Query 022558
Match_columns 295
No_of_seqs 357 out of 1612
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 04:27:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022558.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022558hhsearch_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 4.6E-48 9.9E-53 368.0 6.0 151 6-167 204-354 (398)
2 KOG1168 Transcription factor A 99.9 6.5E-26 1.4E-30 208.3 1.3 152 7-169 216-371 (385)
3 PF00157 Pou: Pou domain - N-t 99.8 1.9E-21 4.1E-26 147.3 0.9 71 5-75 4-74 (75)
4 KOG0484 Transcription factor P 99.7 1.7E-18 3.7E-23 138.2 6.5 69 98-171 13-81 (125)
5 KOG0489 Transcription factor z 99.7 1E-17 2.2E-22 155.4 7.0 67 100-171 157-223 (261)
6 KOG0488 Transcription factor B 99.7 5.1E-17 1.1E-21 153.9 5.6 67 98-169 168-234 (309)
7 KOG2251 Homeobox transcription 99.7 4.6E-16 1E-20 139.1 11.2 68 97-169 32-99 (228)
8 KOG0842 Transcription factor t 99.6 1.2E-16 2.7E-21 150.1 5.3 69 98-171 149-217 (307)
9 KOG0843 Transcription factor E 99.6 3.4E-16 7.3E-21 136.0 7.4 64 101-169 101-164 (197)
10 KOG0850 Transcription factor D 99.6 4.7E-16 1E-20 139.7 7.5 67 97-168 117-183 (245)
11 PF00046 Homeobox: Homeobox do 99.6 1.1E-15 2.3E-20 109.5 5.9 57 103-164 1-57 (57)
12 KOG0487 Transcription factor A 99.6 3.5E-16 7.6E-21 147.1 4.1 66 100-170 233-298 (308)
13 KOG0492 Transcription factor M 99.6 9.4E-16 2E-20 135.9 5.6 68 97-169 139-206 (246)
14 KOG0485 Transcription factor N 99.6 1.1E-15 2.4E-20 136.2 4.4 68 99-171 101-168 (268)
15 KOG0494 Transcription factor C 99.6 3.3E-15 7.2E-20 136.2 5.1 66 101-171 140-205 (332)
16 KOG4577 Transcription factor L 99.5 8.7E-14 1.9E-18 128.6 12.4 115 50-170 108-230 (383)
17 KOG0848 Transcription factor C 99.5 1.1E-14 2.3E-19 133.4 3.5 67 98-169 195-261 (317)
18 TIGR01565 homeo_ZF_HD homeobox 99.5 8.1E-14 1.8E-18 101.2 4.7 52 103-159 2-57 (58)
19 smart00389 HOX Homeodomain. DN 99.4 1E-13 2.3E-18 98.3 5.2 56 103-163 1-56 (56)
20 smart00352 POU Found in Pit-Oc 99.4 4.2E-14 9.2E-19 107.3 3.3 71 5-75 4-74 (75)
21 cd00086 homeodomain Homeodomai 99.4 1.6E-13 3.5E-18 98.0 6.2 57 104-165 2-58 (59)
22 KOG0847 Transcription factor, 99.4 9.7E-14 2.1E-18 124.1 5.8 82 100-186 165-246 (288)
23 KOG0486 Transcription factor P 99.4 1E-13 2.2E-18 129.5 5.0 68 98-170 108-175 (351)
24 KOG0844 Transcription factor E 99.4 6.2E-14 1.4E-18 130.4 2.7 66 98-168 177-242 (408)
25 KOG0491 Transcription factor B 99.4 1.6E-13 3.4E-18 117.9 3.5 66 101-171 99-164 (194)
26 KOG0493 Transcription factor E 99.4 2.4E-13 5.2E-18 124.2 4.6 60 103-167 247-306 (342)
27 KOG0483 Transcription factor H 99.3 4.9E-13 1.1E-17 119.3 4.0 61 103-168 51-111 (198)
28 COG5576 Homeodomain-containing 99.3 1.2E-12 2.6E-17 112.9 6.0 64 101-169 50-113 (156)
29 KOG0490 Transcription factor, 99.2 3.6E-11 7.9E-16 107.7 5.9 78 84-167 43-120 (235)
30 KOG0849 Transcription factor P 98.9 5.6E-09 1.2E-13 101.1 10.2 66 98-168 172-237 (354)
31 KOG0775 Transcription factor S 98.7 5.3E-08 1.1E-12 90.1 9.3 51 109-164 183-233 (304)
32 KOG0774 Transcription factor P 98.7 9.6E-10 2.1E-14 100.8 -3.8 64 101-168 187-252 (334)
33 PF05920 Homeobox_KN: Homeobox 98.2 9.7E-07 2.1E-11 59.5 2.7 33 125-161 8-40 (40)
34 KOG2252 CCAAT displacement pro 98.1 3.4E-06 7.4E-11 84.6 5.2 57 101-162 419-475 (558)
35 KOG0490 Transcription factor, 97.9 7.5E-06 1.6E-10 73.3 4.1 64 99-167 150-213 (235)
36 KOG1146 Homeobox protein [Gene 97.6 8.8E-05 1.9E-09 80.9 5.5 63 101-168 902-964 (1406)
37 PF11569 Homez: Homeodomain le 95.9 0.0063 1.4E-07 44.0 2.6 42 114-160 10-51 (56)
38 KOG3623 Homeobox transcription 95.7 0.04 8.7E-07 57.7 8.4 52 114-170 568-619 (1007)
39 KOG0773 Transcription factor M 94.9 0.024 5.1E-07 54.5 3.6 63 102-168 239-303 (342)
40 PF04218 CENP-B_N: CENP-B N-te 89.2 1 2.2E-05 31.8 5.0 47 103-159 1-47 (53)
41 PF08880 QLQ: QLQ; InterPro: 84.7 1.3 2.7E-05 29.4 3.1 22 42-63 2-23 (37)
42 PF04545 Sigma70_r4: Sigma-70, 63.6 18 0.0004 24.4 4.6 46 108-163 4-49 (50)
43 KOG3755 SATB1 matrix attachmen 60.7 9 0.0002 40.0 3.6 21 147-167 739-759 (769)
44 PF04967 HTH_10: HTH DNA bindi 60.3 11 0.00023 26.9 2.9 39 109-153 1-42 (53)
45 PF08281 Sigma70_r4_2: Sigma-7 60.2 16 0.00034 25.0 3.8 43 109-161 11-53 (54)
46 cd06171 Sigma70_r4 Sigma70, re 59.5 12 0.00026 24.3 3.0 43 109-161 11-53 (55)
47 PF01527 HTH_Tnp_1: Transposas 56.0 14 0.00031 26.9 3.1 44 104-156 2-45 (76)
48 cd00569 HTH_Hin_like Helix-tur 52.6 37 0.00081 19.4 4.2 37 109-155 6-42 (42)
49 COG3413 Predicted DNA binding 50.6 22 0.00047 31.8 4.1 49 108-164 155-206 (215)
50 PRK09646 RNA polymerase sigma 43.7 44 0.00096 28.9 4.8 48 109-166 143-190 (194)
51 PRK03975 tfx putative transcri 42.5 54 0.0012 28.0 5.0 51 107-168 5-55 (141)
52 PRK06759 RNA polymerase factor 41.9 40 0.00088 27.6 4.1 47 108-164 106-152 (154)
53 PRK09652 RNA polymerase sigma 41.7 48 0.001 27.6 4.6 48 108-165 128-175 (182)
54 KOG1146 Homeobox protein [Gene 41.6 43 0.00093 38.2 5.2 61 101-166 704-764 (1406)
55 PF00196 GerE: Bacterial regul 40.9 46 0.00099 23.2 3.7 45 108-163 3-47 (58)
56 PF10668 Phage_terminase: Phag 40.6 17 0.00037 26.6 1.4 19 133-155 25-43 (60)
57 TIGR02937 sigma70-ECF RNA poly 40.2 50 0.0011 26.0 4.3 46 109-164 111-156 (158)
58 PF13936 HTH_38: Helix-turn-he 39.3 26 0.00057 23.5 2.1 40 107-156 3-42 (44)
59 PRK12526 RNA polymerase sigma 37.9 56 0.0012 28.7 4.6 31 132-166 171-201 (206)
60 PRK04217 hypothetical protein; 36.7 1E+02 0.0022 25.2 5.6 51 107-167 41-91 (110)
61 PRK12533 RNA polymerase sigma 36.6 73 0.0016 28.5 5.2 33 133-169 153-185 (216)
62 KOG3623 Homeobox transcription 36.0 58 0.0012 35.1 4.9 106 44-168 582-687 (1007)
63 PRK12512 RNA polymerase sigma 35.5 72 0.0016 27.0 4.8 49 109-167 132-180 (184)
64 PRK12519 RNA polymerase sigma 35.4 51 0.0011 28.2 3.9 31 131-165 158-188 (194)
65 PRK11924 RNA polymerase sigma 35.4 66 0.0014 26.6 4.5 30 133-166 144-173 (179)
66 PF00424 REV: REV protein (ant 34.8 44 0.00096 26.5 3.0 37 114-169 14-50 (91)
67 PRK00118 putative DNA-binding 34.5 79 0.0017 25.6 4.5 47 109-165 18-64 (104)
68 PRK09642 RNA polymerase sigma 34.2 87 0.0019 25.8 5.0 48 109-166 107-154 (160)
69 PF06056 Terminase_5: Putative 34.1 28 0.00061 25.1 1.7 20 133-156 16-35 (58)
70 PRK12514 RNA polymerase sigma 33.2 82 0.0018 26.6 4.8 29 133-165 148-176 (179)
71 TIGR02999 Sig-70_X6 RNA polyme 32.8 77 0.0017 26.7 4.5 46 109-164 135-180 (183)
72 TIGR02948 SigW_bacill RNA poly 31.9 74 0.0016 26.8 4.3 30 132-165 154-183 (187)
73 PRK09648 RNA polymerase sigma 31.4 83 0.0018 26.8 4.5 47 108-164 139-185 (189)
74 PRK12515 RNA polymerase sigma 31.4 86 0.0019 26.8 4.6 49 109-167 132-180 (189)
75 smart00421 HTH_LUXR helix_turn 31.3 1E+02 0.0022 20.1 4.1 41 108-159 3-43 (58)
76 PRK09413 IS2 repressor TnpA; R 31.2 95 0.0021 25.2 4.6 41 106-156 10-51 (121)
77 TIGR02985 Sig70_bacteroi1 RNA 30.8 1E+02 0.0022 24.9 4.8 46 109-164 114-159 (161)
78 PRK09480 slmA division inhibit 30.7 50 0.0011 27.9 3.0 37 118-160 20-56 (194)
79 PRK09644 RNA polymerase sigma 29.7 84 0.0018 26.2 4.2 49 109-167 109-157 (165)
80 smart00027 EH Eps15 homology d 29.3 1.1E+02 0.0024 23.4 4.6 46 107-156 2-51 (96)
81 TIGR02983 SigE-fam_strep RNA p 29.0 1E+02 0.0023 25.3 4.6 47 110-166 112-158 (162)
82 TIGR02989 Sig-70_gvs1 RNA poly 28.9 91 0.002 25.5 4.2 46 108-163 111-156 (159)
83 PRK12541 RNA polymerase sigma 28.8 90 0.002 25.8 4.2 46 109-164 113-158 (161)
84 PF02796 HTH_7: Helix-turn-hel 28.7 71 0.0015 21.3 2.9 38 108-155 5-42 (45)
85 PF13384 HTH_23: Homeodomain-l 28.5 40 0.00087 22.5 1.7 22 132-157 19-40 (50)
86 PRK09639 RNA polymerase sigma 28.5 1E+02 0.0022 25.4 4.5 47 109-166 113-159 (166)
87 TIGR02959 SigZ RNA polymerase 28.3 1.1E+02 0.0023 25.9 4.7 50 108-167 100-149 (170)
88 PRK12537 RNA polymerase sigma 28.1 1.1E+02 0.0024 26.0 4.7 28 133-164 152-179 (182)
89 cd04761 HTH_MerR-SF Helix-Turn 28.1 42 0.00091 22.0 1.7 20 133-156 3-22 (49)
90 PRK05602 RNA polymerase sigma 27.7 96 0.0021 26.4 4.3 31 133-167 147-177 (186)
91 PRK09047 RNA polymerase factor 27.0 1.3E+02 0.0027 24.7 4.8 47 109-165 107-153 (161)
92 PRK09637 RNA polymerase sigma 26.9 1.1E+02 0.0024 26.2 4.5 49 109-167 107-155 (181)
93 PRK06930 positive control sigm 26.8 1.1E+02 0.0024 26.6 4.5 50 108-167 114-163 (170)
94 PRK12546 RNA polymerase sigma 26.6 1.1E+02 0.0023 26.6 4.5 31 133-167 132-162 (188)
95 COG4367 Uncharacterized protei 26.4 83 0.0018 25.0 3.2 40 108-152 2-41 (97)
96 PRK12530 RNA polymerase sigma 25.9 1.2E+02 0.0025 26.2 4.5 29 133-165 153-181 (189)
97 PRK12536 RNA polymerase sigma 25.7 1.2E+02 0.0026 25.7 4.5 30 132-165 147-176 (181)
98 PRK05657 RNA polymerase sigma 25.4 1.1E+02 0.0025 29.2 4.7 54 108-167 262-315 (325)
99 TIGR02939 RpoE_Sigma70 RNA pol 25.1 96 0.0021 26.2 3.8 31 131-165 155-185 (190)
100 TIGR02952 Sig70_famx2 RNA poly 24.9 1.4E+02 0.003 24.6 4.7 28 133-164 141-168 (170)
101 PRK12543 RNA polymerase sigma 24.8 1.3E+02 0.0028 25.4 4.6 32 133-168 136-167 (179)
102 PF13443 HTH_26: Cro/C1-type H 24.5 51 0.0011 23.0 1.6 27 132-162 12-38 (63)
103 PRK12547 RNA polymerase sigma 24.3 1.4E+02 0.0029 25.0 4.5 47 109-165 113-159 (164)
104 PRK12523 RNA polymerase sigma 23.7 1.6E+02 0.0036 24.6 5.0 48 109-166 120-167 (172)
105 PRK07037 extracytoplasmic-func 23.5 1.5E+02 0.0032 24.4 4.6 47 109-165 110-156 (163)
106 PRK12529 RNA polymerase sigma 23.5 1.4E+02 0.003 25.4 4.5 48 108-165 127-174 (178)
107 PRK12524 RNA polymerase sigma 23.5 1.5E+02 0.0032 25.6 4.7 31 133-167 155-185 (196)
108 TIGR02954 Sig70_famx3 RNA poly 23.4 1.4E+02 0.0031 24.8 4.5 30 132-165 137-166 (169)
109 PF00376 MerR: MerR family reg 22.9 59 0.0013 21.3 1.6 19 133-155 2-20 (38)
110 PF13518 HTH_28: Helix-turn-he 22.3 76 0.0016 21.0 2.1 23 133-159 15-37 (52)
111 cd04762 HTH_MerR-trunc Helix-T 22.1 65 0.0014 20.5 1.7 23 133-159 3-25 (49)
112 PRK12538 RNA polymerase sigma 21.9 1.2E+02 0.0027 27.3 4.1 31 133-167 190-220 (233)
113 PRK06986 fliA flagellar biosyn 21.8 1.4E+02 0.003 26.8 4.3 30 132-165 202-231 (236)
114 PRK12532 RNA polymerase sigma 21.8 1.5E+02 0.0033 25.4 4.4 31 133-167 155-185 (195)
115 PF13411 MerR_1: MerR HTH fami 21.8 55 0.0012 23.2 1.4 19 133-155 3-21 (69)
116 PRK12516 RNA polymerase sigma 21.6 1.7E+02 0.0038 25.2 4.8 31 133-167 135-165 (187)
117 TIGR03879 near_KaiC_dom probab 21.4 42 0.00091 25.5 0.7 23 131-157 33-55 (73)
118 PRK06811 RNA polymerase factor 21.4 1.5E+02 0.0033 25.4 4.3 49 109-167 132-180 (189)
119 PRK13919 putative RNA polymera 21.3 1.8E+02 0.0038 24.6 4.7 29 133-165 154-182 (186)
120 cd06170 LuxR_C_like C-terminal 21.2 1.9E+02 0.0042 18.9 4.0 36 110-156 2-37 (57)
121 PRK10072 putative transcriptio 21.0 58 0.0013 25.9 1.5 40 109-160 33-72 (96)
122 PRK09645 RNA polymerase sigma 20.9 2E+02 0.0043 24.0 4.9 47 109-165 119-165 (173)
123 PRK12531 RNA polymerase sigma 20.2 2E+02 0.0043 24.7 4.8 29 133-165 160-188 (194)
124 PRK12539 RNA polymerase sigma 20.1 2E+02 0.0044 24.4 4.8 47 109-165 132-178 (184)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=4.6e-48 Score=368.04 Aligned_cols=151 Identities=20% Similarity=0.232 Sum_probs=134.1
Q ss_pred HHHHHHHHHHhhhhhhhhcCCccCCCcccccccccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccchhcccCCC
Q 022558 6 IREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGRLG 85 (295)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~g~~~s~~~i~~l~~qi~~~~~ic~~~~~~~k~ls~~~~~~sg~~~g 85 (295)
..||||||||+||||||||||||+|||+|+|+|||||||||+||||||++++|+||||+++++.|||++++...+...
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~-- 281 (398)
T KOG3802|consen 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGS-- 281 (398)
T ss_pred CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCC--
Confidence 368999999999999999999999999999999999999999999999999999999999999999999887432221
Q ss_pred CcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 86 NIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 86 ~~~~~p~~~s~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
.|.+.... ...++||+||.|+...+..||++|.. |++|+.++|..||.+| +|++.+|+|||||||+|+||.
T Consensus 282 --~~~~e~i~--a~~RkRKKRTSie~~vr~aLE~~F~~-npKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 282 --PNSIEKIG--AQSRKRKKRTSIEVNVRGALEKHFLK-NPKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred --CCCHHHhh--ccccccccccceeHHHHHHHHHHHHh-CCCCCHHHHHHHHHHh----ccccceEEEEeeccccccccC
Confidence 12222222 22267889999999999999999999 7999999999999999 999999999999999999998
Q ss_pred hh
Q 022558 166 QL 167 (295)
Q Consensus 166 ~~ 167 (295)
..
T Consensus 353 ~~ 354 (398)
T KOG3802|consen 353 TP 354 (398)
T ss_pred CC
Confidence 76
No 2
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.91 E-value=6.5e-26 Score=208.35 Aligned_cols=152 Identities=16% Similarity=0.165 Sum_probs=125.4
Q ss_pred HHHHHHHHHhhhhhhhhcCCccCCCccccccc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccchhcc-c
Q 022558 7 REAAQQETQTQNQNQNQRGGENDNNNVVNGVM---YVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAA-G 82 (295)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~---~g~~~s~~~i~~l~~qi~~~~~ic~~~~~~~k~ls~~~~~~sg-~ 82 (295)
-.|||-||..|||||||||-||+|||-|+.-| -+-.+||.+|||||.+.++-.||.-+++-++.||+++....-- .
T Consensus 216 PReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~ 295 (385)
T KOG1168|consen 216 PRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKD 295 (385)
T ss_pred HHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhc
Confidence 46899999999999999999999999665444 5778999999999999999999999999999999877542211 1
Q ss_pred CCCCcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHH
Q 022558 83 RLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 162 (295)
Q Consensus 83 ~~g~~~~~p~~~s~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~ 162 (295)
..+ ... .. ..++ -+||+||.+.....+.||.+|.. .+.|+.+.|..||++| +|.+.+|+|||||.|+|.
T Consensus 296 ~~p--d~~-~l-~~~~--ekKRKRTSIAAPEKRsLEayFav-QPRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQ 364 (385)
T KOG1168|consen 296 TKP--DIN-EL-LPGG--EKKRKRTSIAAPEKRSLEAYFAV-QPRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQ 364 (385)
T ss_pred cCC--chh-hc-cCcc--ccccccccccCcccccHHHHhcc-CCCCchhHHHHHHHhh----hhhhceEEEEeeccHHHH
Confidence 110 000 11 1123 35789999999999999999999 8999999999999999 999999999999999999
Q ss_pred HHHhhhh
Q 022558 163 KRKQLVS 169 (295)
Q Consensus 163 Kr~~~~~ 169 (295)
||.....
T Consensus 365 KRm~~Sa 371 (385)
T KOG1168|consen 365 KRMKRSA 371 (385)
T ss_pred HHhhhhh
Confidence 9976654
No 3
>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=99.82 E-value=1.9e-21 Score=147.33 Aligned_cols=71 Identities=13% Similarity=0.128 Sum_probs=66.0
Q ss_pred hHHHHHHHHHHhhhhhhhhcCCccCCCcccccccccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhccc
Q 022558 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAH 75 (295)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~g~~~s~~~i~~l~~qi~~~~~ic~~~~~~~k~ls~~ 75 (295)
...+||++||+.||||||++||||+|||.++|.+||++|||++|||||++++++++||+.+|.+.+|+.++
T Consensus 4 ~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~ea 74 (75)
T PF00157_consen 4 PDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhc
Confidence 35689999999999999999999999999999999999999999999999999999999999999999764
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.75 E-value=1.7e-18 Score=138.18 Aligned_cols=69 Identities=32% Similarity=0.494 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhcc
Q 022558 98 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 171 (295)
Q Consensus 98 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~~ 171 (295)
..++.||-||+|+..||..||+.|.. ++||++..|++||.++ .|++..|+|||||||+|.||+.+....
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 999999999999999999999887644
No 5
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=1e-17 Score=155.37 Aligned_cols=67 Identities=33% Similarity=0.384 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhcc
Q 022558 100 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 171 (295)
Q Consensus 100 ~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~~ 171 (295)
...||.||.||..|+.+||+.|.. |+|.++.+|.+||..| .|+|+||+|||||||+||||..+....
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 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.67 E-value=5.1e-17 Score=153.92 Aligned_cols=67 Identities=28% Similarity=0.354 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 98 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 98 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
..+++|+.||.||..||..||+.|++ .+|.+..+|.+||..| ||+..||++||||||+||||.....
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 44778889999999999999999999 7999999999999999 9999999999999999999988774
No 7
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.66 E-value=4.6e-16 Score=139.05 Aligned_cols=68 Identities=35% Similarity=0.574 Sum_probs=64.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 97 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 97 g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
.+.++.||.||+|+..|+.+||.+|.+ ++||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
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 367889999999999999999999999 8999999999999999 9999999999999999999998875
No 8
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.64 E-value=1.2e-16 Score=150.06 Aligned_cols=69 Identities=29% Similarity=0.388 Sum_probs=64.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhcc
Q 022558 98 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 171 (295)
Q Consensus 98 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~~ 171 (295)
+.+++||.|..|+..|+.+||+.|.+ ++|++.++|++||..| .||++||||||||||.|.||+++....
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 34567778899999999999999999 8999999999999999 999999999999999999999988755
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.64 E-value=3.4e-16 Score=136.02 Aligned_cols=64 Identities=38% Similarity=0.447 Sum_probs=61.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 101 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
+.||.||.|+.+||..||.+|+. ++|....+|+.||..| +|++.||+|||||||.|.||.+.+.
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 10
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.63 E-value=4.7e-16 Score=139.68 Aligned_cols=67 Identities=31% Similarity=0.405 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 97 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 97 g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
++.+|.|++||.++.-||..|.+.|++ ++|+..++|.+||..| ||+.+||+|||||||.|.||..+.
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 466788899999999999999999999 7999999999999999 999999999999999999998883
No 11
>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=1.1e-15 Score=109.45 Aligned_cols=57 Identities=42% Similarity=0.663 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 103 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 103 rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
||+|+.|+.+|+.+|+.+|.. ++||+..++..||..| ||+..+|++||+|||+++||
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 12
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.60 E-value=3.5e-16 Score=147.08 Aligned_cols=66 Identities=29% Similarity=0.321 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhc
Q 022558 100 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 170 (295)
Q Consensus 100 ~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~ 170 (295)
+..|+||..+|+.|+.+||+.|.. |.|.+.+.|.+|+..| +|+++||+|||||||+|.||..++..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf-N~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF-NMYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH-HHHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhhh
Confidence 567889999999999999999999 8999999999999999 99999999999999999999987543
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.60 E-value=9.4e-16 Score=135.87 Aligned_cols=68 Identities=37% Similarity=0.428 Sum_probs=63.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 97 GGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 97 g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
.+++..|++||.||..||..||+.|.. .+|.++.+|.+++..| .|+++||+|||||||+|.||.+...
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 378888999999999999999999999 7999999999999999 9999999999999999999987753
No 14
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.58 E-value=1.1e-15 Score=136.20 Aligned_cols=68 Identities=29% Similarity=0.356 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhcc
Q 022558 99 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 171 (295)
Q Consensus 99 ~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~~ 171 (295)
..++||.||+|+..|+..||..|+. .+|.+..+|.-||.+| .|++.||+|||||||.||||+-...-.
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~-krYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFEL-KRYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHH-HhhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 3467789999999999999999999 7999999999999999 999999999999999999998776544
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.55 E-value=3.3e-15 Score=136.18 Aligned_cols=66 Identities=24% Similarity=0.314 Sum_probs=60.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhcc
Q 022558 101 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 171 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~~ 171 (295)
++|+-||.||..|+..||+.|+. .+||+...|+.||.++ .|.+.+|+|||||||+||||..+.-..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFke-aHYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~wg~ 205 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKE-AHYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRWGG 205 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhh-ccCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence 34444999999999999999999 6999999999999999 999999999999999999999887533
No 16
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.53 E-value=8.7e-14 Score=128.62 Aligned_cols=115 Identities=23% Similarity=0.308 Sum_probs=88.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccccchhcccCCCCcccCCCcc--------CCCCCCCCCCCCCCCCHHHHHHHHHHH
Q 022558 50 TLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGRLGNIYCDPLMT--------SGGGHKISARQRWTPTPVQLQILESIF 121 (295)
Q Consensus 50 ~l~~qi~~~~~ic~~~~~~~k~ls~~~~~~sg~~~g~~~~~p~~~--------s~g~~~~~rR~Rt~ft~~Ql~~LE~~F 121 (295)
.-+||-.+|---|-+.+--.+.|..-+.+. .+..+-..|..-.. ...+....||+||++|..||..|+.+|
T Consensus 108 VRkAqd~VYHl~CF~C~iC~R~L~TGdEFY-LmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AY 186 (383)
T KOG4577|consen 108 VRKAQDFVYHLHCFACFICKRQLATGDEFY-LMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAY 186 (383)
T ss_pred HHHhhcceeehhhhhhHhhhcccccCCeeE-EeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHh
Confidence 357888899888888776666665554433 23223333432110 111445678999999999999999999
Q ss_pred hhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhc
Q 022558 122 DQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 170 (295)
Q Consensus 122 ~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~ 170 (295)
.. .++|.+..|++|+... ||.-++|||||||||||+||.++.+.
T Consensus 187 n~-SpKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 187 NT-SPKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred cC-CCchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhcc
Confidence 99 5999999999999999 99999999999999999999888753
No 17
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.49 E-value=1.1e-14 Score=133.38 Aligned_cols=67 Identities=27% Similarity=0.347 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 98 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 98 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
+.+.+-+-|.++|..|+.+||+.|.. .+|.++.++.+||..| +|+|+||+|||||||+|+||..++.
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh~-SryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFHT-SRYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhcc-ccceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 33444456889999999999999999 6999999999999999 9999999999999999999988876
No 18
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.45 E-value=8.1e-14 Score=101.25 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=50.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHHhhcCCCccchhhhhhhhhh
Q 022558 103 ARQRWTPTPVQLQILESIFDQGTGT----PSKQKIKEITVELSQHGQISETNVYNWFQNRR 159 (295)
Q Consensus 103 rR~Rt~ft~~Ql~~LE~~F~~~n~~----Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRR 159 (295)
||.||.||.+|+..||..|+. ++| |+..+|.+||..| ||++.+|+|||||.+
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 799 9999999999999 999999999999975
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.45 E-value=1e-13 Score=98.32 Aligned_cols=56 Identities=43% Similarity=0.629 Sum_probs=52.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHH
Q 022558 103 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 163 (295)
Q Consensus 103 rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~K 163 (295)
++.|+.|+..|+.+|+.+|.. ++||+..++..||..| ||+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~-~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQK-NPYPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 356788999999999999999 7999999999999999 9999999999999998854
No 20
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=99.45 E-value=4.2e-14 Score=107.26 Aligned_cols=71 Identities=11% Similarity=0.126 Sum_probs=67.6
Q ss_pred hHHHHHHHHHHhhhhhhhhcCCccCCCcccccccccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhccc
Q 022558 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAH 75 (295)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~g~~~g~~~s~~~i~~l~~qi~~~~~ic~~~~~~~k~ls~~ 75 (295)
....|+|.|+..|+++|+++|+||++|+-++|++||..+||.+|++|++.+++++++|+..|.+.+|+.+.
T Consensus 4 ~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~ 74 (75)
T smart00352 4 TDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhc
Confidence 44578999999999999999999999999999999999999999999999999999999999999999764
No 21
>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=99.45 E-value=1.6e-13 Score=97.97 Aligned_cols=57 Identities=44% Similarity=0.653 Sum_probs=53.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 104 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 104 R~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
+.|+.++..++.+||.+|.. ++||+..++..||..| ||++.+|++||+|||++.++.
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 56788999999999999999 7999999999999999 999999999999999998864
No 22
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.44 E-value=9.7e-14 Score=124.07 Aligned_cols=82 Identities=29% Similarity=0.400 Sum_probs=67.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhccccccCCCC
Q 022558 100 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSANTLHNGG 179 (295)
Q Consensus 100 ~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~~~~~~~~gg 179 (295)
.+++..|.+|+-.|+..||+.|++ ++|+-.++|.+||..| ++++.+|+|||||||.||||+...+.......+.+
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 355667889999999999999999 8999999999999999 99999999999999999999988765544444444
Q ss_pred CCCCCCC
Q 022558 180 GGGAGAG 186 (295)
Q Consensus 180 ~g~~~~~ 186 (295)
+.+-+.+
T Consensus 240 ~ae~~~g 246 (288)
T KOG0847|consen 240 GAERGAG 246 (288)
T ss_pred ccccccc
Confidence 4433333
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.43 E-value=1e-13 Score=129.46 Aligned_cols=68 Identities=32% Similarity=0.424 Sum_probs=64.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhc
Q 022558 98 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 170 (295)
Q Consensus 98 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~ 170 (295)
+.+++||.||.|+..||..||.+|.+ |.||+...|++||.-. +|++..|+|||.|||+||||+++-..
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 24
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.42 E-value=6.2e-14 Score=130.40 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 98 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 98 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
....-||.||.||.+|+..||+.|-+ .-|-+++.|.+||..| +|.+..|+|||||||+|+||+...
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 33457899999999999999999999 4699999999999999 999999999999999999998766
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.39 E-value=1.6e-13 Score=117.94 Aligned_cols=66 Identities=32% Similarity=0.408 Sum_probs=61.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhcc
Q 022558 101 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 171 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~~ 171 (295)
++++-||+|+..|+..||+.|+. .+|.+.++|.+||..| +|+++||+.||||||+|.||.++....
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 45677999999999999999999 7999999999999999 999999999999999999999887543
No 26
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.39 E-value=2.4e-13 Score=124.23 Aligned_cols=60 Identities=33% Similarity=0.476 Sum_probs=56.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 103 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 103 rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
||+||.|+.+||..|+..|+. |+|.+...|.+||.+| +|.+.||+|||||+|+|-||..-
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 99999999999999999998543
No 27
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.35 E-value=4.9e-13 Score=119.28 Aligned_cols=61 Identities=34% Similarity=0.480 Sum_probs=56.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 103 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 103 rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
.+++.+|+.+|+..||..|+. +.+..+.++..||..| ||.++||.|||||||||||.++..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~-~~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFES-EKKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred ccccccccHHHHHHhHHhhcc-ccccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhh
Confidence 345567899999999999999 7999999999999999 999999999999999999998876
No 28
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.34 E-value=1.2e-12 Score=112.90 Aligned_cols=64 Identities=30% Similarity=0.421 Sum_probs=58.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 101 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
..+++|++.+..|+.+|++.|+. ++||+...|..|+..| +|+++.|++||||||++.|+.....
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 45667777799999999999999 7999999999999999 9999999999999999999976653
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.16 E-value=3.6e-11 Score=107.71 Aligned_cols=78 Identities=28% Similarity=0.331 Sum_probs=66.2
Q ss_pred CCCcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHH
Q 022558 84 LGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 163 (295)
Q Consensus 84 ~g~~~~~p~~~s~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~K 163 (295)
.|..+|....... ...++||.|+.|+..|+.+||+.|+. ++||+...|+.||..+ .+++..|+|||||||+||+
T Consensus 43 ~g~~~~~~d~~~~-~~~~~rr~rt~~~~~ql~~ler~f~~-~h~Pd~~~r~~la~~~----~~~e~rVqvwFqnrrak~r 116 (235)
T KOG0490|consen 43 DGSIYCKRDYQRE-FKFSKRCARCKFTISQLDELERAFEK-VHLPCFACRECLALLL----TGDEFRVQVWFQNRRAKDR 116 (235)
T ss_pred CCcccccccchhh-hhccccccCCCCCcCHHHHHHHhhcC-CCcCccchHHHHhhcC----CCCeeeeehhhhhhcHhhh
Confidence 4555555433321 24567889999999999999999999 7999999999999999 9999999999999999999
Q ss_pred HHhh
Q 022558 164 RKQL 167 (295)
Q Consensus 164 r~~~ 167 (295)
+..+
T Consensus 117 ~~~~ 120 (235)
T KOG0490|consen 117 KEER 120 (235)
T ss_pred hhhc
Confidence 9875
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.92 E-value=5.6e-09 Score=101.05 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 98 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 98 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
..++.+|.||+|+..|+..||+.|+. ++||+...|+.||.++ ++++..|+|||+|||+|++|....
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 44567778999999999999999999 7899999999999999 999999999999999999998854
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.73 E-value=5.3e-08 Score=90.05 Aligned_cols=51 Identities=27% Similarity=0.440 Sum_probs=46.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
|...-+..|..+|.+ ++||+..++.+||+.+ ||+..||-+||+|||+|+|-
T Consensus 183 FKekSR~~LrewY~~-~~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ-NPYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhc-CCCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhhh
Confidence 344456799999999 7999999999999999 99999999999999999993
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.67 E-value=9.6e-10 Score=100.85 Aligned_cols=64 Identities=27% Similarity=0.388 Sum_probs=58.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhh--cCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 101 ISARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~--~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
..||+|..|++.-..+|..+|.. .|+||+.+.+++||+++ +++..||-+||.|+|-+.||....
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 45788999999999999999976 67999999999999999 999999999999999999986443
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=98.21 E-value=9.7e-07 Score=59.53 Aligned_cols=33 Identities=33% Similarity=0.598 Sum_probs=28.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHH
Q 022558 125 TGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 161 (295)
Q Consensus 125 n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK 161 (295)
+|||+.+++..||.++ ||+..||..||-|.|.|
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 99999999999999875
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.10 E-value=3.4e-06 Score=84.59 Aligned_cols=57 Identities=30% Similarity=0.483 Sum_probs=53.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHH
Q 022558 101 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 162 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~ 162 (295)
..||+|.+||..|++.|..+|+. +++|+.+..+.|+.+| +|....|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke-~~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE-NKRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc-CCCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 56778999999999999999999 8999999999999999 999999999999988775
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.95 E-value=7.5e-06 Score=73.28 Aligned_cols=64 Identities=34% Similarity=0.525 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 99 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 99 ~~~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..+.++.|+.+...|+..|+..|.. +++|+...+..|+..+ +++...|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRA-TPKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccC-CCCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 3467788999999999999999999 7999999999999999 99999999999999999998765
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.57 E-value=8.8e-05 Score=80.86 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=58.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 101 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
.+|+.|+.++..||.+|..+|.. ..||...+++.|-..+ +++.++|+|||||-|+|.|+....
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 46789999999999999999999 7999999999999999 999999999999999999997763
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.92 E-value=0.0063 Score=43.98 Aligned_cols=42 Identities=21% Similarity=0.405 Sum_probs=30.8
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhH
Q 022558 114 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 160 (295)
Q Consensus 114 l~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRa 160 (295)
+.-|+.+|.. .+.+...+...|..+. +|+..+|+.||--|+.
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 3459999999 7999999999999999 9999999999976644
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=95.74 E-value=0.04 Score=57.72 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=47.5
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhhc
Q 022558 114 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 170 (295)
Q Consensus 114 l~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~~ 170 (295)
+..|..+|.. |..|+..+...||.++ ||+.++|++||++++++..+.++...
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 6788999999 7999999999999999 99999999999999999988876554
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.89 E-value=0.024 Score=54.45 Aligned_cols=63 Identities=21% Similarity=0.228 Sum_probs=50.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh--cCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 102 SARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 102 ~rR~Rt~ft~~Ql~~LE~~F~~--~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
..|++..+......+|+.+... ..+||+..++..||.++ ||+..+|.+||-|.|-|..+-...
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 4455567888889999987433 23799999999999999 999999999999998876654443
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=89.24 E-value=1 Score=31.82 Aligned_cols=47 Identities=19% Similarity=0.271 Sum_probs=35.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhh
Q 022558 103 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRR 159 (295)
Q Consensus 103 rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRR 159 (295)
+|+|..+|-++...+-..++.+ . ....||..+ |++..+|..|..|+.
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 4788999999988888888873 3 356899999 999999999998863
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=84.68 E-value=1.3 Score=29.39 Aligned_cols=22 Identities=36% Similarity=0.501 Sum_probs=19.7
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 022558 42 VMTDEQLETLRKQIAVYATICE 63 (295)
Q Consensus 42 ~~s~~~i~~l~~qi~~~~~ic~ 63 (295)
.||.+|+..||+||..|+-+.+
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 5899999999999999987665
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=63.60 E-value=18 Score=24.44 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 163 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~K 163 (295)
.+++.+..+|...|.. . + ...+||..| |++...|+.+...-..|-|
T Consensus 4 ~L~~~er~vi~~~y~~-~-~----t~~eIa~~l----g~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-G-L----TLEEIAERL----GISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS-T------SHHHHHHHH----TSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-C-C----CHHHHHHHH----CCcHHHHHHHHHHHHHHhc
Confidence 4678899999999855 2 2 245889999 9999999888765555544
No 43
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=60.68 E-value=9 Score=39.98 Aligned_cols=21 Identities=38% Similarity=0.691 Sum_probs=17.0
Q ss_pred ccchhhhhhhhhhHHHHHHhh
Q 022558 147 SETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 147 s~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..+.|+.||.|||+++||.+.
T Consensus 739 ~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 739 ESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhcchHHHHHHHHHHHhhhhc
Confidence 445789999999999998654
No 44
>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=60.32 E-value=11 Score=26.94 Aligned_cols=39 Identities=28% Similarity=0.365 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHH---HHHHHHHHHhhcCCCccchhhh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQ---KIKEITVELSQHGQISETNVYN 153 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~---~r~~LA~~L~~~~~Ls~~~V~v 153 (295)
+|+.|+.+|...|+. .|-+.+ ...+||..| |++...|..
T Consensus 1 LT~~Q~e~L~~A~~~--GYfd~PR~~tl~elA~~l----gis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYEL--GYFDVPRRITLEELAEEL----GISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHc--CCCCCCCcCCHHHHHHHh----CCCHHHHHH
Confidence 478899999999988 355544 456899999 999976543
No 45
>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=60.18 E-value=16 Score=24.98 Aligned_cols=43 Identities=28% Similarity=0.255 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 161 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK 161 (295)
+++.+..++.-.|..+ ....+||..+ |+++..|++|.+.-|.+
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 4566777777766652 2345889999 99999999999754443
No 46
>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=59.49 E-value=12 Score=24.28 Aligned_cols=43 Identities=19% Similarity=0.224 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 161 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK 161 (295)
+++.+..++...|..+ + ...++|..+ |++...|+.|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~--~----~~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG--L----SYEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 5677788888777552 2 345789999 99999999998655443
No 47
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=55.96 E-value=14 Score=26.90 Aligned_cols=44 Identities=25% Similarity=0.376 Sum_probs=27.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhh
Q 022558 104 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 156 (295)
Q Consensus 104 R~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQ 156 (295)
++|..|++++...+-..+.. ....+.++|..+ ||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~-----~g~sv~~va~~~----gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE-----SGESVSEVAREY----GISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH-----HHCHHHHHHHHH----TS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH-----CCCceEeeeccc----ccccccccHHHH
Confidence 45677898877766555533 124567899999 999999999974
No 48
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=52.56 E-value=37 Score=19.39 Aligned_cols=37 Identities=24% Similarity=0.508 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 155 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWF 155 (295)
++......+...|.. .+ ...++|..+ +++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~--~~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA--GE----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHhC
Confidence 456666666666655 23 345788899 99999998884
No 49
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=50.64 E-value=22 Score=31.79 Aligned_cols=49 Identities=29% Similarity=0.268 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHH---HHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKI---KEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r---~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
.+|..|+.+|..+|.. .|-+.+.+ .+||++| |+++.. +|..=|||..|-
T Consensus 155 ~LTdrQ~~vL~~A~~~--GYFd~PR~~~l~dLA~~l----GISkst--~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKM--GYFDYPRRVSLKDLAKEL----GISKST--LSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHc--CCCCCCccCCHHHHHHHh----CCCHHH--HHHHHHHHHHHH
Confidence 6899999999999998 46666654 6789999 999975 455556665543
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=43.66 E-value=44 Score=28.86 Aligned_cols=48 Identities=15% Similarity=0.133 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
+++.+..+|.-.|..+ ....+||..| |++...|+++...-|.+-|+.-
T Consensus 143 L~~~~r~vl~l~~~~~------~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAYYGG------LTYREVAERL----AVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCChHhHHHHHHHHHHHHHHHh
Confidence 4555566665544441 2345889999 9999999999976666666543
No 51
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=42.53 E-value=54 Score=27.99 Aligned_cols=51 Identities=22% Similarity=0.178 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 107 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 107 t~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
..+++.|+.+|... .. .+ ...+||..| |++...|..|-...+.|.|+....
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 56789999999884 34 22 234899999 999999999999888777765544
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=41.93 E-value=40 Score=27.55 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
.+++.+..++.-.|..+ ....+||..| |++...|++|...-|.|-|+
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 34555666665555441 2356889999 99999999998765555544
No 53
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.71 E-value=48 Score=27.56 Aligned_cols=48 Identities=13% Similarity=-0.011 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
.+++.++.+|.-.|..+ + ...+||..| |++...|+.|...-+.+.|+.
T Consensus 128 ~L~~~~r~vl~l~~~~~--~----s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG--L----SYEEIAEIM----GCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666655441 2 234889999 999999999998666666554
No 54
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=41.59 E-value=43 Score=38.18 Aligned_cols=61 Identities=26% Similarity=0.346 Sum_probs=53.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 101 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 101 ~~rR~Rt~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
+.++.|..+-.+++.+|-.+|-. +--|+...+..|.... ..+.+++.+||+|-|.|.++..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~-~~sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQ-DNSPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccC-CCCHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 44567788888999999999999 6789999999999888 8999999999999999988876
No 55
>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=40.89 E-value=46 Score=23.17 Aligned_cols=45 Identities=27% Similarity=0.228 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 163 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~K 163 (295)
.+|+.++.+|.-+..- + ...+||..| ++++..|+.+..+=+.|..
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 4788888888877654 2 345899999 9999999999887666643
No 56
>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=40.59 E-value=17 Score=26.64 Aligned_cols=19 Identities=32% Similarity=0.693 Sum_probs=16.7
Q ss_pred HHHHHHHHhhcCCCccchhhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWF 155 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWF 155 (295)
-.+||.+| |+++.+|+.|=
T Consensus 25 lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred HHHHHHHH----CCCHHHHHHHh
Confidence 34789999 99999999995
No 57
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=40.22 E-value=50 Score=25.98 Aligned_cols=46 Identities=22% Similarity=0.215 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
+++.+..+|...|.. .+ ...+||..+ |+++..|+.|...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~~~--g~----s~~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE--GL----SYKEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 456666666555443 12 345889999 99999999998876666554
No 58
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.25 E-value=26 Score=23.47 Aligned_cols=40 Identities=28% Similarity=0.365 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhh
Q 022558 107 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 156 (295)
Q Consensus 107 t~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQ 156 (295)
..+|.+++..++.++..+ ....+||..| |.+...|..|..
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 457888899999888762 2345789999 999999988764
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=37.86 E-value=56 Score=28.66 Aligned_cols=31 Identities=13% Similarity=0.137 Sum_probs=24.4
Q ss_pred HHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 132 KIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 132 ~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
...+||..| |+++..|+++...-|.+.|+..
T Consensus 171 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQL----NVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 345889999 9999999999877666666544
No 60
>PRK04217 hypothetical protein; Provisional
Probab=36.65 E-value=1e+02 Score=25.16 Aligned_cols=51 Identities=14% Similarity=0.132 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 107 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 107 t~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..++.+++.++...|... + ...+||+.| +++...|+..+..-+.+.|..-.
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 457888888888877652 2 456899999 99999999999877777666543
No 61
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=36.57 E-value=73 Score=28.53 Aligned_cols=33 Identities=15% Similarity=0.080 Sum_probs=26.0
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
.++||..| |+++..|+++...-|.+.|+.-...
T Consensus 153 ~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 153 YREIAAIA----DVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHccc
Confidence 45889999 9999999999987777777665443
No 62
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=36.04 E-value=58 Score=35.15 Aligned_cols=106 Identities=19% Similarity=0.275 Sum_probs=60.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccchhcccCCCCcccCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhh
Q 022558 44 TDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGRLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQ 123 (295)
Q Consensus 44 s~~~i~~l~~qi~~~~~ic~~~~~~~k~ls~~~~~~sg~~~g~~~~~p~~~s~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~ 123 (295)
+.+++.-+..|+..-....+.|.+-.+.-+-.-. + .|.+.++ . ..-+.|+.....+-..|..+++.
T Consensus 582 s~eelskia~qvglp~~vvk~wfE~~~a~e~sv~-----r------sps~psg-~--~p~kv~sp~k~~dq~ql~~a~el 647 (1007)
T KOG3623|consen 582 SEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE-----R------SPSQPSG-E--RPVKVRSPIKEEDQQQLKQAYEL 647 (1007)
T ss_pred CHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc-----c------CccCCCC-C--CCccccCCCCccchhhhHhhhhc
Confidence 5566666666666655555555543332111100 0 0111111 1 12334455556666667777777
Q ss_pred cCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 124 GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 124 ~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
+-.++-.+-..++..| ...+.+|.|||++|+..-+....-
T Consensus 648 -q~s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 648 -QASPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred -ccCccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCccc
Confidence 4555555555666777 888899999999999877665443
No 63
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=35.46 E-value=72 Score=27.04 Aligned_cols=49 Identities=27% Similarity=0.198 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
+++.+..+|.-.|.. .....+||..| |++...|++++..-|.+.|+.-.
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 344445555544433 12345889999 99999999999877777776543
No 64
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=35.41 E-value=51 Score=28.23 Aligned_cols=31 Identities=16% Similarity=0.047 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 131 QKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 131 ~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
....+||..| |++...|++|+..-|.+.|+.
T Consensus 158 ~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 158 LSQSEIAKRL----GIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 3456889999 999999999997766666654
No 65
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=35.35 E-value=66 Score=26.63 Aligned_cols=30 Identities=17% Similarity=0.139 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
..+||..| |++...|+.|..--|.+.|+.-
T Consensus 144 ~~eIA~~l----gis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 144 YREIAEIL----GVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45889999 9999999999987777666543
No 66
>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=34.81 E-value=44 Score=26.55 Aligned_cols=37 Identities=22% Similarity=0.346 Sum_probs=21.0
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhhh
Q 022558 114 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 169 (295)
Q Consensus 114 l~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~~ 169 (295)
+.+..-.|+. |+||...- -+..= .|||.+||+++.+-
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 3455556777 89998531 11111 68999999988773
No 67
>PRK00118 putative DNA-binding protein; Validated
Probab=34.47 E-value=79 Score=25.58 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
+++.|..++.-.|..+ + ...+||..+ |++...|+.|...-|.+.|..
T Consensus 18 L~ekqRevl~L~y~eg--~----S~~EIAe~l----GIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLDD--Y----SLGEIAEEF----NVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 4566777776666552 2 245789999 999999999998766665553
No 68
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=34.20 E-value=87 Score=25.83 Aligned_cols=48 Identities=13% Similarity=0.066 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
+++.+..++.-.|..+ + ...+||..| |+++..|++....-|.+-|+.-
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 3445555555544441 1 234889999 9999999999987777666643
No 69
>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=34.11 E-value=28 Score=25.05 Aligned_cols=20 Identities=45% Similarity=0.831 Sum_probs=17.7
Q ss_pred HHHHHHHHhhcCCCccchhhhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQ 156 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQ 156 (295)
..+||..| |++...|+.|-+
T Consensus 16 ~~eIA~~L----g~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEEL----GVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHH----CCChHHHHHHHH
Confidence 45899999 999999999974
No 70
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=33.18 E-value=82 Score=26.55 Aligned_cols=29 Identities=10% Similarity=0.281 Sum_probs=23.5
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
.++||..| |+++..|+++...-|.+.|+.
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 55889999 999999999988666666553
No 71
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=32.79 E-value=77 Score=26.71 Aligned_cols=46 Identities=26% Similarity=0.240 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
+++.+..++.-.|..+ ...++||..| |+++..|++....-|.+-|+
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 2345889999 99999999999877666655
No 72
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=31.91 E-value=74 Score=26.82 Aligned_cols=30 Identities=20% Similarity=0.299 Sum_probs=24.0
Q ss_pred HHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 132 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 132 ~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
..++||..| |++...|+++.+.-|.+-|..
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 73
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=31.41 E-value=83 Score=26.84 Aligned_cols=47 Identities=19% Similarity=0.014 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
.+++.+..++.-.|-.+ ...++||..| |++...|+++...-|.+-|+
T Consensus 139 ~L~~~~r~i~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVVG------LSAEETAEAV----GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 34555555555544431 2355889999 99999999998655555554
No 74
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=31.37 E-value=86 Score=26.82 Aligned_cols=49 Identities=14% Similarity=0.239 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
+++.+..+|.-.|-.+ ....+||..| |+++..|++-...-|.+.|+.-.
T Consensus 132 L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 132 LSPAHREIIDLVYYHE------KSVEEVGEIV----GIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555444331 2344789999 99999999998877777776544
No 75
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=31.32 E-value=1e+02 Score=20.11 Aligned_cols=41 Identities=32% Similarity=0.366 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhh
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRR 159 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRR 159 (295)
.+++.+..++..++ . .+ ...+||..+ +++...|+.|...-+
T Consensus 3 ~l~~~e~~i~~~~~-~--g~----s~~eia~~l----~is~~tv~~~~~~~~ 43 (58)
T smart00421 3 SLTPREREVLRLLA-E--GL----TNKEIAERL----GISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHHHH-c--CC----CHHHHHHHH----CCCHHHHHHHHHHHH
Confidence 35777777776543 3 22 345889999 999999999887443
No 76
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=31.23 E-value=95 Score=25.19 Aligned_cols=41 Identities=15% Similarity=0.375 Sum_probs=27.1
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhh
Q 022558 106 RWTPTPVQLQ-ILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 156 (295)
Q Consensus 106 Rt~ft~~Ql~-~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQ 156 (295)
|..++.++.. ++...+.. .. ...++|..+ |++...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~--g~----sv~evA~e~----gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEP--GM----TVSLVARQH----GVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcC--CC----CHHHHHHHH----CcCHHHHHHHHH
Confidence 3446776654 44444443 23 244789999 999999999953
No 77
>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=30.82 E-value=1e+02 Score=24.87 Aligned_cols=46 Identities=22% Similarity=0.105 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
+++.+..+|.-.|.. .+ ...+||..| |+++..|+++...-|.|.|+
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 344555555554433 12 344789999 99999999988755555543
No 78
>PRK09480 slmA division inhibitor protein; Provisional
Probab=30.75 E-value=50 Score=27.87 Aligned_cols=37 Identities=11% Similarity=0.348 Sum_probs=29.3
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhH
Q 022558 118 ESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 160 (295)
Q Consensus 118 E~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRa 160 (295)
...|.. ++. .......||+.. |++...++.+|.|+-.
T Consensus 20 ~~l~~~-~~G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 20 AQMLES-PPG-ERITTAKLAARV----GVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHh-cCC-CccCHHHHHHHh----CCCHhHHHHHCCCHHH
Confidence 334544 345 777888999999 9999999999999763
No 79
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=29.69 E-value=84 Score=26.16 Aligned_cols=49 Identities=12% Similarity=-0.024 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
+++.+..+|.-.|-.+ ...++||..| |+++..|++|..--|.+-|+.-.
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 4455555555443331 2345889999 99999999999866666666543
No 80
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.29 E-value=1.1e+02 Score=23.35 Aligned_cols=46 Identities=22% Similarity=0.367 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHHHhh----cCCCCCHHHHHHHHHHHhhcCCCccchhhhhhh
Q 022558 107 WTPTPVQLQILESIFDQ----GTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 156 (295)
Q Consensus 107 t~ft~~Ql~~LE~~F~~----~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQ 156 (295)
|.++.+++..|...|.. .+.+.+..+...+-..+ ++++..|..+|.
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 23466777666665566 788877777663
No 81
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=28.99 E-value=1e+02 Score=25.32 Aligned_cols=47 Identities=15% Similarity=0.087 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 110 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 110 t~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
++.+..+|.-.|.. .+ ..++||..| |++...|+++-..-|.+-|+.-
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 345889999 9999999999887777766643
No 82
>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=28.89 E-value=91 Score=25.49 Aligned_cols=46 Identities=17% Similarity=0.288 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 163 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~K 163 (295)
.+++.+..++.-.|-.+ ...++||..| |++...|+++...-|.+-|
T Consensus 111 ~L~~~~r~v~~l~~~~g------~~~~eIA~~l----~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG------VSLTALAEQL----GRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HCCHHHHHHHHHHHhcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHH
Confidence 35566666666644431 2345889999 9999999988754444433
No 83
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=28.76 E-value=90 Score=25.80 Aligned_cols=46 Identities=20% Similarity=0.023 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
+++.|..+|.-.|..+ + ...+||..| |++...|+++...-|.+-|+
T Consensus 113 L~~~~r~v~~l~~~~~--~----s~~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG--F----SYKEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 5555666665555441 2 245889999 99999999998766666554
No 84
>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=28.66 E-value=71 Score=21.32 Aligned_cols=38 Identities=21% Similarity=0.518 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhh
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 155 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWF 155 (295)
.++.++...+-.++..+ + .+.+||..+ |++...|+.++
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 35666677777777762 2 356889999 99999998776
No 85
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=28.48 E-value=40 Score=22.49 Aligned_cols=22 Identities=36% Similarity=0.801 Sum_probs=16.9
Q ss_pred HHHHHHHHHhhcCCCccchhhhhhhh
Q 022558 132 KIKEITVELSQHGQISETNVYNWFQN 157 (295)
Q Consensus 132 ~r~~LA~~L~~~~~Ls~~~V~vWFQN 157 (295)
...+||..| |++...|..|.+.
T Consensus 19 s~~~ia~~l----gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRL----GVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHH----TS-HHHHHHHHT-
T ss_pred CHHHHHHHH----CcCHHHHHHHHHH
Confidence 345889999 9999999999754
No 86
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=28.48 E-value=1e+02 Score=25.41 Aligned_cols=47 Identities=23% Similarity=0.227 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
+++.+..+|.-.| .+ + ...+||..| |++...|+++...-|.+.|+.-
T Consensus 113 L~~~~r~il~l~~-~g--~----s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-SG--Y----SYKEIAEAL----GIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-cC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 4556666666666 42 2 345889999 9999999999976666666643
No 87
>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=28.31 E-value=1.1e+02 Score=25.85 Aligned_cols=50 Identities=16% Similarity=0.052 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
.+++.+..+|.-.|..+ + ..++||..| |+++..|+++-..-|.+.|+.-.
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 45566666666655441 2 345889999 99999999998766666666544
No 88
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.09 E-value=1.1e+02 Score=26.04 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=22.4
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
.++||..| |++...|++|-..-|.+-|+
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 99999999998766655554
No 89
>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=28.08 E-value=42 Score=22.03 Aligned_cols=20 Identities=15% Similarity=0.172 Sum_probs=17.0
Q ss_pred HHHHHHHHhhcCCCccchhhhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQ 156 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQ 156 (295)
..++|+.+ |++...|+.|.+
T Consensus 3 ~~e~a~~~----gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLT----GVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHH
Confidence 45788888 999999999964
No 90
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=27.69 E-value=96 Score=26.38 Aligned_cols=31 Identities=13% Similarity=0.078 Sum_probs=24.2
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..+||..| |++...|+++...-|.+-|+.-.
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 99999999999766666665444
No 91
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.00 E-value=1.3e+02 Score=24.69 Aligned_cols=47 Identities=11% Similarity=0.037 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
+++.+..++.-.|-.+ + ...+||..| |++...|++....-|.+.|+.
T Consensus 107 Lp~~~r~v~~l~~~~g--~----s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 107 LPARQREAFLLRYWED--M----DVAETAAAM----GCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred CCHHHHHHHHHHHHhc--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 4455555555544441 2 245889999 999999999887666665554
No 92
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=26.86 E-value=1.1e+02 Score=26.21 Aligned_cols=49 Identities=18% Similarity=0.032 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
+++.++.+|.-.|-. .....+||..| |++...|+..+..-|.+.|+.-.
T Consensus 107 L~~~~r~i~~l~~~~------g~~~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 107 LPEKYAEALRLTELE------GLSQKEIAEKL----GLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CCHHHHHHHHHHHhc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 344444555444333 12345889999 99999999999766666665443
No 93
>PRK06930 positive control sigma-like factor; Validated
Probab=26.83 E-value=1.1e+02 Score=26.56 Aligned_cols=50 Identities=16% Similarity=0.108 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
.+++.++.+|.-.|..+ ....+||..| |++...|+++...-|.|.++.-.
T Consensus 114 ~L~~rer~V~~L~~~eg------~s~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG------LSYSEIADYL----NIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666544441 1245789999 99999999999887777776543
No 94
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=26.65 E-value=1.1e+02 Score=26.58 Aligned_cols=31 Identities=16% Similarity=0.027 Sum_probs=24.9
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..+||..| |++...|+++...-|.+-|+.-.
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 99999999999877777666543
No 95
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.39 E-value=83 Score=25.03 Aligned_cols=40 Identities=18% Similarity=0.092 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhh
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVY 152 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~ 152 (295)
+++++|+.+-...|+. |--.+.-..++||..| ++++..|.
T Consensus 2 SLn~eq~~~Tk~elqa-n~el~~LS~~~iA~~L----n~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQA-NFELCPLSDEEIATAL----NWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHH-hhhhccccHHHHHHHh----CCCHHHHH
Confidence 3567777766666666 5555556677899999 88886543
No 96
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.88 E-value=1.2e+02 Score=26.16 Aligned_cols=29 Identities=21% Similarity=0.177 Sum_probs=23.4
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
..+||..| |+++..|+++...-|.+-|+.
T Consensus 153 ~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 153 SEQICQEC----DISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 45889999 999999999997666665554
No 97
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.66 E-value=1.2e+02 Score=25.71 Aligned_cols=30 Identities=17% Similarity=0.037 Sum_probs=24.5
Q ss_pred HHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 132 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 132 ~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
..++||..| |++...|++....-|.+.|+.
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 455889999 999999999998777776664
No 98
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=25.39 E-value=1.1e+02 Score=29.24 Aligned_cols=54 Identities=11% Similarity=0.076 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
.+++.++.+|...|.- .+-.....++||..| |++...|+.+...-+.|-|+.-.
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 4667777777776633 123334557899999 99999999999877777776543
No 99
>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=25.06 E-value=96 Score=26.18 Aligned_cols=31 Identities=10% Similarity=0.038 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 131 QKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 131 ~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
....+||..| |+++..|+++...-|.+-|+.
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 999999999997666555554
No 100
>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=24.93 E-value=1.4e+02 Score=24.62 Aligned_cols=28 Identities=21% Similarity=0.064 Sum_probs=20.6
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHH
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKR 164 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr 164 (295)
..+||..| |+++..|++...--|.+-|+
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 99999998887544444443
No 101
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=24.80 E-value=1.3e+02 Score=25.44 Aligned_cols=32 Identities=22% Similarity=0.226 Sum_probs=26.3
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 168 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~~ 168 (295)
..+||..| |++...|++....-|++.|+.-..
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 999999999998888887775443
No 102
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.48 E-value=51 Score=23.01 Aligned_cols=27 Identities=11% Similarity=0.225 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhcCCCccchhhhhhhhhhHHH
Q 022558 132 KIKEITVELSQHGQISETNVYNWFQNRRARS 162 (295)
Q Consensus 132 ~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~ 162 (295)
....||+.+ |++...|..|+.++..+.
T Consensus 12 t~~~La~~~----gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKT----GISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHH----T--HHHHHHHHTTT----
T ss_pred CHHHHHHHH----CcCHHHHHHHHhcccccc
Confidence 345889999 999999999999884443
No 103
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=24.26 E-value=1.4e+02 Score=24.97 Aligned_cols=47 Identities=9% Similarity=-0.043 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
+++.+..++.-.|.. ....++||..| |++...|+++...-|.+-|..
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 344455555444433 12355889999 999999999997666665543
No 104
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.73 E-value=1.6e+02 Score=24.59 Aligned_cols=48 Identities=13% Similarity=0.000 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 166 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~ 166 (295)
+++.+..++.-.|..+ ....+||..| |++...|+++...-+.+.+..-
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 3455555555544331 1244889999 9999999999987777776543
No 105
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=23.54 E-value=1.5e+02 Score=24.40 Aligned_cols=47 Identities=19% Similarity=0.117 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
+++.+..+|.-.|-.+ + ...+||..| |++...|+....--|.+.|+.
T Consensus 110 L~~~~r~v~~l~~~~~--~----s~~EIA~~l----gis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRLHG--E----TQKDIAREL----GVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3445555555444331 1 245889999 999999999876555555543
No 106
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=23.54 E-value=1.4e+02 Score=25.37 Aligned_cols=48 Identities=21% Similarity=0.155 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 108 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 108 ~ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
.+++.|+.++.-.|..+ + ..++||..| |+++..|++....-+.+.+..
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 35566666666555442 1 245889999 999999999998777776553
No 107
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.51 E-value=1.5e+02 Score=25.57 Aligned_cols=31 Identities=13% Similarity=-0.009 Sum_probs=24.5
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
.++||..| |++...|+++..--|.+.|+.-.
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 99999999999866666665443
No 108
>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=23.45 E-value=1.4e+02 Score=24.80 Aligned_cols=30 Identities=23% Similarity=0.356 Sum_probs=23.1
Q ss_pred HHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 132 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 132 ~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
...+||..| |++...|+++..--|.+-|+.
T Consensus 137 s~~eiA~~l----gis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVM----NKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 345889999 999999999887666665553
No 109
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=22.93 E-value=59 Score=21.26 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=15.3
Q ss_pred HHHHHHHHhhcCCCccchhhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWF 155 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWF 155 (295)
+.++|+.+ |++.+.|+.|=
T Consensus 2 i~e~A~~~----gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLL----GVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHH----TS-HHHHHHHH
T ss_pred HHHHHHHH----CCCHHHHHHHH
Confidence 45788999 99999999884
No 110
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.27 E-value=76 Score=21.02 Aligned_cols=23 Identities=39% Similarity=0.820 Sum_probs=18.8
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRR 159 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRR 159 (295)
..++|..+ +++..+|..|.+.-+
T Consensus 15 ~~~~a~~~----gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 15 VREIAREF----GISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHH----CCCHhHHHHHHHHHH
Confidence 44789999 999999999986443
No 111
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=22.08 E-value=65 Score=20.54 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=18.9
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRR 159 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRR 159 (295)
..++|..| +++...|..|.++.+
T Consensus 3 ~~e~a~~l----gvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELL----GVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHHcCC
Confidence 35788899 999999999987543
No 112
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=21.91 E-value=1.2e+02 Score=27.32 Aligned_cols=31 Identities=13% Similarity=0.084 Sum_probs=24.9
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..+||..| |+++..|+++...-|.+-|+.-.
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 99999999999877777666543
No 113
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.80 E-value=1.4e+02 Score=26.75 Aligned_cols=30 Identities=27% Similarity=0.339 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 132 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 132 ~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
...+||..| |++...|+.+...-|.+.|+.
T Consensus 202 s~~EIA~~l----gis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 202 NLKEIGAVL----GVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 356889999 999999999998888777764
No 114
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=21.77 E-value=1.5e+02 Score=25.40 Aligned_cols=31 Identities=19% Similarity=0.112 Sum_probs=25.1
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..+||..| |++...|+++...-|.+-|+.-.
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 99999999999877777666543
No 115
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=21.76 E-value=55 Score=23.21 Aligned_cols=19 Identities=26% Similarity=0.328 Sum_probs=16.5
Q ss_pred HHHHHHHHhhcCCCccchhhhhh
Q 022558 133 IKEITVELSQHGQISETNVYNWF 155 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWF 155 (295)
+.++|+.+ |++...|+.|=
T Consensus 3 i~eva~~~----gvs~~tlr~y~ 21 (69)
T PF13411_consen 3 IKEVAKLL----GVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHHT----TTTHHHHHHHH
T ss_pred HHHHHHHH----CcCHHHHHHHH
Confidence 45788888 99999999994
No 116
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=21.63 E-value=1.7e+02 Score=25.17 Aligned_cols=31 Identities=10% Similarity=-0.010 Sum_probs=24.8
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
..+||..| |+++..|+++...-|.+-|+.-.
T Consensus 135 ~~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 135 YEEAAEIC----GCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 44889999 99999999999877766666544
No 117
>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=21.40 E-value=42 Score=25.53 Aligned_cols=23 Identities=30% Similarity=0.371 Sum_probs=19.7
Q ss_pred HHHHHHHHHHhhcCCCccchhhhhhhh
Q 022558 131 QKIKEITVELSQHGQISETNVYNWFQN 157 (295)
Q Consensus 131 ~~r~~LA~~L~~~~~Ls~~~V~vWFQN 157 (295)
-...+||..| ++++..|++|+.+
T Consensus 33 lS~kEIAe~L----GIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEIAEEL----GRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHH----CcCHHHHHHHHhc
Confidence 3456899999 9999999999875
No 118
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.40 E-value=1.5e+02 Score=25.36 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHHhh
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 167 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~~~ 167 (295)
+++.+..++.-.|-.+ ...++||+.| |++...|++..+--|.+-|+...
T Consensus 132 L~~~~r~i~~l~~~~g------~s~~EIAe~l----gis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 132 LEKLDREIFIRRYLLG------EKIEEIAKKL----GLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred CCHHHHHHHHHHHHcc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHccc
Confidence 4555555555444331 2245889999 99999998888766666555443
No 119
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.35 E-value=1.8e+02 Score=24.58 Aligned_cols=29 Identities=14% Similarity=0.040 Sum_probs=22.0
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
.++||..+ |++...|+++...-|.+-|..
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 999999999887655555543
No 120
>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=21.15 E-value=1.9e+02 Score=18.87 Aligned_cols=36 Identities=33% Similarity=0.414 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhh
Q 022558 110 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 156 (295)
Q Consensus 110 t~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQ 156 (295)
+..+..++..++ . .+ ...++|+.+ +++...|+.|..
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 445666665533 2 22 345889999 999999999886
No 121
>PRK10072 putative transcriptional regulator; Provisional
Probab=21.04 E-value=58 Score=25.91 Aligned_cols=40 Identities=18% Similarity=0.191 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 160 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRa 160 (295)
.+...+..|...-.. + ..+||..+ |++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~gl-----T---Q~elA~~l----GvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGL-----K---IDDFARVL----GVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCC-----C---HHHHHHHh----CCCHHHHHHHHcCCCC
Confidence 356556666442222 2 45889999 9999999999988764
No 122
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=20.94 E-value=2e+02 Score=23.99 Aligned_cols=47 Identities=17% Similarity=0.206 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
+++.+..+|.-.|-.+ + ..++||..| |+++..|++....-|.+-|+.
T Consensus 119 L~~~~r~vl~L~~~~g--~----s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG--W----STAQIAADL----GIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 4455555555544331 2 245889999 999999999887555555553
No 123
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.25 E-value=2e+02 Score=24.73 Aligned_cols=29 Identities=7% Similarity=0.085 Sum_probs=22.5
Q ss_pred HHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 133 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 133 r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
.++||..| |++...|++....-|.+.|+.
T Consensus 160 ~~EIA~~l----gis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 160 HQQVAEMF----DIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HHHHHHHh----CcCHHHHHHHHHHHHHHHHHH
Confidence 45889999 999999988886666655553
No 124
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.06 E-value=2e+02 Score=24.40 Aligned_cols=47 Identities=9% Similarity=-0.058 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHhhcCCCccchhhhhhhhhhHHHHHH
Q 022558 109 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 165 (295)
Q Consensus 109 ft~~Ql~~LE~~F~~~n~~Ps~~~r~~LA~~L~~~~~Ls~~~V~vWFQNRRaK~Kr~ 165 (295)
+++.+..+++-.|-. .....+||..| |++...|+.+...-|.+-|+.
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 12345889999 999999999987666665553
Done!