Query 016077
Match_columns 395
No_of_seqs 171 out of 1302
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 03:35:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016077.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016077hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 99.9 7.4E-22 1.6E-26 201.1 12.3 106 289-395 57-205 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 99.8 1.5E-19 3.3E-24 174.9 10.9 103 292-395 1-104 (298)
3 PRK07406 RNA polymerase sigma 99.8 8.6E-19 1.9E-23 176.5 11.7 105 290-395 61-166 (373)
4 PRK05949 RNA polymerase sigma 99.7 1.3E-17 2.7E-22 164.9 12.1 106 289-395 15-121 (327)
5 PRK07405 RNA polymerase sigma 99.7 1.6E-17 3.5E-22 163.1 11.2 104 291-395 7-111 (317)
6 PRK05901 RNA polymerase sigma 99.5 9.7E-15 2.1E-19 152.5 6.3 95 287-395 206-301 (509)
7 COG0568 RpoD DNA-directed RNA 99.4 2.3E-13 4.9E-18 136.4 7.6 104 291-395 8-132 (342)
8 PRK07921 RNA polymerase sigma 99.3 6E-12 1.3E-16 124.8 8.1 92 290-395 24-116 (324)
9 PRK09210 RNA polymerase sigma 98.7 1.5E-08 3.4E-13 101.8 6.3 67 288-395 92-159 (367)
10 PRK05658 RNA polymerase sigma 98.5 8.7E-08 1.9E-12 102.3 4.4 32 364-395 379-410 (619)
11 PRK06596 RNA polymerase factor 98.3 1.5E-06 3.2E-11 84.5 6.2 67 288-395 10-78 (284)
12 TIGR02392 rpoH_proteo alternat 98.2 2E-06 4.4E-11 82.6 5.6 62 293-395 2-65 (270)
13 PF00140 Sigma70_r1_2: Sigma-7 98.1 7.7E-07 1.7E-11 62.9 0.9 34 291-325 1-35 (37)
14 PRK07500 rpoH2 RNA polymerase 98.1 3.8E-06 8.2E-11 82.0 5.6 64 291-395 5-70 (289)
15 PRK05657 RNA polymerase sigma 97.8 3.8E-05 8.2E-10 76.5 5.6 64 291-395 52-116 (325)
16 PRK07122 RNA polymerase sigma 97.4 7.3E-05 1.6E-09 72.1 1.9 33 363-395 38-70 (264)
17 TIGR02850 spore_sigG RNA polym 97.2 0.00043 9.3E-09 65.9 5.0 54 302-395 11-64 (254)
18 TIGR02394 rpoS_proteo RNA poly 97.2 0.00064 1.4E-08 65.9 6.1 66 289-395 10-76 (285)
19 PRK08215 sporulation sigma fac 96.9 0.0013 2.9E-08 62.6 4.8 54 302-395 14-67 (258)
20 PRK05658 RNA polymerase sigma 96.8 0.0015 3.2E-08 70.4 5.0 34 290-324 102-136 (619)
21 PF04539 Sigma70_r3: Sigma-70 96.5 0.0059 1.3E-07 47.9 5.2 41 322-362 3-43 (78)
22 PRK05803 sporulation sigma fac 96.4 0.0055 1.2E-07 57.5 5.5 61 294-395 18-79 (233)
23 PRK06288 RNA polymerase sigma 96.0 0.006 1.3E-07 58.6 3.8 57 300-395 5-64 (268)
24 PRK05572 sporulation sigma fac 92.2 0.22 4.7E-06 47.5 4.8 54 302-395 9-62 (252)
25 TIGR02846 spore_sigmaK RNA pol 88.4 0.95 2.1E-05 42.4 5.6 60 296-395 19-78 (227)
26 COG1191 FliA DNA-directed RNA 85.2 1.7 3.7E-05 42.7 5.5 40 323-362 110-149 (247)
27 PRK07408 RNA polymerase sigma 82.6 3.1 6.7E-05 40.0 6.1 38 323-360 113-150 (256)
28 PRK08301 sporulation sigma fac 82.4 2.1 4.5E-05 40.0 4.7 59 296-394 23-81 (234)
29 TIGR02850 spore_sigG RNA polym 80.3 4.3 9.4E-05 38.8 6.1 37 324-360 121-157 (254)
30 PRK07122 RNA polymerase sigma 79.8 4.5 9.7E-05 39.3 6.2 37 324-360 128-164 (264)
31 TIGR02393 RpoD_Cterm RNA polym 79.3 5.1 0.00011 37.8 6.2 38 323-360 87-124 (238)
32 PRK07921 RNA polymerase sigma 78.2 5.1 0.00011 40.4 6.2 39 322-360 172-210 (324)
33 PRK05911 RNA polymerase sigma 78.1 5 0.00011 38.7 5.9 37 324-360 111-147 (257)
34 PRK12427 flagellar biosynthesi 77.9 4 8.6E-05 38.8 5.0 37 324-360 102-138 (231)
35 PRK09210 RNA polymerase sigma 76.1 6.3 0.00014 40.3 6.2 38 323-360 216-253 (367)
36 TIGR02835 spore_sigmaE RNA pol 72.8 5.9 0.00013 37.3 4.8 59 296-394 23-81 (234)
37 PF01726 LexA_DNA_bind: LexA D 72.2 11 0.00025 29.6 5.5 29 333-361 19-48 (65)
38 PRK11511 DNA-binding transcrip 71.6 14 0.0003 31.9 6.4 61 324-385 10-84 (127)
39 PRK05901 RNA polymerase sigma 71.0 9.3 0.0002 41.3 6.2 38 323-360 358-395 (509)
40 PRK07406 RNA polymerase sigma 70.3 10 0.00022 39.2 6.2 39 322-360 222-260 (373)
41 PRK07670 RNA polymerase sigma 67.0 12 0.00027 35.6 5.6 39 323-361 109-147 (251)
42 TIGR02885 spore_sigF RNA polym 66.7 11 0.00023 35.3 5.0 37 325-361 99-135 (231)
43 TIGR02479 FliA_WhiG RNA polyme 66.0 14 0.00029 34.5 5.6 39 322-360 82-120 (224)
44 PRK10219 DNA-binding transcrip 65.4 23 0.00049 29.2 6.2 59 325-384 7-79 (107)
45 PRK05949 RNA polymerase sigma 63.5 18 0.0004 36.5 6.3 38 323-360 178-215 (327)
46 PRK07598 RNA polymerase sigma 63.3 12 0.00026 39.5 5.1 39 323-361 262-300 (415)
47 PRK08215 sporulation sigma fac 62.6 20 0.00044 34.3 6.2 37 324-360 124-160 (258)
48 COG0568 RpoD DNA-directed RNA 62.2 19 0.00041 37.3 6.2 43 318-360 184-226 (342)
49 PRK06288 RNA polymerase sigma 60.1 16 0.00034 35.3 5.0 38 323-360 118-155 (268)
50 PF04967 HTH_10: HTH DNA bindi 59.3 26 0.00056 26.9 5.0 27 338-364 22-48 (53)
51 PRK11922 RNA polymerase sigma 59.0 9.2 0.0002 35.9 3.1 50 302-391 7-56 (231)
52 PRK07405 RNA polymerase sigma 58.0 26 0.00057 35.1 6.3 38 323-360 168-205 (317)
53 TIGR01446 DnaD_dom DnaD and ph 56.2 20 0.00043 27.8 4.1 57 331-391 4-66 (73)
54 TIGR02997 Sig70-cyanoRpoD RNA 55.6 32 0.00069 33.9 6.4 37 324-360 162-198 (298)
55 COG4367 Uncharacterized protei 54.2 49 0.0011 28.6 6.3 45 328-372 11-62 (97)
56 PRK15121 right oriC-binding tr 53.2 33 0.00072 33.2 6.0 38 324-361 6-43 (289)
57 PRK13503 transcriptional activ 52.8 39 0.00084 31.8 6.2 59 325-384 173-245 (278)
58 PRK15044 transcriptional regul 50.7 33 0.00072 34.9 5.7 37 325-361 194-230 (295)
59 TIGR02980 SigBFG RNA polymeras 50.4 30 0.00066 32.0 5.1 35 326-360 93-127 (227)
60 PRK07500 rpoH2 RNA polymerase 50.1 27 0.00058 34.5 4.8 26 334-359 143-168 (289)
61 PRK06986 fliA flagellar biosyn 45.8 38 0.00083 31.8 5.0 36 325-360 97-132 (236)
62 PRK15186 AraC family transcrip 43.7 44 0.00094 33.4 5.3 36 327-362 185-220 (291)
63 PRK05572 sporulation sigma fac 40.8 62 0.0013 30.8 5.6 36 323-358 118-153 (252)
64 TIGR03826 YvyF flagellar opero 40.1 64 0.0014 29.3 5.3 38 327-364 34-71 (137)
65 TIGR02941 Sigma_B RNA polymera 39.0 56 0.0012 31.1 5.0 36 325-360 118-153 (255)
66 TIGR02297 HpaA 4-hydroxyphenyl 37.3 69 0.0015 30.3 5.3 33 329-361 192-224 (287)
67 PRK05657 RNA polymerase sigma 35.9 82 0.0018 31.8 5.8 36 325-360 175-210 (325)
68 PRK09393 ftrA transcriptional 34.7 69 0.0015 31.4 5.0 35 327-361 222-256 (322)
69 PRK13239 alkylmercury lyase; P 33.1 72 0.0016 30.9 4.7 27 336-362 33-59 (206)
70 PF04542 Sigma70_r2: Sigma-70 31.6 14 0.00031 27.2 -0.2 25 370-394 1-25 (71)
71 COG4977 Transcriptional regula 31.2 1E+02 0.0023 31.7 5.8 53 326-378 223-289 (328)
72 PF13404 HTH_AsnC-type: AsnC-t 30.1 1.2E+02 0.0025 22.0 4.3 25 338-362 16-40 (42)
73 smart00342 HTH_ARAC helix_turn 30.0 95 0.002 23.0 4.1 23 339-361 1-23 (84)
74 PRK09685 DNA-binding transcrip 29.9 3.4E+02 0.0074 25.9 8.8 60 325-385 199-274 (302)
75 PRK13501 transcriptional activ 29.0 1.5E+02 0.0032 28.5 6.1 55 329-384 182-250 (290)
76 KOG0197 Tyrosine kinases [Sign 28.4 24 0.00051 38.1 0.7 62 289-382 283-345 (468)
77 PF13936 HTH_38: Helix-turn-he 27.9 66 0.0014 23.2 2.7 23 340-362 21-43 (44)
78 COG4785 NlpI Lipoprotein NlpI, 26.9 2.9E+02 0.0062 28.0 7.7 80 288-390 162-252 (297)
79 PRK15185 transcriptional regul 26.3 2E+02 0.0043 29.6 6.7 38 324-361 207-244 (309)
80 TIGR02394 rpoS_proteo RNA poly 25.6 1.8E+02 0.004 28.3 6.2 35 326-360 136-170 (285)
81 PRK10572 DNA-binding transcrip 25.5 1.3E+02 0.0028 28.7 5.1 58 326-384 186-257 (290)
82 PF02796 HTH_7: Helix-turn-hel 25.3 1.1E+02 0.0023 22.0 3.5 22 340-361 22-43 (45)
83 PRK10371 DNA-binding transcrip 25.1 2.5E+02 0.0054 27.6 7.1 37 325-361 193-229 (302)
84 PRK06596 RNA polymerase factor 23.1 1.4E+02 0.0031 29.3 4.9 25 336-360 148-172 (284)
85 PF12324 HTH_15: Helix-turn-he 22.9 1E+02 0.0023 25.7 3.3 27 336-362 35-61 (77)
86 COG3413 Predicted DNA binding 22.3 1.7E+02 0.0036 27.5 5.0 54 305-373 154-209 (215)
87 PF14711 Nitr_red_bet_C: Respi 22.1 2E+02 0.0042 24.2 4.8 51 293-353 31-82 (83)
88 PRK12519 RNA polymerase sigma 21.2 2.4E+02 0.0051 25.2 5.6 38 337-374 155-192 (194)
89 cd05491 Bromo_TBP7_like Bromod 21.2 88 0.0019 28.0 2.7 40 349-388 63-102 (119)
90 TIGR02844 spore_III_D sporulat 20.9 4E+02 0.0087 22.1 6.4 36 325-363 8-43 (80)
91 cd05499 Bromo_BDF1_2_II Bromod 20.9 1.1E+02 0.0023 25.6 3.1 40 351-390 46-85 (102)
92 PF08279 HTH_11: HTH domain; 20.8 1.9E+02 0.004 20.9 4.0 24 339-362 15-38 (55)
93 cd06170 LuxR_C_like C-terminal 20.7 2E+02 0.0044 19.9 4.1 38 340-380 16-54 (57)
94 PF08281 Sigma70_r4_2: Sigma-7 20.2 2.3E+02 0.0051 20.3 4.5 29 336-364 23-51 (54)
95 PF04545 Sigma70_r4: Sigma-70, 20.0 2.9E+02 0.0064 19.7 4.9 30 335-364 16-45 (50)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=99.87 E-value=7.4e-22 Score=201.12 Aligned_cols=106 Identities=34% Similarity=0.558 Sum_probs=97.5
Q ss_pred CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHHHcCCCCChHHHHH
Q 016077 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA 347 (395)
Q Consensus 289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~--------------------LE~ir~~L~e~lGrePT~~EWAe 347 (395)
..+|+++ ||++| |+.+|||++||++|+++||++++ |++++.+|++++|++||..|||+
T Consensus 57 ~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~ 135 (415)
T PRK07598 57 RSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK 135 (415)
T ss_pred CCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 4589999 99999 99999999999999999999999 89999999999999999999997
Q ss_pred HhcCcHHHHHHhh----------------------hhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 348 AAGVDQRELRRRL----------------------NYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 348 A~Gms~~eLr~~L----------------------~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
++|+++.+|+.+| ..|+.|+++||++|+|||++||++|.|+|++++|+
T Consensus 136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDL 205 (415)
T PRK07598 136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDL 205 (415)
T ss_pred HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHH
Confidence 7776666666654 67889999999999999999999999999999985
No 2
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=99.80 E-value=1.5e-19 Score=174.90 Aligned_cols=103 Identities=45% Similarity=0.685 Sum_probs=100.0
Q ss_pred ChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHH
Q 016077 292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 370 (395)
Q Consensus 292 D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerL 370 (395)
|++. ||+++ +++||||++||.+|+++|+.++.+++++.+|+++.|++||..+||+++|++..+|..++..|..|+++|
T Consensus 1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 79 (298)
T TIGR02997 1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM 79 (298)
T ss_pred CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence 4677 99999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 371 ITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 371 VkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
|++|+|||++||++|.|+|++++|+
T Consensus 80 v~~~lrlV~~iA~~y~~~~~~~eDL 104 (298)
T TIGR02997 80 IKANLRLVVSVAKKYQNRGLELLDL 104 (298)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHH
Confidence 9999999999999999999999885
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=99.78 E-value=8.6e-19 Score=176.50 Aligned_cols=105 Identities=40% Similarity=0.619 Sum_probs=102.2
Q ss_pred CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHH
Q 016077 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368 (395)
Q Consensus 290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARe 368 (395)
..|+++ ||++| +++||||++||++|+++|++++.+++++.+|+++.|++|+..+||+++|++..+|++++..|..|++
T Consensus 61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 139 (373)
T PRK07406 61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE 139 (373)
T ss_pred CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence 468899 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 369 KMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 369 rLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
+||.+|++||++||++|.|+|++++|+
T Consensus 140 ~Li~~~l~lV~~iA~ry~~~~~~~eDL 166 (373)
T PRK07406 140 KMVQSNLRLVVSIAKKYMNRGLSFQDL 166 (373)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence 999999999999999999999999885
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=99.74 E-value=1.3e-17 Score=164.90 Aligned_cols=106 Identities=32% Similarity=0.513 Sum_probs=102.5
Q ss_pred CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHH
Q 016077 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 367 (395)
Q Consensus 289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~AR 367 (395)
..+|++. ||++| +++||||++||++|+++||.++.+++.+..|++++|++|+..+||++++|+..+|...+..|..|+
T Consensus 15 ~~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~ 93 (327)
T PRK05949 15 FSADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAK 93 (327)
T ss_pred CCCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHH
Confidence 3578999 99999 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 368 DKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 368 erLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
++||++|+++|++||++|.+.|++++|+
T Consensus 94 ~~Li~~~~~~V~~iA~~y~~~~~~~eDL 121 (327)
T PRK05949 94 QKMIEANLRLVVAIAKKYQKRNMEFLDL 121 (327)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCCHHHH
Confidence 9999999999999999999999999885
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.73 E-value=1.6e-17 Score=163.13 Aligned_cols=104 Identities=38% Similarity=0.547 Sum_probs=101.2
Q ss_pred CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHH
Q 016077 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 369 (395)
Q Consensus 291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARer 369 (395)
+|++. ||++| +++||||++||++|+++|++++.+++++..|++++|++|+..+||++++|+..+|..++..|..|+++
T Consensus 7 ~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 7 TDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 67899 99999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 370 MITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 370 LVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
||.+|+++|++||++|.|.|.+++|+
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDL 111 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDL 111 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence 99999999999999999999999884
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.52 E-value=9.7e-15 Score=152.53 Aligned_cols=95 Identities=28% Similarity=0.383 Sum_probs=79.1
Q ss_pred cCCCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHH
Q 016077 287 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365 (395)
Q Consensus 287 ~~~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ 365 (395)
.....|+++ ||++| +++++||++||++|+++|+.+..++... . ...+|+.. +..+|+++++.|..
T Consensus 206 ~~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~~---~~~~l~~~~~~g~~ 271 (509)
T PRK05901 206 LTATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDPE---LRRDLQWIGRDGKR 271 (509)
T ss_pred ccccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchhh---hhhhhhhhccchHH
Confidence 344578999 99999 9999999999999999999885544422 1 11234422 56889999999999
Q ss_pred HHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 366 CKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 366 ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
||++||.+|||||++||++|.|+|++|+|+
T Consensus 272 Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDL 301 (509)
T PRK05901 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDL 301 (509)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHH
Confidence 999999999999999999999999999985
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.42 E-value=2.3e-13 Score=136.36 Aligned_cols=104 Identities=34% Similarity=0.469 Sum_probs=92.7
Q ss_pred CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HcCCCCChH---------------HHHHHhcCcH
Q 016077 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ 353 (395)
Q Consensus 291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e-~lGrePT~~---------------EWAeA~Gms~ 353 (395)
.|.+. |+.++ +..++++.++|.++.+.++....+......|.. .++..|+.. +|+..+..++
T Consensus 8 ~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 8 ADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred hhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 56788 99999 899999999999999999998888888888877 778999987 7777777666
Q ss_pred -HHHHHhhhhcHH---HHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 354 -RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 354 -~eLr~~L~~G~~---ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
..|..++..|.. |+.+||.+||||||||||+|.|+||+|.|+
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DL 132 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDL 132 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHH
Confidence 778899988865 999999999999999999999999999995
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.29 E-value=6e-12 Score=124.80 Aligned_cols=92 Identities=30% Similarity=0.421 Sum_probs=77.5
Q ss_pred CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHH
Q 016077 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368 (395)
Q Consensus 290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARe 368 (395)
.+|++. ||+++ +++++||++||++|+++|+.+..++.. |+..+|.... ...+|+.+++.|..|++
T Consensus 24 ~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~ 89 (324)
T PRK07921 24 AADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR 89 (324)
T ss_pred CCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence 468899 99999 999999999999999999998765554 2233332111 45789999999999999
Q ss_pred HHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 369 KMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 369 rLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
+||.+|++||++||++|.|.|++++|+
T Consensus 90 ~Lv~~~~~lV~~iA~r~~~~~~~~eDL 116 (324)
T PRK07921 90 HLLEANLRLVVSLAKRYTGRGMPLLDL 116 (324)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence 999999999999999999999999885
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=98.72 E-value=1.5e-08 Score=101.80 Aligned_cols=67 Identities=39% Similarity=0.596 Sum_probs=61.7
Q ss_pred CCCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHH
Q 016077 288 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC 366 (395)
Q Consensus 288 ~~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~A 366 (395)
...+|+++ ||++| +++|+||++||.+|+++++.| +..|
T Consensus 92 ~~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A 130 (367)
T PRK09210 92 VKINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEEG----------------------------------------DEEA 130 (367)
T ss_pred cccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHhh----------------------------------------HHHH
Confidence 34578999 99999 999999999999999999887 5789
Q ss_pred HHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 367 KDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 367 RerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
+++||++|++||++||++|.|+|++++|+
T Consensus 131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDL 159 (367)
T PRK09210 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDL 159 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence 99999999999999999999999999884
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=98.49 E-value=8.7e-08 Score=102.29 Aligned_cols=32 Identities=41% Similarity=0.504 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 364 ILCKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 364 ~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
..|+++||.+|||||++||++|.|+|++|+|+
T Consensus 379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DL 410 (619)
T PRK05658 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 410 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHH
Confidence 47999999999999999999999999999985
No 11
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=98.25 E-value=1.5e-06 Score=84.51 Aligned_cols=67 Identities=25% Similarity=0.430 Sum_probs=59.5
Q ss_pred CCCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHH
Q 016077 288 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQ-DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365 (395)
Q Consensus 288 ~~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ-~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ 365 (395)
+.+.+++. |++++ ++.|+|+.++|.+|+.+++ .| +..
T Consensus 10 ~~~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~~G----------------------------------------d~~ 48 (284)
T PRK06596 10 LSPEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLREHG----------------------------------------DLE 48 (284)
T ss_pred CCCccHHHHHHHHH-hccCCCCHHHHHHHHHHHHHcC----------------------------------------CHH
Confidence 34567888 99999 9999999999999998854 44 678
Q ss_pred HHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 366 CKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 366 ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
|+++||..|++||.+||++|.+.|++++||
T Consensus 49 a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDL 78 (284)
T PRK06596 49 AAKQLVLSHLRFVVHIARGYRGYGLPQADL 78 (284)
T ss_pred HHHHHHHHhHHHHHHHHHHhcCCCCCHHHH
Confidence 999999999999999999999999999885
No 12
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=98.19 E-value=2e-06 Score=82.59 Aligned_cols=62 Identities=31% Similarity=0.504 Sum_probs=55.8
Q ss_pred hhH-HHHHhcCCCCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHH
Q 016077 293 PLR-YLRATTSSSRLLTANEEMQLSAGI-QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 370 (395)
Q Consensus 293 ~lr-YLrei~g~~~LLTaeEEveLa~~I-Q~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerL 370 (395)
++. ||+++ +++++|+.++|.+|+.++ +.+ +..|+++|
T Consensus 2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~~g----------------------------------------d~~a~~~L 40 (270)
T TIGR02392 2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLREHG----------------------------------------DLDAAKKL 40 (270)
T ss_pred hHHHHHHHH-hcCCCCCHHHHHHHHHHHHHCC----------------------------------------CHHHHHHH
Confidence 567 99999 999999999999999885 343 67899999
Q ss_pred HHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 371 ITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 371 VkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
|..|++||.++|++|.+.|.+++|+
T Consensus 41 v~~~~~lV~~~a~~~~~~~~~~eDL 65 (270)
T TIGR02392 41 VLSHLRFVVKIARGYRGYGLPQADL 65 (270)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHH
Confidence 9999999999999999999999885
No 13
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 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 [, ]. ; 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: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.13 E-value=7.7e-07 Score=62.92 Aligned_cols=34 Identities=41% Similarity=0.526 Sum_probs=30.0
Q ss_pred CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHH
Q 016077 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKL 325 (395)
Q Consensus 291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~L 325 (395)
+|+++ ||++| ++++|||++||++|+++|+.|...
T Consensus 1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~~~ 35 (37)
T PF00140_consen 1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKGDEA 35 (37)
T ss_dssp HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhHHh
Confidence 37899 99999 999999999999999999998644
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=98.11 E-value=3.8e-06 Score=82.00 Aligned_cols=64 Identities=22% Similarity=0.277 Sum_probs=57.4
Q ss_pred CChhH-HHHHhcCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHH
Q 016077 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQ-DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368 (395)
Q Consensus 291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ-~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARe 368 (395)
.+.++ ||+++ .++++||.++|.+|.++++ .+ +..|++
T Consensus 5 ~~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~~g----------------------------------------d~~A~~ 43 (289)
T PRK07500 5 ASADRSMIRSA-MKAPYLEREEEHALAYRWKDHR----------------------------------------DEDALH 43 (289)
T ss_pred hhHHHHHHHHH-hcCCCCCHHHHHHHHHHHHHCC----------------------------------------CHHHHH
Confidence 34566 99999 8999999999999999875 33 688999
Q ss_pred HHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 369 KMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 369 rLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
+||..|+++|.+||++|.+.|.+++|+
T Consensus 44 ~Lv~~~~~lV~~~a~~~~~~~~~~eDL 70 (289)
T PRK07500 44 RIISAHMRLVISMAGKFRRFGLPMNDL 70 (289)
T ss_pred HHHHHhHHHHHHHHHHHcCCCCCHHHH
Confidence 999999999999999999999998885
No 15
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=97.75 E-value=3.8e-05 Score=76.50 Aligned_cols=64 Identities=34% Similarity=0.427 Sum_probs=58.8
Q ss_pred CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHH
Q 016077 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 369 (395)
Q Consensus 291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARer 369 (395)
.|.++ |+.+| +..|+||+++|.+|..+++.| +..|.++
T Consensus 52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~G----------------------------------------d~~A~~~ 90 (325)
T PRK05657 52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALRG----------------------------------------DFAARQR 90 (325)
T ss_pred ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHH
Confidence 56778 99999 999999999999999999887 6889999
Q ss_pred HHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 370 MITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 370 LVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
||..|+++|.++|++|.+.|.+.+|+
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDL 116 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDL 116 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHH
Confidence 99999999999999999999888774
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=97.38 E-value=7.3e-05 Score=72.10 Aligned_cols=33 Identities=21% Similarity=0.302 Sum_probs=30.5
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 363 GILCKDKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 363 G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
...+|++||.+|||||++||++|.++|++++|+
T Consensus 38 ~~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DL 70 (264)
T PRK07122 38 FQRQRDRIVTRCLPLADHIARRFDGRGEPRDDL 70 (264)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHH
Confidence 356999999999999999999999999999985
No 17
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=97.21 E-value=0.00043 Score=65.88 Aligned_cols=54 Identities=24% Similarity=0.369 Sum_probs=48.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHH
Q 016077 302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381 (395)
Q Consensus 302 g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSI 381 (395)
+++|+|+++||.+|...++.+ +..|+++|+..|+++|.++
T Consensus 11 ~~~~~l~~~~~~~li~~~~~g----------------------------------------d~~a~~~L~~~~~~~v~~~ 50 (254)
T TIGR02850 11 SKLPVLKNQEMRELFIRMQSG----------------------------------------DTTAREKLINGNLRLVLSV 50 (254)
T ss_pred cCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhHHHHHHH
Confidence 678999999999999888765 6789999999999999999
Q ss_pred HHhccCCCCCCCCC
Q 016077 382 AKNYQGAGRMSRPC 395 (395)
Q Consensus 382 AKrY~GrGLsf~D~ 395 (395)
|++|.+.+.+.+|+
T Consensus 51 a~~~~~~~~~aeDl 64 (254)
T TIGR02850 51 IQRFNNRGEYVDDL 64 (254)
T ss_pred HHHHhCCCCCHHHH
Confidence 99999999888774
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. 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 RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=97.20 E-value=0.00064 Score=65.88 Aligned_cols=66 Identities=35% Similarity=0.397 Sum_probs=60.3
Q ss_pred CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHH
Q 016077 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 367 (395)
Q Consensus 289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~AR 367 (395)
-..|.++ ||.+| +.++.|+.++|.+|...++.+ +..|.
T Consensus 10 ~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~g----------------------------------------d~~a~ 48 (285)
T TIGR02394 10 RVADVTQLYLREI-GFKPLLTAEEEIAYARRALAG----------------------------------------DFEAR 48 (285)
T ss_pred CcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHcC----------------------------------------CHHHH
Confidence 3478899 99999 999999999999999999887 68899
Q ss_pred HHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077 368 DKMITSNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 368 erLVkSNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
+.|+..+..+|.++|.+|.+.|.+.+|+
T Consensus 49 ~~L~~~y~~~v~~~a~~~~~~~~~aeDL 76 (285)
T TIGR02394 49 KVMIESNLRLVVSIAKHYVNRGLPLLDL 76 (285)
T ss_pred HHHHHHhHHHHHHHHHHHhcCCCCHHHH
Confidence 9999999999999999999999988874
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=96.85 E-value=0.0013 Score=62.58 Aligned_cols=54 Identities=24% Similarity=0.355 Sum_probs=48.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHH
Q 016077 302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381 (395)
Q Consensus 302 g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSI 381 (395)
.++|+|+++|+..|...++.+ +..++++|+..|+++|..|
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~g----------------------------------------d~~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQNG----------------------------------------DKEAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHHHHHHHHH
Confidence 457899999999999888765 6789999999999999999
Q ss_pred HHhccCCCCCCCCC
Q 016077 382 AKNYQGAGRMSRPC 395 (395)
Q Consensus 382 AKrY~GrGLsf~D~ 395 (395)
|++|.+.+.+.+|+
T Consensus 54 a~~~~~~~~~aeDl 67 (258)
T PRK08215 54 IQRFNNRGENVDDL 67 (258)
T ss_pred HHHHhCCCCCHHHH
Confidence 99999999888774
No 20
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.78 E-value=0.0015 Score=70.36 Aligned_cols=34 Identities=32% Similarity=0.529 Sum_probs=32.1
Q ss_pred CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHH
Q 016077 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK 324 (395)
Q Consensus 290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~ 324 (395)
.+||++ ||++| |+.+|||.++|++++++|..|.+
T Consensus 102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHHHH
Confidence 599999 99999 99999999999999999998865
No 21
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=96.47 E-value=0.0059 Score=47.89 Aligned_cols=41 Identities=32% Similarity=0.404 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 322 ~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
+.++.+.+.+|..++||+||..|.|+.+||+.++++..+..
T Consensus 3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 34567889999999999999999999999999999887753
No 22
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=96.40 E-value=0.0055 Score=57.47 Aligned_cols=61 Identities=23% Similarity=0.336 Sum_probs=54.0
Q ss_pred hH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHH
Q 016077 294 LR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 372 (395)
Q Consensus 294 lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVk 372 (395)
+. |+.++ ++.++||+++|.+|...++.+ +..|.+.|+.
T Consensus 18 ~~~~~~~~-~~~~~~~~~~e~~l~~~~~~g----------------------------------------d~~a~~~l~~ 56 (233)
T PRK05803 18 LVSYVKNN-SFPQPLSEEEERKYLELMKEG----------------------------------------DEEARNILIE 56 (233)
T ss_pred HHHHHHHh-cccCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHH
Confidence 45 99999 889999999999888887765 6789999999
Q ss_pred HhHHHHHHHHHhccCCCCCCCCC
Q 016077 373 SNIRLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 373 SNLRLVVSIAKrY~GrGLsf~D~ 395 (395)
.+.++|.++|.+|.|.+.+.+||
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDl 79 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDL 79 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHH
Confidence 99999999999999998887775
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=96.04 E-value=0.006 Score=58.57 Aligned_cols=57 Identities=12% Similarity=0.027 Sum_probs=46.6
Q ss_pred hcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHH
Q 016077 300 TTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 379 (395)
Q Consensus 300 i~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVV 379 (395)
++|++++||.++|.+|...++.+ .+..+.+.|+..|++||.
T Consensus 5 ~~~~~~~~~~~~e~~l~~~~~~~---------------------------------------~d~~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 5 MSGKIPKYAQQDETELWREYKKT---------------------------------------GDPKIREYLILKYSPLVK 45 (268)
T ss_pred ccCCCccccchHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHH
Confidence 34789999999999999987754 167799999999999999
Q ss_pred HHHHhcc-C--CCCCCCCC
Q 016077 380 SIAKNYQ-G--AGRMSRPC 395 (395)
Q Consensus 380 SIAKrY~-G--rGLsf~D~ 395 (395)
.||++|. | .+.+.+|+
T Consensus 46 ~~a~~~~~~~~~~~~~eDl 64 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDL 64 (268)
T ss_pred HHHHHHHhcCCCCCCHHHH
Confidence 9999986 2 45556653
No 24
>PRK05572 sporulation sigma factor SigF; Validated
Probab=92.16 E-value=0.22 Score=47.45 Aligned_cols=54 Identities=22% Similarity=0.289 Sum_probs=46.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHH
Q 016077 302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381 (395)
Q Consensus 302 g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSI 381 (395)
...|.||.+++.+|...++.+ +..|.++|+..+.++|..+
T Consensus 9 ~~~~~l~~~~~~~li~~~~~g----------------------------------------d~~a~~~L~~~y~~~v~~~ 48 (252)
T PRK05572 9 KKKPQLKDEENKELIKKSQDG----------------------------------------DQEARDTLVEKNLRLVWSV 48 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhHHHHHHH
Confidence 347899999999888777655 5789999999999999999
Q ss_pred HHhccCCCCCCCCC
Q 016077 382 AKNYQGAGRMSRPC 395 (395)
Q Consensus 382 AKrY~GrGLsf~D~ 395 (395)
|++|.+.+.+.+|+
T Consensus 49 a~~~~~~~~~aeDl 62 (252)
T PRK05572 49 VQRFLNRGYEPDDL 62 (252)
T ss_pred HHHHccCCCCHHHH
Confidence 99999998877763
No 25
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=88.43 E-value=0.95 Score=42.44 Aligned_cols=60 Identities=22% Similarity=0.323 Sum_probs=48.9
Q ss_pred HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhH
Q 016077 296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 375 (395)
Q Consensus 296 YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNL 375 (395)
|...-.+..+.|++.+|.+|...++.+ +..|.+.|+..+.
T Consensus 19 ~~~~~~~~~~~~~~~~~~~li~~~~~g----------------------------------------d~~af~~l~~~y~ 58 (227)
T TIGR02846 19 YVTNNGSFPQPLSEEEEKKYLDRLKEG----------------------------------------DEEARNVLIERNL 58 (227)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhH
Confidence 666553456789999999998888776 6788999999999
Q ss_pred HHHHHHHHhccCCCCCCCCC
Q 016077 376 RLVISIAKNYQGAGRMSRPC 395 (395)
Q Consensus 376 RLVVSIAKrY~GrGLsf~D~ 395 (395)
++|.++|.+|.+...+.+||
T Consensus 59 ~~v~~~~~~~~~~~~dAEDl 78 (227)
T TIGR02846 59 RLVAHIVKKFSNTGEDVDDL 78 (227)
T ss_pred HHHHHHHHHhcCCCCCHHHH
Confidence 99999999998877766664
No 26
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=85.16 E-value=1.7 Score=42.69 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
.+++.+..+|+.++||+||+.|.|+..|++.+++...+..
T Consensus 110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~ 149 (247)
T COG1191 110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLA 149 (247)
T ss_pred HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 3455678899999999999999999999999988776643
No 27
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=82.64 E-value=3.1 Score=39.99 Aligned_cols=38 Identities=21% Similarity=0.232 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.++.+.+.+|...+|++||..|.|+.+|+++++++..+
T Consensus 113 ~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 113 RQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 34566788899999999999999999999999887653
No 28
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=82.43 E-value=2.1 Score=40.04 Aligned_cols=59 Identities=22% Similarity=0.327 Sum_probs=45.0
Q ss_pred HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhH
Q 016077 296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 375 (395)
Q Consensus 296 YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNL 375 (395)
|+++.-.-.+.++..++.+|...++.+ +..|.+.|+..+.
T Consensus 23 ~~~~~~~~~~~~~~~~~~~L~~~~~~g----------------------------------------d~~af~~l~~~y~ 62 (234)
T PRK08301 23 YIGGSEALPPPLSKEEEEYLLNKLPKG----------------------------------------DEAVRSLLIERNL 62 (234)
T ss_pred HhccccccCCcCCHHHHHHHHHHHHcc----------------------------------------CHHHHHHHHHHhH
Confidence 777772235667777877777776655 5678888999999
Q ss_pred HHHHHHHHhccCCCCCCCC
Q 016077 376 RLVISIAKNYQGAGRMSRP 394 (395)
Q Consensus 376 RLVVSIAKrY~GrGLsf~D 394 (395)
++|..+|++|.+.+.+.+|
T Consensus 63 ~~l~~~a~~~~~~~~~AeD 81 (234)
T PRK08301 63 RLVVYIARKFENTGINIED 81 (234)
T ss_pred HHHHHHHHHhhcCCCCHHH
Confidence 9999999999888776655
No 29
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=80.26 E-value=4.3 Score=38.76 Aligned_cols=37 Identities=27% Similarity=0.241 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
++.+.+.+|...+|++||..|.|+.+|++++.+...+
T Consensus 121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445667888889999999999999999998876654
No 30
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=79.83 E-value=4.5 Score=39.28 Aligned_cols=37 Identities=35% Similarity=0.492 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
++.+...+|...+|++||..|.|+.+|++++++...+
T Consensus 128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455677888899999999999999999999887655
No 31
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=79.26 E-value=5.1 Score=37.84 Aligned_cols=38 Identities=24% Similarity=0.260 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.++.+...+|...+|++||..|.|+.+|++.++++..+
T Consensus 87 ~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~ 124 (238)
T TIGR02393 87 NKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIK 124 (238)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34556678888999999999999999999999987754
No 32
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=78.24 E-value=5.1 Score=40.44 Aligned_cols=39 Identities=21% Similarity=0.336 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 322 ~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
..++.+++.+|...+|++||..|.|+.+|++.+.++..+
T Consensus 172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~ 210 (324)
T PRK07921 172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLL 210 (324)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 345666788899999999999999999999998887654
No 33
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=78.06 E-value=5 Score=38.65 Aligned_cols=37 Identities=24% Similarity=0.315 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
++.+....|...+|++||..|.|+.+|++.+++...+
T Consensus 111 ~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 111 KLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 3445566788899999999999999999999887654
No 34
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=77.88 E-value=4 Score=38.82 Aligned_cols=37 Identities=22% Similarity=0.352 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
++.+...+|...+|++||..|.|+.+|++.+++...+
T Consensus 102 ~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 102 KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455677888899999999999999999998886654
No 35
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=76.08 E-value=6.3 Score=40.25 Aligned_cols=38 Identities=24% Similarity=0.263 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.++.+...+|...+|++||..|.|+.+||+++.++..+
T Consensus 216 ~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~ 253 (367)
T PRK09210 216 NKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREIL 253 (367)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34566778899999999999999999999999988754
No 36
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=72.84 E-value=5.9 Score=37.31 Aligned_cols=59 Identities=25% Similarity=0.356 Sum_probs=44.8
Q ss_pred HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhH
Q 016077 296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 375 (395)
Q Consensus 296 YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNL 375 (395)
|+.+.-...+.|++++|.+|...++.+ +..|.+.|+....
T Consensus 23 ~~~~~~~~~~~~~~~~~~~l~~~~~~~----------------------------------------d~~a~~~l~~~y~ 62 (234)
T TIGR02835 23 YIGGSEALPPPLTGEEEEALLQKLTQG----------------------------------------DESAKSTLIERNL 62 (234)
T ss_pred HhcccccCCCcCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhH
Confidence 444442246778888888877766654 6788999999999
Q ss_pred HHHHHHHHhccCCCCCCCC
Q 016077 376 RLVISIAKNYQGAGRMSRP 394 (395)
Q Consensus 376 RLVVSIAKrY~GrGLsf~D 394 (395)
++|.+++.+|.+.+.+-+|
T Consensus 63 ~~l~~~~~~~~~~~~~AED 81 (234)
T TIGR02835 63 RLVVYIARKFENTGIGIED 81 (234)
T ss_pred HHHHHHHHHhccCCCCHHH
Confidence 9999999999888876655
No 37
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=72.19 E-value=11 Score=29.65 Aligned_cols=29 Identities=31% Similarity=0.444 Sum_probs=20.3
Q ss_pred HHHcCCCCChHHHHHHhcCc-HHHHHHhhh
Q 016077 333 SERCGGSPTFAQWAAAAGVD-QRELRRRLN 361 (395)
Q Consensus 333 ~e~lGrePT~~EWAeA~Gms-~~eLr~~L~ 361 (395)
.+..|.+||..|.|+++|+. ...+...|.
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 35789999999999999996 666665553
No 38
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=71.56 E-value=14 Score=31.91 Aligned_cols=61 Identities=13% Similarity=0.238 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh--------------cHHHHHHHHHHhHHHHHHHHHhc
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY--------------GILCKDKMITSNIRLVISIAKNY 385 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~--------------G~~ARerLVkSNLRLVVSIAKrY 385 (395)
.+.++..-+...+...++..++|+.+||+...|.+.... -..|++.|...++. |..||..+
T Consensus 10 ~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L~~t~~~-i~eIA~~~ 84 (127)
T PRK11511 10 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEP-ILYLAERY 84 (127)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHHh
Confidence 345666677788888999999999999999998887742 13455666666544 45666553
No 39
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=70.98 E-value=9.3 Score=41.30 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.++.+++.+|...+|++||..|.|+.+||+.+.++..+
T Consensus 358 ~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34666788999999999999999999999998887764
No 40
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=70.32 E-value=10 Score=39.23 Aligned_cols=39 Identities=23% Similarity=0.291 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 322 ~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
..++.+.+..|...+|++||..|.|+.+|++.+.++..+
T Consensus 222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~ 260 (373)
T PRK07406 222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIA 260 (373)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 344556678888999999999999999999998887653
No 41
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=66.97 E-value=12 Score=35.56 Aligned_cols=39 Identities=28% Similarity=0.283 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
.++.+...++...+|++|+..++|+..|++.++++..+.
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 109 KKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 344556677888999999999999999999988777653
No 42
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=66.71 E-value=11 Score=35.26 Aligned_cols=37 Identities=32% Similarity=0.466 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
+.+....|...+|++||..|.|+.+|++++++...+.
T Consensus 99 ~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 99 IRYMKEELSKELGREPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445677888899999999999999999988776543
No 43
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=65.99 E-value=14 Score=34.46 Aligned_cols=39 Identities=36% Similarity=0.420 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 322 ~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
..++.+...+|...+|++|+..|.|+.+|++++.++..+
T Consensus 82 ~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 82 ARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 345666778888999999999999999999998887765
No 44
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=65.43 E-value=23 Score=29.16 Aligned_cols=59 Identities=17% Similarity=0.186 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh--------------cHHHHHHHHHHhHHHHHHHHHh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY--------------GILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~--------------G~~ARerLVkSNLRLVVSIAKr 384 (395)
++++..-+.+.+...++.++.|+.+|++...|.+.... -..|++.|....+. |..||..
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~~~i~~~Rl~~a~~~L~~~~~~-i~~iA~~ 79 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERP-IFDIAMD 79 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHccCCC-HHHHHHH
Confidence 45566677778889999999999999999988877642 34567777665433 4556654
No 45
>PRK05949 RNA polymerase sigma factor; Validated
Probab=63.46 E-value=18 Score=36.51 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
-++.+.+.++...+|++||..|.|+.+|++.+.++..+
T Consensus 178 ~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~ 215 (327)
T PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYL 215 (327)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 33455667788889999999999999999998887763
No 46
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=63.32 E-value=12 Score=39.49 Aligned_cols=39 Identities=21% Similarity=0.281 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
.++.+.+.+|...+|+.||..|.|+.+||+.+.++..+.
T Consensus 262 ~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 262 NKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 346667788889999999999999999999999988754
No 47
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=62.62 E-value=20 Score=34.25 Aligned_cols=37 Identities=27% Similarity=0.237 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
++.+...++...+|++|+..|.|+.+|++++++...+
T Consensus 124 ~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~ 160 (258)
T PRK08215 124 KALQVREKLINENSKEPTVEEIAKELEVPREEVVFAL 160 (258)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3445677888899999999999999999988877643
No 48
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=62.22 E-value=19 Score=37.27 Aligned_cols=43 Identities=26% Similarity=0.353 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 318 ~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.+....+|.+++.+|...+|++|+.++.|+.+|++.+.++..+
T Consensus 184 ~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~ 226 (342)
T COG0568 184 QVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREML 226 (342)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3445566778889999999999999999999999987776655
No 49
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=60.10 E-value=16 Score=35.27 Aligned_cols=38 Identities=24% Similarity=0.327 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.++.+.+..|+..+|++||..|.|+..|++.+.+...+
T Consensus 118 ~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 118 RQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 35667778899999999999999999999998876654
No 50
>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=59.26 E-value=26 Score=26.94 Aligned_cols=27 Identities=15% Similarity=0.214 Sum_probs=24.1
Q ss_pred CCCChHHHHHHhcCcHHHHHHhhhhcH
Q 016077 338 GSPTFAQWAAAAGVDQRELRRRLNYGI 364 (395)
Q Consensus 338 rePT~~EWAeA~Gms~~eLr~~L~~G~ 364 (395)
|..|..+.|+.+|++...+-.+|+.+.
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 788999999999999999998887654
No 51
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=58.97 E-value=9.2 Score=35.88 Aligned_cols=50 Identities=14% Similarity=0.078 Sum_probs=34.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHH
Q 016077 302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381 (395)
Q Consensus 302 g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSI 381 (395)
...|+|+...+.+|...++.+ +..+-+.|+..+..+|..+
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~g----------------------------------------d~~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLAG----------------------------------------DEAAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHcC----------------------------------------CHHHHHHHHHHHHHHHHHH
Confidence 357899999988888887755 4556666666666666666
Q ss_pred HHhccCCCCC
Q 016077 382 AKNYQGAGRM 391 (395)
Q Consensus 382 AKrY~GrGLs 391 (395)
|.+|.+.+-+
T Consensus 47 a~~~~~~~~~ 56 (231)
T PRK11922 47 ARAILRNDAE 56 (231)
T ss_pred HHHHhCChhh
Confidence 6666555433
No 52
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=57.97 E-value=26 Score=35.08 Aligned_cols=38 Identities=21% Similarity=0.332 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.++.+.+.++...+|++||..|.|+.+|++.+.+...+
T Consensus 168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~ 205 (317)
T PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYL 205 (317)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34556677888899999999999999999988877654
No 53
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=56.16 E-value=20 Score=27.83 Aligned_cols=57 Identities=16% Similarity=0.285 Sum_probs=41.0
Q ss_pred HHHHHcCCCCCh------HHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCC
Q 016077 331 VLSERCGGSPTF------AQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRM 391 (395)
Q Consensus 331 ~L~e~lGrePT~------~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLs 391 (395)
.+++..||.||. .+|.+..|++.+.+...++... .+ -+.|++.|-.|++++...|+.
T Consensus 4 ~~e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~---~~-~~~~~~Yi~~Il~~W~~~gi~ 66 (73)
T TIGR01446 4 FFEENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAV---SN-NKANYKYIDAILNNWKNNGIK 66 (73)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHH---Hc-CCCCHHHHHHHHHHHHHcCCC
Confidence 345567777773 4688888888777766665532 22 246899999999999999873
No 54
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=55.61 E-value=32 Score=33.86 Aligned_cols=37 Identities=27% Similarity=0.447 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
++.+.+.++...+|++||..+.|+.+|++.+.+...+
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~ 198 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELL 198 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3455567778889999999999999999988876554
No 55
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.23 E-value=49 Score=28.58 Aligned_cols=45 Identities=13% Similarity=0.053 Sum_probs=34.7
Q ss_pred HHHHHHHHcC-CCCChHHHHHHhcCcHHHHHHhh------hhcHHHHHHHHH
Q 016077 328 LREVLSERCG-GSPTFAQWAAAAGVDQRELRRRL------NYGILCKDKMIT 372 (395)
Q Consensus 328 ir~~L~e~lG-rePT~~EWAeA~Gms~~eLr~~L------~~G~~ARerLVk 372 (395)
.+.+|++.+. ...|.++.|+++|.++..|++.| +.++.-|+-|++
T Consensus 11 Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW~lRd~l~~ 62 (97)
T COG4367 11 TKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRPADVWRLRDFLVQ 62 (97)
T ss_pred HHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhccchhHHHHHHHHH
Confidence 4455665554 77899999999999999999988 456777776654
No 56
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=53.24 E-value=33 Score=33.23 Aligned_cols=38 Identities=21% Similarity=0.205 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
.++++..-+++.+...++..+||+.+|++...|.+...
T Consensus 6 ~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~ 43 (289)
T PRK15121 6 IIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFK 43 (289)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34566677888889999999999999999999888774
No 57
>PRK13503 transcriptional activator RhaS; Provisional
Probab=52.77 E-value=39 Score=31.76 Aligned_cols=59 Identities=20% Similarity=0.224 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh--------------hcHHHHHHHHHHhHHHHHHHHHh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN--------------YGILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~--------------~G~~ARerLVkSNLRLVVSIAKr 384 (395)
+.++..-+.+......|.++||+.+||+...|.+..+ +-..|++.|...|+. |-.||.+
T Consensus 173 i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~LL~~~~~s-I~eIA~~ 245 (278)
T PRK13503 173 LNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDAS-VTDIAYR 245 (278)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 3445556677788899999999999999988877663 345577666666654 5566655
No 58
>PRK15044 transcriptional regulator SirC; Provisional
Probab=50.74 E-value=33 Score=34.87 Aligned_cols=37 Identities=16% Similarity=0.108 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
++++..-+.+.++++++.++||+.+||+...|.+++.
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk 230 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLA 230 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4566777888899999999999999999999998775
No 59
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=50.45 E-value=30 Score=32.04 Aligned_cols=35 Identities=37% Similarity=0.503 Sum_probs=28.9
Q ss_pred HHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 326 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 326 E~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.+....+...+|++||..|.|+.+|++++++...+
T Consensus 93 ~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~ 127 (227)
T TIGR02980 93 NKATEELTQRLGRSPTIAEIAEELGVSEEEVVEAL 127 (227)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34456778888999999999999999998886544
No 60
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=50.13 E-value=27 Score=34.49 Aligned_cols=26 Identities=19% Similarity=0.169 Sum_probs=22.9
Q ss_pred HHcCCCCChHHHHHHhcCcHHHHHHh
Q 016077 334 ERCGGSPTFAQWAAAAGVDQRELRRR 359 (395)
Q Consensus 334 e~lGrePT~~EWAeA~Gms~~eLr~~ 359 (395)
..+|++||..|.|+.+|++++++...
T Consensus 143 ~~l~~~pt~~eiA~~l~~~~~~v~~~ 168 (289)
T PRK07500 143 EELTKQEIHREIATALGVSLSDVEMM 168 (289)
T ss_pred cccCCCCCHHHHHHHhCcCHHHHHHH
Confidence 46899999999999999999888654
No 61
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=45.76 E-value=38 Score=31.77 Aligned_cols=36 Identities=25% Similarity=0.293 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
+.+....+...+|++||..++|+.+|++++.+...+
T Consensus 97 ~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~ 132 (236)
T PRK06986 97 VAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREML 132 (236)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 445567777789999999999999999998866544
No 62
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=43.73 E-value=44 Score=33.38 Aligned_cols=36 Identities=8% Similarity=0.135 Sum_probs=30.4
Q ss_pred HHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 327 ~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
++...+........|.++||+.+||+...|.+.+..
T Consensus 185 ~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~ 220 (291)
T PRK15186 185 NIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344556778889999999999999999999998865
No 63
>PRK05572 sporulation sigma factor SigF; Validated
Probab=40.78 E-value=62 Score=30.83 Aligned_cols=36 Identities=28% Similarity=0.339 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHH
Q 016077 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (395)
Q Consensus 323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~ 358 (395)
.++.+.+.++...+|++|+..+.|+..|++++.+..
T Consensus 118 ~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~ 153 (252)
T PRK05572 118 NKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVL 153 (252)
T ss_pred HHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 345556677788889999999999999998877654
No 64
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=40.07 E-value=64 Score=29.33 Aligned_cols=38 Identities=13% Similarity=0.211 Sum_probs=31.0
Q ss_pred HHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcH
Q 016077 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 364 (395)
Q Consensus 327 ~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~ 364 (395)
+++.-|.+.-++..|..+.++++|++++.+.+.++.|+
T Consensus 34 kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 34 KVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 34444566778889999999999999999999887665
No 65
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=38.98 E-value=56 Score=31.07 Aligned_cols=36 Identities=17% Similarity=0.284 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
+......+...+|+.|+..+.|+.+|++.+.+...+
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~ 153 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIM 153 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 445567788889999999999999999998876543
No 66
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=37.28 E-value=69 Score=30.31 Aligned_cols=33 Identities=12% Similarity=0.211 Sum_probs=26.1
Q ss_pred HHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 329 REVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 329 r~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
...+.+......|.++||+.+||+..-|.+..+
T Consensus 192 ~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk 224 (287)
T TIGR02297 192 NFLIEENYKQHLRLPEYADRLGISESRLNDICR 224 (287)
T ss_pred HHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344556677889999999999999988876654
No 67
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=35.87 E-value=82 Score=31.79 Aligned_cols=36 Identities=14% Similarity=0.109 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
+.+....|+..+|++||..+.|+.+|++++++++.+
T Consensus 175 ~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l 210 (325)
T PRK05657 175 YLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRML 210 (325)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 445566788889999999999999999998887765
No 68
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=34.67 E-value=69 Score=31.39 Aligned_cols=35 Identities=26% Similarity=0.297 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 327 ~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
++...+.+.+...+|..++|+.+||+...|.++.+
T Consensus 222 ~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk 256 (322)
T PRK09393 222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFE 256 (322)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33445566778889999999999999999988775
No 69
>PRK13239 alkylmercury lyase; Provisional
Probab=33.08 E-value=72 Score=30.88 Aligned_cols=27 Identities=26% Similarity=0.212 Sum_probs=25.4
Q ss_pred cCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 336 CGGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 336 lGrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
.|++||..+.|+++|.+++++++.|+.
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 799999999999999999999998875
No 70
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 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 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; 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: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=31.57 E-value=14 Score=27.21 Aligned_cols=25 Identities=16% Similarity=0.256 Sum_probs=19.4
Q ss_pred HHHHhHHHHHHHHHhccCCCCCCCC
Q 016077 370 MITSNIRLVISIAKNYQGAGRMSRP 394 (395)
Q Consensus 370 LVkSNLRLVVSIAKrY~GrGLsf~D 394 (395)
|++.+..+|..++.+|.+.+.+.+|
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD 25 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAED 25 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHH
Confidence 6778888888888888887765554
No 71
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=31.23 E-value=1e+02 Score=31.69 Aligned_cols=53 Identities=13% Similarity=0.177 Sum_probs=40.6
Q ss_pred HHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh--------------hcHHHHHHHHHHhHHHH
Q 016077 326 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN--------------YGILCKDKMITSNIRLV 378 (395)
Q Consensus 326 E~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~--------------~G~~ARerLVkSNLRLV 378 (395)
.++...++..++.+-|.++.|..+||+...|+++-. +=..||+-|.++|+-+.
T Consensus 223 ~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~lG~sP~~yy~~lRL~~Ar~LL~~t~~si~ 289 (328)
T COG4977 223 LRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRAELGVSPARYYLRLRLERARRLLEQTRLSIA 289 (328)
T ss_pred HHHHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCCcHH
Confidence 344455677889999999999999999988877653 34568888888887653
No 72
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=30.13 E-value=1.2e+02 Score=21.99 Aligned_cols=25 Identities=28% Similarity=0.590 Sum_probs=19.7
Q ss_pred CCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 338 GSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 338 rePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
..-++.+.|+.+|++...+.+|+..
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 5567899999999999999888764
No 73
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=29.98 E-value=95 Score=22.98 Aligned_cols=23 Identities=30% Similarity=0.447 Sum_probs=19.6
Q ss_pred CCChHHHHHHhcCcHHHHHHhhh
Q 016077 339 SPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 339 ePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
++|..++|+.+|++...|.+.+.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 46888999999999999888775
No 74
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=29.95 E-value=3.4e+02 Score=25.91 Aligned_cols=60 Identities=17% Similarity=0.177 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHcCCC-CChHHHHHHhcCcHHHHHHhhhh-------------cHHHHHHHHHHh--HHHHHHHHHhc
Q 016077 325 LEGLREVLSERCGGS-PTFAQWAAAAGVDQRELRRRLNY-------------GILCKDKMITSN--IRLVISIAKNY 385 (395)
Q Consensus 325 LE~ir~~L~e~lGre-PT~~EWAeA~Gms~~eLr~~L~~-------------G~~ARerLVkSN--LRLVVSIAKrY 385 (395)
+.+++.-+.+.+..+ .|.+++|+++||++.-|.+.... =..|++.| ... -+=|-.||.+.
T Consensus 199 l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~~~yi~~~RL~~A~~lL-~~~~~~~sI~eIA~~~ 274 (302)
T PRK09685 199 FQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCADDL-RPAADDEKITSIAYKW 274 (302)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh-hhhccCCCHHHHHHHh
Confidence 446677778888876 79999999999999888765531 23455555 431 12366677653
No 75
>PRK13501 transcriptional activator RhaR; Provisional
Probab=29.04 E-value=1.5e+02 Score=28.49 Aligned_cols=55 Identities=16% Similarity=0.122 Sum_probs=39.4
Q ss_pred HHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh--------------hcHHHHHHHHHHhHHHHHHHHHh
Q 016077 329 REVLSERCGGSPTFAQWAAAAGVDQRELRRRLN--------------YGILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 329 r~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~--------------~G~~ARerLVkSNLRLVVSIAKr 384 (395)
...+++.+....+..++|+.+|++...|.+... +-..|++-|...|+ -|-.||.+
T Consensus 182 ~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~~qyi~~~Ri~~A~~LL~~t~~-sI~eIA~~ 250 (290)
T PRK13501 182 MSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEH-RISDIAAR 250 (290)
T ss_pred HHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCC-CHHHHHHH
Confidence 344555667778999999999999988877663 34567777777766 46666654
No 76
>KOG0197 consensus Tyrosine kinases [Signal transduction mechanisms]
Probab=28.41 E-value=24 Score=38.06 Aligned_cols=62 Identities=16% Similarity=0.304 Sum_probs=48.0
Q ss_pred CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHH
Q 016077 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 367 (395)
Q Consensus 289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~AR 367 (395)
-....+. ||+.- ....|...+...++.+|-.||...+- ++-+|++..||
T Consensus 283 m~~GsLl~yLr~~--~~~~l~~~~Ll~~a~qIaeGM~YLes----------------------------~~~IHRDLAAR 332 (468)
T KOG0197|consen 283 MPKGSLLDYLRTR--EGGLLNLPQLLDFAAQIAEGMAYLES----------------------------KNYIHRDLAAR 332 (468)
T ss_pred cccCcHHHHhhhc--CCCccchHHHHHHHHHHHHHHHHHHh----------------------------CCccchhhhhh
Confidence 3456777 99983 46899999999999999998743222 34678899999
Q ss_pred HHHHHHhHHHHHHHH
Q 016077 368 DKMITSNIRLVISIA 382 (395)
Q Consensus 368 erLVkSNLRLVVSIA 382 (395)
+-||..|+ |+.||
T Consensus 333 NiLV~~~~--~vKIs 345 (468)
T KOG0197|consen 333 NILVDEDL--VVKIS 345 (468)
T ss_pred heeeccCc--eEEEc
Confidence 99999998 66554
No 77
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=27.90 E-value=66 Score=23.18 Aligned_cols=23 Identities=17% Similarity=0.228 Sum_probs=14.8
Q ss_pred CChHHHHHHhcCcHHHHHHhhhh
Q 016077 340 PTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 340 PT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
.|..+.|+.+|.+...+.+-|..
T Consensus 21 ~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 21 MSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp --HHHHHHHTT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCcHHHHHHHhc
Confidence 57788888888888887776654
No 78
>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]
Probab=26.88 E-value=2.9e+02 Score=28.05 Aligned_cols=80 Identities=20% Similarity=0.289 Sum_probs=48.1
Q ss_pred CCCCChhH----HHHHhcCCCCCCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHH-----h-cCcHHHH
Q 016077 288 VDYSDPLR----YLRATTSSSRLLTANEE-MQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAA-----A-GVDQREL 356 (395)
Q Consensus 288 ~~~~D~lr----YLrei~g~~~LLTaeEE-veLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA-----~-Gms~~eL 356 (395)
-|++||.| ||.|. -+.+.+- .+|.++.+.. +.++|--. . .++++.|
T Consensus 162 ~D~~DPfR~LWLYl~E~-----k~dP~~A~tnL~qR~~~~------------------d~e~WG~~iV~~yLgkiS~e~l 218 (297)
T COG4785 162 DDPNDPFRSLWLYLNEQ-----KLDPKQAKTNLKQRAEKS------------------DKEQWGWNIVEFYLGKISEETL 218 (297)
T ss_pred cCCCChHHHHHHHHHHh-----hCCHHHHHHHHHHHHHhc------------------cHhhhhHHHHHHHHhhccHHHH
Confidence 35678888 66665 3455442 2344444332 34567643 2 3689999
Q ss_pred HHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCC
Q 016077 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGR 390 (395)
Q Consensus 357 r~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGL 390 (395)
.+++..+-.-...+.+.=----..++|+|.+.|.
T Consensus 219 ~~~~~a~a~~n~~~Ae~LTEtyFYL~K~~l~~G~ 252 (297)
T COG4785 219 MERLKADATDNTSLAEHLTETYFYLGKYYLSLGD 252 (297)
T ss_pred HHHHHhhccchHHHHHHHHHHHHHHHHHHhcccc
Confidence 9998776654444444333344678999988874
No 79
>PRK15185 transcriptional regulator HilD; Provisional
Probab=26.31 E-value=2e+02 Score=29.56 Aligned_cols=38 Identities=16% Similarity=0.132 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
..++++.-+.+..+...|.++||+.+||+...|.+++.
T Consensus 207 ~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK 244 (309)
T PRK15185 207 LKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLA 244 (309)
T ss_pred HHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34556677788889999999999999999999988864
No 80
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. 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 RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=25.58 E-value=1.8e+02 Score=28.29 Aligned_cols=35 Identities=17% Similarity=0.215 Sum_probs=28.1
Q ss_pred HHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 326 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 326 E~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.+....+...+|++|+..+.|...|+++.+++..+
T Consensus 136 ~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~ 170 (285)
T TIGR02394 136 LRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVL 170 (285)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34445567788999999999999999998887654
No 81
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=25.48 E-value=1.3e+02 Score=28.69 Aligned_cols=58 Identities=12% Similarity=0.084 Sum_probs=38.8
Q ss_pred HHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh--------------hcHHHHHHHHHHhHHHHHHHHHh
Q 016077 326 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN--------------YGILCKDKMITSNIRLVISIAKN 384 (395)
Q Consensus 326 E~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~--------------~G~~ARerLVkSNLRLVVSIAKr 384 (395)
+++...+...+....|.+++|+.+|++..-|.+..+ +-..|+..|...|+. |-.||..
T Consensus 186 ~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~~~l~~~Rl~~A~~lL~~t~~s-I~eIA~~ 257 (290)
T PRK10572 186 REACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMP-IATIGRN 257 (290)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 334455666778899999999999999888777663 234566666555533 3445543
No 82
>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=25.29 E-value=1.1e+02 Score=22.02 Aligned_cols=22 Identities=32% Similarity=0.369 Sum_probs=16.6
Q ss_pred CChHHHHHHhcCcHHHHHHhhh
Q 016077 340 PTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 340 PT~~EWAeA~Gms~~eLr~~L~ 361 (395)
-|..+.|+.+|++...+.+.|.
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHHC
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 5788899999999999888765
No 83
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=25.13 E-value=2.5e+02 Score=27.61 Aligned_cols=37 Identities=8% Similarity=0.056 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~ 361 (395)
++++...+.+.....+|..+||+.+||+...|.+..+
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk 229 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQ 229 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4445556677778899999999999999998777664
No 84
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=23.06 E-value=1.4e+02 Score=29.28 Aligned_cols=25 Identities=20% Similarity=0.150 Sum_probs=21.7
Q ss_pred cCCCCChHHHHHHhcCcHHHHHHhh
Q 016077 336 CGGSPTFAQWAAAAGVDQRELRRRL 360 (395)
Q Consensus 336 lGrePT~~EWAeA~Gms~~eLr~~L 360 (395)
.+++||..|.|+.+|+++++++..+
T Consensus 148 ~~~~~t~~eiA~~l~~~~~~v~~~~ 172 (284)
T PRK06596 148 WLNPEEVEMVAEELGVSEEEVREME 172 (284)
T ss_pred cCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3599999999999999999987764
No 85
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=22.88 E-value=1e+02 Score=25.68 Aligned_cols=27 Identities=37% Similarity=0.305 Sum_probs=20.4
Q ss_pred cCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077 336 CGGSPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 336 lGrePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
.|++.|..+.|.++|.+.++++..|..
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 499999999999999999999888753
No 86
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=22.28 E-value=1.7e+02 Score=27.48 Aligned_cols=54 Identities=17% Similarity=0.150 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--CCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHH
Q 016077 305 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCG--GSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 373 (395)
Q Consensus 305 ~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lG--rePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkS 373 (395)
.-||+.|..-|-..+..| .+. |..+..+.|+.+|++...+...|+ +|-.+|+..
T Consensus 154 ~~LTdrQ~~vL~~A~~~G------------YFd~PR~~~l~dLA~~lGISkst~~ehLR---rAe~Kl~~~ 209 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMG------------YFDYPRRVSLKDLAKELGISKSTLSEHLR---RAERKLIEA 209 (215)
T ss_pred ccCCHHHHHHHHHHHHcC------------CCCCCccCCHHHHHHHhCCCHHHHHHHHH---HHHHHHHHH
Confidence 479999988777777766 333 788999999999999999988875 455666654
No 87
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=22.07 E-value=2e+02 Score=24.23 Aligned_cols=51 Identities=27% Similarity=0.533 Sum_probs=27.8
Q ss_pred hhHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HcCCCCChHHHHHHhcCcH
Q 016077 293 PLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFAQWAAAAGVDQ 353 (395)
Q Consensus 293 ~lrYLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e-~lGrePT~~EWAeA~Gms~ 353 (395)
|++||-.+ ||+-+|.-.-..++.++-+ |.-+.. .+|.++ ..++.+.+|++.
T Consensus 31 Pi~YLAnL------ftAGd~~~V~~~L~rL~Am---R~ymR~~~v~~~~-~~~~l~~~glt~ 82 (83)
T PF14711_consen 31 PIEYLANL------FTAGDEEPVRRALKRLLAM---RSYMRAKNVGGEP-DEEVLEAVGLTE 82 (83)
T ss_dssp -HHHHHHH------HSTT-HHHHHHHHHHHHHH---HHHHHHHHTT-S----HHHHHTT--H
T ss_pred cHHHHHHH------HccCChHHHHHHHHHHHHH---HHHHHHHHhCCCC-cHHHHHHcCCCC
Confidence 56688775 7777777766666665544 433333 445544 488999999875
No 88
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=21.22 E-value=2.4e+02 Score=25.23 Aligned_cols=38 Identities=13% Similarity=0.162 Sum_probs=29.7
Q ss_pred CCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHh
Q 016077 337 GGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN 374 (395)
Q Consensus 337 GrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSN 374 (395)
-..-|..|.|+.+|++...++.+++.+...-.+.+..|
T Consensus 155 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 192 (194)
T PRK12519 155 YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDL 192 (194)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999999987766544444444
No 89
>cd05491 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi. TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
Probab=21.18 E-value=88 Score=28.05 Aligned_cols=40 Identities=20% Similarity=0.238 Sum_probs=36.8
Q ss_pred hcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCC
Q 016077 349 AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGA 388 (395)
Q Consensus 349 ~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~Gr 388 (395)
..||...++++|..|.++.-+...+-++|+++=|+.|.++
T Consensus 63 y~MDL~tIe~RL~ng~Y~tp~~F~~DiklI~~Nc~~ynd~ 102 (119)
T cd05491 63 YNMDLDTIEERLWNGYYATPKDFLKDIKRIVRDAKTIGDR 102 (119)
T ss_pred eccCHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCH
Confidence 5689999999999999999999999999999999999765
No 90
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=20.91 E-value=4e+02 Score=22.09 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhc
Q 016077 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG 363 (395)
Q Consensus 325 LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G 363 (395)
++.|.+.|.+ ..+|..+.|+.+|++...+.+.|..+
T Consensus 8 ~~~I~e~l~~---~~~ti~dvA~~~gvS~~TVsr~L~~~ 43 (80)
T TIGR02844 8 VLEIGKYIVE---TKATVRETAKVFGVSKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHHHH---CCCCHHHHHHHhCCCHHHHHHHhcCC
Confidence 4455555554 66789999999999999999999764
No 91
>cd05499 Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=20.85 E-value=1.1e+02 Score=25.57 Aligned_cols=40 Identities=18% Similarity=0.366 Sum_probs=34.3
Q ss_pred CcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCC
Q 016077 351 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGR 390 (395)
Q Consensus 351 ms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGL 390 (395)
||...++++|..|.+.--.-+.+.++||.+=|+.|-+.|-
T Consensus 46 ~dL~~I~~kl~~~~Y~s~~ef~~D~~li~~N~~~yn~~~s 85 (102)
T cd05499 46 MDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGT 85 (102)
T ss_pred CCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Confidence 6778888888888887777888999999999999988874
No 92
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=20.83 E-value=1.9e+02 Score=20.93 Aligned_cols=24 Identities=29% Similarity=0.407 Sum_probs=19.8
Q ss_pred CCChHHHHHHhcCcHHHHHHhhhh
Q 016077 339 SPTFAQWAAAAGVDQRELRRRLNY 362 (395)
Q Consensus 339 ePT~~EWAeA~Gms~~eLr~~L~~ 362 (395)
..|..+.|+.+|++...+++-|..
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHH
Confidence 389999999999999998877754
No 93
>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=20.67 E-value=2e+02 Score=19.92 Aligned_cols=38 Identities=21% Similarity=0.229 Sum_probs=27.9
Q ss_pred CChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHH-HhHHHHHH
Q 016077 340 PTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT-SNIRLVIS 380 (395)
Q Consensus 340 PT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVk-SNLRLVVS 380 (395)
-+..+.|+.+|++...++.+++ +++.+|.- .|..||..
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~---~~~~~l~~~~~~~l~~~ 54 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLR---NIMRKLGVKSRTQLVAY 54 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH---HHHHHhCCCCHHHHHHH
Confidence 4889999999999999998886 44555555 44555543
No 94
>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=20.25 E-value=2.3e+02 Score=20.30 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=20.6
Q ss_pred cCCCCChHHHHHHhcCcHHHHHHhhhhcH
Q 016077 336 CGGSPTFAQWAAAAGVDQRELRRRLNYGI 364 (395)
Q Consensus 336 lGrePT~~EWAeA~Gms~~eLr~~L~~G~ 364 (395)
.-..-|..|.|+..|++...++..++.+.
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34445788999999999999999887754
No 95
>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=20.01 E-value=2.9e+02 Score=19.68 Aligned_cols=30 Identities=23% Similarity=0.310 Sum_probs=23.6
Q ss_pred HcCCCCChHHHHHHhcCcHHHHHHhhhhcH
Q 016077 335 RCGGSPTFAQWAAAAGVDQRELRRRLNYGI 364 (395)
Q Consensus 335 ~lGrePT~~EWAeA~Gms~~eLr~~L~~G~ 364 (395)
.+...-|..|.|+..|++...+++++..+.
T Consensus 16 ~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 16 RYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 446677899999999999999988876543
Done!