 1gv2_A           54 VKKTSWTEEEDRIIYQAHKRLG----NRWAEIAKLLPGRTDNAIKNHWNSTMR  102 (105)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHS----SCHHHHHTTCTTCCHHHHHHHHHHHTC
T ss_pred             ccccCCCHHHHHHHHHHHHHhC----CCHHHHHHHcCCCCHHHHHHHHHHHHh
Confidence            4567999999999999999996    479999999999999999999997653

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A

Probab=99.43  E-value=3e-13  Score=89.48  Aligned_cols=52  Identities=19%  Similarity=0.436  Sum_probs=47.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      ...+.||.|||++|..++.+|+    .+|..||+.|||||..||++||..|...+.
T Consensus        60 ~~~~~WT~eEd~~L~~~v~~~G----~~W~~Ia~~l~gRt~~~~k~rw~~l~~k~~  111 (126)
T 3osg_A           60 ISHTPWTAEEDALLVQKIQEYG----RQWAIIAKFFPGRTDIHIKNRWVTISNKLG  111 (126)
T ss_dssp             SCCSCCCHHHHHHHHHHHHHHC----SCHHHHHTTSTTCCHHHHHHHHHHHHHHTT
T ss_pred             cccccCCHHHHHHHHHHHHHHC----cCHHHHHHHcCCCCHHHHHHHHHHHHHhcC
Confidence            3467999999999999999996    479999999999999999999999988755

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A

Probab=99.43  E-value=2.3e-13  Score=87.78  Aligned_cols=46  Identities=7%  Similarity=0.307  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      +.||.|||.+|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus         2 ~~Wt~eED~~L~~~v~~~g~---~~W~~Ia~~~~~Rt~~qcr~Rw~~~L   47 (107)
T 2k9n_A            2 VKFTEEEDLKLQQLVMRYGA---KDWIRISQLMITRNPRQCRERWNNYI   47 (107)
T ss_dssp             CSSCHHHHHHHHHHHHHHCS---SCHHHHHHHTTTSCHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHHHHCC---CCHHHHhhhcCCCCHHHHHHHHHHHH
Confidence            58999999999999999974   47999999999999999999998753

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A

Probab=99.42  E-value=1.9e-13  Score=87.42  Aligned_cols=47  Identities=17%  Similarity=0.441  Sum_probs=42.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      ..+.||.|||++|..++.+|+.   .+|..||+.|||||..||++||..+
T Consensus         3 ~k~~WT~eED~~L~~~v~~~g~---~~W~~Ia~~l~~Rt~~qcr~Rw~~~   49 (105)
T 1gv2_A            3 IKGPWTKEEDQRVIKLVQKYGP---KRWSVIAKHLKGRIGKQCRERWHNH   49 (105)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHCT---TCHHHHHTTSTTCCHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHhCC---CcHHHHhhhhcCCCHHHHHHHHHhc
Confidence            3578999999999999999974   4799999999999999999999874

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3

Probab=99.40  E-value=4.9e-13  Score=88.33  Aligned_cols=50  Identities=16%  Similarity=0.464  Sum_probs=44.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ....+.||.|||++|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus        24 ~~~k~~Wt~eED~~L~~~v~~~g~---~~W~~Ia~~l~~Rt~~qcr~Rw~~~l   73 (128)
T 1h8a_C           24 ELNKGPWTKEEDQRVIEHVQKYGP---KRWSDIAKHLKGRIGKQCRERWHNHL   73 (128)
T ss_dssp             TCCCSCCCHHHHHHHHHHHHHTCS---CCHHHHHHHSSSCCHHHHHHHHHHTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCC---CCHHHHHHHhcCCcHHHHHHHHHHhc
Confidence            345689999999999999999974   47999999999999999999998743

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A

Probab=99.37  E-value=9e-13  Score=87.20  Aligned_cols=50  Identities=10%  Similarity=0.307  Sum_probs=44.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697            9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus         9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      .....+.||.|||++|..++.+|+.    +|..||+.|||||..||++||..++
T Consensus         7 ~~~kk~~WT~eED~~L~~~v~~~G~----~W~~Ia~~~~~Rt~~qcr~Rw~~~l   56 (126)
T 3osg_A            7 KAAKKQKFTPEEDEMLKRAVAQHGS----DWKMIAATFPNRNARQCRDRWKNYL   56 (126)
T ss_dssp             CBCSSCCCCHHHHHHHHHHHHHHTT----CHHHHHHTCTTCCHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhCC----CHHHHHHHcCCCCHHHHHHHHhhhc
Confidence            3445689999999999999999963    7999999999999999999998753

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3

Probab=99.35  E-value=8.5e-13  Score=87.16  Aligned_cols=48  Identities=27%  Similarity=0.523  Sum_probs=43.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ...++||.|||.+|..++.+|+    .+|..||+.|||||..||++||..++
T Consensus        77 ~~~~~WT~eEd~~L~~~~~~~G----~~W~~Ia~~l~gRt~~~~k~r~~~~~  124 (128)
T 1h8a_C           77 VKKTSWTEEEDRIIYQAHKRLG----NRWAEIAKLLPGRTDNAVKNHWNSTM  124 (128)
T ss_dssp             SCCSCCCHHHHHHHHHHHHHHC----SCHHHHGGGSTTCCHHHHHHHHHTTT
T ss_pred             cccccCCHHHHHHHHHHHHHHC----cCHHHHHHHCCCCCHHHHHHHHHHHH
Confidence            3567999999999999999996    47999999999999999999998764

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}

Probab=99.34  E-value=5.3e-13  Score=88.69  Aligned_cols=46  Identities=4%  Similarity=0.200  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      +.||.|||++|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus         3 g~Wt~eED~~L~~~v~~~g~---~~W~~Ia~~~~~Rt~~qcr~Rw~~~l   48 (131)
T 3zqc_A            3 GPFTEAEDDLIREYVKENGP---QNWPRITSFLPNRSPKQCRERWFNHL   48 (131)
T ss_dssp             SSCCHHHHHHHHHHHHHHCS---CCGGGGTTSCTTSCHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhCc---CCHHHHHHHHCCCCHHHHHHHHhhcc
Confidence            68999999999999999974   47999999999999999999997653

>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A

Probab=99.33  E-value=3.2e-12  Score=80.50  Aligned_cols=48  Identities=21%  Similarity=0.412  Sum_probs=43.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH----cCCCCHHHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKA----VSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~----vpgRT~~qc~~ry~~L~~d   64 (86)
                      .+||.|||..|..++.+|+.+   +|..|++.    ++|||..||++||..++..
T Consensus         1 r~WT~eEd~~L~~gv~k~G~g---~W~~I~~~~~~~~~~RT~~~lKdrWrnllk~   52 (83)
T 2ckx_A            1 RPFSVAEVEALVEAVEHLGTG---RWRDVKMRAFDNADHRTYVDLKDKWKTLVHT   52 (83)
T ss_dssp             CCCCHHHHHHHHHHHHHHCSS---CHHHHHHHHCTTCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCCC---CcHHHHHhhccccCCCCHHHHHHHHHHHHHh
Confidence            379999999999999999754   89999996    8999999999999998753

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}

Probab=99.32  E-value=2.9e-12  Score=85.10  Aligned_cols=52  Identities=15%  Similarity=0.350  Sum_probs=45.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      ...+.||.|||.+|..++.+|+    .+|..||+.|||||..||++||..++....
T Consensus        52 ~~~~~Wt~eEd~~L~~~~~~~G----~~W~~Ia~~l~gRt~~~~k~rw~~~l~~~~  103 (131)
T 3zqc_A           52 VVKHAWTPEEDETIFRNYLKLG----SKWSVIAKLIPGRTDNAIKNRWNSSISKRI  103 (131)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHSC----SCHHHHTTTSTTCCHHHHHHHHHHTTGGGC
T ss_pred             ccCCCCCHHHHHHHHHHHHHHC----cCHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence            3457899999999999999996    479999999999999999999998765543

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C

Probab=99.26  E-value=8e-12  Score=84.97  Aligned_cols=49  Identities=16%  Similarity=0.421  Sum_probs=43.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ...++||.|||.+|..++.+|+.   .+|..||+.|||||..||++||..++
T Consensus        56 ~~~~~Wt~eEd~~L~~~v~~~g~---~~W~~Ia~~l~~Rt~~qcr~Rw~~~l  104 (159)
T 1h89_C           56 LIKGPWTKEEDQRVIKLVQKYGP---KRWSVIAKHLKGRIGKQCRERWHNHL  104 (159)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHCS---CCHHHHHHTSTTCCHHHHHHHHHHTT
T ss_pred             cCCCCCChHHHHHHHHHHHHhCc---ccHHHHHHHcCCCCHHHHHHHHHHHh
Confidence            35689999999999999999974   47999999999999999999998743

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C

Probab=99.26  E-value=5.1e-12  Score=85.97  Aligned_cols=48  Identities=25%  Similarity=0.521  Sum_probs=43.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ....+||.+||.+|..++.+|+    .+|..||++|||||..||++||..++
T Consensus       108 ~~~~~WT~eEd~~L~~~~~~~g----~~W~~Ia~~l~gRt~~~~knr~~~~~  155 (159)
T 1h89_C          108 VKKTSWTEEEDRIIYQAHKRLG----NRWAEIAKLLPGRTDNAIKNHWNSTM  155 (159)
T ss_dssp             SCCSCCCHHHHHHHHHHHHHHC----SCHHHHHTTSTTCCHHHHHHHHHTTT
T ss_pred             ccccCCChHHHHHHHHHHHHHC----CCHHHHHHHCCCCCHHHHHHHHHHHH
Confidence            4567999999999999999996    47999999999999999999998764

>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3

Probab=99.18  E-value=5.3e-11  Score=77.88  Aligned_cols=52  Identities=21%  Similarity=0.376  Sum_probs=46.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc----CCCCHHHHHHHHHHHHH
Q 034697            9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV----SGKTVEDVKKHYELLVK   63 (86)
Q Consensus         9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v----pgRT~~qc~~ry~~L~~   63 (86)
                      ..-...+||.|||..|..++.+|+.+   +|..|++.+    +|||..+|++||..|+.
T Consensus         9 ~rr~r~~WT~EEd~~L~~gV~k~G~g---~W~~I~~~~~~~f~~RT~v~lKdrWrnllk   64 (105)
T 2aje_A            9 QRRIRRPFSVAEVEALVQAVEKLGTG---RWRDVKLCAFEDADHRTYVDLKDKWKTLVH   64 (105)
T ss_dssp             CCCCCCSCCHHHHHHHHHHHHHHCSS---SHHHHHSSSSSSTTCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhCCC---ChHHHHHHhccccCCCCHHHHHHHHHHHHh
Confidence            34457899999999999999999754   899999976    89999999999999884

>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B*

Probab=99.17  E-value=9.4e-11  Score=85.78  Aligned_cols=50  Identities=16%  Similarity=0.345  Sum_probs=44.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697            7 TSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus         7 ~~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      ..+......||.||.++|++||.+|++    +|..||+.|||||+.||+.+|..
T Consensus       127 e~~~k~s~~WTeEE~~lFleAl~kYGK----DW~~IAk~VgTKT~~QcKnfY~~  176 (235)
T 2iw5_B          127 EVIQKCNARWTTEEQLLAVQAIRKYGR----DFQAISDVIGNKSVVQVKNFFVN  176 (235)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHHSS----CHHHHHHHHSSCCHHHHHHHHHH
T ss_pred             CCCCccCCCCCHHHHHHHHHHHHHHCc----CHHHHHHHcCCCCHHHHHHHHHH
Confidence            334455779999999999999999975    59999999999999999999975

>2yqk_A Arginine-glutamic acid dipeptide repeats protein; structure genomics, SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.14  E-value=1.4e-10  Score=69.16  Aligned_cols=46  Identities=22%  Similarity=0.374  Sum_probs=41.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHH-HcCCCCHHHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAK-AVSGKTVEDVKKHYE   59 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~-~vpgRT~~qc~~ry~   59 (86)
                      ......||++|.++|+++|.+|++    .|.+||+ .||+||..||...|.
T Consensus         6 ~~~~~~WT~eE~~~Fe~~l~~yGK----df~~I~~~~v~~Kt~~~~v~fYY   52 (63)
T 2yqk_A            6 SGIEKCWTEDEVKRFVKGLRQYGK----NFFRIRKELLPNKETGELITFYY   52 (63)
T ss_dssp             CCCCCSCCHHHHHHHHHHHHHTCS----CHHHHHHHSCTTSCHHHHHHHHH
T ss_pred             CcCCCCcCHHHHHHHHHHHHHhCc----cHHHHHHHHcCCCcHHHHHHHHh
Confidence            345679999999999999999986    4999999 599999999999885

>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa}

Probab=99.14  E-value=1.4e-10  Score=77.74  Aligned_cols=49  Identities=22%  Similarity=0.365  Sum_probs=44.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc----CCCCHHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV----SGKTVEDVKKHYELLVK   63 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v----pgRT~~qc~~ry~~L~~   63 (86)
                      ....||.|||..|.+++.+|+.+   +|..|++..    +|||..||++||..++.
T Consensus        30 ~r~~WT~EEd~~L~~gV~k~G~g---~W~~I~~~~~~~~~~RT~vdlKdRWrnllk   82 (122)
T 2roh_A           30 IRRPFTVAEVELLVEAVEHLGTG---RWRDVKFRAFENVHHRTYVDLKDKWKTLVH   82 (122)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHSSS---CHHHHHHHHHSSSCCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCC---ChHHHHHHhccccCCCCHHHHHHHHHHHHh
Confidence            46789999999999999999754   899999985    89999999999999874

>2crg_A Metastasis associated protein MTA3; transcription factor, helix turn helix, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.3

Probab=99.12  E-value=2e-10  Score=69.85  Aligned_cols=47  Identities=21%  Similarity=0.405  Sum_probs=42.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHH-HcCCCCHHHHHHHHH
Q 034697            9 SRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAK-AVSGKTVEDVKKHYE   59 (86)
Q Consensus         9 ~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~-~vpgRT~~qc~~ry~   59 (86)
                      +......||++|.++|+++|.+|++    .|..|++ .||+||+.||...|.
T Consensus         4 ~r~~~~~WT~eE~~~Fe~~l~~yGK----df~~I~~~~v~~Kt~~~~v~fYY   51 (70)
T 2crg_A            4 GSSGMEEWSASEACLFEEALEKYGK----DFNDIRQDFLPWKSLTSIIEYYY   51 (70)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHHTCS----CHHHHHHTTCSSSCHHHHHHHHH
T ss_pred             cccCCCCCCHHHHHHHHHHHHHhCc----cHHHHHHHHcCCCCHHHHHHHHH
Confidence            4456789999999999999999986    4999999 699999999999986

>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa}

Probab=99.11  E-value=8.9e-11  Score=78.54  Aligned_cols=51  Identities=20%  Similarity=0.369  Sum_probs=45.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc----CCCCHHHHHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV----SGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v----pgRT~~qc~~ry~~L~~d   64 (86)
                      -....||.|||..|..++.+|+.   .+|..|++.+    +|||..||++||..|+..
T Consensus        15 r~r~~WT~EEd~~L~~gV~k~G~---G~W~~Ia~~~~~~f~~RT~v~lKdRWrnllk~   69 (121)
T 2juh_A           15 RIRRPFSVAEVEALVEAVEHLGT---GRWRDVKMRAFDNADHRTYVDLKDKWKTLVHT   69 (121)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHGG---GCHHHHHHHHCSCCSSCCSHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCC---CCHHHHHHHhccccCCCCHHHHHHHHHHHHhh
Confidence            35689999999999999999975   4899999995    899999999999998764

>1x58_A Hypothetical protein 4930532D21RIK; MUS musculus adult MALE testis cDNA, riken FULL-length enriched library, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.09  E-value=3e-10  Score=68.35  Aligned_cols=53  Identities=15%  Similarity=0.318  Sum_probs=45.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHH---HHcCCCCHHHHHHHHHHHHHH
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVA---KAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA---~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      |.+....+||+||+..|.+.+.+|+.    +|..|+   ..+++||..+++++|+.|...
T Consensus         3 ~~~~~r~~WT~EE~~~L~~gV~k~G~----~W~~I~~~y~f~~~RT~VdLKdk~r~L~k~   58 (62)
T 1x58_A            3 SGSSGRKDFTKEEVNYLFHGVKTMGN----HWNSILWSFPFQKGRRAVDLAHKYHRLISG   58 (62)
T ss_dssp             CCCCCSSSCCHHHHHHHHHHHHHHCS----CHHHHHHHSCCCTTCCHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhH----hHHHHHHhCCCccCcccchHHHHHHHHHhc
Confidence            34556789999999999999999963    799999   477899999999999998643

>1ign_A Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, DNA binding protein/DNA complex; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.6 a.4.1.6 PDB: 3ukg_A

Probab=99.09  E-value=6.1e-11  Score=87.29  Aligned_cols=53  Identities=11%  Similarity=0.238  Sum_probs=44.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCC--CCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKD--TPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~--~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      ....||.|||++|.+++.+||..  +...|..||++|||||..||++||..++..
T Consensus         7 ~k~~FT~EED~~Ile~v~k~Gn~r~ghk~W~~IAk~LpGRT~nsIRnRw~~~L~~   61 (246)
T 1ign_A            7 NKASFTDEEDEFILDVVRKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLSK   61 (246)
T ss_dssp             -CCCCCHHHHHHHHHHHHTSGGGTTCSHHHHHHTTTSTTSCHHHHHHHHHHTTGG
T ss_pred             CCCCCCHHHHHHHHHHHHHhCcCccccccHHHHHHHcCCCCHHHHHHHHHHHHhh
Confidence            45699999999999999999742  223399999999999999999999986544

>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A

Probab=98.97  E-value=1.3e-09  Score=69.66  Aligned_cols=44  Identities=20%  Similarity=0.313  Sum_probs=40.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      ...||++|..+|++++.+||+    .|.+||+.||+||..||..+|..
T Consensus        43 ~~~WT~eE~~~F~~~~~~~gK----~F~~Ia~~l~~Kt~~~cV~~YY~   86 (94)
T 4a69_C           43 MNMWSEQEKETFREKFMQHPK----NFGLIASFLERKTVAECVLYYYL   86 (94)
T ss_dssp             TCCCCHHHHHHHHHHHHHSTT----CHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCC----CHHHHHHHcCCCCHHHHHHHHhc
Confidence            578999999999999999986    59999999999999999999854

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*

Probab=98.72  E-value=4.5e-08  Score=77.66  Aligned_cols=46  Identities=17%  Similarity=0.385  Sum_probs=41.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      .....||.+|..+|+++|.+|++    .|..||+.|++||+.||+.+|..
T Consensus       378 ~~~~~WT~eE~~~f~~al~~yGk----dw~~IA~~VgTKT~~Qvk~fy~~  423 (482)
T 2xag_B          378 KCNARWTTEEQLLAVQAIRKYGR----DFQAISDVIGNKSVVQVKNFFVN  423 (482)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHTT----CHHHHHHHHSSCCHHHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHHHHHHHCc----CHHHHHHHhCCCCHHHHHHHHHH
Confidence            34579999999999999999975    59999999999999999999975

>1ug2_A 2610100B20RIK gene product; hypothetical protein, MYB-like DNA binding domain, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: a.4.1.3

Probab=98.66  E-value=1.7e-07  Score=60.20  Aligned_cols=55  Identities=15%  Similarity=0.241  Sum_probs=47.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDI   68 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~i   68 (86)
                      .--||.|||..++.+..+-+. .++.|..||+.|++||.+||.+||+.|..-+...
T Consensus        33 VvlWTRe~DR~IL~~cQ~~G~-s~~tFa~iA~~L~Nks~nqV~~RFq~Lm~Lf~~~   87 (95)
T 1ug2_A           33 VVLWTREADRVILTMCQEQGA-QPHTFSVISQQLGNKTPVEVSHRFRELMQLFHTA   87 (95)
T ss_dssp             CSSSCHHHHHHHHHHHHHTTS-CTTTHHHHHHHHSSCCHHHHHHHHHHHHHHHHHC
T ss_pred             EEEeccccCHHHHHHHHhcCC-ChhHHHHHHHHHccCCHHHHHHHHHHHHHHHHHH
Confidence            356999999999999888654 3679999999999999999999999998877653

>3hm5_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin, structural genomics consortium, SGC, activator, chromatin regulator; HET: DNA; 1.80A {Homo sapiens}

Probab=98.62  E-value=1.4e-07  Score=60.48  Aligned_cols=52  Identities=17%  Similarity=0.368  Sum_probs=46.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc-----CCCCHHHHHHHHHHHHHHHhhhh
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV-----SGKTVEDVKKHYELLVKDINDIE   69 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v-----pgRT~~qc~~ry~~L~~dv~~ie   69 (86)
                      .+||.||...|.+++.+|.    .||-.|+...     ++||++++++||..+...+....
T Consensus        31 ~~WTkEETd~Lf~L~~~fd----lRW~vI~DRy~~~~~~~Rt~EdLK~RyY~v~~~l~~~r   87 (93)
T 3hm5_A           31 DAWTKAETDHLFDLSRRFD----LRFVVIHDRYDHQQFKKRSVEDLKERYYHICAKLANVR   87 (93)
T ss_dssp             TTBCHHHHHHHHHHHHHTT----TCHHHHHHHSCTTTSCCCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhC----CCeeeehhhhccCCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            7999999999999999996    4899999999     58999999999998877766543

>1fex_A TRF2-interacting telomeric RAP1 protein; helix turn helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Synthetic} SCOP: a.4.1.3

Probab=98.54  E-value=1.9e-07  Score=55.00  Aligned_cols=49  Identities=12%  Similarity=0.184  Sum_probs=43.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCC-----CCchHHHHHH-HcCCCCHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKD-----TPDRWDNVAK-AVSGKTVEDVKKHYELL   61 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~-----~~~rW~~IA~-~vpgRT~~qc~~ry~~L   61 (86)
                      ...||.|||+.|.+.|..|...     ...-|..+|+ .+|++|-++|++||.+.
T Consensus         2 R~~FT~edD~~L~~~v~~~~~~~~~~~Gn~iwk~la~~~~~~HtwqSwRdRy~k~   56 (59)
T 1fex_A            2 RIAFTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSLTQHSWQSLKDRYLKH   56 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHTCCSTTTTTSSHHHHHHHHSCSSSCCSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhccccCCCccHHHHHHHHHhHCCCCCHHHHHHHHHHH
Confidence            5689999999999999999421     4688999999 89999999999999864

>2lr8_A CAsp8-associated protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, apoptosis; NMR {Homo sapiens}

Probab=97.82  E-value=2.4e-08  Score=61.12  Aligned_cols=53  Identities=13%  Similarity=0.202  Sum_probs=45.1

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      .-.||.|||..+..+..+-+. .+..|..||+.+ +||++||.+||+.|..-+..
T Consensus        14 vvlWTReeDR~IL~~cq~~G~-s~~tfa~iA~~L-nks~~QV~~RF~~Lm~Lf~k   66 (70)
T 2lr8_A           14 IILWTRNDDRVILLECQKRGP-SSKTFAYLAAKL-DKNPNQVSERFQQLMKLFEK   66 (70)
Confidence            457999999999988777554 357999999999 89999999999998876654

>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase, SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A {Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13 a.187.1.1 PDB: 2nog_A

Probab=98.26  E-value=1.3e-06  Score=65.92  Aligned_cols=51  Identities=33%  Similarity=0.444  Sum_probs=45.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv   65 (86)
                      +=..||..+...|+.|+.+|+.+   .|+.||+.|+|||.+||+.+|..+.+..
T Consensus       109 GF~~W~rrdf~~Fi~a~~kyGr~---~~~~IA~ev~~Kt~eEV~~Y~~vFw~ry  159 (304)
T 1ofc_X          109 GFTAWTKRDFNQFIKANEKYGRD---DIDNIAKDVEGKTPEEVIEYNAVFWERC  159 (304)
T ss_dssp             SCTTCCHHHHHHHHHHHHHHCTT---CHHHHTTSSTTCCHHHHHHHHHHHHHHG
T ss_pred             hhcccCHHHHHHHHHHHHHhCHH---HHHHHHHHhcCCCHHHHHHHHHHHHHhH
Confidence            34579999999999999999864   7999999999999999998888877766

>2ebi_A DNA binding protein GT-1; DNA-binding domain, phosphorylation; HET: DNA; NMR {Arabidopsis thaliana} PDB: 2jmw_A*

Probab=98.05  E-value=8.6e-06  Score=50.17  Aligned_cols=58  Identities=9%  Similarity=0.303  Sum_probs=47.1

Q ss_pred             CCCCCHHHHHHHHHHHHhc------CCCCCchHHHHHHHcC----CCCHHHHHHHHHHHHHHHhhhhc
Q 034697           13 GSSWTVKQNKQFETALAFY------DKDTPDRWDNVAKAVS----GKTVEDVKKHYELLVKDINDIEA   70 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~------~~~~~~rW~~IA~~vp----gRT~~qc~~ry~~L~~dv~~ie~   70 (86)
                      ...||.+|-.+|+.+....      +......|+.||..|.    .||++||+.+|+.|...-+.+..
T Consensus         4 ~~~Wt~~Et~~Li~~~~e~~~~f~~~~~~~~~W~~Ia~~m~~~G~~rs~~qC~~K~~nL~k~Yk~~k~   71 (86)
T 2ebi_A            4 AETWVQDETRSLIMFRRGMDGLFNTSKSNKHLWEQISSKMREKGFDRSPDMCTDKWRNLLKEFKKAKH   71 (86)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCSCSS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3579999999999997652      1223468999999975    59999999999999998887654

>4iej_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin regulator, repressor, structural joint center for structural genomics; HET: DNA; 1.45A {Homo sapiens} PDB: 3hm5_A*

Probab=97.93  E-value=5e-05  Score=48.65  Aligned_cols=51  Identities=18%  Similarity=0.375  Sum_probs=44.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-----CCCHHHHHHHHHHHHHHHhhh
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-----GKTVEDVKKHYELLVKDINDI   68 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-----gRT~~qc~~ry~~L~~dv~~i   68 (86)
                      ..||.||-..|-+++.+|.    -||-.|+....     .||+++.++||..+...+...
T Consensus        31 ~~WT~eETd~LfdLc~~fd----lRw~vI~DRy~~~~~~~RtvEdLK~RYY~V~~~l~~~   86 (93)
T 4iej_A           31 DAWTKAETDHLFDLSRRFD----LRFVVIHDRYDHQQFKKRSVEDLKERYYHICAKLANV   86 (93)
T ss_dssp             TTBCHHHHHHHHHHHHHTT----TCHHHHHHHCCTTTSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcC----CCeEEEeeccccCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence            6899999999999999996    48999999984     699999999999887776654

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11

Probab=97.79  E-value=0.00015  Score=43.44  Aligned_cols=56  Identities=14%  Similarity=0.191  Sum_probs=47.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC--CCCHHHHHHHHHHHHHHHhh
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS--GKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp--gRT~~qc~~ry~~L~~dv~~   67 (86)
                      -..-.||+|....|..|+.+++. ....+..|-+.|+  |.|..+|+.|.+++.-.++.
T Consensus         5 k~r~~WT~elH~~Fv~Av~~LG~-~~AtPk~Il~~M~v~gLT~~~VkSHLQKYR~~l~r   62 (64)
T 1irz_A            5 KPRVLWTHELHNKFLAAVDHLGV-ERAVPKKILDLMNVDKLTRENVASHLQKFRVALKK   62 (64)
T ss_dssp             CSSCSSCHHHHHHHHHHHHHHCT-TTCCHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHS
T ss_pred             CCCCcCCHHHHHHHHHHHHHhCC-CCCCcHHHHHHcCCCCCCHHHHHHHHHHHHHHHHc
Confidence            34568999999999999999984 3456999999865  89999999999988777664

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*

Probab=97.65  E-value=6.6e-06  Score=65.31  Aligned_cols=43  Identities=26%  Similarity=0.541  Sum_probs=0.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYE   59 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~   59 (86)
                      ...||.+|.++|+++|.+|++    .|.+|+++||+||..+|..+|.
T Consensus       189 ~d~WT~eE~~lFe~al~~yGK----dF~~I~~~lp~Ksv~e~V~yYY  231 (482)
T 2xag_B          189 PDEWTVEDKVLFEQAFSFHGK----TFHRIQQMLPDKSIASLVKFYY  231 (482)
T ss_dssp             -----------------------------------------------
T ss_pred             ccccCHHHHHHHHHHHHHcCc----cHHHHHHHcCCCCHHHHHHHhc
Confidence            458999999999999999986    4999999999999999998864

>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens}

Probab=97.19  E-value=0.0013  Score=45.64  Aligned_cols=52  Identities=15%  Similarity=0.268  Sum_probs=41.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH--cCCCCHHHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKA--VSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~--vpgRT~~qc~~ry~~L~~d   64 (86)
                      ....||..|-..|..++.+|+.. .+||+.|++.  +.+||.++++..|..+...
T Consensus         6 ~~~~~t~~E~r~fira~~kfG~~-~~r~~~I~~da~L~~Ks~~~v~~y~~~f~~~   59 (211)
T 4b4c_A            6 NIKGFSDAEIRRFIKSYKKFGGP-LERLDAIARDAELVDKSETDLRRLGELVHNG   59 (211)
T ss_dssp             --CCSCHHHHHHHHHHHTTCSSG-GGCHHHHHHHTTCTTSCHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHCCc-hhHHHHHHHHhccCCCCHHHHHHHHHHHHHH
Confidence            45689999999999999999732 4699999976  6799999999877765444

>1ign_A Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, DNA binding protein/DNA complex; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.6 a.4.1.6 PDB: 3ukg_A

Probab=97.03  E-value=0.0021  Score=47.23  Aligned_cols=28  Identities=7%  Similarity=0.151  Sum_probs=25.3

Q ss_pred             hHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697           38 RWDNVAKAVSGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus        38 rW~~IA~~vpgRT~~qc~~ry~~L~~dv   65 (86)
                      +|..||+.+|++|....++||.+++.+.
T Consensus       173 ~fk~ia~~~P~HT~~SWRdRyrKfl~~~  200 (246)
T 1ign_A          173 FFKHFAEEHAAHTENAWRDRFRKFLLAY  200 (246)
T ss_dssp             HHHHHHHHTTTSCHHHHHHHHHHTHHHH
T ss_pred             HHHHHHHHCCCCChhhHHHHHHHHHhhc
Confidence            8999999999999999999999866543

>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase, SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A {Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13 a.187.1.1 PDB: 2nog_A

Probab=96.88  E-value=0.0034  Score=47.22  Aligned_cols=55  Identities=13%  Similarity=0.263  Sum_probs=46.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHH------------HcCCCCHHHHHHHHHHHHHHHh
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAK------------AVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~------------~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      ....||.+||..|.-+|.+|+-+..+.|++|-.            .+-.||+.++..|...|+.-|.
T Consensus       211 k~k~yteeEDRfLL~~l~k~G~~~~g~we~Ir~~Ir~~p~FrFDwf~kSRTp~el~rRc~tLi~~ie  277 (304)
T 1ofc_X          211 KGKNYTEIEDRFLVCMLHKLGFDKENVYEELRAAIRASPQFRFDWFIKSRTALELQRRCNTLITLIE  277 (304)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHCGGGTTCHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCccCHHHHHHHHHHHHHhcCCCcchHHHHHHHHHhCcchhhhHHHhcCCHHHHHHHHHHHHHHHH
Confidence            567899999999999999999876789999974            4557999999999988875543

>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear protein complex, chromatin remodeling nucleosome remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A

Probab=95.99  E-value=0.024  Score=43.81  Aligned_cols=56  Identities=13%  Similarity=0.225  Sum_probs=47.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH------------cCCCCHHHHHHHHHHHHHHHh
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKA------------VSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~------------vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      +....||.+||..|+-+|-+|+-+..+.|++|-..            +-.||+.++..|...|+.-|.
T Consensus       226 ~k~k~yteeEDRfLL~~l~k~G~~~~g~we~Ir~~Ir~~p~FrFDwF~kSRT~~EL~rRc~tLi~~Ie  293 (374)
T 2y9y_A          226 NNKRTYSEEEDRFILLMLFKYGLDRDDVYELVRDEIRDCPLFELDFYFRSRTPVELARRGNTLLQCLE  293 (374)
T ss_dssp             SSCCCSCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHCSGGGSCHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCHHHHHHHHHHHHHhccCCCChHHHHHHHHHhCcchhhhHHHhcCCHHHHHHHHHHHHHHHH
Confidence            35678999999999999999997666789999666            457999999999999887654

>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear protein complex, chromatin remodeling nucleosome remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A

Probab=95.73  E-value=0.014  Score=45.14  Aligned_cols=47  Identities=21%  Similarity=0.402  Sum_probs=40.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC-CCCHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS-GKTVEDVKKHYELLV   62 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp-gRT~~qc~~ry~~L~   62 (86)
                      =..||.-+=..|..|+.+|+.+   .-..||..|+ |||.+||+..++.+.
T Consensus       123 F~~WnrrDF~~FI~a~~kyGR~---d~~~IA~ev~~~Kt~eEV~~Y~~vFw  170 (374)
T 2y9y_A          123 FTNWNKLEFRKFITVSGKYGRN---SIQAIARELAPGKTLEEVRAYAKAFW  170 (374)
T ss_dssp             CCCSCHHHHHHHHHHHHHHCTT---CHHHHHSSCCCSSSHHHHHHHHHHHH
T ss_pred             hcccCHHHHHHHHHHHHHhCHh---HHHHHHHHHccCCCHHHHHHHHHHHH
Confidence            3579999999999999999864   7999999998 999999996555443

>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens}

Probab=94.44  E-value=0.23  Score=34.00  Aligned_cols=52  Identities=12%  Similarity=0.298  Sum_probs=40.1

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc--C----------C--CCHHHHHHHHHHHHHHHh
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV--S----------G--KTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v--p----------g--RT~~qc~~ry~~L~~dv~   66 (86)
                      -...||.+||..|...+.+|+-+   +|+.|-.-.  +          .  .++.++..|...|+.-+.
T Consensus       133 ~~~~W~~~~D~~LL~Gi~k~G~g---~w~~Ir~D~~l~~~~k~~~~~~~k~p~a~~L~rR~~~Ll~~l~  198 (211)
T 4b4c_A          133 FDIDWGKEDDSNLLIGIYEYGYG---SWEMIKMDPDLSLTHKILPDDPDKKPQAKQLQTRADYLIKLLS  198 (211)
T ss_dssp             SSSCCCHHHHHHHHHHHHHHCTT---CHHHHHHCSSSSCTTTSSCSSTTSSCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHHHHHHCcC---cHHHHHhChhcCccccccccccccCCChHHHHHHHHHHHHHHH
Confidence            35679999999999999999854   799998732  1          2  357789999877766554

>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A

Probab=92.62  E-value=0.42  Score=35.16  Aligned_cols=48  Identities=13%  Similarity=0.138  Sum_probs=39.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH--cCCCCHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKA--VSGKTVEDVKKHYELL   61 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~--vpgRT~~qc~~ry~~L   61 (86)
                      ...||..|-..|.+++.+|+.- ..||+.|+.-  |+.|+...++.-|..|
T Consensus         3 ~~~ltekEiR~l~Ra~~kfG~~-~~R~e~I~~dA~L~~ks~~~i~~~~~~l   52 (270)
T 2xb0_X            3 LGSIGESEVRALYKAILKFGNL-KEILDELIADGTLPVKSFEKYGETYDEM   52 (270)
T ss_dssp             TCCCCHHHHHHHHHHHHHHSSC-TTCHHHHHHTTSSCCCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhCCH-HHHHHHHHHhcccccCCHHHHHHHHHHH
Confidence            3579999999999999999842 4699999765  5679999988877654

>2hzd_A Transcriptional enhancer factor TEF-1; DNA-binding, helix-turn-helix, gene regulation; NMR {Homo sapiens}

Probab=89.57  E-value=1.5  Score=27.04  Aligned_cols=54  Identities=20%  Similarity=0.385  Sum_probs=38.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCC------------CchHHHHHHHc-----CCCCHHHHHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDT------------PDRWDNVAKAV-----SGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~------------~~rW~~IA~~v-----pgRT~~qc~~ry~~L~~dv   65 (86)
                      +...|+++=+..|.+||..||+..            ..|=+-||.++     .-||.+||-.|-+.|....
T Consensus         5 ~e~vW~~~lE~aF~eaL~~yp~~g~~k~~ls~~gk~~gRNelIs~yI~~~tGk~RtrKQVSShiQvlk~~~   75 (82)
T 2hzd_A            5 AEGVWSPDIEQSFQEALSIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRK   75 (82)
T ss_dssp             GSCCSCHHHHHHHHHHHHHSCSSSCCCCCHHHHCCCCCTHHHHHHHHHHHHSCCCCSHHHHHHHHHHHHHH
T ss_pred             cCCcCCHHHHHHHHHHHHHcCCCCccceeecccccccchhHHHHHHHHHHHcccCCccchhHHHHHHHHHH
Confidence            467899999999999999998541            12333444444     2488999998888776553

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=86.19  E-value=3.8  Score=24.54  Aligned_cols=58  Identities=14%  Similarity=0.127  Sum_probs=45.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      +|.++...+|.++-..|+......+--....=+.||+.+ |-|..||+.=|++-....+
T Consensus         2 ~~g~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~t-gLte~qIkvWFqNrR~k~K   59 (76)
T 2ecc_A            2 SSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQIT-GLPRPEIIQWFGDTRYALK   59 (76)
T ss_dssp             CCSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHT-CCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH-CcCHHHhhHHhHhhHHHHH
Confidence            456778899999999999997776533456778899999 6999999987776554443

>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A

Probab=85.96  E-value=0.69  Score=34.01  Aligned_cols=29  Identities=17%  Similarity=0.520  Sum_probs=25.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAK   44 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~   44 (86)
                      ...|+.+||..|...|-+|+-|   .|+.|-.
T Consensus       168 ~c~W~~~dD~~LLvGIykyGyG---~We~Ir~  196 (270)
T 2xb0_X          168 SSNWTKEEDEKLLIGVFKYGYG---SWTQIRD  196 (270)
T ss_dssp             SSCCCHHHHHHHHHHHHHHCTT---CHHHHHH
T ss_pred             CCCcChHHHHHHHHHHHHHcCC---cHHHHhc
Confidence            4689999999999999999865   7999964

>2cxy_A BAF250B subunit, HBAF250B; DNA-binding domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.60A {Homo sapiens} PDB: 2eh9_A 1ryu_A

Probab=85.19  E-value=1.8  Score=27.78  Aligned_cols=45  Identities=29%  Similarity=0.446  Sum_probs=31.2

Q ss_pred             chHHHHHHHcCCCC----HHHHHHHHHHHHHHHhh-hhcCCCCCCCCCCC
Q 034697           37 DRWDNVAKAVSGKT----VEDVKKHYELLVKDIND-IEAGRYPHPNYRST   81 (86)
Q Consensus        37 ~rW~~IA~~vpgRT----~~qc~~ry~~L~~dv~~-ie~g~v~~P~y~~~   81 (86)
                      ..|..||..++--+    ..+++.+|.+++-.... .+.|..|+|+--+.
T Consensus        73 ~~W~~Va~~lg~~~~~s~~~~Lk~~Y~k~L~~yE~~~~~g~~~p~~i~~~  122 (125)
T 2cxy_A           73 KKWRELATNLNVGTSSSAASSLKKQYIQYLFAFECKIERGEEPPPEVFST  122 (125)
T ss_dssp             TCHHHHHHHTTSCSSHHHHHHHHHHHHHHTHHHHHHHHHCCCCCCSCC--
T ss_pred             CcHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHcCCCCChhHhcc
Confidence            58999999997433    45778889876555543 46888888775443

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=81.32  E-value=5.2  Score=23.42  Aligned_cols=47  Identities=11%  Similarity=0.145  Sum_probs=35.8

Q ss_pred             CHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           17 TVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        17 T~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      |.+.+..+..+|...+.+..-.=..||+.+ |.+...|..|-..|.+.
T Consensus        12 ~~~~~~~IL~~L~~~~~~~~~t~~eLA~~L-gvs~~tV~~~L~~L~~~   58 (77)
T 1qgp_A           12 YQDQEQRILKFLEELGEGKATTAHDLSGKL-GTPKKEINRVLYSLAKK   58 (77)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCEEHHHHHHHH-CCCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCCCcCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            455667777888888755556789999999 58888888887777543

---

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	86
d2cjja1	63	a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Anti	3e-18
d2cqqa1	59	a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1	4e-18
d2cqra1	60	a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1	7e-09
d1xc5a1	68	a.4.1.3 (A:413-480) Nuclear receptor corepressor 2	3e-05
d2iw5b1	65	a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Hu	0.001
d2crga1	57	a.4.1.3 (A:8-64) Metastasis associated protein MTA	0.001
d1ofcx1	52	a.4.1.3 (X:799-850) SANT domain of the nucleosome	0.001

>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]} Length = 63

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Radialis
species: Garden snapdragon (Antirrhinum majus) [TaxId: 4151]

 Score = 69.2 bits (169), Expect = 3e-18
 Identities = 41/62 (66%), Positives = 50/62 (80%)

Query: 13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGR 72
          G  W+ K+NK FE ALA YDKDTPDRW NVA+AV G+T E+VKKHYE+LV+DI  IE+G+
Sbjct: 1  GRPWSAKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDIKYIESGK 60

Query: 73 YP 74
           P
Sbjct: 61 VP 62

>d2cqqa1 a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: DnaJ homolog subfamily C member 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.7 bits (168), Expect = 4e-18
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI 65
            WT +   Q   ++  +   TP RW+ +A  + G++V DV    + L   +
Sbjct: 2  PEWTEEDLSQLTRSMVKFPGGTPGRWEKIAHEL-GRSVTDVTTKAKQLKDSV 52

>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: DnaJ homolog subfamily C member 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 7e-09
 Identities = 22/60 (36%), Positives = 30/60 (50%)

Query: 2  ASNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL 61
           S     +RS+   WT  Q K  E AL  Y + + D WD +A+ V  K+ ED    Y+LL
Sbjct: 1  GSLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLL 60

>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Nuclear receptor corepressor 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 3e-05
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 5  TMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD 64
           +   R   + W+ ++ + F      + K+    +  +A  +  KTV +   +Y L  K+
Sbjct: 9  KVYKDRQVMNMWSEQEKETFREKFMQHPKN----FGLIASFLERKTVAECVLYYYLTKKN 64

Query: 65 IN 66
           N
Sbjct: 65 EN 66

>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: REST corepressor 1, CoREST
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.1 bits (73), Expect = 0.001
 Identities = 10/57 (17%), Positives = 23/57 (40%), Gaps = 4/57 (7%)

Query: 10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN 66
          +   + WT ++      A+  Y +D    +  ++  +  K+V  VK  +    +  N
Sbjct: 2  QKCNARWTTEEQLLAVQAIRKYGRD----FQAISDVIGNKSVVQVKNFFVNYRRRFN 54

>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Metastasis associated protein MTA3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 32.1 bits (73), Expect = 0.001
 Identities = 10/45 (22%), Positives = 23/45 (51%), Gaps = 5/45 (11%)

Query: 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKA-VSGKTVEDVKKHY 58
           W+  +   FE AL  Y KD    ++++ +  +  K++  + ++Y
Sbjct: 3  EWSASEACLFEEALEKYGKD----FNDIRQDFLPWKSLTSIIEYY 43

>d1ofcx1 a.4.1.3 (X:799-850) SANT domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: SANT domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 31.6 bits (72), Expect = 0.001
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIE 69
          +WT +   QF  A   Y +D     DN+AK V GKT E+V ++  +  +   +++
Sbjct: 1  AWTKRDFNQFIKANEKYGRD---DIDNIAKDVEGKTPEEVIEYNAVFWERCTELQ 52

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	86
d2cjja1	63	Radialis {Garden snapdragon (Antirrhinum majus) [T	99.92
d2cqra1	60	DnaJ homolog subfamily C member 1 {Human (Homo sap	99.81
d2cqqa1	59	DnaJ homolog subfamily C member 1 {Human (Homo sap	99.8
d1x41a1	47	Transcriptional adaptor 2-like, TADA2L, isoform b	99.65
d1guua_	50	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	99.63
d1gvda_	52	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	99.63
d1gv2a2	47	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	99.6
d2cu7a1	65	MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 960	99.56
d1w0ta_	52	DNA-binding domain of human telomeric protein, hTR	99.49
d1w0ua_	55	Telomeric repeat binding factor 2, TRF2 {Human (Ho	99.47
d1igna1	86	DNA-binding domain of rap1 {Baker's yeast (Sacchar	99.47
d2iw5b1	65	REST corepressor 1, CoREST {Human (Homo sapiens) [	99.44
d1xc5a1	68	Nuclear receptor corepressor 2 {Human (Homo sapien	99.37
d2ckxa1	83	Telomere binding protein TBP1 {Tobacco (Nicotiana	99.32
d1ug2a_	95	2610100b20rik gene product {Mouse (Mus musculus) [	99.29
d1wgxa_	73	Hypothetical protein C14orf106 (KIAA1903) {Human (	99.18
d2crga1	57	Metastasis associated protein MTA3 {Mouse (Mus mus	99.1
d1irza_	64	Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId	98.25
d1ofcx1	52	SANT domain of the nucleosome remodeling ATPase IS	97.94
d1fexa_	59	Rap1 {Human (Homo sapiens) [TaxId: 9606]}	96.92
d1ofcx2	128	SLIDE domain of the nucleosome remodeling ATPase I	95.97
d1x58a1	49	Hypothetical protein 4930532d21rik {Mouse (Mus mus	94.85
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	93.76
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.16
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	90.36
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	89.66
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.33
d1fs1b1	55	Cyclin A/CDK2-associated p45, Skp1 {Human (Homo sa	88.07
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	85.94
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	85.67
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	85.21
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	83.55
d1kkxa_	102	Transcription regulator Adr6 (Swi1) {Baker's yeast	83.25
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	82.63
d1nexa1	70	Centromere DNA-binding protein complex Cbf3 subuni	82.6
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	82.58

>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Radialis
species: Garden snapdragon (Antirrhinum majus) [TaxId: 4151]

Probab=99.92  E-value=1.8e-25  Score=132.86  Aligned_cols=62  Identities=65%  Similarity=1.102  Sum_probs=60.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcCCCCC
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPH   75 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g~v~~   75 (86)
                      ++||.|||++|++||.+|+.+.+++|.+||++|||||++||++||+.|.+||+.||+|+|||
T Consensus         2 ~~WT~eEd~~L~~~v~~~~~~~~~~W~~Ia~~l~gRt~~qc~~r~~~L~~dik~iesg~vpf   63 (63)
T d2cjja1           2 RPWSAKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDIKYIESGKVPF   63 (63)
T ss_dssp             CSCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHSTTCCHHHHHHHHHHHHHHHHHHHHSSCCC
T ss_pred             cCCCHHHHHHHHHHHHHHCCCCchHHHHHHHHcCCCCHHHHHHHHHHHHHHhhccccCCCCC
Confidence            58999999999999999999888999999999999999999999999999999999999986

>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: DnaJ homolog subfamily C member 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.7e-20  Score=109.10  Aligned_cols=59  Identities=37%  Similarity=0.613  Sum_probs=52.8

Q ss_pred             CCcCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697            3 SNTMTSSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus         3 ~~~~~~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      |-....+......||.|||++|+.||..|+.+.+.+|.+||++|||||+.||+.||+.|
T Consensus         2 s~~~~~~~~~~~~WT~eEd~~L~~~v~~~~~~~~~~W~~IA~~l~~Rt~~qc~~R~~~L   60 (60)
T d2cqra1           2 SLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLL   60 (60)
T ss_dssp             CCCCCTTTCSSCCCCHHHHHHHHHHHHHSCSSSHHHHHHHGGGCSSSCHHHHHHHHHHH
T ss_pred             CCccccCCcCCCCcCHHHHHHHHHHHHHcCCccchHHHHHHHHcCCCCHHHHHHHHHHC
Confidence            34455667778899999999999999999988788999999999999999999999876

>d2cqqa1 a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: DnaJ homolog subfamily C member 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=4.5e-20  Score=109.03  Aligned_cols=57  Identities=25%  Similarity=0.557  Sum_probs=51.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhhhhcCC
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGR   72 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~ie~g~   72 (86)
                      ..||.+|+++|++||.+||+++++||++||++| |||++||+.||+.|.+++. +.+|.
T Consensus         2 ~eWT~ee~~~le~Al~~~P~gt~~RW~~IA~~v-gkt~~ev~~~~k~l~e~~~-~~~g~   58 (59)
T d2cqqa1           2 PEWTEEDLSQLTRSMVKFPGGTPGRWEKIAHEL-GRSVTDVTTKAKQLKDSVT-CSPGM   58 (59)
T ss_dssp             CCCCHHHHHHHHHHHHHSCTTCTTHHHHHHHHH-TSCHHHHHHHHHHHHHSCC-CCSCC
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCcHHHHHHHHHH-CCCHHHHHHHHHHHHHhcc-cCCCC
Confidence            589999999999999999999999999999999 8999999999999998874 34443

>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Transcriptional adaptor 2-like, TADA2L, isoform b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.4e-16  Score=89.39  Aligned_cols=45  Identities=29%  Similarity=0.485  Sum_probs=41.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      ..||.+||.+|.++|.+|+.+   +|..||+.|||||+.||+.||.+.
T Consensus         2 ~~Wt~eEd~~L~~~v~~~G~~---nW~~Ia~~~~~Rt~~Qcr~r~~~~   46 (47)
T d1x41a1           2 PSWTAQEEMALLEAVMDCGFG---NWQDVANQMCTKTKEECEKHYMKY   46 (47)
T ss_dssp             SSSCHHHHHHHHHHHHHTCTT---CHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHHCCc---cHHHHHHHcCCCCHHHHHHHHHHh
Confidence            369999999999999999743   799999999999999999999864

>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: c-Myb, DNA-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=3e-16  Score=88.82  Aligned_cols=46  Identities=13%  Similarity=0.427  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      +.||.+||.+|..++.+|+.   .+|..||+.|||||..||++||.+++
T Consensus         2 ~~WT~eED~~L~~~v~~~g~---~~W~~Ia~~~~~Rt~~qcr~Rw~~~L   47 (50)
T d1guua_           2 TRWTREEDEKLKKLVEQNGT---DDWKVIANYLPNRTDVQCQHRWQKVL   47 (50)
T ss_dssp             CCCCHHHHHHHHHHHHHHCS---SCHHHHHHTSTTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCC---CCHHHHHHHHCCCCHHHHHHHHHhhC
Confidence            57999999999999999974   37999999999999999999998754

>d1gvda_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: c-Myb, DNA-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.9e-16  Score=90.49  Aligned_cols=46  Identities=17%  Similarity=0.477  Sum_probs=42.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      .++||.+||++|.+++.+|+.   .+|..||+.|||||..||++||..+
T Consensus         3 rg~WT~eED~~L~~~v~~~g~---~~W~~Ia~~l~~Rt~~qc~~Rw~~~   48 (52)
T d1gvda_           3 KGPWTKEEDQRLIKLVQKYGP---KRWSVIAKHLKGRIGKQCRERWHNH   48 (52)
T ss_dssp             CCSCCHHHHHHHHHHHHHHCT---TCHHHHHTTSTTCCHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHCC---CCHHHHHHHHCCCCHHHHHHHHHhh
Confidence            578999999999999999974   3799999999999999999999864

>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: c-Myb, DNA-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=5.6e-16  Score=87.05  Aligned_cols=45  Identities=27%  Similarity=0.570  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ++||.|||++|..++.+|+    .+|..||++|||||..||++||..++
T Consensus         2 ~~WT~eED~~L~~~v~~~G----~~W~~Ia~~~~gRt~~~~knr~~~~l   46 (47)
T d1gv2a2           2 TSWTEEEDRIIYQAHKRLG----NRWAEIAKLLPGRTDNAIKNHWNSTM   46 (47)
T ss_dssp             CCCCHHHHHHHHHHHHHHS----SCHHHHHTTCTTCCHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHHh----hHHHHHHhHcCCCCHHHHHHHHHHHc
Confidence            6899999999999999996    37999999999999999999998764

>d2cu7a1 a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: MYSM1 (KIAA1915)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.3e-15  Score=87.21  Aligned_cols=49  Identities=29%  Similarity=0.566  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      ..||.|||.+|.++|.+|+.    +|..||+.|||||..||+.||..++....
T Consensus         3 ~~WT~eEd~~l~~~~~~~G~----~W~~Ia~~~~~Rt~~q~k~ry~~~~~~~~   51 (65)
T d2cu7a1           3 VKWTIEEKELFEQGLAKFGR----RWTKISKLIGSRTVLQVKSYARQYFKNKV   51 (65)
T ss_dssp             CCCCHHHHHHHHHHHHHTCS----CHHHHHHHHSSSCHHHHHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHHHhcc----hHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            57999999999999999973    79999999999999999999988766543

>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: DNA-binding domain of telomeric protein
domain: DNA-binding domain of human telomeric protein, hTRF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=3.9e-14  Score=80.62  Aligned_cols=47  Identities=13%  Similarity=0.391  Sum_probs=42.1

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC--CCCHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS--GKTVEDVKKHYELLV   62 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp--gRT~~qc~~ry~~L~   62 (86)
                      ..+||+|||.+|..+|.+|+.+   +|..||+.++  |||..||++||..|.
T Consensus         2 r~~WT~eED~~L~~~v~~~G~~---~W~~I~~~~~~~~Rt~~q~r~Rw~nl~   50 (52)
T d1w0ta_           2 RQAWLWEEDKNLRSGVRKYGEG---NWSKILLHYKFNNRTSVMLKDRWRTMK   50 (52)
T ss_dssp             CCCCCHHHHHHHHHHHHHHCTT---CHHHHHHHSCCSSCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHCCC---CHHHHHhhcCCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999754   7999999865  899999999998875

>d1w0ua_ a.4.1.4 (A:) Telomeric repeat binding factor 2, TRF2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: DNA-binding domain of telomeric protein
domain: Telomeric repeat binding factor 2, TRF2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=7.8e-14  Score=80.07  Aligned_cols=48  Identities=17%  Similarity=0.465  Sum_probs=42.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH--cCCCCHHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKA--VSGKTVEDVKKHYELLVK   63 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~--vpgRT~~qc~~ry~~L~~   63 (86)
                      ...||.|||++|..+|.+|+.+   +|..||+.  +++||..||++||+.|..
T Consensus         2 r~~WT~eEd~~L~~~V~~~G~~---~W~~I~~~~~~~~Rt~~q~k~Rwrn~~k   51 (55)
T d1w0ua_           2 KQKWTVEESEWVKAGVQKYGEG---NWAAISKNYPFVNRTAVMIKDRWRTMKR   51 (55)
T ss_dssp             CCCCCHHHHHHHHHHHHHHCTT---CHHHHHHHSCCSSCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHhCCC---hHHHHHhhcCCCCcCHHHHHHHHHHHhc
Confidence            3589999999999999999743   79999998  459999999999998764

>d1igna1 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: DNA-binding domain of rap1
domain: DNA-binding domain of rap1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.47  E-value=1.8e-14  Score=89.79  Aligned_cols=53  Identities=15%  Similarity=0.284  Sum_probs=44.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCC--CCchHHHHHHHcCCCCHHHHHHHHHH-HHHHHh
Q 034697           14 SSWTVKQNKQFETALAFYDKD--TPDRWDNVAKAVSGKTVEDVKKHYEL-LVKDIN   66 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~--~~~rW~~IA~~vpgRT~~qc~~ry~~-L~~dv~   66 (86)
                      +.||.|||++|.+++.+|+..  ....|..||+.|||||..||++||.. |...+.
T Consensus         2 ~~WT~eED~~L~~~v~~~g~~~~~~~~W~~IA~~lpgRt~~qcr~Rw~~~L~p~l~   57 (86)
T d1igna1           2 ASFTDEEDEFILDVVRKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLSKRLE   57 (86)
T ss_dssp             CCCCHHHHHHHHHHHHTSGGGTTCSHHHHHHTTTSTTSCHHHHHHHHHHTTGGGCC
T ss_pred             CCCCHHHHHHHHHHHHHhCcCcCCccCHHHHHHHcCCCCHHHHHHHHHHHcCcccc
Confidence            589999999999999999742  34569999999999999999999986 445544

>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: REST corepressor 1, CoREST
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=8.1e-14  Score=81.90  Aligned_cols=46  Identities=17%  Similarity=0.369  Sum_probs=41.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV   62 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~   62 (86)
                      ...||++|+.+|..++..|+.    +|..||+.|||||+.||+.||..+.
T Consensus         5 ~~~WT~eE~~~f~~~~~~~G~----~w~~Ia~~~~~kt~~q~~~~y~~~~   50 (65)
T d2iw5b1           5 NARWTTEEQLLAVQAIRKYGR----DFQAISDVIGNKSVVQVKNFFVNYR   50 (65)
T ss_dssp             CSSCCHHHHHHHHHHHHHHSS----CHHHHHHHHSSCCHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHhCc----hHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            357999999999999999974    5999999999999999999998653

>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Nuclear receptor corepressor 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=2.4e-13  Score=80.52  Aligned_cols=48  Identities=21%  Similarity=0.305  Sum_probs=42.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHH
Q 034697           10 RSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELL   61 (86)
Q Consensus        10 ~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L   61 (86)
                      ......||.||+.+|..++.+|+.    +|..||+.|||||..||+.||...
T Consensus        14 ~~~~~~WT~eE~~~f~~~~~~~G~----~w~~Ia~~~~~rt~~q~~~~yy~~   61 (68)
T d1xc5a1          14 RQVMNMWSEQEKETFREKFMQHPK----NFGLIASFLERKTVAECVLYYYLT   61 (68)
T ss_dssp             TTTTTCCCTTTHHHHHHHHHHTTS----CSSSHHHHTTTSCHHHHHHHHHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHCC----cHHHHHHHcCCCCHHHHHHHHHHH
Confidence            334578999999999999999974    599999999999999999999754

>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Telomere binding protein TBP1
species: Tobacco (Nicotiana tabacum) [TaxId: 4097]

Probab=99.32  E-value=2e-12  Score=79.42  Aligned_cols=47  Identities=21%  Similarity=0.421  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHH----cCCCCHHHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKA----VSGKTVEDVKKHYELLVK   63 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~----vpgRT~~qc~~ry~~L~~   63 (86)
                      .+||.|||..|..+|.+|+.+   +|..||+.    ++|||..||++||+.++.
T Consensus         1 r~WT~eEd~~L~~~V~~~G~~---~W~~I~~~~~~~~~~Rt~~qck~RWrn~l~   51 (83)
T d2ckxa1           1 RPFSVAEVEALVEAVEHLGTG---RWRDVKMRAFDNADHRTYVDLKDKWKTLVH   51 (83)
T ss_dssp             CCCCHHHHHHHHHHHHHHCSS---CHHHHHHHHCTTCTTSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHCcc---cHHHHHHHHHhhccCCCHHHHHHHHHHHhh
Confidence            379999999999999999754   79999986    689999999999998764

>d1ug2a_ a.4.1.3 (A:) 2610100b20rik gene product {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: 2610100b20rik gene product
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=8.6e-12  Score=79.06  Aligned_cols=54  Identities=15%  Similarity=0.250  Sum_probs=46.9

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      ...||.|||++|+..+.+++. ...-|..||+.|+|||..||++||+.|..-+..
T Consensus        33 ~~~WTrEEDriIL~~~q~~G~-~~~tw~~Ia~~L~~Rs~~qvr~Rf~~Lm~lf~~   86 (95)
T d1ug2a_          33 VVLWTREADRVILTMCQEQGA-QPHTFSVISQQLGNKTPVEVSHRFRELMQLFHT   86 (95)
T ss_dssp             CSSSCHHHHHHHHHHHHHTTS-CTTTHHHHHHHHSSCCHHHHHHHHHHHHHHHHH
T ss_pred             cCCcCHHHHHHHHHHHHHcCC-cHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            467999999999999999873 245599999999999999999999998877653

>d1wgxa_ a.4.1.3 (A:) Hypothetical protein C14orf106 (KIAA1903) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Hypothetical protein C14orf106 (KIAA1903)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.18  E-value=4.8e-11  Score=71.88  Aligned_cols=49  Identities=27%  Similarity=0.518  Sum_probs=46.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL   60 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~   60 (86)
                      ....|+++|...|..|+..+|++.+..|.+||..||.||++||...|+.
T Consensus         7 ~d~~W~e~ELqkLh~A~~SlPkh~~gfW~~VA~~VGtRSaeECQ~ky~~   55 (73)
T d1wgxa_           7 GDKEWNEKELQKLHCAFASLPKHKPGFWSEVAAAVGSRSPEECQRKYME   55 (73)
T ss_dssp             SSSCCCHHHHHHHHHHHHHSCSSSSSHHHHHHHHTTTSCHHHHHHHHHH
T ss_pred             cccccCHHHHHHHHHHHHhcCCCCCccHHHHHHHHccCCHHHHHHHHHh
Confidence            4568999999999999999999999999999999999999999998875

>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Metastasis associated protein MTA3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.10  E-value=1e-10  Score=67.32  Aligned_cols=43  Identities=21%  Similarity=0.469  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHH-HcCCCCHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAK-AVSGKTVEDVKKHYEL   60 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~-~vpgRT~~qc~~ry~~   60 (86)
                      ..||+||..+|+++|.+|++    .|.+|++ .||+||..||..+|-.
T Consensus         2 d~WT~eE~~~F~~~~~~yGK----df~~I~~~~v~~Ks~~~~v~fYY~   45 (57)
T d2crga1           2 EEWSASEACLFEEALEKYGK----DFNDIRQDFLPWKSLTSIIEYYYM   45 (57)
T ss_dssp             CCCCHHHHHHHHHHHHHTCS----CHHHHHHTTCSSSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcc----cHHHHHHHHcCCCCHHHHHHHHHH
Confidence            57999999999999999986    5999998 5799999999999853

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: GARP response regulators
domain: Arr10-B
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.25  E-value=2.3e-06  Score=49.98  Aligned_cols=52  Identities=19%  Similarity=0.289  Sum_probs=42.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchH--HHHHHH--cCCCCHHHHHHHHHHHHHHHhh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRW--DNVAKA--VSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW--~~IA~~--vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      .-.||+|+...|..||.+++.+   +|  ..|.+.  ++|+|..||+.|.+++.-.+++
T Consensus         7 R~~WT~elH~~Fv~Av~~lG~~---~atpk~I~~~m~v~~lT~~qV~SHlQKYrl~l~k   62 (64)
T d1irza_           7 RVLWTHELHNKFLAAVDHLGVE---RAVPKKILDLMNVDKLTRENVASHLQKFRVALKK   62 (64)
T ss_dssp             SCSSCHHHHHHHHHHHHHHCTT---TCCHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHHHhCcc---ccchHHHHHHcCCCCCCHHHHHHHHHHHHHHHHh
Confidence            4579999999999999999643   44  677776  6789999999999988766654

>d1ofcx1 a.4.1.3 (X:799-850) SANT domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: SANT domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=97.94  E-value=1.4e-05  Score=44.89  Aligned_cols=50  Identities=34%  Similarity=0.496  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697           15 SWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        15 ~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      .||..|=..|..|+.+|+.+   .-+.||..|.|||.+||+..++..-+....
T Consensus         1 ~WnrrdF~~Fi~a~ekyGR~---d~~~Ia~e~~~Kt~eEV~~Y~~vFw~ry~e   50 (52)
T d1ofcx1           1 AWTKRDFNQFIKANEKYGRD---DIDNIAKDVEGKTPEEVIEYNAVFWERCTE   50 (52)
T ss_dssp             TCCHHHHHHHHHHHHHHCTT---CHHHHTTSSTTCCHHHHHHHHHHHHHHGGG
T ss_pred             CCCHHHHHHHHHHHHHHHHh---hHHHHHHHhcCCCHHHHHHHHHHHHHHHHh
Confidence            59999999999999999864   689999999999999998877665554443

>d1fexa_ a.4.1.3 (A:) Rap1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Myb/SANT domain
domain: Rap1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.92  E-value=0.0015  Score=37.00  Aligned_cols=50  Identities=12%  Similarity=0.183  Sum_probs=42.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCC-----CCchHHHHHH-HcCCCCHHHHHHHHHHH
Q 034697           12 SGSSWTVKQNKQFETALAFYDKD-----TPDRWDNVAK-AVSGKTVEDVKKHYELL   61 (86)
Q Consensus        12 ~~~~WT~eEdk~Le~al~~~~~~-----~~~rW~~IA~-~vpgRT~~qc~~ry~~L   61 (86)
                      +..++|.+||+.|.+.|+.+...     ...-|+.+++ .+|..|-+.-++||.+.
T Consensus         1 GR~~fT~eeD~~l~~yv~~~~~~~~~~~Gn~iwk~l~~~~~~~HtwQSwrdRY~K~   56 (59)
T d1fexa_           1 GRIAFTDADDVAILTYVKENARSPSSVTGNALWKAMEKSSLTQHSWQSLKDRYLKH   56 (59)
T ss_dssp             CCCCCCHHHHHHHHHHHHHTCCSTTTTTSSHHHHHHHHSCSSSCCSHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCcCCccHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            35689999999999999998422     4678999996 68999999999999753

>d1ofcx2 a.4.1.13 (X:851-978) SLIDE domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SLIDE domain
domain: SLIDE domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.97  E-value=0.017  Score=36.99  Aligned_cols=57  Identities=14%  Similarity=0.285  Sum_probs=47.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHc------------CCCCHHHHHHHHHHHHHHHhh
Q 034697           11 SSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAV------------SGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        11 ~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~v------------pgRT~~qc~~ry~~L~~dv~~   67 (86)
                      +.....|.|||..|.-++-+|+-+..+=|+.|-..+            -.||+.++..|...|+.-|.+
T Consensus        47 nk~k~yteeEDRfLl~~~~~~G~~~~~~~e~ir~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~k  115 (128)
T d1ofcx2          47 NKGKNYTEIEDRFLVCMLHKLGFDKENVYEELRAAIRASPQFRFDWFIKSRTALELQRRCNTLITLIER  115 (128)
T ss_dssp             CCCSSCCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHCGGGTTCHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             cCCCccCHHHHHHHHHHHHHhcCCCccHHHHHHHHHHhCcchhhhhHhccCCHHHHHHHHHHHHHHHHH
Confidence            345579999999999999999987666699997655            579999999999988766653

>d1x58a1 a.4.1.1 (A:8-56) Hypothetical protein 4930532d21rik {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hypothetical protein 4930532d21rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.85  E-value=0.099  Score=28.02  Aligned_cols=44  Identities=14%  Similarity=0.357  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcC---CCCHHHHHHHHHHH
Q 034697           14 SSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVS---GKTVEDVKKHYELL   61 (86)
Q Consensus        14 ~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vp---gRT~~qc~~ry~~L   61 (86)
                      ..||.||---|...+.+++    ..|..|-=..|   ||+..+.-..|..|
T Consensus         2 knft~eEv~YL~~GVK~~G----~~WNsILWs~PF~~GR~~vdLA~Ky~~l   48 (49)
T d1x58a1           2 KDFTKEEVNYLFHGVKTMG----NHWNSILWSFPFQKGRRAVDLAHKYHRL   48 (49)
T ss_dssp             SSCCHHHHHHHHHHHHHHC----SCHHHHHHHSCCCTTCCHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHhc----chhhhhhhccCCCCCchhhHHHHHHHhh
Confidence            4799999999999999996    46999987775   99999999988876

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.76  E-value=0.28  Score=27.77  Aligned_cols=59  Identities=14%  Similarity=0.127  Sum_probs=47.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697            8 SSRSSGSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus         8 ~~~~~~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      ++.++....|.++-.+|+......+--....=..||..+ |-+..+|+.=|++-...++.
T Consensus         2 s~~s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~-gL~~~qV~~WF~NrR~k~k~   60 (76)
T d2ecca1           2 SSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQIT-GLPRPEIIQWFGDTRYALKH   60 (76)
T ss_dssp             CCSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHT-CCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHH-ccCHHHHHHHHHHHHHHHHh
Confidence            345566789999999999998877644567788999999 69999999999887776664

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=91.16  E-value=0.35  Score=26.19  Aligned_cols=40  Identities=18%  Similarity=0.238  Sum_probs=33.6

Q ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           21 NKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        21 dk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      |+.+..+|..-+.   -.+..||+.+ |-|...|..|.+.|.+.
T Consensus         7 D~~IL~~L~~~~r---~s~~eiA~~l-~ls~~~v~~Ri~rL~~~   46 (63)
T d2cg4a1           7 DRGILEALMGNAR---TAYAELAKQF-GVSPETIHVRVEKMKQA   46 (63)
T ss_dssp             HHHHHHHHHHCTT---SCHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            6677788887653   4799999999 69999999999998765

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=90.36  E-value=0.5  Score=25.26  Aligned_cols=41  Identities=15%  Similarity=0.159  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        20 Edk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      =|..+..+|.+-+.   -.+..||+.+ |-|...|..|.++|.+.
T Consensus         4 ~D~~Il~~L~~n~r---~s~~eiA~~l-~ls~~~v~~Ri~~L~~~   44 (60)
T d2cyya1           4 IDKKIIKILQNDGK---APLREISKIT-GLAESTIHERIRKLRES   44 (60)
T ss_dssp             HHHHHHHHHHHCTT---CCHHHHHHHH-CSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            36778888888543   4799999999 69999999999998766

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=89.66  E-value=0.49  Score=25.68  Aligned_cols=41  Identities=7%  Similarity=-0.013  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        20 Edk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      =|+.+..+|.+-+.   -....||+.+ |-|...|..|.++|.+.
T Consensus         6 ~D~~IL~~L~~n~r---~s~~~iA~~l-gis~~tv~~Ri~~L~~~   46 (63)
T d2cfxa1           6 IDLNIIEELKKDSR---LSMRELGRKI-KLSPPSVTERVRQLESF   46 (63)
T ss_dssp             HHHHHHHHHHHCSC---CCHHHHHHHH-TCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            36778888887653   3699999999 79999999999998764

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=88.33  E-value=0.84  Score=24.40  Aligned_cols=41  Identities=20%  Similarity=0.267  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 034697           20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKD   64 (86)
Q Consensus        20 Edk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~d   64 (86)
                      =|+.+..+|.+-+.   -....||+.+ |-|...|..|.++|.+.
T Consensus         4 ~D~kIl~~L~~n~r---~s~~~lA~~~-gls~~~v~~Ri~~L~~~   44 (60)
T d1i1ga1           4 RDKIILEILEKDAR---TPFTEIAKKL-GISETAVRKRVKALEEK   44 (60)
T ss_dssp             HHHHHHHHHHHCTT---CCHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCC---CCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence            36778888887543   3699999999 69999999999998776

>d1fs1b1 a.157.1.1 (B:86-140) Cyclin A/CDK2-associated p45, Skp1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Skp1 dimerisation domain-like
superfamily: Skp1 dimerisation domain-like
family: Skp1 dimerisation domain-like
domain: Cyclin A/CDK2-associated p45, Skp1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.07  E-value=0.14  Score=27.95  Aligned_cols=19  Identities=37%  Similarity=0.714  Sum_probs=17.1

Q ss_pred             HHHHHHcCCCCHHHHHHHH
Q 034697           40 DNVAKAVSGKTVEDVKKHY   58 (86)
Q Consensus        40 ~~IA~~vpgRT~~qc~~ry   58 (86)
                      ..||..+.|||++|+|+.|
T Consensus        36 ~~vA~~ikgKt~eeiR~~f   54 (55)
T d1fs1b1          36 KTVANMIKGKTPEEIRKTF   54 (55)
T ss_dssp             HHHHHHHTTCCHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHh
Confidence            5799999999999999865

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=85.94  E-value=1.5  Score=23.34  Aligned_cols=52  Identities=10%  Similarity=0.061  Sum_probs=41.9

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv   65 (86)
                      ...+|.++-..|+......+.-+...=..||..+ |-+..+|+.=|++-....
T Consensus         3 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l-~l~~~~V~~WFqNrR~k~   54 (58)
T d1au7a1           3 RTTISIAAKDALERHFGEHSKPSSQEIMRMAEEL-NLEKEVVRVWFCNRRQRE   54 (58)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHH-TCCHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHh-CCCHHHHHHHHHHHhHHH
Confidence            4578999999999998887654556678999999 699999998887765543

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.67  E-value=1.5  Score=23.21  Aligned_cols=52  Identities=12%  Similarity=0.035  Sum_probs=41.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDI   65 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv   65 (86)
                      ...||.++-..|+......+--+...=+.||..+ |-|..+|+--|++-....
T Consensus         4 Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l-~l~~~~V~~WFqNrR~k~   55 (58)
T d1ig7a_           4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSL-SLTETQVKIWFQNRRAKA   55 (58)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHT-TCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHh-CCChhheeecCcchHhHh
Confidence            3579999999999998776543567788999999 699999988777654443

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=85.21  E-value=1.7  Score=23.56  Aligned_cols=46  Identities=17%  Similarity=0.225  Sum_probs=36.6

Q ss_pred             CHHHHHHHHHHHHhcCC--CCCchHHHHHHHcCCCCHHHHHHHHHHHHH
Q 034697           17 TVKQNKQFETALAFYDK--DTPDRWDNVAKAVSGKTVEDVKKHYELLVK   63 (86)
Q Consensus        17 T~eEdk~Le~al~~~~~--~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~   63 (86)
                      |.+|+++.++....|-.  ..|..+..||..+ |-+.++++...+.|..
T Consensus         2 s~~q~~l~~~I~~~~~~~g~~PP~vrdl~~~l-~~~e~~~~~lL~~l~~   49 (64)
T d1lvaa3           2 SETQKKLLKDLEDKYRVSRWQPPSFKEVAGSF-NLDPSELEELLHYLVR   49 (64)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTSCCBHHHHHHHT-TCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence            67888888888777742  2688999999999 6899999887777654

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=83.55  E-value=1.9  Score=22.84  Aligned_cols=31  Identities=16%  Similarity=0.139  Sum_probs=25.2

Q ss_pred             CchHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Q 034697           36 PDRWDNVAKAVSGKTVEDVKKHYELLVKDIND   67 (86)
Q Consensus        36 ~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~~   67 (86)
                      +-....||+.+ |.|...|+.|.......++.
T Consensus        37 ~~s~~eIA~~l-gis~~tv~~~~~ra~~~Lr~   67 (71)
T d1rp3a2          37 ELPAKEVAKIL-ETSVSRVSQLKAKALERLRE   67 (71)
T ss_dssp             CCCHHHHHHHT-TSCHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence            35789999999 69999999998776666654

>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: Transcription regulator Adr6 (Swi1)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.25  E-value=0.89  Score=26.92  Aligned_cols=44  Identities=9%  Similarity=0.177  Sum_probs=31.2

Q ss_pred             HHHHHHHhcCCC----CCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           23 QFETALAFYDKD----TPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        23 ~Le~al~~~~~~----~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      .|-.++.+++.-    ....|..||..++--...+.+..|.+++....
T Consensus        38 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~lr~~Y~~~L~~yE   85 (102)
T d1kkxa_          38 YLYMLVQKFGGADQVTRTQQWSMVAQRLQISDYQQLESIYFRILLPYE   85 (102)
T ss_dssp             HHHHHHTTTSCHHHHTTSHHHHHHHHHHTCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcChHHhcccCcHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence            345556665421    35679999999987788888888987665543

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.63  E-value=2.7  Score=23.64  Aligned_cols=53  Identities=23%  Similarity=0.211  Sum_probs=41.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      ...+|.++-..|+......+--....=+.||..+ |-+..+|+-=|++-....+
T Consensus        17 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l-~l~~~qV~iWFqNrR~k~k   69 (77)
T d1pufa_          17 RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLL-NLTERQVKIWFQNRRMKMK   69 (77)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHh-CCCHHHhhhhhhhhHHHHH
Confidence            4679999999999998887644456667899999 7999999887776544433

>d1nexa1 a.157.1.1 (A:116-185) Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Skp1 dimerisation domain-like
superfamily: Skp1 dimerisation domain-like
family: Skp1 dimerisation domain-like
domain: Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.60  E-value=0.45  Score=26.82  Aligned_cols=20  Identities=20%  Similarity=0.617  Sum_probs=17.7

Q ss_pred             HHHHHHcCCCCHHHHHHHHH
Q 034697           40 DNVAKAVSGKTVEDVKKHYE   59 (86)
Q Consensus        40 ~~IA~~vpgRT~~qc~~ry~   59 (86)
                      ..||..+.|||++|+|+.|.
T Consensus        37 ~~vA~~ikgkt~eeiR~~f~   56 (70)
T d1nexa1          37 KVVAEMIRGRSPEEIRRTFN   56 (70)
T ss_dssp             HHHHHHHTTCCHHHHHHHHT
T ss_pred             HHHHHHHccCCHHHHHHHhC
Confidence            57999999999999998774

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=82.58  E-value=2.4  Score=22.98  Aligned_cols=53  Identities=9%  Similarity=0.104  Sum_probs=42.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCCchHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Q 034697           13 GSSWTVKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDIN   66 (86)
Q Consensus        13 ~~~WT~eEdk~Le~al~~~~~~~~~rW~~IA~~vpgRT~~qc~~ry~~L~~dv~   66 (86)
                      ...+|.++...|+......+--....=..||..+ |-+..+|+.-|++-....+
T Consensus         6 Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~l-gl~~~~V~~WFqNrR~k~k   58 (65)
T d1fjla_           6 RTTFSASQLDELERAFERTQYPDIYTREELAQRT-NLTEARIQVWFQNRRARLR   58 (65)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHh-CCCHHHhhHhhhhHHHHHH
Confidence            4579999999999998876644567788999999 6999999888877655444