Query 005863
Match_columns 673
No_of_seqs 310 out of 986
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 14:51:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005863.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005863hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07526 POX: Associated with 100.0 2.8E-42 6.1E-47 325.1 13.9 138 221-360 1-139 (140)
2 smart00574 POX domain associat 100.0 1.1E-41 2.4E-46 318.5 13.7 138 217-360 1-139 (140)
3 KOG0773 Transcription factor M 100.0 5.1E-33 1.1E-37 292.4 11.4 259 219-481 45-312 (342)
4 KOG0774 Transcription factor P 99.9 8.4E-23 1.8E-27 207.3 11.7 175 265-472 77-252 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 7.4E-16 1.6E-20 117.7 4.3 40 426-465 1-40 (40)
6 KOG0775 Transcription factor S 99.6 5.9E-15 1.3E-19 151.6 8.6 70 395-467 160-232 (304)
7 cd00086 homeodomain Homeodomai 99.3 3.1E-12 6.7E-17 101.4 6.9 57 410-469 2-58 (59)
8 PF00046 Homeobox: Homeobox do 99.3 5.9E-12 1.3E-16 100.4 5.9 57 409-468 1-57 (57)
9 smart00389 HOX Homeodomain. DN 99.3 9.2E-12 2E-16 98.3 6.8 54 411-467 3-56 (56)
10 KOG0843 Transcription factor E 98.7 3.5E-08 7.6E-13 97.3 7.1 63 407-472 101-163 (197)
11 KOG0487 Transcription factor A 98.7 1.4E-08 3.1E-13 107.4 3.7 59 408-469 235-293 (308)
12 KOG0850 Transcription factor D 98.6 4.8E-08 1E-12 99.4 6.2 61 405-468 119-179 (245)
13 KOG0483 Transcription factor H 98.6 4.3E-08 9.4E-13 98.3 5.2 66 408-476 50-115 (198)
14 KOG0488 Transcription factor B 98.6 4.8E-08 1E-12 103.8 5.9 64 405-471 169-232 (309)
15 KOG0489 Transcription factor z 98.6 3.8E-08 8.3E-13 102.0 4.0 59 408-469 159-217 (261)
16 KOG0842 Transcription factor t 98.5 6.1E-08 1.3E-12 102.7 4.0 61 410-473 154-215 (307)
17 KOG0493 Transcription factor E 98.5 6.4E-08 1.4E-12 99.9 4.0 60 407-469 245-304 (342)
18 TIGR01565 homeo_ZF_HD homeobox 98.4 3.7E-07 8E-12 75.4 5.3 52 409-463 2-57 (58)
19 KOG0484 Transcription factor P 98.4 7.8E-07 1.7E-11 81.3 7.5 65 409-476 18-82 (125)
20 KOG2251 Homeobox transcription 98.3 7.5E-07 1.6E-11 90.4 4.7 62 405-469 34-95 (228)
21 KOG3802 Transcription factor O 98.3 5.7E-07 1.2E-11 97.6 3.6 57 410-469 296-352 (398)
22 COG5576 Homeodomain-containing 98.2 1.2E-06 2.7E-11 85.1 4.9 60 407-469 50-109 (156)
23 KOG0485 Transcription factor N 98.2 1.2E-06 2.6E-11 88.7 4.0 58 411-471 107-164 (268)
24 KOG0492 Transcription factor M 98.1 2.8E-06 6.1E-11 85.7 5.3 63 408-473 144-206 (246)
25 KOG0491 Transcription factor B 98.1 1.6E-06 3.6E-11 84.7 2.1 55 412-469 104-158 (194)
26 KOG0486 Transcription factor P 98.0 2.4E-06 5.2E-11 90.4 2.7 57 410-469 114-170 (351)
27 KOG0848 Transcription factor C 98.0 3.3E-06 7.2E-11 87.7 3.3 52 415-469 206-257 (317)
28 KOG0494 Transcription factor C 98.0 6.7E-06 1.5E-10 85.2 5.2 55 412-469 145-199 (332)
29 KOG4577 Transcription factor L 97.8 2.1E-05 4.6E-10 82.6 5.8 61 405-468 164-224 (383)
30 KOG2252 CCAAT displacement pro 97.7 4.6E-05 9.9E-10 85.8 5.8 56 408-466 420-475 (558)
31 KOG0844 Transcription factor E 97.4 5E-05 1.1E-09 80.4 1.2 58 411-471 184-241 (408)
32 KOG0847 Transcription factor, 97.4 0.00011 2.4E-09 75.0 2.9 57 412-471 171-227 (288)
33 KOG0849 Transcription factor P 97.4 0.00016 3.4E-09 78.6 4.2 59 408-469 176-234 (354)
34 PF03792 PBC: PBC domain; Int 97.3 0.00084 1.8E-08 67.4 7.7 133 222-361 32-169 (191)
35 KOG0773 Transcription factor M 97.2 0.00017 3.7E-09 77.0 2.1 58 410-468 97-154 (342)
36 KOG0490 Transcription factor, 97.1 0.00028 6E-09 70.0 2.3 59 408-469 60-118 (235)
37 KOG1168 Transcription factor A 96.6 0.00062 1.3E-08 71.9 0.9 56 410-468 311-366 (385)
38 PF11569 Homez: Homeodomain le 96.3 0.0032 7E-08 52.1 3.0 43 420-465 10-52 (56)
39 PF03791 KNOX2: KNOX2 domain ; 94.5 0.047 1E-06 44.7 3.8 43 306-356 7-51 (52)
40 KOG0490 Transcription factor, 93.9 0.052 1.1E-06 53.9 3.6 60 407-469 152-211 (235)
41 KOG1146 Homeobox protein [Gene 86.7 0.7 1.5E-05 57.7 4.4 57 412-471 907-963 (1406)
42 KOG3623 Homeobox transcription 73.4 7.8 0.00017 46.5 6.7 44 420-466 568-611 (1007)
43 PF04218 CENP-B_N: CENP-B N-te 72.2 6.7 0.00015 31.8 4.3 46 410-463 2-47 (53)
44 cd06171 Sigma70_r4 Sigma70, re 63.1 13 0.00028 27.5 4.0 46 414-467 10-55 (55)
45 PF11285 DUF3086: Protein of u 60.8 65 0.0014 34.7 9.8 57 294-366 7-63 (283)
46 PF04545 Sigma70_r4: Sigma-70, 58.4 14 0.00031 28.8 3.6 47 414-468 4-50 (50)
47 PF08281 Sigma70_r4_2: Sigma-7 56.8 17 0.00037 28.5 3.9 45 414-466 10-54 (54)
48 cd00569 HTH_Hin_like Helix-tur 55.8 27 0.00059 22.9 4.3 39 413-459 4-42 (42)
49 PF01527 HTH_Tnp_1: Transposas 55.1 16 0.00035 30.3 3.7 46 410-463 2-48 (76)
50 PF13443 HTH_26: Cro/C1-type H 44.5 26 0.00056 28.1 3.2 36 423-465 2-37 (63)
51 smart00421 HTH_LUXR helix_turn 43.6 63 0.0014 24.3 5.1 49 414-471 3-51 (58)
52 PRK09642 RNA polymerase sigma 41.7 48 0.001 31.1 5.0 49 414-470 106-154 (160)
53 cd00131 PAX Paired Box domain 40.6 1.3E+02 0.0027 28.6 7.6 48 412-462 73-127 (128)
54 PRK12530 RNA polymerase sigma 39.8 42 0.0009 32.9 4.4 54 414-475 134-187 (189)
55 PRK09644 RNA polymerase sigma 39.8 41 0.00089 31.8 4.3 49 413-469 107-155 (165)
56 PRK06759 RNA polymerase factor 39.5 39 0.00084 31.3 4.0 47 414-468 106-152 (154)
57 PRK00118 putative DNA-binding 38.9 40 0.00086 31.4 3.8 48 414-469 17-64 (104)
58 TIGR02937 sigma70-ECF RNA poly 37.9 47 0.001 29.4 4.1 47 414-468 110-156 (158)
59 PRK12514 RNA polymerase sigma 36.0 44 0.00095 32.0 3.8 48 414-469 129-176 (179)
60 TIGR02939 RpoE_Sigma70 RNA pol 35.2 36 0.00077 32.6 3.1 50 413-470 137-186 (190)
61 TIGR02985 Sig70_bacteroi1 RNA 34.7 74 0.0016 29.1 5.0 47 414-468 113-159 (161)
62 PRK11511 DNA-binding transcrip 34.2 98 0.0021 28.8 5.7 44 415-462 6-49 (127)
63 PRK09646 RNA polymerase sigma 34.0 48 0.001 32.4 3.8 48 414-469 142-189 (194)
64 PRK03975 tfx putative transcri 33.7 83 0.0018 30.8 5.3 51 413-472 5-55 (141)
65 PF00196 GerE: Bacterial regul 33.5 72 0.0016 25.6 4.1 53 414-475 3-55 (58)
66 PRK09652 RNA polymerase sigma 33.4 75 0.0016 29.8 4.9 49 414-470 128-176 (182)
67 PRK06811 RNA polymerase factor 33.3 69 0.0015 31.2 4.8 51 413-471 130-180 (189)
68 PRK15369 two component system 32.3 1.2E+02 0.0025 28.0 5.9 54 413-475 148-201 (211)
69 PRK12512 RNA polymerase sigma 32.2 48 0.001 31.9 3.4 49 414-470 131-179 (184)
70 PRK11924 RNA polymerase sigma 32.0 64 0.0014 30.2 4.2 48 414-469 125-172 (179)
71 TIGR02941 Sigma_B RNA polymera 31.0 55 0.0012 33.6 3.8 49 414-470 205-253 (255)
72 PRK08583 RNA polymerase sigma 30.9 63 0.0014 33.2 4.3 48 414-469 205-252 (257)
73 PF10168 Nup88: Nuclear pore c 30.6 4.6E+02 0.01 32.1 11.8 17 413-429 680-696 (717)
74 PF12998 ING: Inhibitor of gro 30.2 3.8E+02 0.0083 23.6 9.6 69 298-366 15-84 (105)
75 TIGR02989 Sig-70_gvs1 RNA poly 30.1 67 0.0015 29.8 4.0 48 413-468 110-157 (159)
76 PRK12541 RNA polymerase sigma 30.0 86 0.0019 29.4 4.7 49 413-469 111-159 (161)
77 PRK12526 RNA polymerase sigma 29.0 66 0.0014 32.0 3.9 48 414-469 153-200 (206)
78 KOG2033 Low density lipoprotei 29.0 1.2E+02 0.0026 36.8 6.5 27 440-466 197-223 (863)
79 PRK09648 RNA polymerase sigma 28.9 69 0.0015 31.0 3.9 49 413-469 138-186 (189)
80 PRK12519 RNA polymerase sigma 28.5 64 0.0014 31.3 3.6 49 414-470 141-189 (194)
81 PRK12532 RNA polymerase sigma 27.9 78 0.0017 30.8 4.2 49 414-470 136-184 (195)
82 PRK04217 hypothetical protein; 27.4 92 0.002 29.3 4.3 49 413-469 41-89 (110)
83 PF13518 HTH_28: Helix-turn-he 27.2 62 0.0013 24.7 2.7 24 441-464 15-38 (52)
84 TIGR02999 Sig-70_X6 RNA polyme 27.1 79 0.0017 30.2 3.9 48 414-469 134-181 (183)
85 PRK12536 RNA polymerase sigma 26.8 80 0.0017 30.5 3.9 48 414-469 129-176 (181)
86 PRK05602 RNA polymerase sigma 26.5 72 0.0016 30.8 3.6 48 414-469 128-175 (186)
87 PRK12547 RNA polymerase sigma 26.4 81 0.0018 29.9 3.8 48 414-469 112-159 (164)
88 cd01392 HTH_LacI Helix-turn-he 26.3 55 0.0012 25.2 2.2 21 443-463 2-22 (52)
89 PRK13919 putative RNA polymera 25.2 89 0.0019 30.0 3.9 49 413-469 134-182 (186)
90 PRK12545 RNA polymerase sigma 25.1 1E+02 0.0023 30.5 4.5 50 414-471 139-188 (201)
91 PF09325 Vps5: Vps5 C terminal 24.9 4.3E+02 0.0094 26.4 8.9 69 295-364 35-103 (236)
92 PRK09047 RNA polymerase factor 24.8 1.2E+02 0.0025 28.3 4.5 50 413-470 105-154 (161)
93 TIGR02479 FliA_WhiG RNA polyme 24.6 93 0.002 31.3 4.1 48 414-469 175-222 (224)
94 cd06170 LuxR_C_like C-terminal 24.6 2E+02 0.0044 21.7 5.2 46 415-469 1-46 (57)
95 cd07307 BAR The Bin/Amphiphysi 24.4 5.7E+02 0.012 23.6 9.3 67 295-361 4-79 (194)
96 TIGR02980 SigBFG RNA polymeras 24.1 82 0.0018 31.6 3.6 48 414-469 178-225 (227)
97 TIGR02948 SigW_bacill RNA poly 24.1 1.2E+02 0.0026 28.9 4.6 49 413-469 135-183 (187)
98 PF13730 HTH_36: Helix-turn-he 24.1 2.3E+02 0.0049 22.2 5.4 48 414-464 2-51 (55)
99 PRK12544 RNA polymerase sigma 24.0 1.7E+02 0.0036 29.4 5.7 52 413-472 147-198 (206)
100 PRK06930 positive control sigm 23.8 98 0.0021 30.8 4.0 52 414-473 114-165 (170)
101 PRK12520 RNA polymerase sigma 23.5 1.7E+02 0.0036 28.5 5.5 50 414-471 131-180 (191)
102 PRK12851 groEL chaperonin GroE 22.9 3E+02 0.0064 32.2 8.2 60 289-349 358-430 (541)
103 TIGR02943 Sig70_famx1 RNA poly 22.7 1.3E+02 0.0027 29.6 4.5 50 414-471 131-180 (188)
104 PRK12531 RNA polymerase sigma 22.1 1.1E+02 0.0024 30.0 3.9 49 413-469 140-188 (194)
105 PRK06986 fliA flagellar biosyn 22.1 1.1E+02 0.0023 31.2 4.0 48 414-469 184-231 (236)
106 PRK12546 RNA polymerase sigma 22.0 96 0.0021 30.6 3.5 48 414-469 113-160 (188)
107 TIGR02954 Sig70_famx3 RNA poly 22.0 1.1E+02 0.0023 29.0 3.8 48 414-469 119-166 (169)
108 PRK09639 RNA polymerase sigma 21.8 1.1E+02 0.0024 28.7 3.8 47 414-469 112-158 (166)
109 TIGR02983 SigE-fam_strep RNA p 21.3 1.1E+02 0.0025 28.5 3.8 48 414-469 110-157 (162)
110 PRK12537 RNA polymerase sigma 21.3 1.1E+02 0.0025 29.4 3.8 49 413-469 132-180 (182)
111 PRK12535 RNA polymerase sigma 21.2 1E+02 0.0022 30.5 3.6 49 414-470 133-181 (196)
112 TIGR03001 Sig-70_gmx1 RNA poly 20.9 1.6E+02 0.0034 30.7 5.0 51 413-471 160-210 (244)
113 PRK12516 RNA polymerase sigma 20.8 1.8E+02 0.004 28.5 5.2 48 414-469 116-163 (187)
114 PRK09647 RNA polymerase sigma 20.6 1.7E+02 0.0037 29.3 5.0 48 414-469 138-185 (203)
115 PRK12515 RNA polymerase sigma 20.6 1.4E+02 0.003 28.9 4.3 49 413-469 130-178 (189)
116 PRK12538 RNA polymerase sigma 20.4 1.7E+02 0.0038 30.0 5.1 50 414-471 171-220 (233)
117 CHL00093 groEL chaperonin GroE 20.2 5.4E+02 0.012 30.0 9.5 59 289-348 357-428 (529)
118 PRK11677 hypothetical protein; 20.1 6.5E+02 0.014 24.6 8.6 47 301-360 32-78 (134)
119 PRK12523 RNA polymerase sigma 20.1 1.9E+02 0.004 27.6 5.0 48 413-468 118-165 (172)
No 1
>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=2.8e-42 Score=325.12 Aligned_cols=138 Identities=54% Similarity=0.688 Sum_probs=105.1
Q ss_pred ccccCCccchHHHHHHHHHHhhhhhccC-CCCCCCCccccCCCCCCCCCCcCCCCCCCCCCCCCCCccCCHHHHHHHHHH
Q 005863 221 STILKSKHLKAAQQLLDEAVNIQKALKL-PNSNKNDAKETDGRSSSMLPAFHGILSNPTESVSNSSSELSHAERQELLNK 299 (673)
Q Consensus 221 ~~l~~Sryl~~aQelL~e~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~ls~~e~~e~q~k 299 (673)
++|++|||||||||||||||+|++..+. ......+ ... ....+......+..+....+.....++++++||+|+|+|
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~q~k 78 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSG-APG-GANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQELQRK 78 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhccc-ccc-ccccCCCCCCCCCCCCCccccCCCCCCCChhhHHHHHHH
Confidence 5899999999999999999999863111 1111110 000 011111111112222233333445678999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHHHHHhhhhHHHHH
Q 005863 300 KTKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTISRHFRSLRDAIS 360 (673)
Q Consensus 300 k~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~is~~fr~Lrd~i~ 360 (673)
|+|||.||||||+||+|||+|||+||++||+|||.|+|+|||+|||||||||||||||+|+
T Consensus 79 K~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~ 139 (140)
T PF07526_consen 79 KAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999996
No 2
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=1.1e-41 Score=318.46 Aligned_cols=138 Identities=54% Similarity=0.631 Sum_probs=110.0
Q ss_pred ccccccccCCccchHHHHHHHHHHhhhhhccCCCCCCCCccccCCCCCCCCCCcCCCCCCC-CCCCCCCCccCCHHHHHH
Q 005863 217 IGFNSTILKSKHLKAAQQLLDEAVNIQKALKLPNSNKNDAKETDGRSSSMLPAFHGILSNP-TESVSNSSSELSHAERQE 295 (673)
Q Consensus 217 ~~~a~~l~~Sryl~~aQelL~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~s~~ls~~e~~e 295 (673)
+||+.+|++|||||||||||||||+|++.++.....+. .+....... ..+.+.+. ..+..+..++|+++||+|
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~-~~~~~~~~~-----~~~~~~~~~g~s~~~~~~~ls~~~r~e 74 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSG-NDSPVSTSS-----NEGGGENLSGGSSSSEVPPLSTAERQE 74 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcccHHhhccccccc-ccccccccc-----cCCCcCCCCCCCCCCCCCCCchhHHHH
Confidence 46899999999999999999999999988876543221 000000000 00011111 112234567999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHHHHHhhhhHHHHH
Q 005863 296 LLNKKTKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTISRHFRSLRDAIS 360 (673)
Q Consensus 296 ~q~kk~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~is~~fr~Lrd~i~ 360 (673)
+|+||+||+.||+|||+||+|||+|||+||++||+|||.|+|+|||+||||+||||||||||+|+
T Consensus 75 ~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 75 LQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999996
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.98 E-value=5.1e-33 Score=292.41 Aligned_cols=259 Identities=40% Similarity=0.528 Sum_probs=194.2
Q ss_pred ccccccCCccchHHHHHHHHHHhhhhhccCCCCCCCCccccCCCCCCCCCCcCCCCCCCCCCCCCCCccCCHHHHHHHHH
Q 005863 219 FNSTILKSKHLKAAQQLLDEAVNIQKALKLPNSNKNDAKETDGRSSSMLPAFHGILSNPTESVSNSSSELSHAERQELLN 298 (673)
Q Consensus 219 ~a~~l~~Sryl~~aQelL~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~ls~~e~~e~q~ 298 (673)
+...+..++||++||+||+++|++.................+..... .......-.+. ...++......++++++.
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~n~-~~~s~~~~~~~~~~~~~~ 120 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSP---PEDKGARRGNA-TRESATLKAWLEEHRLNP 120 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccC---ccccccccccc-cccccccccchhhhhhcc
Confidence 56678899999999999999999875543322211100100000000 00000000000 011123345679999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHHHHHhhhhHH--HHHHHHHHhhhccCCccc-
Q 005863 299 KKTKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTISRHFRSLRD--AISDQIQVTGRSLGEQET- 375 (673)
Q Consensus 299 kk~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~is~~fr~Lrd--~i~~qi~~~~~~~ge~~~- 375 (673)
+++|++.|+.+|+.+|.+||..|+.|...|+.+.|.+.+.+|+..++..+++||+++++ +|.+|+......+++.+.
T Consensus 121 ~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~ 200 (342)
T KOG0773|consen 121 YPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQD 200 (342)
T ss_pred CchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999998 788888877766654332
Q ss_pred -CCCC---CCCCCcccccchHHHHHHHH-hhcC-CccccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhC
Q 005863 376 -SSNG---QASIPRLRFVDHQSRQQRAL-QQLG-VMRHAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTG 449 (673)
Q Consensus 376 -s~~~---~~~~~r~~~~D~~l~qqr~~-~~l~-~~r~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTG 449 (673)
.... ...++..+..++.+++++.. ...+ .-...||++++||+.++.+|+.||++|+.||||++.+|.+||++||
T Consensus 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TG 280 (342)
T KOG0773|consen 201 DSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTG 280 (342)
T ss_pred ccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcC
Confidence 1111 11245556667777776531 1111 1245899999999999999999999999999999999999999999
Q ss_pred CChHhHhhhhhhhHhhccchhHHHHHHHhhCC
Q 005863 450 LSKNQVANWFINARVRLWKPMIEEMYKEEFGD 481 (673)
Q Consensus 450 LS~~QVsNWF~NaR~RlkKp~i~e~~~~~~~~ 481 (673)
|++.||+|||||+|+|+|+|+++++|..+...
T Consensus 281 Ls~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 281 LSRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred CCcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 99999999999999999999999999987775
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.88 E-value=8.4e-23 Score=207.30 Aligned_cols=175 Identities=24% Similarity=0.339 Sum_probs=127.7
Q ss_pred CCCCCcCCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhhhhcCccchhhhHH
Q 005863 265 SMLPAFHGILSNPTESVSNSSSELSHAERQELLNKKTKLLSMLEEVDRGYKQYYHQMQ-IVASSFDMVAGHGAAKSYTVL 343 (673)
Q Consensus 265 ~~~~~~~~~~~~~~~~~~~~s~~ls~~e~~e~q~kk~kLl~ml~Evd~ry~qy~~qmq-~vvssfe~vaG~~aa~pyt~l 343 (673)
+|+.++++.+.+..+..+ .+.+..++-||+.|+.+++.+|++..++|+|.|.++. .|.+ .+..++..+|+
T Consensus 77 nML~AEGVagPekgga~~---~~Asgg~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~n---lL~eQsr~RPi--- 147 (334)
T KOG0774|consen 77 NMLLAEGVAGPEKGGARA---AAASGGDHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMN---LLREQSRTRPI--- 147 (334)
T ss_pred HHHHHhcccCccccchhh---hhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHhcccCCC---
Confidence 677777776655544221 2334446789999999999999999999999999985 5554 44568889998
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHhhhccCCcccCCCCCCCCCcccccchHHHHHHHHhhcCCccccCCCCCCCChhHHHHH
Q 005863 344 ALQTISRHFRSLRDAISDQIQVTGRSLGEQETSSNGQASIPRLRFVDHQSRQQRALQQLGVMRHAWRPQRGLPESSVSIL 423 (673)
Q Consensus 344 al~~is~~fr~Lrd~i~~qi~~~~~~~ge~~~s~~~~~~~~r~~~~D~~l~qqr~~~~l~~~r~~~R~rR~Lpk~a~~iL 423 (673)
+.+.|++....+...++..-..++.+.+| ++-+.|.+++| ++||||+|+|.++.||
T Consensus 148 ~~ke~e~m~~~i~~kF~~iq~~lkqstce-------~vmiLr~r~ld-----------------arRKRRNFsK~aTeiL 203 (334)
T KOG0774|consen 148 MPKEIERMVQIISKKFSHIQMQLKQSTCE-------AVMILRSRFLD-----------------ARRKRRNFSKQATEIL 203 (334)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHH-----------------HHHhhcccchhHHHHH
Confidence 44444444444333333211111111111 22233333333 5689999999999999
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHH
Q 005863 424 RAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIE 472 (673)
Q Consensus 424 r~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~ 472 (673)
..||..|+.||||++++|+.||++++++.+||+|||.|.|.|.||.+..
T Consensus 204 neyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 204 NEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 9999999999999999999999999999999999999999999988773
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.59 E-value=7.4e-16 Score=117.66 Aligned_cols=40 Identities=65% Similarity=1.152 Sum_probs=36.5
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhh
Q 005863 426 WLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVR 465 (673)
Q Consensus 426 Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~R 465 (673)
||.+|+.||||+.+||.+||++|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 6
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.56 E-value=5.9e-15 Score=151.55 Aligned_cols=70 Identities=39% Similarity=0.675 Sum_probs=65.0
Q ss_pred HHHHHhhcCCccccCCCCCC---CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhcc
Q 005863 395 QQRALQQLGVMRHAWRPQRG---LPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLW 467 (673)
Q Consensus 395 qqr~~~~l~~~r~~~R~rR~---Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~Rlk 467 (673)
+-|.++++|.+|++|....+ |.++++.+||+||.. +|||+++||++||++|||+..||+|||+|||.|.+
T Consensus 160 KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 160 KYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred cceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 45677899999999998766 999999999999997 99999999999999999999999999999999954
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=99.33 E-value=3.1e-12 Score=101.39 Aligned_cols=57 Identities=32% Similarity=0.535 Sum_probs=53.0
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 410 RPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 410 R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
+++..|++.++.+|++||.. +|||+..++..||.+|||+..||.+||.|+|.|.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45667999999999999999 9999999999999999999999999999999997653
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=5.9e-12 Score=100.35 Aligned_cols=57 Identities=35% Similarity=0.623 Sum_probs=53.4
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 409 WRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 409 ~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
+|+++.|+++++.+|+.+|.. +|||+.+++..||.++||+..||.+||.|+|.+.+|
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 367788999999999999998 999999999999999999999999999999999764
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.27 E-value=9.2e-12 Score=98.25 Aligned_cols=54 Identities=30% Similarity=0.489 Sum_probs=50.1
Q ss_pred CCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhcc
Q 005863 411 PQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLW 467 (673)
Q Consensus 411 ~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~Rlk 467 (673)
++..|+++++.+|++||.. +|||+.+++..||.++||+..||.+||+|+|+|.+
T Consensus 3 ~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4455999999999999998 89999999999999999999999999999999853
No 10
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.68 E-value=3.5e-08 Score=97.26 Aligned_cols=63 Identities=24% Similarity=0.274 Sum_probs=56.9
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHH
Q 005863 407 HAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIE 472 (673)
Q Consensus 407 ~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~ 472 (673)
+.+|.|+.|+.++...|+..|.. +-|-.-.||+.||+..+|+..||+.||+|+|.|+||..-+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 45566777999999999999998 8999999999999999999999999999999999886443
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.65 E-value=1.4e-08 Score=107.38 Aligned_cols=59 Identities=19% Similarity=0.275 Sum_probs=52.7
Q ss_pred cCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 408 AWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 408 ~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.+|||-.++|.++..|++-|+- |=|.|.+-|.+|++.++||..||+.||+|||+|+||-
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 4444455999999999888887 7899999999999999999999999999999998874
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.62 E-value=4.8e-08 Score=99.37 Aligned_cols=61 Identities=25% Similarity=0.360 Sum_probs=56.1
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 405 MRHAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 405 ~r~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
.++.|++|+-++.-+.+.|++-|.+ .-|--..||.+||...|||..||+.||+|+|-|.||
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KK 179 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKK 179 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHH
Confidence 4566777778999999999999998 899999999999999999999999999999999776
No 13
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.60 E-value=4.3e-08 Score=98.33 Aligned_cols=66 Identities=30% Similarity=0.362 Sum_probs=59.3
Q ss_pred cCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHHHHH
Q 005863 408 AWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEEMYK 476 (673)
Q Consensus 408 ~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e~~~ 476 (673)
.++++++|+.+++..|+.-|.. +-|-.+.+|..||++.||...||..||+|||.|+|.+..+..|.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~ 115 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYE 115 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHH
Confidence 5678999999999999999988 67888899999999999999999999999999988877765544
No 14
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.60 E-value=4.8e-08 Score=103.75 Aligned_cols=64 Identities=20% Similarity=0.363 Sum_probs=55.8
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 405 MRHAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 405 ~r~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
+++.++.|.-|+..++..|+.-|.. --|-+..||+.||+..|||-.||..||+|||+|+|+...
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 3455566666999999999999988 789999999999999999999999999999999666533
No 15
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.57 E-value=3.8e-08 Score=102.03 Aligned_cols=59 Identities=22% Similarity=0.321 Sum_probs=54.5
Q ss_pred cCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 408 AWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 408 ~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.+|.|+.|+..++..|+.-|.- |.|-+...|++||..+.|+..||++||+|||+|+||.
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 5567778999999999999988 8999999999999999999999999999999997763
No 16
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.52 E-value=6.1e-08 Score=102.65 Aligned_cols=61 Identities=25% Similarity=0.346 Sum_probs=54.9
Q ss_pred CCCCC-CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHH
Q 005863 410 RPQRG-LPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEE 473 (673)
Q Consensus 410 R~rR~-Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e 473 (673)
||+|. |++.+|-.|+.-|.+ .-|-+-.||+.||..++||..||+.||+|+|-|.||..+++
T Consensus 154 RKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 154 RKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 44444 999999999999998 89999999999999999999999999999999998875543
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.52 E-value=6.4e-08 Score=99.85 Aligned_cols=60 Identities=27% Similarity=0.484 Sum_probs=56.2
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 407 HAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 407 ~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
...|+|..|+.++.+.|+.-|.+ |.|.++.-|+.||.+.||...||+.||+|+|.++||.
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 35677888999999999999999 8999999999999999999999999999999998874
No 18
>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=98.42 E-value=3.7e-07 Score=75.43 Aligned_cols=52 Identities=12% Similarity=0.245 Sum_probs=48.7
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhCCChHhHhhhhhhhH
Q 005863 409 WRPQRGLPESSVSILRAWLFEHFLHPY----PNDSEKIMLAKQTGLSKNQVANWFINAR 463 (673)
Q Consensus 409 ~R~rR~Lpk~a~~iLr~Wf~eH~~nPY----PS~~EK~~LA~qTGLS~~QVsNWF~NaR 463 (673)
+|+|+.|+.+++..|+..|.. .+| |+..++..||..+||+..+|..||+|-+
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 467778999999999999999 999 9999999999999999999999999964
No 19
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.40 E-value=7.8e-07 Score=81.31 Aligned_cols=65 Identities=22% Similarity=0.319 Sum_probs=57.2
Q ss_pred CCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHHHHH
Q 005863 409 WRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEEMYK 476 (673)
Q Consensus 409 ~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e~~~ 476 (673)
+|-|.+|+..+...|+..|.+ .-||..-.+++||.+..|+...|+.||+|+|.+.+|......++
T Consensus 18 RRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 355677999999999999999 78999999999999999999999999999999998875544444
No 20
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.27 E-value=7.5e-07 Score=90.36 Aligned_cols=62 Identities=23% Similarity=0.382 Sum_probs=56.5
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 405 MRHAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 405 ~r~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
+|+.+|.|+.|+..+..+|++-|.+ --||....+++||.+.+|.+.+|.+||.|+|.+.++.
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 4556677778999999999999999 8999999999999999999999999999999997664
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.25 E-value=5.7e-07 Score=97.57 Aligned_cols=57 Identities=21% Similarity=0.352 Sum_probs=52.6
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 410 RPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 410 R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
|||+.|.-.++..|++.|.+ +|-|+.+|.-.||.+.+|.+..|..||+|||.|+|+.
T Consensus 296 KKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 296 KKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred ccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 34444999999999999999 9999999999999999999999999999999998875
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.22 E-value=1.2e-06 Score=85.06 Aligned_cols=60 Identities=22% Similarity=0.337 Sum_probs=55.2
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 407 HAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 407 ~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
...++|+..+..++.+|+.-|.. +|||+..+|..|+..++++++-|..||+|+|.+.++.
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence 35567788999999999999998 9999999999999999999999999999999998764
No 23
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.18 E-value=1.2e-06 Score=88.74 Aligned_cols=58 Identities=22% Similarity=0.271 Sum_probs=52.4
Q ss_pred CCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 411 PQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 411 ~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
.|..|+..++..|+.-|.. ..|-+..||.-||++..||+.||+.||+|+|.|+|+...
T Consensus 107 tRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 107 TRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred chhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 4455999999999999988 789999999999999999999999999999999776543
No 24
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.13 E-value=2.8e-06 Score=85.67 Aligned_cols=63 Identities=21% Similarity=0.302 Sum_probs=55.8
Q ss_pred cCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHH
Q 005863 408 AWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEE 473 (673)
Q Consensus 408 ~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e 473 (673)
-+++|..|+..+...|++-|.+ ..|-+.+|+.+++....||..||+.||+|||.|.|+-.-.|
T Consensus 144 nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 4456777999999999999999 89999999999999999999999999999999987754333
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.06 E-value=1.6e-06 Score=84.69 Aligned_cols=55 Identities=27% Similarity=0.383 Sum_probs=50.5
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 412 QRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 412 rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
|..|+..+...|++-|.. --|-+-.|+++||...+|+.+||+.||+|+|++.||.
T Consensus 104 Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 104 RTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred cccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 445899999999999987 6799999999999999999999999999999998875
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.03 E-value=2.4e-06 Score=90.38 Aligned_cols=57 Identities=26% Similarity=0.390 Sum_probs=52.3
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 410 RPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 410 R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
|-|..|+..+.+.|+.||.. |-||+.+.|++||.-|+||...|++||.|+|.+++|.
T Consensus 114 rQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 114 RQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 33445999999999999999 9999999999999999999999999999999997665
No 27
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.01 E-value=3.3e-06 Score=87.75 Aligned_cols=52 Identities=29% Similarity=0.309 Sum_probs=49.2
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 415 LPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 415 Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
++..++-.|++-|.. .+|.|..-|-+||...||++.||+.||+|||.|.+|.
T Consensus 206 YTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred ecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 788999999999988 8999999999999999999999999999999998775
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.00 E-value=6.7e-06 Score=85.21 Aligned_cols=55 Identities=25% Similarity=0.399 Sum_probs=50.9
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 412 QRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 412 rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
|+.|+..+...|++-|.+ --||..-.|++||.+|+|...+|..||+|||.|++|.
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 455999999999999999 7899999999999999999999999999999996653
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.85 E-value=2.1e-05 Score=82.56 Aligned_cols=61 Identities=23% Similarity=0.350 Sum_probs=55.8
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 405 MRHAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 405 ~r~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
-....|+|++++.++...|+.-|.. .|-|-.--|++|+.+|||....|+.||+|+|.+.|+
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKR 224 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKR 224 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHh
Confidence 3457799999999999999999988 899999999999999999999999999999987654
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.70 E-value=4.6e-05 Score=85.79 Aligned_cols=56 Identities=25% Similarity=0.341 Sum_probs=52.1
Q ss_pred cCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhc
Q 005863 408 AWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRL 466 (673)
Q Consensus 408 ~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~Rl 466 (673)
..|+|-.|+..+++.|++.|.+ ++||+.+..+.|+.+.+|.+.-|.|||-|+|+|-
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 4456667999999999999999 9999999999999999999999999999999994
No 31
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.41 E-value=5e-05 Score=80.39 Aligned_cols=58 Identities=16% Similarity=0.324 Sum_probs=51.0
Q ss_pred CCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 411 PQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 411 ~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
=|+.|+.++...|++-|++ --|-+...|.+||.+.+|.+..|+.||+|+|+|.|+..+
T Consensus 184 YRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 184 YRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 3456999999999776665 469999999999999999999999999999999988766
No 32
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.36 E-value=0.00011 Score=74.97 Aligned_cols=57 Identities=19% Similarity=0.329 Sum_probs=51.5
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 412 QRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 412 rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
+.+|.-.+...|+.-|.+ .-||--.++.+||...|++..||..||+|||.+++|.-.
T Consensus 171 rPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 171 RPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred CCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 455999999999999988 789999999999999999999999999999999777544
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.36 E-value=0.00016 Score=78.58 Aligned_cols=59 Identities=29% Similarity=0.507 Sum_probs=53.7
Q ss_pred cCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 408 AWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 408 ~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.+|.|..|...+...|.+||.. .|||....++.||++|+|+...|..||.|+|.|.+|.
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~ 234 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQ 234 (354)
T ss_pred ccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhc
Confidence 4455667999999999999988 7899999999999999999999999999999997765
No 34
>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=97.26 E-value=0.00084 Score=67.36 Aligned_cols=133 Identities=12% Similarity=0.087 Sum_probs=79.9
Q ss_pred cccCCccchHHHHHHHHHHhhhhhccCCCC-CCCCccccCCCCCCCCCCcCCCCCCCCCCCCC---CCccCCHHHHHHHH
Q 005863 222 TILKSKHLKAAQQLLDEAVNIQKALKLPNS-NKNDAKETDGRSSSMLPAFHGILSNPTESVSN---SSSELSHAERQELL 297 (673)
Q Consensus 222 ~l~~Sryl~~aQelL~e~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~s~~ls~~e~~e~q 297 (673)
.|+..||-.+-+.+|=|+=.- ..+..... +............+|+.++++.+.+..+..+. ...+-.+.|..+|+
T Consensus 32 ~l~~hr~k~ALfsVLcE~KEk-t~LSir~~qee~p~dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~~~d~~dYr 110 (191)
T PF03792_consen 32 ALNCHRMKPALFSVLCEIKEK-TVLSIRNIQEEDPPDPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADNSIDHSDYR 110 (191)
T ss_pred hhcCCCCchhhHHHHHHHHhh-cCccccccCCcCCCchhhhhhhcchhhhcCcCCCCcccchhhhhccCcccccchHHHH
Confidence 466777777777777554320 01110000 00000001122347888877776655543321 12224456888999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhhhhcCccchhhhHHHHHHHHHHhhhhHHHHHH
Q 005863 298 NKKTKLLSMLEEVDRGYKQYYHQMQ-IVASSFDMVAGHGAAKSYTVLALQTISRHFRSLRDAISD 361 (673)
Q Consensus 298 ~kk~kLl~ml~Evd~ry~qy~~qmq-~vvssfe~vaG~~aa~pyt~lal~~is~~fr~Lrd~i~~ 361 (673)
.|++++..++++..++|++.|.++. +|.+ .+..++.++|+|.- .|++....+.+.++.
T Consensus 111 ~kL~~ir~~y~~el~kye~ac~eF~~hV~~---lLreQs~~RPIs~k---eiE~m~~~i~~Kf~~ 169 (191)
T PF03792_consen 111 AKLSQIRQIYHSELEKYEQACNEFTEHVMN---LLREQSEFRPISPK---EIERMVNIIHRKFSK 169 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhHHHHHH---HHHHhcccCCCCHH---HHHHHHHHHHHHHHH
Confidence 9999999999999999999999985 5555 34468899999654 445555555555544
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.18 E-value=0.00017 Score=77.01 Aligned_cols=58 Identities=48% Similarity=0.724 Sum_probs=53.7
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 410 RPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 410 R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
+++.+++.+. .+|+.|+.+|..+|||+.-++.+|+..++++..||++||+|+|+|+++
T Consensus 97 ~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 97 ARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred cccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 3456688888 999999999999999999999999999999999999999999999765
No 36
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.08 E-value=0.00028 Score=69.98 Aligned_cols=59 Identities=19% Similarity=0.085 Sum_probs=53.3
Q ss_pred cCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 408 AWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 408 ~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.+|.|.+|+..+...|+.-|.. .+||...-++.||..++++...|.+||+|+|.++++.
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 4566777999999999999988 6999999999999999999999999999999997654
No 37
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=96.65 E-value=0.00062 Score=71.94 Aligned_cols=56 Identities=25% Similarity=0.430 Sum_probs=48.9
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 410 RPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 410 R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
|||+.+-..-++.|+++|.. .|-|+.+....+|.+..|.+..|..||+|+|.+.|+
T Consensus 311 RKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 311 RKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred cccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 34444655668899999998 899999999999999999999999999999999776
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.32 E-value=0.0032 Score=52.10 Aligned_cols=43 Identities=19% Similarity=0.374 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhh
Q 005863 420 VSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVR 465 (673)
Q Consensus 420 ~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~R 465 (673)
.+.|+++|.. |.+..+.+-..|+.+++|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4559999999 799999999999999999999999999987654
No 39
>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=94.52 E-value=0.047 Score=44.73 Aligned_cols=43 Identities=14% Similarity=0.238 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhh--hHHHHHHHHHHhhhhH
Q 005863 306 MLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSY--TVLALQTISRHFRSLR 356 (673)
Q Consensus 306 ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~py--t~lal~~is~~fr~Lr 356 (673)
..+|+|+++++||. |..+|.. ...+|+ ++.+++.|+.++..|.
T Consensus 7 ~dpELDqFMeaYc~----~L~kyke----eL~~p~~EA~~f~~~ie~qL~~Lt 51 (52)
T PF03791_consen 7 ADPELDQFMEAYCD----MLVKYKE----ELQRPFQEAMEFCREIEQQLSSLT 51 (52)
T ss_pred CCccHHHHHHHHHH----HHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34789999999999 5666774 567898 7889999999998764
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=93.91 E-value=0.052 Score=53.92 Aligned_cols=60 Identities=30% Similarity=0.565 Sum_probs=53.1
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 407 HAWRPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 407 ~~~R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
...+.+..+.......|..-|.. .+||....+..|+..+|++...|..||+|.|.+.++.
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 35556677888899999888877 8999999999999999999999999999999998765
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=86.65 E-value=0.7 Score=57.72 Aligned_cols=57 Identities=25% Similarity=0.360 Sum_probs=51.7
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 412 QRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 412 rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
|..+...++++|+..|.. .-||+.++.+.|-...+|.+..|..||+|+|.+-+|+..
T Consensus 907 ~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred ccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 334788899999999988 889999999999999999999999999999999998744
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=73.45 E-value=7.8 Score=46.50 Aligned_cols=44 Identities=27% Similarity=0.449 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhc
Q 005863 420 VSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRL 466 (673)
Q Consensus 420 ~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~Rl 466 (673)
..+|+++|.. |+.|+.+|-..+|.+.||...-|+.||.+.+...
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 7889999988 9999999999999999999999999999998874
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=72.22 E-value=6.7 Score=31.79 Aligned_cols=46 Identities=22% Similarity=0.218 Sum_probs=30.5
Q ss_pred CCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhH
Q 005863 410 RPQRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINAR 463 (673)
Q Consensus 410 R~rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR 463 (673)
|+|+.|+-+.+-.+-.-+.. .+ -+..||++.|++..+|++|..|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 56777887775555444544 33 488899999999999999999954
No 44
>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=63.14 E-value=13 Score=27.47 Aligned_cols=46 Identities=22% Similarity=0.201 Sum_probs=35.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhcc
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLW 467 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~Rlk 467 (673)
.|+...+.++..++.+. -.-..+|..+|++...|..|....+.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777888888877542 22567899999999999999998887753
No 45
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=60.79 E-value=65 Score=34.73 Aligned_cols=57 Identities=25% Similarity=0.406 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHHHHHhhhhHHHHHHHHHHh
Q 005863 294 QELLNKKTKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTISRHFRSLRDAISDQIQVT 366 (673)
Q Consensus 294 ~e~q~kk~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~is~~fr~Lrd~i~~qi~~~ 366 (673)
.+|+.+|..|..-++++++|-++-.++|+ ++| ||. -+.|-+..+-.+|.+.+.++-.
T Consensus 7 ~eL~qrk~~Lq~eIe~LerR~~ri~~Emr---tsF---aG~----------Sq~lA~RVqGFkdYLvGsLQDL 63 (283)
T PF11285_consen 7 KELEQRKQALQIEIEQLERRRERIEKEMR---TSF---AGQ----------SQDLAIRVQGFKDYLVGSLQDL 63 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---ccc---ccc----------hHHHHHHHhhhHHHHHHHHHHH
Confidence 58999999999999999999999999874 334 333 2445566666677777655443
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=58.43 E-value=14 Score=28.78 Aligned_cols=47 Identities=26% Similarity=0.345 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
.||++.+.+|...|.+. + .-.++|...|++...|..|...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~~----~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG----L----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST---------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC----C----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 58889999998887542 2 24678999999999999999999888763
No 47
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=56.83 E-value=17 Score=28.46 Aligned_cols=45 Identities=27% Similarity=0.336 Sum_probs=33.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhc
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRL 466 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~Rl 466 (673)
.||+..+.++...+.+. -.-.++|+.+|++...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 57888888887766553 2356799999999999999999999874
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=55.82 E-value=27 Score=22.89 Aligned_cols=39 Identities=15% Similarity=0.226 Sum_probs=27.2
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhh
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWF 459 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF 459 (673)
+.++.+.+..+..++.. .+ ....+|+..|++...|.+|.
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 34666666666555543 33 35678999999999999984
No 49
>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=55.05 E-value=16 Score=30.29 Aligned_cols=46 Identities=22% Similarity=0.276 Sum_probs=29.7
Q ss_pred CCCCCCChhHHHHH-HHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhH
Q 005863 410 RPQRGLPESSVSIL-RAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINAR 463 (673)
Q Consensus 410 R~rR~Lpk~a~~iL-r~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR 463 (673)
++++.|+++.+..+ ...+.. ......+|++.|++..+|.+|-.-.+
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 45677888875544 555343 35688899999999999999977665
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=44.53 E-value=26 Score=28.15 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=23.3
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhh
Q 005863 423 LRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVR 465 (673)
Q Consensus 423 Lr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~R 465 (673)
|+.++.+ +-+ ....||+.+|+++.+|+.|+.+...+
T Consensus 2 L~~~m~~---~~i----t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 2 LKELMAE---RGI----TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp HHHHHHH---TT------HHHHHHHHT--HHHHHHHHTTT---
T ss_pred HHHHHHH---cCC----CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 5566666 332 36779999999999999999987444
No 51
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=43.56 E-value=63 Score=24.29 Aligned_cols=49 Identities=20% Similarity=0.186 Sum_probs=36.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
.|++....++..+ .. .+ ....+|+.+|++...|..|....+.++.-...
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~ 51 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRSR 51 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence 4777778877554 32 22 34779999999999999999988888755443
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=41.65 E-value=48 Score=31.06 Aligned_cols=49 Identities=22% Similarity=0.188 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
.||+..+.++...+.+. .+ -.++|..+|++...|.+++.-+|+++++.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999997766653 23 357999999999999999999999987754
No 53
>cd00131 PAX Paired Box domain
Probab=40.57 E-value=1.3e+02 Score=28.59 Aligned_cols=48 Identities=19% Similarity=0.063 Sum_probs=33.8
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-------ChHhHhhhhhhh
Q 005863 412 QRGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGL-------SKNQVANWFINA 462 (673)
Q Consensus 412 rR~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGL-------S~~QVsNWF~Na 462 (673)
.+.+.......+..+..+ ||.-+..|-..+-...|+ +...|+.||.++
T Consensus 73 pr~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 73 PRVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 344555666666767776 898888887666335576 899999997663
No 54
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=39.83 E-value=42 Score=32.86 Aligned_cols=54 Identities=11% Similarity=0.214 Sum_probs=43.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHHHH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEEMY 475 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e~~ 475 (673)
.||+..+.++.--+.+. .+ -.++|..+|++...|.++..-+|+++++.+.+.+|
T Consensus 134 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 187 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--LS------SEQICQECDISTSNLHVLLYRARLQLQACLSKNWF 187 (189)
T ss_pred hCCHHHHHHHhHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 68888999888776652 22 46799999999999999999999999887655544
No 55
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=39.81 E-value=41 Score=31.81 Aligned_cols=49 Identities=16% Similarity=0.044 Sum_probs=41.1
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||+..+.++..++.++ .+ -.++|..+|++...|.+|..-+|+++++-
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--LT------YEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468999999999887764 33 46799999999999999999999998764
No 56
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=39.52 E-value=39 Score=31.31 Aligned_cols=47 Identities=19% Similarity=0.106 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
.||+..+.++..-|.+. .+ -.++|..+|++...|.+|...+|+++++
T Consensus 106 ~L~~~~r~ii~l~~~~~--~s------~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--KT------MGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 68889999887665553 22 4679999999999999999999999865
No 57
>PRK00118 putative DNA-binding protein; Validated
Probab=38.90 E-value=40 Score=31.38 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++..++.+. + .-..+|+.+|+++.-|.+|...+|+++++-
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 57889999998887763 2 245699999999999999999999997663
No 58
>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=37.88 E-value=47 Score=29.43 Aligned_cols=47 Identities=26% Similarity=0.285 Sum_probs=36.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
.||+..+.++..-+.. .++ ...+|+..|+++..|.+|....+.++++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~s----~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GLS----YKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5778888887654433 332 4579999999999999999999998765
No 59
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=35.96 E-value=44 Score=31.99 Aligned_cols=48 Identities=17% Similarity=0.263 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||++.+.++...+.+. ++ -..+|..+|++...|.+++..+|+++++.
T Consensus 129 ~L~~~~r~i~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG----LS----YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 58999999998888763 22 46699999999999999999999998764
No 60
>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=35.15 E-value=36 Score=32.64 Aligned_cols=50 Identities=16% Similarity=0.122 Sum_probs=39.5
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
..||+..+.++.--+.++ + .-.++|..+|++...|.+|.-.+|+++++.+
T Consensus 137 ~~L~~~~r~v~~l~~~~~----~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 137 EALPEDLRTAITLRELEG----L----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred HcCCHHHhhhhhhhhhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 357888888887665553 2 2467999999999999999999999987653
No 61
>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=34.72 E-value=74 Score=29.11 Aligned_cols=47 Identities=28% Similarity=0.241 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
.||++.+.+|...+.+ .++ -..+|+.+|++...|.++...+|+++++
T Consensus 113 ~L~~~~r~il~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKS----YKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 6888889998876554 232 3558999999999999999999999775
No 62
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=34.19 E-value=98 Score=28.82 Aligned_cols=44 Identities=14% Similarity=0.292 Sum_probs=35.4
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhh
Q 005863 415 LPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINA 462 (673)
Q Consensus 415 Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~Na 462 (673)
-....+..+.+|+.+|+..| ++ -..||+.+|+++.++..||...
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 34455778889999988776 55 4668999999999999999876
No 63
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.96 E-value=48 Score=32.43 Aligned_cols=48 Identities=10% Similarity=0.090 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.+|..-+.+. .+ -.++|+.+|++...|.+|...+|+++++.
T Consensus 142 ~L~~~~r~vl~l~~~~~--~s------~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--LT------YREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 58999999998766653 22 46789999999999999999999998764
No 64
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=33.71 E-value=83 Score=30.82 Aligned_cols=51 Identities=22% Similarity=0.139 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHH
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIE 472 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~ 472 (673)
..|++.++.+|+.. .+ .+ .-.++|...|++...|++|...+|.++++-+..
T Consensus 5 ~~Lt~rqreVL~lr-~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLR-ER----GL----TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45899999999773 33 22 245799999999999999999999998776554
No 65
>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=33.54 E-value=72 Score=25.56 Aligned_cols=53 Identities=19% Similarity=0.176 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHHHH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEEMY 475 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e~~ 475 (673)
.|++....+|+.+..- + ...++|...+++.+.|..+..+.++|+.-+...+++
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l~ 55 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAELI 55 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHHH
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHHH
Confidence 4778888888877654 2 256799999999999999999999998766555444
No 66
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.38 E-value=75 Score=29.81 Aligned_cols=49 Identities=20% Similarity=0.174 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
.||+..+.++..-+... .+ -..+|+.+|++...|.+|...+|+++++.+
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LS------YEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888887655442 23 356899999999999999999999987643
No 67
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=33.29 E-value=69 Score=31.21 Aligned_cols=51 Identities=20% Similarity=0.229 Sum_probs=41.6
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
..||++.+.++.-.|.+. .+ -.++|+.+|++...|.+...-+|+++++..+
T Consensus 130 ~~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HhCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 368999999998766553 33 4679999999999999999999999887643
No 68
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=32.25 E-value=1.2e+02 Score=28.00 Aligned_cols=54 Identities=22% Similarity=0.177 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHHHH
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEEMY 475 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e~~ 475 (673)
..|++..+++|+-+ .++ |. .+++|+..+++.+.|.+|..+.|+|+.-.-..+++
T Consensus 148 ~~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~ 201 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201 (211)
T ss_pred cCCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHH
Confidence 45999999999885 342 32 46889999999999999999999998654444433
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=32.17 E-value=48 Score=31.87 Aligned_cols=49 Identities=14% Similarity=0.080 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
.||+..+.++..-+.+. .+ -.++|..+|++...|.+++..+|+++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--AS------IKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 68999999998876663 23 467999999999999999999999987643
No 70
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.97 E-value=64 Score=30.18 Aligned_cols=48 Identities=19% Similarity=0.152 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++..-+.+. + .-..+|+..|++...|.+|..-+|.++++.
T Consensus 125 ~L~~~~r~i~~l~~~~~----~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG----L----SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888887655442 2 236799999999999999999999998764
No 71
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=30.99 E-value=55 Score=33.65 Aligned_cols=49 Identities=20% Similarity=0.183 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
.||+..+.++...|.+.+ . -.++|..+|++...|..|...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g~--s------~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--S------QKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--C------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 689999999988876632 1 367999999999999999999999987643
No 72
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=30.90 E-value=63 Score=33.24 Aligned_cols=48 Identities=19% Similarity=0.215 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.+|...|++. .+ -.++|..+|++...|.+|...+|+++++.
T Consensus 205 ~L~~~~r~vl~l~~~~g--~s------~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN--LS------QKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58999999998877653 22 36799999999999999999999998754
No 73
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=30.57 E-value=4.6e+02 Score=32.06 Aligned_cols=17 Identities=24% Similarity=0.165 Sum_probs=14.6
Q ss_pred CCCChhHHHHHHHHHHH
Q 005863 413 RGLPESSVSILRAWLFE 429 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~e 429 (673)
-.|++.+.+.+++-+.+
T Consensus 680 ~~L~~~Q~~~I~~iL~~ 696 (717)
T PF10168_consen 680 IVLSESQKRTIKEILKQ 696 (717)
T ss_pred ccCCHHHHHHHHHHHHH
Confidence 35999999999998887
No 74
>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=30.21 E-value=3.8e+02 Score=23.55 Aligned_cols=69 Identities=10% Similarity=0.187 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccch-hhhHHHHHHHHHHhhhhHHHHHHHHHHh
Q 005863 298 NKKTKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAK-SYTVLALQTISRHFRSLRDAISDQIQVT 366 (673)
Q Consensus 298 ~kk~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~-pyt~lal~~is~~fr~Lrd~i~~qi~~~ 366 (673)
..+.+.+..+.|+|.++....+++...+..|-...+..... +=..-.++.|...+..++..-...|..+
T Consensus 15 ~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~deKv~lA 84 (105)
T PF12998_consen 15 AELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDEKVALA 84 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45668888888999999999999887777777665542222 2235566777777766655544444443
No 75
>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=30.11 E-value=67 Score=29.80 Aligned_cols=48 Identities=29% Similarity=0.284 Sum_probs=38.4
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
..||+..+.++..-+.+. ++ -..+|..+|++...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~g----~~----~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG----VS----LTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 468899999998855542 22 4568999999999999999999998765
No 76
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=30.05 E-value=86 Score=29.45 Aligned_cols=49 Identities=20% Similarity=0.094 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||+.++.++.-.+.+. .+ -.++|..+|++...|..+...+|+++++.
T Consensus 111 ~~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG--FS------YKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHCCHHHHHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 368999999998876653 33 35699999999999999999999998763
No 77
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=29.00 E-value=66 Score=31.96 Aligned_cols=48 Identities=21% Similarity=0.259 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||++.+.+|..-+++. .. -..+|..+|++...|.+++..+|+++++.
T Consensus 153 ~L~~~~r~vl~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--LS------QEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 68999999998766553 22 46799999999999999999999997664
No 78
>KOG2033 consensus Low density lipoprotein B-like protein [Lipid transport and metabolism]
Probab=29.00 E-value=1.2e+02 Score=36.81 Aligned_cols=27 Identities=19% Similarity=0.159 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCChHhHhhhhhhhHhhc
Q 005863 440 EKIMLAKQTGLSKNQVANWFINARVRL 466 (673)
Q Consensus 440 EK~~LA~qTGLS~~QVsNWF~NaR~Rl 466 (673)
.-..+|---+.++.||-.-|-+.|.-.
T Consensus 197 aL~aiaLLdesdpsqvLelFL~~Rk~~ 223 (863)
T KOG2033|consen 197 ALAAIALLDESDPSQVLELFLEKRKEH 223 (863)
T ss_pred HHHHHHHhccCCHHHHHHHHHHHHHHH
Confidence 344566667889999999999998774
No 79
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.89 E-value=69 Score=31.01 Aligned_cols=49 Identities=22% Similarity=0.096 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||+..+.++..-+++. .+ -.++|..+|++...|.++...+|+++++.
T Consensus 138 ~~L~~~~r~i~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 138 DTLPEKQREILILRVVVG--LS------AEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 368899999998766653 22 56799999999999999999999998764
No 80
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.47 E-value=64 Score=31.28 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
.||++.+.++..-+++. .+ -.++|...|++...|.+|+..+|+++++.+
T Consensus 141 ~L~~~~~~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYEG--LS------QSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 68888888887765552 22 466999999999999999999999988753
No 81
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.92 E-value=78 Score=30.84 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
.||+..+.++.-.+.+. .. -..+|..+|++...|.++...+|+++++.+
T Consensus 136 ~L~~~~r~i~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG--FS------SDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 68888888887655553 22 467999999999999999999999988764
No 82
>PRK04217 hypothetical protein; Provisional
Probab=27.43 E-value=92 Score=29.30 Aligned_cols=49 Identities=18% Similarity=0.143 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..|+++.+.++..++.+.+ .-.++|+.+|++...|.+.+..+|.+++..
T Consensus 41 ~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3488899999988876632 356699999999999999999999887654
No 83
>PF13518 HTH_28: Helix-turn-helix domain
Probab=27.19 E-value=62 Score=24.74 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChHhHhhhhhhhHh
Q 005863 441 KIMLAKQTGLSKNQVANWFINARV 464 (673)
Q Consensus 441 K~~LA~qTGLS~~QVsNWF~NaR~ 464 (673)
...+|++.|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456999999999999999887665
No 84
>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=27.07 E-value=79 Score=30.23 Aligned_cols=48 Identities=17% Similarity=0.121 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||++.+.++.-.+.+. .+ -.++|..+|++...|.+.+..+|.++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG--LT------VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998887663 22 36799999999999999999999997763
No 85
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=26.84 E-value=80 Score=30.49 Aligned_cols=48 Identities=21% Similarity=0.069 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++...+.+. .+ -.++|+.+|++...|.+.+..+|+++++.
T Consensus 129 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG--LS------VAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888877665553 22 46799999999999999999999998764
No 86
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.50 E-value=72 Score=30.78 Aligned_cols=48 Identities=17% Similarity=0.201 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||++.+.++..-+++. .+ -.++|+.+|++...|.++...+|+++++.
T Consensus 128 ~L~~~~r~i~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 128 ALPERQREAIVLQYYQG--LS------NIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred hCCHHHHHHhhHHHhcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 57888888887655552 22 45689999999999999999999998764
No 87
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=26.39 E-value=81 Score=29.94 Aligned_cols=48 Identities=15% Similarity=-0.040 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++.-.+.+. .. -.++|..+|++...|.++..-+|+++++.
T Consensus 112 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASG--FS------YEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 68999999988876664 22 45689999999999999999999997753
No 88
>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=26.26 E-value=55 Score=25.18 Aligned_cols=21 Identities=19% Similarity=0.230 Sum_probs=18.8
Q ss_pred HHHHHhCCChHhHhhhhhhhH
Q 005863 443 MLAKQTGLSKNQVANWFINAR 463 (673)
Q Consensus 443 ~LA~qTGLS~~QVsNWF~NaR 463 (673)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999874
No 89
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.16 E-value=89 Score=30.02 Aligned_cols=49 Identities=14% Similarity=0.133 Sum_probs=39.6
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||+..+.+|...+.+. .. -.++|...|++...|.++...+|.++++.
T Consensus 134 ~~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 134 KALSPEERRVIEVLYYQG--YT------HREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 358999999998766553 22 46799999999999999999999997663
No 90
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=25.12 E-value=1e+02 Score=30.47 Aligned_cols=50 Identities=20% Similarity=0.181 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
.||+..+.++.--+++. .+ -.++|..+|++..-|.+....+|+++++.+-
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 68899999988776653 23 3568999999999999999999999887543
No 91
>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=24.88 E-value=4.3e+02 Score=26.45 Aligned_cols=69 Identities=22% Similarity=0.297 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHHHHHhhhhHHHHHHHHH
Q 005863 295 ELLNKKTKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTISRHFRSLRDAISDQIQ 364 (673)
Q Consensus 295 e~q~kk~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~is~~fr~Lrd~i~~qi~ 364 (673)
.|+.++.+|...++.+-++-+.++..+..+..+|..++..+...+. .-+|..++..+..+++.+..+..
T Consensus 35 ~le~~Lk~l~~~~~~l~~~~~~l~~~~~e~~~~~~~la~~E~~~~l-~~~l~~l~~~~~~~~~~~~~~a~ 103 (236)
T PF09325_consen 35 KLEEQLKKLYKSLERLVKRRQELASALAEFGSSFSQLAKSEEEKSL-SEALSQLAEAFEKISELLEEQAN 103 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCchh-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677888888888888888888888888888889888877665443 55677888888887777665543
No 92
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.78 E-value=1.2e+02 Score=28.29 Aligned_cols=50 Identities=20% Similarity=0.157 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
..||+..+.++.--+++. .+ -.++|..+|++...|.++..-+|+++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWED--MD------VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468999999998766653 22 467999999999999999999999987643
No 93
>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=24.64 E-value=93 Score=31.27 Aligned_cols=48 Identities=19% Similarity=0.284 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.+|...|.+. + .-..+|+.+|++...|..|...+++++++.
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 68999999999887663 2 246799999999999999999999997753
No 94
>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=24.62 E-value=2e+02 Score=21.67 Aligned_cols=46 Identities=22% Similarity=0.184 Sum_probs=32.4
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 415 LPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 415 Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
|++....++..++ . .+ ....+|+.++++...|..|..-.++++..+
T Consensus 1 l~~~e~~i~~~~~-~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLLA-E----GK----TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 3556666665443 2 22 357789999999999999998777776543
No 95
>cd07307 BAR The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-
Probab=24.40 E-value=5.7e+02 Score=23.64 Aligned_cols=67 Identities=10% Similarity=0.058 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchh-------h--hHHHHHHHHHHhhhhHHHHHH
Q 005863 295 ELLNKKTKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKS-------Y--TVLALQTISRHFRSLRDAISD 361 (673)
Q Consensus 295 e~q~kk~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~p-------y--t~lal~~is~~fr~Lrd~i~~ 361 (673)
+++....||+......-....+++.....+..+|..++......+ . ..-+++.|...+..+.+.|..
T Consensus 4 ~~~~~~~kl~k~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~ 79 (194)
T cd07307 4 ELEKLLKKLIKDTKKLLDSLKELPAAAEKLSEALQELGKELPDLSNTDLGEALEKFGKIQKELEEFRDQLEQKLEN 79 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667788888777777777777777778887877664433222 2 234455665555555554443
No 96
>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=24.14 E-value=82 Score=31.63 Aligned_cols=48 Identities=27% Similarity=0.365 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++...+.+. + .-..+|+.+|++...|..|...+++++++.
T Consensus 178 ~L~~~~r~vl~l~y~~~----~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 178 ALPERERRILLLRFFED----K----TQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred cCCHHHHHHHHHHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 68999999998877652 1 256799999999999999999999998764
No 97
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.14 E-value=1.2e+02 Score=28.94 Aligned_cols=49 Identities=16% Similarity=0.133 Sum_probs=38.4
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||+..+.++..-+.+. .+ -.++|..+|++...|.+++..+|+++++.
T Consensus 135 ~~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 135 QALPPKYRMVIVLKYMED--LS------LKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhCCHHHhHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 368888999987744442 22 46789999999999999999999997653
No 98
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.09 E-value=2.3e+02 Score=22.19 Aligned_cols=48 Identities=17% Similarity=0.132 Sum_probs=30.2
Q ss_pred CCChhHHHHHHHHH--HHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHh
Q 005863 414 GLPESSVSILRAWL--FEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARV 464 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf--~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~ 464 (673)
+|+..++.++-.-+ .......||+ ...||+.+|+++..|..+...-+.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35555555543221 1122347887 667999999999999888765443
No 99
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=24.04 E-value=1.7e+02 Score=29.43 Aligned_cols=52 Identities=19% Similarity=0.240 Sum_probs=41.8
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHH
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIE 472 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~ 472 (673)
..||++.+.++.--+++. .+ -.++|..+|++...|.++..-+|+++++.+..
T Consensus 147 ~~L~~~~r~v~~L~~~~g--~s------~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE--LE------TNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 368888888887766663 33 46799999999999999999999998886543
No 100
>PRK06930 positive control sigma-like factor; Validated
Probab=23.75 E-value=98 Score=30.77 Aligned_cols=52 Identities=13% Similarity=0.029 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhHHH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMIEE 473 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i~e 473 (673)
.||+..+.++...+.+. .+ -..+|..+|++...|.++...+|.++++.+-++
T Consensus 114 ~L~~rer~V~~L~~~eg--~s------~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG--LS------YSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 58888888888765542 22 356899999999999999999999987754443
No 101
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=23.51 E-value=1.7e+02 Score=28.47 Aligned_cols=50 Identities=12% Similarity=0.121 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
.||++.+.++.-.+.+. .+ -.++|..+|++..-|.+....+|+++++.+-
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 58999999998776663 33 3679999999999999999999999877543
No 102
>PRK12851 groEL chaperonin GroEL; Reviewed
Probab=22.87 E-value=3e+02 Score=32.21 Aligned_cols=60 Identities=23% Similarity=0.300 Sum_probs=45.6
Q ss_pred CHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHHH
Q 005863 289 SHAERQELLNKKTKLL-------------SMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTIS 349 (673)
Q Consensus 289 s~~e~~e~q~kk~kLl-------------~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~is 349 (673)
++.+|..|+.++++|- .+++|+.++++-...-++..+.. -.|.|.|++.-+.+.+|+...
T Consensus 358 ~~~~~~~l~~ri~~l~g~~~tI~irG~t~~~l~E~er~i~DAl~a~~~al~~-g~VpGGGa~e~~~s~~L~~~~ 430 (541)
T PRK12851 358 SDYDREKLQERLAKLAGGVAVIRVGASTEVEVKEKKDRVDDALHATRAAVEE-GIVPGGGVALLRAVKALDKLE 430 (541)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEecCCCHHHHHHHHHHHHHHHHHHHHHHHc-CcccCchHHHHHHHHHHHHHh
Confidence 4457778888876663 36788999998888888877777 499999998777776676543
No 103
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=22.75 E-value=1.3e+02 Score=29.55 Aligned_cols=50 Identities=14% Similarity=0.141 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
.||+..+.++..-+++. .+ -..+|..+|++..-|.++..-+|+++++.+-
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--FE------SDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 68888989988876664 22 4679999999999999999999999877543
No 104
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=22.15 E-value=1.1e+02 Score=29.97 Aligned_cols=49 Identities=20% Similarity=0.249 Sum_probs=39.6
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||++.+.++..-+.+. .+ -.++|..+|++...|.+.+..+|+++++.
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 468999999998755553 33 35699999999999999999999987764
No 105
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.07 E-value=1.1e+02 Score=31.17 Aligned_cols=48 Identities=23% Similarity=0.269 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++..-|.+. + .-..+|+.+|++...|.+|...+|+++++.
T Consensus 184 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE----L----NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58899999988776553 2 246799999999999999999999998764
No 106
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.02 E-value=96 Score=30.61 Aligned_cols=48 Identities=21% Similarity=0.088 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++.-++.+. .+ -.++|...|++...|.+++.-+|+++++.
T Consensus 113 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 113 QLPDEQREALILVGASG--FS------YEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred hCCHHHhHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 68999999998886663 22 35689999999999999999999998764
No 107
>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=21.98 E-value=1.1e+02 Score=29.03 Aligned_cols=48 Identities=13% Similarity=0.099 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||++.+.++..-+++. .+ -..+|+.+|++...|.++..-+|+++++.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~s------~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--LT------IKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888899997776663 22 45689999999999999999999998764
No 108
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.80 E-value=1.1e+02 Score=28.65 Aligned_cols=47 Identities=17% Similarity=0.258 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.+|..-+ +. + .-..+|...|++...|.++...+|.++++-
T Consensus 112 ~L~~~~r~il~l~~-~g----~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG----Y----SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-cC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888887766 53 2 246799999999999999999999997764
No 109
>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=21.33 E-value=1.1e+02 Score=28.53 Aligned_cols=48 Identities=21% Similarity=0.293 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++..-+.+. ++ -.++|..+|++...|.++...+|.++++.
T Consensus 110 ~L~~~~r~i~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRYYED----LS----EAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHHHhc----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 68888888887766553 22 35689999999999999999999997763
No 110
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.27 E-value=1.1e+02 Score=29.45 Aligned_cols=49 Identities=12% Similarity=0.137 Sum_probs=38.7
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||++.+.++..-+.+. -+ -..+|..+|++...|.+|...+|+++++.
T Consensus 132 ~~L~~~~r~i~~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVDG--CS------HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 368888888777666553 22 46799999999999999999999987653
No 111
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=21.24 E-value=1e+02 Score=30.54 Aligned_cols=49 Identities=16% Similarity=0.034 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchh
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPM 470 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~ 470 (673)
.||+..+.++..-+++. .. -.++|..+|++...|.++...+|+++++-+
T Consensus 133 ~Lp~~~r~v~~l~~~~g--~s------~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 133 ALPPERREALILTQVLG--YT------YEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred cCCHHHHHHhhhHHHhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58898999887776664 22 467999999999999999999999977643
No 112
>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=20.87 E-value=1.6e+02 Score=30.71 Aligned_cols=51 Identities=20% Similarity=0.289 Sum_probs=42.0
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
..||+..+.++.-.+.+. .+ -.++|..+|++..-|.++...+|+++++.+.
T Consensus 160 ~~Lp~~~R~v~~L~~~eg--~S------~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 160 AALSERERHLLRLHFVDG--LS------MDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 368999999998887764 22 3568999999999999999999999887544
No 113
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.85 E-value=1.8e+02 Score=28.52 Aligned_cols=48 Identities=17% Similarity=0.059 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++.-.+.+. .+ -.++|+.+|++...|.++...+|+++++.
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s------~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FA------YEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58889999988776653 33 35689999999999999999999998764
No 114
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.61 E-value=1.7e+02 Score=29.27 Aligned_cols=48 Identities=17% Similarity=0.104 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
.||+..+.++..-+.+. .+ -.++|..+|++..-|.++..-+|+++++.
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LS------YEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 68888888776665553 33 36799999999999999999999998764
No 115
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=20.56 E-value=1.4e+02 Score=28.93 Aligned_cols=49 Identities=14% Similarity=0.196 Sum_probs=39.3
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccch
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKP 469 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp 469 (673)
..||++.+.+|..-+.+. .+ -..+|...|++...|.+.+..+|+++++.
T Consensus 130 ~~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHE--KS------VEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 368999999997765552 22 46799999999999999999999997764
No 116
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.39 E-value=1.7e+02 Score=30.04 Aligned_cols=50 Identities=16% Similarity=0.105 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccchhH
Q 005863 414 GLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWKPMI 471 (673)
Q Consensus 414 ~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkKp~i 471 (673)
.||+..+.++.-.+.+. .+ -.++|..+|++...|.++...+|+++++.+-
T Consensus 171 ~Lp~~~R~v~~L~~~eg--~s------~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN--MS------NGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hCCHHHHHHhhhHHhcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 57888888876665552 23 4679999999999999999999999887543
No 117
>CHL00093 groEL chaperonin GroEL
Probab=20.16 E-value=5.4e+02 Score=29.99 Aligned_cols=59 Identities=19% Similarity=0.216 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHH
Q 005863 289 SHAERQELLNKKTKLL-------------SMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTI 348 (673)
Q Consensus 289 s~~e~~e~q~kk~kLl-------------~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~i 348 (673)
+..|++.|+.++++|- ..++|.+++++-...-++..+.. -.|.|.|++.-..+.+|+..
T Consensus 357 ~~~~~~~l~eR~~~l~g~~~~I~irg~t~~~l~E~er~i~DAl~a~r~a~~~-gvVpGGGa~e~~~s~~L~~~ 428 (529)
T CHL00093 357 SSYEKEKLQERLAKLSGGVAVIKVGAATETEMKDKKLRLEDAINATKAAVEE-GIVPGGGATLVHLSENLKTW 428 (529)
T ss_pred CHHHHHHHHHHHHHhcCCeEEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHc-CcccCCcHHHHHHHHHHHHH
Confidence 4467888888888874 46888888888888888877776 58999999877766666654
No 118
>PRK11677 hypothetical protein; Provisional
Probab=20.08 E-value=6.5e+02 Score=24.60 Aligned_cols=47 Identities=21% Similarity=0.371 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccchhhhHHHHHHHHHHhhhhHHHHH
Q 005863 301 TKLLSMLEEVDRGYKQYYHQMQIVASSFDMVAGHGAAKSYTVLALQTISRHFRSLRDAIS 360 (673)
Q Consensus 301 ~kLl~ml~Evd~ry~qy~~qmq~vvssfe~vaG~~aa~pyt~lal~~is~~fr~Lrd~i~ 360 (673)
.+|-.=|++.....++|.++ |+..|.. |+-.|..|.+.|+.|-.-+.
T Consensus 32 ~~le~eLe~~k~ele~Ykqe---V~~HFa~----------TA~Ll~~L~~~Y~~Ly~HlA 78 (134)
T PRK11677 32 QALQYELEKNKAELEEYRQE---LVSHFAR----------SAELLDTMAKDYRQLYQHMA 78 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHH----------HHHHHHHHHHHHHHHHHHHH
Confidence 44555666777788889888 8888883 56678888888887766554
No 119
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.07 E-value=1.9e+02 Score=27.64 Aligned_cols=48 Identities=10% Similarity=0.125 Sum_probs=39.0
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChHhHhhhhhhhHhhccc
Q 005863 413 RGLPESSVSILRAWLFEHFLHPYPNDSEKIMLAKQTGLSKNQVANWFINARVRLWK 468 (673)
Q Consensus 413 R~Lpk~a~~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF~NaR~RlkK 468 (673)
..||++.+.++.-.+.+. .+ -.++|..+|++..-|.++...+|+|++.
T Consensus 118 ~~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 368999999998776653 33 3569999999999999999999999754
Done!