Query 038021
Match_columns 675
No_of_seqs 314 out of 982
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 06:43:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038021.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038021hhsearch_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 9.1E-42 2E-46 319.1 13.5 139 205-350 1-139 (140)
2 PF07526 POX: Associated with 100.0 1.4E-41 3E-46 320.5 13.6 138 209-350 1-139 (140)
3 KOG0773 Transcription factor M 100.0 3.6E-33 7.8E-38 293.4 10.7 260 207-473 45-312 (342)
4 KOG0774 Transcription factor P 99.9 3.2E-24 6.8E-29 217.6 10.1 153 277-464 96-252 (334)
5 KOG0775 Transcription factor S 99.6 4.1E-16 8.9E-21 160.0 8.9 78 374-459 139-232 (304)
6 PF05920 Homeobox_KN: Homeobox 99.6 1E-15 2.2E-20 116.9 4.1 40 418-457 1-40 (40)
7 cd00086 homeodomain Homeodomai 99.3 3.5E-12 7.6E-17 101.0 6.7 57 402-461 2-58 (59)
8 PF00046 Homeobox: Homeobox do 99.3 6.3E-12 1.4E-16 100.2 6.0 57 401-460 1-57 (57)
9 smart00389 HOX Homeodomain. DN 99.3 1E-11 2.2E-16 98.0 6.6 55 402-459 2-56 (56)
10 KOG0487 Transcription factor A 98.7 1E-08 2.2E-13 108.5 3.5 59 400-461 235-293 (308)
11 KOG0493 Transcription factor E 98.6 3.4E-08 7.5E-13 101.8 4.5 61 398-461 244-304 (342)
12 KOG0842 Transcription factor t 98.6 3.5E-08 7.6E-13 104.5 3.9 61 400-463 152-213 (307)
13 KOG0489 Transcription factor z 98.5 6.4E-08 1.4E-12 100.4 3.8 59 400-461 159-217 (261)
14 KOG0843 Transcription factor E 98.5 1.5E-07 3.3E-12 92.9 6.2 62 400-464 102-163 (197)
15 KOG0483 Transcription factor H 98.5 1.7E-07 3.7E-12 94.1 5.2 70 400-472 50-119 (198)
16 TIGR01565 homeo_ZF_HD homeobox 98.4 2.7E-07 5.8E-12 76.3 5.2 52 401-455 2-57 (58)
17 KOG0850 Transcription factor D 98.4 3.7E-07 8E-12 93.0 4.9 59 400-461 122-180 (245)
18 KOG0488 Transcription factor B 98.3 6E-07 1.3E-11 95.5 5.7 59 402-463 174-232 (309)
19 COG5576 Homeodomain-containing 98.2 1.1E-06 2.3E-11 85.5 4.9 59 400-461 51-109 (156)
20 KOG0485 Transcription factor N 98.2 1.2E-06 2.5E-11 88.9 4.2 61 400-463 104-164 (268)
21 KOG0492 Transcription factor M 98.1 3.8E-06 8.3E-11 84.8 5.8 60 400-462 144-203 (246)
22 KOG3802 Transcription factor O 98.1 2.6E-06 5.6E-11 92.6 3.7 59 400-461 294-352 (398)
23 KOG2251 Homeobox transcription 98.0 4.3E-06 9.4E-11 85.0 4.6 59 400-461 37-95 (228)
24 KOG0484 Transcription factor P 98.0 1.1E-05 2.3E-10 74.1 6.3 60 401-463 18-77 (125)
25 KOG4577 Transcription factor L 98.0 1.1E-05 2.5E-10 84.6 6.7 61 399-462 166-226 (383)
26 KOG0848 Transcription factor C 98.0 4.5E-06 9.7E-11 86.9 3.4 56 406-464 205-260 (317)
27 KOG0494 Transcription factor C 97.9 9.4E-06 2E-10 84.2 4.9 55 404-461 145-199 (332)
28 KOG0486 Transcription factor P 97.9 6.3E-06 1.4E-10 87.3 3.5 59 400-461 112-170 (351)
29 KOG0491 Transcription factor B 97.8 1E-05 2.2E-10 79.4 2.3 56 403-461 103-158 (194)
30 KOG2252 CCAAT displacement pro 97.7 4.8E-05 1.1E-09 85.6 5.6 56 400-458 420-475 (558)
31 KOG0844 Transcription factor E 97.6 3E-05 6.5E-10 82.0 1.7 61 400-463 181-241 (408)
32 PF03792 PBC: PBC domain; Int 97.5 0.00049 1.1E-08 69.0 9.5 86 279-381 102-191 (191)
33 KOG0773 Transcription factor M 97.3 0.0001 2.2E-09 78.6 2.1 60 401-461 96-155 (342)
34 KOG0849 Transcription factor P 97.0 0.00054 1.2E-08 74.5 4.3 58 401-461 177-234 (354)
35 KOG0490 Transcription factor, 97.0 0.00039 8.5E-09 68.9 2.3 59 400-461 60-118 (235)
36 KOG1168 Transcription factor A 96.9 0.00037 8E-09 73.6 1.2 59 399-460 308-366 (385)
37 KOG0847 Transcription factor, 96.8 0.00073 1.6E-08 69.1 3.1 56 405-463 172-227 (288)
38 PF11569 Homez: Homeodomain le 96.2 0.004 8.7E-08 51.6 3.0 43 412-457 10-52 (56)
39 KOG0490 Transcription factor, 93.0 0.081 1.8E-06 52.5 3.3 59 400-461 153-211 (235)
40 PF03791 KNOX2: KNOX2 domain ; 92.5 0.12 2.5E-06 42.5 2.9 42 297-346 8-51 (52)
41 KOG1146 Homeobox protein [Gene 85.9 0.61 1.3E-05 58.2 3.5 59 402-463 905-963 (1406)
42 KOG3623 Homeobox transcription 74.6 4.4 9.5E-05 48.5 5.2 44 412-458 568-611 (1007)
43 PF04218 CENP-B_N: CENP-B N-te 72.9 6.4 0.00014 31.9 4.3 47 401-456 1-48 (53)
44 PF11285 DUF3086: Protein of u 71.4 40 0.00087 36.2 10.8 58 284-357 7-64 (283)
45 cd06171 Sigma70_r4 Sigma70, re 64.8 9.4 0.0002 28.2 3.5 45 407-459 11-55 (55)
46 PF04545 Sigma70_r4: Sigma-70, 64.6 8.5 0.00018 30.0 3.3 47 406-460 4-50 (50)
47 PF01527 HTH_Tnp_1: Transposas 62.6 12 0.00027 31.0 4.2 46 402-455 2-48 (76)
48 cd00569 HTH_Hin_like Helix-tur 59.6 23 0.0005 23.2 4.5 39 405-451 4-42 (42)
49 PF08281 Sigma70_r4_2: Sigma-7 59.5 14 0.00031 28.9 3.9 45 406-458 10-54 (54)
50 PRK09642 RNA polymerase sigma 48.8 28 0.00061 32.6 4.6 49 407-463 107-155 (160)
51 PRK12530 RNA polymerase sigma 47.7 27 0.00057 34.2 4.4 54 406-467 134-187 (189)
52 TIGR02985 Sig70_bacteroi1 RNA 44.9 36 0.00079 31.2 4.7 48 406-461 113-160 (161)
53 PRK12514 RNA polymerase sigma 43.9 36 0.00079 32.6 4.6 48 406-461 129-176 (179)
54 PRK09644 RNA polymerase sigma 43.6 31 0.00068 32.6 4.1 50 405-462 107-156 (165)
55 PRK00118 putative DNA-binding 43.5 27 0.00058 32.5 3.5 48 406-461 17-64 (104)
56 PRK06759 RNA polymerase factor 43.1 28 0.00061 32.3 3.6 47 406-460 106-152 (154)
57 TIGR02937 sigma70-ECF RNA poly 43.1 36 0.00079 30.1 4.2 48 406-461 110-157 (158)
58 PRK09652 RNA polymerase sigma 42.4 31 0.00067 32.4 3.8 49 406-462 128-176 (182)
59 PF13443 HTH_26: Cro/C1-type H 42.2 32 0.00069 27.6 3.4 37 415-458 2-38 (63)
60 PRK06811 RNA polymerase factor 39.3 38 0.00083 33.0 4.1 50 406-463 131-180 (189)
61 PRK12520 RNA polymerase sigma 38.9 45 0.00098 32.4 4.5 52 406-465 131-182 (191)
62 PRK03975 tfx putative transcri 38.6 50 0.0011 32.3 4.7 50 405-463 5-54 (141)
63 TIGR02939 RpoE_Sigma70 RNA pol 38.0 39 0.00084 32.4 3.8 49 406-462 138-186 (190)
64 PRK11924 RNA polymerase sigma 37.8 43 0.00093 31.3 4.0 49 407-463 126-174 (179)
65 PRK12545 RNA polymerase sigma 37.0 58 0.0013 32.2 5.0 50 406-463 139-188 (201)
66 PRK12532 RNA polymerase sigma 37.0 52 0.0011 32.1 4.6 52 406-465 136-187 (195)
67 PRK09646 RNA polymerase sigma 36.8 42 0.0009 32.9 3.9 49 406-462 142-190 (194)
68 PRK12512 RNA polymerase sigma 36.2 36 0.00079 32.7 3.3 49 406-462 131-179 (184)
69 PRK12541 RNA polymerase sigma 35.2 51 0.0011 31.0 4.1 48 406-461 112-159 (161)
70 cd00131 PAX Paired Box domain 35.0 1.9E+02 0.0042 27.4 7.9 47 405-454 74-127 (128)
71 PRK09648 RNA polymerase sigma 34.8 61 0.0013 31.4 4.7 48 406-461 139-186 (189)
72 PRK09047 RNA polymerase factor 34.3 56 0.0012 30.4 4.2 50 405-462 105-154 (161)
73 TIGR02999 Sig-70_X6 RNA polyme 34.0 65 0.0014 30.8 4.6 47 407-461 135-181 (183)
74 PRK11511 DNA-binding transcrip 33.9 77 0.0017 29.5 5.0 47 405-455 4-50 (127)
75 PRK08583 RNA polymerase sigma 33.5 55 0.0012 33.7 4.3 48 406-461 205-252 (257)
76 PRK12544 RNA polymerase sigma 33.4 77 0.0017 31.8 5.3 52 406-465 148-199 (206)
77 TIGR02393 RpoD_Cterm RNA polym 33.2 74 0.0016 32.5 5.1 56 406-465 176-231 (238)
78 PRK12526 RNA polymerase sigma 33.1 65 0.0014 32.0 4.6 49 406-462 153-201 (206)
79 TIGR02941 Sigma_B RNA polymera 33.1 50 0.0011 34.0 3.9 49 406-462 205-253 (255)
80 TIGR02989 Sig-70_gvs1 RNA poly 33.1 68 0.0015 29.8 4.5 47 406-460 111-157 (159)
81 smart00421 HTH_LUXR helix_turn 32.8 86 0.0019 23.5 4.3 45 406-459 3-47 (58)
82 PRK04217 hypothetical protein; 32.0 78 0.0017 29.8 4.6 50 405-462 41-90 (110)
83 PRK12519 RNA polymerase sigma 31.6 50 0.0011 32.0 3.5 49 406-462 141-189 (194)
84 TIGR02943 Sig70_famx1 RNA poly 30.7 72 0.0016 31.2 4.5 51 406-464 131-181 (188)
85 PRK12536 RNA polymerase sigma 30.5 65 0.0014 31.1 4.0 48 407-462 130-177 (181)
86 TIGR03001 Sig-70_gmx1 RNA poly 30.3 86 0.0019 32.6 5.1 50 406-463 161-210 (244)
87 PRK12546 RNA polymerase sigma 30.1 53 0.0011 32.4 3.4 49 406-462 113-161 (188)
88 PRK12547 RNA polymerase sigma 29.9 83 0.0018 29.9 4.6 48 406-461 112-159 (164)
89 PRK12523 RNA polymerase sigma 29.8 79 0.0017 30.2 4.5 47 406-460 119-165 (172)
90 PRK12531 RNA polymerase sigma 29.4 80 0.0017 30.9 4.5 50 405-462 140-189 (194)
91 PRK13919 putative RNA polymera 29.3 87 0.0019 30.1 4.7 48 406-461 135-182 (186)
92 TIGR02980 SigBFG RNA polymeras 29.3 55 0.0012 32.8 3.4 48 406-461 178-225 (227)
93 PRK09647 RNA polymerase sigma 28.9 82 0.0018 31.5 4.6 49 406-462 138-186 (203)
94 PRK05602 RNA polymerase sigma 28.8 81 0.0018 30.4 4.4 47 407-461 129-175 (186)
95 PRK12533 RNA polymerase sigma 28.7 73 0.0016 32.4 4.2 48 406-461 134-181 (216)
96 PRK06930 positive control sigm 28.2 70 0.0015 31.8 3.9 52 406-465 114-165 (170)
97 TIGR02983 SigE-fam_strep RNA p 28.0 89 0.0019 29.2 4.4 48 406-461 110-157 (162)
98 PF00196 GerE: Bacterial regul 28.0 1.1E+02 0.0023 24.6 4.3 49 406-463 3-51 (58)
99 TIGR02954 Sig70_famx3 RNA poly 27.7 69 0.0015 30.4 3.6 48 406-461 119-166 (169)
100 PRK12535 RNA polymerase sigma 27.7 67 0.0015 31.9 3.7 50 406-463 133-182 (196)
101 PRK12516 RNA polymerase sigma 27.6 1E+02 0.0022 30.3 4.9 49 407-463 117-165 (187)
102 TIGR02948 SigW_bacill RNA poly 27.5 86 0.0019 29.9 4.3 48 406-461 136-183 (187)
103 cd01392 HTH_LacI Helix-turn-he 27.4 56 0.0012 25.1 2.5 21 435-455 2-22 (52)
104 PHA00542 putative Cro-like pro 27.3 1.7E+02 0.0038 25.5 5.8 35 432-466 33-67 (82)
105 PRK12524 RNA polymerase sigma 27.3 95 0.0021 30.4 4.6 48 406-461 136-183 (196)
106 PRK15369 two component system 27.1 78 0.0017 29.1 3.8 48 405-461 148-195 (211)
107 PRK12515 RNA polymerase sigma 26.5 1.2E+02 0.0026 29.4 5.1 48 406-461 131-178 (189)
108 PRK06986 fliA flagellar biosyn 26.3 82 0.0018 32.0 4.1 47 407-461 185-231 (236)
109 PRK12537 RNA polymerase sigma 25.9 76 0.0016 30.7 3.6 48 406-461 133-180 (182)
110 TIGR02479 FliA_WhiG RNA polyme 25.7 95 0.0021 31.2 4.4 48 406-461 175-222 (224)
111 PRK12538 RNA polymerase sigma 25.5 1.2E+02 0.0025 31.3 5.1 49 407-463 172-220 (233)
112 PRK09639 RNA polymerase sigma 25.4 1.3E+02 0.0028 28.2 4.9 47 407-462 113-159 (166)
113 PF13518 HTH_28: Helix-turn-he 25.0 68 0.0015 24.6 2.5 24 433-456 15-38 (52)
114 PRK07598 RNA polymerase sigma 24.6 1.5E+02 0.0032 33.9 6.0 59 406-468 350-408 (415)
115 PRK12529 RNA polymerase sigma 24.3 1.1E+02 0.0023 29.6 4.3 47 406-460 127-173 (178)
116 PF08933 DUF1864: Domain of un 23.8 50 0.0011 37.1 2.1 78 285-363 255-343 (387)
117 PRK07670 RNA polymerase sigma 23.6 1.1E+02 0.0024 31.4 4.6 48 406-461 201-248 (251)
118 cd06170 LuxR_C_like C-terminal 23.5 1.3E+02 0.0029 22.7 3.9 45 407-460 1-45 (57)
119 PRK11923 algU RNA polymerase s 23.4 1.2E+02 0.0026 29.4 4.4 48 407-462 139-186 (193)
120 PRK12527 RNA polymerase sigma 23.2 1.3E+02 0.0029 28.1 4.6 47 407-461 106-152 (159)
121 PF09325 Vps5: Vps5 C terminal 23.2 5.8E+02 0.013 25.6 9.4 69 285-354 35-103 (236)
122 PRK09637 RNA polymerase sigma 23.1 1.4E+02 0.003 29.2 4.8 48 406-461 106-153 (181)
123 PRK12528 RNA polymerase sigma 23.0 1.3E+02 0.0028 28.3 4.5 46 406-459 113-158 (161)
124 PRK12513 RNA polymerase sigma 22.9 65 0.0014 31.3 2.5 49 406-462 139-187 (194)
125 TIGR02947 SigH_actino RNA poly 22.8 70 0.0015 31.1 2.7 50 406-463 131-180 (193)
126 PRK09415 RNA polymerase factor 22.5 1.1E+02 0.0024 29.6 4.0 48 406-461 127-174 (179)
127 PRK12517 RNA polymerase sigma 22.4 1.7E+02 0.0036 28.8 5.3 50 406-463 128-177 (188)
128 PRK07037 extracytoplasmic-func 22.3 1.5E+02 0.0032 27.8 4.7 49 406-462 109-157 (163)
129 PRK07408 RNA polymerase sigma 22.3 1.1E+02 0.0025 31.7 4.3 49 406-462 203-251 (256)
130 PRK09649 RNA polymerase sigma 22.0 96 0.0021 30.2 3.5 47 406-460 130-176 (185)
131 PRK12522 RNA polymerase sigma 21.9 1.5E+02 0.0034 28.1 4.8 50 406-463 119-168 (173)
132 PRK12543 RNA polymerase sigma 21.7 1.4E+02 0.0031 28.7 4.6 50 406-463 117-166 (179)
133 PRK06288 RNA polymerase sigma 21.4 1.1E+02 0.0024 31.8 4.0 49 406-462 212-260 (268)
134 PRK05657 RNA polymerase sigma 21.3 1.4E+02 0.0031 32.4 5.0 53 406-462 262-314 (325)
135 PRK08295 RNA polymerase factor 21.3 1.4E+02 0.003 29.2 4.4 47 406-461 155-201 (208)
136 PRK12542 RNA polymerase sigma 21.1 1.5E+02 0.0032 28.6 4.6 48 406-461 122-169 (185)
137 TIGR02959 SigZ RNA polymerase 20.9 1.6E+02 0.0034 28.3 4.7 48 406-461 100-147 (170)
138 PRK12518 RNA polymerase sigma 20.8 71 0.0015 30.3 2.3 48 407-462 121-168 (175)
139 PF12998 ING: Inhibitor of gro 20.8 5.8E+02 0.013 22.4 9.8 59 288-346 15-74 (105)
140 PF04967 HTH_10: HTH DNA bindi 20.5 1.9E+02 0.0041 23.9 4.4 48 407-455 1-48 (53)
141 PRK09641 RNA polymerase sigma 20.4 1.2E+02 0.0025 29.0 3.7 48 406-461 136-183 (187)
142 PF07638 Sigma70_ECF: ECF sigm 20.0 1.5E+02 0.0033 29.1 4.5 47 407-461 136-182 (185)
No 1
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=9.1e-42 Score=319.11 Aligned_cols=139 Identities=56% Similarity=0.767 Sum_probs=110.7
Q ss_pred CcccccccCCcchhHHHHHHHHHhhhhccccCCCCcccchhhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q 038021 205 PSIARAIPSSKYLKAAQQLLDEVVNVRKALRQPDGEKSQSTHEQRMNNSKDGDGGSKDVTSNTQESPSNSPNELSHAERQ 284 (675)
Q Consensus 205 ~~~~~~l~~Sryl~~aQeLL~e~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~e~~ 284 (675)
+||+++|++|||||||||||||||+|++.++.....+...... . ....+.++...+ ..+..+..++|+++||+
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~-----g~s~~~~~~~ls~~~r~ 73 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSGNDSPV-S-TSSNEGGGENLS-----GGSSSSEVPPLSTAERQ 73 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcccHHhhcccccccccccc-c-ccccCCCcCCCC-----CCCCCCCCCCCchhHHH
Confidence 4789999999999999999999999998877654332110000 0 011111111111 11223456899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhhHHHHHHHHHHhhhhhhHHHH
Q 038021 285 ELQNKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPYTALALQTISRHFRCLRDAIC 350 (675)
Q Consensus 285 e~q~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~pyt~lALq~IsrhFr~LrdaI~ 350 (675)
|+|+||+||+.||+|||+||+|||+|||+||++||+|+|.|+|+|||+||||+||||||||||+|+
T Consensus 74 e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 74 ELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999999999996
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=1.4e-41 Score=320.46 Aligned_cols=138 Identities=57% Similarity=0.784 Sum_probs=103.7
Q ss_pred ccccCCcchhHHHHHHHHHhhhhccccCCC-CcccchhhhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q 038021 209 RAIPSSKYLKAAQQLLDEVVNVRKALRQPD-GEKSQSTHEQRMNNSKDGDGGSKDVTSNTQESPSNSPNELSHAERQELQ 287 (675)
Q Consensus 209 ~~l~~Sryl~~aQeLL~e~~~v~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~e~~e~q 287 (675)
++|++|||||||||||||||+|++..+... ........ ........ .+....+....+.....++++++||+|+|
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~~~--~~~~~~~~--~~~~~~~~~~~~~~~~~~~ls~~~~~e~q 76 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGAPG--GANSSGSS--SSSGGSSSSSSSSDSSSPELSPAERQELQ 76 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhcccccc--ccccCCCC--CCCCCCCCCccccCCCCCCCChhhHHHHH
Confidence 479999999999999999999986311111 10100000 00000000 00011122223334556899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhhHHHHHHHHHHhhhhhhHHHH
Q 038021 288 NKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPYTALALQTISRHFRCLRDAIC 350 (675)
Q Consensus 288 ~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~pyt~lALq~IsrhFr~LrdaI~ 350 (675)
+||+|||.||||||+||+|||+|||+||++||+|||.|+|+|||+|||||||||||||||+|+
T Consensus 77 ~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~ 139 (140)
T PF07526_consen 77 RKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999999996
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=100.00 E-value=3.6e-33 Score=293.44 Aligned_cols=260 Identities=41% Similarity=0.563 Sum_probs=194.6
Q ss_pred ccccccCCcchhHHHHHHHHHhhhhccccCCCCcccchhhhhhcCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCHHHHHH
Q 038021 207 IARAIPSSKYLKAAQQLLDEVVNVRKALRQPDGEKSQSTHEQRMNNSKDGDGGSKDV-TSNTQESPSNSPNELSHAERQE 285 (675)
Q Consensus 207 ~~~~l~~Sryl~~aQeLL~e~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ls~~e~~e 285 (675)
+...+..++||++||+||+++|++............... ............ ....+..... ....+..++++
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~n~~~~s-~~~~~~~~~~~ 117 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVP------RSPASLSPPEDKGARRGNATRES-ATLKAWLEEHR 117 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccc------cccccccCccccccccccccccc-cccccchhhhh
Confidence 556788999999999999999999754422221111000 000000000000 0000001111 33446678999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhhHHHHHHHHHHhhhhhhH--HHHHHHHHHHhhhCcc
Q 038021 286 LQNKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPYTALALQTISRHFRCLRD--AICGQIRATRKSLGEQ 363 (675)
Q Consensus 286 ~q~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~pyt~lALq~IsrhFr~Lrd--aI~~qi~~~~~~lge~ 363 (675)
++.+++|++.|+.+|+.+|.+||..|+.|..+|+.+.|.+.+.+++..++..+++||+++++ +|.+|+......+++.
T Consensus 118 ~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~ 197 (342)
T KOG0773|consen 118 LNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGES 197 (342)
T ss_pred hccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999998 7888888777766543
Q ss_pred cc-ccCCc---CcccccchhhhHHHHHhHH-hhhcccccccCCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 038021 364 EN-SENSK---GVGITRLRYVDQQLRQQRA-LQHLGMMQQHAWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLAR 438 (675)
Q Consensus 364 ~~-s~~~~---~~~~~rlr~~Dqel~~qra-lq~lg~~~~~~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~ 438 (675)
.. +.... ...+...+..++.+++++. ....+..+..+||++++||+.++.+|+.||++|+.||||++.+|..||+
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~ 277 (342)
T KOG0773|consen 198 EQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAK 277 (342)
T ss_pred cccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccch
Confidence 21 11111 1124555666666666654 2233334456999999999999999999999999999999999999999
Q ss_pred HhCCChhhHhhhhhhhhhhhchhhHHHHHHHHhhc
Q 038021 439 QTGLTRSQVSNWFINARVRLWKPMVEEMYKEEFAD 473 (675)
Q Consensus 439 ~TGLS~~QVsNWFiNaR~RlkKp~ie~~~ke~~~~ 473 (675)
+|||++.||+|||||+|+|+|+||+++++..+...
T Consensus 278 ~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 278 QTGLSRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred hcCCCcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 99999999999999999999999999999877665
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.90 E-value=3.2e-24 Score=217.64 Aligned_cols=153 Identities=29% Similarity=0.485 Sum_probs=129.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhhHH----HHHHHHHHhhhhhhHHHHHH
Q 038021 277 ELSHAERQELQNKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPYTA----LALQTISRHFRCLRDAICGQ 352 (675)
Q Consensus 277 ~ls~~e~~e~q~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~pyt~----lALq~IsrhFr~LrdaI~~q 352 (675)
+.+..++.+|+.|+.+++.++++..++|+|.|.++...|. +.+..++.++|++. -..+.|++.|. .|.-+
T Consensus 96 ~Asgg~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~--nlL~eQsr~RPi~~ke~e~m~~~i~~kF~----~iq~~ 169 (334)
T KOG0774|consen 96 AASGGDHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVM--NLLREQSRTRPIMPKEIERMVQIISKKFS----HIQMQ 169 (334)
T ss_pred hccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHhcccCCCCHHHHHHHHHHHHHHHH----HHHHH
Confidence 3444567899999999999999999999999999866554 58889999999964 44567788887 45556
Q ss_pred HHHHHhhhCccccccCCcCcccccchhhhHHHHHhHHhhhcccccccCCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHH
Q 038021 353 IRATRKSLGEQENSENSKGVGITRLRYVDQQLRQQRALQHLGMMQQHAWRPQRGLPESSVSILRAWLFEHFLHPYPKDTD 432 (675)
Q Consensus 353 i~~~~~~lge~~~s~~~~~~~~~rlr~~Dqel~~qralq~lg~~~~~~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~e 432 (675)
|+ +++| .++.+.|.|++| ++||||+|.|.++.||.+||..|+.||||++++
T Consensus 170 lk--------qstc---e~vmiLr~r~ld------------------arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~ 220 (334)
T KOG0774|consen 170 LK--------QSTC---EAVMILRSRFLD------------------ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEA 220 (334)
T ss_pred HH--------HHHH---HHHHHHHHHHHH------------------HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHH
Confidence 65 2222 246778888887 668999999999999999999999999999999
Q ss_pred HHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 038021 433 KIMLARQTGLTRSQVSNWFINARVRLWKPMVE 464 (675)
Q Consensus 433 K~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie 464 (675)
|++||++++++..||+|||.|+|.|.+|.+..
T Consensus 221 K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 221 KEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 99999999999999999999999999998773
No 5
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.64 E-value=4.1e-16 Score=160.03 Aligned_cols=78 Identities=40% Similarity=0.660 Sum_probs=71.2
Q ss_pred cccchhhhHHHHHhHHhhhcccccccCCCCCCCCC----------------hhHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 038021 374 ITRLRYVDQQLRQQRALQHLGMMQQHAWRPQRGLP----------------ESSVSILRAWLFEHFLHPYPKDTDKIMLA 437 (675)
Q Consensus 374 ~~rlr~~Dqel~~qralq~lg~~~~~~~RkRR~LP----------------k~a~~iLr~Wf~eH~~nPYPS~~eK~~LA 437 (675)
..+++|.++|..++|+|+.++ |+|-||+|| ++++.+||+||.. +|||++++|++||
T Consensus 139 Wl~AhY~EAek~RGR~LgaV~-----KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~---~~YPsp~eKReLA 210 (304)
T KOG0775|consen 139 WLKAHYKEAEKLRGRPLGAVD-----KYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQ---NPYPSPREKRELA 210 (304)
T ss_pred HHHHHHHHHHHhcCCcCCccc-----cceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhc---CCCCChHHHHHHH
Confidence 466789999999999999988 667777765 7889999999997 8999999999999
Q ss_pred HHhCCChhhHhhhhhhhhhhhc
Q 038021 438 RQTGLTRSQVSNWFINARVRLW 459 (675)
Q Consensus 438 ~~TGLS~~QVsNWFiNaR~Rlk 459 (675)
++|||+..||.|||+|+|.|.+
T Consensus 211 ~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 211 EATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HHhCCchhhhhhhhhhhhhhhh
Confidence 9999999999999999999987
No 6
>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=1e-15 Score=116.94 Aligned_cols=40 Identities=63% Similarity=1.145 Sum_probs=36.5
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 038021 418 WLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVR 457 (675)
Q Consensus 418 Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~R 457 (675)
||.+|+.||||+++||.+||++|||+.+||+|||+|+|+|
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 9999999999999999999999999999999999999997
No 7
>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=99.32 E-value=3.5e-12 Score=101.04 Aligned_cols=57 Identities=30% Similarity=0.522 Sum_probs=53.2
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 402 RPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 402 RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
+++..+++.++.+|++||.. +|||+.+++..||.++||+..||.+||.|+|.+.++.
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 46678999999999999999 7999999999999999999999999999999998763
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=99.27 E-value=6.3e-12 Score=100.20 Aligned_cols=57 Identities=33% Similarity=0.609 Sum_probs=53.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 401 WRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 401 ~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
+|+|+.|+++++.+|+.+|.. +|||+.+++..||..+||+..||.+||.|+|.+.+|
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 478889999999999999998 799999999999999999999999999999999764
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.26 E-value=1e-11 Score=98.00 Aligned_cols=55 Identities=27% Similarity=0.486 Sum_probs=50.6
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 038021 402 RPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLW 459 (675)
Q Consensus 402 RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rlk 459 (675)
++|..|+++++.+|++||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
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 34556999999999999998 69999999999999999999999999999999864
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.68 E-value=1e-08 Score=108.48 Aligned_cols=59 Identities=22% Similarity=0.279 Sum_probs=52.9
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.+|||-.++|.++..|++-|.- |-|.+++-|.+|++.++||..||+.||+|||+|+||-
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~ 293 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKV 293 (308)
T ss_pred cccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhh
Confidence 4456667999999999877777 5999999999999999999999999999999999875
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.60 E-value=3.4e-08 Score=101.83 Aligned_cols=61 Identities=28% Similarity=0.480 Sum_probs=57.5
Q ss_pred ccCCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 398 QHAWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 398 ~~~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
++.+|+|.-|+.++.+.|+.-|.+ |.|.++..|+.||.+.+|.+.||+.||+|+|.++||.
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 447899999999999999999999 6999999999999999999999999999999999875
No 12
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.57 E-value=3.5e-08 Score=104.45 Aligned_cols=61 Identities=25% Similarity=0.305 Sum_probs=55.0
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 400 AWRPQRG-LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 400 ~~RkRR~-LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
++||||- |++.+|-.|++-|.+ ..|-+..||+.||+..+||.+||+.||+|+|-|.||..+
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~ 213 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQK 213 (307)
T ss_pred cccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhh
Confidence 4455554 899999999999998 699999999999999999999999999999999998754
No 13
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.51 E-value=6.4e-08 Score=100.41 Aligned_cols=59 Identities=22% Similarity=0.312 Sum_probs=54.9
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.+|.|..|+..++..|+.-|.- |.|-+...|++||..+.|++.||++||+|+|+|.||.
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 5677888999999999999988 6999999999999999999999999999999998764
No 14
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.51 E-value=1.5e-07 Score=92.90 Aligned_cols=62 Identities=21% Similarity=0.273 Sum_probs=56.7
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVE 464 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie 464 (675)
.+|.|..|+.+++..|+..|.. +-|-.-.||..||+..+|+..||+.||+|+|.|.||...+
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 5677788999999999999998 7999999999999999999999999999999999886443
No 15
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.46 E-value=1.7e-07 Score=94.11 Aligned_cols=70 Identities=26% Similarity=0.289 Sum_probs=60.3
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHHhh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEEMYKEEFA 472 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~~~ke~~~ 472 (675)
.++++++|+.+++..|+.=|..| -|-.+++|..||++.||...||..||+|+|+|.|.+-.+..|..-..
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~---~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~ 119 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE---KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKR 119 (198)
T ss_pred cccccccccHHHHHHhHHhhccc---cccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHH
Confidence 45778889999999999999984 77888999999999999999999999999999988877655543333
No 16
>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=98.45 E-value=2.7e-07 Score=76.30 Aligned_cols=52 Identities=13% Similarity=0.266 Sum_probs=49.3
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 038021 401 WRPQRGLPESSVSILRAWLFEHFLHPY----PKDTDKIMLARQTGLTRSQVSNWFINAR 455 (675)
Q Consensus 401 ~RkRR~LPk~a~~iLr~Wf~eH~~nPY----PS~~eK~~LA~~TGLS~~QVsNWFiNaR 455 (675)
+|+|..|+.+++..|+..|.. ++| |+..++..||..+||+..+|..||+|.+
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 678889999999999999999 799 9999999999999999999999999964
No 17
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.36 E-value=3.7e-07 Score=93.05 Aligned_cols=59 Identities=25% Similarity=0.366 Sum_probs=53.2
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.|++|.-+..-+...|++-|.+ .-|..-.||.+||...|||..||+.||+|+|-|.||-
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 4455666899999999999998 6999999999999999999999999999999998774
No 18
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.32 E-value=6e-07 Score=95.54 Aligned_cols=59 Identities=25% Similarity=0.421 Sum_probs=52.3
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 402 RPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 402 RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
+.|.-|+..++..|+.-|.. --|-+..||..||+..|||-.||+.||+|||.|+|+.+.
T Consensus 174 ksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 174 KSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred cchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 34455999999999998888 599999999999999999999999999999998776644
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.24 E-value=1.1e-06 Score=85.50 Aligned_cols=59 Identities=22% Similarity=0.346 Sum_probs=55.3
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.+++|+..+..++.+|+.-|.. +|||+..+|..|+..++++.+-|+.||+|+|.+.++.
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred CcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence 5677888999999999999998 7999999999999999999999999999999998875
No 20
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.20 E-value=1.2e-06 Score=88.91 Aligned_cols=61 Identities=21% Similarity=0.253 Sum_probs=55.8
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
|+|+|.-|+..++..|+.-|.. ..|-+..||.-||++..|++.||+.||+|+|.|.|+...
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 6677888999999999999988 499999999999999999999999999999999877643
No 21
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.11 E-value=3.8e-06 Score=84.75 Aligned_cols=60 Identities=20% Similarity=0.307 Sum_probs=55.0
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.+++|..|+..+...|++-|.+ .-|-+.+|+.+++....||..||+.||+|+|.|.|+-.
T Consensus 144 nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 4577888999999999999999 59999999999999999999999999999999987753
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.06 E-value=2.6e-06 Score=92.60 Aligned_cols=59 Identities=17% Similarity=0.309 Sum_probs=53.8
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
+||||..|.-.++..|+..|.+ ||-|+.+|.-.||.+.+|.+..|..||+|||.|.|+.
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred ccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 4455556899999999999999 7999999999999999999999999999999999875
No 23
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.03 E-value=4.3e-06 Score=84.98 Aligned_cols=59 Identities=24% Similarity=0.376 Sum_probs=54.3
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
-+|.|..|+.++..+|++-|.+ .-||....+++||.+.+|.+.+|++||+|+|++.++.
T Consensus 37 qRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred cccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 4567778999999999999999 6999999999999999999999999999999988764
No 24
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.02 E-value=1.1e-05 Score=74.08 Aligned_cols=60 Identities=23% Similarity=0.330 Sum_probs=54.3
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 401 WRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 401 ~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
+|-|..|+..+...|+.-|.+ .-||..-.+++||-+..|+...|+.||+|+|.+.+|...
T Consensus 18 RRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 455667999999999999999 589999999999999999999999999999999988644
No 25
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.99 E-value=1.1e-05 Score=84.61 Aligned_cols=61 Identities=23% Similarity=0.336 Sum_probs=55.7
Q ss_pred cCCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 399 HAWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 399 ~~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
..+|+|..++.++...|+.-|.. .|-|..--|++|+..|||....|+.||+|+|++.|+-+
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 37899999999999999999887 69999999999999999999999999999998775543
No 26
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=97.97 E-value=4.5e-06 Score=86.86 Aligned_cols=56 Identities=25% Similarity=0.235 Sum_probs=50.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVE 464 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie 464 (675)
-++..++-.|++-|.- .+|.+...|.+||..+||++.||+.||+|||.|.+|...+
T Consensus 205 VYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred Eecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 3789999999999887 7999999999999999999999999999999998876443
No 27
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=97.93 E-value=9.4e-06 Score=84.19 Aligned_cols=55 Identities=25% Similarity=0.368 Sum_probs=50.8
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 404 QRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 404 RR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
|..|+.-+...|++-|.+ --||.--.|++||.+|+|.+.+|+.||+|+|.|.+|.
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 456999999999999999 5899999999999999999999999999999987664
No 28
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=97.92 E-value=6.3e-06 Score=87.34 Aligned_cols=59 Identities=25% Similarity=0.364 Sum_probs=53.3
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
++|-|..|+..+.+.|+.||.+ |-||+.+.+++||--|+|+...|.+||+|+|.+.+|.
T Consensus 112 qrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 3445556999999999999999 7999999999999999999999999999999987665
No 29
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=97.80 E-value=1e-05 Score=79.38 Aligned_cols=56 Identities=23% Similarity=0.363 Sum_probs=50.6
Q ss_pred CCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 403 PQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 403 kRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.|.-|...+...|.+-|.. -.|-+-.|+++||...+|+.+||+.||+|+|++.||.
T Consensus 103 ~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 103 ARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred hcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 3456888899999999987 4899999999999999999999999999999999875
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.67 E-value=4.8e-05 Score=85.60 Aligned_cols=56 Identities=27% Similarity=0.328 Sum_probs=52.8
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRL 458 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rl 458 (675)
.+|+|-.|+..+++.|++.|.+ ++||+.+..+.|+.+.+|.+.-|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 4567778999999999999999 7999999999999999999999999999999996
No 31
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.55 E-value=3e-05 Score=82.01 Aligned_cols=61 Identities=16% Similarity=0.308 Sum_probs=53.8
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.+|-|.-|+.+++..|++-|++ --|-+...|.+||...+|.+..|+.||+|+|+|.|+.++
T Consensus 181 mRRYRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 3456778999999999777776 379999999999999999999999999999999988765
No 32
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=97.51 E-value=0.00049 Score=69.02 Aligned_cols=86 Identities=20% Similarity=0.364 Sum_probs=66.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhhHHHHHHHH----HHhhhhhhHHHHHHHH
Q 038021 279 SHAERQELQNKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPYTALALQTI----SRHFRCLRDAICGQIR 354 (675)
Q Consensus 279 s~~e~~e~q~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~pyt~lALq~I----srhFr~LrdaI~~qi~ 354 (675)
.+.|..+|+.|+++++.++++..++|++.|.++...|. +.+..++.++|+|...+.+| ++.|. +|.-||+
T Consensus 102 ~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~--~lLreQs~~RPIs~keiE~m~~~i~~Kf~----~iq~qLK 175 (191)
T PF03792_consen 102 NSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVM--NLLREQSEFRPISPKEIERMVNIIHRKFS----KIQMQLK 175 (191)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH--HHHHHhcccCCCCHHHHHHHHHHHHHHHH----HHHHHHH
Confidence 34578899999999999999999999999999866555 47789999999998877554 55554 5655655
Q ss_pred HHHhhhCccccccCCcCcccccchhhh
Q 038021 355 ATRKSLGEQENSENSKGVGITRLRYVD 381 (675)
Q Consensus 355 ~~~~~lge~~~s~~~~~~~~~rlr~~D 381 (675)
+.+|+ ++.+.|.||+|
T Consensus 176 --------QstCE---aVm~LRsRflD 191 (191)
T PF03792_consen 176 --------QSTCE---AVMILRSRFLD 191 (191)
T ss_pred --------HHHHH---HHHHHHHHhcC
Confidence 33332 46788888876
No 33
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.30 E-value=0.0001 Score=78.64 Aligned_cols=60 Identities=48% Similarity=0.685 Sum_probs=55.3
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 401 WRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 401 ~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.+++.+++.++ .+|+.|+.+|..+|||++-++.+|+-.++++..||++||+|+|+|+++.
T Consensus 96 ~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 96 GARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred ccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 34567789999 9999999999999999999999999999999999999999999998654
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.04 E-value=0.00054 Score=74.50 Aligned_cols=58 Identities=28% Similarity=0.515 Sum_probs=52.8
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 401 WRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 401 ~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
+|.|..|...+...|.+||.. .|||.-..++.||++++|+...|..||.|+|.|.+|.
T Consensus 177 rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~ 234 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQ 234 (354)
T ss_pred cccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhc
Confidence 344566999999999999998 6899999999999999999999999999999998775
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.97 E-value=0.00039 Score=68.89 Aligned_cols=59 Identities=19% Similarity=0.072 Sum_probs=53.8
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.+|.|..|+..+..+|+.-|.. .+||....++.||..++++...|.+||+|+|.+.++.
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 5677778999999999999998 4999999999999999999999999999999987664
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=96.87 E-value=0.00037 Score=73.63 Aligned_cols=59 Identities=20% Similarity=0.357 Sum_probs=52.4
Q ss_pred cCCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 399 HAWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 399 ~~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
+++|||..+-.--++-|+++|.. -|-|+-+....+|++..|.++.|..||+|.|.+.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 36777777766668899999998 599999999999999999999999999999998877
No 37
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=96.85 E-value=0.00073 Score=69.14 Aligned_cols=56 Identities=25% Similarity=0.351 Sum_probs=49.7
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
-.|.-.+...|..-|.+ ..||--+++.+||...|.++.||..||+|+|.+.+|.-.
T Consensus 172 PTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 172 PTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred CCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 34888999999998888 589999999999999999999999999999998776543
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.21 E-value=0.004 Score=51.58 Aligned_cols=43 Identities=19% Similarity=0.383 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 038021 412 VSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVR 457 (675)
Q Consensus 412 ~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~R 457 (675)
.+.|+++|..| .+..+.+...|+.+++|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~h---~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKH---KQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHc---CCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 34599999995 99999999999999999999999999877543
No 39
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=93.00 E-value=0.081 Score=52.52 Aligned_cols=59 Identities=31% Similarity=0.557 Sum_probs=51.9
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 400 AWRPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 400 ~~RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.++.+..+......+|..-|.. .+||....+..|+..+|++...|..||.|.|.+.++.
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred cCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 4456667888888888888777 7999999999999999999999999999999998775
No 40
>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=92.47 E-value=0.12 Score=42.54 Aligned_cols=42 Identities=17% Similarity=0.316 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhh--HHHHHHHHHHhhhhhh
Q 038021 297 LDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPY--TALALQTISRHFRCLR 346 (675)
Q Consensus 297 l~Evd~ry~qy~~qmq~vvssfe~vag~gaa~py--t~lALq~IsrhFr~Lr 346 (675)
.+|+|+++++||+- ++ .|. ....+|+ |..|++.|+.+++.|.
T Consensus 8 dpELDqFMeaYc~~---L~-kyk----eeL~~p~~EA~~f~~~ie~qL~~Lt 51 (52)
T PF03791_consen 8 DPELDQFMEAYCDM---LV-KYK----EELQRPFQEAMEFCREIEQQLSSLT 51 (52)
T ss_pred CccHHHHHHHHHHH---HH-HHH----HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47899999999993 33 344 1335888 7889999999888653
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=85.95 E-value=0.61 Score=58.19 Aligned_cols=59 Identities=20% Similarity=0.304 Sum_probs=52.0
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 402 RPQRGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 402 RkRR~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
+.|..+...++++|+..|.. --||+.++.+.|.+..+|....|..||+|+|.+.+|+..
T Consensus 905 a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 905 AYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 34445677889999999888 689999999999999999999999999999999998854
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=74.62 E-value=4.4 Score=48.45 Aligned_cols=44 Identities=25% Similarity=0.447 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 038021 412 VSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRL 458 (675)
Q Consensus 412 ~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rl 458 (675)
+.+|+++|.. |+.|+.+|...+|.+.||...-|+.||.+.+...
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 7789999888 7999999999999999999999999999998754
No 43
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=72.89 E-value=6.4 Score=31.95 Aligned_cols=47 Identities=30% Similarity=0.354 Sum_probs=30.4
Q ss_pred CCCCCCCChhH-HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhh
Q 038021 401 WRPQRGLPESS-VSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARV 456 (675)
Q Consensus 401 ~RkRR~LPk~a-~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~ 456 (675)
+|+|+.|+-+. .++++. +.. .+ -+..||+..|++..+|.+|..|+..
T Consensus 1 krkR~~LTl~eK~~iI~~-~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKR-LEE---GE-----SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSSS--HHHHHHHHHH-HHC---TT------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCCccCCHHHHHHHHHH-HHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 46778888555 455544 444 23 5788999999999999999999643
No 44
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=71.40 E-value=40 Score=36.25 Aligned_cols=58 Identities=21% Similarity=0.434 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhhHHHHHHHHHHhhhhhhHHHHHHHHHHH
Q 038021 284 QELQNKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPYTALALQTISRHFRCLRDAICGQIRATR 357 (675)
Q Consensus 284 ~e~q~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~pyt~lALq~IsrhFr~LrdaI~~qi~~~~ 357 (675)
.+++.+|..|..-++++++|-++-.++|. ++|- |.+ +.|.+..+-.+|-..+.++...
T Consensus 7 ~eL~qrk~~Lq~eIe~LerR~~ri~~Emr---tsFa---G~S----------q~lA~RVqGFkdYLvGsLQDLa 64 (283)
T PF11285_consen 7 KELEQRKQALQIEIEQLERRRERIEKEMR---TSFA---GQS----------QDLAIRVQGFKDYLVGSLQDLA 64 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---cccc---cch----------HHHHHHHhhhHHHHHHHHHHHH
Confidence 48899999999999999999999999873 3332 332 4555666666777777766543
No 45
>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=64.84 E-value=9.4 Score=28.23 Aligned_cols=45 Identities=24% Similarity=0.248 Sum_probs=35.8
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLW 459 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rlk 459 (675)
||...+.++..++.+. + .-..+|..+|++...|..|....+.+++
T Consensus 11 l~~~~~~~~~~~~~~~----~----~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 11 LPEREREVILLRFGEG----L----SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred CCHHHHHHHHHHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 7888888888877652 2 3566899999999999999988887753
No 46
>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=64.57 E-value=8.5 Score=30.03 Aligned_cols=47 Identities=28% Similarity=0.360 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
.||++.+.+|...|++ ++ .-.++|+..|+|...|..+...+..++++
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 4889999999888865 33 35679999999999999999999888764
No 47
>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=62.55 E-value=12 Score=31.02 Aligned_cols=46 Identities=24% Similarity=0.341 Sum_probs=30.1
Q ss_pred CCCCCCChhHH-HHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 038021 402 RPQRGLPESSV-SILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINAR 455 (675)
Q Consensus 402 RkRR~LPk~a~-~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR 455 (675)
++|+.||++.+ +++...+.. ......+|+..|++..+|.+|-.-.+
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 45677887774 455555454 35788999999999999999976665
No 48
>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=59.56 E-value=23 Score=23.24 Aligned_cols=39 Identities=21% Similarity=0.270 Sum_probs=27.0
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWF 451 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWF 451 (675)
+.++.+.+..+..++.+ .+ ....+|+..|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34666666655555543 33 35578999999999999984
No 49
>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=59.45 E-value=14 Score=28.91 Aligned_cols=45 Identities=27% Similarity=0.344 Sum_probs=33.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRL 458 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rl 458 (675)
.||+..+.++.--+.+. + .-.++|+.+|++...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~g----~----s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG----M----SYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC----c----CHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 38888888887766663 2 456799999999999999999998864
No 50
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.80 E-value=28 Score=32.62 Aligned_cols=49 Identities=22% Similarity=0.174 Sum_probs=40.1
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
||+..+.++.-.+.+. .+ -.++|+.+|++...|.+++.-+|.++++.+-
T Consensus 107 Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 107 LPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred CCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 8999999997776663 22 2569999999999999999999999877543
No 51
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=47.72 E-value=27 Score=34.23 Aligned_cols=54 Identities=11% Similarity=0.236 Sum_probs=43.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEEMY 467 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~~~ 467 (675)
.||+..+.++.--+++. + .-.++|..+|++...|.++..-+|+++++.+.+.++
T Consensus 134 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 187 (189)
T PRK12530 134 HLPAQQARVFMMREYLE----L----SSEQICQECDISTSNLHVLLYRARLQLQACLSKNWF 187 (189)
T ss_pred hCCHHHHHHHhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 38999999998777662 2 246799999999999999999999999887665443
No 52
>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=44.93 E-value=36 Score=31.16 Aligned_cols=48 Identities=25% Similarity=0.216 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+....++.-.+.+ .++ -.++|+.+|++...|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKS----YKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4889999999876655 442 34599999999999999999999988753
No 53
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=43.90 E-value=36 Score=32.56 Aligned_cols=48 Identities=15% Similarity=0.236 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||++.+.++...+++ .+ .-.++|+.+|++...|.+++..+|+++++.
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 3899999999888877 33 246699999999999999999999998764
No 54
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=43.65 E-value=31 Score=32.63 Aligned_cols=50 Identities=14% Similarity=0.042 Sum_probs=41.4
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
..||+..+.++.-++.++ . .-.++|..+|++...|.+|..-+|+++++..
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--L------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 348999999998887774 2 3467999999999999999999999987653
No 55
>PRK00118 putative DNA-binding protein; Validated
Probab=43.48 E-value=27 Score=32.50 Aligned_cols=48 Identities=15% Similarity=0.139 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++..++.+. + .-..+|+.+|+++.-|.+|...+|.++++-
T Consensus 17 ~L~ekqRevl~L~y~eg----~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD----Y----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 37999999998887773 2 345699999999999999999999988764
No 56
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=43.08 E-value=28 Score=32.26 Aligned_cols=47 Identities=21% Similarity=0.094 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
.||+..+.++..-+.+. + .-.++|+.+|++...|.+|...+|.++++
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 38999999987666652 2 24679999999999999999999998865
No 57
>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=43.08 E-value=36 Score=30.13 Aligned_cols=48 Identities=23% Similarity=0.255 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++..-+.. .+ ....+|+..|+++..|.+|...++.++++.
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4788888887554444 44 345799999999999999999999887653
No 58
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=42.38 E-value=31 Score=32.41 Aligned_cols=49 Identities=20% Similarity=0.179 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.++..-++. -+ .-.++|+.+|++...|.+|...+|+++++.+
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 3889999988765554 22 2356999999999999999999999988754
No 59
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=42.16 E-value=32 Score=27.62 Aligned_cols=37 Identities=27% Similarity=0.321 Sum_probs=23.4
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 038021 415 LRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRL 458 (675)
Q Consensus 415 Lr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rl 458 (675)
|+.++.++ -+ ....||+.+|+++.+|+.|+.+...+.
T Consensus 2 L~~~m~~~---~i----t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 2 LKELMAER---GI----TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp HHHHHHHT---T------HHHHHHHHT--HHHHHHHHTTT----
T ss_pred HHHHHHHc---CC----CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 56666663 32 567799999999999999999874433
No 60
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=39.33 E-value=38 Score=32.97 Aligned_cols=50 Identities=24% Similarity=0.255 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||++.+.++.-.+.+. .+ -.++|+.+|++...|.+...-+|.++++...
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 48999999998766662 23 3669999999999999999999999887644
No 61
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=38.87 E-value=45 Score=32.40 Aligned_cols=52 Identities=13% Similarity=0.120 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEE 465 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~ 465 (675)
.||++.+.++.-.+++. .+ -.++|..+|++..-|.+....+|+++++.+-.+
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 38999999998777663 23 366999999999999999999999998765533
No 62
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=38.57 E-value=50 Score=32.30 Aligned_cols=50 Identities=24% Similarity=0.165 Sum_probs=40.4
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
..||+.++.+|+. +.+ .+ .-.++|+.+|++...|++|...+|.++++-+.
T Consensus 5 ~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999977 433 33 44679999999999999999999998877644
No 63
>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=38.04 E-value=39 Score=32.37 Aligned_cols=49 Identities=18% Similarity=0.135 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.++.--++++ + .-.++|+.+|++...|.++.-.+|+++++.+
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 37888888887666553 2 3467999999999999999999999987754
No 64
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=37.77 E-value=43 Score=31.33 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=39.3
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
||+..+.++..-+.+ .+ .-.++|+..|++...|.+|..-+|.++++.+.
T Consensus 126 L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 126 LPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 888888888765554 22 34679999999999999999999999887543
No 65
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=36.99 E-value=58 Score=32.25 Aligned_cols=50 Identities=22% Similarity=0.178 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||+..+.++.--+++. .+ -.++|..+|++..-|.+....+|+++++.+.
T Consensus 139 ~Lp~~~r~v~~L~~~eg--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD--FE------IDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 38999999988776663 22 3569999999999999999999999987654
No 66
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=36.95 E-value=52 Score=32.06 Aligned_cols=52 Identities=15% Similarity=0.200 Sum_probs=41.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEE 465 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~ 465 (675)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++...+|+++++.+.+.
T Consensus 136 ~L~~~~r~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 136 NLPENTARVFTLKEILG----F----SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred hCCHHHHHHhhhHHHhC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 48999999987666652 2 3467999999999999999999999998865433
No 67
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=36.79 E-value=42 Score=32.86 Aligned_cols=49 Identities=10% Similarity=0.114 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.+|.--+.+. + .-.++|+.+|++...|.+|...+|+++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~----~----s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----L----TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 38999999997776663 2 3467999999999999999999999887653
No 68
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=36.18 E-value=36 Score=32.70 Aligned_cols=49 Identities=12% Similarity=0.072 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.++.--+.+. . .-.++|+.+|++...|.+++..+|.++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--A------SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998876663 2 3467999999999999999999999987653
No 69
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=35.19 E-value=51 Score=31.00 Aligned_cols=48 Identities=19% Similarity=0.100 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+.++.++.-.+.+. .+ -.++|..+|++...|..+...+|+++++.
T Consensus 112 ~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--FS------YKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 48999999998877663 22 35699999999999999999999998764
No 70
>cd00131 PAX Paired Box domain
Probab=35.03 E-value=1.9e+02 Score=27.36 Aligned_cols=47 Identities=17% Similarity=0.067 Sum_probs=32.1
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-------ChhhHhhhhhhh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGL-------TRSQVSNWFINA 454 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGL-------S~~QVsNWFiNa 454 (675)
+.+.......+..+..+ ||.-+..|...+-...|+ +...|+.||.++
T Consensus 74 r~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 34455555656666666 698888777666335566 899999998764
No 71
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=34.83 E-value=61 Score=31.36 Aligned_cols=48 Identities=25% Similarity=0.116 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++..-+++. + .-.++|..+|++...|.++...+|.++++.
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 48999999998766662 2 356799999999999999999999998764
No 72
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=34.31 E-value=56 Score=30.38 Aligned_cols=50 Identities=18% Similarity=0.149 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
..||+..+.++.--+++ -++ -.++|..+|++...|.+...-+|+++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DMD----VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34899999999876666 332 367999999999999999999999887654
No 73
>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=34.00 E-value=65 Score=30.80 Aligned_cols=47 Identities=15% Similarity=0.128 Sum_probs=39.9
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
||++.+.++.-.+++. + .-.++|..+|++...|.+.+..+|.++++.
T Consensus 135 Lp~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG----L----TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 9999999998887773 2 236799999999999999999999988764
No 74
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=33.93 E-value=77 Score=29.54 Aligned_cols=47 Identities=11% Similarity=0.297 Sum_probs=36.5
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINAR 455 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR 455 (675)
+.-....+..+.+|+.+|+..| + .-..||+.+|+++.++..||...=
T Consensus 4 ~~~~~~~i~~~~~~I~~~~~~~-~---sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 4 RNTDAITIHSILDWIEDNLESP-L---SLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred ccccHHHHHHHHHHHHHhcCCC-C---CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3344556777889999987776 3 346689999999999999998763
No 75
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=33.54 E-value=55 Score=33.68 Aligned_cols=48 Identities=19% Similarity=0.232 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.+|.-.|++. + .-.++|+.+|++...|.+|...+|+++++.
T Consensus 205 ~L~~~~r~vl~l~~~~g----~----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----L----SQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998877663 2 236799999999999999999999998764
No 76
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=33.45 E-value=77 Score=31.80 Aligned_cols=52 Identities=19% Similarity=0.264 Sum_probs=42.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEE 465 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~ 465 (675)
.||++.+.++.--+++. .+ -.++|..+|++...|.++..-+|+++++.+.+.
T Consensus 148 ~L~~~~r~v~~L~~~~g--~s------~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--LE------TNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999988887777663 23 367999999999999999999999998876543
No 77
>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=33.20 E-value=74 Score=32.50 Aligned_cols=56 Identities=18% Similarity=0.101 Sum_probs=43.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEE 465 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~ 465 (675)
.||+..+.+|...|.-+-..++ .-.++|+..|++...|+.+...+++++++.+...
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 4899999999887621101233 4677999999999999999999999999875443
No 78
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=33.12 E-value=65 Score=32.04 Aligned_cols=49 Identities=22% Similarity=0.297 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||++.+.++..-+++. + .-.++|..+|++...|.+++..+|+++++.+
T Consensus 153 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38999999998766653 2 3467999999999999999999999887653
No 79
>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=33.08 E-value=50 Score=33.97 Aligned_cols=49 Identities=20% Similarity=0.173 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.++...|++. + .-.++|+.+|++...|..+...++.++++.+
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 48999999998887763 2 2367999999999999999999999987753
No 80
>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=33.05 E-value=68 Score=29.79 Aligned_cols=47 Identities=30% Similarity=0.268 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
.||+..+.++..-+.+ .+ .-.++|+.+|++...|.++..-+|+++++
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 4899999999886655 33 33569999999999999999999988765
No 81
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.75 E-value=86 Score=23.54 Aligned_cols=45 Identities=20% Similarity=0.232 Sum_probs=33.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLW 459 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rlk 459 (675)
.|++....++..+ .+ .+ ...++|+.+|++...|..|....+.++.
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 4777778877543 33 22 4477999999999999999988877764
No 82
>PRK04217 hypothetical protein; Provisional
Probab=32.03 E-value=78 Score=29.80 Aligned_cols=50 Identities=16% Similarity=0.153 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
..|+++.+.++..++.+. + .-.++|+.+|++...|.+.+..+|.+++..+
T Consensus 41 ~~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 347888889998887763 2 4566999999999999999999988886643
No 83
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=31.60 E-value=50 Score=32.04 Aligned_cols=49 Identities=20% Similarity=0.296 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||++.+.++.--+++. + .-.++|..+|++...|.+|+..+|+++++.+
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 48998888887766552 2 3366999999999999999999999988754
No 84
>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=30.73 E-value=72 Score=31.23 Aligned_cols=51 Identities=14% Similarity=0.153 Sum_probs=41.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVE 464 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie 464 (675)
.||+..+.++.--+++. . .-.++|..+|++..-|.++..-+|+++++.+-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--F------ESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999988777763 2 346799999999999999999999999876543
No 85
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.49 E-value=65 Score=31.10 Aligned_cols=48 Identities=21% Similarity=0.109 Sum_probs=39.1
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
||+..+.++.--+.+. + .-.++|+.+|+++..|.+.+..+|+++++.+
T Consensus 130 L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 130 LPDRQRLPIVHVKLEG----L----SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 7888888876666653 2 3467999999999999999999999988753
No 86
>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=30.30 E-value=86 Score=32.61 Aligned_cols=50 Identities=26% Similarity=0.341 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||++.+.++.-.+++. + .-.++|..+|++..-|.++...+|+++++.+.
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 38999999998887774 2 23679999999999999999999999988654
No 87
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=30.13 E-value=53 Score=32.44 Aligned_cols=49 Identities=20% Similarity=0.132 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.++.-++++ -+ .-.++|...|++...|.+++.-+|+++++.+
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 4899999999888776 33 2356899999999999999999999987653
No 88
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.90 E-value=83 Score=29.85 Aligned_cols=48 Identities=15% Similarity=-0.007 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++..-+|+++++.
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 38999999998877763 2 246799999999999999999999998754
No 89
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=29.83 E-value=79 Score=30.17 Aligned_cols=47 Identities=11% Similarity=0.114 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
.||++.+.++.-.+++. .+| .++|+.+|++..-|.++...+|+|++.
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s~------~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MGH------AEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 38999999998776663 333 569999999999999999999999854
No 90
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=29.41 E-value=80 Score=30.90 Aligned_cols=50 Identities=22% Similarity=0.268 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
..||++.+.++.--+.+. .+ -.++|..+|++...|.+.+..+|+++++.+
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 348999999998766653 23 356999999999999999999998887653
No 91
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=29.28 E-value=87 Score=30.08 Aligned_cols=48 Identities=17% Similarity=0.187 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++...+|.++++.
T Consensus 135 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG----Y----THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 38999999998776663 2 346799999999999999999999988764
No 92
>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=29.27 E-value=55 Score=32.83 Aligned_cols=48 Identities=27% Similarity=0.360 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++...+.+ .+ .-.++|+.+|++...|..|...+++++++.
T Consensus 178 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 178 ALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4899999999887765 22 356799999999999999999999988764
No 93
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.87 E-value=82 Score=31.53 Aligned_cols=49 Identities=18% Similarity=0.189 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.++.--+++. .+| .++|+.+|++..-|.++..-+|+++++.+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LSY------EEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38888888776666553 333 66999999999999999999999987643
No 94
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.77 E-value=81 Score=30.44 Aligned_cols=47 Identities=15% Similarity=0.197 Sum_probs=38.1
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
||++.+.++..-+++. + .-.++|+.+|++...|.++...+|+++++.
T Consensus 129 L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 129 LPERQREAIVLQYYQG----L----SNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CCHHHHHHhhHHHhcC----C----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 7888898886666552 2 235699999999999999999999988765
No 95
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=28.74 E-value=73 Score=32.45 Aligned_cols=48 Identities=21% Similarity=0.122 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.-.++++ -+ -.++|+.+|++...|.++...+|+++++.
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MS------YREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998888774 23 25689999999999999999999988765
No 96
>PRK06930 positive control sigma-like factor; Validated
Probab=28.24 E-value=70 Score=31.80 Aligned_cols=52 Identities=13% Similarity=0.047 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEE 465 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~ 465 (675)
.||+..+.++.-.+.+ .+ .-.++|..+|++...|.++...+|.++++.+-++
T Consensus 114 ~L~~rer~V~~L~~~e----g~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 114 VLTEREKEVYLMHRGY----GL----SYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3899999988876655 22 2366999999999999999999999988765443
No 97
>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=28.04 E-value=89 Score=29.25 Aligned_cols=48 Identities=19% Similarity=0.277 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++..-+.+ .+ .-.++|..+|++...|.++...+|.++++.
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 4899999998776665 33 235689999999999999999999988764
No 98
>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=28.02 E-value=1.1e+02 Score=24.58 Aligned_cols=49 Identities=16% Similarity=0.139 Sum_probs=36.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.|++....+|+-+..- + ...++|...+++.+-|..+..+.++|+.-+-.
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 3788888888665443 3 45679999999999999999999998854433
No 99
>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=27.69 E-value=69 Score=30.36 Aligned_cols=48 Identities=13% Similarity=0.102 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++..-+++. + .-.++|+.+|++...|.++..-+|+++++-
T Consensus 119 ~L~~~~r~i~~l~~~~g----~----s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----L----TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999997777663 2 235699999999999999999999988764
No 100
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=27.67 E-value=67 Score=31.86 Aligned_cols=50 Identities=16% Similarity=0.097 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||+..+.++.--+++. + .-.++|..+|++...|.++...+|+++++-+.
T Consensus 133 ~Lp~~~r~v~~l~~~~g----~----s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 133 ALPPERREALILTQVLG----Y----TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred cCCHHHHHHhhhHHHhC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 38999999887777663 2 34679999999999999999999998876544
No 101
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=27.56 E-value=1e+02 Score=30.28 Aligned_cols=49 Identities=18% Similarity=0.133 Sum_probs=40.2
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
||+..+.++.-.+.+. .+| .++|+.+|++...|.++...+|+++++.+.
T Consensus 117 Lp~~~r~i~~L~~~~g--~s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGASG--FAY------EEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 8999999998877763 232 569999999999999999999999877543
No 102
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=27.46 E-value=86 Score=29.94 Aligned_cols=48 Identities=17% Similarity=0.125 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++..-+++ .+ .-.++|+.+|++...|.+++..+|+++++-
T Consensus 136 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4899999998765554 22 236699999999999999999999988764
No 103
>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=27.38 E-value=56 Score=25.14 Aligned_cols=21 Identities=24% Similarity=0.286 Sum_probs=19.0
Q ss_pred HHHHHhCCChhhHhhhhhhhh
Q 038021 435 MLARQTGLTRSQVSNWFINAR 455 (675)
Q Consensus 435 ~LA~~TGLS~~QVsNWFiNaR 455 (675)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999875
No 104
>PHA00542 putative Cro-like protein
Probab=27.31 E-value=1.7e+02 Score=25.50 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 038021 432 DKIMLARQTGLTRSQVSNWFINARVRLWKPMVEEM 466 (675)
Q Consensus 432 eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~~ 466 (675)
...+||+.+|++...|..|......+.....++++
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 45569999999999999999888655544444443
No 105
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=27.29 E-value=95 Score=30.42 Aligned_cols=48 Identities=15% Similarity=0.069 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||++.+.++.--+++ -|+ -.++|+.+|++...|.+++.-+|+++++.
T Consensus 136 ~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4899999888776655 332 35699999999999999999999998765
No 106
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=27.09 E-value=78 Score=29.12 Aligned_cols=48 Identities=21% Similarity=0.126 Sum_probs=38.6
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 405 RGLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 405 R~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
..|++...++|+-+ .++ | ...++|+..+++.+.|.+|..+.|+|+.-.
T Consensus 148 ~~lt~~e~~vl~l~-~~g----~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG----Y----TNRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred cCCCHHHHHHHHHH-HCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 44899999999875 442 2 246899999999999999999999998533
No 107
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.47 E-value=1.2e+02 Score=29.45 Aligned_cols=48 Identities=17% Similarity=0.179 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||++.+.+|.--+++ .+ .-.++|+..|++...|.+.+..+|+++++.
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 346799999999999999999999888764
No 108
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=26.29 E-value=82 Score=32.01 Aligned_cols=47 Identities=26% Similarity=0.280 Sum_probs=39.6
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
||+..+.++..-|++ .+ .-.++|+.+|++...|.++...+|+++++.
T Consensus 185 L~~~~r~vl~l~~~~----g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 185 LPEREQLVLSLYYQE----EL----NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHhHhcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 899999999777665 22 346799999999999999999999999774
No 109
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=25.91 E-value=76 Score=30.66 Aligned_cols=48 Identities=13% Similarity=0.144 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||++.+.++..-+++. + .-.++|+.+|++...|.+|...+|+++++.
T Consensus 133 ~L~~~~r~i~~l~~~~~----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVDG----C----SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 48999988776666652 2 336799999999999999999999988653
No 110
>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=25.68 E-value=95 Score=31.23 Aligned_cols=48 Identities=25% Similarity=0.305 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.+|...|++. + .-.++|+.+|++...|..+...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE----L----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998887763 2 347799999999999999999999988764
No 111
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=25.52 E-value=1.2e+02 Score=31.28 Aligned_cols=49 Identities=18% Similarity=0.135 Sum_probs=39.7
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
||+..+.++.-.+++. + .-.++|+.+|++...|.++...+|+++++.+-
T Consensus 172 Lp~~~R~v~~L~~~eg----~----s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 172 LPEQQRIAVILSYHEN----M----SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHhhhHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 7999999876666552 2 23679999999999999999999999987643
No 112
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=25.36 E-value=1.3e+02 Score=28.24 Aligned_cols=47 Identities=19% Similarity=0.262 Sum_probs=38.3
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
||+..+.+|.--+ + -+ .-.++|+..|++...|.++...+|.++++-+
T Consensus 113 L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 8888888887666 5 33 3467999999999999999999999987753
No 113
>PF13518 HTH_28: Helix-turn-helix domain
Probab=25.04 E-value=68 Score=24.55 Aligned_cols=24 Identities=33% Similarity=0.513 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChhhHhhhhhhhhh
Q 038021 433 KIMLARQTGLTRSQVSNWFINARV 456 (675)
Q Consensus 433 K~~LA~~TGLS~~QVsNWFiNaR~ 456 (675)
...+|++.|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456999999999999999887665
No 114
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=24.63 E-value=1.5e+02 Score=33.91 Aligned_cols=59 Identities=19% Similarity=0.182 Sum_probs=46.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMVEEMYK 468 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ie~~~k 468 (675)
.||+..+.+|+-.|.-.-..|+ .-.++|+.+|+++..|..+...+++++++|......+
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~ 408 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIR 408 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHH
Confidence 3899999999887762211244 4577999999999999999999999999887655544
No 115
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.28 E-value=1.1e+02 Score=29.62 Aligned_cols=47 Identities=11% Similarity=0.064 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
.||++.+.++.-.+.+. | .-.++|..+|++..-|......+++++..
T Consensus 127 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG----M----KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 39999999998877763 2 23679999999999999999999988754
No 116
>PF08933 DUF1864: Domain of unknown function (DUF1864); InterPro: IPR015029 This protein has no known function. It is found in various hypothetical and conserved domain proteins. ; PDB: 2NWB_A 1ZEE_B 2X66_A 2V7L_A 2V7M_A 2V7K_A 2X67_A 2X68_A 2V7J_A 2V7I_A.
Probab=23.76 E-value=50 Score=37.09 Aligned_cols=78 Identities=17% Similarity=0.150 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhh---HHHHH--------HHHHHhhhhhhHHHHHHH
Q 038021 285 ELQNKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPY---TALAL--------QTISRHFRCLRDAICGQI 353 (675)
Q Consensus 285 e~q~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~py---t~lAL--------q~IsrhFr~LrdaI~~qi 353 (675)
.-|.+.+|++-|++|-...|++|-. ++.++..|=.+++.....+| ..++| .+|.+|++-+.+-|..-.
T Consensus 255 Ysq~lvdkf~Ym~P~dqailr~~mr-~~SL~d~~l~~~~~~~~~~~~~~~~lfl~vc~~hG~tAlqhh~qlv~~Fia~~~ 333 (387)
T PF08933_consen 255 YSQFLVDKFLYMMPEDQAILRDCMR-RPSLMDRFLAEAGAPGEPWYQENLRLFLEVCELHGLTALQHHNQLVEKFIARPS 333 (387)
T ss_dssp HHHHHHCCGGGS-HHHHHHHHHHCT-S--HHHHHHHCHHHCCTHHCCHHHHHHHHHHHHHHHHHHHHHHCHCCCHCHHHH
T ss_pred HHHHHHHHhcccCHHHHHHHHHHcC-CchHHHHHHHhhccccCcchhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHhcHH
Confidence 4567889999999999999999877 57778777766666555555 35544 489999998877777666
Q ss_pred HHHHhhhCcc
Q 038021 354 RATRKSLGEQ 363 (675)
Q Consensus 354 ~~~~~~lge~ 363 (675)
+...+..-++
T Consensus 334 ~~~~~~~~~~ 343 (387)
T PF08933_consen 334 KLAEQAYMAG 343 (387)
T ss_dssp HHHHHHHT--
T ss_pred HHHHHHHhcC
Confidence 6565554433
No 117
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=23.62 E-value=1.1e+02 Score=31.42 Aligned_cols=48 Identities=19% Similarity=0.181 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.-.+++ .+ .-.++|..+|+|...|.+++..+|+++++-
T Consensus 201 ~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3899999999877765 22 346799999999999999999999998763
No 118
>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=23.45 E-value=1.3e+02 Score=22.70 Aligned_cols=45 Identities=20% Similarity=0.166 Sum_probs=31.6
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
||+....++..+ .. .+ ...++|+.++++...|..|..-.+.++..
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 455666666443 32 22 45778999999999999999877766544
No 119
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=23.35 E-value=1.2e+02 Score=29.40 Aligned_cols=48 Identities=21% Similarity=0.165 Sum_probs=38.5
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
||+..+.++.--+.+ .| .-.++|+.+|++...|.+...-+|+++++.+
T Consensus 139 L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 139 LPEDLRTALTLREFD----GL----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCHHHhHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 788888877665555 44 3366999999999999999999999988754
No 120
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.20 E-value=1.3e+02 Score=28.13 Aligned_cols=47 Identities=21% Similarity=0.225 Sum_probs=39.7
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
||++.+.++.-.+.+. .+ -.++|..+|++..-|.+....+|+++++.
T Consensus 106 L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 106 LPPACRDSFLLRKLEG--LS------HQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 8999999998887774 23 36799999999999999999999888765
No 121
>PF09325 Vps5: Vps5 C terminal like; InterPro: IPR015404 Vps5 is a sorting nexin that functions in membrane trafficking. This is the C-terminal dimerisation domain [].
Probab=23.20 E-value=5.8e+02 Score=25.56 Aligned_cols=69 Identities=22% Similarity=0.304 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchhhHHHHHHHHHHhhhhhhHHHHHHHH
Q 038021 285 ELQNKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKPYTALALQTISRHFRCLRDAICGQIR 354 (675)
Q Consensus 285 e~q~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~pyt~lALq~IsrhFr~LrdaI~~qi~ 354 (675)
.++.++.+|...++.+-++-+.....+..+..+|..++......+ ..-+|..++..+..+.+.+..+..
T Consensus 35 ~le~~Lk~l~~~~~~l~~~~~~l~~~~~e~~~~~~~la~~E~~~~-l~~~l~~l~~~~~~~~~~~~~~a~ 103 (236)
T PF09325_consen 35 KLEEQLKKLYKSLERLVKRRQELASALAEFGSSFSQLAKSEEEKS-LSEALSQLAEAFEKISELLEEQAN 103 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCch-hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467777788888888888888888888888888998887776544 355677777777777666555433
No 122
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.07 E-value=1.4e+02 Score=29.20 Aligned_cols=48 Identities=27% Similarity=0.294 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||++.+.++.--+.+ .+ .-.++|...|++...|.+++..+|+++++.
T Consensus 106 ~L~~~~r~i~~l~~~~----g~----~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 106 ALPEKYAEALRLTELE----GL----SQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred hCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3899999998776665 33 346699999999999999999999888764
No 123
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.96 E-value=1.3e+02 Score=28.28 Aligned_cols=46 Identities=17% Similarity=0.208 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLW 459 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~Rlk 459 (675)
.||++.+.++.-.+++. .+ -.++|+.+|++...|.++...+++++.
T Consensus 113 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--LG------YGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 38999999997777663 23 356999999999999999999988764
No 124
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.88 E-value=65 Score=31.33 Aligned_cols=49 Identities=16% Similarity=0.176 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.++.--+++ .+ .-.++|+.+|++...|.++...+|+++++.+
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 3888888888765555 23 2356899999999999999999999988753
No 125
>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=22.84 E-value=70 Score=31.15 Aligned_cols=50 Identities=24% Similarity=0.223 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++..-+|+++++.+-
T Consensus 131 ~Lp~~~r~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG----F----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 38888888886665552 2 34679999999999999999999999887643
No 126
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=22.46 E-value=1.1e+02 Score=29.55 Aligned_cols=48 Identities=21% Similarity=0.256 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.--+.+. .+ -.++|+.+|++...|.++..-+|.++++-
T Consensus 127 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE--LS------IKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred hCCHHHhhHhHhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999987766663 22 36799999999999999999999988764
No 127
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=22.40 E-value=1.7e+02 Score=28.78 Aligned_cols=50 Identities=16% Similarity=0.087 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||+..+.++.-.+.++ .+ -.++|..+|++..-|.++..-+|.++++.+-
T Consensus 128 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG--FS------GEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999998887774 22 3569999999999999999999999877654
No 128
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=22.28 E-value=1.5e+02 Score=27.81 Aligned_cols=49 Identities=18% Similarity=0.204 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||++.+.++.--+++ .+ .-.++|+.+|++...|..+..-+|+++++.+
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 3899999999776665 22 2466999999999999999988888887653
No 129
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=22.27 E-value=1.1e+02 Score=31.69 Aligned_cols=49 Identities=18% Similarity=0.167 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.+|...|.+ .+ .-.++|..+|++...|..+..-++.++++.+
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 4899999998877765 32 3467999999999999999999999987653
No 130
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.02 E-value=96 Score=30.23 Aligned_cols=47 Identities=15% Similarity=0.007 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWK 460 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkK 460 (675)
.||++.+.++.-.+++. + .-.++|..+|++...|.++..-+|+++++
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 48999999998777763 2 23669999999999999999999998876
No 131
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=21.87 E-value=1.5e+02 Score=28.15 Aligned_cols=50 Identities=12% Similarity=0.122 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||+..+.++.--+.+. .+ -.++|..+|++...|..+...+|+++++.+-
T Consensus 119 ~L~~~~r~i~~l~~~~~--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--YS------YKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 38888888886655552 23 3669999999999999999999999887543
No 132
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.72 E-value=1.4e+02 Score=28.73 Aligned_cols=50 Identities=12% Similarity=0.060 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPMV 463 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~i 463 (675)
.||+..+.++.--++++ - .-.++|..+|++...|.+....+|.++++-+-
T Consensus 117 ~Lp~~~r~i~~l~~~e~--~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--Y------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999998887766664 1 23669999999999999999999999987654
No 133
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=21.35 E-value=1.1e+02 Score=31.82 Aligned_cols=49 Identities=22% Similarity=0.372 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.+|...|++. + .-.++|..+|++...|..+...+++++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED----L----TLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998877762 2 3567999999999999999999999987754
No 134
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.32 E-value=1.4e+02 Score=32.41 Aligned_cols=53 Identities=23% Similarity=0.160 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
.||+..+.+|..-|.-+...++ .-.++|+.+|++...|..+...+++++++.+
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 4899999998765522222333 4577999999999999999999999998764
No 135
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=21.29 E-value=1.4e+02 Score=29.21 Aligned_cols=47 Identities=15% Similarity=0.085 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.. +++ .| .-.++|..+|++...|.+.+..+|+++++.
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 489999999877 555 23 336699999999999999888888887664
No 136
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=21.06 E-value=1.5e+02 Score=28.64 Aligned_cols=48 Identities=23% Similarity=0.278 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.-.+++. + .-.++|+.+|++...|.+....+|.++++-
T Consensus 122 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN----L----TYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998766652 2 236699999999999999999999988664
No 137
>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=20.92 E-value=1.6e+02 Score=28.28 Aligned_cols=48 Identities=21% Similarity=0.223 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.++.--+.+ -| .-.++|+.+|++...|.++..-+|+++++-
T Consensus 100 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 100 ELPDEYREAIRLTELE----GL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4899999999877666 33 346799999999999999999999888764
No 138
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=71 Score=30.29 Aligned_cols=48 Identities=21% Similarity=0.206 Sum_probs=39.3
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKPM 462 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp~ 462 (675)
||+..+.+|.--+++ .++ -.++|..+|++...|.+.+..+|+++++.+
T Consensus 121 L~~~~r~vl~l~~~~----g~s----~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 121 LSLEHRAVLVLHDLE----DLP----QKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCHHHeeeeeehHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 888888888776665 332 467999999999999999999999987753
No 139
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=20.83 E-value=5.8e+02 Score=22.40 Aligned_cols=59 Identities=15% Similarity=0.272 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCchh-hHHHHHHHHHHhhhhhh
Q 038021 288 NKLTKLLSMLDEVDRRYKQYYHQMQIVVSSFDVIAGCGAAKP-YTALALQTISRHFRCLR 346 (675)
Q Consensus 288 ~k~~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vag~gaa~p-yt~lALq~IsrhFr~Lr 346 (675)
..+.+.+..+.|+|.++....+++...+.-|-...+.+...| =....++.|...+..++
T Consensus 15 ~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~ 74 (105)
T PF12998_consen 15 AELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERAL 74 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHH
Confidence 345678888888999998888888777776765555432222 23445566666665443
No 140
>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=20.46 E-value=1.9e+02 Score=23.92 Aligned_cols=48 Identities=25% Similarity=0.319 Sum_probs=36.0
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINAR 455 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR 455 (675)
|++.++.+|+.-+..=+- -+|-...-..||+..|++..-+..-+.++=
T Consensus 1 LT~~Q~e~L~~A~~~GYf-d~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF-DVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCHHHHHHHHHHHHcCCC-CCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 577888888877766432 247888899999999999998876554443
No 141
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=20.37 E-value=1.2e+02 Score=29.01 Aligned_cols=48 Identities=19% Similarity=0.159 Sum_probs=36.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 406 GLPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 406 ~LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
.||+..+.+|.--+.+ .+ .-.++|..+|++...|.++...+|+++++-
T Consensus 136 ~L~~~~r~il~l~~~~----~~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHHHHhhhHHhh----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3788888888544333 22 336699999999999999999999998764
No 142
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.02 E-value=1.5e+02 Score=29.12 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=37.8
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 038021 407 LPESSVSILRAWLFEHFLHPYPKDTDKIMLARQTGLTRSQVSNWFINARVRLWKP 461 (675)
Q Consensus 407 LPk~a~~iLr~Wf~eH~~nPYPS~~eK~~LA~~TGLS~~QVsNWFiNaR~RlkKp 461 (675)
++++..+++.-.++. .| ...++|+.+|+|...|.+.+..+|.++.+.
T Consensus 136 l~~~~~~~v~l~~~~----Gl----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE----GL----SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred cCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 677778888777666 66 456789999999999999999999776553
Done!