Query 020690
Match_columns 322
No_of_seqs 143 out of 360
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 04:23:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020690.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020690hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03162 golden-2 like transcr 100.0 3.6E-30 7.9E-35 250.7 8.2 133 109-268 231-367 (526)
2 TIGR01557 myb_SHAQKYF myb-like 99.9 1.1E-21 2.5E-26 146.0 6.5 55 113-167 1-56 (57)
3 PF00249 Myb_DNA-binding: Myb- 98.1 9.6E-06 2.1E-10 56.9 5.5 48 115-165 1-48 (48)
4 smart00426 TEA TEA domain. 94.9 0.032 6.9E-07 44.2 3.5 45 117-163 5-67 (68)
5 cd00167 SANT 'SWI3, ADA2, N-Co 94.7 0.12 2.7E-06 33.5 5.6 44 117-164 1-44 (45)
6 smart00717 SANT SANT SWI3, AD 94.7 0.14 3.1E-06 33.5 5.8 43 116-163 2-45 (49)
7 PF12776 Myb_DNA-bind_3: Myb/S 89.1 0.55 1.2E-05 36.2 3.7 59 117-175 1-72 (96)
8 PF01285 TEA: TEA/ATTS domain 87.8 0.41 8.9E-06 48.5 2.9 52 112-164 46-112 (431)
9 KOG3841 TEF-1 and related tran 85.3 2.3 5E-05 43.5 6.6 52 113-164 74-141 (455)
10 PF13921 Myb_DNA-bind_6: Myb-l 80.7 4.1 8.9E-05 29.2 4.7 41 118-163 1-41 (60)
11 KOG0457 Histone acetyltransfer 70.5 8.4 0.00018 39.8 5.5 52 112-167 69-120 (438)
12 PRK11923 algU RNA polymerase s 63.2 24 0.00051 30.1 6.1 49 120-171 126-185 (193)
13 PRK12541 RNA polymerase sigma 57.4 38 0.00082 28.0 6.2 47 123-172 103-160 (161)
14 PRK09646 RNA polymerase sigma 56.6 34 0.00074 29.5 6.0 54 119-175 129-193 (194)
15 PLN03212 Transcription repress 55.6 26 0.00056 34.0 5.5 34 113-148 23-56 (249)
16 KOG0842 Transcription factor t 54.9 9.5 0.00021 37.7 2.5 59 108-173 150-213 (307)
17 cd00086 homeodomain Homeodomai 53.4 58 0.0013 22.4 5.7 56 113-170 2-57 (59)
18 PRK12533 RNA polymerase sigma 53.2 49 0.0011 29.9 6.6 50 120-172 122-182 (216)
19 PRK09642 RNA polymerase sigma 53.1 43 0.00094 27.5 5.8 49 121-172 95-154 (160)
20 TIGR02989 Sig-70_gvs1 RNA poly 52.8 44 0.00094 27.2 5.7 50 118-170 97-157 (159)
21 PLN03091 hypothetical protein; 52.5 34 0.00073 35.8 6.0 36 111-148 10-45 (459)
22 PRK12540 RNA polymerase sigma 51.7 38 0.00083 29.3 5.5 47 124-173 103-160 (182)
23 TIGR02983 SigE-fam_strep RNA p 50.3 51 0.0011 27.1 5.8 50 120-172 98-158 (162)
24 PRK12530 RNA polymerase sigma 50.1 49 0.0011 28.6 5.9 49 120-171 122-181 (189)
25 cd06171 Sigma70_r4 Sigma70, re 49.9 39 0.00084 21.8 4.1 31 136-169 25-55 (55)
26 PF00046 Homeobox: Homeobox do 49.1 53 0.0012 23.0 5.0 57 112-170 1-57 (57)
27 PRK09640 RNA polymerase sigma 48.7 61 0.0013 27.7 6.2 52 117-171 119-181 (188)
28 TIGR02985 Sig70_bacteroi1 RNA 48.6 62 0.0013 25.9 5.9 48 120-170 101-159 (161)
29 PRK09643 RNA polymerase sigma 48.6 55 0.0012 28.3 6.0 57 120-179 122-189 (192)
30 PRK11924 RNA polymerase sigma 48.0 59 0.0013 26.6 5.8 48 121-171 114-172 (179)
31 PRK12522 RNA polymerase sigma 48.0 47 0.001 27.9 5.3 52 117-171 104-166 (173)
32 TIGR02950 SigM_subfam RNA poly 46.9 67 0.0015 26.0 5.9 47 122-171 95-152 (154)
33 PRK06759 RNA polymerase factor 46.8 69 0.0015 26.0 6.0 48 121-171 95-153 (154)
34 PRK09652 RNA polymerase sigma 46.3 69 0.0015 26.3 6.0 48 121-171 117-175 (182)
35 PRK12519 RNA polymerase sigma 45.9 69 0.0015 27.3 6.1 32 137-171 157-188 (194)
36 TIGR02960 SigX5 RNA polymerase 44.7 56 0.0012 30.3 5.7 49 122-173 132-191 (324)
37 PRK13919 putative RNA polymera 44.7 64 0.0014 27.2 5.7 45 124-171 127-182 (186)
38 PRK12514 RNA polymerase sigma 43.9 65 0.0014 27.1 5.6 33 136-171 144-176 (179)
39 TIGR02943 Sig70_famx1 RNA poly 43.3 71 0.0015 27.6 5.9 49 121-172 120-179 (188)
40 PRK12543 RNA polymerase sigma 43.2 66 0.0014 27.3 5.6 48 121-171 106-164 (179)
41 KOG0724 Zuotin and related mol 43.1 9 0.00019 36.3 0.3 55 113-172 51-105 (335)
42 TIGR02947 SigH_actino RNA poly 42.7 73 0.0016 27.3 5.8 48 122-172 121-179 (193)
43 PF13837 Myb_DNA-bind_4: Myb/S 42.2 35 0.00076 25.8 3.4 58 115-172 1-71 (90)
44 PRK09415 RNA polymerase factor 42.0 85 0.0018 26.7 6.0 49 120-171 115-174 (179)
45 TIGR02952 Sig70_famx2 RNA poly 41.3 95 0.0021 25.5 6.1 48 121-171 111-169 (170)
46 TIGR02948 SigW_bacill RNA poly 40.8 76 0.0016 26.6 5.5 51 118-171 122-183 (187)
47 PF08281 Sigma70_r4_2: Sigma-7 40.4 83 0.0018 21.9 4.8 30 136-168 25-54 (54)
48 PRK09047 RNA polymerase factor 39.6 83 0.0018 25.6 5.5 50 119-171 93-153 (161)
49 KOG0848 Transcription factor C 39.5 53 0.0011 32.8 4.9 59 106-170 194-256 (317)
50 PRK12515 RNA polymerase sigma 38.5 91 0.002 26.6 5.7 50 121-173 120-180 (189)
51 PRK12544 RNA polymerase sigma 38.4 83 0.0018 27.9 5.7 49 121-172 137-196 (206)
52 PRK12545 RNA polymerase sigma 37.9 97 0.0021 27.1 5.9 45 124-171 131-186 (201)
53 PRK12520 RNA polymerase sigma 37.7 1E+02 0.0022 26.4 5.9 49 121-172 120-179 (191)
54 PRK12516 RNA polymerase sigma 37.2 1E+02 0.0022 26.8 5.9 47 124-173 108-165 (187)
55 TIGR02959 SigZ RNA polymerase 36.8 1.1E+02 0.0024 25.9 5.9 51 119-172 87-148 (170)
56 PRK09644 RNA polymerase sigma 36.7 1.1E+02 0.0023 25.5 5.8 51 119-172 95-156 (165)
57 cd08783 Death_MALT1 Death doma 36.7 65 0.0014 27.4 4.4 47 114-163 36-83 (97)
58 PRK11922 RNA polymerase sigma 36.7 89 0.0019 28.0 5.6 54 116-172 133-197 (231)
59 TIGR02894 DNA_bind_RsfA transc 36.3 13 0.00029 33.9 0.3 57 105-166 38-94 (161)
60 TIGR03001 Sig-70_gmx1 RNA poly 35.7 87 0.0019 29.0 5.5 51 118-171 147-208 (244)
61 PRK08241 RNA polymerase factor 35.6 94 0.002 29.2 5.8 46 122-170 143-199 (339)
62 PF00690 Cation_ATPase_N: Cati 35.4 51 0.0011 24.4 3.3 28 139-166 5-35 (69)
63 PRK12536 RNA polymerase sigma 35.3 1.1E+02 0.0025 25.9 5.8 48 121-171 118-176 (181)
64 COG5114 Histone acetyltransfer 35.3 55 0.0012 33.5 4.4 47 116-166 64-110 (432)
65 PRK12513 RNA polymerase sigma 35.1 1.3E+02 0.0028 25.7 6.2 49 121-172 128-187 (194)
66 PRK12526 RNA polymerase sigma 34.9 1.1E+02 0.0024 26.8 5.8 49 121-172 142-201 (206)
67 PRK09636 RNA polymerase sigma 34.8 99 0.0022 28.7 5.8 51 119-172 102-163 (293)
68 PLN03091 hypothetical protein; 34.8 1.1E+02 0.0023 32.3 6.4 42 116-162 68-109 (459)
69 PRK09647 RNA polymerase sigma 34.6 1.1E+02 0.0025 27.0 5.9 49 121-172 127-186 (203)
70 PRK05602 RNA polymerase sigma 34.5 1.3E+02 0.0028 25.6 6.0 50 120-172 116-176 (186)
71 PRK12538 RNA polymerase sigma 33.8 1.2E+02 0.0025 27.7 6.0 48 122-172 161-219 (233)
72 PRK12532 RNA polymerase sigma 33.7 1.2E+02 0.0026 26.0 5.8 48 122-172 126-184 (195)
73 PRK12518 RNA polymerase sigma 33.6 1.3E+02 0.0029 24.9 5.9 48 122-172 110-168 (175)
74 TIGR02939 RpoE_Sigma70 RNA pol 33.6 1.4E+02 0.003 25.0 6.0 50 119-171 125-185 (190)
75 PRK09649 RNA polymerase sigma 33.3 1.3E+02 0.0028 25.9 5.9 45 123-170 121-176 (185)
76 PRK06811 RNA polymerase factor 32.9 1.6E+02 0.0034 25.3 6.3 51 119-172 118-179 (189)
77 COG1595 RpoE DNA-directed RNA 32.7 87 0.0019 26.7 4.7 51 120-173 115-176 (182)
78 TIGR02957 SigX4 RNA polymerase 32.6 1.1E+02 0.0025 28.3 5.8 52 117-171 93-155 (281)
79 PRK12524 RNA polymerase sigma 32.4 1.1E+02 0.0025 26.3 5.4 53 116-171 120-183 (196)
80 TIGR02954 Sig70_famx3 RNA poly 32.3 1.3E+02 0.0029 25.0 5.7 45 124-171 111-166 (169)
81 TIGR02984 Sig-70_plancto1 RNA 32.1 1.5E+02 0.0032 24.7 5.9 46 123-171 131-187 (189)
82 PRK09648 RNA polymerase sigma 31.4 1.5E+02 0.0032 25.2 5.9 47 122-171 129-186 (189)
83 PRK12531 RNA polymerase sigma 31.1 1.3E+02 0.0028 25.9 5.6 47 122-171 131-188 (194)
84 PRK07037 extracytoplasmic-func 29.8 1.8E+02 0.0039 23.9 5.9 46 123-171 100-156 (163)
85 PRK09635 sigI RNA polymerase s 29.3 1.1E+02 0.0025 28.9 5.3 54 115-171 101-165 (290)
86 PRK09645 RNA polymerase sigma 29.1 1.7E+02 0.0036 24.4 5.7 45 125-172 111-166 (173)
87 PLN03212 Transcription repress 28.0 1.8E+02 0.004 28.3 6.4 41 116-161 79-119 (249)
88 PRK12539 RNA polymerase sigma 27.8 1.8E+02 0.0039 24.7 5.8 49 121-172 120-179 (184)
89 PRK12542 RNA polymerase sigma 27.7 1.8E+02 0.004 24.6 5.8 45 125-172 115-170 (185)
90 TIGR02937 sigma70-ECF RNA poly 26.9 2E+02 0.0043 22.1 5.4 30 138-170 127-156 (158)
91 PF11888 DUF3408: Protein of u 25.7 1E+02 0.0022 26.3 4.0 47 116-171 83-129 (136)
92 PF08671 SinI: Anti-repressor 25.5 56 0.0012 22.3 1.8 18 145-163 11-28 (30)
93 PRK09641 RNA polymerase sigma 25.2 2.4E+02 0.0051 23.6 6.0 45 124-171 128-183 (187)
94 smart00389 HOX Homeodomain. DN 25.2 2.3E+02 0.005 19.4 5.0 52 113-166 2-53 (56)
95 PRK06704 RNA polymerase factor 23.4 2.2E+02 0.0047 26.4 5.9 49 121-172 105-164 (228)
96 PRK12534 RNA polymerase sigma 22.9 2.4E+02 0.0053 23.8 5.7 49 120-171 125-184 (187)
97 KOG3161 Predicted E3 ubiquitin 22.7 2.2E+02 0.0048 31.8 6.5 86 199-300 421-519 (861)
98 PRK06986 fliA flagellar biosyn 22.5 2.8E+02 0.006 24.9 6.2 48 121-171 173-231 (236)
99 PRK04217 hypothetical protein; 22.4 1.4E+02 0.0031 25.3 4.2 42 128-172 49-90 (110)
100 KOG0850 Transcription factor D 22.0 88 0.0019 30.4 3.1 60 108-173 119-182 (245)
101 PF14075 UBN_AB: Ubinuclein co 21.8 1.5E+02 0.0032 27.8 4.4 22 110-131 147-168 (214)
102 PRK09639 RNA polymerase sigma 21.7 2.7E+02 0.0059 22.8 5.6 32 137-171 127-158 (166)
103 PRK12535 RNA polymerase sigma 21.6 2.5E+02 0.0053 24.7 5.6 47 124-173 125-182 (196)
104 PRK12546 RNA polymerase sigma 20.9 3E+02 0.0065 24.0 6.0 50 124-176 105-165 (188)
105 PRK09637 RNA polymerase sigma 20.9 3.1E+02 0.0068 23.6 6.0 49 121-172 95-154 (181)
106 PRK09638 RNA polymerase sigma 20.8 3E+02 0.0066 22.8 5.8 46 123-171 117-173 (176)
No 1
>PLN03162 golden-2 like transcription factor; Provisional
Probab=99.96 E-value=3.6e-30 Score=250.67 Aligned_cols=133 Identities=35% Similarity=0.586 Sum_probs=100.3
Q ss_pred cCCCCCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcCCCCCCCCCCCCCCCC
Q 020690 109 RTLKRPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQGLSGGGGGGAGGVNGG 188 (322)
Q Consensus 109 ~~~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ls~~g~~~~~~~~~~ 188 (322)
.+.||+||+||+|||+|||+||++||.++||||+||++|||+|||++||||||||||++++++.......+.
T Consensus 231 ~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~s-------- 302 (526)
T PLN03162 231 PGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAAS-------- 302 (526)
T ss_pred CCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhcc--------
Confidence 457899999999999999999999999999999999999999999999999999999999987655444322
Q ss_pred CCCCCCCCCCCcccccccCCCCCCccCCCCCCCCCCCCCC-ceecchhhHHHHHHHHHhcCCCccCCccc---ccccccC
Q 020690 189 GSGAAGVNADPATDHLFASSPVPAHFLHPGARGNSDHFLP-YVPVAALHQQQMAVAAAVGNPHLQGHQYH---RQMSHFG 264 (322)
Q Consensus 189 ~~~~~~~~~~~~~~~lfa~sPvp~~~l~p~~r~~~~~~~p-~vp~~~~~~~~~~~~a~~~~~~~~~~~~h---r~~~~~g 264 (322)
+...+++..+|.+ |-+.....| +|||+.++.|..+.++++.+|.++. ++| |++-.||
T Consensus 303 ----------wt~kr~~~~~P~~--------rs~~~~g~p~~~pigfP~~~P~P~~~~~~~P~~~~-~Hhpf~rPLhVWG 363 (526)
T PLN03162 303 ----------WTHRRAYTQAPWP--------RSSRRDGLPYLVPIHTPHIQPRPSMAMAMQPQLQT-PHHPISTPLKVWG 363 (526)
T ss_pred ----------chhhhhhccCCcc--------cCCCCCCCccccccCCCCCCCCCCccCCCCCCccc-ccccccccceecc
Confidence 1334455555433 222222234 4777777766556666777888776 444 8888888
Q ss_pred CCCC
Q 020690 265 SPAN 268 (322)
Q Consensus 265 ~p~~ 268 (322)
.|+-
T Consensus 364 hPtv 367 (526)
T PLN03162 364 YPTV 367 (526)
T ss_pred CCCC
Confidence 7653
No 2
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=99.85 E-value=1.1e-21 Score=146.02 Aligned_cols=55 Identities=64% Similarity=1.016 Sum_probs=53.1
Q ss_pred CCccccChHHHHHHHHHHHHhCC-CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhh
Q 020690 113 RPRLVWTPQLHKRFVDAVAHLGI-KNAVPKTIMQLMSVDGLTRENVASHLQKYRLY 167 (322)
Q Consensus 113 KpRl~WT~ELH~rFVeAV~qLG~-dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~ 167 (322)
|+|++||+|+|.+||+||++||. +.|+||+|+++|++++||+.||+|||||||++
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 68999999999999999999996 89999999999999999999999999999985
No 3
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=98.06 E-value=9.6e-06 Score=56.95 Aligned_cols=48 Identities=27% Similarity=0.353 Sum_probs=42.2
Q ss_pred ccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhH
Q 020690 115 RLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYR 165 (322)
Q Consensus 115 Rl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYR 165 (322)
|..||+|.+++|++||.++|.+ .++.|.+.|+ .+-|..++++|.++|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~--~W~~Ia~~~~-~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD--NWKKIAKRMP-GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT--HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCc--HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence 5689999999999999999965 6999999999 6789999999999985
No 4
>smart00426 TEA TEA domain.
Probab=94.85 E-value=0.032 Score=44.18 Aligned_cols=45 Identities=31% Similarity=0.429 Sum_probs=30.3
Q ss_pred ccChHHHHHHHHHHHHhCCCCCChH-H-----------------HHHhhCCCCCCHHHHHHHhhh
Q 020690 117 VWTPQLHKRFVDAVAHLGIKNAVPK-T-----------------IMQLMSVDGLTRENVASHLQK 163 (322)
Q Consensus 117 ~WT~ELH~rFVeAV~qLG~dkAtPK-~-----------------ILelM~V~GLTrenVkSHLQK 163 (322)
+|.++|-..|++|++.+=. ..+-| + |...-|. --|+.||.||+|.
T Consensus 5 vWp~~lE~Af~~aL~~~~~-~g~~kik~~~r~k~~gRNelIs~YI~~~tGk-~Rt~KQVsShIQv 67 (68)
T smart00426 5 VWSPDIEQAFQEALAIYPP-CGRRKIILSDEGKMYGRNELIARYIKLRTGK-TRTRKQVSSHIQV 67 (68)
T ss_pred cCcHHHHHHHHHHHHHcCc-cCcccchhhhcCcccchhHHHHHHHHHHhCC-ccchhhhcchhee
Confidence 7999999999999997642 11111 2 2222221 2499999999995
No 5
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=94.75 E-value=0.12 Score=33.47 Aligned_cols=44 Identities=16% Similarity=0.218 Sum_probs=37.0
Q ss_pred ccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhh
Q 020690 117 VWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKY 164 (322)
Q Consensus 117 ~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKY 164 (322)
.||.+-.+.|+.++.++|. ..++.|.+.|+- -|..+|+.+.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~--~~w~~Ia~~~~~--rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK--NNWEKIAKELPG--RTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc--CCHHHHHhHcCC--CCHHHHHHHHHHh
Confidence 4999999999999999993 239999999865 5999999887654
No 6
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=94.65 E-value=0.14 Score=33.52 Aligned_cols=43 Identities=19% Similarity=0.281 Sum_probs=36.7
Q ss_pred cccChHHHHHHHHHHHHhC-CCCCChHHHHHhhCCCCCCHHHHHHHhhh
Q 020690 116 LVWTPQLHKRFVDAVAHLG-IKNAVPKTIMQLMSVDGLTRENVASHLQK 163 (322)
Q Consensus 116 l~WT~ELH~rFVeAV~qLG-~dkAtPK~ILelM~V~GLTrenVkSHLQK 163 (322)
-.||++-...|+++++++| .+ ++.|.+.|. +-|..+|+.+..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~---w~~Ia~~~~--~rt~~~~~~~~~~ 45 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNN---WEKIAKELP--GRTAEQCRERWNN 45 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCC---HHHHHHHcC--CCCHHHHHHHHHH
Confidence 4699999999999999999 44 999999987 6699999877554
No 7
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=89.11 E-value=0.55 Score=36.15 Aligned_cols=59 Identities=15% Similarity=0.265 Sum_probs=42.7
Q ss_pred ccChHHHHHHHHHHHHh---CC-------CCCChHHHHHhhCC---CCCCHHHHHHHhhhhHhhhhhhcCCC
Q 020690 117 VWTPQLHKRFVDAVAHL---GI-------KNAVPKTIMQLMSV---DGLTRENVASHLQKYRLYLKRMQGLS 175 (322)
Q Consensus 117 ~WT~ELH~rFVeAV~qL---G~-------dkAtPK~ILelM~V---~GLTrenVkSHLQKYRl~lkr~~~ls 175 (322)
+||++..+.||+++... |. ++...+.|.+.++- ..+|..||++|+...|..-+....+-
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~ 72 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELR 72 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 59999999999998633 42 23456678877774 45899999999988776665444443
No 8
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=87.81 E-value=0.41 Score=48.52 Aligned_cols=52 Identities=27% Similarity=0.398 Sum_probs=29.8
Q ss_pred CCCccccChHHHHHHHHHHHHh---CCCCCC------------hHHHHHhhCCCCCCHHHHHHHhhhh
Q 020690 112 KRPRLVWTPQLHKRFVDAVAHL---GIKNAV------------PKTIMQLMSVDGLTRENVASHLQKY 164 (322)
Q Consensus 112 kKpRl~WT~ELH~rFVeAV~qL---G~dkAt------------PK~ILelM~V~GLTrenVkSHLQKY 164 (322)
++..-+|++++...|++|+..+ |..|-. -..|...-| .--|++||.||+|..
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg-~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTG-KTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS-----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhC-cccchhHHHHHHHHH
Confidence 4567899999999999999966 433200 112222222 235999999999998
No 9
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=85.27 E-value=2.3 Score=43.53 Aligned_cols=52 Identities=27% Similarity=0.500 Sum_probs=34.8
Q ss_pred CCccccChHHHHHHHHHHHHh---CCCC----------CChHHHHHhhCC---CCCCHHHHHHHhhhh
Q 020690 113 RPRLVWTPQLHKRFVDAVAHL---GIKN----------AVPKTIMQLMSV---DGLTRENVASHLQKY 164 (322)
Q Consensus 113 KpRl~WT~ELH~rFVeAV~qL---G~dk----------AtPK~ILelM~V---~GLTrenVkSHLQKY 164 (322)
-.--+|+++.-+.|.||+..+ |..| ..=.-|-..++. +--||.||.||.|..
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVl 141 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVL 141 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHH
Confidence 345689999999999999966 4211 111223333333 346999999999974
No 10
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=80.68 E-value=4.1 Score=29.19 Aligned_cols=41 Identities=17% Similarity=0.298 Sum_probs=33.5
Q ss_pred cChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhh
Q 020690 118 WTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQK 163 (322)
Q Consensus 118 WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQK 163 (322)
||+|--.+.+++|...|.+ ++.|-+.|+ .-|..+|+.+..+
T Consensus 1 WT~eEd~~L~~~~~~~g~~---W~~Ia~~l~--~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGND---WKKIAEHLG--NRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS----HHHHHHHST--TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcC---HHHHHHHHC--cCCHHHHHHHHHH
Confidence 9999999999999999964 999999996 4688999877666
No 11
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=70.53 E-value=8.4 Score=39.80 Aligned_cols=52 Identities=19% Similarity=0.230 Sum_probs=45.3
Q ss_pred CCCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhh
Q 020690 112 KRPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLY 167 (322)
Q Consensus 112 kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~ 167 (322)
..-...||-+--..+++|++.+|+.+ |..|-+.||.. |.++++.|--|+...
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GN--W~dIA~hIGtK--tkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGN--WQDIADHIGTK--TKEECKEHYLKHFVN 120 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCc--HHHHHHHHccc--chHHHHHHHHHHHhc
Confidence 34567899999999999999999876 99999999955 999999998887653
No 12
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=63.22 E-value=24 Score=30.08 Aligned_cols=49 Identities=12% Similarity=0.144 Sum_probs=35.6
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.++++.+.++++.|.. +.-+.+.|-+.||+ |...|++++++-|.+|++.
T Consensus 126 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 126 DEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQC---PVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred HHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 3556778888888862 33446666666655 6889999999999888763
No 13
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=57.38 E-value=38 Score=27.98 Aligned_cols=47 Identities=17% Similarity=0.228 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 123 HKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 123 H~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
...+++++..|.. +.-+.+.|-+.||+ |...|++||.+=|.+|++..
T Consensus 103 ~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgi---s~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 103 IASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGL---SLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHhhc
Confidence 3567788888873 34556666666655 68889999999999998754
No 14
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=56.64 E-value=34 Score=29.49 Aligned_cols=54 Identities=15% Similarity=0.178 Sum_probs=39.5
Q ss_pred ChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcCCC
Q 020690 119 TPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQGLS 175 (322)
Q Consensus 119 T~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ls 175 (322)
+.++.+.+.+++.+|.. +.-+.+.|-+.||+ +..+|+++|.+=|.+|++.-..|
T Consensus 129 ~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgi---s~~tVk~~l~ra~~~Lr~~l~~~ 193 (194)
T PRK09646 129 ARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAV---PLGTVKTRMRDGLIRLRDCLGVS 193 (194)
T ss_pred HHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCC---ChHhHHHHHHHHHHHHHHHhccC
Confidence 34666778889988872 34556666666655 78999999999999888766543
No 15
>PLN03212 Transcription repressor MYB5; Provisional
Probab=55.61 E-value=26 Score=33.96 Aligned_cols=34 Identities=15% Similarity=0.127 Sum_probs=27.9
Q ss_pred CCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhC
Q 020690 113 RPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMS 148 (322)
Q Consensus 113 KpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~ 148 (322)
-.|-.||+|.-++-+++|+.+|.. .++.|.+.|+
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~--nW~~IAk~~g 56 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEG--RWRSLPKRAG 56 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcc--cHHHHHHhhh
Confidence 446789999999999999999953 3888877775
No 16
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=54.94 E-value=9.5 Score=37.70 Aligned_cols=59 Identities=22% Similarity=0.313 Sum_probs=42.5
Q ss_pred CcCCCCCccccCh----HHHHHHHHHHHHhCCCC-CChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 108 ARTLKRPRLVWTP----QLHKRFVDAVAHLGIKN-AVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 108 ~~~~kKpRl~WT~----ELH~rFVeAV~qLG~dk-AtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
.+..||+|+-.|. ||-+||-.-=..=+.++ ..=+.| .||-.|||.=-|..|-+.||.+-
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~L-------rLT~TQVKIWFQNrRYK~KR~~~ 213 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSL-------RLTPTQVKIWFQNRRYKTKRQQK 213 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhc-------CCCchheeeeeecchhhhhhhhh
Confidence 3567899999986 89999966543334331 111222 68999999999999999998765
No 17
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=53.44 E-value=58 Score=22.42 Aligned_cols=56 Identities=25% Similarity=0.220 Sum_probs=40.3
Q ss_pred CCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 113 RPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 113 KpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
+.|..++.+- ...++++.... ...+...|.++...-|||..+|..-.+.-|...++
T Consensus 2 ~~r~~~~~~~-~~~Le~~f~~~-~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQ-LEELEKEFEKN-PYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHH-HHHHHHHHHhC-CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4556666665 44555555443 35567788888888899999999998888877665
No 18
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=53.22 E-value=49 Score=29.91 Aligned_cols=50 Identities=18% Similarity=0.189 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
.|..+.+.++++.|.. +.-+-+.|-+.|| ++...|++||.+=|.+|++.-
T Consensus 122 ~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~Lg---iS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 122 AEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIAD---VPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred HHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHH
Confidence 3455678888888873 3445566666664 589999999999999998654
No 19
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=53.14 E-value=43 Score=27.52 Aligned_cols=49 Identities=12% Similarity=0.109 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
++-..+..++++|.. +.-+.+.|-+.|| ++...|++||.+-|..|++.-
T Consensus 95 e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 95 EQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEK---IEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHH
Confidence 444556777777762 3455666666665 478999999999999988653
No 20
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=52.84 E-value=44 Score=27.23 Aligned_cols=50 Identities=12% Similarity=0.155 Sum_probs=36.4
Q ss_pred cChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 118 WTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 118 WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
+..+++..+.++++.|.. +.-+.+.|-+.||+ |...|++++.+=|..|+.
T Consensus 97 ~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~i---s~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 97 RSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGR---TVNAVYKALSRLRVRLRD 157 (159)
T ss_pred hHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCC---CHHHHHHHHHHHHHHHHh
Confidence 345667788888888872 34556666666654 788999999988888875
No 21
>PLN03091 hypothetical protein; Provisional
Probab=52.52 E-value=34 Score=35.79 Aligned_cols=36 Identities=11% Similarity=0.301 Sum_probs=29.2
Q ss_pred CCCCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhC
Q 020690 111 LKRPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMS 148 (322)
Q Consensus 111 ~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~ 148 (322)
.+..|-+||+|.-++.+++|+++|.. .++.|-+.|+
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~--nWs~IAk~~g 45 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHG--CWSSVPKQAG 45 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcC--CHHHHhhhhc
Confidence 34566789999999999999999953 4888877775
No 22
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=51.66 E-value=38 Score=29.28 Aligned_cols=47 Identities=13% Similarity=0.110 Sum_probs=33.6
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 124 KRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 124 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
..+.+++++|.. +.-+-+.|-+.|++ |...|+++|.+=|..|++...
T Consensus 103 ~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgi---s~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 103 EEFRAALDKLPQDQREALILVGASGFSYEDAAAICGC---AVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred HHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHH
Confidence 346677777762 34456666666654 688899999999999987655
No 23
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=50.32 E-value=51 Score=27.11 Aligned_cols=50 Identities=14% Similarity=0.212 Sum_probs=36.1
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
.+......+++++|-. +.-+.+.|-+.||+ +...|++||.+=|..|++.-
T Consensus 98 ~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgi---s~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 98 VALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGI---SVGTVKSRLSRALARLRELL 158 (162)
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCC---CHHHHHHHHHHHHHHHHHHh
Confidence 3455566667766652 34557777777765 69999999999999998754
No 24
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=50.09 E-value=49 Score=28.56 Aligned_cols=49 Identities=20% Similarity=0.227 Sum_probs=35.0
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.++...+..++++|.. +.-+-+.|-+.|| +|...|++||.+=|..|++.
T Consensus 122 ~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lg---is~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 122 EEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECD---ISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHH
Confidence 3556677888888873 2344555555554 47899999999999888864
No 25
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=49.89 E-value=39 Score=21.75 Aligned_cols=31 Identities=16% Similarity=0.303 Sum_probs=23.6
Q ss_pred CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhh
Q 020690 136 KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLK 169 (322)
Q Consensus 136 dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lk 169 (322)
+.-+.+.|-+.||+ +...|++++++.+.+++
T Consensus 25 ~~~~~~~ia~~~~~---s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 25 EGLSYEEIAEILGI---SRSTVRQRLHRALKKLR 55 (55)
T ss_pred cCCCHHHHHHHHCc---CHHHHHHHHHHHHHHcC
Confidence 34568888888874 78889999888877654
No 26
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=49.06 E-value=53 Score=23.01 Aligned_cols=57 Identities=23% Similarity=0.173 Sum_probs=38.8
Q ss_pred CCCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 112 KRPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 112 kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
||.|..+|.+-.....+.++ .. ...+...|.++...-|||..+|..=-|.-|...||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~-~~-~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQ-EN-PYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHH-HS-SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHH-Hh-ccccccccccccccccccccccccCHHHhHHHhCc
Confidence 46788888765555444444 44 23445566666665689999999988888877664
No 27
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=48.70 E-value=61 Score=27.71 Aligned_cols=52 Identities=10% Similarity=0.037 Sum_probs=39.6
Q ss_pred ccChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 117 VWTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 117 ~WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.+..++.....+++++|.. +.-+.+.|-+.||+ |...|+++|.+=|..|++.
T Consensus 119 ~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgi---s~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 119 APKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHM---GLSATKMRYKRALDKLREK 181 (188)
T ss_pred cccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 3566788888999999972 24556777777765 6799999999988888764
No 28
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=48.63 E-value=62 Score=25.86 Aligned_cols=48 Identities=19% Similarity=0.223 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
.++...+.+++..|.. +.-+.+.|-+.||+ |...|++++.+-|.+|++
T Consensus 101 ~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgi---s~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 101 KELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGI---SVKTVEYHISKALKELRK 159 (161)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHh
Confidence 4566667777776652 34556667666654 899999999998888875
No 29
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=48.60 E-value=55 Score=28.31 Aligned_cols=57 Identities=18% Similarity=0.215 Sum_probs=39.6
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcCCCCCCC
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQGLSGGGG 179 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ls~~g~ 179 (322)
.++.....+++..|-. +.-+.+.|-+.||+ |...|+++|.+=|..|++.-.....|+
T Consensus 122 ~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~---s~~tV~~rl~rar~~Lr~~l~~~~~~~ 189 (192)
T PRK09643 122 VETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGV---AEGTVKSRCARGRARLAELLGYLRAGG 189 (192)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3455556666666651 34567777777765 789999999998888887766554444
No 30
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=47.99 E-value=59 Score=26.58 Aligned_cols=48 Identities=19% Similarity=0.252 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
++-..+.++++.|.. +.-+.+.|-+.||+ |...|++++.+-|.++++.
T Consensus 114 e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgi---s~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 114 DDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGV---PVGTVKSRLRRARQLLREC 172 (179)
T ss_pred HHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 344556666666652 34456666666654 7889999999998888764
No 31
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=47.97 E-value=47 Score=27.85 Aligned_cols=52 Identities=8% Similarity=0.071 Sum_probs=37.9
Q ss_pred ccChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 117 VWTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 117 ~WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.|..+.-+....++++|.. +.-+-+.|-+.||+ +...|++||.+-|..|++.
T Consensus 104 ~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgi---s~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 104 FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNI---PIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCC---CHHHHHHHHHHHHHHHHHH
Confidence 5666666677777877762 34556667677765 6999999999999888764
No 32
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=46.88 E-value=67 Score=25.97 Aligned_cols=47 Identities=23% Similarity=0.286 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
....+.+++++|.. +.-+-+.|-+.||+ |...|+++|.+-|.+|++.
T Consensus 95 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgi---s~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 95 EQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNL---SLAKVKSNLFRARKELKKL 152 (154)
T ss_pred HHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 44567888888872 23456666666655 6888999999999988864
No 33
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=46.85 E-value=69 Score=25.99 Aligned_cols=48 Identities=10% Similarity=-0.016 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
++.....+++.+|.. +.-+-+.|-+.|| ++...|++++.+=+.+|++.
T Consensus 95 ~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~---is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 95 DVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETE---MTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHhhc
Confidence 445667777777762 4455666666664 47888999999988888753
No 34
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=46.31 E-value=69 Score=26.25 Aligned_cols=48 Identities=21% Similarity=0.232 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
+....+.+++..|.. +.-+.+.|-+.||+ +...|++++.+=+.+|++.
T Consensus 117 ~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi---s~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 117 ELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGC---PIGTVRSRIFRAREALRAK 175 (182)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 355667777777762 45567777777765 7888999988877777753
No 35
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=45.92 E-value=69 Score=27.27 Aligned_cols=32 Identities=13% Similarity=0.175 Sum_probs=24.9
Q ss_pred CCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 137 NAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 137 kAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.-+-+.|-+.||+ |...|+++|++-|.+|++.
T Consensus 157 g~s~~EIA~~lgi---s~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRLGI---PLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHhCC---CHHHHHHHHHHHHHHHHHH
Confidence 4556666666655 7899999999999999864
No 36
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=44.70 E-value=56 Score=30.25 Aligned_cols=49 Identities=22% Similarity=0.245 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhCCC-----------CCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 122 LHKRFVDAVAHLGIK-----------NAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 122 LH~rFVeAV~qLG~d-----------kAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
+...+.+++++|..+ .-+-+.|-+.|| ++...|++||++=|.+|++...
T Consensus 132 ~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lg---is~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 132 VRLAFVAAIQYLPPRQRAVLLLRDVLGWRAAETAELLG---TSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HHHHHHHHHHhCCHHHhhHhhhHHHhCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHhcc
Confidence 556788888888732 334555555554 4788999999999999987543
No 37
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=44.70 E-value=64 Score=27.19 Aligned_cols=45 Identities=16% Similarity=0.197 Sum_probs=34.5
Q ss_pred HHHHHHHHHhC-----------CCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 124 KRFVDAVAHLG-----------IKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 124 ~rFVeAV~qLG-----------~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
....+++..|. .+.-+.+.|-+.||+ |..+|+++|++-|.+|++.
T Consensus 127 ~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi---s~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 127 TRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGL---PLGTLKTRARRALSRLKEV 182 (186)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHH
Confidence 44567777776 245668888888866 6899999999999999864
No 38
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=43.94 E-value=65 Score=27.07 Aligned_cols=33 Identities=15% Similarity=0.172 Sum_probs=25.8
Q ss_pred CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 136 KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 136 dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
+.-+.+.|-+.||+ |...|+++|++-|..|++.
T Consensus 144 ~g~s~~eIA~~lgi---s~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 144 EGLSYKELAERHDV---PLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred cCCCHHHHHHHHCC---ChHHHHHHHHHHHHHHHHH
Confidence 34557777777765 7889999999999999864
No 39
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=43.33 E-value=71 Score=27.62 Aligned_cols=49 Identities=20% Similarity=0.214 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
+....+.+++.+|.. +.-+-+.|-+.|| +|...|+++|.+=|..|++.-
T Consensus 120 e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 120 EFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELE---ISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHHHH
Confidence 344556667777752 3344555555554 589999999999999988654
No 40
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=43.21 E-value=66 Score=27.28 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
+....+.+++..|.. +.-+.+.|-+.||+ +...|++||.+-|.+|++.
T Consensus 106 ~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgi---s~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 106 ESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQI---PIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 344556677777762 34567777777765 5788999999999988764
No 41
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=43.14 E-value=9 Score=36.35 Aligned_cols=55 Identities=15% Similarity=0.098 Sum_probs=42.2
Q ss_pred CCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 113 RPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 113 KpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
...-+||++.|.+|.++|... +..+.+|.+..+.. +..++.+|-|+|...+.+..
T Consensus 51 ~~~~~~t~~~~~~~~~~l~~~---~~~~~~~~~~~~~~--~~v~~~~~~~~~~p~~~~~~ 105 (335)
T KOG0724|consen 51 DDEPRRTPDSWDKFAEALPLE---KRLEDKIEEYIGLV--FDVNIRESGQKPFPKYGKSD 105 (335)
T ss_pred ccccccchhhhhHHHhcCccc---cccchhHHhhhhhH--HHHhhhhccCCCccccCccc
Confidence 344569999999888887543 55678887777664 88899999999988887753
No 42
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=42.67 E-value=73 Score=27.27 Aligned_cols=48 Identities=23% Similarity=0.224 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
......+++++|.. +.-+.+.|-+.||+ |...|+++|.+=|..|++.-
T Consensus 121 ~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 121 PDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGT---PIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 34566778888862 34556666666654 78999999999999888654
No 43
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=42.19 E-value=35 Score=25.76 Aligned_cols=58 Identities=22% Similarity=0.358 Sum_probs=36.3
Q ss_pred ccccChHHHHHHHHHHHH------h---C-CCC-CChHHHHHhhCCCCC--CHHHHHHHhhhhHhhhhhhc
Q 020690 115 RLVWTPQLHKRFVDAVAH------L---G-IKN-AVPKTIMQLMSVDGL--TRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 115 Rl~WT~ELH~rFVeAV~q------L---G-~dk-AtPK~ILelM~V~GL--TrenVkSHLQKYRl~lkr~~ 172 (322)
|-.||.+.-..|++++.. + + ..+ .+.+.|.+.|+.-|. |-.|++...-.-+...++..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k 71 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIK 71 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 557999999999999887 2 1 122 368888888876665 88888877655444444443
No 44
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=41.96 E-value=85 Score=26.71 Aligned_cols=49 Identities=27% Similarity=0.321 Sum_probs=36.5
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.+...+...++.+|.. +.-+.+.|-+.||+ +...|++||.+-|.+|++.
T Consensus 115 ~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~i---s~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 115 NAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGV---NENTVKTRLKKAKELLKKG 174 (179)
T ss_pred HHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 4556667778888872 34556777777765 7899999999999998864
No 45
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=41.29 E-value=95 Score=25.46 Aligned_cols=48 Identities=15% Similarity=0.122 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
+....+.+++++|.. +.-+-+.|-+.||+ +...|+++|.+=|..||+.
T Consensus 111 ~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~i---s~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 111 EANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGK---TEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHh
Confidence 344567788888873 23445555555544 5777888888888887763
No 46
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=40.81 E-value=76 Score=26.55 Aligned_cols=51 Identities=14% Similarity=0.259 Sum_probs=35.4
Q ss_pred cChHHHHHHHHHHHHhC-----------CCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 118 WTPQLHKRFVDAVAHLG-----------IKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 118 WT~ELH~rFVeAV~qLG-----------~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
+..++.....+++.+|. .+.-+.+.|-+.||+ |..+|+++|++-|.+|++.
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 122 ISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEILDL---PVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 33444455566677765 245667777777766 7899999999988888754
No 47
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=40.37 E-value=83 Score=21.85 Aligned_cols=30 Identities=17% Similarity=0.300 Sum_probs=18.8
Q ss_pred CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhh
Q 020690 136 KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYL 168 (322)
Q Consensus 136 dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~l 168 (322)
+.-+.+.|-+.|| +|...|+++|++=|.+|
T Consensus 25 ~g~s~~eIa~~l~---~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 25 QGMSYAEIAEILG---ISESTVKRRLRRARKKL 54 (54)
T ss_dssp S---HHHHHHHCT---S-HHHHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHC---cCHHHHHHHHHHHHhhC
Confidence 3445777777775 47888888888766543
No 48
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=39.63 E-value=83 Score=25.65 Aligned_cols=50 Identities=14% Similarity=0.151 Sum_probs=36.1
Q ss_pred ChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 119 TPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 119 T~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
..++...+..++++|-. +.-+-+.|-+.|| ++...|+++|.+=|..|++.
T Consensus 93 ~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 93 RAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMG---CSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHH
Confidence 44667778888888862 3445566666665 47889999999988888764
No 49
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=39.47 E-value=53 Score=32.77 Aligned_cols=59 Identities=24% Similarity=0.292 Sum_probs=36.5
Q ss_pred CCCcCCCCCccccCh----HHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 106 EPARTLKRPRLVWTP----QLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 106 ~~~~~~kKpRl~WT~----ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
.+.||.-|-|+|.|+ ||-+.|-.- .. .|-.+--||--.=|||..|||.-.|.-|.+=+|
T Consensus 194 ~KtRTkDKYRvVYTDhQRLELEKEfh~S-ry-----ITirRKSELA~~LgLsERQVKIWFQNRRAKERK 256 (317)
T KOG0848|consen 194 VKTRTKDKYRVVYTDHQRLELEKEFHTS-RY-----ITIRRKSELAATLGLSERQVKIWFQNRRAKERK 256 (317)
T ss_pred ceeecccceeEEecchhhhhhhhhhccc-cc-----eeeehhHHHHHhhCccHhhhhHhhhhhhHHHHH
Confidence 355778899999997 444444211 01 122222344444589999999999987765443
No 50
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.52 E-value=91 Score=26.60 Aligned_cols=50 Identities=10% Similarity=0.139 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
++...+.+++..|.. +.-+.+.|-+.||+ |...|+++|.+=|..|++...
T Consensus 120 ~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgi---s~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 120 DTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGI---PESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHHH
Confidence 445667777777762 35566777777765 789999999999888886543
No 51
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=38.41 E-value=83 Score=27.94 Aligned_cols=49 Identities=20% Similarity=0.228 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
++...+..++.+|.. +.-+-+.|-+.|| +|...|++||++=|..|++.-
T Consensus 137 e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lg---is~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 137 QFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVD---LSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHH
Confidence 344567778888862 3344566666665 488999999999999888753
No 52
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=37.92 E-value=97 Score=27.07 Aligned_cols=45 Identities=18% Similarity=0.173 Sum_probs=32.7
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 124 KRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 124 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
..+.+++.+|.. +.-+-+.|-+.||+ +...|+++|.+=|..|++.
T Consensus 131 ~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgi---s~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 131 TLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTL---TANHCSVLLYRARTRLRTC 186 (201)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHH
Confidence 456678888762 34556666666654 7899999999998888764
No 53
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=37.68 E-value=1e+02 Score=26.38 Aligned_cols=49 Identities=18% Similarity=0.172 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
++...+.+++.+|-. +.-+-+.|-+.|| ++...|+++|.+=|..|++.-
T Consensus 120 ~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 120 EFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQ---ITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHH
Confidence 334556677777762 3344556666664 478899999999888887653
No 54
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.25 E-value=1e+02 Score=26.77 Aligned_cols=47 Identities=13% Similarity=0.160 Sum_probs=33.7
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 124 KRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 124 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
..+..++++|.. +.-+-+.|-+.||+ +...|++||.+=|..|++.-.
T Consensus 108 ~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgi---s~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 108 QDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGC---AVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHH
Confidence 457788888862 34445566666654 688999999999999986543
No 55
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=36.79 E-value=1.1e+02 Score=25.90 Aligned_cols=51 Identities=16% Similarity=0.179 Sum_probs=35.1
Q ss_pred ChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 119 TPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 119 T~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
..++...+.++++.|.. +.-+.+.|-+.||+ |...|+++|++=|..|++.-
T Consensus 87 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 87 VKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGL---SLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 34455566777777752 34456666666654 68899999999888887654
No 56
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=36.70 E-value=1.1e+02 Score=25.51 Aligned_cols=51 Identities=14% Similarity=0.208 Sum_probs=35.3
Q ss_pred ChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 119 TPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 119 T~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
..++...+..++..|.. +.-+-+.|-+.||+ +...|+++|++-|.+|++.-
T Consensus 95 ~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 95 AKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDL---KLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 34566777788888873 23445555555544 77889999999999988653
No 57
>cd08783 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins
Probab=36.69 E-value=65 Score=27.45 Aligned_cols=47 Identities=17% Similarity=0.282 Sum_probs=40.1
Q ss_pred CccccCh-HHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhh
Q 020690 114 PRLVWTP-QLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQK 163 (322)
Q Consensus 114 pRl~WT~-ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQK 163 (322)
.|++-++ |++++-+..+..-|-- -|.+|+.|++.|-|..+.-.-||+
T Consensus 36 ~~fr~S~~el~~cslkvl~p~gSP---sk~LL~~~~~rg~Tv~~Ll~~L~~ 83 (97)
T cd08783 36 GRFRLSCLDLEQCSLKVLEPEGSP---SRSLLKLLGERGCTVTELSEFLQA 83 (97)
T ss_pred CccccCHHHHHHHHHHHhcCCCCc---hHHHHHHHHHcCCcHHHHHHHHHH
Confidence 4788887 8999999888877743 578899999999999999998887
No 58
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=36.66 E-value=89 Score=27.99 Aligned_cols=54 Identities=15% Similarity=0.162 Sum_probs=39.5
Q ss_pred cccChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 116 LVWTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 116 l~WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
..+..++.+..-+++..|.. +.-+.+.|-+.||+ |...|+++|.+-|.+|++..
T Consensus 133 ~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgi---s~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 133 AAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGL---PEETVKTRLHRARRLLRESL 197 (231)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHH
Confidence 34556666777888888872 34556677777765 68999999999999988764
No 59
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=36.32 E-value=13 Score=33.86 Aligned_cols=57 Identities=21% Similarity=0.255 Sum_probs=41.5
Q ss_pred CCCCcCCCCCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHh
Q 020690 105 DEPARTLKRPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRL 166 (322)
Q Consensus 105 ~~~~~~~kKpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl 166 (322)
+.-.+|.....|||...+-+++.++|+.---.+-.++.. ...||+++|-+-||.|..
T Consensus 38 ~~L~RTsAACGFRWNs~VRkqY~~~i~~AKkqRk~~~~~-----~~~ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 38 RALNRTAAACGFRWNAYVRKQYEEAIELAKKQRKELKRE-----AGSLTLQDVISFLQNLKT 94 (161)
T ss_pred HHHcccHHHhcchHHHHHHHHHHHHHHHHHHHHhccccC-----cccCCHHHHHHHHHHHHh
Confidence 344567778999999999999999998654211111111 256999999999999975
No 60
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=35.70 E-value=87 Score=28.97 Aligned_cols=51 Identities=18% Similarity=0.208 Sum_probs=36.2
Q ss_pred cChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 118 WTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 118 WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
|..++.....+++.+|-. +.-+-+.|-+.||+ +...|++||.+=|..|++.
T Consensus 147 ~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgi---s~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 147 YRQDFRQALREALAALSERERHLLRLHFVDGLSMDRIGAMYQV---HRSTVSRWVAQARERLLER 208 (244)
T ss_pred hHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHH
Confidence 445566777888888872 34556666666655 7888999999988877643
No 61
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=35.59 E-value=94 Score=29.20 Aligned_cols=46 Identities=26% Similarity=0.299 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
+...+..++++|.. +.-+-+.|-+.||+ +...|+++|.+=|.+|++
T Consensus 143 ~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 143 VRLAFVAALQHLPPRQRAVLILRDVLGWSAAEVAELLDT---SVAAVNSALQRARATLAE 199 (339)
T ss_pred HHHHHHHHHHhCCHHHhhhhhhHHhhCCCHHHHHHHhCC---CHHHHHHHHHHHHHHHhh
Confidence 44567888888872 23455666666654 788999999999999986
No 62
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=35.41 E-value=51 Score=24.37 Aligned_cols=28 Identities=21% Similarity=0.414 Sum_probs=22.8
Q ss_pred ChHHHHHhhC---CCCCCHHHHHHHhhhhHh
Q 020690 139 VPKTIMQLMS---VDGLTRENVASHLQKYRL 166 (322)
Q Consensus 139 tPK~ILelM~---V~GLTrenVkSHLQKYRl 166 (322)
+...|++.++ ..|||.++|+..+++|=.
T Consensus 5 ~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G~ 35 (69)
T PF00690_consen 5 SVEEVLKRLNTSSSQGLSSEEVEERRKKYGP 35 (69)
T ss_dssp SHHHHHHHHTTBTSSBBTHHHHHHHHHHHSS
T ss_pred CHHHHHHHHCcCCCCCCCHHHHHHHHHhccc
Confidence 3567888887 479999999999999943
No 63
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=35.32 E-value=1.1e+02 Score=25.91 Aligned_cols=48 Identities=10% Similarity=0.054 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
++...+.++++.|.. +.-+.+.|-+.||+ +...|+++|..=|.+|++.
T Consensus 118 ~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~i---s~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 118 EARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGL---SESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 556667788887762 34566777777765 7888999998888888763
No 64
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=35.28 E-value=55 Score=33.51 Aligned_cols=47 Identities=19% Similarity=0.309 Sum_probs=40.9
Q ss_pred cccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHh
Q 020690 116 LVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRL 166 (322)
Q Consensus 116 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl 166 (322)
--|+.+.--.|+++++-||+.+ |..|.+.+|.. +.+.||||-=||-+
T Consensus 64 e~WgadEEllli~~~~TlGlGN--W~dIadyiGsr--~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGN--WEDIADYIGSR--AKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCc--HHHHHHHHhhh--hhHHHHHHHHHHHh
Confidence 4599999999999999999765 99999999954 89999999888655
No 65
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=35.14 E-value=1.3e+02 Score=25.68 Aligned_cols=49 Identities=20% Similarity=0.203 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
++-..+.+++..|.. +.-+.+.|-+.|| ++...|+++|.+-|..|++.-
T Consensus 128 ~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 128 RDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTG---VPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred HHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHH
Confidence 344567777777762 4566778888886 478999999999888888643
No 66
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=34.93 E-value=1.1e+02 Score=26.84 Aligned_cols=49 Identities=18% Similarity=0.169 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
+++..+.+++..|.. +.-+-+.|-+.||+ |...|+++|.+=+.+|++..
T Consensus 142 ~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgi---s~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 142 LMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNV---PLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 345678888888872 34556666666665 68889999999888888764
No 67
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=34.84 E-value=99 Score=28.70 Aligned_cols=51 Identities=10% Similarity=0.042 Sum_probs=37.6
Q ss_pred ChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 119 TPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 119 T~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
..++...+..++++|.. +.-+-+.|-+.|| +|...|+++|++=|..|++..
T Consensus 102 ~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg---~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 102 AEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLG---RSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHhhC
Confidence 44556678888888873 3445666666664 588999999999999998753
No 68
>PLN03091 hypothetical protein; Provisional
Probab=34.80 E-value=1.1e+02 Score=32.28 Aligned_cols=42 Identities=17% Similarity=0.182 Sum_probs=35.9
Q ss_pred cccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhh
Q 020690 116 LVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQ 162 (322)
Q Consensus 116 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQ 162 (322)
-.||+|.-++.++.+..+|-+ +.+|-+.| +|-|-.+||.+..
T Consensus 68 gpWT~EED~lLLeL~k~~GnK---WskIAk~L--PGRTDnqIKNRWn 109 (459)
T PLN03091 68 GTFSQQEENLIIELHAVLGNR---WSQIAAQL--PGRTDNEIKNLWN 109 (459)
T ss_pred CCCCHHHHHHHHHHHHHhCcc---hHHHHHhc--CCCCHHHHHHHHH
Confidence 469999999999999999964 99999886 7889999986543
No 69
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=34.63 E-value=1.1e+02 Score=27.02 Aligned_cols=49 Identities=18% Similarity=0.176 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
++-..+.+++++|-. +.-+-+.|-+.||+ +...|+++|.+=|.+|++.-
T Consensus 127 ~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgi---s~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 127 RLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGV---KLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 344556677777762 33445666666655 67899999999999998654
No 70
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=34.46 E-value=1.3e+02 Score=25.56 Aligned_cols=50 Identities=20% Similarity=0.169 Sum_probs=34.4
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
.+.-.....+++.|.. +.-+.+.|-+.| |+|...|+++|.+=|..|++..
T Consensus 116 ~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l---gis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 116 RQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVM---DISVDALESLLARGRRALRAQL 176 (186)
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHh---CcCHHHHHHHHHHHHHHHHHHH
Confidence 3445567777777762 234455555555 4588999999999999988654
No 71
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=33.82 E-value=1.2e+02 Score=27.73 Aligned_cols=48 Identities=25% Similarity=0.251 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
+-....+++++|.. +.-+.+.|-+.||+ +...|+++|++=|.+|++.-
T Consensus 161 ~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgi---s~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 161 LSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDT---TVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred HHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHH
Confidence 33456677777762 34556666666655 78899999999999998654
No 72
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=33.75 E-value=1.2e+02 Score=25.95 Aligned_cols=48 Identities=15% Similarity=0.181 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
+-..+.+++.+|.. +.-+-+.|-+.||+ |...|++||.+=|..|++.-
T Consensus 126 ~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 126 FQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGI---STSNYHTIMHRARESLRQCL 184 (195)
T ss_pred HHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 34456667777762 23445555555544 78889999998888887653
No 73
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=33.64 E-value=1.3e+02 Score=24.94 Aligned_cols=48 Identities=17% Similarity=0.257 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
+.....++++.|.. +.-+.+.|-+.||+ |...|+++|.+=|.+|++.-
T Consensus 110 ~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~---s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 110 YQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNI---PVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHH
Confidence 34556677888872 45567788888866 68999999999999888653
No 74
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=33.57 E-value=1.4e+02 Score=25.02 Aligned_cols=50 Identities=18% Similarity=0.166 Sum_probs=34.5
Q ss_pred ChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 119 TPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 119 T~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
..++.+.+.++++.|.. +.-+-+.|-+.|| +|..+|+++|.+-|.+|++.
T Consensus 125 ~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lg---is~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 125 SRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIARIMD---CPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred HHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHH
Confidence 34556667778888862 2344555555555 57899999998888888754
No 75
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=33.28 E-value=1.3e+02 Score=25.87 Aligned_cols=45 Identities=11% Similarity=0.014 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 123 HKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 123 H~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
.....+++.+|.. +.-+-+.|-+.||+ +...|+++|.+-|..|++
T Consensus 121 ~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgi---s~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 121 LVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGC---PVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHh
Confidence 3456677888762 34556667677765 789999999999999987
No 76
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=32.88 E-value=1.6e+02 Score=25.31 Aligned_cols=51 Identities=16% Similarity=0.216 Sum_probs=34.9
Q ss_pred ChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 119 TPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 119 T~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
..+......+++..|-. +.-+.+.|-+.|| +|..+|+++|++-|..|++..
T Consensus 118 ~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lg---is~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 118 LKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLG---LTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHcc
Confidence 34455556677777652 2344556666665 478999999999999998754
No 77
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=32.69 E-value=87 Score=26.72 Aligned_cols=51 Identities=20% Similarity=0.269 Sum_probs=38.5
Q ss_pred hHHHHHHHHHHHHhC-----------CCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 120 PQLHKRFVDAVAHLG-----------IKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG-----------~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
.+...++.+|+..|- ++.-+.+.|-+.|++ +...|+|+|..=|.++++...
T Consensus 115 ~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i---~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 115 EEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGI---SVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred HHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHh
Confidence 466677788888776 245667777777766 588899999999999887654
No 78
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=32.64 E-value=1.1e+02 Score=28.32 Aligned_cols=52 Identities=12% Similarity=0.085 Sum_probs=39.2
Q ss_pred ccChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 117 VWTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 117 ~WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
...+++...+..++++|.. +.-+.+.|-+.|| +|...|+++|++=|.+|++.
T Consensus 93 ~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg---~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 93 ELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVG---KSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHhh
Confidence 3445666778889988872 3456677777776 58899999999999999864
No 79
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=32.42 E-value=1.1e+02 Score=26.32 Aligned_cols=53 Identities=17% Similarity=0.117 Sum_probs=37.2
Q ss_pred cccChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 116 LVWTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 116 l~WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
..+..++.+....++++|.. +.-..+.|-+.||+ +...|+++|.+=|..|++.
T Consensus 120 ~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgi---s~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 120 ALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEI---GVEAVESLTARGKRALAAL 183 (196)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHH
Confidence 34555666666677777762 34556666666655 7889999999999888865
No 80
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=32.29 E-value=1.3e+02 Score=24.95 Aligned_cols=45 Identities=20% Similarity=0.201 Sum_probs=34.1
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 124 KRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 124 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
..+.+|+++|.. +.-+.+.|-+.||+ |...|+++|.+=|.+|++.
T Consensus 111 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgi---s~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 111 LDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNK---PEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred HHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 367788888872 34566777777765 8999999999999988864
No 81
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=32.10 E-value=1.5e+02 Score=24.74 Aligned_cols=46 Identities=15% Similarity=0.113 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 123 HKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 123 H~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
......++++|.. +.-+-+.|-+.| |+|...|+++|.+-|.+|++.
T Consensus 131 ~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eIA~~l---gis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 131 AVRLAQALAKLPEDYREVILLRHLEGLSFAEVAERM---DRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHHHH---CcCHHHHHHHHHHHHHHHHHH
Confidence 3445556666652 233445555555 458899999999999999864
No 82
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=31.40 E-value=1.5e+02 Score=25.22 Aligned_cols=47 Identities=13% Similarity=0.066 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
..+....++.+|.. +.-+-+.|-+.| |++...|++++.+-|.+|++.
T Consensus 129 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~l---gis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 129 SSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAV---GSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHH---CCCHHHHHHHHHHHHHHHHHH
Confidence 44455566666662 234455555556 457888999999988888865
No 83
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=31.14 E-value=1.3e+02 Score=25.91 Aligned_cols=47 Identities=13% Similarity=0.178 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 122 LHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 122 LH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
+.....+++.+|.. +.-+.+.|-+.||+ +...|+++|.+=|..|++.
T Consensus 131 ~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgi---s~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 131 LKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDI---PLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCc---CHHHHHHHHHHHHHHHHHH
Confidence 34556677777762 34566777777755 7888999999888888764
No 84
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=29.79 E-value=1.8e+02 Score=23.90 Aligned_cols=46 Identities=15% Similarity=0.188 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 123 HKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 123 H~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.+.+..++..|.. +.-+.+.|-+.||+ +...|+++|.+=+..+++.
T Consensus 100 ~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgi---s~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 100 LRHVADALSELPARTRYAFEMYRLHGETQKDIARELGV---SPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 3455666666652 33456666666655 7888999998888888764
No 85
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=29.30 E-value=1.1e+02 Score=28.91 Aligned_cols=54 Identities=9% Similarity=0.081 Sum_probs=40.1
Q ss_pred ccccChHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 115 RLVWTPQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 115 Rl~WT~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
...+..++...|..++++|.. ..-+-+.|-+.|+ +|...|+++|+.=|.+|++.
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lg---is~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIG---SQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHhh
Confidence 355677888899999999973 2344555555554 47899999999999999864
No 86
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=29.07 E-value=1.7e+02 Score=24.38 Aligned_cols=45 Identities=20% Similarity=0.138 Sum_probs=32.4
Q ss_pred HHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 125 RFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 125 rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
.+.+|+++|.. +.-+-+.|-+.||+ +...|+++|.+=|..|++.-
T Consensus 111 ~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgi---s~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 111 LVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGI---PEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHh
Confidence 46677777762 34556666666655 68889999999999988754
No 87
>PLN03212 Transcription repressor MYB5; Provisional
Probab=27.98 E-value=1.8e+02 Score=28.33 Aligned_cols=41 Identities=15% Similarity=0.021 Sum_probs=34.2
Q ss_pred cccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHh
Q 020690 116 LVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHL 161 (322)
Q Consensus 116 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHL 161 (322)
-.||.|.-+.-++++..+|-+ +..|-+.| +|-|-.+||.+.
T Consensus 79 gpWT~EED~lLlel~~~~GnK---Ws~IAk~L--pGRTDnqIKNRW 119 (249)
T PLN03212 79 GGITSDEEDLILRLHRLLGNR---WSLIAGRI--PGRTDNEIKNYW 119 (249)
T ss_pred CCCChHHHHHHHHHHHhcccc---HHHHHhhc--CCCCHHHHHHHH
Confidence 468899889999999999954 99998876 777999998764
No 88
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=27.81 E-value=1.8e+02 Score=24.74 Aligned_cols=49 Identities=8% Similarity=-0.029 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
+......+++..|-. +.-+-+.|-+.||+ +...|+++|.+=|..|++.-
T Consensus 120 e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgi---s~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 120 ESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGM---SESAVKVSVHRGLKALAALI 179 (184)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHH
Confidence 444567777777752 34456666666665 78999999999999888643
No 89
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=27.69 E-value=1.8e+02 Score=24.65 Aligned_cols=45 Identities=20% Similarity=0.258 Sum_probs=31.5
Q ss_pred HHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 125 RFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 125 rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
....++.+|.. +.-+-+.|-+.|| +|...|+++|.+=|..|++.-
T Consensus 115 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lg---is~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 115 QIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMG---ITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHH
Confidence 34556666652 3445666666665 489999999999999988653
No 90
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=26.86 E-value=2e+02 Score=22.06 Aligned_cols=30 Identities=20% Similarity=0.314 Sum_probs=21.1
Q ss_pred CChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhh
Q 020690 138 AVPKTIMQLMSVDGLTRENVASHLQKYRLYLKR 170 (322)
Q Consensus 138 AtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr 170 (322)
-+.+.|-+.||+ |...|..++++-+.++++
T Consensus 127 ~s~~eIA~~l~~---s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 127 LSYKEIAEILGI---SVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHHCC---CHHHHHHHHHHHHHHHHh
Confidence 346666666664 688888888887777764
No 91
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=25.74 E-value=1e+02 Score=26.35 Aligned_cols=47 Identities=17% Similarity=0.337 Sum_probs=35.5
Q ss_pred cccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 116 LVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 116 l~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
+-=+.|+|++....|..||..+.+--.+++-+ ++-||..|+.-+++.
T Consensus 83 vyI~~e~h~~l~~Iv~~ig~~~~si~~yidNI---------L~~Hle~~~eeI~~l 129 (136)
T PF11888_consen 83 VYISRETHERLSRIVRVIGERKMSISGYIDNI---------LRHHLEEYREEINEL 129 (136)
T ss_pred eEECHHHHHHHHHHHHHHCCCCCcHHHHHHHH---------HHHHHHHHHHHHHHH
Confidence 77788999999999999987766666553321 566999999887754
No 92
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=25.46 E-value=56 Score=22.30 Aligned_cols=18 Identities=22% Similarity=0.447 Sum_probs=11.3
Q ss_pred HhhCCCCCCHHHHHHHhhh
Q 020690 145 QLMSVDGLTRENVASHLQK 163 (322)
Q Consensus 145 elM~V~GLTrenVkSHLQK 163 (322)
+.|+ -|||.++|+..|+-
T Consensus 11 eA~~-~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 11 EAKE-SGLSKEEIREFLEF 28 (30)
T ss_dssp HHHH-TT--HHHHHHHHHH
T ss_pred HHHH-cCCCHHHHHHHHHh
Confidence 3444 49999999988863
No 93
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.21 E-value=2.4e+02 Score=23.59 Aligned_cols=45 Identities=16% Similarity=0.271 Sum_probs=30.4
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 124 KRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 124 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
....++++.|.. +.-+.+.|-+.||+ |..+|+++|.+-|.+|++.
T Consensus 128 ~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~~lgi---s~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 128 ETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDL---PVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 345556666652 34446666666655 6899999999988888764
No 94
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=25.16 E-value=2.3e+02 Score=19.38 Aligned_cols=52 Identities=19% Similarity=0.185 Sum_probs=34.1
Q ss_pred CCccccChHHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHh
Q 020690 113 RPRLVWTPQLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRL 166 (322)
Q Consensus 113 KpRl~WT~ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl 166 (322)
|.|..+|++--. .++++..-.. ..+...|.++...-|||..+|..=.+.-|.
T Consensus 2 k~r~~~~~~~~~-~L~~~f~~~~-~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 2 RKRTSFTPEQLE-ELEKEFQKNP-YPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCcCCHHHHH-HHHHHHHhCC-CCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 455667766444 4444444442 456778888888889999999876665554
No 95
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=23.45 E-value=2.2e+02 Score=26.43 Aligned_cols=49 Identities=22% Similarity=0.247 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
++++....++++|.. +.-+=+.|-+.||+ +...||++|.+=|..|++..
T Consensus 105 ~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~Lgi---S~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 105 DLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSV---SEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred HHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHH
Confidence 455666778888873 23445666666654 78889999999999998764
No 96
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=22.95 E-value=2.4e+02 Score=23.80 Aligned_cols=49 Identities=14% Similarity=0.094 Sum_probs=33.5
Q ss_pred hHHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 120 PQLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 120 ~ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.+......+|+.+|.. +.-+.+.|-+.|| +|...|+++|.+=|.+|++.
T Consensus 125 ~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lg---is~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 125 ASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTD---TPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhC---CChhHHHHHHHHHHHHHHHH
Confidence 3455666677777762 3445555655554 47888999999988888764
No 97
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.75 E-value=2.2e+02 Score=31.77 Aligned_cols=86 Identities=22% Similarity=0.406 Sum_probs=50.8
Q ss_pred Cccc-ccccCCCCCCccCCCCCCCCCCCCCCceecchhhHHHHHHHHHhcCCCccCCcccccc-cccCCCC---CCCccc
Q 020690 199 PATD-HLFASSPVPAHFLHPGARGNSDHFLPYVPVAALHQQQMAVAAAVGNPHLQGHQYHRQM-SHFGSPA---NGQFEH 273 (322)
Q Consensus 199 ~~~~-~lfa~sPvp~~~l~p~~r~~~~~~~p~vp~~~~~~~~~~~~a~~~~~~~~~~~~hr~~-~~~g~p~---~~~f~~ 273 (322)
+.+. .|.-+--||...+-+..-+..+||-+|+|-.-.-+- .||-.. --||.|+ .|.+..
T Consensus 421 ~~~~~~l~r~~nv~~~s~prgs~~~~~H~s~~~pr~r~r~~----------------~yqm~~P~~~~~pP~Vpsg~~~p 484 (861)
T KOG3161|consen 421 APCVPRLVRSNNVPESSLPRGSMPYADHYSTFSPRDRMRSS----------------PYQMPPPQPYGPPPPVPSGMYAP 484 (861)
T ss_pred cCcchhhhhccCCCcccCCCCCCCcccccCccCcccchhcC----------------CCCCCCCCcCCCCCCCCccccCC
Confidence 3444 345555677777777777889999999987643322 222111 1144443 466666
Q ss_pred chhhhhc-CcccccccC-------CccccCCCCch
Q 020690 274 HLFARQA-QPQQVHRMG-------APVHSTVPSSY 300 (322)
Q Consensus 274 ~~~~r~~-~~~~~~r~~-------~~~~~~~~~~~ 300 (322)
++=.|.. -|+|.+||- .||-+|-++-|
T Consensus 485 p~~~~~~~~PP~~q~~~~~~~~~mPpm~~M~~~~y 519 (861)
T KOG3161|consen 485 PYDSRRIWRPPMYQRDDIIRSNSMPPMDVMHSSVY 519 (861)
T ss_pred CcccccCCCCCCCCcccchhccCCCCcccccccee
Confidence 6666655 456677764 45666666666
No 98
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.51 E-value=2.8e+02 Score=24.90 Aligned_cols=48 Identities=19% Similarity=0.207 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHhC-----------CCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 121 QLHKRFVDAVAHLG-----------IKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 121 ELH~rFVeAV~qLG-----------~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
++...+..+++.|- .+.-+-+.|-+.||+ |...|+.++.+=+..|++.
T Consensus 173 ~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgi---s~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 173 ELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGV---SESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHhHhccCCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 45566777777775 234556666666654 7888888888887777753
No 99
>PRK04217 hypothetical protein; Provisional
Probab=22.38 E-value=1.4e+02 Score=25.28 Aligned_cols=42 Identities=19% Similarity=0.182 Sum_probs=31.9
Q ss_pred HHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 128 DAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 128 eAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
+++..+..+..+-+.|-+.|++ +...|+++|+.-+..|+..-
T Consensus 49 eai~l~~~eGlS~~EIAk~LGI---S~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 49 EALRLVDYEGLTQEEAGKRMGV---SRGTVWRALTSARKKVAQML 90 (110)
T ss_pred HHHHHHHHcCCCHHHHHHHHCc---CHHHHHHHHHHHHHHHHHHH
Confidence 5555555556678888888866 78899999999888887654
No 100
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=22.03 E-value=88 Score=30.44 Aligned_cols=60 Identities=27% Similarity=0.532 Sum_probs=43.2
Q ss_pred CcCCCCCccccCh----HHHHHHHHHHHHhCCCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 108 ARTLKRPRLVWTP----QLHKRFVDAVAHLGIKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 108 ~~~~kKpRl~WT~----ELH~rFVeAV~qLG~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
.+..+|+|-..+. .|.+||-.. ..| |.|.+- ||--+=|||..|||.-.|.-|.++||+..
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkT-QYL----ALPERA-eLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQT-QYL----ALPERA-ELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhc-chh----cCcHHH-HHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3456788888875 677888553 222 344432 33334599999999999999999999887
No 101
>PF14075 UBN_AB: Ubinuclein conserved middle domain
Probab=21.82 E-value=1.5e+02 Score=27.82 Aligned_cols=22 Identities=18% Similarity=0.440 Sum_probs=18.9
Q ss_pred CCCCCccccChHHHHHHHHHHH
Q 020690 110 TLKRPRLVWTPQLHKRFVDAVA 131 (322)
Q Consensus 110 ~~kKpRl~WT~ELH~rFVeAV~ 131 (322)
...|.|+.||+++-..+.+.|.
T Consensus 147 ~~PrKkF~Wtde~R~lL~~lv~ 168 (214)
T PF14075_consen 147 KGPRKKFQWTDEIRELLCELVK 168 (214)
T ss_pred CCCCcCCCCCHHHHHHHHHHHH
Confidence 4567899999999999988876
No 102
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.74 E-value=2.7e+02 Score=22.82 Aligned_cols=32 Identities=13% Similarity=0.280 Sum_probs=23.7
Q ss_pred CCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 137 NAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 137 kAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
.-+.+.|-+.||+ |...|++++.+-|.+|++.
T Consensus 127 g~s~~eIA~~lgi---s~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 127 GYSYKEIAEALGI---KESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CCCHHHHHHHHCC---CHHHHHHHHHHHHHHHHHH
Confidence 3446666666654 7888999999888888764
No 103
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=21.59 E-value=2.5e+02 Score=24.66 Aligned_cols=47 Identities=11% Similarity=0.024 Sum_probs=33.0
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcC
Q 020690 124 KRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQG 173 (322)
Q Consensus 124 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ 173 (322)
..+.+++++|.. +.-+-+.|-+.||+ +...|+++|.+-|..|++.-+
T Consensus 125 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgi---s~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 125 IDVRTLIDALPPERREALILTQVLGYTYEEAAKIADV---RVGTIRSRVARARADLIAATA 182 (196)
T ss_pred HHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCC---CHHHHHHHHHHHHHHHHHHhc
Confidence 357777877762 23445555555554 788999999999999987654
No 104
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=20.91 E-value=3e+02 Score=24.04 Aligned_cols=50 Identities=18% Similarity=0.149 Sum_probs=34.0
Q ss_pred HHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhcCCCC
Q 020690 124 KRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQGLSG 176 (322)
Q Consensus 124 ~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~~ls~ 176 (322)
..+.+++++|-. +.-+-+.|-+.|| +|...|++||++=|..|++.-....
T Consensus 105 ~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~Lg---iS~~tVk~~l~Rar~~Lr~~l~~~~ 165 (188)
T PRK12546 105 SDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCG---VAVGTVKSRANRARARLAELLQLEE 165 (188)
T ss_pred HHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHhccc
Confidence 345677777752 2344555555555 4788999999999999987665443
No 105
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=20.85 E-value=3.1e+02 Score=23.56 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhCC-----------CCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhhc
Q 020690 121 QLHKRFVDAVAHLGI-----------KNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRMQ 172 (322)
Q Consensus 121 ELH~rFVeAV~qLG~-----------dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~~ 172 (322)
++...+..+++.|.. +.-..+.|-+.||+ +...|+++|.+=|..|++.-
T Consensus 95 e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgi---s~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 95 ELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGL---SLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCC---CHHHHHHHHHHHHHHHHHHH
Confidence 445556666666652 33445566666654 67889999999888887653
No 106
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.76 E-value=3e+02 Score=22.84 Aligned_cols=46 Identities=15% Similarity=0.237 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhC-----------CCCCChHHHHHhhCCCCCCHHHHHHHhhhhHhhhhhh
Q 020690 123 HKRFVDAVAHLG-----------IKNAVPKTIMQLMSVDGLTRENVASHLQKYRLYLKRM 171 (322)
Q Consensus 123 H~rFVeAV~qLG-----------~dkAtPK~ILelM~V~GLTrenVkSHLQKYRl~lkr~ 171 (322)
-..+.+++..|. .+.-+++.|-+.||+ +..+|+++|.+=|..|++.
T Consensus 117 ~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~i---s~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 117 WSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNI---PEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred HHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCC---ChhHHHHHHHHHHHHHHHH
Confidence 345666777776 245668888888876 7899999999888888764
Done!