Query 022516
Match_columns 296
No_of_seqs 354 out of 1608
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 04:08:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022516.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022516hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802 Transcription factor O 100.0 1.6E-41 3.4E-46 323.4 6.3 151 6-168 204-354 (398)
2 KOG1168 Transcription factor A 99.8 4.4E-22 9.5E-27 183.1 2.3 153 7-170 216-371 (385)
3 KOG0484 Transcription factor P 99.7 3.5E-18 7.6E-23 136.3 6.7 69 99-172 13-81 (125)
4 KOG0489 Transcription factor z 99.7 3.1E-18 6.7E-23 158.9 7.1 67 101-172 157-223 (261)
5 KOG0488 Transcription factor B 99.7 1.7E-17 3.6E-22 157.2 6.2 67 99-170 168-234 (309)
6 KOG0842 Transcription factor t 99.7 2.5E-17 5.5E-22 154.7 6.3 69 99-172 149-217 (307)
7 KOG0843 Transcription factor E 99.7 1.1E-16 2.3E-21 139.1 7.3 64 102-170 101-164 (197)
8 KOG2251 Homeobox transcription 99.7 2.7E-16 5.9E-21 140.5 9.7 68 98-170 32-99 (228)
9 KOG0850 Transcription factor D 99.6 2.2E-16 4.8E-21 141.7 6.8 67 98-169 117-183 (245)
10 KOG0487 Transcription factor A 99.6 1E-16 2.3E-21 150.6 4.3 67 100-171 232-298 (308)
11 KOG4577 Transcription factor L 99.6 3.5E-15 7.6E-20 137.7 11.9 115 50-171 108-230 (383)
12 KOG0492 Transcription factor M 99.6 5.6E-16 1.2E-20 137.2 6.1 68 98-170 139-206 (246)
13 PF00046 Homeobox: Homeobox do 99.6 8.2E-16 1.8E-20 110.1 5.8 57 104-165 1-57 (57)
14 PF00157 Pou: Pou domain - N-t 99.6 1.3E-16 2.7E-21 121.0 0.7 70 5-74 4-73 (75)
15 KOG0485 Transcription factor N 99.6 5.7E-16 1.2E-20 138.1 4.3 67 99-170 100-166 (268)
16 KOG0494 Transcription factor C 99.6 3.4E-15 7.3E-20 136.1 6.3 65 102-171 140-204 (332)
17 KOG0848 Transcription factor C 99.5 2.3E-15 5E-20 137.7 3.5 65 101-170 197-261 (317)
18 KOG0844 Transcription factor E 99.5 1.1E-14 2.3E-19 135.4 2.8 66 99-169 177-242 (408)
19 smart00389 HOX Homeodomain. DN 99.5 6.8E-14 1.5E-18 99.3 5.1 55 105-164 2-56 (56)
20 cd00086 homeodomain Homeodomai 99.5 1.1E-13 2.4E-18 98.8 6.0 57 105-166 2-58 (59)
21 TIGR01565 homeo_ZF_HD homeobox 99.5 7.7E-14 1.7E-18 101.3 5.0 52 104-160 2-57 (58)
22 KOG0847 Transcription factor, 99.5 5.4E-14 1.2E-18 125.7 4.6 75 101-180 165-239 (288)
23 KOG0491 Transcription factor B 99.4 7E-14 1.5E-18 120.0 3.4 66 102-172 99-164 (194)
24 KOG0486 Transcription factor P 99.4 1.2E-13 2.5E-18 129.1 5.0 68 99-171 108-175 (351)
25 KOG0493 Transcription factor E 99.4 1.1E-13 2.3E-18 126.5 4.4 60 104-168 247-306 (342)
26 KOG0483 Transcription factor H 99.4 2.2E-13 4.8E-18 121.5 3.9 62 104-170 51-112 (198)
27 COG5576 Homeodomain-containing 99.3 1.3E-12 2.8E-17 112.8 6.0 64 102-170 50-113 (156)
28 KOG0490 Transcription factor, 99.2 2.7E-11 5.9E-16 108.6 5.5 78 85-168 43-120 (235)
29 smart00352 POU Found in Pit-Oc 99.0 2.6E-10 5.7E-15 86.6 3.1 70 5-74 4-73 (75)
30 KOG0849 Transcription factor P 98.9 8.3E-10 1.8E-14 106.8 5.0 66 99-169 172-237 (354)
31 KOG0775 Transcription factor S 98.8 2.9E-08 6.4E-13 91.7 9.2 50 110-164 183-232 (304)
32 KOG0774 Transcription factor P 98.7 4.8E-10 1E-14 102.7 -3.6 64 102-169 187-252 (334)
33 PF05920 Homeobox_KN: Homeobox 98.3 4.5E-07 9.7E-12 61.2 2.5 33 126-162 8-40 (40)
34 KOG2252 CCAAT displacement pro 98.1 5E-06 1.1E-10 83.4 6.6 58 101-163 418-475 (558)
35 KOG0490 Transcription factor, 97.9 7.5E-06 1.6E-10 73.3 4.0 65 99-168 149-213 (235)
36 KOG1146 Homeobox protein [Gene 97.4 0.00017 3.6E-09 78.8 5.4 63 102-169 902-964 (1406)
37 PF11569 Homez: Homeodomain le 96.4 0.0023 5E-08 46.2 2.1 42 115-161 10-51 (56)
38 KOG3623 Homeobox transcription 96.3 0.019 4.2E-07 60.0 9.1 52 115-171 568-619 (1007)
39 KOG0773 Transcription factor M 95.5 0.013 2.9E-07 56.2 3.7 63 103-169 239-303 (342)
40 PF04218 CENP-B_N: CENP-B N-te 89.6 0.88 1.9E-05 32.2 4.8 47 104-160 1-47 (53)
41 PF08880 QLQ: QLQ; InterPro: 88.2 0.63 1.4E-05 30.8 3.0 22 42-63 2-23 (37)
42 PF04545 Sigma70_r4: Sigma-70, 63.2 15 0.00032 24.9 4.1 46 109-164 4-49 (50)
43 cd06171 Sigma70_r4 Sigma70, re 61.8 10 0.00023 24.6 3.0 44 109-162 10-53 (55)
44 PF08281 Sigma70_r4_2: Sigma-7 59.2 15 0.00032 25.1 3.5 43 110-162 11-53 (54)
45 PF01527 HTH_Tnp_1: Transposas 59.2 10 0.00023 27.6 2.9 44 105-157 2-45 (76)
46 KOG3755 SATB1 matrix attachmen 54.7 4.6 0.0001 42.0 0.4 50 119-169 708-760 (769)
47 KOG3623 Homeobox transcription 54.3 46 0.00099 35.9 7.4 107 43-169 581-687 (1007)
48 PF04967 HTH_10: HTH DNA bindi 54.2 17 0.00036 25.9 3.1 38 110-153 1-41 (53)
49 cd00569 HTH_Hin_like Helix-tur 51.1 35 0.00075 19.5 3.9 38 109-156 5-42 (42)
50 PRK09652 RNA polymerase sigma 46.8 34 0.00073 28.5 4.4 49 109-167 128-176 (182)
51 PF00424 REV: REV protein (ant 44.8 26 0.00057 27.8 3.1 37 115-170 14-50 (91)
52 KOG1146 Homeobox protein [Gene 43.4 8.1 0.00018 43.6 0.1 65 103-172 444-508 (1406)
53 TIGR02937 sigma70-ECF RNA poly 42.8 40 0.00087 26.5 4.1 47 109-165 110-156 (158)
54 PRK09646 RNA polymerase sigma 42.6 48 0.001 28.6 4.9 48 110-167 143-190 (194)
55 PRK06759 RNA polymerase factor 42.1 36 0.00077 27.9 3.8 47 109-165 106-152 (154)
56 PRK03975 tfx putative transcri 41.9 54 0.0012 28.0 4.9 51 108-169 5-55 (141)
57 PF10668 Phage_terminase: Phag 41.6 15 0.00032 27.0 1.2 19 134-156 25-43 (60)
58 PF00196 GerE: Bacterial regul 40.4 44 0.00095 23.3 3.5 45 109-164 3-47 (58)
59 PF11336 DUF3138: Protein of u 39.6 1.4E+02 0.003 30.4 7.9 83 33-124 12-94 (514)
60 PRK09642 RNA polymerase sigma 39.6 59 0.0013 26.9 4.8 48 110-167 107-154 (160)
61 COG3413 Predicted DNA binding 39.1 43 0.00093 29.9 4.1 48 109-164 155-205 (215)
62 PRK12533 RNA polymerase sigma 38.3 62 0.0013 29.0 5.0 32 134-169 153-184 (216)
63 PRK12526 RNA polymerase sigma 38.1 49 0.0011 29.0 4.3 30 134-167 172-201 (206)
64 PRK11924 RNA polymerase sigma 37.7 56 0.0012 27.0 4.4 31 134-168 144-174 (179)
65 PRK12519 RNA polymerase sigma 37.5 46 0.001 28.5 4.0 30 133-166 159-188 (194)
66 TIGR02948 SigW_bacill RNA poly 36.5 53 0.0012 27.7 4.1 30 133-166 154-183 (187)
67 PRK04217 hypothetical protein; 36.3 93 0.002 25.4 5.3 51 108-168 41-91 (110)
68 PF13936 HTH_38: Helix-turn-he 36.2 27 0.00059 23.4 1.8 40 108-157 3-42 (44)
69 TIGR02985 Sig70_bacteroi1 RNA 36.0 70 0.0015 25.9 4.7 46 110-165 114-159 (161)
70 PRK09413 IS2 repressor TnpA; R 35.9 64 0.0014 26.2 4.3 41 107-157 10-51 (121)
71 PRK12512 RNA polymerase sigma 35.9 72 0.0016 27.1 4.9 49 110-168 132-180 (184)
72 TIGR02983 SigE-fam_strep RNA p 35.8 65 0.0014 26.6 4.5 47 111-167 112-158 (162)
73 PRK09644 RNA polymerase sigma 34.6 73 0.0016 26.6 4.6 49 110-168 109-157 (165)
74 PRK12541 RNA polymerase sigma 34.5 59 0.0013 26.9 4.0 47 110-166 113-159 (161)
75 PRK12515 RNA polymerase sigma 34.2 79 0.0017 27.0 4.9 50 109-168 131-180 (189)
76 TIGR02999 Sig-70_X6 RNA polyme 33.3 75 0.0016 26.8 4.5 46 110-165 135-180 (183)
77 PRK00118 putative DNA-binding 33.2 87 0.0019 25.3 4.6 48 110-167 18-65 (104)
78 TIGR02959 SigZ RNA polymerase 33.1 74 0.0016 26.9 4.5 50 109-168 100-149 (170)
79 TIGR02989 Sig-70_gvs1 RNA poly 32.3 73 0.0016 26.1 4.2 46 109-164 111-156 (159)
80 PRK12514 RNA polymerase sigma 32.3 89 0.0019 26.3 4.9 29 134-166 148-176 (179)
81 smart00027 EH Eps15 homology d 32.1 84 0.0018 24.1 4.3 46 108-157 2-51 (96)
82 PRK09639 RNA polymerase sigma 32.1 82 0.0018 26.1 4.5 48 110-168 113-160 (166)
83 PRK09047 RNA polymerase factor 31.4 89 0.0019 25.6 4.6 49 109-167 106-154 (161)
84 PRK12546 RNA polymerase sigma 31.0 76 0.0017 27.5 4.3 31 134-168 132-162 (188)
85 PRK09637 RNA polymerase sigma 30.8 81 0.0018 27.1 4.4 31 134-168 125-155 (181)
86 PRK09648 RNA polymerase sigma 30.6 78 0.0017 27.0 4.2 47 109-165 139-185 (189)
87 PRK05602 RNA polymerase sigma 30.4 82 0.0018 26.8 4.3 31 134-168 147-177 (186)
88 smart00421 HTH_LUXR helix_turn 30.4 94 0.002 20.3 3.8 40 109-159 3-42 (58)
89 TIGR02952 Sig70_famx2 RNA poly 29.5 96 0.0021 25.6 4.5 28 134-165 141-168 (170)
90 COG4367 Uncharacterized protei 28.7 68 0.0015 25.5 3.1 39 109-152 2-40 (97)
91 PRK12537 RNA polymerase sigma 28.6 1.1E+02 0.0023 26.1 4.7 28 134-165 152-179 (182)
92 PRK12524 RNA polymerase sigma 28.3 1E+02 0.0022 26.6 4.6 31 134-168 155-185 (196)
93 PRK09480 slmA division inhibit 27.9 55 0.0012 27.6 2.8 40 116-161 17-56 (194)
94 TIGR02939 RpoE_Sigma70 RNA pol 27.7 82 0.0018 26.6 3.8 31 132-166 155-185 (190)
95 PRK06930 positive control sigm 27.3 1.2E+02 0.0026 26.4 4.8 50 109-168 114-163 (170)
96 PF02796 HTH_7: Helix-turn-hel 27.3 66 0.0014 21.5 2.5 38 109-156 5-42 (45)
97 PRK05657 RNA polymerase sigma 27.3 90 0.002 29.9 4.4 54 109-168 262-315 (325)
98 PF06056 Terminase_5: Putative 27.2 40 0.00087 24.3 1.5 25 134-164 16-40 (58)
99 PRK12523 RNA polymerase sigma 27.0 1.2E+02 0.0026 25.5 4.7 48 110-167 120-167 (172)
100 PRK12530 RNA polymerase sigma 26.7 1.1E+02 0.0024 26.3 4.5 30 134-167 153-182 (189)
101 PRK07037 extracytoplasmic-func 26.2 1.2E+02 0.0026 25.0 4.5 47 110-166 110-156 (163)
102 cd04761 HTH_MerR-SF Helix-Turn 26.2 42 0.00091 22.0 1.4 20 134-157 3-22 (49)
103 PRK12545 RNA polymerase sigma 25.7 1.4E+02 0.003 26.0 5.0 31 134-168 158-188 (201)
104 PRK12535 RNA polymerase sigma 25.5 1.4E+02 0.0031 26.0 5.0 31 134-168 152-182 (196)
105 PRK12516 RNA polymerase sigma 25.4 1.3E+02 0.0029 25.9 4.8 49 110-168 117-165 (187)
106 PRK13919 putative RNA polymera 25.3 1.3E+02 0.0029 25.4 4.8 29 134-166 154-182 (186)
107 PRK09645 RNA polymerase sigma 25.3 1.4E+02 0.0029 25.0 4.7 48 110-167 119-166 (173)
108 PF13384 HTH_23: Homeodomain-l 25.0 45 0.00098 22.2 1.4 21 134-158 20-40 (50)
109 PF13443 HTH_26: Cro/C1-type H 24.9 44 0.00095 23.3 1.4 28 133-164 12-39 (63)
110 PRK12529 RNA polymerase sigma 24.8 1.3E+02 0.0028 25.6 4.5 48 109-166 127-174 (178)
111 PRK12547 RNA polymerase sigma 24.6 1.3E+02 0.0029 25.0 4.5 47 110-166 113-159 (164)
112 TIGR02954 Sig70_famx3 RNA poly 24.2 1.4E+02 0.003 24.9 4.6 29 134-166 138-166 (169)
113 PRK12536 RNA polymerase sigma 24.1 1.3E+02 0.0029 25.4 4.5 30 133-166 147-176 (181)
114 PRK12532 RNA polymerase sigma 24.1 1.3E+02 0.0027 25.9 4.4 31 134-168 155-185 (195)
115 PRK12538 RNA polymerase sigma 24.0 1.1E+02 0.0024 27.7 4.1 31 134-168 190-220 (233)
116 PF13518 HTH_28: Helix-turn-he 23.6 64 0.0014 21.4 2.0 23 134-160 15-37 (52)
117 PRK12543 RNA polymerase sigma 23.6 1.3E+02 0.0028 25.5 4.3 32 134-169 136-167 (179)
118 PRK09647 RNA polymerase sigma 23.4 1.6E+02 0.0034 25.9 5.0 31 134-168 157-187 (203)
119 PRK06811 RNA polymerase factor 23.0 1.3E+02 0.0029 25.7 4.3 50 109-168 131-180 (189)
120 PRK12520 RNA polymerase sigma 22.4 1.6E+02 0.0036 25.1 4.8 51 110-170 132-182 (191)
121 PRK11923 algU RNA polymerase s 22.3 1.5E+02 0.0033 25.2 4.6 31 134-168 157-187 (193)
122 PRK12511 RNA polymerase sigma 22.0 1.6E+02 0.0034 25.4 4.6 49 110-168 112-160 (182)
123 PRK12531 RNA polymerase sigma 22.0 1.8E+02 0.0038 25.1 4.9 30 134-167 160-189 (194)
124 PRK09649 RNA polymerase sigma 21.7 1.4E+02 0.003 25.6 4.1 28 134-165 149-176 (185)
125 PRK12528 RNA polymerase sigma 21.7 1.5E+02 0.0033 24.4 4.3 45 109-163 113-157 (161)
126 PRK12540 RNA polymerase sigma 21.6 2.7E+02 0.0059 23.8 6.0 49 110-168 112-160 (182)
127 PRK12539 RNA polymerase sigma 21.4 1.7E+02 0.0036 24.9 4.6 47 110-166 132-178 (184)
128 PF12720 DUF3807: Protein of u 21.2 61 0.0013 28.6 1.8 14 41-54 48-61 (172)
129 PRK06986 fliA flagellar biosyn 21.1 1.4E+02 0.003 26.8 4.1 31 133-167 202-232 (236)
130 PRK12542 RNA polymerase sigma 20.9 1.6E+02 0.0035 25.0 4.4 48 110-167 123-170 (185)
131 TIGR03879 near_KaiC_dom probab 20.7 37 0.0008 25.8 0.3 22 133-158 34-55 (73)
132 PRK08583 RNA polymerase sigma 20.5 1.6E+02 0.0035 26.7 4.5 48 109-166 205-252 (257)
133 cd06170 LuxR_C_like C-terminal 20.3 1.8E+02 0.0039 19.0 3.7 36 111-157 2-37 (57)
134 PRK08295 RNA polymerase factor 20.2 1.7E+02 0.0036 25.2 4.4 29 134-166 173-201 (208)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=1.6e-41 Score=323.38 Aligned_cols=151 Identities=19% Similarity=0.211 Sum_probs=131.1
Q ss_pred HHHHHHHHHHhhhhhhhccCCCCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCC
Q 022516 6 IREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRL 85 (296)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~t~~~l~~lr~qi~~~~~ic~~~~~~~k~l~~~~~~~~sg~~~ 85 (296)
..||||||||+||||||||||||+|||+|+|+|||||||+++||||+++..+|++||++++.+.|||........
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~----- 278 (398)
T KOG3802|consen 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRES----- 278 (398)
T ss_pred CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccc-----
Confidence 368999999999999999999999999999999999999999999999999999999999999999976544211
Q ss_pred CCcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 86 GNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 86 g~~~~~p~~~s~~~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
.+..+.+.... ...++||+||.|+...+..||++|.. |++|+..+|..||.+| +|...+|+|||||||.|+||
T Consensus 279 ~~~~~~~e~i~--a~~RkRKKRTSie~~vr~aLE~~F~~-npKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 279 TGSPNSIEKIG--AQSRKRKKRTSIEVNVRGALEKHFLK-NPKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred cCCCCCHHHhh--ccccccccccceeHHHHHHHHHHHHh-CCCCCHHHHHHHHHHh----ccccceEEEEeecccccccc
Confidence 11111111111 12267889999999999999999999 7999999999999999 99999999999999999999
Q ss_pred Hhh
Q 022516 166 KQL 168 (296)
Q Consensus 166 ~~~ 168 (296)
...
T Consensus 352 ~~~ 354 (398)
T KOG3802|consen 352 ITP 354 (398)
T ss_pred CCC
Confidence 876
No 2
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.84 E-value=4.4e-22 Score=183.12 Aligned_cols=153 Identities=16% Similarity=0.187 Sum_probs=123.9
Q ss_pred HHHHHHHHHhhhhhhhccCCCCCCCcccCccc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCC
Q 022516 7 REAAQQETQTQNQNQNQRGGENDNNNVVNGVM---YVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGG 83 (296)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~---~~~~~t~~~l~~lr~qi~~~~~ic~~~~~~~k~l~~~~~~~~sg~ 83 (296)
-.|||-||..|||||||||-||+|||-|+--| -|-.+|+.+||||+-+..+-.+|.-+++.++.||.........-.
T Consensus 216 PReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~ 295 (385)
T KOG1168|consen 216 PRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKD 295 (385)
T ss_pred HHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhc
Confidence 45899999999999999999999999664433 678899999999999999999999999999999965433221111
Q ss_pred CCCCcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHH
Q 022516 84 RLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (296)
Q Consensus 84 ~~g~~~~~p~~~s~~~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~ 163 (296)
..+. ..-+ ..++. ++|+||.+.....+.||.+|.. ++.|+.+.+..||++| .|...+|+|||||.|+|.
T Consensus 296 ~~pd--~~~l--~~~~e--kKRKRTSIAAPEKRsLEayFav-QPRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQ 364 (385)
T KOG1168|consen 296 TKPD--INEL--LPGGE--KKRKRTSIAAPEKRSLEAYFAV-QPRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQ 364 (385)
T ss_pred cCCc--hhhc--cCccc--cccccccccCcccccHHHHhcc-CCCCchhHHHHHHHhh----hhhhceEEEEeeccHHHH
Confidence 1110 0001 11133 4778999999999999999999 8999999999999999 999999999999999999
Q ss_pred HHHhhhh
Q 022516 164 KRKQLVS 170 (296)
Q Consensus 164 Kr~~~~~ 170 (296)
||.....
T Consensus 365 KRm~~Sa 371 (385)
T KOG1168|consen 365 KRMKRSA 371 (385)
T ss_pred HHhhhhh
Confidence 9976654
No 3
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.74 E-value=3.5e-18 Score=136.29 Aligned_cols=69 Identities=32% Similarity=0.494 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhcc
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (296)
..++.||-||+||..||..||+.|.. ++||++-.|++||.++ .|++..|+|||||||+|.||+.+....
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~E-THYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAE-THYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHh-hcCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 45678899999999999999999999 8999999999999999 999999999999999999998876544
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=3.1e-18 Score=158.90 Aligned_cols=67 Identities=33% Similarity=0.384 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhcc
Q 022516 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (296)
Q Consensus 101 ~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (296)
...||.||.||..|+.+||+.|.. |+|+++..|.|||..| .|+|+||||||||||+||||..+....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhf-N~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHF-NKYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcc-ccccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhccccc
Confidence 357899999999999999999999 8999999999999999 999999999999999999999887655
No 5
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.69 E-value=1.7e-17 Score=157.24 Aligned_cols=67 Identities=28% Similarity=0.354 Sum_probs=63.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
..+++|+.||.||..||..||+.|++ .+|.+..+|.+||..| ||+..||++||||||+||||.....
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~-QKYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEK-QKYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHH-hhcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhh
Confidence 55788899999999999999999999 8999999999999999 9999999999999999999988873
No 6
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.69 E-value=2.5e-17 Score=154.68 Aligned_cols=69 Identities=29% Similarity=0.388 Sum_probs=64.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhcc
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (296)
+.+++||+|..|++.|+.+||+.|.+ ++|++.+||++||..| .||++||||||||||.|+||+++....
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrq-QRYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQ-QRYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHh-hhccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhhh
Confidence 46677888999999999999999999 8999999999999999 999999999999999999999987755
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=1.1e-16 Score=139.08 Aligned_cols=64 Identities=38% Similarity=0.447 Sum_probs=61.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
+.+|.||.|+++||..||..|+. ++|....+|+.||..| +|++.||+|||||||.|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~-~~Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG-NQYVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc-CCeeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 67889999999999999999999 7999999999999999 9999999999999999999998874
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.66 E-value=2.7e-16 Score=140.48 Aligned_cols=68 Identities=35% Similarity=0.574 Sum_probs=65.2
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 98 ~~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
.+.++.||.||+|+..|+.+||.+|.+ ++||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~k-TqYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAK-TQYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHh-hcCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 478899999999999999999999999 8999999999999999 9999999999999999999998865
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.64 E-value=2.2e-16 Score=141.73 Aligned_cols=67 Identities=31% Similarity=0.405 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 98 ~~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
++.+|.|++||.++.-||..|.+.|++ ++|+..+||.+||..| ||+.+||||||||||.|.||..+.
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQk-TQYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQ-TQYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhh-cchhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhc
Confidence 467788999999999999999999999 7999999999999999 999999999999999999999883
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.64 E-value=1e-16 Score=150.62 Aligned_cols=67 Identities=28% Similarity=0.312 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhc
Q 022516 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (296)
Q Consensus 100 ~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (296)
.+..|++|..+|+.|+.+||+.|.. |.|++++.|.+|++.| +|+++||+|||||||+|+||..++..
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlf-N~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLF-NMYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHH-HHHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhhh
Confidence 3567889999999999999999999 8999999999999999 99999999999999999999987543
No 11
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.62 E-value=3.5e-15 Score=137.73 Aligned_cols=115 Identities=23% Similarity=0.299 Sum_probs=95.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCcccCCCcc--------CCCCCCCCCCCCCCCCHHHHHHHHHH
Q 022516 50 TLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMT--------SGGGHKISARQRWTPTPVQLQILESI 121 (296)
Q Consensus 50 ~lr~qi~~~~~ic~~~~~~~k~l~~~~~~~~sg~~~g~~~~~p~~~--------s~~~~~~~rR~Rt~ft~~Ql~~LE~~ 121 (296)
..++|..+|...|.+++...+.|.....+. -+..+.+.|..... ...+....+|+||++|..||+.|+.+
T Consensus 108 VRkAqd~VYHl~CF~C~iC~R~L~TGdEFY--LmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~A 185 (383)
T KOG4577|consen 108 VRKAQDFVYHLHCFACFICKRQLATGDEFY--LMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQA 185 (383)
T ss_pred HHHhhcceeehhhhhhHhhhcccccCCeeE--EeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHH
Confidence 348999999999999999999988877766 44445555532111 11144567899999999999999999
Q ss_pred HhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhc
Q 022516 122 FDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (296)
Q Consensus 122 F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (296)
|+. .++|.+..|++|+.++ ||..++|+|||||||||+||.++.+.
T Consensus 186 Yn~-SpKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 186 YNT-SPKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred hcC-CCchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhcc
Confidence 999 5999999999999999 99999999999999999999988753
No 12
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.61 E-value=5.6e-16 Score=137.25 Aligned_cols=68 Identities=37% Similarity=0.428 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 98 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 98 ~~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
.+++..|++||.||..||..||+.|.. .+|.++.+|.+++..| .|+++||+|||||||+|.||.+...
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfre-kqYLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFRE-KQYLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhH-hhhhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHH
Confidence 477888999999999999999999999 7999999999999999 9999999999999999999987653
No 13
>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=99.61 E-value=8.2e-16 Score=110.11 Aligned_cols=57 Identities=42% Similarity=0.663 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
||+|+.|+.+|+.+|+.+|.. ++||+..++..||..| ||+..+|++||+|||+++||
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-NPYPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH-SSSCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH-hccccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 578999999999999999999 7999999999999999 99999999999999999986
No 14
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=99.60 E-value=1.3e-16 Score=121.03 Aligned_cols=70 Identities=13% Similarity=0.134 Sum_probs=65.1
Q ss_pred hHHHHHHHHHHhhhhhhhccCCCCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 022516 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSA 74 (296)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~t~~~l~~lr~qi~~~~~ic~~~~~~~k~l~~ 74 (296)
...+|+++||+.||||||++||||.|||.++|.+||++||+++|+||+++..+++++|+.++.+.+|+..
T Consensus 4 ~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~e 73 (75)
T PF00157_consen 4 PDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEE 73 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHh
Confidence 3568999999999999999999999999999999999999999999999999999999999999999864
No 15
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.60 E-value=5.7e-16 Score=138.05 Aligned_cols=67 Identities=31% Similarity=0.403 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
+..++|+.||+|+..|+..||..|+. .+|++..+|..||+.| .|+|+||+|||||||.||||+-...
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~-krYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFEL-KRYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHH-HhhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 34467889999999999999999999 7999999999999999 9999999999999999999987654
No 16
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.56 E-value=3.4e-15 Score=136.12 Aligned_cols=65 Identities=25% Similarity=0.316 Sum_probs=59.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhc
Q 022516 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (296)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (296)
++|+-||.||..|+..||+.|.. .+||+...|+.||.++ .|.+.+|+|||||||+||||..+.-.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFke-aHYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKE-AHYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhh-ccCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 34444999999999999999999 6999999999999999 99999999999999999999988753
No 17
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.54 E-value=2.3e-15 Score=137.68 Aligned_cols=65 Identities=28% Similarity=0.364 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 101 ~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
+.+-+.|.++|..|+.+||+.|.. .+|.++.++.|||..| +|+|+||+|||||||||+||..++.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~-SryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHT-SRYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecccceeEEecchhhhhhhhhhcc-ccceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 334467899999999999999999 6999999999999999 9999999999999999999998876
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.48 E-value=1.1e-14 Score=135.41 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
....-||.||.||.+||..||+.|.+ .-|.+++.|.|||..| +|.+..|+|||||||+|+||+...
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyr-ENYVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYR-ENYVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHH-hccccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhh
Confidence 34456899999999999999999999 4799999999999999 999999999999999999998775
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.46 E-value=6.8e-14 Score=99.29 Aligned_cols=55 Identities=44% Similarity=0.644 Sum_probs=51.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
+.|+.|+++|+.+|+..|.. ++||+..++..||..| ||+..+|++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~-~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK-NPYPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 56788999999999999999 7999999999999999 9999999999999999864
No 20
>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=99.46 E-value=1.1e-13 Score=98.80 Aligned_cols=57 Identities=44% Similarity=0.653 Sum_probs=53.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
+.|+.|+..|+.+||.+|.. ++||+..++..||..| ||+..+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~-~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK-NPYPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 56789999999999999999 7999999999999999 999999999999999998864
No 21
>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=99.46 E-value=7.7e-14 Score=101.32 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHHhhcCCcccchhhchhhhhH
Q 022516 104 ARQRWTPTPVQLQILESIFDQGTGT----PSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (296)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~y----Ps~~~r~~LA~~L~~~~gLs~~qV~vWFQNRR 160 (296)
+|.||.||.+|+..||..|+. ++| |+..+|.+||..| ||++++|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~-~~y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEK-LGWKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHH-cCCCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 789999999999999999999 899 9999999999999 999999999999965
No 22
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.45 E-value=5.4e-14 Score=125.68 Aligned_cols=75 Identities=27% Similarity=0.343 Sum_probs=64.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhccccccCCCC
Q 022516 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSANTLHNGG 180 (296)
Q Consensus 101 ~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~~~~~~~gg 180 (296)
.+++..|.+|+-.|+..||+.|+. ++|+-.++|.+||..| |+++.+|+|||||||.||||+...+.........+
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq-tkylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds 239 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ-TKYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDS 239 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh-hhcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhhccccCCC
Confidence 345667889999999999999999 8999999999999999 99999999999999999999987664444333333
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.42 E-value=7e-14 Score=120.05 Aligned_cols=66 Identities=32% Similarity=0.408 Sum_probs=61.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhcc
Q 022516 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (296)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (296)
++++.|++|+..|+..||+.|+. .+|.+.++|.|||..| +|+++||+.||||||+|.||.++....
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~-QrYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFER-QRYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HhhhhcccccCccccccHHHHhh-hhhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 45678999999999999999999 8999999999999999 999999999999999999999887654
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.42 E-value=1.2e-13 Score=129.07 Aligned_cols=68 Identities=32% Similarity=0.424 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhc
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (296)
+.+++||.|+.|+..||..||..|.+ |+||+-..|++||.-+ +|++.+|+|||.|||+||||++....
T Consensus 108 ki~KqrrQrthFtSqqlqele~tF~r-NrypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 108 KISKQRRQRTHFTSQQLQELEATFQR-NRYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhhHHHHHHHHHHHHhh-ccCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 44588999999999999999999999 8999999999999999 99999999999999999999988765
No 25
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.42 E-value=1.1e-13 Score=126.48 Aligned_cols=60 Identities=33% Similarity=0.476 Sum_probs=56.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
+|+||.||.+||..|+..|+. |+|.+...|.+||.+| +|.+.||+|||||+|+|.||..-
T Consensus 247 KRPRTAFtaeQL~RLK~EF~e-nRYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQE-NRYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cCccccccHHHHHHHHHHHhh-hhhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhccC
Confidence 578999999999999999999 8999999999999999 99999999999999999998643
No 26
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.38 E-value=2.2e-13 Score=121.47 Aligned_cols=62 Identities=34% Similarity=0.472 Sum_probs=56.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
.+++.+|+.+|+..||..|+. +.|....++..||..| ||.++||.|||||||||||.++...
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~-~~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFES-EKKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccccccHHHHHHhHHhhcc-ccccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhh
Confidence 344457999999999999999 7999999999999999 9999999999999999999998863
No 27
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.34 E-value=1.3e-12 Score=112.80 Aligned_cols=64 Identities=30% Similarity=0.421 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
..+++|++.+.+|+.+|++.|+. ++||+...|..|+..| +|+++.|++||||||++.|+.....
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i-~p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI-NPYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc-CCCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccc
Confidence 34566777799999999999999 7999999999999999 9999999999999999999976643
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.17 E-value=2.7e-11 Score=108.59 Aligned_cols=78 Identities=28% Similarity=0.331 Sum_probs=65.9
Q ss_pred CCCcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 85 LGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 85 ~g~~~~~p~~~s~~~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
.|..+|...... ....+.||.|+.|+..|+.+||+.|+. ++||+...|+.||..+ .+++..|+|||||||+||+
T Consensus 43 ~g~~~~~~d~~~-~~~~~~rr~rt~~~~~ql~~ler~f~~-~h~Pd~~~r~~la~~~----~~~e~rVqvwFqnrrak~r 116 (235)
T KOG0490|consen 43 DGSIYCKRDYQR-EFKFSKRCARCKFTISQLDELERAFEK-VHLPCFACRECLALLL----TGDEFRVQVWFQNRRAKDR 116 (235)
T ss_pred CCcccccccchh-hhhccccccCCCCCcCHHHHHHHhhcC-CCcCccchHHHHhhcC----CCCeeeeehhhhhhcHhhh
Confidence 444555443322 124567899999999999999999999 7999999999999999 9999999999999999999
Q ss_pred HHhh
Q 022516 165 RKQL 168 (296)
Q Consensus 165 r~~~ 168 (296)
+...
T Consensus 117 ~~~~ 120 (235)
T KOG0490|consen 117 KEER 120 (235)
T ss_pred hhhc
Confidence 9875
No 29
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.99 E-value=2.6e-10 Score=86.60 Aligned_cols=70 Identities=11% Similarity=0.131 Sum_probs=66.5
Q ss_pred hHHHHHHHHHHhhhhhhhccCCCCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 022516 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSA 74 (296)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~t~~~l~~lr~qi~~~~~ic~~~~~~~k~l~~ 74 (296)
....|+|.++..++++|+++|+||.+++-++|++||..+|+.+|++|+....+++++|+..+.+.+|+..
T Consensus 4 ~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~ 73 (75)
T smart00352 4 TDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEE 73 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHh
Confidence 4457899999999999999999999999999999999999999999999999999999999999999864
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.93 E-value=8.3e-10 Score=106.82 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
..++.+|.|++|++.|+..||+.|+. ++||+...|+.||.++ ++++..|+|||+|||+|++|....
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~r-t~yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQR-TPYPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccchHHHHHHHhcC-CCCCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 55667788999999999999999999 7899999999999999 999999999999999999998853
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.78 E-value=2.9e-08 Score=91.71 Aligned_cols=50 Identities=28% Similarity=0.452 Sum_probs=45.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
|...-+..|..+|.. ++||+..++.+||+.+ ||+..||-+||+|||+|+|
T Consensus 183 FKekSR~~LrewY~~-~~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ-NPYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhc-CCCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhh
Confidence 334457899999999 7999999999999999 9999999999999999999
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.74 E-value=4.8e-10 Score=102.74 Aligned_cols=64 Identities=27% Similarity=0.388 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhh--cCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 102 ISARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~--~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
..||+|..|++.-..+|..+|.. +|+||+.+.+++||+++ +++..||.+||.|+|-+.||....
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhhh
Confidence 35778889999999999999976 68999999999999999 999999999999999999986543
No 33
>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=98.29 E-value=4.5e-07 Score=61.16 Aligned_cols=33 Identities=33% Similarity=0.598 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHH
Q 022516 126 TGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (296)
Q Consensus 126 n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK 162 (296)
++||+..++.+||..+ ||+..||..||-|.|.|
T Consensus 8 nPYPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NPYPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp SGS--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 7999999999999999 99999999999999975
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.11 E-value=5e-06 Score=83.43 Aligned_cols=58 Identities=29% Similarity=0.462 Sum_probs=54.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHH
Q 022516 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (296)
Q Consensus 101 ~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~ 163 (296)
-..+|+|.+||..|++.|..+|+. +++|+.+..+.|+.+| +|..+.|.+||-|.|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke-~~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKE-NKRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhc-CCCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 356778999999999999999999 8999999999999999 999999999999998876
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.95 E-value=7.5e-06 Score=73.33 Aligned_cols=65 Identities=34% Similarity=0.519 Sum_probs=59.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
...+.++.|+.+...|+..|+..|.. +.+|+...+..|+..+ +++++.|+|||+|+|++.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRA-TPKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccC-CCCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 33567788999999999999999999 7999999999999999 99999999999999999998765
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.43 E-value=0.00017 Score=78.79 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=58.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
.+|+.|+.++..||.+|..+|.. ..||.-.+.+.|-..+ ++..++|.|||||-|+|.|+....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~-q~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEA-QRTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhh-ccCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhhc
Confidence 46778999999999999999999 7999999999999999 999999999999999999998773
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.37 E-value=0.0023 Score=46.20 Aligned_cols=42 Identities=21% Similarity=0.405 Sum_probs=30.9
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHH
Q 022516 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (296)
Q Consensus 115 l~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRa 161 (296)
+..|+.+|.. .+++...+...|..+. +|+..||+.||--|+.
T Consensus 10 ~~pL~~Yy~~-h~~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLK-HKQLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHH-T----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHH-cCCccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 4569999999 7999999999999999 9999999999976543
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=96.30 E-value=0.019 Score=59.95 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=47.6
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhc
Q 022516 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (296)
Q Consensus 115 l~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (296)
+..|..+|.. |..|+..+...||... ||+.+.|++||++++++..+..+...
T Consensus 568 ~sllkayyal-n~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYAL-NGLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7789999999 8999999999999999 99999999999999999988876544
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.47 E-value=0.013 Score=56.22 Aligned_cols=63 Identities=21% Similarity=0.228 Sum_probs=50.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh--cCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 103 SARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~--~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
..|++..+......+|+.+... ..+||+..++..||.++ ||+..||.+||-|.|.|..+-...
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc----CCCcccCCchhhhcccccCCchHH
Confidence 4455567889999999988433 23799999999999999 999999999999999887665443
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=89.61 E-value=0.88 Score=32.17 Aligned_cols=47 Identities=19% Similarity=0.271 Sum_probs=34.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhH
Q 022516 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (296)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRR 160 (296)
+|+|..+|-++...+-..++.+ . ...+||..+ |++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~-----s~~~ia~~f----gv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E-----SKRDIAREF----GVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T------HHHHHHHH----T--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C-----CHHHHHHHh----CCCHHHHHHHHHhHH
Confidence 4678899999888888888873 3 456899999 999999999998864
No 41
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=88.19 E-value=0.63 Score=30.84 Aligned_cols=22 Identities=36% Similarity=0.501 Sum_probs=20.2
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 022516 42 VMTDEQLETLRKQIAVYATICE 63 (296)
Q Consensus 42 ~~t~~~l~~lr~qi~~~~~ic~ 63 (296)
.||.+|+..||+||.+|+.+.+
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 5999999999999999998766
No 42
>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=63.23 E-value=15 Score=24.89 Aligned_cols=46 Identities=17% Similarity=0.294 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
.+++.+..+|...|.. .+ .-.++|..+ |++...|+.+...-..|-|
T Consensus 4 ~L~~~er~vi~~~y~~--~~----t~~eIa~~l----g~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE--GL----TLEEIAERL----GISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS--T-----SHHHHHHHH----TSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC--CC----CHHHHHHHH----CCcHHHHHHHHHHHHHHhc
Confidence 4678899999998855 22 245899999 9999999888765555544
No 43
>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=61.76 E-value=10 Score=24.61 Aligned_cols=44 Identities=16% Similarity=0.162 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK 162 (296)
.+++.+..++...|.. . + ...++|..+ |++...|+.|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~-~-~----~~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGE-G-L----SYEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhc-C-C----CHHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 3567788888777754 1 2 244789999 99999999998755443
No 44
>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=59.24 E-value=15 Score=25.15 Aligned_cols=43 Identities=28% Similarity=0.255 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK 162 (296)
+++.+..++.-.|..+ ....++|..+ |+++..|++|...-|.+
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHHHHhh
Confidence 4566777777666552 3345899999 99999999999755443
No 45
>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=59.19 E-value=10 Score=27.61 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=28.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhh
Q 022516 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (296)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (296)
+.|..|++++...+-..+... ...+.++|..+ ||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~-----g~sv~~va~~~----gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES-----GESVSEVAREY----GISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH-----HCHHHHHHHHH----TS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC-----CCceEeeeccc----ccccccccHHHH
Confidence 456788998877776666331 24567899999 999999999964
No 46
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=54.72 E-value=4.6 Score=42.02 Aligned_cols=50 Identities=24% Similarity=0.250 Sum_probs=33.9
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHHhh---cCCcccchhhchhhhhHHHHHHHhhh
Q 022516 119 ESIFDQGTGTPSKQKIKEITVELSQ---HGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 119 E~~F~~~n~yPs~~~r~~LA~~L~~---~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
+.+|.. +..++...+.+..+++.. .-....+.|+.||.|||+++|+.+..
T Consensus 708 ~~w~~k-~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLK-TRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheec-ccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 555666 677777777666655500 00224578999999999999997654
No 47
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=54.27 E-value=46 Score=35.86 Aligned_cols=107 Identities=18% Similarity=0.247 Sum_probs=66.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q 022516 43 MTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIF 122 (296)
Q Consensus 43 ~t~~~l~~lr~qi~~~~~ic~~~~~~~k~l~~~~~~~~sg~~~g~~~~~p~~~s~~~~~~~rR~Rt~ft~~Ql~~LE~~F 122 (296)
.+.+++..+..|+.+-....+.|.+-.++-..... . .|.++++ . ...+.|+....++-..|..++
T Consensus 581 ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~----r--------sps~psg-~--~p~kv~sp~k~~dq~ql~~a~ 645 (1007)
T KOG3623|consen 581 PSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE----R--------SPSQPSG-E--RPVKVRSPIKEEDQQQLKQAY 645 (1007)
T ss_pred CCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc----c--------CccCCCC-C--CCccccCCCCccchhhhHhhh
Confidence 46677888888888777777777665543211100 0 0111111 1 122334555666666777777
Q ss_pred hhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 123 DQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 123 ~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
+. +--+...+-..++.+| ...+.+|.|||++|+..-+....-
T Consensus 646 el-q~s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 646 EL-QASPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred hc-ccCccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCccc
Confidence 77 5556665555667777 888899999999999877665544
No 48
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=54.24 E-value=17 Score=25.89 Aligned_cols=38 Identities=32% Similarity=0.483 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhcCCC---CCHHHHHHHHHHHhhcCCcccchhh
Q 022516 110 PTPVQLQILESIFDQGTGT---PSKQKIKEITVELSQHGQISETNVY 153 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~y---Ps~~~r~~LA~~L~~~~gLs~~qV~ 153 (296)
+|+.|+.+|...|+. .| |-.....+||+.| |++...|.
T Consensus 1 LT~~Q~e~L~~A~~~--GYfd~PR~~tl~elA~~l----gis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYEL--GYFDVPRRITLEELAEEL----GISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHc--CCCCCCCcCCHHHHHHHh----CCCHHHHH
Confidence 578999999999988 35 4445667899999 99987654
No 49
>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=51.10 E-value=35 Score=19.54 Aligned_cols=38 Identities=24% Similarity=0.496 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWF 156 (296)
.++.++...+...|.. .+ ...++|..+ +++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~--~~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA--GE----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHhC
Confidence 3566666666666655 23 345788899 99999988884
No 50
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=46.82 E-value=34 Score=28.53 Aligned_cols=49 Identities=12% Similarity=-0.021 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
.+++.+..+|...|.. .+ ...+||..| |+++..|+.|...-+.+.|+.-
T Consensus 128 ~L~~~~r~vl~l~~~~--~~----s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIE--GL----SYEEIAEIM----GCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 3556666666655544 12 234889999 9999999999986666665543
No 51
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=44.81 E-value=26 Score=27.83 Aligned_cols=37 Identities=22% Similarity=0.346 Sum_probs=21.1
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 115 l~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
+.+..-+|+. |+||...- -+..= .|||.+||+++.+-
T Consensus 14 vRiIk~Lyqs-nPyP~~~G---Tr~aR---------------RnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQS-NPYPSPEG---TRQAR---------------RNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHT-S-S--S-S----HHHH---------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHcc-ccCCCCCC---ccccc---------------cchhhhHHHHHHHH
Confidence 4455556877 89998531 11111 69999999988763
No 52
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=43.43 E-value=8.1 Score=43.59 Aligned_cols=65 Identities=11% Similarity=0.009 Sum_probs=54.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhhcc
Q 022516 103 SARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (296)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (296)
.+-.|++++.-|+.+|-..|.. ..||.-.+...++..| ++..+.+..||++++.++.....+...
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt-~~cpkc~~~yk~a~~L----~vhmRskhp~~~~~~c~~gq~~~~~ar 508 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKT-LKCPKCNWHYKLAQTL----GVHMRSKHPESQSAYCKAGQNHPRLAR 508 (1406)
T ss_pred hhhhhhcccccceeeeeccccc-ccCCccchhhhhHHHh----hhcccccccccchhHhHhccccccccc
Confidence 3445778888899999999988 7999999999999999 999999999999988888776555443
No 53
>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=42.81 E-value=40 Score=26.54 Aligned_cols=47 Identities=21% Similarity=0.211 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
.+++.+..++...|.. .+ ...+||..+ |+++..|+.|...-+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~--g~----s~~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE--GL----SYKEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 3456666666555433 22 344889999 99999999998866666554
No 54
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=42.55 E-value=48 Score=28.64 Aligned_cols=48 Identities=13% Similarity=0.080 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
+++.+..+|.-.|.. .....+||..| |++...|+++...-|.+.|+.-
T Consensus 143 L~~~~r~vl~l~~~~------~~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAYYG------GLTYREVAERL----AVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHHHc------CCCHHHHHHHh----CCChHhHHHHHHHHHHHHHHHh
Confidence 455555555544433 12345889999 9999999999976666666544
No 55
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=42.06 E-value=36 Score=27.91 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
.+++.+..++...|-.+ ....+||..| |++...|++|...-|.+.|+
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHhh
Confidence 34555666665544441 2355899999 99999999998766655554
No 56
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=41.87 E-value=54 Score=28.01 Aligned_cols=51 Identities=22% Similarity=0.178 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
..+++.|+.+|... .. .+ ...+||..| |++...|..|-...+.|.|+....
T Consensus 5 ~~Lt~rqreVL~lr-~~--Gl----Tq~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLR-ER--GL----TQQEIADIL----GTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHH-Hc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999874 34 22 234899999 999999999999877777665543
No 57
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=41.56 E-value=15 Score=26.95 Aligned_cols=19 Identities=32% Similarity=0.693 Sum_probs=16.7
Q ss_pred HHHHHHHHhhcCCcccchhhchh
Q 022516 134 IKEITVELSQHGQISETNVYNWF 156 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWF 156 (296)
-.+||.+| |+++.+|+.|=
T Consensus 25 lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred HHHHHHHH----CCCHHHHHHHh
Confidence 34889999 99999999995
No 58
>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=40.39 E-value=44 Score=23.28 Aligned_cols=45 Identities=27% Similarity=0.228 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
.||+.++.+|.-+..- + ...++|..+ ++++..|+.+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G---~----~~~eIA~~l----~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---M----SNKEIAEEL----GISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT---S-----HHHHHHHH----TSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc---C----CcchhHHhc----CcchhhHHHHHHHHHHHhC
Confidence 5788889988776654 2 245899999 9999999998877666643
No 59
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=39.59 E-value=1.4e+02 Score=30.38 Aligned_cols=83 Identities=14% Similarity=0.132 Sum_probs=51.9
Q ss_pred ccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhcCCCCCCcccCCCccCCCCCCCCCCCCCCCCH
Q 022516 33 VVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTP 112 (296)
Q Consensus 33 ~~~g~~~~~~~t~~~l~~lr~qi~~~~~ic~~~~~~~k~l~~~~~~~~sg~~~g~~~~~p~~~s~~~~~~~rR~Rt~ft~ 112 (296)
++++++....-+-.+|+.|.+|+..... +..++.+.+.+.+.....+...+.....+...+. ...++.+|+
T Consensus 12 ~al~~~a~a~a~a~~i~~L~~ql~aLq~---~v~eL~~~laa~~~aa~~gA~~~~~~~a~~~aP~------~~a~~~~T~ 82 (514)
T PF11336_consen 12 GALPGAAMAAATADQIKALQAQLQALQD---QVNELRAKLAAKPAAAPGGAAIGPAATAAAAAPS------SDAQAGLTN 82 (514)
T ss_pred hhccccccccCCHHHHHHHHHHHHHHHH---HHHHHHHHHhcCCCCCCccccccccccccccCCC------cccccccCh
Confidence 4566666677788899999999876554 4446677776655544333333333332222111 125789999
Q ss_pred HHHHHHHHHHhh
Q 022516 113 VQLQILESIFDQ 124 (296)
Q Consensus 113 ~Ql~~LE~~F~~ 124 (296)
+++..+..-+..
T Consensus 83 d~~~~~~qqiAn 94 (514)
T PF11336_consen 83 DDATEMRQQIAN 94 (514)
T ss_pred HHHHHHHHHHHh
Confidence 999888776655
No 60
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=39.57 E-value=59 Score=26.85 Aligned_cols=48 Identities=13% Similarity=0.066 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
+++.+..++.-.|..+ + ...+||..| |+++..|++....-|.+.|+.-
T Consensus 107 Lp~~~r~v~~l~~~~g--~----s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE--K----SYQEIALQE----KIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 3445555555444331 1 234889999 9999999999987777766654
No 61
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=39.05 E-value=43 Score=29.90 Aligned_cols=48 Identities=31% Similarity=0.438 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHhhcCCC---CCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGT---PSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~y---Ps~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
.+|+.|+.+|..+|.. .| |-.....+||+.| |++...+ |..=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~--GYFd~PR~~~l~dLA~~l----GISkst~--~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKM--GYFDYPRRVSLKDLAKEL----GISKSTL--SEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHc--CCCCCCccCCHHHHHHHh----CCCHHHH--HHHHHHHHHH
Confidence 6999999999999998 35 4445567889999 9998763 4444455444
No 62
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=38.34 E-value=62 Score=29.01 Aligned_cols=32 Identities=16% Similarity=0.071 Sum_probs=25.5
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
.++||..| |+++..|+++...-|.+.|+.-..
T Consensus 153 ~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 153 YREIAAIA----DVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHcc
Confidence 45889999 999999999998777776666533
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=38.10 E-value=49 Score=29.02 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=24.1
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
..+||..| |+++..|+++...-|.+.|+..
T Consensus 172 ~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 172 QEQLAQQL----NVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45889999 9999999999877666666554
No 64
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=37.73 E-value=56 Score=27.05 Aligned_cols=31 Identities=16% Similarity=0.104 Sum_probs=24.8
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |++...|+.|...-|.+.|+.-.
T Consensus 144 ~~eIA~~l----gis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 144 YREIAEIL----GVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999999877777665433
No 65
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=37.54 E-value=46 Score=28.53 Aligned_cols=30 Identities=17% Similarity=0.066 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
...+||..+ |++...|++|+..-|.+.|+.
T Consensus 159 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 159 SQSEIAKRL----GIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 456889999 999999999998777766654
No 66
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=36.52 E-value=53 Score=27.74 Aligned_cols=30 Identities=20% Similarity=0.299 Sum_probs=24.0
Q ss_pred HHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
...++|..| |+++..|+++...-|.+.|..
T Consensus 154 s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 154 SLKEISEIL----DLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 345889999 999999999998666666654
No 67
>PRK04217 hypothetical protein; Provisional
Probab=36.26 E-value=93 Score=25.41 Aligned_cols=51 Identities=14% Similarity=0.132 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..++.+++.++...|... + ...+||+.+ |++...|+..+..-+.+.|..-.
T Consensus 41 ~~Lt~eereai~l~~~eG--l----S~~EIAk~L----GIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG--L----TQEEAGKRM----GVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 457889988888777652 2 345899999 99999999999877777666544
No 68
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=36.21 E-value=27 Score=23.40 Aligned_cols=40 Identities=28% Similarity=0.365 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhh
Q 022516 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (296)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (296)
..+|.+++..++.++..+ ....+||+.| |.+...|..|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G------~s~~~IA~~l----g~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG------MSIREIAKRL----GRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT----T--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC------CCHHHHHHHH----CcCcHHHHHHHh
Confidence 467888999999887762 2344799999 999999887764
No 69
>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=36.02 E-value=70 Score=25.89 Aligned_cols=46 Identities=22% Similarity=0.105 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
+++.+..+|.-.|.. .+ ...+||..| |+++..|+++...-|.|.|+
T Consensus 114 L~~~~r~il~l~~~~--~~----~~~eIA~~l----gis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRFE--GK----SYKEIAEEL----GISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 344555555543433 22 244789999 99999999988765555553
No 70
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.95 E-value=64 Score=26.20 Aligned_cols=41 Identities=15% Similarity=0.375 Sum_probs=27.0
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhh
Q 022516 107 RWTPTPVQLQ-ILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (296)
Q Consensus 107 Rt~ft~~Ql~-~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (296)
|..|+.+... ++...+.. .++ ..++|..+ ||+...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~--g~s----v~evA~e~----gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEP--GMT----VSLVARQH----GVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcC--CCC----HHHHHHHH----CcCHHHHHHHHH
Confidence 3456776654 44444443 332 34789999 999999999953
No 71
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=35.89 E-value=72 Score=27.07 Aligned_cols=49 Identities=27% Similarity=0.198 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
+++.+..+|.-.|.. .....+||..| |++...|++++..-|.+.|+.-.
T Consensus 132 L~~~~r~v~~l~~~~------g~s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 132 LPPRQRDVVQSISVE------GASIKETAAKL----SMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCHHHHHHHHHHHHc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhh
Confidence 344455555544433 12345889999 99999999999877777776544
No 72
>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=35.77 E-value=65 Score=26.62 Aligned_cols=47 Identities=15% Similarity=0.087 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 111 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 111 t~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
++.+..+|.-.|.. .+ ..++||..| |++...|+++-..-|.+.|+.-
T Consensus 112 ~~~~r~i~~l~~~~--g~----s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 112 PARQRAVVVLRYYE--DL----SEAQVAEAL----GISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHhhhHHHh--cC----CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHh
Confidence 44555555554433 12 244889999 9999999999987777776654
No 73
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=34.55 E-value=73 Score=26.55 Aligned_cols=49 Identities=12% Similarity=-0.024 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
+++.+..++.-.|-.+ ...++||..| |+++..|++|...-|.+.|+.-.
T Consensus 109 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 109 LPVIEAQAILLCDVHE------LTYEEAASVL----DLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHhHHHhc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555443331 2245889999 99999999999877777666544
No 74
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=34.49 E-value=59 Score=26.93 Aligned_cols=47 Identities=19% Similarity=0.008 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
+++.|..+|.-.|-. .+ ...+||..| |++...|+++...-|.+.|+.
T Consensus 113 L~~~~r~v~~l~~~~--~~----s~~eIA~~l----gis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 113 LPLERRNVLLLRDYY--GF----SYKEIAEMT----GLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHhhhHHhc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHhh
Confidence 555566666555544 12 234889999 999999999987666665543
No 75
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=34.24 E-value=79 Score=27.05 Aligned_cols=50 Identities=14% Similarity=0.234 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
.+++.+..+|+-.|... ....+||..| |+++..|++-...-|.+.|+.-.
T Consensus 131 ~L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE------KSVEEVGEIV----GIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 34455555554444331 2244888999 99999999998877777776544
No 76
>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=33.26 E-value=75 Score=26.81 Aligned_cols=46 Identities=26% Similarity=0.240 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
+++.+..++.-.|..+ ...++||..| |+++..|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG------LTVEEIAELL----GVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4555555555554441 2245889999 99999999999877666665
No 77
>PRK00118 putative DNA-binding protein; Validated
Probab=33.16 E-value=87 Score=25.33 Aligned_cols=48 Identities=19% Similarity=0.215 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
+++.|..++...|..+ + ...+||..+ |++...|+.|...-|.+.|..-
T Consensus 18 L~ekqRevl~L~y~eg--~----S~~EIAe~l----GIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 18 LTEKQRNYMELYYLDD--Y----SLGEIAEEF----NVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 4566777776666552 2 234789999 9999999999987776666543
No 78
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=33.10 E-value=74 Score=26.85 Aligned_cols=50 Identities=16% Similarity=0.052 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
.+++.+..+|.-.|-.. + ..++||..| |+++..|+++-..-|.+.|+.-.
T Consensus 100 ~L~~~~r~v~~l~~~~g--~----s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--L----SQQEIAEKL----GLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666555441 2 245889999 99999999999776666666544
No 79
>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=32.33 E-value=73 Score=26.08 Aligned_cols=46 Identities=15% Similarity=0.233 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
.+++.+..++...|-. ....++||..| |++...|+++...-|.+.|
T Consensus 111 ~L~~~~r~v~~l~~~~------g~~~~eIA~~l----~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 111 KLPERQRELLQLRYQR------GVSLTALAEQL----GRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HCCHHHHHHHHHHHhc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHH
Confidence 3556666666664443 12345899999 9999999988764444443
No 80
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=32.28 E-value=89 Score=26.34 Aligned_cols=29 Identities=10% Similarity=0.281 Sum_probs=23.6
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
.++||..| |+++..|+++...-|.+.|+.
T Consensus 148 ~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 148 YKELAERH----DVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HHHHHHHH----CCChHHHHHHHHHHHHHHHHH
Confidence 45889999 999999999988666666653
No 81
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=32.08 E-value=84 Score=24.08 Aligned_cols=46 Identities=22% Similarity=0.367 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHhh----cCCCCCHHHHHHHHHHHhhcCCcccchhhchhh
Q 022516 108 WTPTPVQLQILESIFDQ----GTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (296)
Q Consensus 108 t~ft~~Ql~~LE~~F~~----~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (296)
|.++.+|+..|...|.. .+.+.+..+...+-..+ ++++..|.-+|.
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~----~~~~~ev~~i~~ 51 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKS----GLPQTLLAKIWN 51 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHc----CCCHHHHHHHHH
Confidence 45788999999999877 23567777766666666 888777776663
No 82
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=32.07 E-value=82 Score=26.06 Aligned_cols=48 Identities=23% Similarity=0.202 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
+++.+..+|.-.| .+ + ...+||..| |++...|+++...-|.+.|+.-.
T Consensus 113 L~~~~r~il~l~~-~g--~----s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 113 MTERDRTVLLLRF-SG--Y----SYKEIAEAL----GIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCHHHHHHHHHHH-cC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 5556666666666 41 2 345889999 99999999999766666666443
No 83
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=31.42 E-value=89 Score=25.63 Aligned_cols=49 Identities=10% Similarity=0.017 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
.+++.+..++.-.|-.+ ++ ..+||..| |++...|++....-|.+.|+.-
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s----~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 106 KLPARQREAFLLRYWED--MD----VAETAAAM----GCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred hCCHHHHHHHHHHHHhc--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 34555555555544441 22 45889999 9999999998876666655543
No 84
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=31.05 E-value=76 Score=27.55 Aligned_cols=31 Identities=16% Similarity=0.027 Sum_probs=25.2
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |++...|+++...-|.+.|+.-.
T Consensus 132 ~~EIA~~L----giS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 132 YEEAAEMC----GVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHh
Confidence 45889999 99999999999877777766544
No 85
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.79 E-value=81 Score=27.07 Aligned_cols=31 Identities=26% Similarity=0.193 Sum_probs=24.1
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |++...|++.+..-|.+.|+.-.
T Consensus 125 ~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 125 QKEIAEKL----GLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred HHHHHHHh----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999999866666665443
No 86
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=30.58 E-value=78 Score=27.03 Aligned_cols=47 Identities=17% Similarity=-0.041 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
.+++.+..++...|.. ....++||..| |++...|+++...-|.+-|+
T Consensus 139 ~L~~~~r~i~~l~~~~------g~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVV------GLSAEETAEAV----GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHc------CCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 3445555555554433 12355889999 99999999998655555554
No 87
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=30.41 E-value=82 Score=26.83 Aligned_cols=31 Identities=13% Similarity=0.078 Sum_probs=24.5
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |++...|+++...-|.+.|+.-.
T Consensus 147 ~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 147 NIEAAAVM----DISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999999766666666544
No 88
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=30.36 E-value=94 Score=20.30 Aligned_cols=40 Identities=33% Similarity=0.390 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNR 159 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNR 159 (296)
.+++.++.++..++ . .+ ...+||..+ +++...|+.|...-
T Consensus 3 ~l~~~e~~i~~~~~-~--g~----s~~eia~~l----~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLA-E--GL----TNKEIAERL----GISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHH-c--CC----CHHHHHHHH----CCCHHHHHHHHHHH
Confidence 36777888776533 3 22 345889999 99999999888643
No 89
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=29.47 E-value=96 Score=25.62 Aligned_cols=28 Identities=21% Similarity=0.064 Sum_probs=20.7
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
..+||..| |+++..|++...--|.+.|+
T Consensus 141 ~~eIA~~l----~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 141 IAEVARIL----GKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 45889999 99999998877544444443
No 90
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.74 E-value=68 Score=25.48 Aligned_cols=39 Identities=18% Similarity=0.118 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNV 152 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV 152 (296)
+++++|+.+-...|+. |--.+.-..+++|..| ++++..|
T Consensus 2 SLn~eq~~~Tk~elqa-n~el~~LS~~~iA~~L----n~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQA-NFELCPLSDEEIATAL----NWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHH-hhhhccccHHHHHHHh----CCCHHHH
Confidence 4678888887777777 5666667778999999 8887543
No 91
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.59 E-value=1.1e+02 Score=26.09 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=22.6
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
.++||..+ |++...|++|-..-|.+.|+
T Consensus 152 ~~eIA~~l----gis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 152 HAEIAQRL----GAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred HHHHHHHH----CCChhhHHHHHHHHHHHHHH
Confidence 45889999 99999999998766665554
No 92
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.27 E-value=1e+02 Score=26.65 Aligned_cols=31 Identities=13% Similarity=-0.009 Sum_probs=24.6
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
.++||..| |++...|+++..--|.+.|+.-.
T Consensus 155 ~~eIA~~l----gis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 155 NPEIAEVM----EIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999999866666666543
No 93
>PRK09480 slmA division inhibitor protein; Provisional
Probab=27.92 E-value=55 Score=27.63 Aligned_cols=40 Identities=15% Similarity=0.371 Sum_probs=30.7
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHH
Q 022516 116 QILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (296)
Q Consensus 116 ~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRa 161 (296)
......|.. ++. ......+||++. |++...++.+|.|+-.
T Consensus 17 ~aa~~l~~~-~~G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 17 QALAQMLES-PPG-ERITTAKLAARV----GVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHh-cCC-CccCHHHHHHHh----CCCHhHHHHHCCCHHH
Confidence 333344554 345 777888999999 9999999999999874
No 94
>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=27.73 E-value=82 Score=26.64 Aligned_cols=31 Identities=10% Similarity=0.038 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 132 QKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 132 ~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
..-.+||..| |+++..|+++...-|.+-|+.
T Consensus 155 ~s~~EIA~~l----gis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 155 LSYEDIARIM----DCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 3456889999 999999999997656555554
No 95
>PRK06930 positive control sigma-like factor; Validated
Probab=27.30 E-value=1.2e+02 Score=26.36 Aligned_cols=50 Identities=16% Similarity=0.110 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
.+++.++.++.-.|..+ + ...+||..| |++...|+++...-|.|.++.-.
T Consensus 114 ~L~~rer~V~~L~~~eg--~----s~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG--L----SYSEIADYL----NIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666554441 1 234889999 99999999999888777776544
No 96
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=27.27 E-value=66 Score=21.49 Aligned_cols=38 Identities=21% Similarity=0.518 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWF 156 (296)
.++.+++..+...+... + .+.+||+.+ |++...|+-++
T Consensus 5 ~~~~~~~~~i~~l~~~G--~----si~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG--M----SIAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC--C----CHHHHHHHH----CcCHHHHHHHH
Confidence 46776777777777772 2 355899999 99999988765
No 97
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=27.26 E-value=90 Score=29.92 Aligned_cols=54 Identities=11% Similarity=0.076 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
.+++.++.+|...|.- .|-.....++||..| |++...|+.+...-+.|.|+.-.
T Consensus 262 ~L~~~~R~vl~lrygL--~~~e~~s~~EIA~~L----gis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGL--LGYEAATLEDVAREI----GLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhcc--CCCCCcCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 5667777777776633 123334456899999 99999999999877777776543
No 98
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=27.24 E-value=40 Score=24.26 Aligned_cols=25 Identities=40% Similarity=0.697 Sum_probs=19.7
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
..+||..| |++.+.|+.|-+ |.+|.
T Consensus 16 ~~eIA~~L----g~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 16 IKEIAEEL----GVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred HHHHHHHH----CCChHHHHHHHH--hhCcc
Confidence 44899999 999999999974 44443
No 99
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.03 E-value=1.2e+02 Score=25.46 Aligned_cols=48 Identities=13% Similarity=0.000 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
+++.+..++.-.|-.+ ....+||..| |+++..|+++...-+.+.+..-
T Consensus 120 Lp~~~r~v~~L~~~~g------~s~~EIA~~l----gis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 120 LSSKARAAFLYNRLDG------MGHAEIAERL----GVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHh
Confidence 3455555555444331 2234889999 9999999999987777776543
No 100
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=26.68 E-value=1.1e+02 Score=26.29 Aligned_cols=30 Identities=20% Similarity=0.153 Sum_probs=24.1
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
..+||..| |+++..|+++...-|.+.|+..
T Consensus 153 ~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 153 SEQICQEC----DISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45889999 9999999999976666666543
No 101
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.22 E-value=1.2e+02 Score=25.03 Aligned_cols=47 Identities=19% Similarity=0.130 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
+++.+..+|.-.|-.. ....+||..| |++...|+.....-|.+.|+.
T Consensus 110 L~~~~r~v~~l~~~~~------~s~~EIA~~l----gis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRLHG------ETQKDIAREL----GVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3445555555444331 1245889999 999999999876555555543
No 102
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.18 E-value=42 Score=22.03 Aligned_cols=20 Identities=15% Similarity=0.172 Sum_probs=16.9
Q ss_pred HHHHHHHHhhcCCcccchhhchhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQ 157 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQ 157 (296)
..++|+.+ |++...|+.|.+
T Consensus 3 ~~e~a~~~----gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLT----GVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHH
Confidence 35788888 999999999964
No 103
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=25.72 E-value=1.4e+02 Score=25.98 Aligned_cols=31 Identities=19% Similarity=0.253 Sum_probs=25.1
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |+++..|++....-|.+-|+.-.
T Consensus 158 ~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 158 IDDICTEL----TLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999998877777666554
No 104
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=25.55 E-value=1.4e+02 Score=25.99 Aligned_cols=31 Identities=10% Similarity=0.005 Sum_probs=24.0
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |++...|+++...-|.+.|+.-.
T Consensus 152 ~~EIAe~l----gis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 152 YEEAAKIA----DVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred HHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhc
Confidence 45889999 99999999998766666555443
No 105
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=25.36 E-value=1.3e+02 Score=25.89 Aligned_cols=49 Identities=10% Similarity=-0.037 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
+++.+..++.-.|.. .+ ...+||..| |+++..|+++...-|.+.|+.-.
T Consensus 117 Lp~~~r~i~~L~~~~--g~----s~~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGAS--GF----AYEEAAEIC----GCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 344455555444333 12 234889999 99999999999877776666544
No 106
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.28 E-value=1.3e+02 Score=25.35 Aligned_cols=29 Identities=14% Similarity=0.040 Sum_probs=22.2
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
..+||..+ |++...|+++...-|.+.|..
T Consensus 154 ~~eIA~~l----gis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 154 HREAAQLL----GLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred HHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 45788889 999999999887656555543
No 107
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.27 E-value=1.4e+02 Score=25.01 Aligned_cols=48 Identities=17% Similarity=0.191 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
+++.+..+|.-.|..+ + ..++||..| |+++..|++....-|.+.|+.-
T Consensus 119 L~~~~r~vl~L~~~~g--~----s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG--W----STAQIAADL----GIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHh
Confidence 4455555555544331 2 245889999 9999999998876665555543
No 108
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.00 E-value=45 Score=22.23 Aligned_cols=21 Identities=38% Similarity=0.838 Sum_probs=16.8
Q ss_pred HHHHHHHHhhcCCcccchhhchhhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQN 158 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQN 158 (296)
..++|..| |++...|..|.+.
T Consensus 20 ~~~ia~~l----gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 20 IREIAKRL----GVSRSTVYRWIKR 40 (50)
T ss_dssp HHHHHHHH----TS-HHHHHHHHT-
T ss_pred HHHHHHHH----CcCHHHHHHHHHH
Confidence 45899999 9999999999754
No 109
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.89 E-value=44 Score=23.35 Aligned_cols=28 Identities=11% Similarity=0.219 Sum_probs=18.0
Q ss_pred HHHHHHHHHhhcCCcccchhhchhhhhHHHHH
Q 022516 133 KIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (296)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (296)
...+||+.+ |++...|..|+.++..+..
T Consensus 12 t~~~La~~~----gis~~tl~~~~~~~~~~~~ 39 (63)
T PF13443_consen 12 TQKDLARKT----GISRSTLSRILNGKPSNPS 39 (63)
T ss_dssp -HHHHHHHH----T--HHHHHHHHTTT-----
T ss_pred CHHHHHHHH----CcCHHHHHHHHhccccccc
Confidence 345889999 9999999999998844433
No 110
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.77 E-value=1.3e+02 Score=25.61 Aligned_cols=48 Identities=21% Similarity=0.155 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
.+++.|..++.-.|..+ + ..++||..| |+++..|++....-+.+.+..
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~----s~~EIA~~l----gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--M----KQKDIAQAL----DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHh
Confidence 35566666666554441 2 245889999 999999999998777776554
No 111
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.63 E-value=1.3e+02 Score=25.01 Aligned_cols=47 Identities=9% Similarity=-0.043 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
+++.+..++.-.|.. ....++||..| |+++..|+++...-|.+-|..
T Consensus 113 L~~~~r~v~~l~~~~------g~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 113 LSADQREAIILIGAS------GFSYEDAAAIC----GCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHHHHHHc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 444555555544433 12345889999 999999999997666665543
No 112
>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=24.18 E-value=1.4e+02 Score=24.90 Aligned_cols=29 Identities=24% Similarity=0.367 Sum_probs=22.9
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
..+||..| |+++..|+++...-|.+.|+.
T Consensus 138 ~~eiA~~l----gis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 138 IKEIAEVM----NKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 45889999 999999999887666666553
No 113
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=24.14 E-value=1.3e+02 Score=25.43 Aligned_cols=30 Identities=17% Similarity=0.037 Sum_probs=24.5
Q ss_pred HHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
...+||..| |+++..|++....-|.+.|+.
T Consensus 147 s~~EIA~~l----~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLT----GLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 355889999 999999999998777776664
No 114
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=24.11 E-value=1.3e+02 Score=25.88 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=25.5
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |++...|+++...-|.+.|+.-.
T Consensus 155 ~~EIA~~l----gis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 155 SDEIQQMC----GISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999999877777776654
No 115
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.99 E-value=1.1e+02 Score=27.71 Aligned_cols=31 Identities=13% Similarity=0.084 Sum_probs=25.1
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |+++..|+++...-|.+.|+.-.
T Consensus 190 ~~EIA~~L----gis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 190 NGEIAEVM----DTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999999877777766544
No 116
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.64 E-value=64 Score=21.39 Aligned_cols=23 Identities=39% Similarity=0.820 Sum_probs=18.8
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRR 160 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRR 160 (296)
..++|..+ ||+..+|..|.+.-+
T Consensus 15 ~~~~a~~~----gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 15 VREIAREF----GISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHH----CCCHhHHHHHHHHHH
Confidence 34789999 999999999986444
No 117
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=23.61 E-value=1.3e+02 Score=25.53 Aligned_cols=32 Identities=22% Similarity=0.226 Sum_probs=26.6
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (296)
..+||..| |+++..|++....-|.+.|+.-..
T Consensus 136 ~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~l~~ 167 (179)
T PRK12543 136 QEEIAQLL----QIPIGTVKSRIHAALKKLRQKEQI 167 (179)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 999999999998888888776544
No 118
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=23.39 E-value=1.6e+02 Score=25.91 Aligned_cols=31 Identities=16% Similarity=0.182 Sum_probs=24.5
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |+++..|+++...-|.+.|+.-.
T Consensus 157 ~~EIA~~L----gis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 157 YEEIAATL----GVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 44788899 99999999999876666666544
No 119
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.01 E-value=1.3e+02 Score=25.70 Aligned_cols=50 Identities=20% Similarity=0.349 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
.+++.+..++.-.|-.+ ...++||..| |++...|++..+.-|.+.|+...
T Consensus 131 ~L~~~~r~i~~l~~~~g------~s~~EIAe~l----gis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG------EKIEEIAKKL----GLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred hCCHHHHHHHHHHHHcc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHccc
Confidence 34555555555444331 2245889999 99999998888766666555443
No 120
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=22.43 E-value=1.6e+02 Score=25.07 Aligned_cols=51 Identities=22% Similarity=0.137 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhhhh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (296)
+++.+..++.-.|-.+ + ...+||..| |+++..|++....-|.+.|+.-...
T Consensus 132 Lp~~~r~v~~l~~~~g--~----s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 132 LPPRTGRVFMMREWLE--L----ETEEICQEL----QITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555444331 2 245889999 9999999999987777766655443
No 121
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.26 E-value=1.5e+02 Score=25.20 Aligned_cols=31 Identities=13% Similarity=0.089 Sum_probs=24.9
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
..+||..| |+++..|++....-|.+-|+.-+
T Consensus 157 ~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 157 YEDIASVM----QCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45889999 99999999999877777666543
No 122
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=22.03 E-value=1.6e+02 Score=25.37 Aligned_cols=49 Identities=16% Similarity=0.074 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
+++.+..++.-.|..+ + ...+||..| |++...|+++...-|.+.|+...
T Consensus 112 Lp~~~R~v~~L~~~eg--~----s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 112 LPEEQRAALHLVAIEG--L----SYQEAAAVL----GIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555544331 2 245889999 99999999998766666555444
No 123
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=22.00 E-value=1.8e+02 Score=25.07 Aligned_cols=30 Identities=7% Similarity=0.071 Sum_probs=22.9
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
.++||..| |++...|++....-|.+.|+.-
T Consensus 160 ~~EIA~~l----gis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 160 HQQVAEMF----DIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HHHHHHHh----CcCHHHHHHHHHHHHHHHHHHh
Confidence 45889999 9999999888866666655543
No 124
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.71 E-value=1.4e+02 Score=25.63 Aligned_cols=28 Identities=4% Similarity=-0.079 Sum_probs=21.8
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (296)
.++||..| |+++..|+++...-|.+.|+
T Consensus 149 ~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 149 YADAAAVC----GCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 45889999 99999999998655555544
No 125
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=21.66 E-value=1.5e+02 Score=24.40 Aligned_cols=45 Identities=22% Similarity=0.211 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~ 163 (296)
.+++.|..++.-.|-.+ ++ ..+||..| |++...|+++...-+.+.
T Consensus 113 ~L~~~~r~v~~L~~~~g--~s----~~EIA~~l----~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--LG----YGEIATEL----GISLATVKRYLNKAAMRC 157 (161)
T ss_pred HCCHHHHHHHHHHHHcC--CC----HHHHHHHH----CCCHHHHHHHHHHHHHHH
Confidence 34566666666655442 22 34889999 999999999886554443
No 126
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.62 E-value=2.7e+02 Score=23.81 Aligned_cols=49 Identities=6% Similarity=-0.079 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHhh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (296)
+++.+..++.-.|.. .....+||..| |+++..|++....-|.+-|+.-.
T Consensus 112 Lp~~~R~v~~L~~~~------g~s~~EIA~~L----gis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 112 LPQDQREALILVGAS------GFSYEDAAAIC----GCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHhhHHHHc------CCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 344444554444433 12345889999 99999999998766666655544
No 127
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=21.38 E-value=1.7e+02 Score=24.90 Aligned_cols=47 Identities=9% Similarity=-0.058 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
+++.+..+++-.|-. .....+||..| |++...|+++...-|.+.|+.
T Consensus 132 L~~~~r~v~~l~~~~------g~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 132 LPEKMRLAIQAVKLE------GLSVAEAATRS----GMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CCHHHHHHHHHHHHc------CCcHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 445555555543333 22345889999 999999999987666666554
No 128
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=21.17 E-value=61 Score=28.60 Aligned_cols=14 Identities=43% Similarity=0.769 Sum_probs=12.5
Q ss_pred ccCCHHHHHHHHHH
Q 022516 41 KVMTDEQLETLRKQ 54 (296)
Q Consensus 41 ~~~t~~~l~~lr~q 54 (296)
+.|||+||+.||.-
T Consensus 48 RTLTDEQI~IFRHS 61 (172)
T PF12720_consen 48 RTLTDEQIEIFRHS 61 (172)
T ss_pred ccccHHHHHHHHHH
Confidence 68999999999965
No 129
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.15 E-value=1.4e+02 Score=26.79 Aligned_cols=31 Identities=26% Similarity=0.311 Sum_probs=25.8
Q ss_pred HHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
...+||..| |++...|+.+...-|.+.|+.-
T Consensus 202 s~~EIA~~l----gis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 202 NLKEIGAVL----GVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 356889999 9999999999988888777653
No 130
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.94 E-value=1.6e+02 Score=24.97 Aligned_cols=48 Identities=21% Similarity=0.212 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHHh
Q 022516 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (296)
Q Consensus 110 ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (296)
+++.+..++.-.|-. ....++||..| |+++..|++....-|.+.|+.-
T Consensus 123 L~~~~r~i~~l~~~~------g~s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 123 LNESNRQVFKYKVFY------NLTYQEISSVM----GITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CCHHHHHHHHHHHHc------CCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 344555555443333 12245889999 9999999998876666665543
No 131
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=20.71 E-value=37 Score=25.82 Aligned_cols=22 Identities=32% Similarity=0.365 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhcCCcccchhhchhhh
Q 022516 133 KIKEITVELSQHGQISETNVYNWFQN 158 (296)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQN 158 (296)
...+||..| ++++..|++|+.+
T Consensus 34 S~kEIAe~L----GIS~~TVk~~l~~ 55 (73)
T TIGR03879 34 TASEIAEEL----GRTEQTVRNHLKG 55 (73)
T ss_pred CHHHHHHHH----CcCHHHHHHHHhc
Confidence 456899999 9999999999864
No 132
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.55 E-value=1.6e+02 Score=26.68 Aligned_cols=48 Identities=17% Similarity=0.156 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
.+++.+..+|.-.|... + ...+||..| |++...|+.|...-+.|.|+.
T Consensus 205 ~L~~~~r~vl~l~~~~g--~----s~~eIA~~l----~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN--L----SQKETGERL----GISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666655441 2 235889999 999999999987666666554
No 133
>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=20.26 E-value=1.8e+02 Score=19.04 Aligned_cols=36 Identities=33% Similarity=0.414 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCcccchhhchhh
Q 022516 111 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (296)
Q Consensus 111 t~~Ql~~LE~~F~~~n~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (296)
++.+..++..++ . .+ ...++|..+ +++...|+.|..
T Consensus 2 ~~~e~~i~~~~~-~--~~----s~~eia~~l----~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA-E--GK----TNKEIADIL----GISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH-c--CC----CHHHHHHHH----CCCHHHHHHHHH
Confidence 455666665433 2 22 345889999 999999999886
No 134
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=20.22 E-value=1.7e+02 Score=25.20 Aligned_cols=29 Identities=21% Similarity=0.230 Sum_probs=22.8
Q ss_pred HHHHHHHHhhcCCcccchhhchhhhhHHHHHHH
Q 022516 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (296)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (296)
..+||..| |++...|++....-|.+.|+.
T Consensus 173 ~~EIA~~l----gis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 173 YQEIAEEL----NRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 45889999 999999998877666666554
Done!