Query 018065
Match_columns 361
No_of_seqs 166 out of 1294
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:50:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018065.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018065hhsearch_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 3E-23 6.4E-28 208.6 11.1 109 253-361 58-208 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 99.9 2.1E-21 4.6E-26 185.1 10.3 106 255-360 1-106 (298)
3 PRK07406 RNA polymerase sigma 99.8 5E-20 1.1E-24 183.0 11.0 109 253-361 61-169 (373)
4 PRK05949 RNA polymerase sigma 99.8 5.2E-19 1.1E-23 172.3 11.4 108 253-360 16-123 (327)
5 PRK07405 RNA polymerase sigma 99.8 4.4E-19 9.5E-24 171.7 10.7 108 253-360 6-113 (317)
6 PRK05901 RNA polymerase sigma 99.6 1.2E-15 2.5E-20 157.4 6.5 96 253-361 209-304 (509)
7 COG0568 RpoD DNA-directed RNA 99.5 1.6E-14 3.5E-19 142.8 6.9 108 253-360 7-134 (342)
8 PRK07921 RNA polymerase sigma 99.4 5.5E-13 1.2E-17 130.4 6.8 96 253-361 24-119 (324)
9 PRK09210 RNA polymerase sigma 99.0 6.6E-10 1.4E-14 110.0 6.3 70 252-361 93-162 (367)
10 PRK05658 RNA polymerase sigma 98.8 3.4E-09 7.3E-14 111.3 4.3 35 327-361 379-413 (619)
11 PRK06596 RNA polymerase factor 98.6 4.4E-08 9.6E-13 93.8 6.4 71 252-361 11-81 (284)
12 TIGR02392 rpoH_proteo alternat 98.6 5.1E-08 1.1E-12 92.2 5.8 67 256-361 2-68 (270)
13 PRK07500 rpoH2 RNA polymerase 98.5 1.1E-07 2.4E-12 91.3 6.2 69 254-361 5-73 (289)
14 PRK05657 RNA polymerase sigma 98.3 1E-06 2.3E-11 86.3 6.1 68 253-360 51-118 (325)
15 PRK07122 RNA polymerase sigma 98.1 1.1E-06 2.5E-11 83.3 1.8 35 327-361 39-73 (264)
16 TIGR02394 rpoS_proteo RNA poly 98.1 5.5E-06 1.2E-10 78.9 6.4 69 252-360 10-78 (285)
17 PF00140 Sigma70_r1_2: Sigma-7 98.1 1.2E-06 2.6E-11 61.3 0.9 34 254-287 1-34 (37)
18 TIGR02850 spore_sigG RNA polym 97.8 2.9E-05 6.3E-10 72.8 5.4 59 263-361 9-67 (254)
19 PRK08215 sporulation sigma fac 97.7 5.6E-05 1.2E-09 70.9 5.3 59 263-361 12-70 (258)
20 PRK05803 sporulation sigma fac 97.5 0.0002 4.3E-09 66.1 6.0 65 256-360 17-81 (233)
21 PRK06288 RNA polymerase sigma 97.1 0.00052 1.1E-08 64.9 4.6 59 264-361 6-67 (268)
22 PRK05658 RNA polymerase sigma 96.9 0.001 2.2E-08 70.6 4.3 35 253-287 102-136 (619)
23 TIGR02941 Sigma_B RNA polymera 96.7 0.0023 5E-08 59.8 5.1 54 268-360 8-61 (255)
24 PF04539 Sigma70_r3: Sigma-70 96.5 0.0038 8.3E-08 48.3 4.2 39 286-324 4-42 (78)
25 PRK08583 RNA polymerase sigma 96.4 0.0046 9.9E-08 57.9 5.1 54 268-360 8-61 (257)
26 PRK05572 sporulation sigma fac 96.0 0.011 2.4E-07 55.4 5.4 59 262-360 6-64 (252)
27 TIGR02846 spore_sigmaK RNA pol 94.2 0.11 2.4E-06 47.9 6.1 64 257-360 16-80 (227)
28 PRK08301 sporulation sigma fac 92.4 0.25 5.4E-06 45.5 5.4 35 326-360 50-84 (234)
29 TIGR02835 spore_sigmaE RNA pol 90.4 0.51 1.1E-05 43.8 5.3 56 265-360 29-84 (234)
30 COG0568 RpoD DNA-directed RNA 86.2 1.9 4E-05 43.9 6.5 33 253-285 65-97 (342)
31 PRK11922 RNA polymerase sigma 86.1 0.76 1.7E-05 42.5 3.5 56 265-360 7-62 (231)
32 PF04542 Sigma70_r2: Sigma-70 82.1 0.58 1.3E-05 34.3 0.7 28 333-360 1-28 (71)
33 COG1191 FliA DNA-directed RNA 82.0 2 4.3E-05 41.7 4.5 62 256-325 88-149 (247)
34 PRK07408 RNA polymerase sigma 80.9 3.1 6.7E-05 39.4 5.3 36 287-322 114-149 (256)
35 TIGR02850 spore_sigG RNA polym 77.8 4.3 9.4E-05 38.2 5.2 35 288-322 122-156 (254)
36 TIGR02393 RpoD_Cterm RNA polym 77.6 4.5 9.8E-05 37.6 5.2 36 287-322 88-123 (238)
37 PRK07122 RNA polymerase sigma 77.3 4.6 0.0001 38.6 5.3 36 288-323 129-164 (264)
38 PRK07921 RNA polymerase sigma 76.6 4.6 0.0001 40.2 5.3 37 286-322 173-209 (324)
39 PRK12427 flagellar biosynthesi 74.2 4.4 9.4E-05 38.0 4.2 35 288-322 103-137 (231)
40 PRK05911 RNA polymerase sigma 73.4 6.4 0.00014 37.4 5.2 35 288-322 112-146 (257)
41 PRK09210 RNA polymerase sigma 73.1 6.2 0.00013 39.7 5.2 36 287-322 217-252 (367)
42 PRK07406 RNA polymerase sigma 68.6 8.9 0.00019 39.2 5.2 37 286-322 223-259 (373)
43 PRK05901 RNA polymerase sigma 67.4 9.3 0.0002 40.8 5.3 36 287-322 359-394 (509)
44 PRK07670 RNA polymerase sigma 66.0 9.3 0.0002 35.8 4.5 37 287-323 110-146 (251)
45 PRK11511 DNA-binding transcrip 65.2 15 0.00033 31.2 5.3 59 288-347 11-83 (127)
46 TIGR02885 spore_sigF RNA polym 63.6 15 0.00031 33.8 5.2 35 289-323 100-134 (231)
47 TIGR02479 FliA_WhiG RNA polyme 63.6 12 0.00027 34.2 4.8 37 287-323 84-120 (224)
48 PRK05949 RNA polymerase sigma 62.9 15 0.00032 36.6 5.5 36 287-322 179-214 (327)
49 PRK07598 RNA polymerase sigma 60.2 14 0.0003 38.6 4.8 38 287-324 263-300 (415)
50 PRK08215 sporulation sigma fac 57.9 20 0.00044 33.7 5.3 34 288-321 125-158 (258)
51 PRK07405 RNA polymerase sigma 56.0 22 0.00048 35.1 5.4 36 287-322 169-204 (317)
52 PRK06288 RNA polymerase sigma 55.9 19 0.00042 34.1 4.8 36 287-322 119-154 (268)
53 PRK10219 DNA-binding transcrip 55.7 29 0.00062 28.2 5.1 59 288-347 7-79 (107)
54 TIGR02997 Sig70-cyanoRpoD RNA 54.5 25 0.00055 34.1 5.4 36 287-322 162-197 (298)
55 PRK09646 RNA polymerase sigma 54.5 11 0.00024 33.6 2.7 35 326-360 28-62 (194)
56 PRK12519 RNA polymerase sigma 51.3 8.4 0.00018 34.0 1.4 35 326-360 27-61 (194)
57 TIGR01446 DnaD_dom DnaD and ph 50.5 15 0.00032 28.1 2.5 55 296-354 6-66 (73)
58 PRK07500 rpoH2 RNA polymerase 49.0 52 0.0011 32.0 6.6 63 256-321 104-167 (289)
59 TIGR02980 SigBFG RNA polymeras 49.0 24 0.00053 32.2 4.1 32 290-321 94-125 (227)
60 PRK15044 transcriptional regul 48.3 31 0.00068 34.6 5.0 59 257-324 172-230 (295)
61 PF01726 LexA_DNA_bind: LexA D 45.8 36 0.00078 26.5 4.0 25 297-321 20-45 (65)
62 PRK15121 right oriC-binding tr 43.6 47 0.001 31.7 5.3 38 288-325 7-44 (289)
63 PRK05572 sporulation sigma fac 41.0 46 0.001 31.2 4.7 34 287-320 119-152 (252)
64 smart00342 HTH_ARAC helix_turn 40.2 46 0.00099 24.3 3.7 23 302-324 1-23 (84)
65 PRK06986 fliA flagellar biosyn 39.0 41 0.0009 31.1 4.0 34 288-321 97-130 (236)
66 PRK12531 RNA polymerase sigma 38.9 26 0.00056 31.2 2.6 36 325-360 24-59 (194)
67 PRK13503 transcriptional activ 38.9 62 0.0013 29.9 5.2 58 289-347 174-245 (278)
68 PRK09685 DNA-binding transcrip 35.9 2.8E+02 0.006 26.1 9.1 37 288-324 199-236 (302)
69 KOG0197 Tyrosine kinases [Sign 35.8 12 0.00027 39.6 0.1 69 246-345 277-345 (468)
70 COG4977 Transcriptional regula 35.1 62 0.0013 32.9 4.8 51 291-341 225-289 (328)
71 TIGR02941 Sigma_B RNA polymera 34.7 51 0.0011 30.9 3.9 34 288-321 118-151 (255)
72 PF04967 HTH_10: HTH DNA bindi 33.6 81 0.0018 24.0 4.1 26 301-326 22-47 (53)
73 PRK15186 AraC family transcrip 33.0 63 0.0014 31.8 4.4 35 291-325 186-220 (291)
74 TIGR03826 YvyF flagellar opero 32.8 71 0.0015 28.7 4.3 32 295-326 39-70 (137)
75 PRK05657 RNA polymerase sigma 32.5 79 0.0017 31.5 5.0 36 288-323 175-210 (325)
76 PRK13239 alkylmercury lyase; P 31.7 55 0.0012 31.3 3.6 27 299-325 33-59 (206)
77 COG1476 Predicted transcriptio 31.7 53 0.0012 26.4 3.0 54 295-360 9-62 (68)
78 PRK09643 RNA polymerase sigma 31.5 33 0.00072 30.6 2.1 37 324-360 23-59 (192)
79 COG4367 Uncharacterized protei 29.9 2E+02 0.0042 24.8 6.2 45 291-335 11-62 (97)
80 PF07261 DnaB_2: Replication i 29.3 25 0.00054 26.7 0.8 25 335-359 47-72 (77)
81 PRK12538 RNA polymerase sigma 27.8 32 0.0007 32.3 1.4 35 326-360 61-95 (233)
82 PRK15185 transcriptional regul 27.7 1.7E+02 0.0036 29.7 6.4 43 289-331 209-252 (309)
83 PF12324 HTH_15: Helix-turn-he 27.3 61 0.0013 26.7 2.7 27 299-325 35-61 (77)
84 TIGR02844 spore_III_D sporulat 26.3 2.2E+02 0.0047 23.3 5.8 37 287-326 7-43 (80)
85 PF10078 DUF2316: Uncharacteri 26.2 2.8E+02 0.006 23.4 6.5 53 270-334 3-62 (89)
86 PRK06596 RNA polymerase factor 26.0 1.9E+02 0.0041 28.0 6.3 23 300-322 149-171 (284)
87 PF13404 HTH_AsnC-type: AsnC-t 23.0 1.2E+02 0.0027 21.5 3.4 29 294-324 11-39 (42)
88 PRK09393 ftrA transcriptional 22.9 1.1E+02 0.0024 29.6 4.1 36 290-325 222-257 (322)
89 TIGR02297 HpaA 4-hydroxyphenyl 22.8 1.2E+02 0.0025 28.3 4.1 32 293-324 193-224 (287)
90 PRK10371 DNA-binding transcrip 22.0 2.1E+02 0.0046 27.7 5.8 38 288-325 193-230 (302)
91 PF13801 Metal_resist: Heavy-m 21.2 4.1E+02 0.0089 20.8 8.6 69 268-346 40-116 (125)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=99.89 E-value=3e-23 Score=208.63 Aligned_cols=109 Identities=41% Similarity=0.642 Sum_probs=101.8
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHHhhCCCCcHHHHHHHh
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI 312 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~--------------------LEkir~~Le~~lGrePT~~EWA~Aa 312 (361)
.+|+++.||++|++.||||++||++|+++||++++ |++++.+|++++|++||..|||.++
T Consensus 58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~ 137 (415)
T PRK07598 58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA 137 (415)
T ss_pred CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence 57999999999999999999999999999999999 8999999999999999999999888
Q ss_pred ccchhhhhhhc----------------------cccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 313 GLSCRDLKSEL----------------------HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 313 G~d~~~Lr~~L----------------------~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
|+++.+|+.+| ..|..|+++||++|+|||++||++|.|+|+.++||||.
T Consensus 138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQE 208 (415)
T PRK07598 138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQE 208 (415)
T ss_pred CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHH
Confidence 77766666665 57889999999999999999999999999999999993
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=99.85 E-value=2.1e-21 Score=185.07 Aligned_cols=106 Identities=49% Similarity=0.758 Sum_probs=103.6
Q ss_pred cHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHH
Q 018065 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334 (361)
Q Consensus 255 D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI 334 (361)
|++..||++++++|+||++||.+|+++|++++.+++++.+|++++|++||..+||+++|++..+|..++..|..|+++||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 335 NANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 335 ~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
.+|+|||++||++|.|+|++++||||
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQ 106 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQ 106 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHH
Confidence 99999999999999999999999998
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=99.82 E-value=5e-20 Score=182.97 Aligned_cols=109 Identities=39% Similarity=0.693 Sum_probs=106.2
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek 332 (361)
..|++..||++++++|+||++||++|+++|++++.|++++.+|++.+|++|+..+||.++|++..+|++++..|..|+++
T Consensus 61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~ 140 (373)
T PRK07406 61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK 140 (373)
T ss_pred CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 333 LINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 333 LI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
||.+|++||++||++|.|+|++++||||.
T Consensus 141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQE 169 (373)
T PRK07406 141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQE 169 (373)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 99999999999999999999999999983
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=99.79 E-value=5.2e-19 Score=172.31 Aligned_cols=108 Identities=41% Similarity=0.643 Sum_probs=105.8
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek 332 (361)
..|++..||++|+++|+||++||++|++.|+.++.+++.+..|+..+|++|+..+||.++|++..+|...+..|..|+++
T Consensus 16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~ 95 (327)
T PRK05949 16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK 95 (327)
T ss_pred CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
||.+|+++|++||++|.|.|++++||||
T Consensus 96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQ 123 (327)
T PRK05949 96 MIEANLRLVVAIAKKYQKRNMEFLDLIQ 123 (327)
T ss_pred HHHHHHHHHHHHHHHHccCCCCHHHHHH
Confidence 9999999999999999999999999998
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.79 E-value=4.4e-19 Score=171.71 Aligned_cols=108 Identities=42% Similarity=0.625 Sum_probs=105.5
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek 332 (361)
.+|++..||++++++|+||++||++|+++|++++.+++++..|++++|++|+..+||.++|++...|...+..|..|+++
T Consensus 6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
||.+|+++|+++|++|.|.|.+++||||
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQ 113 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQ 113 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence 9999999999999999999999999998
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=1.2e-15 Score=157.37 Aligned_cols=96 Identities=38% Similarity=0.507 Sum_probs=80.6
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek 332 (361)
..|+++.||++|+++|+||++||++|+++|+.+..++.. +++ | .+|+. ....+|+.+++.|..||++
T Consensus 209 ~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~--~-----~~~~~---~~~~~l~~~~~~g~~Ar~~ 275 (509)
T PRK05901 209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LAE--G-----EKLDP---ELRRDLQWIGRDGKRAKNH 275 (509)
T ss_pred cccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hhh--c-----ccchh---hhhhhhhhhccchHHHHHH
Confidence 578999999999999999999999999999986443321 111 1 23442 2567899999999999999
Q ss_pred HHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 333 LINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 333 LI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
||.+|||||++||++|.|+|++|+||||.
T Consensus 276 LI~sNLrLVvsIAkrY~~~Gl~~eDLIQE 304 (509)
T PRK05901 276 LLEANLRLVVSLAKRYTNRGLSFLDLIQE 304 (509)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 99999999999999999999999999994
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.51 E-value=1.6e-14 Score=142.80 Aligned_cols=108 Identities=35% Similarity=0.517 Sum_probs=94.4
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-hhCCCCcHH---------------HHHHHhccch
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC 316 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~-~lGrePT~~---------------EWA~AaG~d~ 316 (361)
..|.+..|+.+++..++++.++|.++.+.+++...+......|.. ..|..|+.. +|+.....++
T Consensus 7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 467899999999999999999999999999988888777777777 678888886 6665555544
Q ss_pred -hhhhhhccccHH---HHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 317 -RDLKSELHSGNS---SREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 317 -~~Lr~~L~~G~~---ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
..|..++..|.. |+.+||.+||||||+|||+|.|+|++|.||||
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQ 134 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQ 134 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHh
Confidence 778888888865 99999999999999999999999999999999
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.38 E-value=5.5e-13 Score=130.39 Aligned_cols=96 Identities=38% Similarity=0.523 Sum_probs=80.7
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek 332 (361)
..|++..||++++++|+||++||.+|+++|+.+..++.. |+..+|+... ...+|+.+++.|..|+++
T Consensus 24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~ 90 (324)
T PRK07921 24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH 90 (324)
T ss_pred CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence 357899999999999999999999999999987665543 2223333111 456789999999999999
Q ss_pred HHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 333 LINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 333 LI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
||.+|+++|++||++|.|.|++++||||.
T Consensus 91 Lv~~~~~lV~~iA~r~~~~~~~~eDLvQE 119 (324)
T PRK07921 91 LLEANLRLVVSLAKRYTGRGMPLLDLIQE 119 (324)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 99999999999999999999999999983
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=98.97 E-value=6.6e-10 Score=110.04 Aligned_cols=70 Identities=46% Similarity=0.734 Sum_probs=64.5
Q ss_pred CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHH
Q 018065 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331 (361)
Q Consensus 252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARe 331 (361)
..+|+++.||++|+++|+||.+||.+|++.++. | +..|++
T Consensus 93 ~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A~~ 132 (367)
T PRK09210 93 KINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEAKQ 132 (367)
T ss_pred ccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHHHH
Confidence 357899999999999999999999999998875 4 467999
Q ss_pred HHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 332 KLINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 332 kLI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
+||..|+++|++||++|.|+|+.++||||.
T Consensus 133 ~Li~~~~~lV~~iA~~~~~~~~~~eDLiQE 162 (367)
T PRK09210 133 RLAEANLRLVVSIAKRYVGRGMLFLDLIQE 162 (367)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 999999999999999999999999999983
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=98.79 E-value=3.4e-09 Score=111.35 Aligned_cols=35 Identities=40% Similarity=0.787 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 327 ~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
..|+++||.+|||||++|||+|.|+|++|.||||.
T Consensus 379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQe 413 (619)
T PRK05658 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 413 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHH
Confidence 47999999999999999999999999999999994
No 11
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=98.64 E-value=4.4e-08 Score=93.75 Aligned_cols=71 Identities=30% Similarity=0.551 Sum_probs=63.2
Q ss_pred CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHH
Q 018065 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331 (361)
Q Consensus 252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARe 331 (361)
.+.+++..|+++++++|+|+.++|.+|+..++. .| +..|++
T Consensus 11 ~~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~--------------~G-------------------------d~~a~~ 51 (284)
T PRK06596 11 SPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE--------------HG-------------------------DLEAAK 51 (284)
T ss_pred CCccHHHHHHHHHhccCCCCHHHHHHHHHHHHH--------------cC-------------------------CHHHHH
Confidence 356799999999999999999999999986542 14 578999
Q ss_pred HHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 332 KLINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 332 kLI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
+||..|++||.+||++|.+.|++++||||.
T Consensus 52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQe 81 (284)
T PRK06596 52 QLVLSHLRFVVHIARGYRGYGLPQADLIQE 81 (284)
T ss_pred HHHHHhHHHHHHHHHHhcCCCCCHHHHHHH
Confidence 999999999999999999999999999984
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=98.61 E-value=5.1e-08 Score=92.17 Aligned_cols=67 Identities=30% Similarity=0.582 Sum_probs=60.0
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 018065 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (361)
Q Consensus 256 ~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~ 335 (361)
++..||++++++|+|+.++|.+|+..+.. .| +..|+++||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~--------------~g-------------------------d~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE--------------HG-------------------------DLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHHHH
Confidence 57889999999999999999999986432 13 6789999999
Q ss_pred HhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 336 ANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 336 sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
.|+++|.++|++|.+.|.+++||||.
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQe 68 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQE 68 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 99999999999999999999999984
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=98.54 E-value=1.1e-07 Score=91.32 Aligned_cols=69 Identities=23% Similarity=0.403 Sum_probs=61.6
Q ss_pred CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHH
Q 018065 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333 (361)
Q Consensus 254 ~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekL 333 (361)
.+.+..||+++.++|+||.++|.+|+..++. .| +..|+++|
T Consensus 5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~--------------~g-------------------------d~~A~~~L 45 (289)
T PRK07500 5 ASADRSMIRSAMKAPYLEREEEHALAYRWKD--------------HR-------------------------DEDALHRI 45 (289)
T ss_pred hhHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHH
Confidence 3467789999999999999999999987753 13 67899999
Q ss_pred HHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 334 INANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 334 I~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
|..|+++|.++|++|.+.|.+++||||.
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQe 73 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQE 73 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 9999999999999999999999999983
No 14
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=98.29 E-value=1e-06 Score=86.27 Aligned_cols=68 Identities=38% Similarity=0.576 Sum_probs=62.9
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek 332 (361)
..|.+..|+.+|+..|+||+++|.+|+..++. | +..|.++
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~---------------G-------------------------d~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR---------------G-------------------------DFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHH
Confidence 36788999999999999999999999988775 4 5789999
Q ss_pred HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
||..|+++|.++|++|.+.|.+.+||+|
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQ 118 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIE 118 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHH
Confidence 9999999999999999999999999998
No 15
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=98.10 E-value=1.1e-06 Score=83.33 Aligned_cols=35 Identities=31% Similarity=0.675 Sum_probs=33.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 327 ~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi 361 (361)
..+|++||.+|+|||++||++|.++|++++||||+
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQe 73 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQV 73 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHH
Confidence 56999999999999999999999999999999995
No 16
>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=98.10 E-value=5.5e-06 Score=78.91 Aligned_cols=69 Identities=38% Similarity=0.563 Sum_probs=63.9
Q ss_pred CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHH
Q 018065 252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331 (361)
Q Consensus 252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARe 331 (361)
-..|++..||.+|+..+.|+.++|.+|+..++. | +..|.+
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~a~~ 49 (285)
T TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALA---------------G-------------------------DFEARK 49 (285)
T ss_pred CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHH
Confidence 357899999999999999999999999987775 4 578999
Q ss_pred HHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 332 KLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 332 kLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
.||..+..+|..+|++|.+.|...+||+|
T Consensus 50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQ 78 (285)
T TIGR02394 50 VMIESNLRLVVSIAKHYVNRGLPLLDLIE 78 (285)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHH
Confidence 99999999999999999999999999998
No 17
>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=98.07 E-value=1.2e-06 Score=61.27 Aligned_cols=34 Identities=41% Similarity=0.464 Sum_probs=30.3
Q ss_pred CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH
Q 018065 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (361)
Q Consensus 254 ~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~ 287 (361)
+|+++.||++|+++||||++||++|+++|+.+-.
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 3789999999999999999999999999998654
No 18
>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=97.80 E-value=2.9e-05 Score=72.76 Aligned_cols=59 Identities=39% Similarity=0.623 Sum_probs=52.3
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHH
Q 018065 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (361)
Q Consensus 263 ei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVV 342 (361)
+.+++|+||+++|.+|+..++. | +..|+++|+..|+++|.
T Consensus 9 ~~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~~~~~v~ 48 (254)
T TIGR02850 9 NTSKLPVLKNQEMRELFIRMQS---------------G-------------------------DTTAREKLINGNLRLVL 48 (254)
T ss_pred cccCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHH
Confidence 3578999999999999877764 3 56799999999999999
Q ss_pred HHHHhcCCCCCCccCccCC
Q 018065 343 HVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 343 SIAKrY~grGLsfqDLIQi 361 (361)
++|++|.+.+.+.+||+|.
T Consensus 49 ~~a~~~~~~~~~aeDlvQe 67 (254)
T TIGR02850 49 SVIQRFNNRGEYVDDLFQV 67 (254)
T ss_pred HHHHHHhCCCCCHHHHHHH
Confidence 9999999999999999983
No 19
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=97.68 E-value=5.6e-05 Score=70.86 Aligned_cols=59 Identities=39% Similarity=0.657 Sum_probs=51.8
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHH
Q 018065 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342 (361)
Q Consensus 263 ei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVV 342 (361)
+..++|+|+++||..|+..++. | +..++++||..|+++|.
T Consensus 12 ~~~~~~~l~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~~~~~v~ 51 (258)
T PRK08215 12 NTSKLPVLKNEEMRELFERMQN---------------G-------------------------DKEAREKLINGNLRLVL 51 (258)
T ss_pred cCCCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHH
Confidence 3467789999999999887764 3 57899999999999999
Q ss_pred HHHHhcCCCCCCccCccCC
Q 018065 343 HVAKQYQGRGISLHDLLQI 361 (361)
Q Consensus 343 SIAKrY~grGLsfqDLIQi 361 (361)
.+|++|.+.+.+.+||+|.
T Consensus 52 ~~a~~~~~~~~~aeDlvQe 70 (258)
T PRK08215 52 SVIQRFNNRGENVDDLFQV 70 (258)
T ss_pred HHHHHHhCCCCCHHHHHHH
Confidence 9999999999999999983
No 20
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=97.49 E-value=0.0002 Score=66.15 Aligned_cols=65 Identities=28% Similarity=0.496 Sum_probs=58.8
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 018065 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (361)
Q Consensus 256 ~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~ 335 (361)
++..|+.+++..++||+++|..|...++. | +..|.+.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~---------------g-------------------------d~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE---------------G-------------------------DEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHH
Confidence 67889999999999999999988876654 3 5779999999
Q ss_pred HhHHHHHHHHHhcCCCCCCccCccC
Q 018065 336 ANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 336 sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
.+.++|..+|.+|.|.|.+.+||||
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQ 81 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLIS 81 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHH
Confidence 9999999999999999999999998
No 21
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=97.13 E-value=0.00052 Score=64.87 Aligned_cols=59 Identities=25% Similarity=0.286 Sum_probs=50.2
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHH
Q 018065 264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 343 (361)
Q Consensus 264 i~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVS 343 (361)
.|.+|+||.++|.+|+..++.. | +..+.+.|+..|++||..
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~~--------------~-------------------------d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKKT--------------G-------------------------DPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHH
Confidence 3789999999999999877641 2 578999999999999999
Q ss_pred HHHhcC-C--CCCCccCccCC
Q 018065 344 VAKQYQ-G--RGISLHDLLQI 361 (361)
Q Consensus 344 IAKrY~-g--rGLsfqDLIQi 361 (361)
||++|. | .+.+.+||+|.
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qe 67 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSY 67 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHH
Confidence 999986 3 57789999983
No 22
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.86 E-value=0.001 Score=70.62 Aligned_cols=35 Identities=31% Similarity=0.482 Sum_probs=32.9
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 287 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~ 287 (361)
.+||+++||++||..+|||+|+|++++++|..+.+
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 136 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN 136 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999998764
No 23
>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=96.71 E-value=0.0023 Score=59.77 Aligned_cols=54 Identities=30% Similarity=0.401 Sum_probs=47.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHh
Q 018065 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 268 ~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKr 347 (361)
+.||.++|.+|...++.. | +..|.++|+..|.++|..+|++
T Consensus 8 ~~l~~~~~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~y~~~v~~~a~~ 48 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQN--------------Q-------------------------NGEAQEKLVDHYQNLVYSIAYK 48 (255)
T ss_pred CCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHHHHHHhHHHHHHHHHH
Confidence 668999999888777641 2 4779999999999999999999
Q ss_pred cCCCCCCccCccC
Q 018065 348 YQGRGISLHDLLQ 360 (361)
Q Consensus 348 Y~grGLsfqDLIQ 360 (361)
|.+.|...+||+|
T Consensus 49 ~~~~~~~aeDlvQ 61 (255)
T TIGR02941 49 YSKGGPMHEDLVQ 61 (255)
T ss_pred HhcCCCCHHHHHH
Confidence 9999999999998
No 24
>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=96.49 E-value=0.0038 Score=48.26 Aligned_cols=39 Identities=31% Similarity=0.607 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 286 ~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
.++.+.+.+|+..+||+||..|.|+.+|++.+.++..+.
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 456678899999999999999999999999988876554
No 25
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=96.42 E-value=0.0046 Score=57.86 Aligned_cols=54 Identities=30% Similarity=0.327 Sum_probs=47.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHh
Q 018065 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 268 ~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKr 347 (361)
+.|++++|.+|..+++.. | +..|.+.|+..|.++|..+|++
T Consensus 8 ~~l~~~e~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~~~~~v~~~a~~ 48 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQEN--------------Q-------------------------DEEAQEKLVKHYKNLVESLAYK 48 (257)
T ss_pred CcCChHHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHHHHHH
Confidence 779999999888766530 2 5779999999999999999999
Q ss_pred cCCCCCCccCccC
Q 018065 348 YQGRGISLHDLLQ 360 (361)
Q Consensus 348 Y~grGLsfqDLIQ 360 (361)
|.+.+.+.+||+|
T Consensus 49 ~~~~~~~aeDlvQ 61 (257)
T PRK08583 49 YSKGQSHHEDLVQ 61 (257)
T ss_pred HhcCCCCHHHHHH
Confidence 9999999999998
No 26
>PRK05572 sporulation sigma factor SigF; Validated
Probab=96.04 E-value=0.011 Score=55.40 Aligned_cols=59 Identities=36% Similarity=0.553 Sum_probs=51.2
Q ss_pred hccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHH
Q 018065 262 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV 341 (361)
Q Consensus 262 kei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLV 341 (361)
++-...|.||.+++.+|...++. | +..|.++|+..+.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKSQD---------------G-------------------------DQEARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHH
Confidence 45567899999999988765553 3 5679999999999999
Q ss_pred HHHHHhcCCCCCCccCccC
Q 018065 342 VHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 342 VSIAKrY~grGLsfqDLIQ 360 (361)
..+|++|.+.+.+.+||+|
T Consensus 46 ~~~a~~~~~~~~~aeDl~Q 64 (252)
T PRK05572 46 WSVVQRFLNRGYEPDDLFQ 64 (252)
T ss_pred HHHHHHHccCCCCHHHHHH
Confidence 9999999999999999998
No 27
>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=94.18 E-value=0.11 Score=47.92 Aligned_cols=64 Identities=28% Similarity=0.517 Sum_probs=52.9
Q ss_pred HHHHHh-ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 018065 257 LRLFLW-GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335 (361)
Q Consensus 257 l~~YLk-ei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~ 335 (361)
+-.|.- +-+..+.|++.+|..|...++. | +..|-+.|+.
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~af~~l~~ 55 (227)
T TIGR02846 16 LVGYVTNNGSFPQPLSEEEEKKYLDRLKE---------------G-------------------------DEEARNVLIE 55 (227)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHH
Confidence 344664 3456678999999999877764 4 5678999999
Q ss_pred HhHHHHHHHHHhcCCCCCCccCccC
Q 018065 336 ANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 336 sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
.+.++|..+|.+|.+.+.+.+||+|
T Consensus 56 ~y~~~v~~~~~~~~~~~~dAEDlvQ 80 (227)
T TIGR02846 56 RNLRLVAHIVKKFSNTGEDVDDLIS 80 (227)
T ss_pred HhHHHHHHHHHHhcCCCCCHHHHHH
Confidence 9999999999999998999999998
No 28
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=92.41 E-value=0.25 Score=45.47 Aligned_cols=35 Identities=40% Similarity=0.728 Sum_probs=32.8
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+..|.+.|+..+.++|..+|++|.+.+.+.+||+|
T Consensus 50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQ 84 (234)
T PRK08301 50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLIS 84 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHH
Confidence 56789999999999999999999999999999998
No 29
>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=90.42 E-value=0.51 Score=43.78 Aligned_cols=56 Identities=36% Similarity=0.623 Sum_probs=47.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHH
Q 018065 265 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV 344 (361)
Q Consensus 265 ~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSI 344 (361)
...+.|++++|.+|...++. | +..|.+.|+..+.++|..+
T Consensus 29 ~~~~~~~~~~~~~l~~~~~~---------------~-------------------------d~~a~~~l~~~y~~~l~~~ 68 (234)
T TIGR02835 29 ALPPPLTGEEEEALLQKLTQ---------------G-------------------------DESAKSTLIERNLRLVVYI 68 (234)
T ss_pred cCCCcCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHHH
Confidence 45678888888887765543 3 5789999999999999999
Q ss_pred HHhcCCCCCCccCccC
Q 018065 345 AKQYQGRGISLHDLLQ 360 (361)
Q Consensus 345 AKrY~grGLsfqDLIQ 360 (361)
|++|.+.+.+-+||+|
T Consensus 69 ~~~~~~~~~~AEDlvQ 84 (234)
T TIGR02835 69 ARKFENTGIGIEDLVS 84 (234)
T ss_pred HHHhccCCCCHHHHHH
Confidence 9999999999999998
No 30
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=86.21 E-value=1.9 Score=43.90 Aligned_cols=33 Identities=24% Similarity=0.326 Sum_probs=29.3
Q ss_pred CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHH
Q 018065 253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL 285 (361)
Q Consensus 253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l 285 (361)
..+.+..|+..+...++|+++||.+|+..++.+
T Consensus 65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g 97 (342)
T COG0568 65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRG 97 (342)
T ss_pred hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcC
Confidence 455778899999999999999999999999877
No 31
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=86.10 E-value=0.76 Score=42.46 Aligned_cols=56 Identities=21% Similarity=0.293 Sum_probs=47.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHH
Q 018065 265 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV 344 (361)
Q Consensus 265 ~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSI 344 (361)
...|+|+...+..|...++. | +..+-+.|+..+.++|..+
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLA---------------G-------------------------DEAAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHHHH
Confidence 56788999888888776654 3 5778889999999999999
Q ss_pred HHhcCCCCCCccCccC
Q 018065 345 AKQYQGRGISLHDLLQ 360 (361)
Q Consensus 345 AKrY~grGLsfqDLIQ 360 (361)
|++|.+.+-+-+||+|
T Consensus 47 a~~~~~~~~~AEDlvQ 62 (231)
T PRK11922 47 ARAILRNDAEAEDVVQ 62 (231)
T ss_pred HHHHhCChhhHHHHHH
Confidence 9999998888899988
No 32
>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=82.09 E-value=0.58 Score=34.27 Aligned_cols=28 Identities=29% Similarity=0.415 Sum_probs=26.3
Q ss_pred HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
|++.+.++|..+|++|.+.+.+.+|++|
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~q 28 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQ 28 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhh
Confidence 6889999999999999999999999987
No 33
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=81.99 E-value=2 Score=41.73 Aligned_cols=62 Identities=24% Similarity=0.326 Sum_probs=42.8
Q ss_pred HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 256 ~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
-+..||++-. ..--+---.+++. +++....+|+..+||+||..|.|+..|++.+++...+..
T Consensus 88 ei~d~LR~~~--~v~vpR~~~~~~~------~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~ 149 (247)
T COG1191 88 EILDYLRKND--SVKVPRSLRELGR------RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLA 149 (247)
T ss_pred HHHHHHHhCC--CccCcHHHHHHHH------HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 4556787766 2222223333333 345678889999999999999999999998877665543
No 34
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=80.86 E-value=3.1 Score=39.43 Aligned_cols=36 Identities=28% Similarity=0.458 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
++.+...+|...+|++||..|.|+..|++.++++..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 445677889999999999999999999998877654
No 35
>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=77.82 E-value=4.3 Score=38.21 Aligned_cols=35 Identities=26% Similarity=0.297 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
+.+...+|...+|++||..|.|+..|++.+.+...
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 34456778888999999999999999987776543
No 36
>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=77.58 E-value=4.5 Score=37.62 Aligned_cols=36 Identities=31% Similarity=0.533 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
++.+...+|...+|++||..|.|+..|++.+.++..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~ 123 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREI 123 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 345567788889999999999999999988877654
No 37
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=77.35 E-value=4.6 Score=38.64 Aligned_cols=36 Identities=28% Similarity=0.525 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhc
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L 323 (361)
+.+...+|...+|++||..|.|+..|++.+++...+
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 445677888889999999999999999887776543
No 38
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=76.60 E-value=4.6 Score=40.24 Aligned_cols=37 Identities=30% Similarity=0.377 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 286 ~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
.++.+++.+|...+|++||..|.|+..|++.+.+...
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 3455678888999999999999999999987766653
No 39
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=74.16 E-value=4.4 Score=37.99 Aligned_cols=35 Identities=14% Similarity=0.356 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
+.+....|...+|++||..|.|+..|++.+++...
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~ 137 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEY 137 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHH
Confidence 34566788888999999999999999998776554
No 40
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=73.44 E-value=6.4 Score=37.39 Aligned_cols=35 Identities=26% Similarity=0.370 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
+.+....|...+|++||..|.|+..|++.+++...
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~ 146 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGW 146 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHH
Confidence 33456678888999999999999999988777554
No 41
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=73.08 E-value=6.2 Score=39.73 Aligned_cols=36 Identities=25% Similarity=0.417 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
++.+...+|...+|++||..|.|+..|++.+.++..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~ 252 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREI 252 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 345677888899999999999999999988777653
No 42
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=68.57 E-value=8.9 Score=39.19 Aligned_cols=37 Identities=30% Similarity=0.471 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 286 ~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
.++.+....|...+|++||..|.|+.+|++.+.++..
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 3455677788899999999999999999988777643
No 43
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=67.36 E-value=9.3 Score=40.77 Aligned_cols=36 Identities=31% Similarity=0.513 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
++.+++.+|...+|++||..|.|+..|++.+.++..
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~ 394 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREI 394 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 455678889999999999999999999987776654
No 44
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=66.01 E-value=9.3 Score=35.83 Aligned_cols=37 Identities=22% Similarity=0.393 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhc
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L 323 (361)
++.+....+...+|++|+..++|+..|++.+.++..+
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~ 146 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM 146 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3455667788889999999999999999887766553
No 45
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=65.22 E-value=15 Score=31.24 Aligned_cols=59 Identities=14% Similarity=0.157 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcccc--------------HHHHHHHHHHhHHHHHHHHHh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG--------------NSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G--------------~~ARekLI~sNLRLVVSIAKr 347 (361)
+.++..-+...+..+++..++|+.+|++...|.+.+..- ..|++.|...++. |..||..
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L~~t~~~-i~eIA~~ 83 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEP-ILYLAER 83 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 344555666677888999999999999999888876632 2345555555544 4566655
No 46
>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=63.64 E-value=15 Score=33.83 Aligned_cols=35 Identities=37% Similarity=0.571 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhc
Q 018065 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (361)
Q Consensus 289 Ekir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L 323 (361)
.+....|...+|++||..|.|+..|++.+.+...+
T Consensus 100 ~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~ 134 (231)
T TIGR02885 100 RYMKEELSKELGREPTINELAEALGVSPEEIVMAL 134 (231)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence 34566788889999999999999999887766443
No 47
>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=63.63 E-value=12 Score=34.17 Aligned_cols=37 Identities=32% Similarity=0.636 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhc
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L 323 (361)
++.+...+|...+|++|+..|.|+.+|++.+.++..+
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4556677888899999999999999999887766544
No 48
>PRK05949 RNA polymerase sigma factor; Validated
Probab=62.91 E-value=15 Score=36.62 Aligned_cols=36 Identities=25% Similarity=0.423 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
++.+.+.++...+|++||..|.|+++|++.+.+...
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~ 214 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREY 214 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 445566778888999999999999999988777654
No 49
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=60.20 E-value=14 Score=38.57 Aligned_cols=38 Identities=21% Similarity=0.448 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
++.+.+..|...+||.||..|.|+++|++.+.++..+.
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45677888889999999999999999999888877543
No 50
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=57.95 E-value=20 Score=33.70 Aligned_cols=34 Identities=24% Similarity=0.286 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~ 321 (361)
+.+...++...+|++|+..|.|+..|++.+.+..
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 3345667888899999999999999998766554
No 51
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=56.04 E-value=22 Score=35.10 Aligned_cols=36 Identities=25% Similarity=0.470 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
++.+.+.++...+|++||..|.|+++|++.+.+...
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~ 204 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREY 204 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 455677788889999999999999999977666654
No 52
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=55.91 E-value=19 Score=34.11 Aligned_cols=36 Identities=28% Similarity=0.492 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
.+.+....|+..+|++||..|.|+..|++.+.+...
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~ 154 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSL 154 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 455667788889999999999999999987766554
No 53
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=55.67 E-value=29 Score=28.16 Aligned_cols=59 Identities=12% Similarity=0.070 Sum_probs=39.8
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc--c------------HHHHHHHHHHhHHHHHHHHHh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS--G------------NSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~--G------------~~ARekLI~sNLRLVVSIAKr 347 (361)
++++..-+...+..+++.++.|+.+|++...|.+.+.. | ..|++.|....+. |..||..
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 34455556667788899999999999998888876653 2 3466666654433 4556654
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=54.49 E-value=25 Score=34.08 Aligned_cols=36 Identities=25% Similarity=0.457 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
++.+.+..+...+|++||..+.|+.+|++.+.+...
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~ 197 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVREL 197 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 445566778888999999999999999987766543
No 55
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=54.47 E-value=11 Score=33.59 Aligned_cols=35 Identities=9% Similarity=-0.022 Sum_probs=32.0
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+..+-++|+..+-.+|..+|.+|.+..-+-+|++|
T Consensus 28 ~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQ 62 (194)
T PRK09646 28 DQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQ 62 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 57789999999999999999999998888899987
No 56
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=51.34 E-value=8.4 Score=34.02 Aligned_cols=35 Identities=23% Similarity=0.215 Sum_probs=31.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+..+-+.|+..+.++|..++++|.|..-.-+||+|
T Consensus 27 d~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQ 61 (194)
T PRK12519 27 QSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQ 61 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 57788999999999999999999888878889887
No 57
>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=50.53 E-value=15 Score=28.13 Aligned_cols=55 Identities=24% Similarity=0.414 Sum_probs=37.3
Q ss_pred HHhhCCCCc------HHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCC
Q 018065 296 QSQFGREPT------LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGIS 354 (361)
Q Consensus 296 e~~lGrePT------~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLs 354 (361)
++.+||.|| +.+|....|++.+.+...++.. ..+ -+.|++.|-.|++++...|+.
T Consensus 6 e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a---~~~-~~~~~~Yi~~Il~~W~~~gi~ 66 (73)
T TIGR01446 6 EENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEA---VSN-NKANYKYIDAILNNWKNNGIK 66 (73)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHH---HHc-CCCCHHHHHHHHHHHHHcCCC
Confidence 344566665 5567777777766665555542 222 246899999999999999974
No 58
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=49.00 E-value=52 Score=31.98 Aligned_cols=63 Identities=14% Similarity=0.191 Sum_probs=35.9
Q ss_pred HHHHHHhccCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhh
Q 018065 256 PLRLFLWGPETR-KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (361)
Q Consensus 256 ~l~~YLkei~~~-~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~ 321 (361)
.+..|+++-... +.-+...+..+...++. ++....++...+|++||..|.|+..|++.+++..
T Consensus 104 ~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~ 167 (289)
T PRK07500 104 SIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDVEM 167 (289)
T ss_pred HHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHH
Confidence 344566543322 22233344444444443 2222222333689999999999999998877654
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=48.97 E-value=24 Score=32.20 Aligned_cols=32 Identities=31% Similarity=0.576 Sum_probs=26.6
Q ss_pred HHHHHHHHhhCCCCcHHHHHHHhccchhhhhh
Q 018065 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (361)
Q Consensus 290 kir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~ 321 (361)
+....+...+|++|+..|.|++.|++...+..
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~ 125 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVVE 125 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 35567788889999999999999998877754
No 60
>PRK15044 transcriptional regulator SirC; Provisional
Probab=48.28 E-value=31 Score=34.59 Aligned_cols=59 Identities=22% Similarity=0.195 Sum_probs=43.6
Q ss_pred HHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 257 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 257 l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
+..|++..+..+.|..+..... ++++..-+....+++++..+||+.+|++...|.+++.
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk 230 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLA 230 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHH
Confidence 5567777777666655544332 3445556667788999999999999999999988765
No 61
>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=45.77 E-value=36 Score=26.49 Aligned_cols=25 Identities=32% Similarity=0.485 Sum_probs=16.8
Q ss_pred HhhCCCCcHHHHHHHhccc-hhhhhh
Q 018065 297 SQFGREPTLIEWAKAIGLS-CRDLKS 321 (361)
Q Consensus 297 ~~lGrePT~~EWA~AaG~d-~~~Lr~ 321 (361)
...|.+||..|.|++.|+. ...++.
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHH
Confidence 4569999999999999995 544443
No 62
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=43.62 E-value=47 Score=31.68 Aligned_cols=38 Identities=16% Similarity=0.122 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
++++..-++..+...++..++|+.+|++...|.+.+..
T Consensus 7 i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455566677788899999999999999988887663
No 63
>PRK05572 sporulation sigma factor SigF; Validated
Probab=41.04 E-value=46 Score=31.24 Aligned_cols=34 Identities=32% Similarity=0.656 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhh
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 320 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr 320 (361)
++.+....+...+|++|+..|.|++.|++...+.
T Consensus 119 ~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 3445667777888999999999999998776543
No 64
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=40.23 E-value=46 Score=24.33 Aligned_cols=23 Identities=35% Similarity=0.443 Sum_probs=19.1
Q ss_pred CCcHHHHHHHhccchhhhhhhcc
Q 018065 302 EPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 302 ePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
+++..++|+.+|++...|.+.+.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36788999999999888887776
No 65
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=38.98 E-value=41 Score=31.10 Aligned_cols=34 Identities=32% Similarity=0.558 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~ 321 (361)
+.+....+...+|++|+..++|+..|++.+.+..
T Consensus 97 ~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 97 VAQAIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 3445566777889999999999999998877543
No 66
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=38.93 E-value=26 Score=31.22 Aligned_cols=36 Identities=8% Similarity=0.035 Sum_probs=29.9
Q ss_pred ccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 325 ~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
.+..|-+.|+..+.+.|..+|.+|.|..-.-+||+|
T Consensus 24 ~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQ 59 (194)
T PRK12531 24 RDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQ 59 (194)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 356788889999999999999999887666778877
No 67
>PRK13503 transcriptional activator RhaS; Provisional
Probab=38.86 E-value=62 Score=29.91 Aligned_cols=58 Identities=22% Similarity=0.250 Sum_probs=39.9
Q ss_pred HHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc--------------cHHHHHHHHHHhHHHHHHHHHh
Q 018065 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS--------------GNSSREKLINANLRLVVHVAKQ 347 (361)
Q Consensus 289 Ekir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~--------------G~~ARekLI~sNLRLVVSIAKr 347 (361)
.++..-+.+....+.|..+||+.+|++...|.+.... -..|++.|...|+. |-.||.+
T Consensus 174 ~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~LL~~~~~s-I~eIA~~ 245 (278)
T PRK13503 174 NQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDAS-VTDIAYR 245 (278)
T ss_pred HHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHcCCCC-HHHHHHH
Confidence 3444556667778899999999999998888776542 13466666655553 5566665
No 68
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=35.89 E-value=2.8e+02 Score=26.08 Aligned_cols=37 Identities=19% Similarity=0.162 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhhCCC-CcHHHHHHHhccchhhhhhhcc
Q 018065 288 LEKEKSKLQSQFGRE-PTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 288 LEkir~~Le~~lGre-PT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
+.+++.-+.+.+..+ .|..++|+++|++...|.+...
T Consensus 199 l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 199 FQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334555566677766 7999999999999888876554
No 69
>KOG0197 consensus Tyrosine kinases [Signal transduction mechanisms]
Probab=35.76 E-value=12 Score=39.59 Aligned_cols=69 Identities=20% Similarity=0.301 Sum_probs=53.9
Q ss_pred hccCCCCCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 246 KLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 246 k~~~~~~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
.+..++.+...|..||+. +....|...+...++.+|-++|... +=++-+|+
T Consensus 277 yIVtE~m~~GsLl~yLr~-~~~~~l~~~~Ll~~a~qIaeGM~YL----------------------------es~~~IHR 327 (468)
T KOG0197|consen 277 YIVTEYMPKGSLLDYLRT-REGGLLNLPQLLDFAAQIAEGMAYL----------------------------ESKNYIHR 327 (468)
T ss_pred EEEEEecccCcHHHHhhh-cCCCccchHHHHHHHHHHHHHHHHH----------------------------HhCCccch
Confidence 455667788899999998 7778999999999998888765422 12456889
Q ss_pred cHHHHHHHHHHhHHHHHHHH
Q 018065 326 GNSSREKLINANLRLVVHVA 345 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIA 345 (361)
|-+|||-||..|+ |+.||
T Consensus 328 DLAARNiLV~~~~--~vKIs 345 (468)
T KOG0197|consen 328 DLAARNILVDEDL--VVKIS 345 (468)
T ss_pred hhhhhheeeccCc--eEEEc
Confidence 9999999999998 66554
No 70
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=35.12 E-value=62 Score=32.89 Aligned_cols=51 Identities=22% Similarity=0.289 Sum_probs=38.8
Q ss_pred HHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcccc--------------HHHHHHHHHHhHHHH
Q 018065 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG--------------NSSREKLINANLRLV 341 (361)
Q Consensus 291 ir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G--------------~~ARekLI~sNLRLV 341 (361)
+...++..++.+-+.++.|..+||+...|.++.... ..||+-|.++|+-+.
T Consensus 225 ~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~lG~sP~~yy~~lRL~~Ar~LL~~t~~si~ 289 (328)
T COG4977 225 AIELMEANLEEPLSLEELADRAGLSRRQLERLFRAELGVSPARYYLRLRLERARRLLEQTRLSIA 289 (328)
T ss_pred HHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCCcHH
Confidence 344556677889999999999999999998875522 458888888887643
No 71
>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=34.68 E-value=51 Score=30.88 Aligned_cols=34 Identities=29% Similarity=0.515 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhh
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~ 321 (361)
+.+....+...+|++|+..+.|...|++.+.+..
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3456677888889999999999999998877654
No 72
>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=33.60 E-value=81 Score=23.96 Aligned_cols=26 Identities=31% Similarity=0.406 Sum_probs=21.8
Q ss_pred CCCcHHHHHHHhccchhhhhhhcccc
Q 018065 301 REPTLIEWAKAIGLSCRDLKSELHSG 326 (361)
Q Consensus 301 rePT~~EWA~AaG~d~~~Lr~~L~~G 326 (361)
|..+..|.|+..|++...+-..|..+
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 67899999999999988887777654
No 73
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=33.01 E-value=63 Score=31.81 Aligned_cols=35 Identities=23% Similarity=0.330 Sum_probs=29.0
Q ss_pred HHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 291 ir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
+...+........+..+||+.+||+...|.+.+..
T Consensus 186 i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~ 220 (291)
T PRK15186 186 IYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34456667788999999999999999999988764
No 74
>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=32.81 E-value=71 Score=28.68 Aligned_cols=32 Identities=22% Similarity=0.297 Sum_probs=26.1
Q ss_pred HHHhhCCCCcHHHHHHHhccchhhhhhhcccc
Q 018065 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (361)
Q Consensus 295 Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G 326 (361)
|.+.-|+..|..+.+++.|++++.+.+.|+.|
T Consensus 39 Lr~~p~~~ati~eV~e~tgVs~~~I~~~IreG 70 (137)
T TIGR03826 39 LRKHENRQATVSEIVEETGVSEKLILKFIREG 70 (137)
T ss_pred HHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcC
Confidence 44455677899999999999999999877766
No 75
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=32.47 E-value=79 Score=31.46 Aligned_cols=36 Identities=19% Similarity=0.303 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhc
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 323 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L 323 (361)
+.+....|+..+|++|+..+.|...|++.++++..+
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 334566778889999999999999999877775543
No 76
>PRK13239 alkylmercury lyase; Provisional
Probab=31.71 E-value=55 Score=31.31 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=24.7
Q ss_pred hCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 299 FGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 299 lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
.|++||..+.|++.|.+.++++++|+.
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 499999999999999999999888775
No 77
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=31.67 E-value=53 Score=26.40 Aligned_cols=54 Identities=28% Similarity=0.500 Sum_probs=36.8
Q ss_pred HHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 295 Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
++..+| -|-++.|..+|++...+-.. ..|. -.-+|.|...||+-|. .+++|+++
T Consensus 9 ~R~~~~--ltQ~elA~~vgVsRQTi~~i-Ekgk------y~Psl~La~kia~~f~---~~iedIF~ 62 (68)
T COG1476 9 LRAELG--LTQEELAKLVGVSRQTIIAI-EKGK------YNPSLELALKIARVFG---KTIEDIFQ 62 (68)
T ss_pred HHHHhC--cCHHHHHHHcCcCHHHHHHH-HcCC------CCchHHHHHHHHHHhC---CCHHHHHh
Confidence 334445 67888899999876555322 2221 2567899999999986 77777765
No 78
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=31.53 E-value=33 Score=30.62 Aligned_cols=37 Identities=22% Similarity=0.191 Sum_probs=32.7
Q ss_pred cccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 324 ~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
..+..+-+.|+..+...|..++.++.+....-+||+|
T Consensus 23 ~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQ 59 (192)
T PRK09643 23 AGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQ 59 (192)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHH
Confidence 4467889999999999999999999988888899987
No 79
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.92 E-value=2e+02 Score=24.77 Aligned_cols=45 Identities=24% Similarity=0.155 Sum_probs=31.6
Q ss_pred HHHHHHHhh-CCCCcHHHHHHHhccchhhhhhhc------cccHHHHHHHHH
Q 018065 291 EKSKLQSQF-GREPTLIEWAKAIGLSCRDLKSEL------HSGNSSREKLIN 335 (361)
Q Consensus 291 ir~~Le~~l-GrePT~~EWA~AaG~d~~~Lr~~L------~~G~~ARekLI~ 335 (361)
.+.+|++.+ -...+.++.|.+.|.+...|++.| +.+...|+-|++
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 344455433 346789999999999988888877 456667776554
No 80
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=29.31 E-value=25 Score=26.70 Aligned_cols=25 Identities=12% Similarity=0.413 Sum_probs=18.4
Q ss_pred HHhHHHHHHHHHhcCCCCC-CccCcc
Q 018065 335 NANLRLVVHVAKQYQGRGI-SLHDLL 359 (361)
Q Consensus 335 ~sNLRLVVSIAKrY~grGL-sfqDLI 359 (361)
..|.+.|..|++++...|+ +++|+.
T Consensus 47 ~~~~~Yi~~Il~~W~~~gi~t~e~~~ 72 (77)
T PF07261_consen 47 KRSFNYIEKILNNWKQKGIKTVEDAE 72 (77)
T ss_dssp --SHHHHHHHHHHHHHCT--SCCCCT
T ss_pred CCCHHHHHHHHHHHHHcCCCCHHHHH
Confidence 4579999999999999997 465553
No 81
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.78 E-value=32 Score=32.26 Aligned_cols=35 Identities=14% Similarity=0.229 Sum_probs=30.1
Q ss_pred cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360 (361)
Q Consensus 326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ 360 (361)
+..+-+.|+..+.+.|..++.+|.|..-.-+|++|
T Consensus 61 d~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQ 95 (233)
T PRK12538 61 DEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQ 95 (233)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Confidence 56788889999999999999999887777888887
No 82
>PRK15185 transcriptional regulator HilD; Provisional
Probab=27.67 E-value=1.7e+02 Score=29.68 Aligned_cols=43 Identities=28% Similarity=0.264 Sum_probs=32.0
Q ss_pred HHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc-ccHHHHH
Q 018065 289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH-SGNSSRE 331 (361)
Q Consensus 289 Ekir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~-~G~~ARe 331 (361)
+++..-+....+...+.++||+.+|++...|.+.+. .|....+
T Consensus 209 erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~~~ 252 (309)
T PRK15185 209 ERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFSD 252 (309)
T ss_pred HHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHH
Confidence 345555667778899999999999999999988764 2433333
No 83
>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=27.26 E-value=61 Score=26.72 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=19.8
Q ss_pred hCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 299 FGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 299 lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
.|++.|..+.|.++|.+.++++..|..
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 399999999999999999988877653
No 84
>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=26.27 E-value=2.2e+02 Score=23.34 Aligned_cols=37 Identities=19% Similarity=0.211 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcccc
Q 018065 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG 326 (361)
Q Consensus 287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G 326 (361)
+++.|.+-|.. | .+|+.+.|+.+|++...+.+.|..+
T Consensus 7 R~~~I~e~l~~--~-~~ti~dvA~~~gvS~~TVsr~L~~~ 43 (80)
T TIGR02844 7 RVLEIGKYIVE--T-KATVRETAKVFGVSKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHHHHH--C-CCCHHHHHHHhCCCHHHHHHHhcCC
Confidence 44555555655 4 5799999999999999999999864
No 85
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.18 E-value=2.8e+02 Score=23.44 Aligned_cols=53 Identities=21% Similarity=0.157 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcccc-------HHHHHHHH
Q 018065 270 LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG-------NSSREKLI 334 (361)
Q Consensus 270 LTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G-------~~ARekLI 334 (361)
||++|.+.=...+|.-.+ ..| .|.++.|+..|++...|+++|.-. ...|+-|.
T Consensus 3 Ln~~Q~~~T~~ELq~nf~----------~~~--ls~~~ia~dL~~s~~~le~vL~l~~~~~~~vW~lRdyL~ 62 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFE----------LSG--LSLEQIAADLGTSPEHLEQVLNLKQPFPEDVWILRDYLN 62 (89)
T ss_pred CCHHHHHHHHHHHHHHHH----------HcC--CCHHHHHHHhCCCHHHHHHHHcCCCCCcccchHHHHHHH
Confidence 666666654444443222 124 788999999999999999887743 45565543
No 86
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=25.99 E-value=1.9e+02 Score=28.03 Aligned_cols=23 Identities=13% Similarity=0.134 Sum_probs=19.9
Q ss_pred CCCCcHHHHHHHhccchhhhhhh
Q 018065 300 GREPTLIEWAKAIGLSCRDLKSE 322 (361)
Q Consensus 300 GrePT~~EWA~AaG~d~~~Lr~~ 322 (361)
+++||..|.|+..|++.++++..
T Consensus 149 ~~~~t~~eiA~~l~~~~~~v~~~ 171 (284)
T PRK06596 149 LNPEEVEMVAEELGVSEEEVREM 171 (284)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHH
Confidence 59999999999999998887655
No 87
>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=22.98 E-value=1.2e+02 Score=21.55 Aligned_cols=29 Identities=28% Similarity=0.455 Sum_probs=19.9
Q ss_pred HHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 294 KLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 294 ~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
.|+.. | .-++.+.|+.+|++...+.+++.
T Consensus 11 ~Lq~d-~-r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 11 LLQED-G-RRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp HHHH--T-TS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHc-C-CccHHHHHHHHCcCHHHHHHHHH
Confidence 34443 4 46789999999999988887765
No 88
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=22.95 E-value=1.1e+02 Score=29.56 Aligned_cols=36 Identities=11% Similarity=0.129 Sum_probs=28.4
Q ss_pred HHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 290 kir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
++..-+...++.+.+..++|+.+|++...|.+++..
T Consensus 222 ~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344445566678899999999999999999887763
No 89
>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=22.85 E-value=1.2e+02 Score=28.33 Aligned_cols=32 Identities=19% Similarity=0.292 Sum_probs=25.1
Q ss_pred HHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELH 324 (361)
Q Consensus 293 ~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~ 324 (361)
.-+....+...|.++||+.+|++..-|.+...
T Consensus 193 ~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk 224 (287)
T TIGR02297 193 FLIEENYKQHLRLPEYADRLGISESRLNDICR 224 (287)
T ss_pred HHHHHhhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 33445567788999999999999988877655
No 90
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=22.05 E-value=2.1e+02 Score=27.68 Aligned_cols=38 Identities=8% Similarity=0.114 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065 288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325 (361)
Q Consensus 288 LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~ 325 (361)
++++..-+.......++..+||+.+|++...|.+.+..
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33444555566677899999999999999888776664
No 91
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=21.15 E-value=4.1e+02 Score=20.83 Aligned_cols=69 Identities=14% Similarity=0.246 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHHHHHHHH--------HHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHH
Q 018065 268 KLLTADEEFELIAQIQDLIR--------LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLR 339 (361)
Q Consensus 268 ~LLTaEEE~eL~~~IQ~l~~--------LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLR 339 (361)
--||+++..++-...+.... +...+.+|...+..++ .|...++..+..-..++..|-..-++
T Consensus 40 l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~~~~----------~D~~~i~a~~~~~~~~~~~l~~~~~~ 109 (125)
T PF13801_consen 40 LNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLAAPP----------PDEAAIEALLEEIREAQAELRQERLE 109 (125)
T ss_dssp S-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSS----------S-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC----------CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56999999988877764432 2334445545554333 35566666667777777777777777
Q ss_pred HHHHHHH
Q 018065 340 LVVHVAK 346 (361)
Q Consensus 340 LVVSIAK 346 (361)
.++.+++
T Consensus 110 ~~~~~~~ 116 (125)
T PF13801_consen 110 HLLEIRA 116 (125)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 7777764
Done!