Query 005901
Match_columns 671
No_of_seqs 318 out of 1047
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 15:25:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00574 POX domain associat 100.0 1.4E-41 3.1E-46 317.5 13.8 139 197-343 1-139 (140)
2 PF07526 POX: Associated with 100.0 5.4E-41 1.2E-45 315.7 13.1 139 201-344 1-140 (140)
3 KOG0773 Transcription factor M 100.0 1E-32 2.2E-37 288.5 9.7 256 199-463 45-312 (342)
4 KOG0774 Transcription factor P 99.8 6.1E-19 1.3E-23 179.4 10.3 152 272-455 98-253 (334)
5 KOG0775 Transcription factor S 99.6 1.3E-15 2.9E-20 156.2 8.6 82 361-449 148-232 (304)
6 PF05920 Homeobox_KN: Homeobox 99.6 1.7E-15 3.7E-20 115.7 3.6 40 408-447 1-40 (40)
7 cd00086 homeodomain Homeodomai 99.4 9E-13 2E-17 104.0 6.3 57 392-451 2-58 (59)
8 smart00389 HOX Homeodomain. DN 99.3 2.2E-12 4.7E-17 101.4 6.4 55 392-449 2-56 (56)
9 PF00046 Homeobox: Homeobox do 99.3 1.4E-12 3E-17 103.6 4.9 57 391-450 1-57 (57)
10 KOG0487 Transcription factor A 99.0 1.9E-10 4.1E-15 121.2 3.5 61 390-453 234-295 (308)
11 KOG0842 Transcription factor t 99.0 3.4E-10 7.4E-15 119.2 3.9 63 390-455 152-215 (307)
12 KOG0843 Transcription factor E 98.9 1.3E-09 2.9E-14 107.1 4.2 64 389-455 101-164 (197)
13 KOG0489 Transcription factor z 98.8 2.1E-09 4.4E-14 111.0 3.1 60 390-452 159-218 (261)
14 KOG0483 Transcription factor H 98.8 5.3E-09 1.1E-13 104.6 5.3 81 389-473 49-129 (198)
15 KOG0488 Transcription factor B 98.8 4E-09 8.6E-14 111.6 4.6 57 395-454 177-233 (309)
16 KOG0493 Transcription factor E 98.7 9.3E-09 2E-13 105.9 3.2 60 389-451 245-304 (342)
17 TIGR01565 homeo_ZF_HD homeobox 98.6 5.1E-08 1.1E-12 80.5 5.5 52 391-445 2-57 (58)
18 KOG3802 Transcription factor O 98.6 7.5E-08 1.6E-12 104.1 7.7 60 390-452 293-353 (398)
19 KOG0850 Transcription factor D 98.6 3.2E-08 7E-13 100.6 4.0 58 392-452 124-181 (245)
20 KOG0485 Transcription factor N 98.6 3.6E-08 7.9E-13 99.6 3.7 63 390-455 104-166 (268)
21 COG5576 Homeodomain-containing 98.4 1.8E-07 3.8E-12 90.7 4.3 62 388-452 49-110 (156)
22 KOG0848 Transcription factor C 98.4 1.2E-07 2.6E-12 98.2 2.6 57 396-455 205-261 (317)
23 KOG0484 Transcription factor P 98.4 2.2E-07 4.8E-12 84.9 3.8 63 392-457 19-81 (125)
24 KOG0486 Transcription factor P 98.4 2E-07 4.3E-12 98.4 3.6 61 392-455 113-174 (351)
25 KOG0492 Transcription factor M 98.4 3.3E-07 7.1E-12 92.3 4.8 59 391-452 145-203 (246)
26 KOG2251 Homeobox transcription 98.4 3E-07 6.5E-12 93.1 4.4 60 390-452 37-96 (228)
27 KOG0491 Transcription factor B 98.3 1.5E-07 3.2E-12 91.9 1.0 56 394-452 104-159 (194)
28 KOG0494 Transcription factor C 98.3 4.8E-07 1E-11 93.5 4.5 54 396-452 147-200 (332)
29 KOG0847 Transcription factor, 98.0 3.2E-06 7E-11 85.8 2.6 64 394-460 171-234 (288)
30 KOG4577 Transcription factor L 97.9 5.7E-06 1.2E-10 86.8 3.6 62 387-451 164-225 (383)
31 KOG2252 CCAAT displacement pro 97.9 1.6E-05 3.5E-10 89.2 7.1 56 390-448 420-475 (558)
32 KOG0844 Transcription factor E 97.8 6.9E-06 1.5E-10 86.7 1.6 59 392-453 183-241 (408)
33 KOG0490 Transcription factor, 97.5 5.5E-05 1.2E-09 74.5 2.5 60 390-452 60-119 (235)
34 KOG1168 Transcription factor A 97.5 7.8E-05 1.7E-09 78.5 3.6 59 389-450 308-366 (385)
35 KOG0849 Transcription factor P 97.5 8.4E-05 1.8E-09 80.4 4.0 58 392-452 178-235 (354)
36 KOG0773 Transcription factor M 97.2 0.00013 2.8E-09 77.5 1.8 62 390-452 95-156 (342)
37 PF11569 Homez: Homeodomain le 96.2 0.0044 9.5E-08 51.4 3.1 43 402-447 10-52 (56)
38 KOG0490 Transcription factor, 94.5 0.027 5.8E-07 55.6 2.8 61 390-453 153-213 (235)
39 PF03791 KNOX2: KNOX2 domain ; 92.3 0.46 1E-05 39.1 6.1 42 282-339 10-51 (52)
40 KOG1146 Homeobox protein [Gene 89.8 0.22 4.8E-06 61.7 3.0 57 394-453 907-963 (1406)
41 PF04218 CENP-B_N: CENP-B N-te 78.6 3.4 7.3E-05 33.5 4.1 47 391-445 1-47 (53)
42 PF03792 PBC: PBC domain; Int 76.5 49 0.0011 34.1 12.4 53 271-325 101-153 (191)
43 KOG3623 Homeobox transcription 73.4 4.3 9.4E-05 48.5 4.7 45 402-449 568-612 (1007)
44 cd06171 Sigma70_r4 Sigma70, re 69.0 6.5 0.00014 29.0 3.4 46 396-449 10-55 (55)
45 PRK06759 RNA polymerase factor 68.0 68 0.0015 29.6 10.6 47 396-450 106-152 (154)
46 PF12998 ING: Inhibitor of gro 63.6 1E+02 0.0022 27.2 10.3 72 281-352 15-87 (105)
47 PF01527 HTH_Tnp_1: Transposas 62.2 13 0.00028 30.8 4.2 46 392-445 2-48 (76)
48 PF11285 DUF3086: Protein of u 60.8 96 0.0021 33.5 11.1 119 277-411 7-154 (283)
49 PF04545 Sigma70_r4: Sigma-70, 59.5 7.6 0.00016 30.3 2.2 47 396-450 4-50 (50)
50 PF08281 Sigma70_r4_2: Sigma-7 59.3 11 0.00024 29.5 3.1 45 396-448 10-54 (54)
51 PRK09648 RNA polymerase sigma 56.0 1.2E+02 0.0025 29.3 10.2 49 396-452 139-187 (189)
52 cd00569 HTH_Hin_like Helix-tur 53.5 32 0.00068 22.5 4.3 39 395-441 4-42 (42)
53 smart00421 HTH_LUXR helix_turn 48.9 33 0.00071 25.8 4.2 50 396-454 3-52 (58)
54 PRK12538 RNA polymerase sigma 46.4 1.4E+02 0.0031 30.6 9.6 49 396-452 171-219 (233)
55 PRK09642 RNA polymerase sigma 45.9 18 0.00039 33.8 2.8 49 396-452 106-154 (160)
56 PF00196 GerE: Bacterial regul 45.1 28 0.0006 27.9 3.4 53 396-457 3-55 (58)
57 PF13443 HTH_26: Cro/C1-type H 42.8 19 0.00041 28.9 2.1 27 422-448 12-38 (63)
58 TIGR02985 Sig70_bacteroi1 RNA 42.1 24 0.00052 32.2 3.0 48 396-451 113-160 (161)
59 PRK00118 putative DNA-binding 41.5 36 0.00077 31.7 3.9 56 396-460 17-72 (104)
60 PF10168 Nup88: Nuclear pore c 39.9 4.5E+02 0.0098 32.1 13.7 19 393-411 678-696 (717)
61 TIGR02937 sigma70-ECF RNA poly 39.9 26 0.00057 30.9 2.8 48 396-451 110-157 (158)
62 PRK09644 RNA polymerase sigma 39.8 29 0.00063 32.7 3.2 50 395-452 107-156 (165)
63 PRK03975 tfx putative transcri 39.8 25 0.00055 34.3 2.8 51 395-454 5-55 (141)
64 PRK09645 RNA polymerase sigma 38.8 2.4E+02 0.0052 26.6 9.3 49 396-452 118-166 (173)
65 PRK12514 RNA polymerase sigma 38.3 26 0.00057 33.4 2.7 48 396-451 129-176 (179)
66 PRK05602 RNA polymerase sigma 38.0 77 0.0017 30.5 5.9 49 396-452 128-176 (186)
67 PRK12530 RNA polymerase sigma 37.3 32 0.00069 33.5 3.2 52 396-455 134-185 (189)
68 PRK12512 RNA polymerase sigma 36.5 28 0.00061 33.4 2.6 49 396-452 131-179 (184)
69 PF09712 PHA_synth_III_E: Poly 36.5 2.1E+02 0.0046 30.9 9.4 125 277-437 158-288 (293)
70 PRK11924 RNA polymerase sigma 36.2 31 0.00068 32.1 2.8 49 396-452 125-173 (179)
71 PRK09415 RNA polymerase factor 35.9 3.1E+02 0.0067 26.3 9.7 49 396-452 127-175 (179)
72 PRK09652 RNA polymerase sigma 35.5 32 0.0007 32.1 2.8 49 396-452 128-176 (182)
73 cd00131 PAX Paired Box domain 35.4 1.8E+02 0.0039 27.5 7.7 48 394-444 73-127 (128)
74 PRK15369 two component system 35.1 64 0.0014 29.5 4.6 54 395-457 148-201 (211)
75 cd06170 LuxR_C_like C-terminal 34.8 63 0.0014 24.5 3.9 47 397-452 1-47 (57)
76 PRK12541 RNA polymerase sigma 34.7 32 0.00068 32.3 2.6 47 396-450 112-158 (161)
77 PRK06930 positive control sigm 34.5 32 0.00069 34.1 2.7 55 396-458 114-168 (170)
78 PRK12526 RNA polymerase sigma 33.8 34 0.00073 33.9 2.7 49 396-452 153-201 (206)
79 TIGR02939 RpoE_Sigma70 RNA pol 33.6 28 0.0006 33.2 2.1 49 396-452 138-186 (190)
80 TIGR02989 Sig-70_gvs1 RNA poly 33.6 42 0.00091 31.1 3.2 48 395-450 110-157 (159)
81 PRK09646 RNA polymerase sigma 33.6 33 0.00072 33.4 2.6 49 396-452 142-190 (194)
82 PRK12519 RNA polymerase sigma 32.3 32 0.00069 33.2 2.3 49 396-452 141-189 (194)
83 TIGR02999 Sig-70_X6 RNA polyme 32.3 38 0.00083 32.3 2.7 48 396-451 134-181 (183)
84 PRK06811 RNA polymerase factor 30.6 46 0.00099 32.3 3.0 49 396-452 131-179 (189)
85 TIGR03001 Sig-70_gmx1 RNA poly 30.0 44 0.00095 34.7 2.9 51 396-454 161-211 (244)
86 PRK12547 RNA polymerase sigma 29.6 41 0.00088 31.9 2.4 49 396-452 112-160 (164)
87 PRK12536 RNA polymerase sigma 29.5 44 0.00095 32.2 2.7 49 396-452 129-177 (181)
88 PRK13919 putative RNA polymera 29.1 43 0.00094 32.0 2.6 49 396-452 135-183 (186)
89 TIGR02954 Sig70_famx3 RNA poly 29.1 44 0.00094 31.6 2.5 49 396-452 119-167 (169)
90 TIGR02983 SigE-fam_strep RNA p 28.6 41 0.00089 31.4 2.2 49 396-452 110-158 (162)
91 PRK12515 RNA polymerase sigma 28.4 52 0.0011 31.8 3.0 49 396-452 131-179 (189)
92 PRK09047 RNA polymerase factor 28.4 56 0.0012 30.3 3.1 50 395-452 105-154 (161)
93 PRK12544 RNA polymerase sigma 28.1 43 0.00094 33.5 2.4 52 396-455 148-199 (206)
94 PRK12531 RNA polymerase sigma 28.0 47 0.001 32.4 2.6 50 395-452 140-189 (194)
95 PRK12523 RNA polymerase sigma 27.6 48 0.001 31.6 2.5 48 396-451 119-166 (172)
96 PRK08583 RNA polymerase sigma 27.5 53 0.0012 33.7 3.0 49 396-452 205-253 (257)
97 TIGR02948 SigW_bacill RNA poly 26.6 48 0.0011 31.5 2.4 49 396-452 136-184 (187)
98 PRK12516 RNA polymerase sigma 26.5 53 0.0011 32.2 2.7 49 396-452 116-164 (187)
99 PRK06986 fliA flagellar biosyn 26.2 46 0.001 33.7 2.3 49 396-452 184-232 (236)
100 PRK12546 RNA polymerase sigma 26.1 49 0.0011 32.6 2.4 49 396-452 113-161 (188)
101 TIGR02941 Sigma_B RNA polymera 25.7 56 0.0012 33.5 2.8 49 396-452 205-253 (255)
102 PRK12520 RNA polymerase sigma 25.5 66 0.0014 31.1 3.1 50 396-453 131-180 (191)
103 PRK12533 RNA polymerase sigma 25.3 45 0.00098 33.8 2.0 49 396-452 134-182 (216)
104 PHA03247 large tegument protei 25.2 1.3E+02 0.0027 41.6 6.2 57 268-324 975-1038(3151)
105 PRK12537 RNA polymerase sigma 24.8 62 0.0013 31.2 2.8 49 395-451 132-180 (182)
106 TIGR02980 SigBFG RNA polymeras 24.7 57 0.0012 32.6 2.6 48 396-451 178-225 (227)
107 PRK10778 dksA RNA polymerase-b 24.7 2.6E+02 0.0057 27.6 7.0 30 277-306 35-64 (151)
108 PRK12545 RNA polymerase sigma 24.7 62 0.0013 31.9 2.8 50 396-453 139-188 (201)
109 PRK12532 RNA polymerase sigma 24.6 67 0.0014 31.2 3.0 49 396-452 136-184 (195)
110 PRK04217 hypothetical protein; 24.5 75 0.0016 29.9 3.1 50 395-452 41-90 (110)
111 PRK11511 DNA-binding transcrip 23.7 1.2E+02 0.0025 28.3 4.3 43 398-444 7-49 (127)
112 PRK12524 RNA polymerase sigma 23.5 65 0.0014 31.5 2.7 49 396-452 136-184 (196)
113 TIGR02947 SigH_actino RNA poly 23.4 28 0.00061 33.8 0.1 49 396-452 131-179 (193)
114 PF07765 KIP1: KIP1-like prote 23.2 1.1E+02 0.0025 27.2 3.8 30 272-301 40-70 (74)
115 PF12126 DUF3583: Protein of u 23.1 2.3E+02 0.005 31.3 6.7 36 279-314 48-83 (324)
116 PF13518 HTH_28: Helix-turn-he 22.5 75 0.0016 24.3 2.3 25 422-446 14-38 (52)
117 PRK09649 RNA polymerase sigma 21.9 79 0.0017 30.7 2.9 47 396-450 130-176 (185)
118 PRK09647 RNA polymerase sigma 21.9 90 0.0019 31.2 3.3 49 396-452 138-186 (203)
119 PRK07037 extracytoplasmic-func 21.9 77 0.0017 29.6 2.7 49 396-452 109-157 (163)
120 TIGR02479 FliA_WhiG RNA polyme 21.8 70 0.0015 32.1 2.6 48 396-451 175-222 (224)
121 PRK07408 RNA polymerase sigma 21.7 68 0.0015 33.2 2.5 49 396-452 203-251 (256)
122 PRK09639 RNA polymerase sigma 21.7 67 0.0015 30.0 2.3 48 396-452 112-159 (166)
123 cd07307 BAR The Bin/Amphiphysi 21.5 6.4E+02 0.014 23.2 10.1 67 278-344 4-79 (194)
124 PRK09637 RNA polymerase sigma 20.5 80 0.0017 30.7 2.6 49 396-452 106-154 (181)
125 PRK12542 RNA polymerase sigma 20.4 1.1E+02 0.0024 29.4 3.5 49 396-452 122-170 (185)
126 COG1734 DksA DnaK suppressor p 20.4 7.4E+02 0.016 23.8 8.8 91 277-368 4-95 (120)
127 PRK12513 RNA polymerase sigma 20.4 40 0.00087 32.6 0.5 49 396-452 139-187 (194)
128 TIGR02943 Sig70_famx1 RNA poly 20.3 8.1E+02 0.018 23.9 12.7 49 396-452 131-179 (188)
129 PRK12528 RNA polymerase sigma 20.2 1E+02 0.0022 28.9 3.1 46 396-449 113-158 (161)
130 PF02203 TarH: Tar ligand bind 20.2 3.2E+02 0.007 25.5 6.5 26 319-344 141-166 (171)
131 TIGR02393 RpoD_Cterm RNA polym 20.1 96 0.0021 31.6 3.2 54 396-453 176-229 (238)
132 PRK06288 RNA polymerase sigma 20.0 86 0.0019 32.5 2.9 49 396-452 212-260 (268)
No 1
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=1.4e-41 Score=317.53 Aligned_cols=139 Identities=52% Similarity=0.691 Sum_probs=112.3
Q ss_pred cccccccccCccchHHHHHHHHHhccchhhhcCCCCcchhhHHHHHhhhhccCCccCCCCCCCCCCCCCCCCCccCHHHH
Q 005901 197 SSTQSAILGSKYLKAAQELLDEVVKVESMIIKGSDHHHSAKAAQIKETMKMNRESIDGDQELNGTGDSTKSSFELTTAQR 276 (671)
Q Consensus 197 sGya~~l~~SrYLkpAQeLLdE~~~v~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~g~g~~~~~~~s~~~~~~ls~~er 276 (671)
+||+.+|++|||||||||||||||+|++++.+..... . .+.........++++...++++++..++|+++||
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~-~-------~~~~~~~~~~~~~~~~~~g~s~~~~~~~ls~~~r 72 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQS-G-------NDSPVSTSSNEGGGENLSGGSSSSEVPPLSTAER 72 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcccHHhhcccccc-c-------ccccccccccCCCcCCCCCCCCCCCCCCCchhHH
Confidence 4899999999999999999999999999885322111 0 0000001111111222233455667899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHHHHHHHHHHHHhHHHHHHH
Q 005901 277 QELQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTALALRTISKQFRCLKDAIS 343 (671)
Q Consensus 277 ~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~lal~~iSr~Fr~L~daI~ 343 (671)
+|+|+||+||+.||+|||+||+|||+|||+|+++||+++|+|+|++||+|||++||||||||||+|.
T Consensus 73 ~e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 73 QELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999999999996
No 2
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=100.00 E-value=5.4e-41 Score=315.71 Aligned_cols=139 Identities=51% Similarity=0.682 Sum_probs=105.6
Q ss_pred cccccCccchHHHHHHHHHhccchhhhcCCCCcchhhHHHHHhhhhccCCccCCC-CCCCCCCCCCCCCCccCHHHHHHH
Q 005901 201 SAILGSKYLKAAQELLDEVVKVESMIIKGSDHHHSAKAAQIKETMKMNRESIDGD-QELNGTGDSTKSSFELTTAQRQEL 279 (671)
Q Consensus 201 ~~l~~SrYLkpAQeLLdE~~~v~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~g~-g~~~~~~~s~~~~~~ls~~er~E~ 279 (671)
++|++|||||||||||||||+|+++.......... .............+. +.+....++.....+++++||+|+
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~ 75 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSS-----GAPGGANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQEL 75 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhcc-----ccccccccCCCCCCCCCCCCCccccCCCCCCCChhhHHHH
Confidence 47999999999999999999998742111100000 000000000001111 112233444556789999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHHHHHHHHHHHHhHHHHHHHH
Q 005901 280 QIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTALALRTISKQFRCLKDAISA 344 (671)
Q Consensus 280 q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~lal~~iSr~Fr~L~daI~~ 344 (671)
|+||+||+.||||||+||+|||+|||+|+++||+|||+|+|++||+||||+||||||||||+|.+
T Consensus 76 q~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~~ 140 (140)
T PF07526_consen 76 QRKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAISD 140 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999964
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.97 E-value=1e-32 Score=288.54 Aligned_cols=256 Identities=38% Similarity=0.551 Sum_probs=194.4
Q ss_pred cccccccCccchHHHHHHHHHhccchhhhcCCCCcchhhHHHHHhhhhccCCccC--CCCCCCCCCCCCCCCCccCHHHH
Q 005901 199 TQSAILGSKYLKAAQELLDEVVKVESMIIKGSDHHHSAKAAQIKETMKMNRESID--GDQELNGTGDSTKSSFELTTAQR 276 (671)
Q Consensus 199 ya~~l~~SrYLkpAQeLLdE~~~v~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~--g~g~~~~~~~s~~~~~~ls~~er 276 (671)
+...+..+|||++||+||+++|++.....+........ .. ....... ..+...++..... +......++
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-----~~---~~~~~~~~~~~~~~~~n~~~~s-~~~~~~~~~ 115 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPV-----PR---SPASLSPPEDKGARRGNATRES-ATLKAWLEE 115 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCcc-----cc---ccccccCccccccccccccccc-cccccchhh
Confidence 44568899999999999999999976652211111000 00 0001111 1110111111222 455577899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHHHHHHHHHHHHhHHHH--HHHHHHHHHhhhcC
Q 005901 277 QELQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTALALRTISKQFRCLKD--AISAQIKATSKKLG 354 (671)
Q Consensus 277 ~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~lal~~iSr~Fr~L~d--aI~~Qi~a~~~~l~ 354 (671)
++++.+++|++.|+++|+.+|.+|+..|+.|.+.|+...|++.+.+|+.+++..++++|+++++ +|..|+......++
T Consensus 116 ~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~ 195 (342)
T KOG0773|consen 116 HRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLG 195 (342)
T ss_pred hhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999998 78888887776665
Q ss_pred ccccCC---C---cccCcchhhhhHHHHHHHH-HHhcCC-CCCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHH
Q 005901 355 EDDCLG---A---KAEGSRLRFIDHQIRQQRA-LQHLGM-QHHAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQL 426 (671)
Q Consensus 355 e~d~~g---g---~~e~~~l~~vD~~lrqqRa-~qqlg~-q~~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~L 426 (671)
+.+... . ..........+..+++++. ....+. +..+||++++||++++.+|+.||++|+.||||++.+|..|
T Consensus 196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~L 275 (342)
T KOG0773|consen 196 ESEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLML 275 (342)
T ss_pred cccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhcccc
Confidence 433211 1 1113344555666665543 112222 5568999999999999999999999999999999999999
Q ss_pred HHHhCCChhhhhhhhhhhhhhcCcchhhhhhHHHHHH
Q 005901 427 AKQTGLTRSQVSNWFINARVRLWKPMVEEMYMEELKE 463 (671)
Q Consensus 427 A~~TGLS~kQVsNWFiNaRrR~kKp~iee~~~ee~~~ 463 (671)
|++|||++.||+|||||+|+|+|+||+++++.+++..
T Consensus 276 a~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 276 AKQTGLSRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred chhcCCCcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 9999999999999999999999999999999988776
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.78 E-value=6.1e-19 Score=179.42 Aligned_cols=152 Identities=26% Similarity=0.457 Sum_probs=113.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHH----HHHHHHHHHHhHHHHHHHHHHH
Q 005901 272 TTAQRQELQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTA----LALRTISKQFRCLKDAISAQIK 347 (671)
Q Consensus 272 s~~er~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~----lal~~iSr~Fr~L~daI~~Qi~ 347 (671)
+.-.+.||..|+.|+..+|++-.++|+|-|.++...|.+.-..-+. .+|.+. -+.+.|++-|...+..|
T Consensus 98 sgg~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr--~RPi~~ke~e~m~~~i~~kF~~iq~~l----- 170 (334)
T KOG0774|consen 98 SGGDHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSR--TRPIMPKEIERMVQIISKKFSHIQMQL----- 170 (334)
T ss_pred cCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--cCCCCHHHHHHHHHHHHHHHHHHHHHH-----
Confidence 3334779999999999999999999999999999999988777554 222221 23344445444333222
Q ss_pred HHhhhcCccccCCCcccCcchhhhhHHHHHHHHHHhcCCCCCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHH
Q 005901 348 ATSKKLGEDDCLGAKAEGSRLRFIDHQIRQQRALQHLGMQHHAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLA 427 (671)
Q Consensus 348 a~~~~l~e~d~~gg~~e~~~l~~vD~~lrqqRa~qqlg~q~~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA 427 (671)
..+-|.. +-.-+.+++|. +||||+|+|.+++||..||..|+.||||++++|.+||
T Consensus 171 ------kqstce~--vmiLr~r~lda-----------------rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLA 225 (334)
T KOG0774|consen 171 ------KQSTCEA--VMILRSRFLDA-----------------RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELA 225 (334)
T ss_pred ------HHHHHHH--HHHHHHHHHHH-----------------HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHH
Confidence 1111111 11112233332 4789999999999999999999999999999999999
Q ss_pred HHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 428 KQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 428 ~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
++++++..||+|||-|.|.|.||.+...
T Consensus 226 kqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 226 KQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHcCceehhhccccccceeehhhhhhhh
Confidence 9999999999999999999999987543
No 5
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.60 E-value=1.3e-15 Score=156.17 Aligned_cols=82 Identities=35% Similarity=0.670 Sum_probs=76.1
Q ss_pred CcccCcchhhhhHHHHHHHHHHhcCCCCCCCCCCCC---CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhh
Q 005901 361 AKAEGSRLRFIDHQIRQQRALQHLGMQHHAWRPQRG---LPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQV 437 (671)
Q Consensus 361 g~~e~~~l~~vD~~lrqqRa~qqlg~q~~~kRkrR~---Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQV 437 (671)
++.++..|+.||+| |+++++++++.+|....+ |.++.+.+||+||.. +|||+++||.+||+.|||+..||
T Consensus 148 ek~RGR~LgaV~KY----RvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 148 EKLRGRPLGAVDKY----RVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred HHhcCCcCCccccc----eeeccCCCCCccccCceeeeehhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhh
Confidence 45567889999998 999999999999987654 999999999999997 99999999999999999999999
Q ss_pred hhhhhhhhhhcC
Q 005901 438 SNWFINARVRLW 449 (671)
Q Consensus 438 sNWFiNaRrR~k 449 (671)
.|||+|||.|.+
T Consensus 221 sNWFKNRRQRDR 232 (304)
T KOG0775|consen 221 SNWFKNRRQRDR 232 (304)
T ss_pred hhhhhhhhhhhh
Confidence 999999999998
No 6
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.56 E-value=1.7e-15 Score=115.66 Aligned_cols=40 Identities=65% Similarity=1.219 Sum_probs=36.5
Q ss_pred HHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 005901 408 WLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVR 447 (671)
Q Consensus 408 Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR 447 (671)
||.+|+.||||+++||..||++|||+.+||+|||+|+|+|
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 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=99.37 E-value=9e-13 Score=104.01 Aligned_cols=57 Identities=32% Similarity=0.571 Sum_probs=53.4
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 392 RPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 392 RkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
+++..|+++++.+|++||.. +|||+.+++..||.+|||+..||.+||.|+|.|.++.
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 9999999999999999999999999999999998764
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.33 E-value=2.2e-12 Score=101.43 Aligned_cols=55 Identities=27% Similarity=0.535 Sum_probs=50.9
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 005901 392 RPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLW 449 (671)
Q Consensus 392 RkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~k 449 (671)
+++..|+++++.+|++||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 34556999999999999998 89999999999999999999999999999999864
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.32 E-value=1.4e-12 Score=103.61 Aligned_cols=57 Identities=35% Similarity=0.660 Sum_probs=53.8
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCc
Q 005901 391 WRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWK 450 (671)
Q Consensus 391 kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kK 450 (671)
+|+|+.|+++++.+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.|.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467788999999999999998 999999999999999999999999999999999764
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.00 E-value=1.9e-10 Score=121.18 Aligned_cols=61 Identities=23% Similarity=0.268 Sum_probs=55.1
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchh
Q 005901 390 AWRPQRG-LPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMV 453 (671)
Q Consensus 390 ~kRkrR~-Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~i 453 (671)
.-||||. ++|.|+..||+-|+- |-|.|++-|.+|++.++||++||++||||||+|+||-..
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 3455555 999999999999988 899999999999999999999999999999999998653
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.96 E-value=3.4e-10 Score=119.21 Aligned_cols=63 Identities=24% Similarity=0.344 Sum_probs=57.2
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 390 AWRPQRG-LPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 390 ~kRkrR~-Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
+|||+|. |++.||-.||+-|.+ ..|.+..||+.||+.++||..||+.||||+|.|.||..+++
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 4566666 899999999999998 89999999999999999999999999999999999876544
No 12
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.87 E-value=1.3e-09 Score=107.13 Aligned_cols=64 Identities=22% Similarity=0.325 Sum_probs=58.3
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 389 HAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 389 ~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
..||.|+.|+.++...|+..|.. +-|-.-.||..||+.++|++.||+.||+|+|.|.||...++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 45667777999999999999999 99999999999999999999999999999999999876553
No 13
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.81 E-value=2.1e-09 Score=110.99 Aligned_cols=60 Identities=22% Similarity=0.289 Sum_probs=55.6
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 390 AWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 390 ~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||.|..|+..++..||.-|.- |.|.++..|++||..+.|++.||++||+|||+|.||..
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 4567777999999999999988 99999999999999999999999999999999999854
No 14
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.79 E-value=5.3e-09 Score=104.63 Aligned_cols=81 Identities=30% Similarity=0.327 Sum_probs=67.1
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhhhhHHHHHHHhhcC
Q 005901 389 HAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYMEELKEQEKNG 468 (671)
Q Consensus 389 ~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee~~~ee~~~~~~~~ 468 (671)
..+++|++|+.+++..|+.-|.. +-|-.+++|..||+++||.+.||..||+|||.|.|.+..|. .++..+++.+..
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~-d~~~Lk~~~~~l 124 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK-DYESLKRQLESL 124 (198)
T ss_pred ccccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh-hHHHHHHHHHHH
Confidence 35788899999999999999998 77888899999999999999999999999999988877554 445666665554
Q ss_pred Ccccc
Q 005901 469 SAENI 473 (671)
Q Consensus 469 ~~e~~ 473 (671)
.+++.
T Consensus 125 ~~~~~ 129 (198)
T KOG0483|consen 125 RSEND 129 (198)
T ss_pred hhhhh
Confidence 44443
No 15
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.79 E-value=4e-09 Score=111.57 Aligned_cols=57 Identities=26% Similarity=0.427 Sum_probs=52.5
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhh
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVE 454 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ie 454 (671)
..|+..++..||.-|.. -.|.+..||..||+.+|||..||++||+|||+|+|+...+
T Consensus 177 TaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 177 TAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred hhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 34999999999999998 8999999999999999999999999999999998886633
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.68 E-value=9.3e-09 Score=105.94 Aligned_cols=60 Identities=30% Similarity=0.525 Sum_probs=56.5
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 389 HAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 389 ~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
..||+|.-|+.++.+.|++-|.+ +.|.|+..|..||.+++|.+.||+.||+|+|.|+||.
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 45678888999999999999999 8999999999999999999999999999999999985
No 17
>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=98.63 E-value=5.1e-08 Score=80.47 Aligned_cols=52 Identities=13% Similarity=0.318 Sum_probs=49.1
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 005901 391 WRPQRGLPERAVTILRAWLFEHFLHPY----PKDSDKQQLAKQTGLTRSQVSNWFINAR 445 (671)
Q Consensus 391 kRkrR~Lpk~~~~iLr~Wf~eH~~nPY----PS~~EK~~LA~~TGLS~kQVsNWFiNaR 445 (671)
+|+|+.|+.+++..|+..|.. .+| |+..++..||..+||++.+|..||+|.+
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 577778999999999999998 999 9999999999999999999999999965
No 18
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.61 E-value=7.5e-08 Score=104.10 Aligned_cols=60 Identities=20% Similarity=0.336 Sum_probs=55.2
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 390 AWRPQRG-LPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 390 ~kRkrR~-Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
+|||||+ +...++..|+..|.+ +|-|+.+|.-.||.+++|.+..|++||+|||.|+|+..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 4555555 999999999999999 99999999999999999999999999999999999865
No 19
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.59 E-value=3.2e-08 Score=100.56 Aligned_cols=58 Identities=26% Similarity=0.396 Sum_probs=53.4
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 392 RPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 392 RkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
++|+-++.-+.+.|++.|.+ .-|.--.||.+||..+|||..||+.||+|||-|.||.+
T Consensus 124 KPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 124 KPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred CCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 34445899999999999998 99999999999999999999999999999999999866
No 20
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.57 E-value=3.6e-08 Score=99.56 Aligned_cols=63 Identities=21% Similarity=0.271 Sum_probs=57.0
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 390 AWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 390 ~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
|||.|..|+..++..|+.-|.. ..|.+..||..||+++.|++.||+.||+|+|.|.|+....+
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 5667777999999999999988 89999999999999999999999999999999998866433
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.43 E-value=1.8e-07 Score=90.74 Aligned_cols=62 Identities=19% Similarity=0.295 Sum_probs=57.2
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 388 HHAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 388 ~~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
...+++|++.+..++.+|++.|.. +|||+..+|..|+..++|+++-|..||+|+|.+.|+..
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 345677888999999999999998 99999999999999999999999999999999998755
No 22
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.40 E-value=1.2e-07 Score=98.22 Aligned_cols=57 Identities=25% Similarity=0.279 Sum_probs=52.7
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
.++..++-.||+.|.- .+|.|...|.+||..+||+++||+.||+|||.|++|...+.
T Consensus 205 VYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred Eecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 3899999999999987 99999999999999999999999999999999998866444
No 23
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.39 E-value=2.2e-07 Score=84.94 Aligned_cols=63 Identities=22% Similarity=0.356 Sum_probs=56.3
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhhhh
Q 005901 392 RPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEEMY 457 (671)
Q Consensus 392 RkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee~~ 457 (671)
|-|.+|+..+...|++.|.+ .-||..=.|++||.+..|++..|..||+|+|.+.+|...-..+
T Consensus 19 RIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 19 RIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 44556999999999999999 8999999999999999999999999999999999987644443
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.38 E-value=2e-07 Score=98.36 Aligned_cols=61 Identities=30% Similarity=0.438 Sum_probs=54.3
Q ss_pred CCCCC-CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 392 RPQRG-LPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 392 RkrR~-Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
|++|+ |+..+.+.||.||.+ |.||+.+.|++||.-|+|++..|++||.|+|.+.+|...-.
T Consensus 113 rrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 113 RRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 44444 999999999999999 99999999999999999999999999999999988755333
No 25
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.37 E-value=3.3e-07 Score=92.28 Aligned_cols=59 Identities=20% Similarity=0.352 Sum_probs=53.7
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 391 WRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 391 kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
+++|..|+..+...|++-|.+ .-|.+.+||.+++..+.||+.||+.||+|||.|.|+-.
T Consensus 145 RkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 145 RKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 345556999999999999999 89999999999999999999999999999999998743
No 26
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.37 E-value=3e-07 Score=93.15 Aligned_cols=60 Identities=23% Similarity=0.417 Sum_probs=54.6
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 390 AWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 390 ~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.+|.|++|+..+..+|+..|.+ .-||....+++||.+++|.+.+|.+||.|+|.|.++..
T Consensus 37 qRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred cccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 3455666999999999999999 89999999999999999999999999999999988643
No 27
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.32 E-value=1.5e-07 Score=91.94 Aligned_cols=56 Identities=23% Similarity=0.395 Sum_probs=51.5
Q ss_pred CCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 394 QRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 394 rR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
|..|...+...|++.|.. -.|.+-.|+.+||..++|+++||+.||+|+|+|.||-.
T Consensus 104 Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 104 RTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred cccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 345999999999999998 79999999999999999999999999999999998754
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.31 E-value=4.8e-07 Score=93.49 Aligned_cols=54 Identities=24% Similarity=0.350 Sum_probs=50.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.|+..+...|++-|.+ --||..-.|+.||..|+|.+.+|.+||+|||.|.+|..
T Consensus 147 iFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred hhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 4999999999999999 89999999999999999999999999999999987743
No 29
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.98 E-value=3.2e-06 Score=85.85 Aligned_cols=64 Identities=27% Similarity=0.371 Sum_probs=57.5
Q ss_pred CCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhhhhHHH
Q 005901 394 QRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYMEE 460 (671)
Q Consensus 394 rR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee~~~ee 460 (671)
|.+|.-.++..|+.-|.+ ..||--+++.+||...|+++.||.+||+|||.|.+|...-||..-.
T Consensus 171 rPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasak 234 (288)
T KOG0847|consen 171 RPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAK 234 (288)
T ss_pred CCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhcc
Confidence 345999999999999998 8999999999999999999999999999999999998877766533
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.94 E-value=5.7e-06 Score=86.76 Aligned_cols=62 Identities=24% Similarity=0.394 Sum_probs=57.3
Q ss_pred CCCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 387 QHHAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 387 q~~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
....||+|++++.++.+.|+.-|.. .|-|-.--|+.|+.+|||.-+.|..||+|+|.|.|+-
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 4567899999999999999999987 9999999999999999999999999999999988753
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.93 E-value=1.6e-05 Score=89.22 Aligned_cols=56 Identities=27% Similarity=0.354 Sum_probs=52.9
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 005901 390 AWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRL 448 (671)
Q Consensus 390 ~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~ 448 (671)
.||+|-.|+..+++.|+..|.+ ++||+.+..+.|+.+++|.+.-|.|||-|+|+|.
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 4667777999999999999999 9999999999999999999999999999999996
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.81 E-value=6.9e-06 Score=86.70 Aligned_cols=59 Identities=17% Similarity=0.343 Sum_probs=53.1
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchh
Q 005901 392 RPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMV 453 (671)
Q Consensus 392 RkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~i 453 (671)
|=|+-|+.+++..|++.|++ --|-++-.|.+||..++|.+..|+.||+|||+|.|+..+
T Consensus 183 RYRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 183 RYRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 34556999999999998887 689999999999999999999999999999999998654
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.49 E-value=5.5e-05 Score=74.49 Aligned_cols=60 Identities=17% Similarity=0.061 Sum_probs=54.2
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 390 AWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 390 ~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
++|.|.+|+..+.+.|++-|.. .+||....|+.||..+++++..|.+||+|+|.+.++..
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4455667999999999999998 69999999999999999999999999999999988754
No 34
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.48 E-value=7.8e-05 Score=78.54 Aligned_cols=59 Identities=20% Similarity=0.361 Sum_probs=52.9
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCc
Q 005901 389 HAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWK 450 (671)
Q Consensus 389 ~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kK 450 (671)
.+||||+.+-..-++.|+++|.. -|-|+-+....+|+++.|.+..|..||+|+|.|.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 45666666766678999999998 899999999999999999999999999999999887
No 35
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.48 E-value=8.4e-05 Score=80.43 Aligned_cols=58 Identities=28% Similarity=0.524 Sum_probs=53.4
Q ss_pred CCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 392 RPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 392 RkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
|.|+.|+..+...|+.||.. .|||.-..|+.||++++|+...|..||.|+|.|.+|..
T Consensus 178 r~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 178 RNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 44556999999999999998 88999999999999999999999999999999988865
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.22 E-value=0.00013 Score=77.53 Aligned_cols=62 Identities=44% Similarity=0.611 Sum_probs=56.4
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 390 AWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 390 ~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
..+++.+++.+. .+|+.|+.+|..+|||++.++..|+..++++..||++||+|+|+|.++.+
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 344556789999 99999999999999999999999999999999999999999999988754
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.18 E-value=0.0044 Score=51.42 Aligned_cols=43 Identities=19% Similarity=0.455 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 005901 402 VTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVR 447 (671)
Q Consensus 402 ~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR 447 (671)
.+.|+++|.. |.+..+.+-..|+.+++|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4559999998 899999999999999999999999999877554
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.46 E-value=0.027 Score=55.65 Aligned_cols=61 Identities=31% Similarity=0.564 Sum_probs=53.5
Q ss_pred CCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchh
Q 005901 390 AWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMV 453 (671)
Q Consensus 390 ~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~i 453 (671)
.++.+..+...+..+|..-|.. .+||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3445556899999999988887 999999999999999999999999999999999987553
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=92.27 E-value=0.46 Score=39.14 Aligned_cols=42 Identities=19% Similarity=0.278 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHHHHHHHHHHHHhHHH
Q 005901 282 KKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTALALRTISKQFRCLK 339 (671)
Q Consensus 282 kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~lal~~iSr~Fr~L~ 339 (671)
.++++|+.|+.|..+||+.+ ..+|.+| ..|++.|..++..|.
T Consensus 10 ELDqFMeaYc~~L~kykeeL------~~p~~EA----------~~f~~~ie~qL~~Lt 51 (52)
T PF03791_consen 10 ELDQFMEAYCDMLVKYKEEL------QRPFQEA----------MEFCREIEQQLSSLT 51 (52)
T ss_pred cHHHHHHHHHHHHHHHHHHH------HHHHHHH----------HHHHHHHHHHHHHHh
Confidence 57999999999999999988 7788877 567888888887764
No 40
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=89.79 E-value=0.22 Score=61.73 Aligned_cols=57 Identities=21% Similarity=0.346 Sum_probs=52.3
Q ss_pred CCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchh
Q 005901 394 QRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMV 453 (671)
Q Consensus 394 rR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~i 453 (671)
|..+...++++|+..|.. .-||+.++-+.|.+..+|....|..||+|+|.+.+|+..
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 344889999999999988 899999999999999999999999999999999998763
No 41
>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=78.61 E-value=3.4 Score=33.52 Aligned_cols=47 Identities=26% Similarity=0.278 Sum_probs=30.7
Q ss_pred CCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 005901 391 WRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINAR 445 (671)
Q Consensus 391 kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaR 445 (671)
+|+|+.|+-+..-.+-..+.. .+ -+..||+..|++..+|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 467777887774444344443 33 688999999999999999999954
No 42
>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=76.48 E-value=49 Score=34.09 Aligned_cols=53 Identities=8% Similarity=0.126 Sum_probs=44.2
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHH
Q 005901 271 LTTAQRQELQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTA 325 (671)
Q Consensus 271 ls~~er~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~ 325 (671)
-.+.|..+|..|++++...|++-.++|++-|.++-..|...-..-|. .+|-+.
T Consensus 101 ~~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLreQs~--~RPIs~ 153 (191)
T PF03792_consen 101 DNSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLREQSE--FRPISP 153 (191)
T ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcc--cCCCCH
Confidence 55668889999999999999999999999999999888887776554 455554
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=73.38 E-value=4.3 Score=48.50 Aligned_cols=45 Identities=22% Similarity=0.463 Sum_probs=41.5
Q ss_pred HHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 005901 402 VTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLW 449 (671)
Q Consensus 402 ~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~k 449 (671)
+.+|+++|.. ++.|+.+|-..+|.+.||...-|+.||.+.|....
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~ 612 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEM 612 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhh
Confidence 7889999988 99999999999999999999999999999887654
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=68.99 E-value=6.5 Score=29.00 Aligned_cols=46 Identities=26% Similarity=0.315 Sum_probs=36.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLW 449 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~k 449 (671)
.|+...+.++..++.+. -.-..+|..+|++...|..|....|.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46788888888776542 23567899999999999999998887764
No 45
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=67.96 E-value=68 Score=29.57 Aligned_cols=47 Identities=21% Similarity=0.178 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWK 450 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kK 450 (671)
.||+..+.++..-+.+. -.-.++|+.+|++...|.+|...+|+++++
T Consensus 106 ~L~~~~r~ii~l~~~~~--------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 68899999987665552 235789999999999999999999999875
No 46
>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=63.64 E-value=1e+02 Score=27.20 Aligned_cols=72 Identities=8% Similarity=0.196 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCc-hhhhHHHHHHHHHHHHhHHHHHHHHHHHHHhhh
Q 005901 281 IKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGS-AKSYTALALRTISKQFRCLKDAISAQIKATSKK 352 (671)
Q Consensus 281 ~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~-a~~yt~lal~~iSr~Fr~L~daI~~Qi~a~~~~ 352 (671)
....+.+..+.|+|.++....+++..-+.-|-...+.++ ...=..-.++.|...|..+...-.+.+..+...
T Consensus 15 ~el~r~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~deKv~lA~~~ 87 (105)
T PF12998_consen 15 AELQRNLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDEKVALAQQA 87 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467788899999999999999999999999888776521 111334566777777777777666666666543
No 47
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=62.23 E-value=13 Score=30.85 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=30.7
Q ss_pred CCCCCCChhHHH-HHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 005901 392 RPQRGLPERAVT-ILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINAR 445 (671)
Q Consensus 392 RkrR~Lpk~~~~-iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaR 445 (671)
++++.|+++.+. +++..+.. ......+|+..|++..+|.+|-.-.+
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 456678888754 45555444 37789999999999999999987776
No 48
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=60.83 E-value=96 Score=33.51 Aligned_cols=119 Identities=15% Similarity=0.330 Sum_probs=68.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHHHHHHHHHHHHhHHHHHHHHHHHHHhhhcCcc
Q 005901 277 QELQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTALALRTISKQFRCLKDAISAQIKATSKKLGED 356 (671)
Q Consensus 277 ~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~lal~~iSr~Fr~L~daI~~Qi~a~~~~l~e~ 356 (671)
.|++.+|..|..-++++++|-++...+| ..+|- |. .+.|.+.-+-.+|.+.+.++....+-+.=
T Consensus 7 ~eL~qrk~~Lq~eIe~LerR~~ri~~Em---rtsFa---G~----------Sq~lA~RVqGFkdYLvGsLQDLa~saEqL 70 (283)
T PF11285_consen 7 KELEQRKQALQIEIEQLERRRERIEKEM---RTSFA---GQ----------SQDLAIRVQGFKDYLVGSLQDLAQSAEQL 70 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---Hcccc---cc----------hHHHHHHHhhhHHHHHHHHHHHHHHHHhh
Confidence 5899999999999999999999999888 44553 32 13344555566777776666443221110
Q ss_pred ccC----------------C-Ccc---cCcchhhhhHHHHH-----HHHHHhcCC----CCCCCCCCCCCChhHHHHHHH
Q 005901 357 DCL----------------G-AKA---EGSRLRFIDHQIRQ-----QRALQHLGM----QHHAWRPQRGLPERAVTILRA 407 (671)
Q Consensus 357 d~~----------------g-g~~---e~~~l~~vD~~lrq-----qRa~qqlg~----q~~~kRkrR~Lpk~~~~iLr~ 407 (671)
+.. . ... ......+..+.++. ++.+.++-- --..|+=||+|.+--...+++
T Consensus 71 eLv~~~~~~~psp~~~~~~~~~~~~~~~~~~~~~~~~~F~~~~~~Ir~~l~qyr~~PDyYg~PWqLRRtfe~~hae~v~~ 150 (283)
T PF11285_consen 71 ELVPQPVVVQPSPLDEPAPPPQANAAKNPPTPQFAAQTFQPDERQIRRLLDQYRTQPDYYGPPWQLRRTFEPIHAERVED 150 (283)
T ss_pred ccCCCCcCCCCCcccccccCcccccccCCCCCcchhhhcchHHHHHHHHHHHHhhCCCccCChHHHHhcccHHHHHHHHH
Confidence 000 0 000 01111222222221 123333322 235688888888888888888
Q ss_pred HHHH
Q 005901 408 WLFE 411 (671)
Q Consensus 408 Wf~e 411 (671)
||+.
T Consensus 151 WFF~ 154 (283)
T PF11285_consen 151 WFFN 154 (283)
T ss_pred HHhc
Confidence 9885
No 49
>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=59.49 E-value=7.6 Score=30.27 Aligned_cols=47 Identities=30% Similarity=0.439 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWK 450 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kK 450 (671)
.||++.+.+|...|++ . -.-.++|+.+|++...|..|...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~----~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----G----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----C----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 5889999999888754 2 335789999999999999999999888753
No 50
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=59.28 E-value=11 Score=29.55 Aligned_cols=45 Identities=29% Similarity=0.403 Sum_probs=33.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRL 448 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~ 448 (671)
.||+..+.++...+.+. -.-.++|+.+|++...|.+|...+|+++
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 57888888887766652 3457899999999999999999998864
No 51
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=56.02 E-value=1.2e+02 Score=29.34 Aligned_cols=49 Identities=24% Similarity=0.190 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++..-+.+. -.-.++|..+|++...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 68899999998766652 23578999999999999999999999987643
No 52
>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=53.48 E-value=32 Score=22.48 Aligned_cols=39 Identities=18% Similarity=0.285 Sum_probs=27.2
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWF 441 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWF 441 (671)
+.++.+....+..++.. .+ ....+|+.+|++...|.+|.
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 34666666656555433 33 45688999999999999995
No 53
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=48.91 E-value=33 Score=25.82 Aligned_cols=50 Identities=20% Similarity=0.238 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVE 454 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ie 454 (671)
.|+++...++..+ .. . .....+|+.+|++...|..|....+.++.-....
T Consensus 3 ~l~~~e~~i~~~~-~~----g----~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~~ 52 (58)
T smart00421 3 SLTPREREVLRLL-AE----G----LTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRT 52 (58)
T ss_pred CCCHHHHHHHHHH-Hc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Confidence 4778888887554 32 2 2457899999999999999999888887654433
No 54
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=46.43 E-value=1.4e+02 Score=30.62 Aligned_cols=49 Identities=18% Similarity=0.203 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++.-.+.+. . .-.++|+.+|++...|.++...+|+++++.+
T Consensus 171 ~Lp~~~R~v~~L~~~eg--~------s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN--M------SNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 57888888876665552 2 3478999999999999999999999998755
No 55
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=45.93 E-value=18 Score=33.78 Aligned_cols=49 Identities=24% Similarity=0.228 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.+. .+ -.++|+.+|++...|.+++.-+|.++++.+
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 48999999997766652 22 358999999999999999999999988765
No 56
>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=45.08 E-value=28 Score=27.95 Aligned_cols=53 Identities=19% Similarity=0.235 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhhhh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEEMY 457 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee~~ 457 (671)
.|++....+|+-+... ....++|+..+++++-|..+..+.++|+.-....++.
T Consensus 3 ~LT~~E~~vl~~l~~G---------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l~ 55 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---------MSNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAELI 55 (58)
T ss_dssp SS-HHHHHHHHHHHTT---------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHHH
T ss_pred ccCHHHHHHHHHHHhc---------CCcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHHH
Confidence 4788888999766544 3567899999999999999999999998876655544
No 57
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=42.78 E-value=19 Score=28.88 Aligned_cols=27 Identities=26% Similarity=0.404 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhhhhc
Q 005901 422 DKQQLAKQTGLTRSQVSNWFINARVRL 448 (671)
Q Consensus 422 EK~~LA~~TGLS~kQVsNWFiNaRrR~ 448 (671)
....||+.+|+++.+|+.|+.+.+.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 467899999999999999999774333
No 58
>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=42.09 E-value=24 Score=32.20 Aligned_cols=48 Identities=25% Similarity=0.285 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
.||++...+|...+.+ .+ .-.++|+.+|+++..|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5788889998875554 32 345699999999999999999999998753
No 59
>PRK00118 putative DNA-binding protein; Validated
Probab=41.54 E-value=36 Score=31.70 Aligned_cols=56 Identities=14% Similarity=0.163 Sum_probs=43.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhhhhHHH
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYMEE 460 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee~~~ee 460 (671)
.||+.++.++..++.+. -.-..+|+.+|+++.-|.+|...+|+++++- ++.+..-+
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~-~~~~~~~~ 72 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY-EEKLHLYE 72 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH-HHHHChHH
Confidence 57889999998887762 3346799999999999999999999988773 35555443
No 60
>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=39.90 E-value=4.5e+02 Score=32.06 Aligned_cols=19 Identities=16% Similarity=0.092 Sum_probs=15.7
Q ss_pred CCCCCChhHHHHHHHHHHH
Q 005901 393 PQRGLPERAVTILRAWLFE 411 (671)
Q Consensus 393 krR~Lpk~~~~iLr~Wf~e 411 (671)
+.-.|++.+.+.++.-+.+
T Consensus 678 ~s~~L~~~Q~~~I~~iL~~ 696 (717)
T PF10168_consen 678 KSIVLSESQKRTIKEILKQ 696 (717)
T ss_pred CCccCCHHHHHHHHHHHHH
Confidence 3346999999999999887
No 61
>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=39.85 E-value=26 Score=30.90 Aligned_cols=48 Identities=25% Similarity=0.341 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
.||+..+.++..-+.. .+ .-..+|+.+|+++..|.+|....|.++++.
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5778888887544333 33 346899999999999999999999988753
No 62
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=39.82 E-value=29 Score=32.74 Aligned_cols=50 Identities=14% Similarity=0.090 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
..||++.+.++..++.++ -.-.++|..+|++...|.+|..-+|+++++-.
T Consensus 107 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 368999999998877763 23478999999999999999999999997644
No 63
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=39.76 E-value=25 Score=34.28 Aligned_cols=51 Identities=27% Similarity=0.234 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhh
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVE 454 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ie 454 (671)
..|++.++.+|+. +.+ . -...++|+.+|++...|++|...+|.++++-...
T Consensus 5 ~~Lt~rqreVL~l-r~~----G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----G----LTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHH-HHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999977 333 2 2346899999999999999999999998876644
No 64
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.78 E-value=2.4e+02 Score=26.61 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.+|..-+.+. + .-.++|+.+|++..-|.++..-+|+++++.+
T Consensus 118 ~L~~~~r~vl~L~~~~g----~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG----W----STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998766652 2 2468999999999999999999999988755
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=38.33 E-value=26 Score=33.37 Aligned_cols=48 Identities=15% Similarity=0.282 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
.||++.+.++...+.+. + .-.++|+.+|++...|.+++..+|+++++-
T Consensus 129 ~L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG----L----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 58889999888887762 2 247899999999999999999999998764
No 66
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=38.01 E-value=77 Score=30.50 Aligned_cols=49 Identities=14% Similarity=0.212 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.++..-+++. -.-.++|+.+|++...|.++...+|+++++.+
T Consensus 128 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQG--------LSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhcC--------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887655542 23468999999999999999999999998755
No 67
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=37.26 E-value=32 Score=33.55 Aligned_cols=52 Identities=13% Similarity=0.263 Sum_probs=42.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
.||+..+.++.-.+.+. -.-.++|..+|+++..|.++..-+|+++++-+.+.
T Consensus 134 ~Lp~~~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--------LSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred hCCHHHHHHHhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 58899999988776652 23478999999999999999999999998766433
No 68
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=36.53 E-value=28 Score=33.35 Aligned_cols=49 Identities=14% Similarity=0.163 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.+. -.-.++|..+|++...|.+++..+|+++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998876652 23478999999999999999999999998655
No 69
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=36.48 E-value=2.1e+02 Score=30.90 Aligned_cols=125 Identities=17% Similarity=0.212 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhhhhhhhcCCchhhhHHHHHHHHH-----HHHhHHHHHHHHHHHHHh
Q 005901 277 QELQIKKAKLVNMLDEVEQRYKQYHHQMQVV-VSAFEQAAGFGSAKSYTALALRTIS-----KQFRCLKDAISAQIKATS 350 (671)
Q Consensus 277 ~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v-~ssFe~~ag~~~a~~yt~lal~~iS-----r~Fr~L~daI~~Qi~a~~ 350 (671)
+|.|.++.+|+..+.+..+.+..|...+..+ ..+|+..... ....+. .-+|.|.|.+.+.+..+-
T Consensus 158 Re~q~~~~~l~~a~~~~~~a~~ey~~~l~~~~~~a~~~~~~~---------l~~~~~~g~~~~s~re~~d~Wi~~ae~~~ 228 (293)
T PF09712_consen 158 REHQEQLQALFDAWMEYQRASQEYQAQLSEAWMKAFERMMEK---------LQERAEEGEQIKSWREFYDIWIDAAEEAY 228 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHhhccCCCCcCHHHHHHHHHHHHHHHH
Confidence 5778899999999999999998888777644 4455443110 000000 124555555555444332
Q ss_pred hhcCccccCCCcccCcchhhhhHHHHHHHHHHhcCCCCCCCCCCCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHh
Q 005901 351 KKLGEDDCLGAKAEGSRLRFIDHQIRQQRALQHLGMQHHAWRPQRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQT 430 (671)
Q Consensus 351 ~~l~e~d~~gg~~e~~~l~~vD~~lrqqRa~qqlg~q~~~kRkrR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~T 430 (671)
..+-..+... ...-++++..+ .|.+...++++.++.. -+.||+.|-..|.+.+
T Consensus 229 ~~~~~S~ef~----~~~g~~~~a~m--------------------~~r~~~~~~~e~~L~~---l~lPTr~evd~l~k~l 281 (293)
T PF09712_consen 229 EELFRSEEFA----QAYGQLVNALM--------------------DLRKQQQEVVEEYLRS---LNLPTRSEVDELYKRL 281 (293)
T ss_pred HHHHCCHHHH----HHHHHHHHHHH--------------------HHHHHHHHHHHHHHHH---CCCCCHHHHHHHHHHH
Confidence 2211000000 00001122211 1344557788888887 8999999999999876
Q ss_pred CCChhhh
Q 005901 431 GLTRSQV 437 (671)
Q Consensus 431 GLS~kQV 437 (671)
--.+++|
T Consensus 282 ~eLrre~ 288 (293)
T PF09712_consen 282 HELRREV 288 (293)
T ss_pred HHHHHHH
Confidence 5444443
No 70
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=36.21 E-value=31 Score=32.11 Aligned_cols=49 Identities=18% Similarity=0.218 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++..-+.+ . -.-..+|+.+|++...|.+|..-+|.++++.+
T Consensus 125 ~L~~~~r~i~~l~~~~----~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----G----LSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888765544 2 23478999999999999999999999998755
No 71
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=35.94 E-value=3.1e+02 Score=26.35 Aligned_cols=49 Identities=20% Similarity=0.339 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.+. . .-.++|+.+|++...|.++..-+|.++++-+
T Consensus 127 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE--L------SIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 68999999987766553 2 2368999999999999999999999988644
No 72
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.51 E-value=32 Score=32.12 Aligned_cols=49 Identities=22% Similarity=0.241 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.|++..+.+|...+... .+ -..+|+.+|++...|.+|...+|+++++.+
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 58888899987655441 22 358999999999999999999999998755
No 73
>cd00131 PAX Paired Box domain
Probab=35.42 E-value=1.8e+02 Score=27.54 Aligned_cols=48 Identities=17% Similarity=0.129 Sum_probs=33.7
Q ss_pred CCCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCC-------Chhhhhhhhhhh
Q 005901 394 QRGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGL-------TRSQVSNWFINA 444 (671)
Q Consensus 394 rR~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGL-------S~kQVsNWFiNa 444 (671)
++.+..+....+..+..+ +|.-|..|-..+-...|+ +...|+.||.++
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 334566666667777666 898888776665335566 999999998764
No 74
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=35.06 E-value=64 Score=29.54 Aligned_cols=54 Identities=24% Similarity=0.244 Sum_probs=42.3
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhhhh
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEEMY 457 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee~~ 457 (671)
..|++...++|+-+ .+ .|. ..++|+.++++.+.|.+|..+.|+|+.-.-..++.
T Consensus 148 ~~lt~~e~~vl~l~-~~----g~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~ 201 (211)
T PRK15369 148 PLLTPRERQILKLI-TE----GYT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201 (211)
T ss_pred cCCCHHHHHHHHHH-HC----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHH
Confidence 35999999999875 33 222 47889999999999999999999998765554444
No 75
>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=34.78 E-value=63 Score=24.46 Aligned_cols=47 Identities=21% Similarity=0.257 Sum_probs=33.5
Q ss_pred CChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 397 LPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 397 Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
|++....++..++ . . ....++|+.++++...|..|..-.+.+...+.
T Consensus 1 l~~~e~~i~~~~~-~----~----~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~ 47 (57)
T cd06170 1 LTPREREVLRLLA-E----G----KTNKEIADILGISEKTVKTHLRNIMRKLGVKS 47 (57)
T ss_pred CCHHHHHHHHHHH-c----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCC
Confidence 4556666665432 2 2 24578899999999999999987777766544
No 76
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=34.68 E-value=32 Score=32.27 Aligned_cols=47 Identities=19% Similarity=0.174 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWK 450 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kK 450 (671)
.||+.++.++.-.+.+. . .-.++|..+|++...|..+...+|+|+++
T Consensus 112 ~L~~~~r~v~~l~~~~~--~------s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--F------SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 68999999998866653 2 23689999999999999999999999875
No 77
>PRK06930 positive control sigma-like factor; Validated
Probab=34.47 E-value=32 Score=34.12 Aligned_cols=55 Identities=15% Similarity=0.141 Sum_probs=43.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhhhhH
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEEMYM 458 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee~~~ 458 (671)
.||+..+.++...+.+- -.-..+|..+|++...|.++...+|.++++.+.+++.|
T Consensus 114 ~L~~rer~V~~L~~~eg--------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~~ 168 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG--------LSYSEIADYLNIKKSTVQSMIERAEKKIARQINESLFC 168 (170)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 58888888887765542 23468999999999999999999999998877655544
No 78
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=33.83 E-value=34 Score=33.92 Aligned_cols=49 Identities=27% Similarity=0.330 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.+|..-+++. -.-.++|..+|++...|.+++..+|+++++-+
T Consensus 153 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--------LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998766552 23478999999999999999999999987655
No 79
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=33.62 E-value=28 Score=33.23 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.++ -.-.++|+.+|++...|.+|...+|+++++.+
T Consensus 138 ~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 57888888887665542 23478999999999999999999999988755
No 80
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=33.62 E-value=42 Score=31.06 Aligned_cols=48 Identities=31% Similarity=0.309 Sum_probs=38.9
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCc
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWK 450 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kK 450 (671)
..||+..+.++..-+.+. -.-.++|+.+|++...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~g--------~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG--------VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 358899999998855542 234689999999999999999999998875
No 81
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.59 E-value=33 Score=33.42 Aligned_cols=49 Identities=10% Similarity=0.141 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.+|...+.+. -.-.++|+.+|++...|.+|...+|+++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 58999999997766553 23468999999999999999999999988654
No 82
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=32.34 E-value=32 Score=33.24 Aligned_cols=49 Identities=20% Similarity=0.304 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.++..-+++. -.-.++|..+|++...|.+|+..+|+++++-+
T Consensus 141 ~L~~~~~~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYEG--------LSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 57888888887665542 23468999999999999999999999998754
No 83
>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=32.27 E-value=38 Score=32.26 Aligned_cols=48 Identities=17% Similarity=0.195 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
.||+..+.++...+.+. -.-.++|..+|++...|.+.+..+|.++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG--------LTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998877662 2346899999999999999999999998763
No 84
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=30.62 E-value=46 Score=32.35 Aligned_cols=49 Identities=27% Similarity=0.306 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.++.-.|.+. . .-.++|+.+|++...|.+...-+|+++++..
T Consensus 131 ~L~~~~r~i~~l~~~~g--~------s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--E------KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 68999999998766552 2 3468999999999999999999999988743
No 85
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=30.00 E-value=44 Score=34.66 Aligned_cols=51 Identities=27% Similarity=0.433 Sum_probs=42.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVE 454 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ie 454 (671)
.||+..+.++.-.+.+.+ .-.++|..+|++..-|.++...+|+++++.+..
T Consensus 161 ~Lp~~~R~v~~L~~~eg~--------S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 161 ALSERERHLLRLHFVDGL--------SMDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 589999999988777632 246899999999999999999999999886633
No 86
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.60 E-value=41 Score=31.86 Aligned_cols=49 Identities=14% Similarity=0.006 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++.-.+.+. -.-.++|+.+|++...|.++..-+|+++++-+
T Consensus 112 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASG--------FSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998876663 23468999999999999999999999987543
No 87
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.54 E-value=44 Score=32.16 Aligned_cols=49 Identities=22% Similarity=0.151 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.+. -.-.++|+.+|+++..|.+.+..+|+++++.+
T Consensus 129 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG--------LSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888876665553 23478999999999999999999999998755
No 88
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=29.11 E-value=43 Score=32.03 Aligned_cols=49 Identities=14% Similarity=0.188 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.+|...+.+. -.-.++|+.+|++...|.++...+|.++++.+
T Consensus 135 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG--------YTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998766552 23478999999999999999999999987654
No 89
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=29.07 E-value=44 Score=31.59 Aligned_cols=49 Identities=14% Similarity=0.182 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.++..-+++. -.-.++|+.+|++...|.++..-+|+++++.+
T Consensus 119 ~L~~~~r~i~~l~~~~g--------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 57888889987776652 23468999999999999999999999988754
No 90
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=28.62 E-value=41 Score=31.39 Aligned_cols=49 Identities=22% Similarity=0.346 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++..-+.+. -.-.++|..+|++...|.++...+|.++++.+
T Consensus 110 ~L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYED--------LSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHhc--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58888899987766552 22467999999999999999999999988644
No 91
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=28.44 E-value=52 Score=31.79 Aligned_cols=49 Identities=16% Similarity=0.258 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.+|..-+.+. -.-.++|+.+|++...|.+.+..+|+++++..
T Consensus 131 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE--------KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 68999999997766552 33478999999999999999999999887744
No 92
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.43 E-value=56 Score=30.28 Aligned_cols=50 Identities=20% Similarity=0.207 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
..||+..+.++.-.+.+. .+ -.++|..+|++...|.++..-+|+++++.+
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 368999999998766652 22 468999999999999999999999988655
No 93
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=28.10 E-value=43 Score=33.48 Aligned_cols=52 Identities=19% Similarity=0.345 Sum_probs=42.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchhhh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMVEE 455 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~iee 455 (671)
.||++.+.++..-+++. . .-.++|+.+|++...|.++..-+|+++++.+...
T Consensus 148 ~L~~~~r~v~~L~~~~g--~------s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--L------ETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 68888888887776663 2 2478999999999999999999999999876443
No 94
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=28.02 E-value=47 Score=32.40 Aligned_cols=50 Identities=26% Similarity=0.312 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
..||++.+.++...+.+. .+ -.++|..+|++...|.+.+..+|+++++-+
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 468999999998765552 23 368999999999999999999999888654
No 95
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.64 E-value=48 Score=31.58 Aligned_cols=48 Identities=13% Similarity=0.192 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
.||++.+.++.-.+.+. .+ -.++|+.+|++..-|.++...+|+|++..
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58999999998766653 23 36899999999999999999999998643
No 96
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=27.53 E-value=53 Score=33.68 Aligned_cols=49 Identities=18% Similarity=0.318 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.+|...|++.+ .-.++|+.+|++...|.+|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL--------SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 589999999988776521 2378999999999999999999999987644
No 97
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.60 E-value=48 Score=31.50 Aligned_cols=49 Identities=16% Similarity=0.211 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++..-+.+. -.-.++|+.+|++...|.+++..+|+++++.+
T Consensus 136 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED--------LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 58888899987644441 23478999999999999999999999987643
No 98
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=26.51 E-value=53 Score=32.20 Aligned_cols=49 Identities=16% Similarity=0.120 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++.-.+.+. .+ -.++|+.+|++...|.++...+|+++++-+
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s------~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FA------YEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57899999998776652 22 357999999999999999999999998755
No 99
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=26.16 E-value=46 Score=33.67 Aligned_cols=49 Identities=27% Similarity=0.370 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++..-|.+. -.-.++|+.+|++...|.+|...+|+++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE--------LNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhccC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58899999997766552 23578999999999999999999999998754
No 100
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=26.12 E-value=49 Score=32.56 Aligned_cols=49 Identities=20% Similarity=0.137 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++.-++.+- -.-.++|..+|++...|.+++.-+|+++++-+
T Consensus 113 ~Lp~~~r~v~~L~~~~g--------~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASG--------FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 68999999998876662 23467999999999999999999999998644
No 101
>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=25.68 E-value=56 Score=33.50 Aligned_cols=49 Identities=20% Similarity=0.268 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...|.+.+ .-.++|+.+|++...|..|...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 589999999988776532 2368999999999999999999999988654
No 102
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.51 E-value=66 Score=31.14 Aligned_cols=50 Identities=16% Similarity=0.221 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMV 453 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~i 453 (671)
.||++++.++.-.+.+. .+ -.++|..+|++..-|.+....+|+++++-+.
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 58999999998776662 23 3689999999999999999999999987553
No 103
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=25.26 E-value=45 Score=33.83 Aligned_cols=49 Identities=20% Similarity=0.188 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.++ -+ -.++|+.+|++..-|.++...+|+++++.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MS------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 68999999998877763 22 367999999999999999999999998765
No 104
>PHA03247 large tegument protein UL36; Provisional
Probab=25.24 E-value=1.3e+02 Score=41.62 Aligned_cols=57 Identities=21% Similarity=0.380 Sum_probs=47.3
Q ss_pred CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHhhhhhhhhcCCchhhhH
Q 005901 268 SFELTTAQRQELQIKKAKLVNMLDEVEQRYKQ-------YHHQMQVVVSAFEQAAGFGSAKSYT 324 (671)
Q Consensus 268 ~~~ls~~er~E~q~kk~kLl~ml~EV~~rY~q-------y~~qm~~v~ssFe~~ag~~~a~~yt 324 (671)
...|++..|..+..++..+..|+.+...||+. .|+.|+.+....--..|+.++-.-.
T Consensus 975 ~~~Ls~e~r~rl~~r~~evEt~~~~aR~r~~~i~~~r~~~y~~L~~lLrPl~~FvGLRaa~~~l 1038 (3151)
T PHA03247 975 TDELSPEARERLRARARAIEAMLEEARERAEAARAARERFFQKLQGVLRPLPDFGGLRAAPAVL 1038 (3151)
T ss_pred hcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccHhHH
Confidence 45788999999999999999999999999977 7889999988877777877665433
No 105
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.78 E-value=62 Score=31.15 Aligned_cols=49 Identities=12% Similarity=0.160 Sum_probs=39.0
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
..||++.+.++..-+.+. -.-.++|+.+|++...|.+|...+|+++++-
T Consensus 132 ~~L~~~~r~i~~l~~~~~--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVDG--------CSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 368888888777666552 2347899999999999999999999988753
No 106
>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=24.74 E-value=57 Score=32.60 Aligned_cols=48 Identities=29% Similarity=0.453 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
.||+..+.++...+.+ . -.-.++|+.+|++...|..|...+++++++.
T Consensus 178 ~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 178 ALPERERRILLLRFFE----D----KTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred cCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5899999999887654 1 3457899999999999999999999998754
No 107
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=24.68 E-value=2.6e+02 Score=27.58 Aligned_cols=30 Identities=17% Similarity=0.094 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 005901 277 QELQIKKAKLVNMLDEVEQRYKQYHHQMQV 306 (671)
Q Consensus 277 ~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~ 306 (671)
.+++.-+.+|+.+..++..+..+-...++.
T Consensus 35 ~ql~~fr~~L~~~r~eL~~~i~~~~~~~~~ 64 (151)
T PRK10778 35 AQLAHFKRILEAWRNQLRDEVDRTVTHMQD 64 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 355566777888888887777766666653
No 108
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=24.68 E-value=62 Score=31.94 Aligned_cols=50 Identities=22% Similarity=0.252 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMV 453 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~i 453 (671)
.||+..+.++.--+++. .+ -.++|..+|++..-|.+....+|+++++-+.
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 58999999998766652 22 3689999999999999999999999987653
No 109
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=24.59 E-value=67 Score=31.22 Aligned_cols=49 Identities=16% Similarity=0.226 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++.-.+.+. -.-.++|+.+|++...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG--------FSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888889887655552 23468999999999999999999999998765
No 110
>PRK04217 hypothetical protein; Provisional
Probab=24.52 E-value=75 Score=29.88 Aligned_cols=50 Identities=18% Similarity=0.222 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 395 RGLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 395 R~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
..|+++.+.++..++.+.+ .-.++|+.+|++...|.+.+..+|.+++.-+
T Consensus 41 ~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3489999999988876522 4567999999999999999999998886544
No 111
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=23.68 E-value=1.2e+02 Score=28.25 Aligned_cols=43 Identities=9% Similarity=0.348 Sum_probs=33.9
Q ss_pred ChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 005901 398 PERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINA 444 (671)
Q Consensus 398 pk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNa 444 (671)
....+..+.+|+.+|+..+ -.-..||+.+|+++..+..||...
T Consensus 7 ~~~~i~~~~~~I~~~~~~~----~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNLESP----LSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhcCCC----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4445667788999987665 345779999999999999999866
No 112
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.53 E-value=65 Score=31.46 Aligned_cols=49 Identities=16% Similarity=0.163 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.++.-.+++ -| .-.++|+.+|++...|.+++.-+|+++++-.
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GL----SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999888776554 22 2468999999999999999999999998644
No 113
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=23.45 E-value=28 Score=33.76 Aligned_cols=49 Identities=22% Similarity=0.209 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++.-.+.+. -.-.++|+.+|++...|.++..-+|+++++-+
T Consensus 131 ~Lp~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG--------FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57788887776555442 23468999999999999999999999998765
No 114
>PF07765 KIP1: KIP1-like protein; InterPro: IPR011684 This is a group of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase []. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions []. It has also been suggested that the coiled-coils of the protein allow it to dimerise in vivo [].
Probab=23.17 E-value=1.1e+02 Score=27.17 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=21.9
Q ss_pred CHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Q 005901 272 TTAQRQELQIK-KAKLVNMLDEVEQRYKQYH 301 (671)
Q Consensus 272 s~~er~E~q~k-k~kLl~ml~EV~~rY~qy~ 301 (671)
|.++|.|.--+ +-.|+++++|+.+.|+-..
T Consensus 40 SfakrAEmyy~kRp~Li~~vee~yr~YrsLA 70 (74)
T PF07765_consen 40 SFAKRAEMYYKKRPELISLVEEFYRSYRSLA 70 (74)
T ss_pred hHHHhhHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 45566665544 4599999999999987554
No 115
>PF12126 DUF3583: Protein of unknown function (DUF3583); InterPro: IPR021978 This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with PF00097 from PFAM and PF00643 from PFAM. Most members are promyelocytic leukemia proteins, and this family lies towards the C terminus.
Probab=23.15 E-value=2.3e+02 Score=31.30 Aligned_cols=36 Identities=22% Similarity=0.321 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 005901 279 LQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQA 314 (671)
Q Consensus 279 ~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ 314 (671)
..+-.++=.+||+.|..||...|++|-.-....|.+
T Consensus 48 V~hVqaqEreLLe~v~~rYqR~y~ema~~L~~Leav 83 (324)
T PF12126_consen 48 VAHVQAQERELLEAVEARYQRDYEEMAGQLGRLEAV 83 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 344456667899999999999999997666666665
No 116
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.48 E-value=75 Score=24.27 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhhh
Q 005901 422 DKQQLAKQTGLTRSQVSNWFINARV 446 (671)
Q Consensus 422 EK~~LA~~TGLS~kQVsNWFiNaRr 446 (671)
....+|++.|++..+|..|....+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3456999999999999999887665
No 117
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.91 E-value=79 Score=30.73 Aligned_cols=47 Identities=15% Similarity=0.015 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWK 450 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kK 450 (671)
.||++++.++.-.+.+. -.-.++|+.+|++...|.++..-+|+++++
T Consensus 130 ~Lp~~~r~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLG--------LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 58899999997776653 224689999999999999999999999886
No 118
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.90 E-value=90 Score=31.18 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++..-+.+. .+ -.++|+.+|++..-|.++..-+|+++++.+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LS------YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888776665553 33 368999999999999999999999998755
No 119
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=21.87 E-value=77 Score=29.57 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.++..-+++. -...++|+.+|++...|..+..-+|+++++-+
T Consensus 109 ~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG--------ETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58899999997766552 23478999999999999999988888887654
No 120
>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=21.77 E-value=70 Score=32.06 Aligned_cols=48 Identities=27% Similarity=0.385 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcc
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKP 451 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp 451 (671)
.||+..+.+|...|.+. -.-.++|+.+|++...|..|...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE--------LNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 58999999998877652 2347899999999999999999999988753
No 121
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=21.69 E-value=68 Score=33.24 Aligned_cols=49 Identities=20% Similarity=0.233 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.+|...|.+ . -.-..+|..+|++...|..+..-++.++++.+
T Consensus 203 ~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLH----D----LTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5888889998877765 2 24578999999999999999999999998755
No 122
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.67 E-value=67 Score=30.01 Aligned_cols=48 Identities=21% Similarity=0.275 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.+|...+ +. -.-..+|..+|++...|.++...+|.++++-+
T Consensus 112 ~L~~~~r~il~l~~-~g--------~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG--------YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57888888887666 42 23478999999999999999999999988754
No 123
>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=21.54 E-value=6.4e+02 Score=23.20 Aligned_cols=67 Identities=12% Similarity=0.053 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhh---------hHHHHHHHHHHHHhHHHHHHHH
Q 005901 278 ELQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKS---------YTALALRTISKQFRCLKDAISA 344 (671)
Q Consensus 278 E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~---------yt~lal~~iSr~Fr~L~daI~~ 344 (671)
+++....||+.......+....++.........|...+..-...+ +..-+++.|...+..+.+.|..
T Consensus 4 ~~~~~~~kl~k~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~ 79 (194)
T cd07307 4 ELEKLLKKLIKDTKKLLDSLKELPAAAEKLSEALQELGKELPDLSNTDLGEALEKFGKIQKELEEFRDQLEQKLEN 79 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455667778877777777777777777788888877754433222 2333344454444444444433
No 124
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=20.52 E-value=80 Score=30.69 Aligned_cols=49 Identities=27% Similarity=0.361 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||++.+.++...+.+ - -.-.++|..+|++...|.+++..+|+++++-+
T Consensus 106 ~L~~~~r~i~~l~~~~----g----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELE----G----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhc----C----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5888899998776554 2 23478999999999999999999999887644
No 125
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.37 E-value=1.1e+02 Score=29.43 Aligned_cols=49 Identities=22% Similarity=0.308 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.+. -.-.++|+.+|++...|.+....+|+++++-+
T Consensus 122 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN--------LTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58899999998765552 23468999999999999999999999997754
No 126
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=20.36 E-value=7.4e+02 Score=23.80 Aligned_cols=91 Identities=16% Similarity=0.123 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcCCchhhhHHHHHHHHHHHHhHHHHHHHHHHHHH-hhhcCc
Q 005901 277 QELQIKKAKLVNMLDEVEQRYKQYHHQMQVVVSAFEQAAGFGSAKSYTALALRTISKQFRCLKDAISAQIKAT-SKKLGE 355 (671)
Q Consensus 277 ~E~q~kk~kLl~ml~EV~~rY~qy~~qm~~v~ssFe~~ag~~~a~~yt~lal~~iSr~Fr~L~daI~~Qi~a~-~~~l~e 355 (671)
..++.-|.+|+.+-.+...+.++..+.++.....|...+-.. ...|..-...+...+-+.+...|...+..+ ...+|.
T Consensus 4 ~~~~~fk~~L~~~k~~l~~~~~~~~~~~~~~~~~~~d~aD~a-~~~~~~~~~~~~~~r~r~~l~~i~~al~rIe~gtYG~ 82 (120)
T COG1734 4 EQLEHFKNKLLEWKKDLLEELEQTEEHLQDENEASPDPADRA-TQEEERELELRLRDRERKLLRKIESALDRIEEGTYGI 82 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCchhhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccc
Confidence 356677889999999999999999988887555553332221 222444333444444444444454444332 233555
Q ss_pred cccCCCcccCcch
Q 005901 356 DDCLGAKAEGSRL 368 (671)
Q Consensus 356 ~d~~gg~~e~~~l 368 (671)
|+.-|..+...||
T Consensus 83 Ce~cG~~Ip~~RL 95 (120)
T COG1734 83 CEECGEPIPEARL 95 (120)
T ss_pred hhccCCcCCHHHH
Confidence 6555544443333
No 127
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=20.36 E-value=40 Score=32.63 Aligned_cols=49 Identities=16% Similarity=0.227 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.+. . .-.++|+.+|++...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHGD--L------ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehccC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57788888887655442 2 3467999999999999999999999998754
No 128
>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=20.28 E-value=8.1e+02 Score=23.87 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.++...+.+. -.-.++|+.+|++..-|.++..-+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--------FESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 68888999998776663 33478999999999999999999999998755
No 129
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.18 E-value=1e+02 Score=28.88 Aligned_cols=46 Identities=17% Similarity=0.269 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLW 449 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~k 449 (671)
.||++++.++...+.+. .+ -.++|+.+|++...|.++...+++++.
T Consensus 113 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--LG------YGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 58899999997776653 22 368999999999999999999988764
No 130
>PF02203 TarH: Tar ligand binding domain homologue; InterPro: IPR003122 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors.; GO: 0004888 transmembrane signaling receptor activity, 0006935 chemotaxis, 0007165 signal transduction, 0016020 membrane; PDB: 2ASR_A 3ATP_A 2D4U_A 2LIG_A 1VLS_A 1LIH_A 1WAT_B 1VLT_B 1WAS_A 1JMW_A.
Probab=20.18 E-value=3.2e+02 Score=25.51 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=11.8
Q ss_pred chhhhHHHHHHHHHHHHhHHHHHHHH
Q 005901 319 SAKSYTALALRTISKQFRCLKDAISA 344 (671)
Q Consensus 319 ~a~~yt~lal~~iSr~Fr~L~daI~~ 344 (671)
....|..+..+.+...|....+++..
T Consensus 141 d~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (171)
T PF02203_consen 141 DIAAFMQLPNEKIQPLFDAFTAAWQA 166 (171)
T ss_dssp -HHHHHHSSHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcchhHHHHHHHHHH
Confidence 34444444445555555444444443
No 131
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=20.15 E-value=96 Score=31.58 Aligned_cols=54 Identities=22% Similarity=0.190 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcchh
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPMV 453 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~i 453 (671)
.||+..+.+|...|.-+-..+ -.-.++|+.+|++...|+.+...+++|+|....
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~----~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~ 229 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRP----HTLEEVGKEFNVTRERIRQIESKALRKLRHPSR 229 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCC----ccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHH
Confidence 589999999987762100122 346789999999999999999999999998753
No 132
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.02 E-value=86 Score=32.54 Aligned_cols=49 Identities=27% Similarity=0.443 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcCcch
Q 005901 396 GLPERAVTILRAWLFEHFLHPYPKDSDKQQLAKQTGLTRSQVSNWFINARVRLWKPM 452 (671)
Q Consensus 396 ~Lpk~~~~iLr~Wf~eH~~nPYPS~~EK~~LA~~TGLS~kQVsNWFiNaRrR~kKp~ 452 (671)
.||+..+.+|...|.+. -.-..+|..+|++...|..+...+++++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998877652 23578999999999999999999999988765
Done!