Query 010311
Match_columns 513
No_of_seqs 207 out of 1320
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 23:02:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010311.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010311hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.6 2.8E-16 6E-21 156.1 4.4 66 9-74 156-221 (261)
2 KOG0488 Transcription factor B 99.6 6.8E-16 1.5E-20 157.2 7.2 67 7-73 167-233 (309)
3 KOG0843 Transcription factor E 99.5 9.4E-15 2E-19 138.9 6.4 65 10-74 100-164 (197)
4 KOG0842 Transcription factor t 99.5 9.8E-15 2.1E-19 148.5 6.0 71 9-79 150-220 (307)
5 PF00046 Homeobox: Homeobox do 99.5 1.9E-14 4.1E-19 110.6 6.0 57 13-69 1-57 (57)
6 KOG0484 Transcription factor P 99.5 2.4E-14 5.2E-19 126.3 7.0 67 10-76 15-81 (125)
7 KOG2251 Homeobox transcription 99.5 6.1E-14 1.3E-18 136.8 9.6 67 8-74 33-99 (228)
8 KOG0487 Transcription factor A 99.5 1E-14 2.2E-19 148.4 4.2 63 10-72 233-295 (308)
9 KOG0850 Transcription factor D 99.5 8.9E-14 1.9E-18 136.4 7.1 65 8-72 118-182 (245)
10 KOG0485 Transcription factor N 99.5 4.5E-14 9.8E-19 137.7 4.6 68 9-76 101-168 (268)
11 KOG0494 Transcription factor C 99.4 1.2E-13 2.5E-18 137.7 5.7 63 10-72 138-201 (332)
12 KOG0492 Transcription factor M 99.4 1.5E-13 3.1E-18 133.4 5.2 67 10-76 142-208 (246)
13 KOG0848 Transcription factor C 99.4 1.8E-13 3.9E-18 136.7 3.5 66 10-75 197-262 (317)
14 KOG0486 Transcription factor P 99.4 1.2E-12 2.5E-17 133.2 9.2 65 11-75 111-175 (351)
15 cd00086 homeodomain Homeodomai 99.4 1.1E-12 2.3E-17 100.1 6.3 58 13-70 1-58 (59)
16 smart00389 HOX Homeodomain. DN 99.4 8.7E-13 1.9E-17 100.2 5.8 56 13-68 1-56 (56)
17 KOG0493 Transcription factor E 99.3 1.3E-12 2.7E-17 130.4 5.2 63 9-71 243-305 (342)
18 TIGR01565 homeo_ZF_HD homeobox 99.3 3.3E-12 7.1E-17 101.9 5.2 53 12-64 1-57 (58)
19 KOG3802 Transcription factor O 99.3 1.9E-12 4E-17 135.1 3.8 62 10-71 292-353 (398)
20 KOG0483 Transcription factor H 99.3 4.2E-12 9E-17 122.8 4.8 64 12-75 50-113 (198)
21 KOG0491 Transcription factor B 99.2 4.8E-12 1E-16 119.4 3.8 65 9-73 97-161 (194)
22 COG5576 Homeodomain-containing 99.2 1.7E-11 3.6E-16 114.7 6.9 66 8-73 47-112 (156)
23 KOG4577 Transcription factor L 99.2 1.3E-11 2.8E-16 124.7 5.2 69 8-76 163-231 (383)
24 KOG0847 Transcription factor, 99.1 5.6E-11 1.2E-15 116.5 6.0 68 9-76 164-231 (288)
25 KOG0844 Transcription factor E 99.1 2E-11 4.3E-16 124.1 1.8 64 8-71 177-240 (408)
26 KOG0490 Transcription factor, 99.0 2.1E-10 4.6E-15 108.4 3.0 64 9-72 57-120 (235)
27 KOG0849 Transcription factor P 98.7 7.3E-09 1.6E-13 107.7 5.0 66 6-71 170-235 (354)
28 KOG0775 Transcription factor S 98.7 4.7E-08 1E-12 98.6 9.8 65 5-69 160-233 (304)
29 KOG1168 Transcription factor A 98.7 6.4E-09 1.4E-13 105.6 2.1 63 9-71 306-368 (385)
30 KOG0774 Transcription factor P 98.1 6.8E-06 1.5E-10 83.0 7.8 60 12-71 188-250 (334)
31 PF05920 Homeobox_KN: Homeobox 98.0 4.8E-06 1E-10 62.0 2.8 34 33-66 7-40 (40)
32 KOG0490 Transcription factor, 97.8 2.6E-05 5.6E-10 74.0 4.7 66 7-72 148-213 (235)
33 KOG2252 CCAAT displacement pro 97.7 5.3E-05 1.1E-09 82.8 5.6 58 10-67 418-475 (558)
34 KOG1146 Homeobox protein [Gene 97.1 0.00063 1.4E-08 80.5 5.6 92 10-106 901-992 (1406)
35 KOG0773 Transcription factor M 95.4 0.0086 1.9E-07 61.6 2.4 63 12-74 239-304 (342)
36 PF11569 Homez: Homeodomain le 95.3 0.014 3E-07 47.1 2.7 41 24-64 10-50 (56)
37 KOG3623 Homeobox transcription 90.1 0.38 8.1E-06 55.3 4.8 48 24-71 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 86.9 1.2 2.7E-05 34.8 4.5 46 13-63 1-46 (53)
39 PF04545 Sigma70_r4: Sigma-70, 65.2 12 0.00026 28.1 4.1 46 18-68 4-49 (50)
40 cd06171 Sigma70_r4 Sigma70, re 55.3 14 0.0003 26.1 2.9 43 18-65 10-52 (55)
41 PRK03975 tfx putative transcri 47.3 40 0.00087 31.8 5.3 50 16-71 4-53 (141)
42 PF01527 HTH_Tnp_1: Transposas 46.8 19 0.00041 28.7 2.7 44 14-61 2-45 (76)
43 PF04967 HTH_10: HTH DNA bindi 44.6 33 0.00072 27.3 3.7 40 19-58 1-42 (53)
44 cd00569 HTH_Hin_like Helix-tur 41.9 71 0.0015 19.8 4.5 38 18-60 5-42 (42)
45 PF00196 GerE: Bacterial regul 37.0 59 0.0013 25.1 4.0 45 18-68 3-47 (58)
46 PF10668 Phage_terminase: Phag 36.8 24 0.00053 29.0 1.9 20 41-60 24-43 (60)
47 PF08281 Sigma70_r4_2: Sigma-7 34.4 73 0.0016 23.9 4.1 42 18-64 10-51 (54)
48 COG3413 Predicted DNA binding 31.0 54 0.0012 31.9 3.6 41 18-58 155-197 (215)
49 smart00421 HTH_LUXR helix_turn 30.5 1.2E+02 0.0026 21.8 4.6 40 18-63 3-42 (58)
50 KOG1146 Homeobox protein [Gene 29.3 59 0.0013 40.5 4.1 64 8-71 701-764 (1406)
51 PRK06759 RNA polymerase factor 28.8 1.1E+02 0.0024 27.1 4.9 46 19-69 107-152 (154)
52 PF04910 Tcf25: Transcriptiona 28.6 26 0.00056 37.2 1.0 26 212-239 335-360 (360)
53 PF09607 BrkDBD: Brinker DNA-b 28.4 1E+02 0.0023 25.3 4.2 44 16-61 3-47 (58)
54 PRK12515 RNA polymerase sigma 26.9 1.4E+02 0.0029 27.8 5.4 32 41-72 149-180 (189)
55 PRK09644 RNA polymerase sigma 25.3 1.5E+02 0.0033 26.8 5.3 31 41-71 126-156 (165)
56 PRK09646 RNA polymerase sigma 24.9 1E+02 0.0022 28.9 4.1 48 19-71 143-190 (194)
57 TIGR02937 sigma70-ECF RNA poly 24.8 1.2E+02 0.0027 25.5 4.3 46 19-69 111-156 (158)
58 PRK09642 RNA polymerase sigma 24.2 1.5E+02 0.0032 26.6 4.9 30 42-71 125-154 (160)
59 PF08280 HTH_Mga: M protein tr 23.6 90 0.0019 24.6 3.0 37 21-61 5-41 (59)
60 PRK04217 hypothetical protein; 23.3 1.5E+02 0.0033 26.9 4.8 50 17-71 41-90 (110)
61 cd04761 HTH_MerR-SF Helix-Turn 23.2 67 0.0014 23.3 2.1 22 42-63 3-24 (49)
62 PRK12526 RNA polymerase sigma 23.1 1.4E+02 0.0031 28.4 4.8 32 40-71 170-201 (206)
63 PF13518 HTH_28: Helix-turn-he 22.5 70 0.0015 23.5 2.1 22 41-62 14-35 (52)
64 PRK09652 RNA polymerase sigma 22.4 1.5E+02 0.0032 26.6 4.6 47 19-70 129-175 (182)
65 PF13443 HTH_26: Cro/C1-type H 22.1 89 0.0019 24.0 2.7 30 41-70 12-41 (63)
66 cd06170 LuxR_C_like C-terminal 21.8 2E+02 0.0044 20.7 4.5 36 20-61 2-37 (57)
67 TIGR02985 Sig70_bacteroi1 RNA 21.7 1.8E+02 0.0039 25.4 4.9 29 41-69 131-159 (161)
68 PRK12512 RNA polymerase sigma 21.6 1.5E+02 0.0033 27.3 4.6 32 41-72 149-180 (184)
69 PRK12514 RNA polymerase sigma 21.5 96 0.0021 28.4 3.2 30 41-70 147-176 (179)
70 PRK11924 RNA polymerase sigma 21.5 1.1E+02 0.0025 27.3 3.6 31 41-71 143-173 (179)
71 PF13936 HTH_38: Helix-turn-he 21.3 1E+02 0.0022 23.1 2.8 41 16-61 2-42 (44)
72 PRK09413 IS2 repressor TnpA; R 20.8 1.6E+02 0.0035 26.3 4.4 42 15-60 9-50 (121)
73 TIGR02948 SigW_bacill RNA poly 20.2 1.7E+02 0.0036 26.8 4.5 32 39-70 152-183 (187)
74 TIGR02989 Sig-70_gvs1 RNA poly 20.1 1.8E+02 0.004 25.7 4.6 30 39-68 127-156 (159)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.61 E-value=2.8e-16 Score=156.14 Aligned_cols=66 Identities=30% Similarity=0.429 Sum_probs=61.8
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhh
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDE 74 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e 74 (513)
..+.||.||.||..||.+||+.|..|+|.+...|.|||..|.|+|+||+|||||||+||||..+..
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 356789999999999999999999999999999999999999999999999999999999987444
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.61 E-value=6.8e-16 Score=157.21 Aligned_cols=67 Identities=30% Similarity=0.473 Sum_probs=63.0
Q ss_pred cCCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhh
Q 010311 7 KVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVD 73 (513)
Q Consensus 7 k~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~ 73 (513)
...+|+|+.||.||..||..||+.|++.+|.+..+|.+||..|||+..||++||||||+||||....
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 4457888899999999999999999999999999999999999999999999999999999998754
No 3
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.53 E-value=9.4e-15 Score=138.94 Aligned_cols=65 Identities=31% Similarity=0.541 Sum_probs=61.8
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhh
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDE 74 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e 74 (513)
.+.||.||.||.+||..||..|+.+.|....+|+.||..|+|++.||+|||||||.|.||.+..+
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 37789999999999999999999999999999999999999999999999999999999998654
No 4
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.52 E-value=9.8e-15 Score=148.49 Aligned_cols=71 Identities=31% Similarity=0.447 Sum_probs=64.8
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhhhhCC
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAFVGG 79 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~~~~~ 79 (513)
.++|||.|..|+..|+.+||+.|..++|++..+|+.||..|.||++||+|||||||-|.||+.+++.....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 45778888999999999999999999999999999999999999999999999999999999876655443
No 5
>PF00046 Homeobox: Homeobox domain not present here.; 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 ....
Probab=99.52 E-value=1.9e-14 Score=110.55 Aligned_cols=57 Identities=42% Similarity=0.761 Sum_probs=55.2
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhh
Q 010311 13 NIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69 (513)
Q Consensus 13 RRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR 69 (513)
|++|+.||..|+.+|+..|..++||+..++..||.+|||+..+|++||+|||+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999986
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.51 E-value=2.4e-14 Score=126.34 Aligned_cols=67 Identities=30% Similarity=0.414 Sum_probs=62.4
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhhh
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAF 76 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~~ 76 (513)
++.||-||.||..||..||..|...+||++-.|++||.++.|++.+|||||||||+|.||+.+....
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 5678889999999999999999999999999999999999999999999999999999998755543
No 7
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.50 E-value=6.1e-14 Score=136.75 Aligned_cols=67 Identities=27% Similarity=0.426 Sum_probs=63.5
Q ss_pred CCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhh
Q 010311 8 VSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDE 74 (513)
Q Consensus 8 ~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e 74 (513)
..++.||.||+|+..||++||..|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++..
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 4678899999999999999999999999999999999999999999999999999999999987544
No 8
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.50 E-value=1e-14 Score=148.38 Aligned_cols=63 Identities=35% Similarity=0.463 Sum_probs=60.4
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhh
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk 72 (513)
+..||||..+|+.|+.+||+.|..|.|++.+.|.+|++.|+|++|||+|||||||.|.||..+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 667888999999999999999999999999999999999999999999999999999999874
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.46 E-value=8.9e-14 Score=136.35 Aligned_cols=65 Identities=28% Similarity=0.412 Sum_probs=61.5
Q ss_pred CCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhh
Q 010311 8 VSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72 (513)
Q Consensus 8 ~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk 72 (513)
..+|-||.||.++..||..|.+.|++++|+-..+|.+||..|||+..||+|||||||.|.||..+
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 35677889999999999999999999999999999999999999999999999999999999875
No 10
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.45 E-value=4.5e-14 Score=137.69 Aligned_cols=68 Identities=31% Similarity=0.368 Sum_probs=63.1
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhhh
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAF 76 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~~ 76 (513)
..+|||.||+|+..|+..||..|+..+|.+..+|.-||.+|.|+|.||+|||||||.||||+...+..
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 34788899999999999999999999999999999999999999999999999999999999755543
No 11
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.43 E-value=1.2e-13 Score=137.65 Aligned_cols=63 Identities=29% Similarity=0.428 Sum_probs=58.0
Q ss_pred cCCCCC-CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhh
Q 010311 10 LEKNIK-RRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72 (513)
Q Consensus 10 rkkRRk-RT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk 72 (513)
+++||. ||.||..|++.||+.|+...||+..-|+.||.++.|.+.+|+|||||||+||||.++
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 334444 999999999999999999999999999999999999999999999999999999864
No 12
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.41 E-value=1.5e-13 Score=133.41 Aligned_cols=67 Identities=33% Similarity=0.435 Sum_probs=61.6
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhhh
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAF 76 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~~ 76 (513)
+-.|+.||.||.+||..||+.|...+|.++++|.+++..|.|++.||+|||||||+|.||.+..+..
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 3457889999999999999999999999999999999999999999999999999999998855543
No 13
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.38 E-value=1.8e-13 Score=136.72 Aligned_cols=66 Identities=35% Similarity=0.471 Sum_probs=60.2
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhh
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEA 75 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~ 75 (513)
+.+-|-|.++|..|+.+||+.|..++|+++..+.|||..|||+||||+|||||||+|+||..++..
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 344456889999999999999999999999999999999999999999999999999999876553
No 14
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.38 E-value=1.2e-12 Score=133.23 Aligned_cols=65 Identities=26% Similarity=0.430 Sum_probs=61.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhh
Q 010311 11 EKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEA 75 (513)
Q Consensus 11 kkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~ 75 (513)
|+||.||.||.+||..||.+|+++.||+..+|++||..++|++.+|+|||.|||+||||.+....
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 67788999999999999999999999999999999999999999999999999999999885554
No 15
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.37 E-value=1.1e-12 Score=100.11 Aligned_cols=58 Identities=43% Similarity=0.671 Sum_probs=54.7
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhh
Q 010311 13 NIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70 (513)
Q Consensus 13 RRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~ 70 (513)
++.|+.|+..|+.+|+.+|..++||+..++..||.++||+..+|++||+|||.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3568899999999999999999999999999999999999999999999999998764
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.37 E-value=8.7e-13 Score=100.22 Aligned_cols=56 Identities=41% Similarity=0.662 Sum_probs=52.6
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHh
Q 010311 13 NIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68 (513)
Q Consensus 13 RRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~K 68 (513)
++.|+.|+..|+.+|+.+|..++||+..++..||..+||+..||+.||+|||.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999999999999999999999999999999999998754
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.32 E-value=1.3e-12 Score=130.44 Aligned_cols=63 Identities=32% Similarity=0.511 Sum_probs=59.1
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
...-||.||.||.+||..|+..|+.+.|.+...|.+||.+|||.+.||+|||||+|+|.||..
T Consensus 243 ~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 243 SKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 344578899999999999999999999999999999999999999999999999999999875
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.29 E-value=3.3e-12 Score=101.94 Aligned_cols=53 Identities=23% Similarity=0.354 Sum_probs=50.9
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCChhhhhhhhhchh
Q 010311 12 KNIKRRYKTPAQVMALEKFYNEHKY----PTEEMKSQVAEQIGLTEKQVSGWFCHRR 64 (513)
Q Consensus 12 kRRkRT~FT~~QLevLEk~Fekn~Y----PS~~eReeLA~eLGLSerQVqVWFQNRR 64 (513)
+||.||.||.+|+..|+..|+.++| |+..++.+||..|||++++|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999964
No 19
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.27 E-value=1.9e-12 Score=135.08 Aligned_cols=62 Identities=35% Similarity=0.518 Sum_probs=60.0
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
.+|||+||.|+...+..||++|.+|+.|+..++..||.+|+|...+|+|||||||.|.||..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 47899999999999999999999999999999999999999999999999999999999986
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.25 E-value=4.2e-12 Score=122.77 Aligned_cols=64 Identities=33% Similarity=0.451 Sum_probs=58.4
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhh
Q 010311 12 KNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEA 75 (513)
Q Consensus 12 kRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~ 75 (513)
...++.+|+.+|+..||..|+.+.+.....+..||.+|||.++||.|||||||+|||.++....
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d 113 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKD 113 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhh
Confidence 4456678999999999999999999999999999999999999999999999999999875443
No 21
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.23 E-value=4.8e-12 Score=119.39 Aligned_cols=65 Identities=26% Similarity=0.482 Sum_probs=60.7
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhh
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVD 73 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~ 73 (513)
.-+++|.||.|+..|+..||+.|+.++|.+..+|.|||..|+|++.||+.||||||.|.||.++.
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 34567889999999999999999999999999999999999999999999999999999998743
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.22 E-value=1.7e-11 Score=114.73 Aligned_cols=66 Identities=29% Similarity=0.431 Sum_probs=61.2
Q ss_pred CCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhh
Q 010311 8 VSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVD 73 (513)
Q Consensus 8 ~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~ 73 (513)
.+...+++|++.|..|+.+|+..|+.++||+..+|..|+..|+|+++-||+||||||++.|+....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 346678889999999999999999999999999999999999999999999999999999998643
No 23
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.20 E-value=1.3e-11 Score=124.69 Aligned_cols=69 Identities=30% Similarity=0.444 Sum_probs=63.5
Q ss_pred CCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhhh
Q 010311 8 VSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAF 76 (513)
Q Consensus 8 ~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~~ 76 (513)
.....||+||++|+.||+.|+.+|+..+.|-...|+.|+.++||.-+.|||||||||+|+||.++++..
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 345678899999999999999999999999999999999999999999999999999999999866643
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.13 E-value=5.6e-11 Score=116.50 Aligned_cols=68 Identities=28% Similarity=0.411 Sum_probs=62.2
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhhh
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAF 76 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~~ 76 (513)
.++++..|.+|+..|+..||..|+..+|+-..+|.+||..+|+++.||+|||||||+||||+-..+..
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence 35667788899999999999999999999999999999999999999999999999999998755544
No 25
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.11 E-value=2e-11 Score=124.06 Aligned_cols=64 Identities=27% Similarity=0.414 Sum_probs=60.1
Q ss_pred CCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 8 VSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 8 ~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
...+-||-||.||.+||..||+.|-+..|.+...|.|||..|+|.|..|+|||||||.|+||+.
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 3455678899999999999999999999999999999999999999999999999999999985
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.98 E-value=2.1e-10 Score=108.44 Aligned_cols=64 Identities=23% Similarity=0.286 Sum_probs=60.6
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhh
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk 72 (513)
..++++.|+.|+..|++.||..|+..+||+...|+.||..++|++..|++||||||+||++...
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4577889999999999999999999999999999999999999999999999999999999863
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.75 E-value=7.3e-09 Score=107.70 Aligned_cols=66 Identities=29% Similarity=0.442 Sum_probs=62.1
Q ss_pred ccCCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 6 NKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 6 nk~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
+...++.++.||+|+..|+..|+..|+.++||....|++||.+++|++..|++||+|||++|+|..
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 455677788899999999999999999999999999999999999999999999999999999986
No 28
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.73 E-value=4.7e-08 Score=98.63 Aligned_cols=65 Identities=29% Similarity=0.489 Sum_probs=56.6
Q ss_pred cccCCcCCCCCCc---------cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhh
Q 010311 5 ENKVSLEKNIKRR---------YKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69 (513)
Q Consensus 5 enk~srkkRRkRT---------~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR 69 (513)
+.++.+|..-+|| +|...-+.+|..+|..++||+..++.+||+.+||+..||-.||.|||+|+|-
T Consensus 160 KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 160 KYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred cceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 3455556666676 4677779999999999999999999999999999999999999999999993
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.68 E-value=6.4e-09 Score=105.55 Aligned_cols=63 Identities=30% Similarity=0.535 Sum_probs=59.8
Q ss_pred CcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 9 SLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 9 srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
...|||+||.+..-....||++|..++.|+.+.+..||++|.|....|+|||||+|+|.||.+
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 357889999999999999999999999999999999999999999999999999999999975
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.12 E-value=6.8e-06 Score=83.01 Aligned_cols=60 Identities=32% Similarity=0.542 Sum_probs=55.7
Q ss_pred CCCCCccCCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 12 KNIKRRYKTPAQVMALEKFY---NEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 12 kRRkRT~FT~~QLevLEk~F---ekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
.+|+|..|+....++|..+| ..++||+.+.+++||.++|++..||..||.|.|-+.||-.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 36788899999999999999 5789999999999999999999999999999999998865
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=97.98 E-value=4.8e-06 Score=62.04 Aligned_cols=34 Identities=41% Similarity=0.816 Sum_probs=29.0
Q ss_pred hCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhh
Q 010311 33 EHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLK 66 (513)
Q Consensus 33 kn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK 66 (513)
.++||+..++.+||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 5799999999999999999999999999998864
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.78 E-value=2.6e-05 Score=74.05 Aligned_cols=66 Identities=26% Similarity=0.394 Sum_probs=61.2
Q ss_pred cCCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhh
Q 010311 7 KVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72 (513)
Q Consensus 7 k~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk 72 (513)
....+.++.|+.++..|+..|...|....+|+...+..|+..+|++++.|++||+|+|++.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 445677888999999999999999999999999999999999999999999999999999999764
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.66 E-value=5.3e-05 Score=82.76 Aligned_cols=58 Identities=26% Similarity=0.410 Sum_probs=54.3
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhH
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKE 67 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~ 67 (513)
...||.|.+||..|+..|..+|+.+++|+.++.+.|+.+|+|...-|.+||-|-|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 4667789999999999999999999999999999999999999999999999987664
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.08 E-value=0.00063 Score=80.48 Aligned_cols=92 Identities=21% Similarity=0.350 Sum_probs=75.3
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhhhhhCCCCCCCCCccc
Q 010311 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAFVGGRQDRSSGVIQ 89 (513)
Q Consensus 10 rkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e~~~~~r~d~ssg~iq 89 (513)
-.++..|+.++..||.++...|....||...+.+.|...++|..+.|++||||-|+|.++... ++..+.+.+...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~-----n~~~~ss~~~s~ 975 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL-----NGTAASSTGGSS 975 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh-----cccccccccccc
Confidence 456778999999999999999999999999999999999999999999999999999998764 223444555555
Q ss_pred cCCCCCCCCCCCCCCCC
Q 010311 90 DRGSGLRQDSCGSTKQG 106 (513)
Q Consensus 90 ~~gsgl~p~sc~Ss~~~ 106 (513)
.+++...+..|.-....
T Consensus 976 sp~s~~q~k~~~~~~~~ 992 (1406)
T KOG1146|consen 976 SPLSAAQPKDCPYCDVK 992 (1406)
T ss_pred CcccccCCCcccccCcc
Confidence 66666777666655544
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.44 E-value=0.0086 Score=61.60 Aligned_cols=63 Identities=30% Similarity=0.450 Sum_probs=52.4
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhhhhh
Q 010311 12 KNIKRRYKTPAQVMALEKFYN---EHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDE 74 (513)
Q Consensus 12 kRRkRT~FT~~QLevLEk~Fe---kn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk~e 74 (513)
+.+.+..|......+|+.|.. .++||+..++..||.++||+..||.+||-|.|.|..+-....
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~ 304 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE 304 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence 445566899999999998852 368999999999999999999999999999988866655433
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.33 E-value=0.014 Score=47.06 Aligned_cols=41 Identities=29% Similarity=0.562 Sum_probs=31.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchh
Q 010311 24 VMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64 (513)
Q Consensus 24 LevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRR 64 (513)
+..|+..|...+++.......|..+.+|+..||+.||-.|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 46699999999999999999999999999999999997654
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=90.10 E-value=0.38 Score=55.32 Aligned_cols=48 Identities=29% Similarity=0.510 Sum_probs=44.9
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 24 VMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 24 LevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
+.+|...|..|..|+..+...+|.+.||+.+.|+.||+++++......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 789999999999999999999999999999999999999998877654
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=86.86 E-value=1.2 Score=34.81 Aligned_cols=46 Identities=22% Similarity=0.289 Sum_probs=34.5
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhch
Q 010311 13 NIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHR 63 (513)
Q Consensus 13 RRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNR 63 (513)
|++|..+|-++...+-..++... ....||.++|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 47889999998877777777655 57789999999999999999874
No 39
>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. 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 ....
Probab=65.18 E-value=12 Score=28.08 Aligned_cols=46 Identities=15% Similarity=0.164 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHh
Q 010311 18 YKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68 (513)
Q Consensus 18 ~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~K 68 (513)
.+++.+..+|...|- ....-.++|..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 478899999999982 2234678899999999999988765444433
No 40
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=55.32 E-value=14 Score=26.11 Aligned_cols=43 Identities=12% Similarity=0.072 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhh
Q 010311 18 YKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRL 65 (513)
Q Consensus 18 ~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRa 65 (513)
.++..+..++...|... ....++|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46778888888877422 23567899999999999999865443
No 41
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=47.35 E-value=40 Score=31.80 Aligned_cols=50 Identities=16% Similarity=0.140 Sum_probs=39.4
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 16 RRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 16 RT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
...+++.|+++|...++ . ....++|..||++...|..|.++.+.+.++..
T Consensus 4 ~~~Lt~rqreVL~lr~~--G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLRER--G----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45789999999988432 2 23568999999999999999998777776654
No 42
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=46.78 E-value=19 Score=28.69 Aligned_cols=44 Identities=27% Similarity=0.373 Sum_probs=28.7
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 010311 14 IKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFC 61 (513)
Q Consensus 14 RkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQ 61 (513)
++|..||.++...+-..+.. ......+||.++|+++.+|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 46788999887777666522 235678899999999999999953
No 43
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=44.56 E-value=33 Score=27.33 Aligned_cols=40 Identities=25% Similarity=0.288 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCChhhhhh
Q 010311 19 KTPAQVMALEKFYNEHK--YPTEEMKSQVAEQIGLTEKQVSG 58 (513)
Q Consensus 19 FT~~QLevLEk~Fekn~--YPS~~eReeLA~eLGLSerQVqV 58 (513)
+|..|+++|..+|+.-= +|-.....+||.+||++..-+..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 58899999999997543 36677888999999999877654
No 44
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=41.88 E-value=71 Score=19.84 Aligned_cols=38 Identities=13% Similarity=0.307 Sum_probs=26.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 010311 18 YKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWF 60 (513)
Q Consensus 18 ~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWF 60 (513)
.++..+...+...|.. .. ...++|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 3566666666666653 22 45678899999999888874
No 45
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=37.02 E-value=59 Score=25.07 Aligned_cols=45 Identities=20% Similarity=0.188 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHh
Q 010311 18 YKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68 (513)
Q Consensus 18 ~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~K 68 (513)
.||..++.+|.....-.. ..++|..+++++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~~------~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS------NKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcCC------cchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 588899999988765443 778999999999999999877665544
No 46
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=36.77 E-value=24 Score=28.97 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCChhhhhhhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWF 60 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWF 60 (513)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999994
No 47
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. 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 are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; 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: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=34.42 E-value=73 Score=23.91 Aligned_cols=42 Identities=19% Similarity=0.147 Sum_probs=28.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchh
Q 010311 18 YKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64 (513)
Q Consensus 18 ~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRR 64 (513)
.+++.+..++...|- ....-.++|..+|+++..|+.|.+.-|
T Consensus 10 ~L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp CS-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356677777766553 334577899999999999999987544
No 48
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=30.99 E-value=54 Score=31.86 Aligned_cols=41 Identities=22% Similarity=0.336 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHhhC--CCCCHHHHHHHHHHhCCChhhhhh
Q 010311 18 YKTPAQVMALEKFYNEH--KYPTEEMKSQVAEQIGLTEKQVSG 58 (513)
Q Consensus 18 ~FT~~QLevLEk~Fekn--~YPS~~eReeLA~eLGLSerQVqV 58 (513)
.+|..|+++|..+|..- -||-.....+||+++|+++.-+.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 69999999999999754 447777888999999999876443
No 49
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=30.47 E-value=1.2e+02 Score=21.76 Aligned_cols=40 Identities=23% Similarity=0.318 Sum_probs=29.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhch
Q 010311 18 YKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHR 63 (513)
Q Consensus 18 ~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNR 63 (513)
.++..+..++...+. . ....++|..+|++...|..|.+.-
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 467788887766432 2 245788999999999999987643
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=29.34 E-value=59 Score=40.49 Aligned_cols=64 Identities=17% Similarity=0.267 Sum_probs=57.0
Q ss_pred CCcCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 8 VSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 8 ~srkkRRkRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
.+.+.+.-|..+-..++.+|-.+|-.+.-|+...+.-|......+.+++++||+|-|.|.++..
T Consensus 701 ~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 701 LSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 3445566777788899999999999999999999999999999999999999999999988765
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=28.81 E-value=1.1e+02 Score=27.06 Aligned_cols=46 Identities=11% Similarity=0.001 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhh
Q 010311 19 KTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69 (513)
Q Consensus 19 FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR 69 (513)
+++.|..++...|-. .....+||..+|++...|+.|...-+.+.|+
T Consensus 107 L~~~~r~ii~l~~~~-----~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERFFV-----GKTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 455556665554422 2347789999999999999998765555443
No 52
>PF04910 Tcf25: Transcriptional repressor TCF25; InterPro: IPR006994 This entry appears to represent a novel family of basic helix-loop-helix (bHLH) proteins that control differentiation and development of a variety of organs [, ]. Human Nulp1 (Q2MK75 from SWISSPROT) is a basic helix-loop-helix protein expressed broadly during early embryonic organogenesis. Over expression of human Nulp1 in COS-7 cells inhibits the transcriptional activity of serum response factor (SRF), suggesting that Nulp1 may act as a novel bHLH transcriptional repressor in the SRF signalling pathway to mediate cellular functions [].
Probab=28.56 E-value=26 Score=37.21 Aligned_cols=26 Identities=42% Similarity=0.763 Sum_probs=19.7
Q ss_pred HHHHHHHhCccccccCCCcccccCCCCC
Q 010311 212 ISAVKRQLGRHYREDGPPLGVDFDPLPP 239 (513)
Q Consensus 212 I~aVe~qLG~p~rEDGP~LG~eFDpLPP 239 (513)
+..|-+-|...+.+.+|+. +||||||
T Consensus 335 ~~~~~~~lP~~i~~~~~~~--~fDPLPP 360 (360)
T PF04910_consen 335 FSSLMALLPREIWENQPVY--EFDPLPP 360 (360)
T ss_pred CCcccccCCHHHhcCCCCC--CCCCCCC
Confidence 3445566778888888765 8999998
No 53
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=28.36 E-value=1e+02 Score=25.35 Aligned_cols=44 Identities=18% Similarity=0.233 Sum_probs=22.0
Q ss_pred CccCCHHH-HHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 010311 16 RRYKTPAQ-VMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFC 61 (513)
Q Consensus 16 RT~FT~~Q-LevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQ 61 (513)
|..|+... |.+++-++ .+.---..+|. .|.+.|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~-~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAE-KDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHH-H-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHH-HccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 44566544 44444443 33322223343 49999999999999964
No 54
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.89 E-value=1.4e+02 Score=27.83 Aligned_cols=32 Identities=25% Similarity=0.238 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCChhhhhhhhhchhhhHhhhhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk 72 (513)
...++|..+|+++..|++....-|.+.++...
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999998877777777654
No 55
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=25.33 E-value=1.5e+02 Score=26.81 Aligned_cols=31 Identities=16% Similarity=0.129 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
...+||..+|+++..|++|.+.-|.+.|+..
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999987776666654
No 56
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=24.87 E-value=1e+02 Score=28.93 Aligned_cols=48 Identities=15% Similarity=0.053 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 19 KTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 19 FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
++..+..+|...| .......++|..||++...|+++...-|.+.|+..
T Consensus 143 L~~~~r~vl~l~~-----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAY-----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 4444555554433 22234678899999999999999977666666553
No 57
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=24.81 E-value=1.2e+02 Score=25.50 Aligned_cols=46 Identities=17% Similarity=0.111 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhh
Q 010311 19 KTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69 (513)
Q Consensus 19 FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR 69 (513)
++..|..++...|- ......+||..+|+++..|..|...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45555556554432 22345689999999999999998765555443
No 58
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=24.22 E-value=1.5e+02 Score=26.60 Aligned_cols=30 Identities=20% Similarity=0.009 Sum_probs=24.7
Q ss_pred HHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 42 KSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 42 ReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
-.++|..+|+++..|+++...-|.+.|+..
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999987777666654
No 59
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=23.64 E-value=90 Score=24.60 Aligned_cols=37 Identities=19% Similarity=0.324 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 010311 21 PAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFC 61 (513)
Q Consensus 21 ~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQ 61 (513)
..|+..|+-.+. +...+.. +||..+|++++.|+.-..
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 357888988888 6666655 899999999999876543
No 60
>PRK04217 hypothetical protein; Provisional
Probab=23.30 E-value=1.5e+02 Score=26.86 Aligned_cols=50 Identities=16% Similarity=0.141 Sum_probs=38.0
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 17 RYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 17 T~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
..++.+|++++...|...- ...+||+.+|++...|...+..-+.+.+...
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4678899888877764332 4678999999999999999877666665543
No 61
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.21 E-value=67 Score=23.29 Aligned_cols=22 Identities=9% Similarity=0.080 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChhhhhhhhhch
Q 010311 42 KSQVAEQIGLTEKQVSGWFCHR 63 (513)
Q Consensus 42 ReeLA~eLGLSerQVqVWFQNR 63 (513)
..++|+.+|+++..|+.|.++.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997543
No 62
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.05 E-value=1.4e+02 Score=28.45 Aligned_cols=32 Identities=19% Similarity=0.053 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 40 EMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 40 ~eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
....+||..+|+++..|+++...-+.+.++..
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999876666666554
No 63
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.45 E-value=70 Score=23.47 Aligned_cols=22 Identities=18% Similarity=0.484 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCChhhhhhhhhc
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCH 62 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQN 62 (513)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3556899999999999999853
No 64
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=22.45 E-value=1.5e+02 Score=26.63 Aligned_cols=47 Identities=13% Similarity=-0.038 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhhchhhhHhhh
Q 010311 19 KTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70 (513)
Q Consensus 19 FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~ 70 (513)
+++.+..+|...|- ......++|..+|+++..|+.|...-+.+.++.
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 55556666655432 222356789999999999999988655555554
No 65
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=22.14 E-value=89 Score=24.00 Aligned_cols=30 Identities=10% Similarity=0.143 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChhhhhhhhhchhhhHhhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQNRRaK~KR~ 70 (513)
...+||+.+|++...|..|+.++..+..-.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~ 41 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLD 41 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHH
Confidence 466789999999999999998774444433
No 66
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=21.84 E-value=2e+02 Score=20.73 Aligned_cols=36 Identities=22% Similarity=0.377 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 010311 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFC 61 (513)
Q Consensus 20 T~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQ 61 (513)
+..|..++...+. . ....++|..++++...|..|..
T Consensus 2 ~~~e~~i~~~~~~--~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE--G----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4566666655432 2 2567889999999999999976
No 67
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=21.67 E-value=1.8e+02 Score=25.39 Aligned_cols=29 Identities=17% Similarity=0.272 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChhhhhhhhhchhhhHhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQNRRaK~KR 69 (513)
...+||..+|+++..|+.+...-+.+.|+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999988655555443
No 68
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.60 E-value=1.5e+02 Score=27.26 Aligned_cols=32 Identities=9% Similarity=-0.059 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCChhhhhhhhhchhhhHhhhhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQNRRaK~KR~kk 72 (513)
.-.+||..+|++...|+.++..-|.+.|+...
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 45788999999999999999877777776643
No 69
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.52 E-value=96 Score=28.41 Aligned_cols=30 Identities=17% Similarity=0.267 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCChhhhhhhhhchhhhHhhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQNRRaK~KR~ 70 (513)
...+||..+|+++..|+++...-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 367899999999999999988666666554
No 70
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.48 E-value=1.1e+02 Score=27.25 Aligned_cols=31 Identities=16% Similarity=0.145 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhhhhhhhchhhhHhhhh
Q 010311 41 MKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71 (513)
Q Consensus 41 eReeLA~eLGLSerQVqVWFQNRRaK~KR~k 71 (513)
.-.+||..+|+++..|..|...-|.+.|+..
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999999987666666543
No 71
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.28 E-value=1e+02 Score=23.06 Aligned_cols=41 Identities=17% Similarity=0.214 Sum_probs=20.8
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 010311 16 RRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFC 61 (513)
Q Consensus 16 RT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWFQ 61 (513)
.+.+|.+|+..++..++.. ....+||..+|.+..-|..|..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 3567888888888886532 4456799999999999888764
No 72
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.82 E-value=1.6e+02 Score=26.26 Aligned_cols=42 Identities=31% Similarity=0.298 Sum_probs=27.5
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 010311 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWF 60 (513)
Q Consensus 15 kRT~FT~~QLevLEk~Fekn~YPS~~eReeLA~eLGLSerQVqVWF 60 (513)
+|..++.++....-.....+. ....++|.++|++..+|..|.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHH
Confidence 355677776443333332233 235678999999999999995
No 73
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=20.19 E-value=1.7e+02 Score=26.78 Aligned_cols=32 Identities=13% Similarity=0.114 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhCCChhhhhhhhhchhhhHhhh
Q 010311 39 EEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70 (513)
Q Consensus 39 ~~eReeLA~eLGLSerQVqVWFQNRRaK~KR~ 70 (513)
...-.++|..+|+++..|+++++.-|.+.+..
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999997666666554
No 74
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=20.07 E-value=1.8e+02 Score=25.74 Aligned_cols=30 Identities=23% Similarity=0.228 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhCCChhhhhhhhhchhhhHh
Q 010311 39 EEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68 (513)
Q Consensus 39 ~~eReeLA~eLGLSerQVqVWFQNRRaK~K 68 (513)
.....++|..+|++...|.++...-|.+.+
T Consensus 127 g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 127 GVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 344678999999999999988765444443
Done!