Query 035594
Match_columns 336
No_of_seqs 134 out of 345
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 04:21:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035594.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035594hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.7 5.2E-19 1.1E-23 162.8 1.9 63 85-152 159-221 (261)
2 KOG0484 Transcription factor P 99.7 6.6E-19 1.4E-23 148.9 1.9 63 85-152 17-79 (125)
3 KOG0488 Transcription factor B 99.7 3.2E-18 6.9E-23 162.3 3.8 63 85-152 172-234 (309)
4 PF00046 Homeobox: Homeobox do 99.7 1.3E-17 2.9E-22 118.7 3.1 57 86-147 1-57 (57)
5 KOG0842 Transcription factor t 99.7 3.9E-17 8.5E-22 155.9 6.8 64 84-152 152-215 (307)
6 KOG0843 Transcription factor E 99.7 5.2E-17 1.1E-21 146.9 4.8 64 84-152 101-164 (197)
7 KOG0487 Transcription factor A 99.7 3.8E-17 8.3E-22 156.1 4.2 63 85-152 235-297 (308)
8 KOG0492 Transcription factor M 99.6 1.7E-16 3.8E-21 146.5 5.2 65 85-154 144-209 (246)
9 KOG2251 Homeobox transcription 99.6 2.1E-16 4.6E-21 145.9 4.8 63 85-152 37-99 (228)
10 KOG0494 Transcription factor C 99.6 4.1E-16 8.8E-21 148.0 3.7 63 85-152 141-203 (332)
11 smart00389 HOX Homeodomain. DN 99.6 1.7E-15 3.7E-20 106.5 3.0 56 86-146 1-56 (56)
12 cd00086 homeodomain Homeodomai 99.6 2.5E-15 5.3E-20 105.8 3.5 58 86-148 1-58 (59)
13 KOG0850 Transcription factor D 99.6 3.3E-15 7.1E-20 139.0 5.4 64 85-153 122-185 (245)
14 TIGR01565 homeo_ZF_HD homeobox 99.5 2.4E-14 5.2E-19 108.1 5.3 52 86-142 2-57 (58)
15 KOG0493 Transcription factor E 99.5 2.9E-14 6.3E-19 135.7 4.6 60 85-149 246-305 (342)
16 KOG0848 Transcription factor C 99.5 2.2E-14 4.7E-19 136.5 3.6 59 86-149 200-258 (317)
17 KOG0844 Transcription factor E 99.5 1.3E-14 2.8E-19 140.3 2.1 62 85-151 181-242 (408)
18 KOG0485 Transcription factor N 99.5 2.4E-14 5.2E-19 133.4 3.3 63 85-152 104-166 (268)
19 KOG0491 Transcription factor B 99.4 1.7E-14 3.7E-19 129.8 0.7 65 85-154 100-164 (194)
20 COG5576 Homeodomain-containing 99.4 1.9E-13 4E-18 119.7 5.4 69 79-152 45-113 (156)
21 KOG0486 Transcription factor P 99.4 2.5E-13 5.3E-18 131.2 5.8 65 84-153 111-175 (351)
22 KOG0483 Transcription factor H 99.4 2.1E-13 4.5E-18 123.7 2.2 62 86-152 51-112 (198)
23 KOG0490 Transcription factor, 99.4 2.6E-13 5.7E-18 116.9 2.7 61 85-150 60-120 (235)
24 KOG4577 Transcription factor L 99.2 7.2E-12 1.6E-16 120.9 4.1 64 83-151 165-228 (383)
25 KOG0847 Transcription factor, 99.1 1.6E-11 3.5E-16 115.1 2.4 63 85-152 167-229 (288)
26 KOG0849 Transcription factor P 99.1 2.8E-11 6.1E-16 116.7 2.5 63 85-152 176-238 (354)
27 KOG3802 Transcription factor O 98.7 8.5E-09 1.8E-13 102.1 4.6 61 85-150 294-354 (398)
28 KOG0490 Transcription factor, 98.2 1E-06 2.2E-11 76.2 3.1 61 85-150 153-213 (235)
29 KOG0775 Transcription factor S 97.8 1.7E-05 3.7E-10 76.6 3.3 54 88-146 170-232 (304)
30 KOG0774 Transcription factor P 97.7 2.6E-05 5.5E-10 75.4 3.1 64 85-152 188-253 (334)
31 KOG2252 CCAAT displacement pro 97.6 3.6E-05 7.7E-10 79.5 3.2 58 85-147 420-477 (558)
32 KOG1168 Transcription factor A 97.6 5.1E-05 1.1E-09 74.3 3.7 65 82-151 306-370 (385)
33 PF05920 Homeobox_KN: Homeobox 97.5 1.9E-05 4.2E-10 55.7 -0.2 33 107-144 8-40 (40)
34 KOG1146 Homeobox protein [Gene 96.6 0.0012 2.6E-08 74.0 2.6 61 85-150 903-963 (1406)
35 KOG0773 Transcription factor M 91.7 0.12 2.7E-06 49.0 2.6 59 85-147 239-299 (342)
36 KOG3623 Homeobox transcription 90.3 0.17 3.6E-06 55.3 2.2 51 97-152 568-618 (1007)
37 PF11569 Homez: Homeodomain le 86.4 0.2 4.3E-06 38.6 -0.2 41 97-142 10-50 (56)
38 PF04218 CENP-B_N: CENP-B N-te 72.9 4.6 0.0001 29.7 3.2 47 86-142 1-47 (53)
39 cd06171 Sigma70_r4 Sigma70, re 71.9 1.9 4.2E-05 28.1 0.9 43 91-143 10-52 (55)
40 PF04967 HTH_10: HTH DNA bindi 67.0 4.7 0.0001 30.3 2.2 39 92-134 1-40 (53)
41 PF12824 MRP-L20: Mitochondria 56.9 55 0.0012 29.6 7.5 41 88-135 82-122 (164)
42 COG3413 Predicted DNA binding 55.6 12 0.00027 33.5 3.2 41 89-134 153-195 (215)
43 cd00569 HTH_Hin_like Helix-tur 54.7 17 0.00036 20.9 2.7 40 89-138 3-42 (42)
44 smart00027 EH Eps15 homology d 48.1 16 0.00035 28.6 2.4 45 90-138 2-50 (96)
45 PF01527 HTH_Tnp_1: Transposas 48.0 12 0.00025 27.7 1.5 42 87-138 2-44 (76)
46 PF02796 HTH_7: Helix-turn-hel 44.9 9 0.0002 26.9 0.5 39 89-137 3-41 (45)
47 KOG3755 SATB1 matrix attachmen 44.8 6.4 0.00014 42.7 -0.4 64 85-149 691-758 (769)
48 PRK03975 tfx putative transcri 44.6 17 0.00037 32.2 2.3 52 90-152 5-56 (141)
49 PRK09652 RNA polymerase sigma 41.5 21 0.00046 29.3 2.2 40 91-140 128-167 (182)
50 PRK09413 IS2 repressor TnpA; R 40.1 24 0.00052 29.3 2.4 41 87-137 8-49 (121)
51 smart00421 HTH_LUXR helix_turn 40.1 24 0.00051 23.5 2.0 38 91-139 3-40 (58)
52 PRK09646 RNA polymerase sigma 40.0 26 0.00057 30.2 2.7 39 91-139 142-180 (194)
53 PF04545 Sigma70_r4: Sigma-70, 39.6 19 0.00041 25.1 1.5 38 91-138 4-41 (50)
54 TIGR02937 sigma70-ECF RNA poly 39.2 21 0.00046 27.4 1.8 46 91-146 110-155 (158)
55 PRK09642 RNA polymerase sigma 38.5 27 0.00058 28.8 2.4 46 92-147 107-152 (160)
56 PRK06759 RNA polymerase factor 36.4 23 0.00049 28.8 1.7 40 91-140 106-145 (154)
57 TIGR02948 SigW_bacill RNA poly 34.9 28 0.0006 29.2 2.0 47 91-147 136-182 (187)
58 PRK12526 RNA polymerase sigma 33.9 34 0.00073 30.1 2.4 39 91-139 153-191 (206)
59 PRK11924 RNA polymerase sigma 33.5 38 0.00083 27.7 2.6 46 92-147 126-171 (179)
60 PF13936 HTH_38: Helix-turn-he 33.4 15 0.00033 25.9 0.2 38 90-137 3-40 (44)
61 PF08281 Sigma70_r4_2: Sigma-7 32.6 17 0.00037 25.5 0.3 38 92-139 11-48 (54)
62 PRK04217 hypothetical protein; 30.7 39 0.00084 28.8 2.2 49 90-148 41-89 (110)
63 PF00196 GerE: Bacterial regul 29.2 28 0.0006 25.0 1.0 44 91-145 3-46 (58)
64 TIGR02985 Sig70_bacteroi1 RNA 28.9 45 0.00097 26.7 2.2 44 91-144 113-156 (161)
65 PRK12519 RNA polymerase sigma 28.8 35 0.00075 29.1 1.6 46 92-147 142-187 (194)
66 PF08880 QLQ: QLQ; InterPro: 28.5 45 0.00098 23.6 1.9 13 91-103 2-14 (37)
67 KOG3623 Homeobox transcription 27.8 25 0.00055 39.3 0.8 77 77-158 618-695 (1007)
68 PF13873 Myb_DNA-bind_5: Myb/S 27.6 84 0.0018 23.6 3.4 59 90-148 3-75 (78)
69 PRK12512 RNA polymerase sigma 27.6 49 0.0011 28.0 2.3 50 91-150 131-180 (184)
70 PRK12514 RNA polymerase sigma 26.7 61 0.0013 27.3 2.7 43 92-144 130-172 (179)
71 cd06170 LuxR_C_like C-terminal 26.6 62 0.0014 21.7 2.3 37 92-139 1-37 (57)
72 PRK09480 slmA division inhibit 24.9 62 0.0013 27.0 2.4 36 101-142 20-55 (194)
73 PRK09639 RNA polymerase sigma 24.9 63 0.0014 26.6 2.4 46 91-147 112-157 (166)
74 TIGR02989 Sig-70_gvs1 RNA poly 24.8 50 0.0011 26.9 1.8 38 91-138 111-148 (159)
75 PRK12545 RNA polymerase sigma 24.5 74 0.0016 27.9 2.9 46 92-147 140-185 (201)
76 PF10925 DUF2680: Protein of u 24.3 45 0.00098 25.6 1.4 42 92-138 1-42 (59)
77 PRK12538 RNA polymerase sigma 23.9 60 0.0013 29.7 2.3 47 93-149 173-219 (233)
78 PRK12541 RNA polymerase sigma 23.8 49 0.0011 27.4 1.6 45 91-145 112-156 (161)
79 PRK09637 RNA polymerase sigma 23.6 68 0.0015 27.7 2.5 39 91-139 106-144 (181)
80 PF13565 HTH_32: Homeodomain-l 23.4 1.7E+02 0.0037 21.6 4.3 47 85-137 26-76 (77)
81 TIGR02983 SigE-fam_strep RNA p 23.3 58 0.0013 26.8 2.0 42 91-142 110-151 (162)
82 TIGR00620 sporelyase spore pho 23.2 97 0.0021 29.0 3.6 24 91-115 131-154 (199)
83 PRK09648 RNA polymerase sigma 22.6 64 0.0014 27.5 2.1 39 90-138 138-176 (189)
84 PTZ00183 centrin; Provisional 22.4 2.2E+02 0.0049 22.8 5.1 39 85-123 4-46 (158)
85 PRK09644 RNA polymerase sigma 22.0 72 0.0016 26.6 2.3 47 91-147 108-154 (165)
86 PRK12515 RNA polymerase sigma 21.9 84 0.0018 26.9 2.7 40 90-139 130-169 (189)
87 PRK12546 RNA polymerase sigma 21.8 67 0.0015 28.1 2.1 51 91-151 113-163 (188)
88 PRK10100 DNA-binding transcrip 21.7 46 0.00099 30.2 1.1 51 91-152 155-205 (216)
89 TIGR02959 SigZ RNA polymerase 21.6 67 0.0015 27.2 2.0 39 91-139 100-138 (170)
90 TIGR02939 RpoE_Sigma70 RNA pol 21.5 56 0.0012 27.4 1.5 37 93-139 140-176 (190)
91 KOG2416 Acinus (induces apopto 21.5 38 0.00083 37.0 0.6 45 97-152 652-698 (718)
92 TIGR02999 Sig-70_X6 RNA polyme 21.4 72 0.0016 26.8 2.2 39 92-140 135-173 (183)
93 TIGR02943 Sig70_famx1 RNA poly 20.8 94 0.002 26.9 2.8 48 91-148 131-178 (188)
94 PRK12522 RNA polymerase sigma 20.7 89 0.0019 26.2 2.6 38 92-139 120-157 (173)
95 cd02413 40S_S3_KH K homology R 20.6 74 0.0016 25.4 2.0 28 112-139 48-75 (81)
96 PRK05602 RNA polymerase sigma 20.6 75 0.0016 27.0 2.1 38 92-139 129-166 (186)
97 PF09851 SHOCT: Short C-termin 20.5 2.5E+02 0.0054 18.7 4.2 28 94-123 2-29 (31)
98 PRK12543 RNA polymerase sigma 20.4 87 0.0019 26.6 2.5 52 92-153 118-169 (179)
99 PRK12527 RNA polymerase sigma 20.3 86 0.0019 25.9 2.4 38 92-139 106-143 (159)
100 PRK09047 RNA polymerase factor 20.2 88 0.0019 25.5 2.4 39 91-139 106-144 (161)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=5.2e-19 Score=162.85 Aligned_cols=63 Identities=22% Similarity=0.293 Sum_probs=60.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.+|.||+||.+||.+||+.|..++ |++...|.+||..|. |+|+|||||||||||||||..+..
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L~----LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHALN----LTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhcc----hhHHHHHHHHHHHHHHHHHhhccc
Confidence 699999999999999999999999 999999999999998 999999999999999999987776
No 2
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.73 E-value=6.6e-19 Score=148.92 Aligned_cols=63 Identities=27% Similarity=0.355 Sum_probs=60.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.||-||+||..||.+||++|...+ ||++..|++||..|. |+|++|||||||||||.||+.|--
T Consensus 17 QRRIRTTFTS~QLkELErvF~ETH-YPDIYTREEiA~kid----LTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAETH-YPDIYTREEIALKID----LTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhc-CCcchhHHHHHHhhh----hhHHHHHHHHHhhHHHHHHHHHHH
Confidence 499999999999999999999999 999999999999998 999999999999999999987765
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=3.2e-18 Score=162.34 Aligned_cols=63 Identities=22% Similarity=0.307 Sum_probs=60.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.|+.||.||..||..||+.|++.+ |.+..+|.+||+.|+ |++.|||+||||||+||||+....
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~QK-YLS~~DR~~LA~~Lg----LTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEKQK-YLSVADRIELAASLG----LTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHHhh-cccHHHHHHHHHHcC----CchhhHHHHHhhhhHHHHHHHHhh
Confidence 499999999999999999999999 999999999999998 999999999999999999987764
No 4
>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=99.68 E-value=1.3e-17 Score=118.70 Aligned_cols=57 Identities=33% Similarity=0.542 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 86 GSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 86 rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
+++|+.||++|+.+||+.|..+. ||+.++++.||.+|+ |+..+|++||||||+|+||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~-~p~~~~~~~la~~l~----l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENP-YPSKEEREELAKELG----LTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSS-SCHHHHHHHHHHHHT----SSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhc-ccccccccccccccc----ccccccccCHHHhHHHhCc
Confidence 57899999999999999999998 999999999999998 9999999999999999986
No 5
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.68 E-value=3.9e-17 Score=155.90 Aligned_cols=64 Identities=27% Similarity=0.396 Sum_probs=60.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 84 PLGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 84 ~~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
+.||+|-.||+.|+-+||+.|+.++ |+++.||++||..|+ ||+.||||||||||+|.||++...
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQR-YLSAPERE~LA~~Lr----LT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQR-YLSAPEREHLASSLR----LTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhh-ccccHhHHHHHHhcC----CCchheeeeeecchhhhhhhhhhh
Confidence 3599999999999999999999999 999999999999998 999999999999999999977766
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.66 E-value=5.2e-17 Score=146.87 Aligned_cols=64 Identities=25% Similarity=0.376 Sum_probs=60.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 84 PLGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 84 ~~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.++|.||.||++||..||..|+.++ |....+|++||..|+ |+|.||+|||||||.|.||.+-+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L~----LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSLS----LSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHcC----CChhHhhhhhhhhhHHHHHHHHHh
Confidence 4689999999999999999999999 999999999999998 999999999999999998876553
No 7
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.66 E-value=3.8e-17 Score=156.06 Aligned_cols=63 Identities=24% Similarity=0.320 Sum_probs=60.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.|++|-.+|+.|+.+||+.|--++ |.+.+.|-+|++.|+ |||+||||||||||+|+||-.|+.
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~lN----LTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTLN----LTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhcc----cchhheeeeehhhhhHHhhhhhhh
Confidence 499999999999999999999999 999999999999998 999999999999999999988755
No 8
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.63 E-value=1.7e-16 Score=146.52 Aligned_cols=65 Identities=29% Similarity=0.374 Sum_probs=61.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh-hh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW-ES 154 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~-e~ 154 (336)
-|++||.||..||..||+.|+... |+++++|.+++..|. |+|.|||+||||||||.||.++-+ |.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL~----LTeTqVKIWFQNRRAKaKRlQeae~Ek 209 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSLE----LTETQVKIWFQNRRAKAKRLQEAELEK 209 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhhh----hhhhheehhhhhhhHHHHHHHHHHHHH
Confidence 499999999999999999999999 999999999999998 999999999999999999987776 44
No 9
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.63 E-value=2.1e-16 Score=145.86 Aligned_cols=63 Identities=24% Similarity=0.380 Sum_probs=60.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.||.||+||..||.+||.+|++.+ ||++..|++||.+|+ |.|.+|||||.|||||+|++++++
T Consensus 37 qRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkln----LpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKLN----LPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHhC----CchhhhhhhhccccchhhHhhhhh
Confidence 499999999999999999999999 999999999999998 999999999999999999998876
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.60 E-value=4.1e-16 Score=148.03 Aligned_cols=63 Identities=25% Similarity=0.417 Sum_probs=59.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
+|+-||.||..||.+||+.|...+ ||+...|+-||..+. |.|.+|+||||||||||||+.++.
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaH-YPDv~Are~la~kte----lpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAH-YPDVYAREMLADKTE----LPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhcc----CchhhhhHHhhhhhHHhhhhhhhc
Confidence 455699999999999999999999 999999999998887 999999999999999999998887
No 11
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.56 E-value=1.7e-15 Score=106.45 Aligned_cols=56 Identities=34% Similarity=0.558 Sum_probs=52.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHH
Q 035594 86 GSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARER 146 (336)
Q Consensus 86 rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReK 146 (336)
++.|+.||++|+.+||..|..+. ||+.+++++||.+|+ |+..+|++||+|||+|.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKLG----LSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHhHHHHhhccC
Confidence 36788999999999999999999 999999999999998 999999999999999864
No 12
>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=99.55 E-value=2.5e-15 Score=105.78 Aligned_cols=58 Identities=33% Similarity=0.543 Sum_probs=54.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHh
Q 035594 86 GSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQK 148 (336)
Q Consensus 86 rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRK 148 (336)
++.|..|+++|+.+||+.|..++ ||+.++++.||.+|+ |+..+|++||+|||++.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKELG----LTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHHHHHHHHHHhcc
Confidence 36789999999999999999999 999999999999998 99999999999999998864
No 13
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.55 E-value=3.3e-15 Score=139.00 Aligned_cols=64 Identities=19% Similarity=0.293 Sum_probs=61.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRWE 153 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~e 153 (336)
+|++||.++.-||+.|.+.|++.. |+-..+|.+||+.|+ |+..|||+||||||.|.||.++..+
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsLG----LTQTQVKIWFQNrRSK~KKl~k~g~ 185 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASLG----LTQTQVKIWFQNRRSKFKKLKKQGS 185 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHhC----CchhHhhhhhhhhHHHHHHHHhcCC
Confidence 699999999999999999999999 999999999999998 9999999999999999999988543
No 14
>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=99.50 E-value=2.4e-14 Score=108.09 Aligned_cols=52 Identities=17% Similarity=0.245 Sum_probs=50.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHHhhcCCCCCCcceecccchh
Q 035594 86 GSSRWNPTPEQLLALEEMYRRGTRT----PSAEQIQHIASQLRRFGKIEGKNVFYWFQNHK 142 (336)
Q Consensus 86 rR~Rw~FT~EQLqiLEelF~~g~~Y----Ps~eqRqeIA~eL~~~G~LtEsqVqvWFQNRR 142 (336)
+|.||.||++|++.||+.|+... | |+..+|++||.+|+ |++.+|+|||||-|
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~lg----l~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEIG----VTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHhC----CCHHHeeeecccCC
Confidence 68999999999999999999999 9 99999999999998 99999999999976
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.47 E-value=2.9e-14 Score=135.72 Aligned_cols=60 Identities=23% Similarity=0.370 Sum_probs=57.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKR 149 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKr 149 (336)
-.|+||.||.|||++|...|+.++ |++.+.|++||.+|+ |.|+||++||||+|||-||..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR-YlTEqRRQ~La~ELg----LNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR-YLTEQRRQELAQELG----LNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh-hHHHHHHHHHHHHhC----cCHHHhhHHhhhhhhhhhhcc
Confidence 478999999999999999999999 999999999999998 999999999999999998843
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.47 E-value=2.2e-14 Score=136.50 Aligned_cols=59 Identities=27% Similarity=0.407 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhh
Q 035594 86 GSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKR 149 (336)
Q Consensus 86 rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKr 149 (336)
-+-|-.+|..|..+||+.|..++ |.++.+..+||.-|+ |+|+|||+||||||||+||..
T Consensus 200 DKYRvVYTDhQRLELEKEfh~Sr-yITirRKSELA~~Lg----LsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSR-YITIRRKSELAATLG----LSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred cceeEEecchhhhhhhhhhcccc-ceeeehhHHHHHhhC----ccHhhhhHhhhhhhHHHHHHH
Confidence 34566899999999999999999 999999999999998 999999999999999999843
No 17
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.47 E-value=1.3e-14 Score=140.34 Aligned_cols=62 Identities=24% Similarity=0.373 Sum_probs=59.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRR 151 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr 151 (336)
.||.||.||.|||.+||+.|-+.. |.+...|-+||+.|+ |+|.-|||||||||+|.||+|--
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaLN----LPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAALN----LPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhhC----CCcceeehhhhhchhhhhhhhhh
Confidence 699999999999999999999999 999999999999998 99999999999999999987654
No 18
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.46 E-value=2.4e-14 Score=133.42 Aligned_cols=63 Identities=19% Similarity=0.252 Sum_probs=60.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
-.+.||.|+..|+..||..|+..+ |++..+|.-||++|. |+|.|||+||||||-||||+-...
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~kr-YLSsaeRa~LA~sLq----LTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFELKR-YLSSAERAGLAASLQ----LTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHHHh-hhhHHHHhHHHHhhh----hhhhhhhhhhhhhhHHHHHHHhhh
Confidence 478999999999999999999999 999999999999998 999999999999999999988777
No 19
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.44 E-value=1.7e-14 Score=129.84 Aligned_cols=65 Identities=25% Similarity=0.361 Sum_probs=61.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRWES 154 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~e~ 154 (336)
.++.|+.|+.-||..||+.|+.++ |++..+|++||..|+ |+++||+.||||||+|.||..|..+-
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~Qr-YLS~~e~~ELan~L~----LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQR-YLSTPERQELANALS----LSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred hhhhcccccCccccccHHHHhhhh-hcccHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 588999999999999999999999 999999999999998 99999999999999999999888753
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.41 E-value=1.9e-13 Score=119.70 Aligned_cols=69 Identities=32% Similarity=0.443 Sum_probs=63.5
Q ss_pred ccccCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 79 EFNEQPLGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 79 ~~~~~~~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
..+..+.++.|..-|.+|+.+||+.|..++ ||+...|..|+..|+ |+++.||+||||||++.|++++..
T Consensus 45 ~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~ln----m~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 45 QDGSSPPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLLN----MPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred ccCCCcCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhcC----CChhhhhhhhchHHHHHHHhcccc
Confidence 344456799999999999999999999999 999999999999998 999999999999999999988775
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.40 E-value=2.5e-13 Score=131.24 Aligned_cols=65 Identities=26% Similarity=0.388 Sum_probs=61.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhhh
Q 035594 84 PLGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRWE 153 (336)
Q Consensus 84 ~~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~e 153 (336)
..||.|+-||..||++||..|++++ ||+...|++||.-.+ |+|++|.|||.||||||||..|-++
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNr-ypdMstrEEIavwtN----lTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNR-YPDMSTREEIAVWTN----LTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcc-CCccchhhHHHhhcc----ccchhhhhhcccchhhhhhhhhhHH
Confidence 3699999999999999999999999 999999999999998 9999999999999999999877775
No 22
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.36 E-value=2.1e-13 Score=123.67 Aligned_cols=62 Identities=26% Similarity=0.392 Sum_probs=57.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 86 GSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 86 rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.++.-.||.+|+..||+.|+.+. |...+++.+||.+|+ |..+||.|||||||||||.|+-..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~Lg----L~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKELG----LQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhhC----CChhHHHHHHhhccccccchhhhh
Confidence 45566799999999999999999 999999999999998 999999999999999999987655
No 23
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.36 E-value=2.6e-13 Score=116.91 Aligned_cols=61 Identities=28% Similarity=0.351 Sum_probs=57.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRR 150 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrR 150 (336)
.++.|+.||..|+.+||++|...+ ||+..-|+.+|..+. ++|.+|++||||||+|++++.+
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~~h-~Pd~~~r~~la~~~~----~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEKVH-LPCFACRECLALLLT----GDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcCCC-cCccchHHHHhhcCC----CCeeeeehhhhhhcHhhhhhhc
Confidence 599999999999999999999998 999999998888886 9999999999999999999887
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.21 E-value=7.2e-12 Score=120.89 Aligned_cols=64 Identities=23% Similarity=0.421 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhh
Q 035594 83 QPLGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRR 151 (336)
Q Consensus 83 ~~~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr 151 (336)
++..|+||+.|.-||+.|..+|...+ .|..--|++|+.+.+ |..+.|||||||||||+||-++-
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~Sp-KPARHVREQLsseTG----LDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSP-KPARHVREQLSSETG----LDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCC-chhHHHHHHhhhccC----cceeehhhhhhhhhHHHHhhhhh
Confidence 45699999999999999999999999 899999999999988 99999999999999999997653
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.14 E-value=1.6e-11 Score=115.10 Aligned_cols=63 Identities=24% Similarity=0.313 Sum_probs=58.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
+...|-+|+-.||..||..|+..+ ||-..+|.++|..|+ ++|++|+|||||||.|||||...+
T Consensus 167 rk~srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~lg----mteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQELN----MTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred ccccCCCccchhhhhhhhhhhhhh-cccchhHHHhhcccc----ccHHHHHHHHhcchhhhhhhhccc
Confidence 456788999999999999999999 999999999999998 999999999999999999976554
No 26
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.10 E-value=2.8e-11 Score=116.71 Aligned_cols=63 Identities=30% Similarity=0.427 Sum_probs=59.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.+|.|++||++|+..||+.|+.++ ||++..|++||.+++ ++|.+|++||||||+|++|..+..
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i~----l~e~riqvwf~nrra~~rr~~~~~ 238 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKETG----LPEPRVQVWFQNRRAKWRRQHRDC 238 (354)
T ss_pred ccccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhcc----CCchHHHHHHhhhhhhhhhccccc
Confidence 488899999999999999999999 999999999999998 999999999999999999988653
No 27
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.73 E-value=8.5e-09 Score=102.10 Aligned_cols=61 Identities=26% Similarity=0.416 Sum_probs=56.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRR 150 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrR 150 (336)
.|++||.+......+||+.|.++. .|+.++|.+||.+|+ |+-..|.|||=|||=|+||-..
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~np-KPt~qEIt~iA~~L~----leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLKNP-KPTSQEITHIAESLQ----LEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccceeHHHHHHHHHHHHhCC-CCCHHHHHHHHHHhc----cccceEEEEeeccccccccCCC
Confidence 499999999999999999999999 899999999999998 8888899999999988887554
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.19 E-value=1e-06 Score=76.21 Aligned_cols=61 Identities=28% Similarity=0.482 Sum_probs=57.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRR 150 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrR 150 (336)
.++.|+.++..|+..|+..|.... ||+...+++|+..++ +++..|++||||+|++.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~~----~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEETG----LSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhcC----CChhhhhhhcccHHHHHHhhcc
Confidence 588999999999999999999999 999999999999998 9999999999999999998776
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=97.77 E-value=1.7e-05 Score=76.58 Aligned_cols=54 Identities=26% Similarity=0.369 Sum_probs=47.6
Q ss_pred CCCCCCHHH---------HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHH
Q 035594 88 SRWNPTPEQ---------LLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARER 146 (336)
Q Consensus 88 ~Rw~FT~EQ---------LqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReK 146 (336)
+||...-|| ...|.+.|..+. ||+..+..+||+..+ |+-.||-+||.|||-|.|
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~~~-YPsp~eKReLA~aTg----Lt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQNP-YPSPREKRELAEATG----LTITQVSNWFKNRRQRDR 232 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhcCC-CCChHHHHHHHHHhC----Cchhhhhhhhhhhhhhhh
Confidence 566655555 578999999999 999999999999998 999999999999998876
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.68 E-value=2.6e-05 Score=75.44 Aligned_cols=64 Identities=23% Similarity=0.305 Sum_probs=56.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhc--CCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRR--GTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~--g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.||+|-+|++.=..||.+.|-. +..||+.+..++||.+.+ |+-+||-.||-|+|.|-||---..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCn----ItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCN----ITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcC----ceehhhccccccceeehhhhhhhh
Confidence 4999999999999999999954 344999999999999998 999999999999999999865544
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.62 E-value=3.6e-05 Score=79.45 Aligned_cols=58 Identities=26% Similarity=0.337 Sum_probs=53.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
..++|..||..|...|-.+|..++ +|+.+..+.|+.+|+ |.-+-|.+||-|-|-|.+-
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~~-RPS~Emq~tIS~qL~----L~~sTV~NfFmNaRRRsl~ 477 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKENK-RPSREMQETISQQLN----LELSTVINFFMNARRRSLD 477 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcCC-CCCHHHHHHHHHHhC----CcHHHHHHHHHhhhhhccc
Confidence 588999999999999999999999 899999999999998 9999999999999976633
No 32
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.59 E-value=5.1e-05 Score=74.31 Aligned_cols=65 Identities=23% Similarity=0.376 Sum_probs=56.2
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhh
Q 035594 82 EQPLGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRR 151 (336)
Q Consensus 82 ~~~~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr 151 (336)
..-..|+||..-.-.-+.||..|..++ -|+.+.|..||++|. |-...|.|||=|.|-|.||-++.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQP-RPS~EkIAaIAekLD----LKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQP-RPSGEKIAAIAEKLD----LKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred ccccccccccccCcccccHHHHhccCC-CCchhHHHHHHHhhh----hhhceEEEEeeccHHHHHHhhhh
Confidence 333589999999999999999999999 599999999999998 66777999999999887775443
No 33
>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=97.52 E-value=1.9e-05 Score=55.70 Aligned_cols=33 Identities=30% Similarity=0.535 Sum_probs=27.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhH
Q 035594 107 GTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKAR 144 (336)
Q Consensus 107 g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAR 144 (336)
++ ||+.+++++||.+.+ |+..||..||-|.|.|
T Consensus 8 nP-YPs~~ek~~L~~~tg----ls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NP-YPSKEEKEELAKQTG----LSRKQISNWFINARRR 40 (40)
T ss_dssp SG-S--HHHHHHHHHHHT----S-HHHHHHHHHHHHHH
T ss_pred CC-CCCHHHHHHHHHHcC----CCHHHHHHHHHHhHcc
Confidence 45 999999999999998 9999999999999965
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.58 E-value=0.0012 Score=73.97 Aligned_cols=61 Identities=18% Similarity=0.365 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhh
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRR 150 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrR 150 (336)
+|+.|+.++..||.+|..+|.... ||..++++.+-..+. ++-..|++||||-|+|.|+...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~-~~~~~~~E~l~~~~~----~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQR-TPTMQECEVLEEPIG----LPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhcc-CChHHHHHhhccccc----CCcchhHHhhhhhhhhhhhhhh
Confidence 689999999999999999999999 999999999999887 7778899999999999998665
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=91.70 E-value=0.12 Score=49.01 Aligned_cols=59 Identities=19% Similarity=0.170 Sum_probs=48.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhc--CCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 85 LGSSRWNPTPEQLLALEEMYRR--GTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~--g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
..|++..+-++...+|+.-... ...||+..+...||.+.+ |+-.||.+||-|.|-|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TG----Ls~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTG----LSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcC----CCcccCCchhhhcccccCC
Confidence 4667778999999999865544 223999999999999998 9999999999999966554
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=90.29 E-value=0.17 Score=55.27 Aligned_cols=51 Identities=27% Similarity=0.357 Sum_probs=46.5
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 97 LLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 97 LqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
+..|...|..+. .|+.++...||.+++ |+-..|+.||+++++.+..-.|.-
T Consensus 568 ~sllkayyaln~-~ps~eelskia~qvg----lp~~vvk~wfE~~~a~e~sv~rsp 618 (1007)
T KOG3623|consen 568 TSLLKAYYALNG-LPSEEELSKIAQQVG----LPFAVVKAWFEDEEAEEMSVERSP 618 (1007)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHHHhc----ccHHHHHHHHHhhhhhhhhhccCc
Confidence 788999999999 899999999999998 899999999999999998876654
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=86.45 E-value=0.2 Score=38.58 Aligned_cols=41 Identities=20% Similarity=0.427 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchh
Q 035594 97 LLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHK 142 (336)
Q Consensus 97 LqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRR 142 (336)
++-|++.|.... .+...+.+.|..+-+ |+..+|..||--|+
T Consensus 10 ~~pL~~Yy~~h~-~L~E~DL~~L~~kS~----ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHK-QLQEEDLDELCDKSR----MSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHTT------HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcC-CccHhhHHHHHHHHC----CCHHHHHHHHHHhc
Confidence 456999999988 899999999999998 99999999997554
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=72.87 E-value=4.6 Score=29.66 Aligned_cols=47 Identities=19% Similarity=0.215 Sum_probs=34.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchh
Q 035594 86 GSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHK 142 (336)
Q Consensus 86 rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRR 142 (336)
+|+|..+|-+|-..+=+.++.|. ...+||.+++ |+.+.|..|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~------s~~~ia~~fg----v~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE------SKRDIAREFG----VSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHHHT------CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHhHH
Confidence 47899999998777777788887 2456999998 99999999998864
No 39
>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=71.94 E-value=1.9 Score=28.10 Aligned_cols=43 Identities=14% Similarity=0.088 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhh
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKA 143 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRA 143 (336)
..++.|..+++..|..+. . ..+||..++ ++...|+.|.+.-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~~--~----~~~ia~~~~----~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEGL--S----YEEIAEILG----ISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHH
Confidence 357889999999997665 2 345899998 999999888765443
No 40
>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=67.00 E-value=4.7 Score=30.33 Aligned_cols=39 Identities=26% Similarity=0.325 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHHhhcCCCCCCcc
Q 035594 92 PTPEQLLALEEMYRRGT-RTPSAEQIQHIASQLRRFGKIEGKNV 134 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~-~YPs~eqRqeIA~eL~~~G~LtEsqV 134 (336)
+|+.|.++|..+|..|= -+|-.....+||++|+ |+..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lg----is~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELG----ISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhC----CCHHHH
Confidence 58999999999999983 1587888899999998 776554
No 41
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=56.87 E-value=55 Score=29.59 Aligned_cols=41 Identities=12% Similarity=0.192 Sum_probs=32.6
Q ss_pred CCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcce
Q 035594 88 SRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVF 135 (336)
Q Consensus 88 ~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVq 135 (336)
+.-..|+||++++-++-..++ ..-.+..||++.+ ++.--|-
T Consensus 82 k~y~Lt~e~i~Eir~LR~~DP---~~wTr~~LAkkF~----~S~~fV~ 122 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAEDP---EKWTRKKLAKKFN----CSPLFVS 122 (164)
T ss_pred ccccCCHHHHHHHHHHHHcCc---hHhhHHHHHHHhC----CCHHHHH
Confidence 456899999999999988775 7788889999987 5554444
No 42
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=55.65 E-value=12 Score=33.50 Aligned_cols=41 Identities=24% Similarity=0.366 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHHhhcCCCCCCcc
Q 035594 89 RWNPTPEQLLALEEMYRRG--TRTPSAEQIQHIASQLRRFGKIEGKNV 134 (336)
Q Consensus 89 Rw~FT~EQLqiLEelF~~g--~~YPs~eqRqeIA~eL~~~G~LtEsqV 134 (336)
+-.+|+-|+++|..+|..| . ||-.-..++||++|+ |+.+-+
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYFd-~PR~~~l~dLA~~lG----ISkst~ 195 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYFD-YPRRVSLKDLAKELG----ISKSTL 195 (215)
T ss_pred cccCCHHHHHHHHHHHHcCCCC-CCccCCHHHHHHHhC----CCHHHH
Confidence 3379999999999999998 6 799999999999998 776554
No 43
>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=54.65 E-value=17 Score=20.86 Aligned_cols=40 Identities=20% Similarity=0.376 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecc
Q 035594 89 RWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWF 138 (336)
Q Consensus 89 Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWF 138 (336)
+..++.++...+.+.|..+. ...+||..++ ++...|+.|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~~~------s~~~ia~~~~----is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAAGE------SVAEIARRLG----VSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHhC
Confidence 33467777777777787554 2345888887 7777777773
No 44
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=48.11 E-value=16 Score=28.56 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHHhhcCCCCCCcceecc
Q 035594 90 WNPTPEQLLALEEMYRR----GTRTPSAEQIQHIASQLRRFGKIEGKNVFYWF 138 (336)
Q Consensus 90 w~FT~EQLqiLEelF~~----g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWF 138 (336)
|-+|++|+..|.++|.. +.++.+..+..++-..++ +++..|.-+|
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~----~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSG----LPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcC----CCHHHHHHHH
Confidence 78899999999999976 445666666555544332 6666665544
No 45
>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=48.03 E-value=12 Score=27.67 Aligned_cols=42 Identities=21% Similarity=0.409 Sum_probs=26.2
Q ss_pred CCCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecc
Q 035594 87 SSRWNPTPEQLLALEEMY-RRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWF 138 (336)
Q Consensus 87 R~Rw~FT~EQLqiLEelF-~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWF 138 (336)
+.|..||+++-..+=..+ ..+. .+.++|.+++ |+...++.|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~------sv~~va~~~g----i~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGE------SVSEVAREYG----ISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHC------HHHHHHHHHT----S-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCC------ceEeeecccc----cccccccHHH
Confidence 567888988866555555 5555 4667999998 9999998883
No 46
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=44.87 E-value=9 Score=26.90 Aligned_cols=39 Identities=26% Similarity=0.448 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceec
Q 035594 89 RWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYW 137 (336)
Q Consensus 89 Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvW 137 (336)
+..++++|++.+-+++..|. + +.+||..++ |+-+-|+.+
T Consensus 3 p~~~~~~~~~~i~~l~~~G~--s----i~~IA~~~g----vsr~TvyR~ 41 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAEGM--S----IAEIAKQFG----VSRSTVYRY 41 (45)
T ss_dssp SSSSSHCCHHHHHHHHHTT--------HHHHHHHTT----S-HHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHCCC--C----HHHHHHHHC----cCHHHHHHH
Confidence 34578889999999999997 2 456999998 887777744
No 47
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=44.82 E-value=6.4 Score=42.71 Aligned_cols=64 Identities=16% Similarity=0.172 Sum_probs=38.1
Q ss_pred CCCCCCCCCHHHHHHHHHH-HhcCCCCCCHHHHHHHHHHHhh---cCCCCCCcceecccchhhHHHHhh
Q 035594 85 LGSSRWNPTPEQLLALEEM-YRRGTRTPSAEQIQHIASQLRR---FGKIEGKNVFYWFQNHKARERQKR 149 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEel-F~~g~~YPs~eqRqeIA~eL~~---~G~LtEsqVqvWFQNRRAReKRKr 149 (336)
+++.|-.|=.+|.-.+.+- |.+++ -++--++.+-.+++.. --+.++++|+.||.|||+++|+-+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~-s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTR-SGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheeccc-CchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 3555555555554444333 33333 4555555555554431 012578899999999999998754
No 48
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=44.64 E-value=17 Score=32.17 Aligned_cols=52 Identities=23% Similarity=0.126 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 90 WNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 90 w~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
..+|+-|.++|+. +..+. + .++||..|+ ++...|..|-+.-+-|.|+.+...
T Consensus 5 ~~Lt~rqreVL~l-r~~Gl---T---q~EIAe~LG----iS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 5 SFLTERQIEVLRL-RERGL---T---QQEIADILG----TSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred cCCCHHHHHHHHH-HHcCC---C---HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999988 55665 2 346999998 999999999987666665544443
No 49
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.45 E-value=21 Score=29.28 Aligned_cols=40 Identities=15% Similarity=-0.050 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQN 140 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQN 140 (336)
.+++.|.++|...|-.+. +- ++||..|+ +++..|+.|.+.
T Consensus 128 ~L~~~~r~vl~l~~~~~~--s~----~eIA~~lg----is~~tV~~~l~r 167 (182)
T PRK09652 128 SLPEELRTAITLREIEGL--SY----EEIAEIMG----CPIGTVRSRIFR 167 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--CH----HHHHHHHC----CCHHHHHHHHHH
Confidence 578888899998887766 33 35999998 999999988873
No 50
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=40.12 E-value=24 Score=29.30 Aligned_cols=41 Identities=17% Similarity=0.447 Sum_probs=30.1
Q ss_pred CCCCCCCHHH-HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceec
Q 035594 87 SSRWNPTPEQ-LLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYW 137 (336)
Q Consensus 87 R~Rw~FT~EQ-LqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvW 137 (336)
.+|-.||.++ ++++...+..+. +-. +||.+++ |+...|+.|
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~--sv~----evA~e~g----Is~~tl~~W 49 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM--TVS----LVARQHG----VAASQLFLW 49 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC--CHH----HHHHHHC----cCHHHHHHH
Confidence 3445567665 667777777766 333 4899998 999999999
No 51
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.05 E-value=24 Score=23.49 Aligned_cols=38 Identities=26% Similarity=0.261 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
.+++.|.++++. +..+. . ..+||..|+ ++...|+.|.+
T Consensus 3 ~l~~~e~~i~~~-~~~g~--s----~~eia~~l~----is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRL-LAEGL--T----NKEIAERLG----ISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHH-HHcCC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 368889999876 44554 2 356999998 99999987765
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=39.96 E-value=26 Score=30.24 Aligned_cols=39 Identities=18% Similarity=0.135 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
.+++.|..+|...|-.+. ..++||+.|+ ++...|+++..
T Consensus 142 ~L~~~~r~vl~l~~~~~~------s~~EIA~~Lg----is~~tVk~~l~ 180 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL------TYREVAERLA----VPLGTVKTRMR 180 (194)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHhC----CChHhHHHHHH
Confidence 467788888888777776 2346999998 99999987763
No 53
>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=39.61 E-value=19 Score=25.12 Aligned_cols=38 Identities=21% Similarity=0.272 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWF 138 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWF 138 (336)
.+++.|.++|...|-.+. + .++||..|+ ++...|..+.
T Consensus 4 ~L~~~er~vi~~~y~~~~--t----~~eIa~~lg----~s~~~V~~~~ 41 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL--T----LEEIAERLG----ISRSTVRRIL 41 (50)
T ss_dssp TS-HHHHHHHHHHHTST---S----HHHHHHHHT----SCHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC--C----HHHHHHHHC----CcHHHHHHHH
Confidence 468899999999996666 2 346999998 8988887553
No 54
>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=39.20 E-value=21 Score=27.43 Aligned_cols=46 Identities=20% Similarity=0.127 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARER 146 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReK 146 (336)
.+++.|..+|...|-.+. +.. +||..|+ ++.+.|..|.+.=+.|-|
T Consensus 110 ~L~~~~~~ii~~~~~~g~--s~~----eIA~~l~----~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEGL--SYK----EIAEILG----ISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcCC--CHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 457888888888776655 333 5999998 999999877665444433
No 55
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=38.50 E-value=27 Score=28.82 Aligned_cols=46 Identities=20% Similarity=0.067 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
.++.|-.++.-.|-.+. + .++||+.|+ +++..|+++..-=|.+-|+
T Consensus 107 Lp~~~r~v~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK--S----YQEIALQEK----IEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 56677777777777776 2 235999998 9999999877644444433
No 56
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.38 E-value=23 Score=28.85 Aligned_cols=40 Identities=13% Similarity=0.138 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQN 140 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQN 140 (336)
.+++.|.+++...|-.+. . .++||..|+ +++..|+.|...
T Consensus 106 ~L~~~~r~ii~l~~~~~~--s----~~EIA~~l~----is~~tV~~~~~r 145 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK--T----MGEIALETE----MTYYQVRWIYRQ 145 (154)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHH
Confidence 466778888888887776 2 456999998 999999987643
No 57
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=34.87 E-value=28 Score=29.20 Aligned_cols=47 Identities=13% Similarity=0.152 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
.+++.|-.+|+..|-.+. + .++||+.|+ ++...|+++.+.=|.+-|+
T Consensus 136 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~lg----is~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMEDL--S----LKEISEILD----LPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 466777777777666555 2 345999998 9999999888544444443
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=33.90 E-value=34 Score=30.09 Aligned_cols=39 Identities=15% Similarity=0.148 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
.+++.|..+|...|-.+. ..++||..|+ +++..|+++.+
T Consensus 153 ~L~~~~r~vl~l~~~~g~------s~~EIA~~lg----is~~tV~~~l~ 191 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQEL------SQEQLAQQLN----VPLGTVKSRLR 191 (206)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHHH
Confidence 356677777777776666 2346999998 99999977663
No 59
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.46 E-value=38 Score=27.69 Aligned_cols=46 Identities=17% Similarity=0.094 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
.++.+..+|...|..+. + .++||..|+ ++...|..|.+-=|.|.|+
T Consensus 126 L~~~~r~i~~l~~~~~~--~----~~eIA~~lg----is~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVEGL--S----YREIAEILG----VPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 56667777777776665 2 245999998 9999999887654444444
No 60
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=33.44 E-value=15 Score=25.87 Aligned_cols=38 Identities=29% Similarity=0.296 Sum_probs=17.9
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceec
Q 035594 90 WNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYW 137 (336)
Q Consensus 90 w~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvW 137 (336)
..+|.+|...++.++..|. + ..+||+.|+ ++.+-|..+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~---s---~~~IA~~lg----~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM---S---IREIAKRLG----RSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHTT------HHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC---C---HHHHHHHHC----cCcHHHHHH
Confidence 4578999999999998887 2 345999998 665555443
No 61
>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=32.61 E-value=17 Score=25.47 Aligned_cols=38 Identities=21% Similarity=0.118 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
.++.|-.++...|-.+. + .++||..|+ ++.+.|++|.+
T Consensus 11 L~~~~r~i~~l~~~~g~--s----~~eIa~~l~----~s~~~v~~~l~ 48 (54)
T PF08281_consen 11 LPERQREIFLLRYFQGM--S----YAEIAEILG----ISESTVKRRLR 48 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHCT----S-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCc--C----HHHHHHHHC----cCHHHHHHHHH
Confidence 56788888998888887 3 345999998 99999999875
No 62
>PRK04217 hypothetical protein; Provisional
Probab=30.69 E-value=39 Score=28.79 Aligned_cols=49 Identities=14% Similarity=0.110 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHh
Q 035594 90 WNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQK 148 (336)
Q Consensus 90 w~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRK 148 (336)
-..|.+|.+++...|..+. ..++||+.|+ |+..-|+...+.-+.+.|..
T Consensus 41 ~~Lt~eereai~l~~~eGl------S~~EIAk~LG----IS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL------TQEEAGKRMG----VSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHH
Confidence 3578999999999988777 2456999998 99999997776555444443
No 63
>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=29.25 E-value=28 Score=25.02 Aligned_cols=44 Identities=20% Similarity=0.109 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARE 145 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRARe 145 (336)
.+|+.++++|.-+..... .++||..|+ |+++-|+++..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~~-------~~eIA~~l~----is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS-------NKEIAEELG----ISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHHT----SHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcCC-------cchhHHhcC----cchhhHHHHHHHHHHHh
Confidence 589999999988776655 345999998 99999988765544443
No 64
>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=28.94 E-value=45 Score=26.70 Aligned_cols=44 Identities=18% Similarity=0.074 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKAR 144 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAR 144 (336)
..++.+.++|.-.|-.+. +-. +||..|+ +++..|+.+...=|.|
T Consensus 113 ~L~~~~r~il~l~~~~~~--~~~----eIA~~lg----is~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEGK--SYK----EIAEELG----ISVKTVEYHISKALKE 156 (161)
T ss_pred HCCHHHHHHHHHHHHcCC--CHH----HHHHHHC----CCHHHHHHHHHHHHHH
Confidence 456777778877676554 333 4999998 9999998765443333
No 65
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.82 E-value=35 Score=29.15 Aligned_cols=46 Identities=24% Similarity=0.136 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
+++.|..+|+-.|-.+. ..++||..|+ ++.+.|+.|.+.=|.+-|+
T Consensus 142 L~~~~~~v~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYYEGL------SQSEIAKRLG----IPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhhcCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 56677777777766665 2346999998 9999999998544444333
No 66
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=28.47 E-value=45 Score=23.61 Aligned_cols=13 Identities=38% Similarity=0.358 Sum_probs=11.4
Q ss_pred CCCHHHHHHHHHH
Q 035594 91 NPTPEQLLALEEM 103 (336)
Q Consensus 91 ~FT~EQLqiLEel 103 (336)
.||++|+.+||.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5999999999964
No 67
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=27.76 E-value=25 Score=39.27 Aligned_cols=77 Identities=17% Similarity=0.146 Sum_probs=50.7
Q ss_pred ccccccCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh-hhh
Q 035594 77 VSEFNEQPLGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW-ESE 155 (336)
Q Consensus 77 ~~~~~~~~~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~-e~~ 155 (336)
|+..+..++.+.|.....++-..|-.+|+-+- -|+-.+---++..|. ..+..|.+||++|+.+.+.-.--. -+.
T Consensus 618 ps~psg~~p~kv~sp~k~~dq~ql~~a~elq~-s~~n~~~pl~~t~~~----n~~pv~ev~dhsrsstpsp~pl~ltss~ 692 (1007)
T KOG3623|consen 618 PSQPSGERPVKVRSPIKEEDQQQLKQAYELQA-SPSNDEFPLIATRLQ----NDPPVVEVWDHSRSSTPSPMPLFLTSSA 692 (1007)
T ss_pred ccCCCCCCCccccCCCCccchhhhHhhhhccc-CccCcccchhhhhcc----CCCcchhhcccCCCCCCCCCcccccccc
Confidence 33333444677787777888888999998776 455555555666665 556667999999998776644333 333
Q ss_pred cCC
Q 035594 156 TNN 158 (336)
Q Consensus 156 ~~~ 158 (336)
++.
T Consensus 693 n~~ 695 (1007)
T KOG3623|consen 693 NGA 695 (1007)
T ss_pred cCC
Confidence 443
No 68
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=27.60 E-value=84 Score=23.64 Aligned_cols=59 Identities=20% Similarity=0.185 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHhcCCC-----CCCHH-------HHHHHHHHHhhcCCC--CCCcceecccchhhHHHHh
Q 035594 90 WNPTPEQLLALEEMYRRGTR-----TPSAE-------QIQHIASQLRRFGKI--EGKNVFYWFQNHKARERQK 148 (336)
Q Consensus 90 w~FT~EQLqiLEelF~~g~~-----YPs~e-------qRqeIA~eL~~~G~L--tEsqVqvWFQNRRAReKRK 148 (336)
-+||.+|..+|-+++..... ..+.. -=++||..|+..|+. +-.+|+..++|-+++.|++
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 47999999999988766321 11111 125799999876664 2223556677777776665
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.55 E-value=49 Score=27.97 Aligned_cols=50 Identities=20% Similarity=0.177 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhh
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRR 150 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrR 150 (336)
.+++.|.++|.-.|-.+. . .++||..|+ ++...|+.+...=|.+-|++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~l~----is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA--S----IKETAAKLS----MSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHhC----CCHHHHHHHHHHHHHHHHHHhh
Confidence 456777777877776666 2 346999998 9999999887655555554433
No 70
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.72 E-value=61 Score=27.29 Aligned_cols=43 Identities=12% Similarity=0.263 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhH
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKAR 144 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAR 144 (336)
.++.|-.+|.-.|-.|. ..++||..|+ +++..|+++.+.=|.+
T Consensus 130 L~~~~r~i~~l~~~~g~------s~~eIA~~lg----is~~tV~~~l~Rar~~ 172 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGL------SYKELAERHD----VPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHHC----CChHHHHHHHHHHHHH
Confidence 45566666776776565 2456999998 9999998776543333
No 71
>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=26.57 E-value=62 Score=21.67 Aligned_cols=37 Identities=27% Similarity=0.267 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
+++.|.++++..+ .+. ..++||..++ ++...|+.|..
T Consensus 1 l~~~e~~i~~~~~-~~~------s~~eia~~l~----~s~~tv~~~~~ 37 (57)
T cd06170 1 LTPREREVLRLLA-EGK------TNKEIADILG----ISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHHHH-cCC------CHHHHHHHHC----CCHHHHHHHHH
Confidence 3667888886643 443 2346888887 89888988764
No 72
>PRK09480 slmA division inhibitor protein; Provisional
Probab=24.92 E-value=62 Score=27.00 Aligned_cols=36 Identities=8% Similarity=0.214 Sum_probs=28.3
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchh
Q 035594 101 EEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHK 142 (336)
Q Consensus 101 EelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRR 142 (336)
.++|.... . ....+.+||++.+ |+..-++++|.|+.
T Consensus 20 ~~l~~~~~-G-~~~ti~~Ia~~ag----vs~gt~Y~~F~~K~ 55 (194)
T PRK09480 20 AQMLESPP-G-ERITTAKLAARVG----VSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHhcC-C-CccCHHHHHHHhC----CCHhHHHHHCCCHH
Confidence 44555444 4 5667888999998 99999999999977
No 73
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.88 E-value=63 Score=26.62 Aligned_cols=46 Identities=22% Similarity=0.159 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
.+++.|-.+|.-.| .|. +- ++||..|+ +++..|+++...=|.+.|+
T Consensus 112 ~L~~~~r~il~l~~-~g~--s~----~eIA~~lg----is~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGY--SY----KEIAEALG----IKESSVGTTLARAKKKFRK 157 (166)
T ss_pred cCCHHHHHHHHHHH-cCC--CH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 36777888888888 665 33 35999998 9999999887433333333
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=24.81 E-value=50 Score=26.92 Aligned_cols=38 Identities=24% Similarity=0.263 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWF 138 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWF 138 (336)
.+++.|.+++...|-.|. + .++||+.|+ |+...|+++.
T Consensus 111 ~L~~~~r~v~~l~~~~g~--~----~~eIA~~l~----is~~tv~~~l 148 (159)
T TIGR02989 111 KLPERQRELLQLRYQRGV--S----LTALAEQLG----RTVNAVYKAL 148 (159)
T ss_pred HCCHHHHHHHHHHHhcCC--C----HHHHHHHhC----CCHHHHHHHH
Confidence 477788888888776665 2 345999998 9999999663
No 75
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=24.46 E-value=74 Score=27.85 Aligned_cols=46 Identities=11% Similarity=0.026 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
+++.|-.++.-.|-.+. + .++||..|+ +++..|++....=|.+-|+
T Consensus 140 Lp~~~r~v~~L~~~eg~--s----~~EIA~~lg----is~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 140 LPEQIGRVFMMREFLDF--E----IDDICTELT----LTANHCSVLLYRARTRLRT 185 (201)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHHHHH
Confidence 45556666666666665 2 346999998 9999999876543333333
No 76
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=24.30 E-value=45 Score=25.62 Aligned_cols=42 Identities=19% Similarity=0.135 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecc
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWF 138 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWF 138 (336)
+|.+|...|+++|..=- +.+++|-.+.-.+|.||..+=..|-
T Consensus 1 lT~~Qk~el~~l~~qm~-----e~kK~~idk~Ve~G~iTqeqAd~ik 42 (59)
T PF10925_consen 1 LTDQQKKELKALYKQML-----ELKKQIIDKYVEAGVITQEQADAIK 42 (59)
T ss_pred CCHHHHHHHHHHHHHHH-----HHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 58999999999997643 5677788888889999998855553
No 77
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.86 E-value=60 Score=29.67 Aligned_cols=47 Identities=15% Similarity=0.087 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhh
Q 035594 93 TPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKR 149 (336)
Q Consensus 93 T~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKr 149 (336)
++.|-++|.-.|-.+. ..++||..|+ +++..|+++.+.=|.|.|+..
T Consensus 173 p~~~R~v~~L~~~eg~------s~~EIA~~Lg----is~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 173 PEQQRIAVILSYHENM------SNGEIAEVMD----TTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CHHHHHHhhhHHhcCC------CHHHHHHHHC----cCHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555 2346999998 999999887765444444433
No 78
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=23.79 E-value=49 Score=27.36 Aligned_cols=45 Identities=13% Similarity=-0.045 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARE 145 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRARe 145 (336)
.+++.|..+|+-.|-.+. +. ++||..|+ ++...|+++...=|.|-
T Consensus 112 ~L~~~~r~v~~l~~~~~~--s~----~eIA~~lg----is~~tv~~~l~Rar~~L 156 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGF--SY----KEIAEMTG----LSLAKVKIELHRGRKET 156 (161)
T ss_pred HCCHHHHHHhhhHHhcCC--CH----HHHHHHHC----CCHHHHHHHHHHHHHHH
Confidence 577788888888777776 33 45999998 99999887665433333
No 79
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.59 E-value=68 Score=27.71 Aligned_cols=39 Identities=18% Similarity=0.049 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
.+++.|..+|...|-.|. +- ++||..|+ ++...|+..+.
T Consensus 106 ~L~~~~r~i~~l~~~~g~--~~----~EIA~~lg----is~~tV~~~l~ 144 (181)
T PRK09637 106 ALPEKYAEALRLTELEGL--SQ----KEIAEKLG----LSLSGAKSRVQ 144 (181)
T ss_pred hCCHHHHHHHHHHHhcCC--CH----HHHHHHhC----CCHHHHHHHHH
Confidence 567778888888877776 33 45999998 99999988775
No 80
>PF13565 HTH_32: Homeodomain-like domain
Probab=23.45 E-value=1.7e+02 Score=21.56 Aligned_cols=47 Identities=21% Similarity=0.257 Sum_probs=29.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhc-C---CCCCCcceec
Q 035594 85 LGSSRWNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRF-G---KIEGKNVFYW 137 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~-G---~LtEsqVqvW 137 (336)
..++|. +++|.+.|.++....+ .-+.. +|+..|... | .++.+.|+.|
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~p-~wt~~---~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEHP-RWTPR---EIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhCC-CCCHH---HHHHHHHHHhCCCCCccHhHHHHh
Confidence 355566 8888899999998876 34444 355666533 2 2366656543
No 81
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=23.28 E-value=58 Score=26.78 Aligned_cols=42 Identities=14% Similarity=0.045 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchh
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHK 142 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRR 142 (336)
.+++.|..+|+..|-.+. +. ++||..|+ +++..|+++-..=|
T Consensus 110 ~L~~~~r~i~~l~~~~g~--s~----~eIA~~lg----is~~tV~~~l~ra~ 151 (162)
T TIGR02983 110 RLPARQRAVVVLRYYEDL--SE----AQVAEALG----ISVGTVKSRLSRAL 151 (162)
T ss_pred hCCHHHHHHhhhHHHhcC--CH----HHHHHHhC----CCHHHHHHHHHHHH
Confidence 346778888888776665 33 35999998 99999987654333
No 82
>TIGR00620 sporelyase spore photoproduct lyase. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.24 E-value=97 Score=29.02 Aligned_cols=24 Identities=17% Similarity=0.122 Sum_probs=19.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQ 115 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eq 115 (336)
+||++...++++.|-... +|=.++
T Consensus 131 R~t~~~k~~i~~~fP~s~-l~~~ee 154 (199)
T TIGR00620 131 RFTKPAKRVIEKNYPKTK-LELDEE 154 (199)
T ss_pred EcCHHHHHHHHHhCCCCC-CCccHH
Confidence 699999999999999887 665443
No 83
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=22.64 E-value=64 Score=27.48 Aligned_cols=39 Identities=13% Similarity=-0.169 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecc
Q 035594 90 WNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWF 138 (336)
Q Consensus 90 w~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWF 138 (336)
-.+++.|-.+++-.|-.+. ..++||..|+ ++...|+++.
T Consensus 138 ~~L~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l 176 (189)
T PRK09648 138 DTLPEKQREILILRVVVGL------SAEETAEAVG----STPGAVRVAQ 176 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 3566777788887777766 2456999998 9999998776
No 84
>PTZ00183 centrin; Provisional
Probab=22.44 E-value=2.2e+02 Score=22.77 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=29.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHH
Q 035594 85 LGSSRWNPTPEQLLALEEMYRR----GTRTPSAEQIQHIASQL 123 (336)
Q Consensus 85 ~rR~Rw~FT~EQLqiLEelF~~----g~~YPs~eqRqeIA~eL 123 (336)
++..|..++++|+..|+++|.. +.++.+..+...+-..+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~ 46 (158)
T PTZ00183 4 RRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSL 46 (158)
T ss_pred cccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHh
Confidence 3567888999999999999974 34567777666655554
No 85
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=21.98 E-value=72 Score=26.58 Aligned_cols=47 Identities=11% Similarity=-0.058 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHH
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQ 147 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKR 147 (336)
..++.|-++|.-.|-.+. + .++||..|+ +++..|++|.+-=|.|-|+
T Consensus 108 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~lg----is~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 108 TLPVIEAQAILLCDVHEL--T----YEEAASVLD----LKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred hCCHHHHHHHHhHHHhcC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 456667777776665555 2 345999998 9999998877644444444
No 86
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=21.92 E-value=84 Score=26.86 Aligned_cols=40 Identities=10% Similarity=0.142 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 90 WNPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 90 w~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
-.+++.|-++|+-.|-.+. + .++||+.|+ |+...|++-..
T Consensus 130 ~~L~~~~r~vl~l~~~~~~--s----~~eIA~~lg----is~~tV~~~l~ 169 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHEK--S----VEEVGEIVG----IPESTVKTRMF 169 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHH
Confidence 3567888888888777666 2 345999998 99999987664
No 87
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=21.81 E-value=67 Score=28.12 Aligned_cols=51 Identities=18% Similarity=-0.018 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhh
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRR 151 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr 151 (336)
.+++.|-++|.-.|-.+. +. ++||..|+ |+...|+++.+-=|.+-|+.-..
T Consensus 113 ~Lp~~~r~v~~L~~~~g~--s~----~EIA~~Lg----iS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 113 QLPDEQREALILVGASGF--SY----EEAAEMCG----VAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred hCCHHHhHHhhhHHhcCC--CH----HHHHHHHC----CCHHHHHHHHHHHHHHHHHHHhc
Confidence 346666677776666555 33 45999998 99999998886555555444433
No 88
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.67 E-value=46 Score=30.21 Aligned_cols=51 Identities=24% Similarity=0.133 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhh
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRW 152 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~ 152 (336)
.+|+-|+++|+-+.. |. .+.+ ||+.|. +++..|+.+.++=..|..-+.|.+
T Consensus 155 ~Lt~rE~~Vl~l~~~-G~--s~~e----IA~~L~----iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 155 LLTHREKEILNKLRI-GA--SNNE----IARSLF----ISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCHHHHHHHHHHHc-CC--CHHH----HHHHhC----CCHHHHHHHHHHHHHHhCCCCHHH
Confidence 489999999999988 44 3444 999998 999999998887776666555544
No 89
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=21.58 E-value=67 Score=27.22 Aligned_cols=39 Identities=21% Similarity=0.052 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
.+++.|..+|+-.|-.+. + .++||..|+ +++..|+++-+
T Consensus 100 ~L~~~~r~v~~l~~~~g~--s----~~eIA~~lg----is~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL--S----QQEIAEKLG----LSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 677888888888887776 2 345999998 99999997764
No 90
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=21.54 E-value=56 Score=27.45 Aligned_cols=37 Identities=14% Similarity=-0.028 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 93 TPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 93 T~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
++.|-+++.-.|-.+. ..++||+.|+ +++..|+++..
T Consensus 140 ~~~~r~v~~l~~~~~~------s~~EIA~~lg----is~~tv~~~l~ 176 (190)
T TIGR02939 140 PEDLRTAITLRELEGL------SYEDIARIMD----CPVGTVRSRIF 176 (190)
T ss_pred CHHHhhhhhhhhhcCC------CHHHHHHHHC----cCHHHHHHHHH
Confidence 4555555555554444 2456999998 99999988774
No 91
>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]
Probab=21.48 E-value=38 Score=36.99 Aligned_cols=45 Identities=16% Similarity=0.310 Sum_probs=34.4
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcce--ecccchhhHHHHhhhhh
Q 035594 97 LLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVF--YWFQNHKARERQKRRRW 152 (336)
Q Consensus 97 LqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVq--vWFQNRRAReKRKrRr~ 152 (336)
+..|..+|.+....|.++ |.+|++.||- -=|-|.|+|+++.+-++
T Consensus 652 iklLDdLFkKTka~PcIY-----------yLPLTeEqIAaKEAer~~k~KErrE~~rd 698 (718)
T KOG2416|consen 652 IKLLDDLFKKTKAIPCIY-----------YLPLTEEQIAAKEAERNNKGKERRETTRD 698 (718)
T ss_pred hhHHHHHHHhcccCCcee-----------eecCCHHHHHHHHHHHhhhhhhhhhhhhh
Confidence 788999999998888887 5566666643 56788888888665554
No 92
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=21.40 E-value=72 Score=26.80 Aligned_cols=39 Identities=21% Similarity=0.202 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccc
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQN 140 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQN 140 (336)
+.+.|-.++.-.|-.+. ..++||..|+ +++..|++..+.
T Consensus 135 Lp~~~r~v~~l~~~~g~------s~~EIA~~lg----is~~tVk~~l~R 173 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL------TVEEIAELLG----VSVRTVERDWRF 173 (183)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHHHH
Confidence 66667777777777776 2346999998 999999987653
No 93
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.79 E-value=94 Score=26.93 Aligned_cols=48 Identities=13% Similarity=0.057 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHh
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQK 148 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRK 148 (336)
.+.+.|.++|.-.|-.+. ..++||+.|+ ++...|+....-=|.+-|+.
T Consensus 131 ~L~~~~r~v~~l~~~~g~------s~~EIA~~lg----is~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREVLGF------ESDEICQELE----ISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHHhCC------CHHHHHHHhC----CCHHHHHHHHHHHHHHHHHH
Confidence 455667777777777766 2356999998 99999976554333343333
No 94
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=20.69 E-value=89 Score=26.25 Aligned_cols=38 Identities=16% Similarity=0.105 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
+++.|-+++.-.|-.+. + -++||+.|+ ++...|+++..
T Consensus 120 L~~~~r~i~~l~~~~~~--s----~~EIA~~lg----is~~tV~~~l~ 157 (173)
T PRK12522 120 LNEKYKTVLVLYYYEQY--S----YKEMSEILN----IPIGTVKYRLN 157 (173)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHhC----CCHHHHHHHHH
Confidence 44555566666666665 2 345999998 99999987664
No 95
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.58 E-value=74 Score=25.42 Aligned_cols=28 Identities=11% Similarity=0.160 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 112 SAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 112 s~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
....+++|+..|....+|.+.+|.+|+.
T Consensus 48 ~G~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 48 KGRRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred CchhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 3467888888898888899999999985
No 96
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=20.57 E-value=75 Score=26.99 Aligned_cols=38 Identities=16% Similarity=0.052 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
+++.|-.+|...|-.+. + .++||..|+ ++...|+++.+
T Consensus 129 L~~~~r~i~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~ 166 (186)
T PRK05602 129 LPERQREAIVLQYYQGL--S----NIEAAAVMD----ISVDALESLLA 166 (186)
T ss_pred CCHHHHHHhhHHHhcCC--C----HHHHHHHhC----cCHHHHHHHHH
Confidence 46677777777776666 2 345999998 99999998763
No 97
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=20.49 E-value=2.5e+02 Score=18.75 Aligned_cols=28 Identities=29% Similarity=0.525 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Q 035594 94 PEQLLALEEMYRRGTRTPSAEQIQHIASQL 123 (336)
Q Consensus 94 ~EQLqiLEelF~~g~~YPs~eqRqeIA~eL 123 (336)
.++|..|.++|..|- .+.++=++..+.|
T Consensus 2 ~~~L~~L~~l~~~G~--IseeEy~~~k~~l 29 (31)
T PF09851_consen 2 EDRLEKLKELYDKGE--ISEEEYEQKKARL 29 (31)
T ss_pred hHHHHHHHHHHHcCC--CCHHHHHHHHHHH
Confidence 478999999999998 7887766666554
No 98
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.39 E-value=87 Score=26.60 Aligned_cols=52 Identities=19% Similarity=0.031 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceecccchhhHHHHhhhhhh
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQNHKARERQKRRRWE 153 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQNRRAReKRKrRr~e 153 (336)
+++.|..++.-.|-.+. ..++||+.|+ |++..|++..+.=|.+-|+...+.+
T Consensus 118 Lp~~~r~i~~l~~~e~~------s~~EIA~~lg----is~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY------SQEEIAQLLQ----IPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred CCHHHHHHHHHHHHccC------CHHHHHHHHC----CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666665555 2356999998 9999999877766666666555543
No 99
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=20.29 E-value=86 Score=25.88 Aligned_cols=38 Identities=21% Similarity=0.031 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 92 PTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 92 FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
+++.|-+++...|-.+. + .++||..|+ +++..|++.-.
T Consensus 106 L~~~~r~v~~l~~~~~~--s----~~eIA~~lg----is~~tv~~~l~ 143 (159)
T PRK12527 106 LPPACRDSFLLRKLEGL--S----HQQIAEHLG----ISRSLVEKHIV 143 (159)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHhC----CCHHHHHHHHH
Confidence 66667777777776665 2 345999998 99999986554
No 100
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.16 E-value=88 Score=25.54 Aligned_cols=39 Identities=13% Similarity=0.021 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhcCCCCCCcceeccc
Q 035594 91 NPTPEQLLALEEMYRRGTRTPSAEQIQHIASQLRRFGKIEGKNVFYWFQ 139 (336)
Q Consensus 91 ~FT~EQLqiLEelF~~g~~YPs~eqRqeIA~eL~~~G~LtEsqVqvWFQ 139 (336)
.+++.|.+++.-.|-.+. + .++||+.|+ ++...|++...
T Consensus 106 ~Lp~~~r~v~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYWEDM--D----VAETAAAMG----CSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHHhcC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 456677777777777766 2 346999998 99999986543
Done!