Query 005052
Match_columns 716
No_of_seqs 331 out of 1004
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 17:16:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005052.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005052hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00574 POX domain associat 100.0 6.4E-38 1.4E-42 294.7 8.7 130 281-410 2-139 (140)
2 PF07526 POX: Associated with 100.0 9.9E-38 2.2E-42 294.9 9.7 127 285-411 2-140 (140)
3 KOG0773 Transcription factor M 100.0 1.8E-32 3.9E-37 287.0 10.1 252 282-534 45-312 (342)
4 KOG0774 Transcription factor P 99.6 5.5E-15 1.2E-19 151.7 13.6 64 461-524 188-251 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 9.1E-16 2E-20 118.0 3.6 40 479-518 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.4 1.1E-12 2.4E-17 103.8 6.3 57 463-522 2-58 (59)
7 smart00389 HOX Homeodomain. DN 99.3 2.7E-12 5.9E-17 101.2 6.3 55 463-520 2-56 (56)
8 PF00046 Homeobox: Homeobox do 99.3 1.9E-12 4.2E-17 103.2 5.4 57 462-521 1-57 (57)
9 KOG0775 Transcription factor S 99.3 7.9E-12 1.7E-16 129.5 6.9 51 467-520 182-232 (304)
10 KOG0842 Transcription factor t 98.9 2.2E-09 4.7E-14 113.7 6.3 65 460-527 151-216 (307)
11 KOG0487 Transcription factor A 98.8 1.5E-09 3.3E-14 114.9 3.8 60 461-523 234-294 (308)
12 KOG0843 Transcription factor E 98.7 1.8E-08 3.8E-13 100.0 5.1 64 460-526 101-164 (197)
13 KOG0493 Transcription factor E 98.7 1.9E-08 4.1E-13 104.4 4.6 61 459-522 244-304 (342)
14 KOG0489 Transcription factor z 98.6 1.9E-08 4.2E-13 104.2 3.6 58 461-521 159-216 (261)
15 TIGR01565 homeo_ZF_HD homeobox 98.6 6.8E-08 1.5E-12 80.3 5.5 52 462-516 2-57 (58)
16 KOG0488 Transcription factor B 98.6 4.8E-08 1E-12 103.9 5.4 62 460-524 170-232 (309)
17 KOG0483 Transcription factor H 98.6 5.1E-08 1.1E-12 98.1 4.7 66 461-529 50-115 (198)
18 KOG0850 Transcription factor D 98.6 5.2E-08 1.1E-12 99.6 4.5 57 464-523 125-181 (245)
19 KOG0485 Transcription factor N 98.5 7E-08 1.5E-12 98.2 4.1 64 458-524 101-164 (268)
20 KOG0484 Transcription factor P 98.4 4.1E-07 8.9E-12 83.9 6.2 57 465-524 21-77 (125)
21 COG5576 Homeodomain-containing 98.4 3.9E-07 8.5E-12 88.8 5.0 60 460-522 50-109 (156)
22 KOG3802 Transcription factor O 98.4 3E-07 6.6E-12 100.0 4.3 59 461-522 293-352 (398)
23 KOG2251 Homeobox transcription 98.3 8E-07 1.7E-11 90.7 4.6 58 462-522 38-95 (228)
24 KOG0848 Transcription factor C 98.3 4.6E-07 1E-11 94.6 2.8 57 468-527 206-262 (317)
25 KOG0492 Transcription factor M 98.2 1.3E-06 2.7E-11 88.7 5.5 59 461-522 144-202 (246)
26 KOG0486 Transcription factor P 98.2 1E-06 2.2E-11 93.6 3.9 60 461-523 111-171 (351)
27 KOG0491 Transcription factor B 98.1 8.8E-07 1.9E-11 87.2 1.5 58 462-522 100-158 (194)
28 KOG0494 Transcription factor C 98.1 2.6E-06 5.7E-11 88.7 4.7 53 467-522 147-199 (332)
29 KOG0847 Transcription factor, 98.1 2.9E-06 6.3E-11 86.7 3.8 76 460-538 164-241 (288)
30 KOG4577 Transcription factor L 97.9 6.1E-06 1.3E-10 87.1 3.8 62 459-523 165-226 (383)
31 KOG2252 CCAAT displacement pro 97.9 5.1E-05 1.1E-09 85.7 9.7 57 460-519 419-475 (558)
32 KOG0844 Transcription factor E 97.5 3.2E-05 6.9E-10 82.3 1.1 59 463-524 183-241 (408)
33 KOG0849 Transcription factor P 97.4 0.00011 2.4E-09 79.8 4.1 58 463-523 178-235 (354)
34 KOG0773 Transcription factor M 97.4 7.3E-05 1.6E-09 79.6 1.8 60 463-523 97-156 (342)
35 KOG0490 Transcription factor, 97.3 0.00012 2.7E-09 72.2 2.6 60 460-522 59-118 (235)
36 KOG1168 Transcription factor A 97.1 0.0002 4.4E-09 76.0 1.7 59 460-521 308-366 (385)
37 PF11569 Homez: Homeodomain le 95.6 0.0085 1.8E-07 50.2 2.4 43 473-518 10-52 (56)
38 KOG0490 Transcription factor, 94.8 0.024 5.1E-07 56.1 3.3 61 460-523 152-212 (235)
39 KOG1146 Homeobox protein [Gene 87.7 0.41 8.8E-06 59.9 3.2 57 465-524 907-963 (1406)
40 PF04218 CENP-B_N: CENP-B N-te 79.5 3.2 6.9E-05 33.9 4.2 47 462-516 1-47 (53)
41 KOG3623 Homeobox transcription 68.7 6.4 0.00014 47.5 4.7 44 473-519 568-611 (1007)
42 cd06171 Sigma70_r4 Sigma70, re 68.1 5.9 0.00013 29.4 3.0 45 468-520 11-55 (55)
43 PF11285 DUF3086: Protein of u 66.6 42 0.00092 36.4 9.8 57 343-415 6-62 (283)
44 PF01527 HTH_Tnp_1: Transposas 65.3 9.2 0.0002 31.9 3.9 46 463-516 2-48 (76)
45 PF04545 Sigma70_r4: Sigma-70, 64.8 6.4 0.00014 30.9 2.7 47 467-521 4-50 (50)
46 PF08281 Sigma70_r4_2: Sigma-7 61.5 10 0.00022 30.0 3.3 45 467-519 10-54 (54)
47 cd00569 HTH_Hin_like Helix-tur 57.6 25 0.00054 23.1 4.3 38 467-512 5-42 (42)
48 TIGR02985 Sig70_bacteroi1 RNA 48.7 17 0.00036 33.3 3.0 48 467-522 113-160 (161)
49 PRK06759 RNA polymerase factor 47.4 18 0.00039 33.5 3.1 47 467-521 106-152 (154)
50 PRK09644 RNA polymerase sigma 47.4 20 0.00044 33.9 3.4 50 466-523 107-156 (165)
51 PF13443 HTH_26: Cro/C1-type H 47.1 20 0.00043 29.0 2.9 43 476-525 2-44 (63)
52 PRK09642 RNA polymerase sigma 47.0 21 0.00046 33.5 3.5 49 467-523 106-154 (160)
53 PRK12530 RNA polymerase sigma 45.3 24 0.00052 34.6 3.7 51 467-525 134-184 (189)
54 TIGR02937 sigma70-ECF RNA poly 44.9 20 0.00044 31.7 2.9 47 467-521 110-156 (158)
55 PRK00118 putative DNA-binding 44.7 20 0.00044 33.6 2.9 48 467-522 17-64 (104)
56 PRK12514 RNA polymerase sigma 42.7 33 0.00072 32.8 4.1 48 467-522 129-176 (179)
57 PRK11924 RNA polymerase sigma 41.7 27 0.00058 32.7 3.3 49 467-523 125-173 (179)
58 PRK03975 tfx putative transcri 41.3 37 0.00079 33.5 4.2 49 466-523 5-53 (141)
59 PRK09652 RNA polymerase sigma 40.8 27 0.00059 32.7 3.2 49 467-523 128-176 (182)
60 PRK12512 RNA polymerase sigma 39.6 24 0.00051 34.0 2.6 49 467-523 131-179 (184)
61 PF03791 KNOX2: KNOX2 domain ; 39.2 1.1E+02 0.0024 25.8 6.0 43 332-374 5-50 (52)
62 PF02326 YMF19: Plant ATP synt 39.1 26 0.00056 31.7 2.6 32 13-44 13-44 (86)
63 PRK09646 RNA polymerase sigma 39.1 27 0.00059 34.2 3.0 49 467-523 142-190 (194)
64 TIGR02939 RpoE_Sigma70 RNA pol 38.9 21 0.00046 34.1 2.2 49 467-523 138-186 (190)
65 PRK06811 RNA polymerase factor 38.0 30 0.00065 33.8 3.1 49 467-523 131-179 (189)
66 PRK09648 RNA polymerase sigma 37.9 30 0.00065 33.5 3.0 48 467-522 139-186 (189)
67 PRK12526 RNA polymerase sigma 37.1 30 0.00065 34.4 3.0 49 467-523 153-201 (206)
68 TIGR02989 Sig-70_gvs1 RNA poly 36.6 33 0.00072 31.9 3.0 47 467-521 111-157 (159)
69 TIGR02999 Sig-70_X6 RNA polyme 36.5 33 0.00072 32.8 3.1 48 467-522 134-181 (183)
70 PF00196 GerE: Bacterial regul 35.7 61 0.0013 26.2 4.1 49 467-524 3-51 (58)
71 PRK12519 RNA polymerase sigma 34.9 32 0.0007 33.4 2.8 49 467-523 141-189 (194)
72 smart00421 HTH_LUXR helix_turn 34.8 76 0.0017 23.9 4.3 46 467-521 3-48 (58)
73 PRK12541 RNA polymerase sigma 34.4 34 0.00073 32.2 2.7 48 466-521 111-158 (161)
74 TIGR02941 Sigma_B RNA polymera 33.5 42 0.00091 34.5 3.4 49 467-523 205-253 (255)
75 PRK12520 RNA polymerase sigma 33.4 62 0.0014 31.5 4.5 49 467-523 131-179 (191)
76 PRK05602 RNA polymerase sigma 32.9 36 0.00078 32.9 2.7 49 467-523 128-176 (186)
77 TIGR02980 SigBFG RNA polymeras 32.5 37 0.00079 34.1 2.8 49 467-523 178-226 (227)
78 TIGR02948 SigW_bacill RNA poly 32.4 38 0.00082 32.4 2.8 49 467-523 136-184 (187)
79 PRK08583 RNA polymerase sigma 32.2 51 0.0011 33.9 3.8 49 467-523 205-253 (257)
80 PRK13919 putative RNA polymera 32.1 37 0.00079 32.7 2.6 49 467-523 135-183 (186)
81 PRK12547 RNA polymerase sigma 32.1 42 0.00091 31.9 3.0 48 467-522 112-159 (164)
82 PRK12532 RNA polymerase sigma 31.9 43 0.00094 32.7 3.1 49 467-523 136-184 (195)
83 PRK15369 two component system 31.9 98 0.0021 28.4 5.3 48 466-522 148-195 (211)
84 TIGR02393 RpoD_Cterm RNA polym 31.7 56 0.0012 33.4 4.0 56 467-526 176-231 (238)
85 PRK12546 RNA polymerase sigma 30.7 40 0.00087 33.3 2.7 49 467-523 113-161 (188)
86 PRK04217 hypothetical protein; 30.7 70 0.0015 30.3 4.1 49 467-523 42-90 (110)
87 PRK12536 RNA polymerase sigma 30.6 47 0.001 32.1 3.1 49 467-523 129-177 (181)
88 PRK09047 RNA polymerase factor 30.1 56 0.0012 30.4 3.4 50 466-523 105-154 (161)
89 TIGR02983 SigE-fam_strep RNA p 30.0 51 0.0011 30.9 3.1 48 467-522 110-157 (162)
90 TIGR02954 Sig70_famx3 RNA poly 30.0 49 0.0011 31.4 3.0 49 467-523 119-167 (169)
91 PRK12515 RNA polymerase sigma 29.7 56 0.0012 31.8 3.4 48 467-522 131-178 (189)
92 PHA00542 putative Cro-like pro 29.6 1.3E+02 0.0027 26.6 5.3 35 493-527 33-67 (82)
93 PRK12537 RNA polymerase sigma 29.0 51 0.0011 31.9 3.0 48 466-521 132-179 (182)
94 PRK06986 fliA flagellar biosyn 28.5 42 0.00091 34.1 2.5 49 467-523 184-232 (236)
95 PRK12516 RNA polymerase sigma 28.2 57 0.0012 32.1 3.2 49 467-523 116-164 (187)
96 PRK12544 RNA polymerase sigma 28.1 66 0.0014 32.4 3.7 51 467-525 148-198 (206)
97 PRK12523 RNA polymerase sigma 27.7 58 0.0013 31.1 3.1 47 467-521 119-165 (172)
98 PRK12531 RNA polymerase sigma 27.5 57 0.0012 32.0 3.1 50 466-523 140-189 (194)
99 PRK09647 RNA polymerase sigma 27.3 77 0.0017 31.8 4.0 49 467-523 138-186 (203)
100 TIGR02479 FliA_WhiG RNA polyme 27.0 53 0.0011 33.1 2.8 48 467-522 175-222 (224)
101 PRK12533 RNA polymerase sigma 26.6 69 0.0015 32.7 3.6 49 467-523 134-182 (216)
102 PRK12524 RNA polymerase sigma 26.6 58 0.0013 32.0 3.0 49 467-523 136-184 (196)
103 PRK12545 RNA polymerase sigma 26.5 67 0.0015 31.9 3.4 50 467-524 139-188 (201)
104 PRK09639 RNA polymerase sigma 25.9 70 0.0015 30.0 3.3 48 467-523 112-159 (166)
105 PRK12538 RNA polymerase sigma 25.6 68 0.0015 33.1 3.4 49 467-523 171-219 (233)
106 PF04967 HTH_10: HTH DNA bindi 25.6 1.1E+02 0.0025 25.5 4.0 49 468-517 1-49 (53)
107 PRK07037 extracytoplasmic-func 25.1 68 0.0015 30.1 3.0 49 467-523 109-157 (163)
108 PRK06930 positive control sigm 25.0 69 0.0015 32.0 3.2 50 467-524 114-163 (170)
109 TIGR02947 SigH_actino RNA poly 24.7 41 0.00089 32.8 1.5 49 467-523 131-179 (193)
110 PRK09649 RNA polymerase sigma 24.6 65 0.0014 31.5 2.9 47 467-521 130-176 (185)
111 cd01392 HTH_LacI Helix-turn-he 24.6 57 0.0012 25.3 2.0 21 496-516 2-22 (52)
112 PRK06288 RNA polymerase sigma 24.4 72 0.0016 33.3 3.3 49 467-523 212-260 (268)
113 PRK09641 RNA polymerase sigma 24.4 69 0.0015 30.6 3.0 49 467-523 136-184 (187)
114 TIGR03001 Sig-70_gmx1 RNA poly 24.4 87 0.0019 32.7 3.9 50 467-524 161-210 (244)
115 PRK12529 RNA polymerase sigma 24.2 96 0.0021 30.0 3.9 48 467-522 127-174 (178)
116 PF13518 HTH_28: Helix-turn-he 24.2 64 0.0014 24.8 2.2 25 493-517 14-38 (52)
117 PRK07670 RNA polymerase sigma 24.1 64 0.0014 33.3 2.9 47 467-521 201-247 (251)
118 PRK12513 RNA polymerase sigma 24.1 36 0.00077 33.2 1.0 49 467-523 139-187 (194)
119 TIGR02952 Sig70_famx2 RNA poly 23.9 72 0.0016 29.9 2.9 48 467-522 122-169 (170)
120 PRK11923 algU RNA polymerase s 23.8 95 0.0021 30.1 3.9 49 467-523 138-186 (193)
121 PRK07408 RNA polymerase sigma 23.8 61 0.0013 33.7 2.7 49 467-523 203-251 (256)
122 PRK12527 RNA polymerase sigma 23.6 1.2E+02 0.0025 28.6 4.3 49 467-523 105-153 (159)
123 PRK09413 IS2 repressor TnpA; R 23.3 1.8E+02 0.0039 27.2 5.4 46 463-515 8-53 (121)
124 cd06170 LuxR_C_like C-terminal 23.2 1.7E+02 0.0038 22.2 4.5 45 468-521 1-45 (57)
125 PF10168 Nup88: Nuclear pore c 23.0 1.3E+03 0.028 28.6 13.6 19 464-482 678-696 (717)
126 PRK11511 DNA-binding transcrip 22.8 1.4E+02 0.0029 28.0 4.5 44 468-515 6-49 (127)
127 PRK09637 RNA polymerase sigma 22.6 83 0.0018 30.8 3.2 49 467-523 106-154 (181)
128 PRK12542 RNA polymerase sigma 22.6 79 0.0017 30.6 3.0 49 467-523 122-170 (185)
129 cd00131 PAX Paired Box domain 22.5 3.4E+02 0.0073 25.9 7.1 46 467-515 75-127 (128)
130 PRK07598 RNA polymerase sigma 22.5 1.5E+02 0.0032 34.0 5.5 58 467-528 350-407 (415)
131 TIGR02943 Sig70_famx1 RNA poly 22.4 96 0.0021 30.5 3.6 49 467-523 131-179 (188)
132 PF07638 Sigma70_ECF: ECF sigm 22.2 1.1E+02 0.0024 30.2 4.0 48 468-523 136-183 (185)
133 PRK12540 RNA polymerase sigma 21.8 70 0.0015 31.4 2.5 49 467-523 111-159 (182)
134 PRK05657 RNA polymerase sigma 21.6 1.2E+02 0.0026 33.1 4.4 53 467-523 262-314 (325)
135 PRK09645 RNA polymerase sigma 21.5 81 0.0018 30.0 2.8 49 467-523 118-166 (173)
136 PRK12522 RNA polymerase sigma 21.4 1E+02 0.0022 29.5 3.5 50 467-524 119-168 (173)
137 PRK08295 RNA polymerase factor 21.3 85 0.0018 30.7 3.0 47 467-522 155-201 (208)
138 cd00093 HTH_XRE Helix-turn-hel 21.3 1E+02 0.0023 22.1 2.8 23 494-516 15-37 (58)
139 PRK08301 sporulation sigma fac 21.2 76 0.0017 32.1 2.7 53 467-523 178-230 (234)
140 TIGR02959 SigZ RNA polymerase 21.1 1E+02 0.0022 29.7 3.4 49 467-523 100-148 (170)
141 PRK12539 RNA polymerase sigma 21.0 92 0.002 30.2 3.1 49 467-523 131-179 (184)
142 PRK12543 RNA polymerase sigma 20.6 1.2E+02 0.0026 29.3 3.8 49 467-523 117-165 (179)
143 COG3413 Predicted DNA binding 20.6 1.2E+02 0.0026 30.8 4.0 52 467-519 155-206 (215)
144 PRK12518 RNA polymerase sigma 20.4 61 0.0013 30.8 1.7 49 467-523 120-168 (175)
145 PRK12535 RNA polymerase sigma 20.2 91 0.002 31.0 3.0 49 467-523 133-181 (196)
146 PF12273 RCR: Chitin synthesis 20.1 73 0.0016 30.1 2.2 17 13-29 7-23 (130)
147 TIGR02885 spore_sigF RNA polym 20.0 89 0.0019 31.6 2.9 47 467-521 183-229 (231)
No 1
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=6.4e-38 Score=294.70 Aligned_cols=130 Identities=53% Similarity=0.811 Sum_probs=106.1
Q ss_pred ccceeccCCcchhHHHHHHHHHHccCCccCcchhhhh---h--h--hcccCCCCCCC-CCCcccccChhhHHHHHHHHHH
Q 005052 281 GHQFQLRNSKYLAPAQEILKEFCSLGTKQNDATKLKS---N--K--AKQQWDDENAG-SSSRKQSLCSLEFMELQKRKTK 352 (716)
Q Consensus 281 Gya~~l~~SRyLkPAQeLL~E~c~v~~~~~~~~~~~s---~--~--~~~~~~~~~~~-~~s~~peLssle~~elQ~kK~k 352 (716)
||+++|++||||+||||||+|||+|+........... . . .....+...+. ..+..+++++++++|+|+||+|
T Consensus 2 g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~~~~~~ls~~~r~e~q~kk~k 81 (140)
T smart00574 2 GGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSGNDSPVSTSSNEGGGENLSGGSSSSEVPPLSTAERQELQRKKAK 81 (140)
T ss_pred chhhhccCccccccHHHHHHHHhcccHHhhcccccccccccccccccCCCcCCCCCCCCCCCCCCCchhHHHHHHHHHHH
Confidence 8899999999999999999999999855433221110 0 0 00111111111 2234589999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCccCchhhhHHHhhhcccchhhHH
Q 005052 353 LLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIV 410 (716)
Q Consensus 353 LL~mLEEVd~rY~qY~~qmq~V~sSFe~vaG~gaA~~Yt~lAl~amSrhfr~LrdaI~ 410 (716)
||.||||||+||+|||+|||+|+++||+|+|.|+|.|||+||+++||||||||||+|+
T Consensus 82 Ll~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 82 LLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999996
No 2
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=100.00 E-value=9.9e-38 Score=294.87 Aligned_cols=127 Identities=55% Similarity=0.803 Sum_probs=100.5
Q ss_pred eccCCcchhHHHHHHHHHHccCCccCcch-hhhhh-------hhcccC--CCCC--CCCCCcccccChhhHHHHHHHHHH
Q 005052 285 QLRNSKYLAPAQEILKEFCSLGTKQNDAT-KLKSN-------KAKQQW--DDEN--AGSSSRKQSLCSLEFMELQKRKTK 352 (716)
Q Consensus 285 ~l~~SRyLkPAQeLL~E~c~v~~~~~~~~-~~~s~-------~~~~~~--~~~~--~~~~s~~peLssle~~elQ~kK~k 352 (716)
+|++||||+||||||+|||+|+....... ..+.. ...... .... .+.....+++++++++|+|+||+|
T Consensus 2 ~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~q~kK~K 81 (140)
T PF07526_consen 2 VLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGAPGGANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQELQRKKAK 81 (140)
T ss_pred ccccchhHHHHHHHHHHHHcccchhhhcchhhccccccccccCCCCCCCCCCCCCccccCCCCCCCChhhHHHHHHHHHH
Confidence 69999999999999999999987321100 00000 000000 0000 112234578999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCccCchhhhHHHhhhcccchhhHHH
Q 005052 353 LLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIVG 411 (716)
Q Consensus 353 LL~mLEEVd~rY~qY~~qmq~V~sSFe~vaG~gaA~~Yt~lAl~amSrhfr~LrdaI~~ 411 (716)
||.||||||+||+|||+|||+|+++||+|+|.|+|.|||+||++|||||||||||+|++
T Consensus 82 Ll~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~~ 140 (140)
T PF07526_consen 82 LLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAISD 140 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999963
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.97 E-value=1.8e-32 Score=286.98 Aligned_cols=252 Identities=42% Similarity=0.595 Sum_probs=197.1
Q ss_pred cceeccCCcchhHHHHHHHHHHccCCccCcchhh----hhhhhc-ccC-----CCCCCCCCCcccccChhhHHHHHHHHH
Q 005052 282 HQFQLRNSKYLAPAQEILKEFCSLGTKQNDATKL----KSNKAK-QQW-----DDENAGSSSRKQSLCSLEFMELQKRKT 351 (716)
Q Consensus 282 ya~~l~~SRyLkPAQeLL~E~c~v~~~~~~~~~~----~s~~~~-~~~-----~~~~~~~~s~~peLssle~~elQ~kK~ 351 (716)
+...+..+|||.++|+||+|+|+++......... ...... ... ...+.+..+ ++..+.+++++++.+++
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~ 123 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRES-ATLKAWLEEHRLNPYPS 123 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccc-cccccchhhhhhccCch
Confidence 3567899999999999999999987543221100 000000 000 001111122 45567889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCccCchhhhHHHhhhcccchh--hHHHHHHHHHhhcCCCCCCCCC
Q 005052 352 KLLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRD--GIVGQIQATKKAMGEKDPVAPG 429 (716)
Q Consensus 352 kLL~mLEEVd~rY~qY~~qmq~V~sSFe~vaG~gaA~~Yt~lAl~amSrhfr~Lrd--aI~~Qi~~~~k~mge~d~~~~g 429 (716)
||+.+|.+|+.+|.+||..|+.+.+.|+...|++.+.+|++.++..+++||+++.+ +|..|+......++..+.....
T Consensus 124 k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~ 203 (342)
T KOG0773|consen 124 KLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSE 203 (342)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999998 7888988887777644321111
Q ss_pred ---CCCCCCCcchhhhhhhHhhH-HhhhhccccCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCCh
Q 005052 430 ---TSRGETPRLKIIDQTLRQQR-AFQQMSMMESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSR 505 (716)
Q Consensus 430 ---~~~gEt~rlr~~dq~lrq~r-a~q~~~~~e~~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~ 505 (716)
......+..+..++.+++++ ++......+..+||++++||+.++.+|+.|+++|+.||||++.+|.+||++|||++
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~ 283 (342)
T KOG0773|consen 204 DESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSR 283 (342)
T ss_pred cccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCc
Confidence 11222455555566666654 34445555667899999999999999999999999999999999999999999999
Q ss_pred hhhhhhchhhhhhhchhhHHHHHHHhhhh
Q 005052 506 SQVSNWFINARVRLWKPMVEEMYLEETKE 534 (716)
Q Consensus 506 ~QVsNWFiNaRrRlkKpmiee~~~~~~~~ 534 (716)
.||+|||||+|+|+|+||+++++......
T Consensus 284 ~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 284 PQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred ccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 99999999999999999999999987655
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.61 E-value=5.5e-15 Score=151.75 Aligned_cols=64 Identities=38% Similarity=0.672 Sum_probs=61.8
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 461 PWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 461 ~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
.+||||+|+|.++.||..||..|+.||||++++|++||+++|++..||+|||.|.|.|.||.|.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 4688999999999999999999999999999999999999999999999999999999999885
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.58 E-value=9.1e-16 Score=117.99 Aligned_cols=40 Identities=68% Similarity=1.174 Sum_probs=36.5
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhh
Q 005052 479 WLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 518 (716)
Q Consensus 479 Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrR 518 (716)
||.+|+.||||+++||++||++||||.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.36 E-value=1.1e-12 Score=103.83 Aligned_cols=57 Identities=30% Similarity=0.538 Sum_probs=53.1
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 463 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 463 RkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
+++..|+++++.+|++||.. +|||+..++..||.+|||+..||.+||.|+|.|.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45667999999999999999 7999999999999999999999999999999998763
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.32 E-value=2.7e-12 Score=101.23 Aligned_cols=55 Identities=31% Similarity=0.513 Sum_probs=50.5
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhc
Q 005052 463 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 520 (716)
Q Consensus 463 RkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlk 520 (716)
+++..|+++++.+|+.||.. +|||+.+++..||+.+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 34455999999999999998 69999999999999999999999999999999864
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.32 E-value=1.9e-12 Score=103.18 Aligned_cols=57 Identities=35% Similarity=0.622 Sum_probs=53.7
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 462 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 462 kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
+|+++.|+++++.+|+.+|.. +|||+.+++..||.++||+..||.+||.|+|.|.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467788999999999999998 799999999999999999999999999999999864
No 9
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.25 E-value=7.9e-12 Score=129.52 Aligned_cols=51 Identities=49% Similarity=0.791 Sum_probs=48.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhc
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 520 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlk 520 (716)
.|.++++.+||+||.. +|||++++|++||+.||||..||+|||+|+|.|.+
T Consensus 182 CFKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred ehhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 3889999999999997 89999999999999999999999999999999987
No 10
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.88 E-value=2.2e-09 Score=113.72 Aligned_cols=65 Identities=23% Similarity=0.307 Sum_probs=57.8
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHHHH
Q 005052 460 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 527 (716)
Q Consensus 460 ~~kRkrR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee~ 527 (716)
.+|||+|. |++.||-.|++-|.+ ..|.+..||+.||..++||.+||+.||+|+|.|.||..+++-
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred ccccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 35666666 999999999999998 699999999999999999999999999999999998665443
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.85 E-value=1.5e-09 Score=114.90 Aligned_cols=60 Identities=23% Similarity=0.259 Sum_probs=53.6
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 461 PWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 461 ~kRkrR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
..||||. ++|.|+..|++-|.- |-|.+++-|.+|++.++||..||+.||+|||+|+||-.
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 3455554 999999999999888 69999999999999999999999999999999998744
No 12
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.68 E-value=1.8e-08 Score=100.00 Aligned_cols=64 Identities=23% Similarity=0.336 Sum_probs=58.0
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHHH
Q 005052 460 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 526 (716)
Q Consensus 460 ~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee 526 (716)
++||.|+.|+.+++..|+..|.. +-|-.-.||+.||+.++||++||+.||+|+|.|.||...++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 56777777999999999999998 79999999999999999999999999999999998855443
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.65 E-value=1.9e-08 Score=104.36 Aligned_cols=61 Identities=28% Similarity=0.488 Sum_probs=57.2
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 459 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 459 ~~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
++.||+|+-|+.++++.|+.-|.+ |.|.++..|++||.++||.+.||+.||+|+|.|+||.
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 456888888999999999999999 7999999999999999999999999999999999873
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.62 E-value=1.9e-08 Score=104.17 Aligned_cols=58 Identities=19% Similarity=0.270 Sum_probs=54.0
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 461 PWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 461 ~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.+|.|+.|+..++..|+.-|.- |.|.+...|++||..++||+.||++||+|||+|.||
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk 216 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKK 216 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHH
Confidence 5666667999999999999988 799999999999999999999999999999999887
No 15
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.60 E-value=6.8e-08 Score=80.32 Aligned_cols=52 Identities=12% Similarity=0.248 Sum_probs=48.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhhhhhchhhh
Q 005052 462 WRPQRGLPERSVSVLRAWLFEHFLHPY----PSDVDKHILARQTGLSRSQVSNWFINAR 516 (716)
Q Consensus 462 kRkrR~fpk~qv~iLr~Wf~eH~~nPY----PS~~EK~~LAkqTGLS~~QVsNWFiNaR 516 (716)
+|+|+.|+.+++..|+..|.. ++| |+..++.+||..+||++.+|.+||+|.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 677778999999999999999 799 9999999999999999999999999964
No 16
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.58 E-value=4.8e-08 Score=103.89 Aligned_cols=62 Identities=26% Similarity=0.383 Sum_probs=53.6
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 460 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 460 ~~kRkrR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
+++||.|. |+..++..|+.-|.. =-|.+..||.+||+..|||-.||.+||+|||.|.|+.+.
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 34445444 999999999999987 599999999999999999999999999999998766553
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.56 E-value=5.1e-08 Score=98.11 Aligned_cols=66 Identities=27% Similarity=0.302 Sum_probs=58.6
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHHHHHH
Q 005052 461 PWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMYL 529 (716)
Q Consensus 461 ~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee~~~ 529 (716)
.++++++|+.+++..|+.-|.. +-|-.+.+|..||++.||.+.||..||+|+|+|.|.+-.|.-|.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~ 115 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYE 115 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHH
Confidence 5778899999999999999998 58888899999999999999999999999999988766554443
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.56 E-value=5.2e-08 Score=99.63 Aligned_cols=57 Identities=25% Similarity=0.356 Sum_probs=52.2
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 464 PQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 464 krR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
+|+-++.-++..|++-|.+ .-|..-.||.+||..+|||.+||+.||+|+|-|.||.|
T Consensus 125 PRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 125 PRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred CcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 3444999999999999998 79999999999999999999999999999999998854
No 19
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.51 E-value=7e-08 Score=98.19 Aligned_cols=64 Identities=20% Similarity=0.251 Sum_probs=57.8
Q ss_pred cCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 458 ESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 458 e~~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
+++|||+|+.|+..++..|+.-|.. ..|.+..||..||+++.||++||+.||+|+|.|.|+...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 4567777778999999999999998 599999999999999999999999999999999877553
No 20
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.42 E-value=4.1e-07 Score=83.91 Aligned_cols=57 Identities=21% Similarity=0.352 Sum_probs=52.7
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 465 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 465 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
|..|+..+++.|++.|.+ .-||+.-.|++||-+..||+..|+.||+|+|.+.+|...
T Consensus 21 RTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 21 RTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 445999999999999999 699999999999999999999999999999999988643
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.36 E-value=3.9e-07 Score=88.80 Aligned_cols=60 Identities=25% Similarity=0.373 Sum_probs=55.9
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 460 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 460 ~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
..+++|++.+..++.+|+.-|.. +|||+..+|..|+..++++++-|+.||+|+|.+.|+.
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence 46777888999999999999998 7999999999999999999999999999999998764
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.35 E-value=3e-07 Score=100.01 Aligned_cols=59 Identities=20% Similarity=0.326 Sum_probs=53.6
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 461 PWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 461 ~kRkrR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
+|||||+ +.-.++..|+..|.+ ||.|+.+|.-.||.+.+|.+..|++||+|||.|.|+.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 3454454 999999999999999 7999999999999999999999999999999999874
No 23
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.26 E-value=8e-07 Score=90.65 Aligned_cols=58 Identities=26% Similarity=0.429 Sum_probs=53.3
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 462 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 462 kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
+|.|+.|+.++..+|++-|.+ .-||+...+++||.+++|.+.+|++||.|+|.|.++.
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 355666999999999999999 7999999999999999999999999999999998763
No 24
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.25 E-value=4.6e-07 Score=94.55 Aligned_cols=57 Identities=26% Similarity=0.263 Sum_probs=52.3
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHHHH
Q 005052 468 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 527 (716)
Q Consensus 468 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee~ 527 (716)
++..++-.|++-|.- .+|.+...|.+||..+|||++||+.||+|||.|.+|...++.
T Consensus 206 YTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 899999999999987 799999999999999999999999999999999988655443
No 25
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.24 E-value=1.3e-06 Score=88.72 Aligned_cols=59 Identities=20% Similarity=0.326 Sum_probs=53.7
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 461 PWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 461 ~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.+++|+.|+..+...|++-|.+ .-|.+.+||.+++....||.+||+.||+|+|.|.|+-
T Consensus 144 nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 3455666999999999999999 6999999999999999999999999999999998763
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.19 E-value=1e-06 Score=93.61 Aligned_cols=60 Identities=27% Similarity=0.375 Sum_probs=53.7
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 461 PWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 461 ~kRkrR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
++|++|+ |+..+.+.|+.||.. |.||+.+.|++||--|+||+..|++||.|+|.+.+|..
T Consensus 111 KqrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 3444555 999999999999999 79999999999999999999999999999999977643
No 27
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.12 E-value=8.8e-07 Score=87.23 Aligned_cols=58 Identities=29% Similarity=0.412 Sum_probs=51.9
Q ss_pred CCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 462 WRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 462 kRkrR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
+||.|. |+..+...|++-|.. -.|.+-.|+.+||...+|+++||+.||+|+|.|.||-
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred hhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 444444 999999999999997 4899999999999999999999999999999999873
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.10 E-value=2.6e-06 Score=88.73 Aligned_cols=53 Identities=25% Similarity=0.394 Sum_probs=49.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.|+..+...|++-|.+ --||+-.-|++||.+|+|.+.+|++||+|+|.|.+|.
T Consensus 147 iFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred hhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 3999999999999999 6899999999999999999999999999999997653
No 29
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.05 E-value=2.9e-06 Score=86.72 Aligned_cols=76 Identities=24% Similarity=0.326 Sum_probs=64.5
Q ss_pred CCCCCC--CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHHHHHHHhhhhhcc
Q 005052 460 HPWRPQ--RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMYLEETKEQDN 537 (716)
Q Consensus 460 ~~kRkr--R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee~~~~~~~~~~~ 537 (716)
..+|++ .+|.-.++..|+.-|.+ .-||--.++.+||...|+++.||.+||+|+|.|.+|+-.-||.....+.+..
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds~ 240 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDSG 240 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCCc
Confidence 344543 34999999999999998 6999999999999999999999999999999999888887888776666544
Q ss_pred c
Q 005052 538 N 538 (716)
Q Consensus 538 ~ 538 (716)
.
T Consensus 241 a 241 (288)
T KOG0847|consen 241 A 241 (288)
T ss_pred c
Confidence 3
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.94 E-value=6.1e-06 Score=87.11 Aligned_cols=62 Identities=23% Similarity=0.364 Sum_probs=56.4
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 459 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 459 ~~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
...||||++++.+++..|+.-|.. .|.|..--|++|+.+|||....|+.||+|+|+|.|+-.
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 356899999999999999999887 79999999999999999999999999999999876533
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.87 E-value=5.1e-05 Score=85.71 Aligned_cols=57 Identities=28% Similarity=0.348 Sum_probs=53.4
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhh
Q 005052 460 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 519 (716)
Q Consensus 460 ~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRl 519 (716)
..||+|-.|+..+++.|+..|.+ ++||+.++-+.|+.+++|.++-|.|||-|+|||-
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 45777777999999999999999 7999999999999999999999999999999995
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.50 E-value=3.2e-05 Score=82.32 Aligned_cols=59 Identities=19% Similarity=0.332 Sum_probs=51.8
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 463 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 463 RkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
|=|+-|+++++..|++-|++ --|-+.-.|=+||..++|.++.|+.||+|+|.|.|+..+
T Consensus 183 RYRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 183 RYRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 33456999999999888876 478888899999999999999999999999999987665
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.42 E-value=0.00011 Score=79.76 Aligned_cols=58 Identities=28% Similarity=0.547 Sum_probs=52.6
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 463 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 463 RkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
|.|+.|+..+...|+.||.. .|||....|+.||++|+|+...|+.||.|+|.|.+|..
T Consensus 178 r~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 178 RNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 34456999999999999998 68999999999999999999999999999999987744
No 34
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.36 E-value=7.3e-05 Score=79.59 Aligned_cols=60 Identities=47% Similarity=0.716 Sum_probs=54.7
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 463 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 463 RkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
+++.+++.+. .+|+.|+.+|..+|||++-++..|+..|+++..||++||+|+|+|+++.+
T Consensus 97 ~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 97 ARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred cccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 3445689899 99999999999999999999999999999999999999999999987643
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.32 E-value=0.00012 Score=72.17 Aligned_cols=60 Identities=17% Similarity=0.092 Sum_probs=53.6
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 460 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 460 ~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
..+|.|.+|+..+...|++-|.. .+||+...++.||..+++++..|.+||+|+|++.++.
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 34555666999999999999998 4999999999999999999999999999999998764
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.10 E-value=0.0002 Score=75.96 Aligned_cols=59 Identities=22% Similarity=0.354 Sum_probs=53.1
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 460 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 460 ~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
++||||+.+-..-++-|+++|.. -|-|+.+....+|++..|.+..|..||+|.|.|.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 56777777777778899999998 699999999999999999999999999999999887
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.58 E-value=0.0085 Score=50.18 Aligned_cols=43 Identities=21% Similarity=0.398 Sum_probs=31.1
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhh
Q 005052 473 VSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 518 (716)
Q Consensus 473 v~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrR 518 (716)
.+.|++.|.. |.++.+.+...|..+|+||..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4559999998 599999999999999999999999999877544
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.79 E-value=0.024 Score=56.15 Aligned_cols=61 Identities=34% Similarity=0.572 Sum_probs=53.4
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 460 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 460 ~~kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
..++.+..+...+..+|..-|.. .+||....+..|+..+|++...|.+||+|.|.+.++..
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 34555667999999999888887 79999999999999999999999999999999987644
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=87.66 E-value=0.41 Score=59.88 Aligned_cols=57 Identities=19% Similarity=0.358 Sum_probs=51.7
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 465 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 465 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
|..+...++++|+..|.+ --||++++.+.|.+..+|.+..|..||+|+|.+-+|+..
T Consensus 907 ~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred ccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 344899999999999998 699999999999999999999999999999999988653
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=79.51 E-value=3.2 Score=33.93 Aligned_cols=47 Identities=30% Similarity=0.259 Sum_probs=31.0
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhh
Q 005052 462 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 516 (716)
Q Consensus 462 kRkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaR 516 (716)
+|+|+.|+-+.+--+-.-+.+ .+ -+..||+..|++.++|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 466777888775544444444 23 688999999999999999999853
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=68.67 E-value=6.4 Score=47.46 Aligned_cols=44 Identities=27% Similarity=0.451 Sum_probs=41.0
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhh
Q 005052 473 VSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 519 (716)
Q Consensus 473 v~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRl 519 (716)
..+|++.|.. |+.|+++|...+|.+.||...-|+.||.+.|...
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 7888999888 7999999999999999999999999999998765
No 42
>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=68.13 E-value=5.9 Score=29.38 Aligned_cols=45 Identities=31% Similarity=0.322 Sum_probs=35.9
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhc
Q 005052 468 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 520 (716)
Q Consensus 468 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlk 520 (716)
++++...++...+.+. -.-.++|+.+|++...|..|....|.+++
T Consensus 11 l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 11 LPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred CCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 6778888888777542 24577899999999999999988887764
No 43
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=66.63 E-value=42 Score=36.37 Aligned_cols=57 Identities=28% Similarity=0.512 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCccCchhhhHHHhhhcccchhhHHHHHHH
Q 005052 343 FMELQKRKTKLLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIVGQIQA 415 (716)
Q Consensus 343 ~~elQ~kK~kLL~mLEEVd~rY~qY~~qmq~V~sSFe~vaG~gaA~~Yt~lAl~amSrhfr~LrdaI~~Qi~~ 415 (716)
..+|+.+|..|..-++++++|-.+-..+|.+- | +|-+ +.+.+.-+..+|-.++.++.
T Consensus 6 L~eL~qrk~~Lq~eIe~LerR~~ri~~Emrts---F---aG~S----------q~lA~RVqGFkdYLvGsLQD 62 (283)
T PF11285_consen 6 LKELEQRKQALQIEIEQLERRRERIEKEMRTS---F---AGQS----------QDLAIRVQGFKDYLVGSLQD 62 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc---c---ccch----------HHHHHHHhhhHHHHHHHHHH
Confidence 46899999999999999999999888888763 3 3432 33444444555656665553
No 44
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=65.31 E-value=9.2 Score=31.88 Aligned_cols=46 Identities=26% Similarity=0.331 Sum_probs=30.4
Q ss_pred CCCCCCChhHHH-HHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhh
Q 005052 463 RPQRGLPERSVS-VLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 516 (716)
Q Consensus 463 RkrR~fpk~qv~-iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaR 516 (716)
++++.|+++.+. ++...+.. ......+|++.|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 345678888854 44555444 46889999999999999999977665
No 45
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=64.77 E-value=6.4 Score=30.89 Aligned_cols=47 Identities=34% Similarity=0.419 Sum_probs=37.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||++...+|..-|.+ ++ .-.++|+..|+|...|+.+...+..++|+
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4888999999888755 32 45789999999999999999999988763
No 46
>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=61.46 E-value=10 Score=29.98 Aligned_cols=45 Identities=29% Similarity=0.386 Sum_probs=33.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 519 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRl 519 (716)
.||+..+.++..-+.+. -.-.++|+.+|+|...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 47888888887766652 3567899999999999999999999874
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=57.62 E-value=25 Score=23.13 Aligned_cols=38 Identities=24% Similarity=0.294 Sum_probs=27.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhc
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWF 512 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWF 512 (716)
.++.+....+..++.. .+ ....+|+..|+++..|.+|.
T Consensus 5 ~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 4666666666555543 33 45688999999999999984
No 48
>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=48.73 E-value=17 Score=33.34 Aligned_cols=48 Identities=25% Similarity=0.239 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||++...++...+.+ .+ .-.++|+.+|+|+..|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5788899998876655 33 345699999999999999999999998753
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=47.42 E-value=18 Score=33.52 Aligned_cols=47 Identities=17% Similarity=0.116 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||+..+.++..-+.+. + .-.++|+.+|++...|.+|...+|+++++
T Consensus 106 ~L~~~~r~ii~l~~~~~----~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG----K----TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 58999999987666552 2 35789999999999999999999999875
No 50
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=47.36 E-value=20 Score=33.92 Aligned_cols=50 Identities=14% Similarity=0.085 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 466 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 466 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
..||++.+.++..++.++ -.-.++|..+|++...|.+|..-+|+++++-+
T Consensus 107 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999998887773 24478999999999999999999999987643
No 51
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.05 E-value=20 Score=28.97 Aligned_cols=43 Identities=28% Similarity=0.287 Sum_probs=25.0
Q ss_pred HHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHH
Q 005052 476 LRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 525 (716)
Q Consensus 476 Lr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmie 525 (716)
|+.++.++ -+ ....||+.+|+++.+|+.|+.+...+..-..++
T Consensus 2 L~~~m~~~---~i----t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~ 44 (63)
T PF13443_consen 2 LKELMAER---GI----TQKDLARKTGISRSTLSRILNGKPSNPSLDTLE 44 (63)
T ss_dssp HHHHHHHT---T------HHHHHHHHT--HHHHHHHHTTT-----HHHHH
T ss_pred HHHHHHHc---CC----CHHHHHHHHCcCHHHHHHHHhcccccccHHHHH
Confidence 45566653 22 567899999999999999999875454433333
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=47.01 E-value=21 Score=33.47 Aligned_cols=49 Identities=24% Similarity=0.197 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++.-.+.+. .+ -.++|+.+|++...|.++..-+|+++++.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999997776662 22 368999999999999999999999987755
No 53
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=45.27 E-value=24 Score=34.59 Aligned_cols=51 Identities=16% Similarity=0.247 Sum_probs=42.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 525 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmie 525 (716)
.||++.+.++.--+.+. + .-.++|..+|+|+..|.++..-+|+++++-+.+
T Consensus 134 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~ 184 (189)
T PRK12530 134 HLPAQQARVFMMREYLE----L----SSEQICQECDISTSNLHVLLYRARLQLQACLSK 184 (189)
T ss_pred hCCHHHHHHHhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999988777662 2 357899999999999999999999999876643
No 54
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=44.90 E-value=20 Score=31.67 Aligned_cols=47 Identities=30% Similarity=0.332 Sum_probs=36.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||+..+.++..-+.. .+ .-.++|+.+|+|+..|.+|...+|.++++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4778888887554443 34 45689999999999999999999998875
No 55
>PRK00118 putative DNA-binding protein; Validated
Probab=44.67 E-value=20 Score=33.57 Aligned_cols=48 Identities=15% Similarity=0.114 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||+.++.++..++.+. -.-.++|+.+|+|+.-|.+|...+|+++++-
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 47899999998887762 2446799999999999999999999998763
No 56
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=42.67 E-value=33 Score=32.85 Aligned_cols=48 Identities=15% Similarity=0.253 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||++.+.++...+.+ .+ .-.++|+.+|+|...|.++...+|+++++-
T Consensus 129 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GL----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4899999999888876 33 357899999999999999999999998764
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=41.72 E-value=27 Score=32.68 Aligned_cols=49 Identities=20% Similarity=0.200 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++..-+.+ .+ .-.++|+..|+|+..|.+|..-+|.++++.+
T Consensus 125 ~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3788888888766554 22 3478999999999999999999999998654
No 58
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=41.29 E-value=37 Score=33.45 Aligned_cols=49 Identities=31% Similarity=0.237 Sum_probs=40.1
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 466 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 466 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
..|++.++.+|+. +.+ .+ .-.++|+.+|+|+..|++|-..+|.++++..
T Consensus 5 ~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4589999999977 333 33 4568999999999999999999999987644
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=40.84 E-value=27 Score=32.73 Aligned_cols=49 Identities=20% Similarity=0.205 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.|++..+.++..-+.. -+ .-.++|+.+|+++..|.+|...+|+++++.+
T Consensus 128 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIE----GL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888999988765554 22 2368999999999999999999999998754
No 60
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=39.62 E-value=24 Score=34.00 Aligned_cols=49 Identities=18% Similarity=0.131 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++..-+.+. -.-.++|+.+|+|...|.+++..+|+++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998876662 24578999999999999999999999997654
No 61
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=39.22 E-value=1.1e+02 Score=25.82 Aligned_cols=43 Identities=19% Similarity=0.096 Sum_probs=31.2
Q ss_pred CCcccccChhhHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 005052 332 SSRKQSLCSLEFME---LQKRKTKLLSMLEEVDRRYRHYCDQMKAV 374 (716)
Q Consensus 332 ~s~~peLssle~~e---lQ~kK~kLL~mLEEVd~rY~qY~~qmq~V 374 (716)
.+.+||||--|..- |.++|..|.+.++|....|+.-..|+..+
T Consensus 5 ~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~L 50 (52)
T PF03791_consen 5 IGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSSL 50 (52)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34679999877543 67889999999999966666655555543
No 62
>PF02326 YMF19: Plant ATP synthase F0; InterPro: IPR003319 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. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit 8 (or ymf19) found in the F0 complex of mitochondrial F-ATPases from plants and algae. This subunit is sometimes found in association and N-terminal to IPR009455 from INTERPRO, in higher plants. Subunit 8 differs in sequence between plants, Metazoa (IPR001421 from INTERPRO) and fungi (IPR009230 from INTERPRO) [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=39.13 E-value=26 Score=31.71 Aligned_cols=32 Identities=38% Similarity=0.719 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHHHhhhcchhhhhHhhhhcccc
Q 005052 13 FFFFFFFFLFFFCFVFNITDKIHSLLLLRNWW 44 (716)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 (716)
|++.++|++|+++++..|--+|-..|.+|+.=
T Consensus 13 fW~~i~f~~~y~~~~~~~lP~i~~~lk~R~~~ 44 (86)
T PF02326_consen 13 FWLLIFFFFFYIFLVNFILPKISRILKLRSKL 44 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555566666678899999999999863
No 63
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=39.10 E-value=27 Score=34.19 Aligned_cols=49 Identities=10% Similarity=0.138 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.+|..-+.+. -.-.++|+.+|++...|.++...+|+++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48999999998776663 24478999999999999999999999987644
No 64
>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=38.86 E-value=21 Score=34.14 Aligned_cols=49 Identities=18% Similarity=0.154 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.++ + .-.++|+.+|+|...|.++.-.+|+++++.+
T Consensus 138 ~L~~~~r~v~~l~~~~~----~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----L----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887666552 2 4478999999999999999999999987654
No 65
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=37.96 E-value=30 Score=33.77 Aligned_cols=49 Identities=20% Similarity=0.258 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.-.+.+. . .-.++|+.+|+|...|.+...-+|+++++..
T Consensus 131 ~L~~~~r~i~~l~~~~g--~------s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--E------KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 58999999998766652 2 3478999999999999999999999987754
No 66
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.87 E-value=30 Score=33.54 Aligned_cols=48 Identities=21% Similarity=0.138 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||+..+.++..-+.+. + .-.++|..+|++...|.++...+|+++++.
T Consensus 139 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG----L----SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998776662 2 457899999999999999999999998764
No 67
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=37.07 E-value=30 Score=34.43 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++..-+.+. -.-.++|..+|+|...|.++...+|+++++.+
T Consensus 153 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--------LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 24578999999999999999999999987644
No 68
>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=36.60 E-value=33 Score=31.87 Aligned_cols=47 Identities=30% Similarity=0.290 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||++.+.++..-+.+ .+ .-.++|+.+|+|...|.++..-+|+++++
T Consensus 111 ~L~~~~r~v~~l~~~~----g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQR----GV----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 4899999998886555 23 34689999999999999999999988865
No 69
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=36.47 E-value=33 Score=32.79 Aligned_cols=48 Identities=21% Similarity=0.176 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||++.+.++.-.+.+. + .-.++|..+|++...|.+....+|.++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG----L----TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998887762 2 347899999999999999999999998763
No 70
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=35.73 E-value=61 Score=26.15 Aligned_cols=49 Identities=22% Similarity=0.192 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
.|++....+|+.+..- + ...++|...+++++-|..+..+.++|+.-+-.
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~ 51 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKNR 51 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSH
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCCH
Confidence 4788888888777554 2 56789999999999999999999999865443
No 71
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=34.94 E-value=32 Score=33.38 Aligned_cols=49 Identities=20% Similarity=0.290 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++...++..-+.+. + .-.++|..+|+|...|.+|+..+|+++++.+
T Consensus 141 ~L~~~~~~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYEG----L----SQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888887766552 2 3478999999999999999999999998754
No 72
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=34.84 E-value=76 Score=23.93 Aligned_cols=46 Identities=26% Similarity=0.272 Sum_probs=35.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.|++....++..+ .. .+ ...++|+.+|+++..|..|....+.++.-
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 4777888877554 32 22 45789999999999999999988877754
No 73
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=34.40 E-value=34 Score=32.23 Aligned_cols=48 Identities=23% Similarity=0.175 Sum_probs=39.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 466 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 466 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
..||++++.++.-.+.+. + .-.++|..+|+|...|..+...+|+|+++
T Consensus 111 ~~L~~~~r~v~~l~~~~~----~----s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG----F----SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358999999988876663 2 34689999999999999999999999875
No 74
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=33.48 E-value=42 Score=34.54 Aligned_cols=49 Identities=22% Similarity=0.218 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++...+.+. + .-.++|+.+|+|...|+.+...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998887663 2 3478999999999999999999999998754
No 75
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=33.43 E-value=62 Score=31.47 Aligned_cols=49 Identities=16% Similarity=0.208 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++++.++.-.+.+. .+ -.++|..+|+|..-|.+....+|+++++-+
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999988777662 23 378999999999999999999999997654
No 76
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=32.89 E-value=36 Score=32.89 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++..-+++. + .-.++|+.+|++...|.++...+|+++++.+
T Consensus 128 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQG----L----SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhcC----C----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 37888888886666552 2 3468999999999999999999999987644
No 77
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=32.48 E-value=37 Score=34.14 Aligned_cols=49 Identities=29% Similarity=0.413 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++...+.+ . -.-.++|+.+|+++..|..|...+++++++.+
T Consensus 178 ~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 178 ALPERERRILLLRFFE----D----KTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred cCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5899999999887765 2 24678999999999999999999999987643
No 78
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=32.37 E-value=38 Score=32.35 Aligned_cols=49 Identities=18% Similarity=0.177 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++..-+.+ .+ .-.++|+.+|+|+..|.+++..+|+++++-+
T Consensus 136 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4889999998765554 22 3478999999999999999999999987643
No 79
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=32.24 E-value=51 Score=33.94 Aligned_cols=49 Identities=20% Similarity=0.268 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.+|...+.+. + .-.++|+.+|+++..|.+|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g----~----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----L----SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998877652 2 3478999999999999999999999987643
No 80
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=32.11 E-value=37 Score=32.69 Aligned_cols=49 Identities=18% Similarity=0.223 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++.-.+.+. + .-.++|+.+|+|...|.++...+|.++++.+
T Consensus 135 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG----Y----THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998776652 2 4478999999999999999999999987643
No 81
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=32.06 E-value=42 Score=31.93 Aligned_cols=48 Identities=15% Similarity=0.013 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++..-+|+++++-
T Consensus 112 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASG----F----SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999988877763 2 346899999999999999999999998753
No 82
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=31.92 E-value=43 Score=32.67 Aligned_cols=49 Identities=20% Similarity=0.259 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.-.+.+. + .-.++|+.+|+|...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG----F----SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48899999987665552 2 3478999999999999999999999998755
No 83
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=31.89 E-value=98 Score=28.43 Aligned_cols=48 Identities=23% Similarity=0.172 Sum_probs=39.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 466 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 466 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
..|++...++|+-+ .+ .| ...++|+..+++.+.|.+|..+.|+|+.-.
T Consensus 148 ~~lt~~e~~vl~l~-~~----g~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 148 PLLTPRERQILKLI-TE----GY----TNRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred cCCCHHHHHHHHHH-HC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 34999999999885 44 23 257899999999999999999999998643
No 84
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=31.73 E-value=56 Score=33.44 Aligned_cols=56 Identities=20% Similarity=0.140 Sum_probs=43.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHHH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 526 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee 526 (716)
.||+..+.+|...|.-.-..++ .-.++|+.+|+|+..|+.+...+++|+|..+.++
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~----t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~ 231 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPH----TLEEVGKEFNVTRERIRQIESKALRKLRHPSRSK 231 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCc----cHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHh
Confidence 4899999999887621101232 5788999999999999999999999999876443
No 85
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=30.67 E-value=40 Score=33.34 Aligned_cols=49 Identities=20% Similarity=0.159 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.-.+.+ -+ .-.++|...|+|...|.++..-+|+++++-+
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGAS----GF----SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999888776 23 3467899999999999999999999987644
No 86
>PRK04217 hypothetical protein; Provisional
Probab=30.66 E-value=70 Score=30.33 Aligned_cols=49 Identities=18% Similarity=0.201 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.++++.+.++..++.+. + .-.++|+.+|+|+..|.+.+..+|.+++..+
T Consensus 42 ~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48899999998887763 2 5677999999999999999999998886543
No 87
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.59 E-value=47 Score=32.12 Aligned_cols=49 Identities=24% Similarity=0.139 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++.--+.+. + .-.++|+.+|+++..|.+....+|+++++.+
T Consensus 129 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG----L----SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 37888888876666552 2 4578999999999999999999999998754
No 88
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=30.08 E-value=56 Score=30.43 Aligned_cols=50 Identities=24% Similarity=0.223 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 466 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 466 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
..||++.+.++.--+.+ -+ .-.++|..+|+|...|.+...-+|+++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DM----DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999999877666 23 2478999999999999999999999987654
No 89
>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=30.00 E-value=51 Score=30.93 Aligned_cols=48 Identities=25% Similarity=0.312 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||++.+.++..-+.+ .+ .-.++|..+|++...|.++...+|.++++.
T Consensus 110 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----DL----SEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHHHh----cC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4888999998776665 22 346789999999999999999999998764
No 90
>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=29.97 E-value=49 Score=31.40 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++..-+++. + .-.++|+.+|+|...|.++..-+|+++++.+
T Consensus 119 ~L~~~~r~i~~l~~~~g----~----s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----L----TIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48888999987777662 2 3468999999999999999999999987643
No 91
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=29.71 E-value=56 Score=31.76 Aligned_cols=48 Identities=15% Similarity=0.180 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||++.+.+|.--+.+ .+ .-.++|+..|+|+..|.+-...+|+++++.
T Consensus 131 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYH----EK----SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4899999999776665 22 457899999999999999999999998764
No 92
>PHA00542 putative Cro-like protein
Probab=29.57 E-value=1.3e+02 Score=26.56 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChhhhhhhchhhhhhhchhhHHHH
Q 005052 493 DKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 527 (716)
Q Consensus 493 EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee~ 527 (716)
...+||+.+|+++..|+.|.....++.....++++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki 67 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKL 67 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHH
Confidence 45679999999999999999887655554444443
No 93
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=29.02 E-value=51 Score=31.90 Aligned_cols=48 Identities=13% Similarity=0.161 Sum_probs=38.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 466 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 466 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
..||++.+.++..-+.+. + .-.++|+.+|+|...|.+|...+|+++++
T Consensus 132 ~~L~~~~r~i~~l~~~~~----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 132 EQLEPARRNCILHAYVDG----C----SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 358889988877666652 2 34789999999999999999999998865
No 94
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=28.47 E-value=42 Score=34.12 Aligned_cols=49 Identities=31% Similarity=0.344 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++..-+.+ .+ .-.++|+.+|+|..-|.++...+|+++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~----g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQE----EL----NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999998777665 22 4578999999999999999999999997643
No 95
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=28.18 E-value=57 Score=32.12 Aligned_cols=49 Identities=16% Similarity=0.090 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.-.+.+. .+ -.++|+.+|++...|.++...+|+++++-+
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s------~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FA------YEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999988877762 23 358999999999999999999999997754
No 96
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=28.06 E-value=66 Score=32.36 Aligned_cols=51 Identities=24% Similarity=0.327 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 525 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmie 525 (716)
.||++.+.++.--+.+. . .-.++|+.+|+|..-|.++..-+|+++++.+.+
T Consensus 148 ~L~~~~r~v~~L~~~~g--~------s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--L------ETNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 58899988887777663 2 347899999999999999999999999886643
No 97
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.68 E-value=58 Score=31.12 Aligned_cols=47 Identities=13% Similarity=0.159 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||++.+.++.-.+.+. .+ -.++|+.+|++..-|.++...+|+|++.
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 48999999988776662 23 3689999999999999999999999864
No 98
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.51 E-value=57 Score=31.96 Aligned_cols=50 Identities=22% Similarity=0.221 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 466 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 466 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
..||++.+.++.--+.+. . .-.++|..+|+|...|.+....+|+++++.+
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~------s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--L------PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--C------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 458999999998766652 2 3468999999999999999999999987654
No 99
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=27.32 E-value=77 Score=31.83 Aligned_cols=49 Identities=16% Similarity=0.146 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.+. .+ -.++|+.+|++..-|.++..-+|+++++.+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LS------YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888776666553 33 378999999999999999999999987644
No 100
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=27.00 E-value=53 Score=33.10 Aligned_cols=48 Identities=27% Similarity=0.342 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||+..+.+|...|.+ .+ .-.++|+.+|++...|..+...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~----~~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYE----EL----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4899999999888776 22 357899999999999999999999998763
No 101
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.63 E-value=69 Score=32.70 Aligned_cols=49 Identities=22% Similarity=0.159 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.-.+.++ -+ -.++|+.+|+|..-|.++...+|+++++.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MS------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998887773 23 367999999999999999999999987654
No 102
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.60 E-value=58 Score=31.97 Aligned_cols=49 Identities=16% Similarity=0.142 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.+ -| .-.++|+.+|++...|.+++.-+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GL----SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4899999888776655 33 2478999999999999999999999997643
No 103
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=26.47 E-value=67 Score=31.87 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
.||+..+.++.--+.+. + .-.++|..+|+|..-|.+....+|+++++-+.
T Consensus 139 ~Lp~~~r~v~~L~~~eg----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD----F----EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999988776662 2 24689999999999999999999999987553
No 104
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=25.94 E-value=70 Score=30.04 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.+|.--+ + -+ .-.++|..+|++...|.++...+|.++++-+
T Consensus 112 ~L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887766 5 22 4578999999999999999999999987744
No 105
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=25.65 E-value=68 Score=33.06 Aligned_cols=49 Identities=16% Similarity=0.166 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++.-.+.+. + .-.++|+.+|+|...|.++...+|+++++.+
T Consensus 171 ~Lp~~~R~v~~L~~~eg----~----s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN----M----SNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888988876666552 2 3478999999999999999999999998754
No 106
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=25.61 E-value=1.1e+02 Score=25.50 Aligned_cols=49 Identities=27% Similarity=0.338 Sum_probs=36.9
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhh
Q 005052 468 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARV 517 (716)
Q Consensus 468 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRr 517 (716)
|++.+..+|+.-+..=+ .-+|....-.+||+..|+++.-++.-+.++=+
T Consensus 1 LT~~Q~e~L~~A~~~GY-fd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 1 LTDRQREILKAAYELGY-FDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHHHHHHcCC-CCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 57888889887766532 33488899999999999999988765544433
No 107
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=25.14 E-value=68 Score=30.09 Aligned_cols=49 Identities=22% Similarity=0.261 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.+ .+ .-.++|+.+|+|...|.....-+|+++++.+
T Consensus 109 ~L~~~~r~v~~l~~~~----~~----s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH----GE----TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999999776665 22 3578999999999999999998998887654
No 108
>PRK06930 positive control sigma-like factor; Validated
Probab=24.97 E-value=69 Score=31.97 Aligned_cols=50 Identities=16% Similarity=0.066 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
.||+..+.++.-.+.+. + .-.++|+.+|+|...|.++...+|+++++.+-
T Consensus 114 ~L~~rer~V~~L~~~eg----~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG----L----SYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48889988888766552 2 34789999999999999999999999977553
No 109
>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=24.75 E-value=41 Score=32.78 Aligned_cols=49 Identities=22% Similarity=0.226 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.-.+.+ -+ .-.++|+.+|+|...|.++..-+|+++++.+
T Consensus 131 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE----GF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888887665555 22 3478999999999999999999999998755
No 110
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=24.58 E-value=65 Score=31.47 Aligned_cols=47 Identities=15% Similarity=0.004 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||++++.++.-.+.+. + .-.++|+.+|+|...|.++..-+|+++++
T Consensus 130 ~Lp~~~r~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLG----L----SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 58999999987777662 2 34789999999999999999999999876
No 111
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=24.58 E-value=57 Score=25.26 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=18.9
Q ss_pred HHHHHhCCChhhhhhhchhhh
Q 005052 496 ILARQTGLSRSQVSNWFINAR 516 (716)
Q Consensus 496 ~LAkqTGLS~~QVsNWFiNaR 516 (716)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 112
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=24.39 E-value=72 Score=33.30 Aligned_cols=49 Identities=24% Similarity=0.426 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.+|...|.+. -.-.++|..+|+|...|......+++++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998877762 24678999999999999999999999987654
No 113
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=24.39 E-value=69 Score=30.58 Aligned_cols=49 Identities=20% Similarity=0.222 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++...+|.--+.+ . ..-.++|..+|+|...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~il~l~~~~----~----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE----D----LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhh----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888887544333 2 23478999999999999999999999987643
No 114
>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=24.36 E-value=87 Score=32.70 Aligned_cols=50 Identities=28% Similarity=0.391 Sum_probs=41.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
.||++.+.++.-.+.+. + .-.++|..+|++..-|.++...+|+++++.+.
T Consensus 161 ~Lp~~~R~v~~L~~~eg----~----S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG----L----SMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999988887763 2 34789999999999999999999999987653
No 115
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.17 E-value=96 Score=30.05 Aligned_cols=48 Identities=13% Similarity=0.096 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||++++.++.-.+.+. . .-.++|+.+|+|..-|.+....+++++...
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~------s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--M------KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 48999999998877763 2 347899999999999999999999887543
No 116
>PF13518 HTH_28: Helix-turn-helix domain
Probab=24.16 E-value=64 Score=24.84 Aligned_cols=25 Identities=36% Similarity=0.539 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCChhhhhhhchhhhh
Q 005052 493 DKHILARQTGLSRSQVSNWFINARV 517 (716)
Q Consensus 493 EK~~LAkqTGLS~~QVsNWFiNaRr 517 (716)
...++|++.|+++.+|..|....+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3566999999999999999877665
No 117
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=24.10 E-value=64 Score=33.28 Aligned_cols=47 Identities=23% Similarity=0.224 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||+..+.++...+.+ .+ .-.++|..+|+|...|.+++..+|+++++
T Consensus 201 ~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4899999999877765 22 35789999999999999999999999875
No 118
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=24.09 E-value=36 Score=33.16 Aligned_cols=49 Identities=18% Similarity=0.197 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.+ .+ .-.++|+.+|+|...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHG----DL----ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888887665544 22 3467999999999999999999999998754
No 119
>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=23.91 E-value=72 Score=29.91 Aligned_cols=48 Identities=17% Similarity=0.067 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||+..+.++..-+.+ -+ .-.++|+.+|++...|.+...-+|+++++.
T Consensus 122 ~L~~~~r~vl~l~~~~----g~----s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQ----NL----PIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred hCCHHHHHHHHHHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 5899999999886665 22 347899999999999999998888888753
No 120
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=23.79 E-value=95 Score=30.11 Aligned_cols=49 Identities=20% Similarity=0.173 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.+ .| .-.++|+.+|+|+..|.+...-+|+++++-+
T Consensus 138 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 138 QLPEDLRTALTLREFD----GL----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hCCHHHhHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3788888777665554 44 3478999999999999999999999998755
No 121
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=23.77 E-value=61 Score=33.74 Aligned_cols=49 Identities=24% Similarity=0.221 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.+|..-|.+ .+ .-.++|..+|+|...|..+..-+++|+++.+
T Consensus 203 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLH----DL----TQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4888999998877765 22 4578999999999999999999999987654
No 122
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.62 E-value=1.2e+02 Score=28.59 Aligned_cols=49 Identities=24% Similarity=0.253 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++...++.-.+.+. . .-.++|..+|++..-|.+....+|+++++.+
T Consensus 105 ~L~~~~r~v~~l~~~~~--~------s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG--L------SHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 38999999998887763 2 3478999999999999999999999987654
No 123
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=23.28 E-value=1.8e+02 Score=27.19 Aligned_cols=46 Identities=22% Similarity=0.248 Sum_probs=30.8
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhh
Q 005052 463 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINA 515 (716)
Q Consensus 463 RkrR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNa 515 (716)
+++|+++.+-+...-....+ +.+ ...++|+..|++..+|.+|..-.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 44566877775544333343 232 45778999999999999995443
No 124
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=23.22 E-value=1.7e+02 Score=22.16 Aligned_cols=45 Identities=27% Similarity=0.225 Sum_probs=32.2
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 468 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 468 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
|++....++..+ .. .+ ...++|+.+++++..|..|..-.++++..
T Consensus 1 l~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 355666666543 22 22 55789999999999999999877777654
No 125
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=23.00 E-value=1.3e+03 Score=28.56 Aligned_cols=19 Identities=16% Similarity=0.109 Sum_probs=15.7
Q ss_pred CCCCCChhHHHHHHHHHHH
Q 005052 464 PQRGLPERSVSVLRAWLFE 482 (716)
Q Consensus 464 krR~fpk~qv~iLr~Wf~e 482 (716)
+...|++.+.+.++.-+.+
T Consensus 678 ~s~~L~~~Q~~~I~~iL~~ 696 (717)
T PF10168_consen 678 KSIVLSESQKRTIKEILKQ 696 (717)
T ss_pred CCccCCHHHHHHHHHHHHH
Confidence 3345999999999999887
No 126
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=22.83 E-value=1.4e+02 Score=28.02 Aligned_cols=44 Identities=11% Similarity=0.304 Sum_probs=34.5
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhh
Q 005052 468 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINA 515 (716)
Q Consensus 468 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNa 515 (716)
-....+..+.+|+.+|+..| + .-.+||+.+|+++..+..+|...
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~-~---sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESP-L---SLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCC-C---CHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455677889999987665 3 45789999999999999999865
No 127
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=22.61 E-value=83 Score=30.76 Aligned_cols=49 Identities=29% Similarity=0.349 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++..-+.+ .+ .-.++|...|+|...|.+.+..+|+++++-+
T Consensus 106 ~L~~~~r~i~~l~~~~----g~----~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELE----GL----SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888999998776655 33 3478999999999999999999999987644
No 128
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.59 E-value=79 Score=30.62 Aligned_cols=49 Identities=20% Similarity=0.285 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++.-.+.+. + .-.++|..+|+|..-|.+....+|+++++-+
T Consensus 122 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN----L----TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 2 3468999999999999999999999987644
No 129
>cd00131 PAX Paired Box domain
Probab=22.49 E-value=3.4e+02 Score=25.91 Aligned_cols=46 Identities=17% Similarity=0.070 Sum_probs=32.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------Chhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGL-------SRSQVSNWFINA 515 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGL-------S~~QVsNWFiNa 515 (716)
....+....+..+..+ ||.-+..|-.++-...|+ +...|+.||.++
T Consensus 75 ~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3556666666667666 688888777666335576 999999987653
No 130
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=22.49 E-value=1.5e+02 Score=34.05 Aligned_cols=58 Identities=24% Similarity=0.199 Sum_probs=45.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhHHHHH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMY 528 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmiee~~ 528 (716)
.||+..+.+|+-.|.-.-..|+ .-.++|+.+|+|+..|..+..-+++++++|.....+
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l 407 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRI 407 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHH
Confidence 4899999999888762111244 468899999999999999999999999987654443
No 131
>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=22.37 E-value=96 Score=30.47 Aligned_cols=49 Identities=18% Similarity=0.224 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++..-+.+. . .-.++|+.+|+|..-|.++..-+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--F------ESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58899999988877763 2 4578999999999999999999999998755
No 132
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.24 E-value=1.1e+02 Score=30.24 Aligned_cols=48 Identities=25% Similarity=0.336 Sum_probs=39.0
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 468 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 468 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
++++..+++.-.+++ .| ...++|+.+|+|+..|...+..+|.++.+.+
T Consensus 136 l~~~~~~~v~l~~~~----Gl----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE----GL----SVEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred cCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 677788888777665 55 5678999999999999999999998876543
No 133
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.83 E-value=70 Score=31.35 Aligned_cols=49 Identities=16% Similarity=0.090 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.-.+.+. + .-.++|+.+|+|...|.....-+|+++++.+
T Consensus 111 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 111 KLPQDQREALILVGASG----F----SYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred hCCHHHHHHhhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47999999988776662 2 3468999999999999999999999987654
No 134
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.59 E-value=1.2e+02 Score=33.10 Aligned_cols=53 Identities=23% Similarity=0.186 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.+|..-|.-+...++ .-.++|+.+|+|+..|+.+...+|+++|+.+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~----s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAA----TLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCc----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999998765522212233 5688999999999999999999999998755
No 135
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.55 E-value=81 Score=29.98 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.+|.--+.+. + .-.++|+.+|++..-|.+...-+|+++++.+
T Consensus 118 ~L~~~~r~vl~L~~~~g----~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG----W----STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998777662 3 2468999999999999999999999987644
No 136
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=21.45 E-value=1e+02 Score=29.48 Aligned_cols=50 Identities=14% Similarity=0.157 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhhH
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 524 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpmi 524 (716)
.||++...++.--+.+. . .-.++|..+|++...|..+...+|+++++-+.
T Consensus 119 ~L~~~~r~i~~l~~~~~--~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--Y------SYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888888876655552 2 34789999999999999999999999987553
No 137
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=21.35 E-value=85 Score=30.67 Aligned_cols=47 Identities=17% Similarity=0.104 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 522 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKp 522 (716)
.||+..+.++.. +.+ .| .-.++|..+|+|+..|.+....+|+++++-
T Consensus 155 ~L~~~~r~vl~l-~~e----~~----s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 155 LLSELEKEVLEL-YLD----GK----SYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred hCCHHHHHHHHH-HHc----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888899877 665 23 347899999999999998888888887653
No 138
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=21.33 E-value=1e+02 Score=22.10 Aligned_cols=23 Identities=35% Similarity=0.371 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChhhhhhhchhhh
Q 005052 494 KHILARQTGLSRSQVSNWFINAR 516 (716)
Q Consensus 494 K~~LAkqTGLS~~QVsNWFiNaR 516 (716)
...+|+.+|+++..|.+|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45888999999999999988764
No 139
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=21.20 E-value=76 Score=32.11 Aligned_cols=53 Identities=19% Similarity=0.100 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.-+....+ .-.++|+.+|+|...|.++...+|+++++.+
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~----s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEK----TQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4889998888765521101122 3578999999999999999999999998754
No 140
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=21.09 E-value=1e+02 Score=29.67 Aligned_cols=49 Identities=22% Similarity=0.266 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||++.+.++.--+.+ -| .-.++|+.+|+|...|.++..-+|+++++-+
T Consensus 100 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELE----GL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5889999998877666 23 3478999999999999999999999887643
No 141
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=21.00 E-value=92 Score=30.20 Aligned_cols=49 Identities=22% Similarity=0.173 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++.--+.+. -.-.++|+.+|++..-|.++...+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 24578999999999999999999999987643
No 142
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.60 E-value=1.2e+02 Score=29.31 Aligned_cols=49 Identities=14% Similarity=0.117 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++.--+.+. -.-.++|+.+|+|..-|.+....+|.++++-+
T Consensus 117 ~Lp~~~r~i~~l~~~e~--------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--------YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999887766663 13478999999999999999999999987654
No 143
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.57 E-value=1.2e+02 Score=30.80 Aligned_cols=52 Identities=31% Similarity=0.415 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 519 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRl 519 (716)
.|+++++++|+.-|..= ..=||....-.+||++.|+++.-+..=..++=+|+
T Consensus 155 ~LTdrQ~~vL~~A~~~G-YFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG-YFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 59999999998887753 23468999999999999999998876655555554
No 144
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.40 E-value=61 Score=30.76 Aligned_cols=49 Identities=20% Similarity=0.157 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.+|..-+.+ .+ .-.++|+.+|+|...|.+.+..+|+++++-+
T Consensus 120 ~L~~~~r~vl~l~~~~----g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 120 TLSLEHRAVLVLHDLE----DL----PQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hCCHHHeeeeeehHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888776655 33 3578999999999999999999999987644
No 145
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=20.21 E-value=91 Score=31.02 Aligned_cols=49 Identities=14% Similarity=0.062 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhchhh
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 523 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkKpm 523 (716)
.||+..+.++..-+.+. -.-.++|..+|++...|.++...+|+++++-+
T Consensus 133 ~Lp~~~r~v~~l~~~~g--------~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 133 ALPPERREALILTQVLG--------YTYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred cCCHHHHHHhhhHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999987776663 23578999999999999999999999987654
No 146
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=20.13 E-value=73 Score=30.15 Aligned_cols=17 Identities=12% Similarity=0.526 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHhhhc
Q 005052 13 FFFFFFFFLFFFCFVFN 29 (716)
Q Consensus 13 ~~~~~~~~~~~~~~~~~ 29 (716)
.|+++||++||+|+++|
T Consensus 7 iii~~i~l~~~~~~~~~ 23 (130)
T PF12273_consen 7 IIIVAILLFLFLFYCHN 23 (130)
T ss_pred HHHHHHHHHHHHHHHHH
No 147
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=20.03 E-value=89 Score=31.56 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhchhhhhhhch
Q 005052 467 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 521 (716)
Q Consensus 467 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~~QVsNWFiNaRrRlkK 521 (716)
.||++...++..-|.+ . ..-.++|+.+|+|+..|..+-..+.+|+++
T Consensus 183 ~L~~~e~~i~~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYFK----D----KTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5899999998876654 2 257889999999999999998888888865
Done!