Query 022944
Match_columns 289
No_of_seqs 360 out of 1609
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 07:17:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022944.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022944hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802 Transcription factor O 100.0 1.4E-38 3.1E-43 301.4 6.1 151 6-168 204-354 (398)
2 KOG1168 Transcription factor A 99.8 9.7E-20 2.1E-24 166.7 2.0 153 7-170 216-371 (385)
3 KOG2251 Homeobox transcription 99.8 4.9E-18 1.1E-22 150.7 10.7 71 95-170 29-99 (228)
4 KOG0484 Transcription factor P 99.8 1.2E-18 2.7E-23 137.9 6.1 70 99-173 13-82 (125)
5 KOG0489 Transcription factor z 99.7 3.1E-18 6.7E-23 158.1 7.2 68 101-173 157-224 (261)
6 KOG0850 Transcription factor D 99.7 2.9E-17 6.3E-22 146.5 7.2 68 97-169 116-183 (245)
7 KOG0842 Transcription factor t 99.7 3.9E-17 8.4E-22 152.6 7.9 71 99-174 149-219 (307)
8 KOG0488 Transcription factor B 99.7 2E-17 4.4E-22 155.9 6.1 67 99-170 168-234 (309)
9 KOG0843 Transcription factor E 99.7 7.8E-17 1.7E-21 139.0 7.0 64 102-170 101-164 (197)
10 KOG4577 Transcription factor L 99.7 2.2E-16 4.9E-21 144.7 8.3 115 51-172 109-231 (383)
11 KOG0492 Transcription factor M 99.6 1.5E-16 3.2E-21 140.1 5.6 66 99-169 140-205 (246)
12 KOG0487 Transcription factor A 99.6 9.7E-17 2.1E-21 150.0 4.3 66 100-170 232-297 (308)
13 PF00046 Homeobox: Homeobox do 99.6 7E-16 1.5E-20 109.9 5.8 57 104-165 1-57 (57)
14 KOG0494 Transcription factor C 99.6 5.3E-16 1.1E-20 140.5 6.4 68 99-171 136-204 (332)
15 KOG0485 Transcription factor N 99.6 4.8E-16 1E-20 137.6 4.3 69 99-172 100-168 (268)
16 KOG0848 Transcription factor C 99.5 2.3E-15 4.9E-20 136.9 3.1 63 103-170 199-261 (317)
17 KOG0844 Transcription factor E 99.5 9.1E-15 2E-19 135.1 3.4 66 99-169 177-242 (408)
18 smart00389 HOX Homeodomain. DN 99.5 5.7E-14 1.2E-18 99.2 5.2 56 104-164 1-56 (56)
19 cd00086 homeodomain Homeodomai 99.5 9.7E-14 2.1E-18 98.7 6.0 57 105-166 2-58 (59)
20 TIGR01565 homeo_ZF_HD homeobox 99.5 7.2E-14 1.6E-18 100.8 5.1 52 104-160 2-57 (58)
21 KOG0486 Transcription factor P 99.4 6.2E-14 1.3E-18 130.1 4.6 68 99-171 108-175 (351)
22 KOG0493 Transcription factor E 99.4 8E-14 1.7E-18 126.5 4.4 59 104-167 247-305 (342)
23 KOG0847 Transcription factor, 99.4 1.2E-13 2.7E-18 122.6 4.8 69 101-174 165-233 (288)
24 KOG0491 Transcription factor B 99.4 7.6E-14 1.7E-18 119.0 2.1 67 102-173 99-165 (194)
25 KOG0483 Transcription factor H 99.4 2.2E-13 4.7E-18 120.9 3.9 63 103-170 50-112 (198)
26 COG5576 Homeodomain-containing 99.4 6.8E-13 1.5E-17 113.8 5.9 64 101-169 49-112 (156)
27 PF00157 Pou: Pou domain - N-t 99.4 1.1E-13 2.3E-18 104.4 0.1 70 5-74 4-73 (75)
28 KOG0490 Transcription factor, 99.2 1.1E-11 2.4E-16 110.6 5.4 105 55-168 16-120 (235)
29 KOG0849 Transcription factor P 99.0 4.2E-10 9E-15 108.3 4.9 66 99-169 172-237 (354)
30 KOG0775 Transcription factor S 98.8 1.3E-08 2.9E-13 93.3 8.5 49 111-164 184-232 (304)
31 KOG0774 Transcription factor P 98.6 5.2E-09 1.1E-13 95.5 -0.3 63 103-169 188-252 (334)
32 smart00352 POU Found in Pit-Oc 98.6 3.6E-08 7.7E-13 74.5 2.4 69 5-73 4-72 (75)
33 PF05920 Homeobox_KN: Homeobox 98.3 5E-07 1.1E-11 60.5 2.5 33 126-162 8-40 (40)
34 KOG2252 CCAAT displacement pro 98.0 1.1E-05 2.3E-10 80.7 7.2 57 102-163 419-475 (558)
35 KOG0490 Transcription factor, 98.0 5.8E-06 1.3E-10 73.7 3.9 64 100-168 150-213 (235)
36 KOG1146 Homeobox protein [Gene 97.5 0.00013 2.9E-09 79.1 5.4 63 102-169 902-964 (1406)
37 KOG3623 Homeobox transcription 96.3 0.019 4.2E-07 59.6 8.9 52 115-171 568-619 (1007)
38 PF11569 Homez: Homeodomain le 96.2 0.0031 6.8E-08 45.2 2.0 42 115-161 10-51 (56)
39 KOG0773 Transcription factor M 95.4 0.012 2.5E-07 56.3 3.2 63 103-169 239-303 (342)
40 PF08880 QLQ: QLQ; InterPro: 89.9 0.41 9E-06 31.5 3.1 23 42-64 2-24 (37)
41 PF04218 CENP-B_N: CENP-B N-te 88.4 1.2 2.5E-05 31.3 4.7 47 104-160 1-47 (53)
42 KOG3755 SATB1 matrix attachmen 61.1 6.5 0.00014 40.7 2.6 46 119-169 708-760 (769)
43 KOG3623 Homeobox transcription 60.2 42 0.00092 35.9 8.3 106 44-169 582-687 (1007)
44 PF04545 Sigma70_r4: Sigma-70, 59.8 20 0.00042 24.1 4.1 46 109-164 4-49 (50)
45 PF01527 HTH_Tnp_1: Transposas 58.5 11 0.00024 27.3 3.0 43 105-157 2-45 (76)
46 cd06171 Sigma70_r4 Sigma70, re 58.2 12 0.00026 24.1 2.9 44 109-162 10-53 (55)
47 PF08281 Sigma70_r4_2: Sigma-7 52.8 20 0.00042 24.4 3.3 42 110-161 11-52 (54)
48 cd00569 HTH_Hin_like Helix-tur 49.8 38 0.00083 19.2 4.0 38 109-156 5-42 (42)
49 KOG1146 Homeobox protein [Gene 43.5 37 0.0008 38.4 5.0 61 102-167 704-764 (1406)
50 PF00196 GerE: Bacterial regul 42.4 39 0.00085 23.4 3.5 45 109-164 3-47 (58)
51 PRK03975 tfx putative transcri 41.9 43 0.00093 28.4 4.2 51 108-169 5-55 (141)
52 PF04967 HTH_10: HTH DNA bindi 41.0 41 0.00089 23.7 3.4 38 110-153 1-41 (53)
53 PF10668 Phage_terminase: Phag 38.4 18 0.00039 26.3 1.2 20 134-157 25-44 (60)
54 PRK09652 RNA polymerase sigma 37.9 56 0.0012 27.0 4.4 48 109-166 128-175 (182)
55 COG3413 Predicted DNA binding 35.7 52 0.0011 29.2 4.1 49 109-165 155-206 (215)
56 TIGR02937 sigma70-ECF RNA poly 35.5 61 0.0013 25.4 4.1 47 109-165 110-156 (158)
57 PRK09646 RNA polymerase sigma 35.4 63 0.0014 27.7 4.5 48 110-167 143-190 (194)
58 PRK06759 RNA polymerase factor 34.9 53 0.0012 26.7 3.8 47 109-165 106-152 (154)
59 PRK09413 IS2 repressor TnpA; R 34.8 70 0.0015 25.8 4.4 41 107-157 10-51 (121)
60 PF13936 HTH_38: Helix-turn-he 34.1 29 0.00062 23.1 1.6 40 108-157 3-42 (44)
61 PF00424 REV: REV protein (ant 32.9 51 0.0011 26.0 3.1 36 115-169 14-49 (91)
62 KOG0193 Serine/threonine prote 32.7 33 0.00071 35.9 2.5 63 2-66 386-450 (678)
63 cd00131 PAX Paired Box domain 32.3 2.7E+02 0.0059 22.8 7.5 46 109-159 75-127 (128)
64 PRK12526 RNA polymerase sigma 31.0 74 0.0016 27.7 4.2 30 134-167 172-201 (206)
65 PRK12519 RNA polymerase sigma 30.7 60 0.0013 27.7 3.5 30 133-166 159-188 (194)
66 PRK11924 RNA polymerase sigma 30.1 87 0.0019 25.8 4.3 30 134-167 144-173 (179)
67 smart00027 EH Eps15 homology d 30.0 95 0.0021 23.6 4.2 46 108-157 2-51 (96)
68 PRK09642 RNA polymerase sigma 29.6 1E+02 0.0023 25.2 4.7 48 110-167 107-154 (160)
69 PRK04217 hypothetical protein; 29.3 1.2E+02 0.0025 24.7 4.7 51 108-168 41-91 (110)
70 smart00421 HTH_LUXR helix_turn 28.9 98 0.0021 20.1 3.7 40 109-159 3-42 (58)
71 PRK00118 putative DNA-binding 28.5 1E+02 0.0022 24.8 4.2 47 110-166 18-64 (104)
72 PRK12512 RNA polymerase sigma 28.0 99 0.0022 26.0 4.4 49 110-168 132-180 (184)
73 TIGR02948 SigW_bacill RNA poly 27.7 90 0.002 26.2 4.1 29 134-166 155-183 (187)
74 TIGR02985 Sig70_bacteroi1 RNA 27.4 1.2E+02 0.0026 24.4 4.6 46 110-165 114-159 (161)
75 PRK12514 RNA polymerase sigma 27.4 1E+02 0.0023 25.8 4.4 29 134-166 148-176 (179)
76 PRK09644 RNA polymerase sigma 27.1 1.2E+02 0.0025 25.2 4.6 50 110-169 109-158 (165)
77 PF11336 DUF3138: Protein of u 26.8 3E+02 0.0064 27.9 7.8 82 34-124 13-94 (514)
78 PRK09480 slmA division inhibit 26.7 60 0.0013 27.3 2.8 41 115-161 16-56 (194)
79 cd04761 HTH_MerR-SF Helix-Turn 26.3 42 0.00092 21.9 1.4 21 134-158 3-23 (49)
80 PRK12515 RNA polymerase sigma 26.2 1.3E+02 0.0028 25.5 4.8 51 109-169 131-181 (189)
81 PF06056 Terminase_5: Putative 25.7 44 0.00096 23.8 1.5 20 134-157 16-35 (58)
82 PF13443 HTH_26: Cro/C1-type H 25.6 43 0.00093 23.3 1.4 28 133-164 12-39 (63)
83 PF13384 HTH_23: Homeodomain-l 25.5 45 0.00097 22.1 1.4 21 134-158 20-40 (50)
84 TIGR02959 SigZ RNA polymerase 25.4 1.2E+02 0.0026 25.4 4.5 50 109-168 100-149 (170)
85 PRK09639 RNA polymerase sigma 25.1 1.3E+02 0.0028 24.7 4.5 48 109-167 112-159 (166)
86 TIGR02999 Sig-70_X6 RNA polyme 25.1 1.1E+02 0.0024 25.6 4.2 46 110-165 135-180 (183)
87 TIGR02983 SigE-fam_strep RNA p 24.7 1.3E+02 0.0028 24.6 4.5 47 111-167 112-158 (162)
88 PRK09648 RNA polymerase sigma 24.4 1.2E+02 0.0025 25.8 4.2 47 109-165 139-185 (189)
89 PRK12541 RNA polymerase sigma 24.3 1.1E+02 0.0025 25.1 4.0 46 110-165 113-158 (161)
90 PF02796 HTH_7: Helix-turn-hel 24.0 68 0.0015 21.2 2.1 38 109-156 5-42 (45)
91 PRK09637 RNA polymerase sigma 23.6 1.3E+02 0.0028 25.6 4.3 48 110-167 107-154 (181)
92 PRK12546 RNA polymerase sigma 22.9 1.3E+02 0.0028 25.9 4.3 31 134-168 132-162 (188)
93 TIGR03879 near_KaiC_dom probab 22.7 32 0.0007 26.0 0.3 23 132-158 33-55 (73)
94 PRK05602 RNA polymerase sigma 22.6 1.6E+02 0.0034 24.9 4.7 32 134-169 147-178 (186)
95 TIGR02989 Sig-70_gvs1 RNA poly 22.5 1.4E+02 0.003 24.2 4.2 45 109-163 111-155 (159)
96 PRK09047 RNA polymerase factor 22.3 1.6E+02 0.0035 23.9 4.6 48 109-166 106-153 (161)
97 PF13518 HTH_28: Helix-turn-he 22.2 70 0.0015 21.1 1.9 23 134-160 15-37 (52)
98 PRK12533 RNA polymerase sigma 22.2 1.8E+02 0.0038 25.9 5.0 32 134-169 153-184 (216)
99 PRK06930 positive control sigm 22.1 1.6E+02 0.0034 25.5 4.5 51 109-169 114-164 (170)
100 PRK12537 RNA polymerase sigma 21.7 1.5E+02 0.0033 25.0 4.3 28 134-165 152-179 (182)
101 PRK10072 putative transcriptio 21.3 51 0.0011 26.0 1.2 41 109-161 32-72 (96)
102 TIGR02952 Sig70_famx2 RNA poly 21.2 1.7E+02 0.0037 24.0 4.5 27 134-164 141-167 (170)
103 PRK12530 RNA polymerase sigma 21.2 1.4E+02 0.0031 25.4 4.2 29 134-166 153-181 (189)
104 COG4367 Uncharacterized protei 21.1 1.2E+02 0.0026 24.0 3.1 38 110-152 3-40 (97)
105 PRK05657 RNA polymerase sigma 20.9 1.4E+02 0.0031 28.4 4.4 54 109-168 262-315 (325)
106 PRK07037 extracytoplasmic-func 20.9 1.5E+02 0.0033 24.2 4.1 46 110-165 110-155 (163)
107 PRK12523 RNA polymerase sigma 20.9 1.8E+02 0.0038 24.3 4.6 48 110-167 120-167 (172)
108 PRK12524 RNA polymerase sigma 20.9 2.4E+02 0.0052 24.1 5.5 30 134-167 155-184 (196)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=1.4e-38 Score=301.39 Aligned_cols=151 Identities=21% Similarity=0.269 Sum_probs=130.9
Q ss_pred HHHHHHHHHHhhhhhhcccCCcCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhcchhhhhhcCCCC
Q 022944 6 IREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRL 85 (289)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~l~~~~k~l~~~~~~~~sg~~~ 85 (289)
..||||||||+||||||||||+|+|||+|+|++||+|||+++|+||+++..+|++||++++.+.|||.........+.
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~-- 281 (398)
T KOG3802|consen 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGS-- 281 (398)
T ss_pred CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCC--
Confidence 368999999999999999999999999999999999999999999999999999999999999999965444211111
Q ss_pred CCccCCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 86 GNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 86 ~~~~~~p~~~~~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
....+-+ +...++||+||.|....+..||+.|.+ |++|+..+|..||.+| +|...+|+|||||||.|.||
T Consensus 282 -~~~~e~i----~a~~RkRKKRTSie~~vr~aLE~~F~~-npKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 282 -PNSIEKI----GAQSRKRKKRTSIEVNVRGALEKHFLK-NPKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred -CCCHHHh----hccccccccccceeHHHHHHHHHHHHh-CCCCCHHHHHHHHHHh----ccccceEEEEeecccccccc
Confidence 1111111 123368889999999999999999999 8999999999999999 99999999999999999999
Q ss_pred Hhh
Q 022944 166 KQL 168 (289)
Q Consensus 166 ~~~ 168 (289)
...
T Consensus 352 ~~~ 354 (398)
T KOG3802|consen 352 ITP 354 (398)
T ss_pred CCC
Confidence 776
No 2
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.76 E-value=9.7e-20 Score=166.71 Aligned_cols=153 Identities=17% Similarity=0.203 Sum_probs=122.7
Q ss_pred HHHHHHHHHhhhhhhcccCCcCCCCc--ccCccc-ccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhcchhhhhhcCC
Q 022944 7 REAAQQETQTQNQNQNQRGGENDNNN--VVNGVM-YVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGG 83 (289)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~g~~~--~~~~~~-~~~~~t~~q~~~lr~qi~~~~~ic~~l~~~~k~l~~~~~~~~sg~ 83 (289)
-.|||-||..|||||||||-+|.||| +|+-++ -+-.+++.+|++|+-...+-.+|.-+++.++.||.........-.
T Consensus 216 PReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~ 295 (385)
T KOG1168|consen 216 PRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKD 295 (385)
T ss_pred HHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhc
Confidence 45899999999999999999999996 555553 467899999999999999999999999999999855433221111
Q ss_pred CCCCccCCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHH
Q 022944 84 RLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (289)
Q Consensus 84 ~~~~~~~~p~~~~~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~ 163 (289)
+.+. ...+. .++ -++|+||.+..-+.+.||.+|.. .+.|+.+.+..||++| .|...+|+|||||.|+|.
T Consensus 296 ~~pd--~~~l~--~~~--ekKRKRTSIAAPEKRsLEayFav-QPRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQ 364 (385)
T KOG1168|consen 296 TKPD--INELL--PGG--EKKRKRTSIAAPEKRSLEAYFAV-QPRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQ 364 (385)
T ss_pred cCCc--hhhcc--Ccc--ccccccccccCcccccHHHHhcc-CCCCchhHHHHHHHhh----hhhhceEEEEeeccHHHH
Confidence 1110 01111 112 36778999999999999999999 9999999999999999 999999999999999999
Q ss_pred HHHhhhc
Q 022944 164 KRKQLVS 170 (289)
Q Consensus 164 Kr~~~~~ 170 (289)
||....+
T Consensus 365 KRm~~Sa 371 (385)
T KOG1168|consen 365 KRMKRSA 371 (385)
T ss_pred HHhhhhh
Confidence 9966543
No 3
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.75 E-value=4.9e-18 Score=150.70 Aligned_cols=71 Identities=34% Similarity=0.543 Sum_probs=66.4
Q ss_pred cCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhc
Q 022944 95 TSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (289)
Q Consensus 95 ~~~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (289)
+...+.++.||.||+|+..|+.+||..|.+ ++||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 29 P~~~~pRkqRRERTtFtr~QlevLe~LF~k-TqYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 29 PYSSGPRKQRRERTTFTRKQLEVLEALFAK-TQYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred CcCccchhcccccceecHHHHHHHHHHHHh-hcCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 333478899999999999999999999999 9999999999999999 9999999999999999999998874
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.75 E-value=1.2e-18 Score=137.92 Aligned_cols=70 Identities=31% Similarity=0.485 Sum_probs=64.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhcccc
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSA 173 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~~ 173 (289)
..++.||-||+||..||..||+.|.. ++||++..|++||.++ .|++.+|+|||||||+|.||+.+.+...
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~E-THYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAE-THYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHh-hcCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 35678889999999999999999999 9999999999999999 9999999999999999999988765443
No 5
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.74 E-value=3.1e-18 Score=158.09 Aligned_cols=68 Identities=32% Similarity=0.377 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhcccc
Q 022944 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSA 173 (289)
Q Consensus 101 ~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~~ 173 (289)
.+.||.||.||..||.+||+.|.. |+|.++.+|.|||..| .|+|+||||||||||+||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhf-N~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHF-NKYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcc-ccccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 458899999999999999999999 9999999999999999 9999999999999999999988875444
No 6
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.69 E-value=2.9e-17 Score=146.48 Aligned_cols=68 Identities=31% Similarity=0.401 Sum_probs=64.6
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 97 GGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 97 ~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
.|+.||.|+.||.++..||..|.+.|++ ++|...+||.+||..| ||+.+||||||||||.|.||..+.
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQk-TQYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQ-TQYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhh-cchhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhc
Confidence 4577889999999999999999999999 8999999999999999 999999999999999999999884
No 7
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.69 E-value=3.9e-17 Score=152.59 Aligned_cols=71 Identities=28% Similarity=0.376 Sum_probs=64.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhccccc
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSAN 174 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~~~ 174 (289)
+..++||+|..|++.|+.+||+.|.+ ++|.+.+||++||..| .||++||||||||||.|+||+++...-..
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrq-QRYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQ-QRYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHh-hhccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 35567778999999999999999999 9999999999999999 99999999999999999999998755443
No 8
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.69 E-value=2e-17 Score=155.86 Aligned_cols=67 Identities=28% Similarity=0.354 Sum_probs=63.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhc
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (289)
..||+|+.||.||..||..||+.|++ .+|.+..+|.+||..| ||+..||++||||||+||||.....
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 55788889999999999999999999 9999999999999999 9999999999999999999988773
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=7.8e-17 Score=139.05 Aligned_cols=64 Identities=38% Similarity=0.447 Sum_probs=61.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhc
Q 022944 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (289)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (289)
+.+|.||.|+.+||..||.+|+. ++|....+|+.||..| +|++.||+|||||||.|.||.+.+.
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 78899999999999999999999 9999999999999999 9999999999999999999998874
No 10
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.66 E-value=2.2e-16 Score=144.68 Aligned_cols=115 Identities=23% Similarity=0.302 Sum_probs=96.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhcchhhhhhcCCCCCCccCCCCccC--------CCCCCCCCCCCCCCCHHHHHHHHHHH
Q 022944 51 LRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTS--------GGGHKISARQRWTPTPVQLQILESIF 122 (289)
Q Consensus 51 lr~qi~~~~~ic~~l~~~~k~l~~~~~~~~sg~~~~~~~~~p~~~~--------~g~~~~~rR~Rt~ft~~Ql~~LE~~F 122 (289)
-++|..||+..|.+++.+.+.|.+...+. .+..+.++|...... ..+....+|+||++|..||+.|...|
T Consensus 109 RkAqd~VYHl~CF~C~iC~R~L~TGdEFY--LmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AY 186 (383)
T KOG4577|consen 109 RKAQDFVYHLHCFACFICKRQLATGDEFY--LMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAY 186 (383)
T ss_pred HHhhcceeehhhhhhHhhhcccccCCeeE--EeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHh
Confidence 47899999999999999999999888877 455555544332211 11344588999999999999999999
Q ss_pred hhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhccc
Q 022944 123 DQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (289)
Q Consensus 123 ~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (289)
.. .+.|.+..|++|+.+. ||..++|+|||||||||+||.++.+..
T Consensus 187 n~-SpKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 187 NT-SPKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cC-CCchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhcch
Confidence 99 8999999999999999 999999999999999999999988654
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.64 E-value=1.5e-16 Score=140.05 Aligned_cols=66 Identities=38% Similarity=0.445 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
+++..|++||.||..||..||+.|.. .+|.++.+|.+++..| .|+++||+|||||||+|.||.+..
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfre-kqYLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFRE-KQYLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhH-hhhhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHH
Confidence 67778899999999999999999999 8999999999999999 999999999999999999998876
No 12
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.64 E-value=9.7e-17 Score=149.98 Aligned_cols=66 Identities=29% Similarity=0.318 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhc
Q 022944 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (289)
Q Consensus 100 ~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (289)
-++.|++|..+|+.|+.+||+.|.. |.|.+++.|.+|++.| +|+++||+|||||||+|.||..++.
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlf-N~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLF-NMYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHH-HHHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhhh
Confidence 3568889999999999999999999 9999999999999999 9999999999999999999998753
No 13
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.62 E-value=7e-16 Score=109.89 Aligned_cols=57 Identities=42% Similarity=0.663 Sum_probs=55.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
||.|+.||.+|+.+||.+|.. ++||+..++..||..| ||+..+|++||+|||+++||
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 9999999999999999 99999999999999999986
No 14
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=5.3e-16 Score=140.46 Aligned_cols=68 Identities=26% Similarity=0.356 Sum_probs=61.0
Q ss_pred CCCCCCCC-CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhcc
Q 022944 99 GHKISARQ-RWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (289)
Q Consensus 99 ~~~~~rR~-Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (289)
+.+++||. ||.||..|+..||+.|.. .+||+...|+-||.++ .|.+.+|+|||||||+||||..+.-.
T Consensus 136 kkk~kRRh~RTiFT~~Qle~LEkaFke-aHYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 136 KKKKKRRHFRTIFTSYQLEELEKAFKE-AHYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccccccchhhHHHHHHHHHHHhh-ccCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 33434444 999999999999999999 8999999999999999 99999999999999999999888743
No 15
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.60 E-value=4.8e-16 Score=137.63 Aligned_cols=69 Identities=30% Similarity=0.382 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhccc
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSS 172 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~ 172 (289)
+..++||.||+|+..|+..||..|+. .+|.+..+|..||..| .|+|+||||||||||.||||+-.....
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~-krYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFEL-KRYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHH-HhhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 34567889999999999999999999 8999999999999999 999999999999999999998776433
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.54 E-value=2.3e-15 Score=136.88 Aligned_cols=63 Identities=29% Similarity=0.365 Sum_probs=59.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhc
Q 022944 103 SARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (289)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (289)
+-+.|.++|..|+.+||+.|.. ++|.++.++.+||.-| +|+|+||||||||||+|+||..++.
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~-SryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHT-SRYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhcc-ccceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 3456889999999999999999 9999999999999999 9999999999999999999988874
No 17
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.50 E-value=9.1e-15 Score=135.06 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
....-||.||.||.+|+..||+.|-+ .-|-++++|.+||..| +|.|..|||||||||+|+||+...
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 34568899999999999999999999 6799999999999999 999999999999999999998876
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.47 E-value=5.7e-14 Score=99.20 Aligned_cols=56 Identities=43% Similarity=0.629 Sum_probs=52.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHH
Q 022944 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (289)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (289)
++.|+.|+..++.+||..|.. ++||+..++..||..| ||+..+|++||+|||++.|
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 8999999999999999 9999999999999999864
No 19
>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=99.47 E-value=9.7e-14 Score=98.67 Aligned_cols=57 Identities=44% Similarity=0.653 Sum_probs=54.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 105 RQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
+.|+.++..++.+||.+|.. ++||+..++..||..+ ||++.+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~-~~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK-NPYPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 56789999999999999999 8999999999999999 999999999999999998864
No 20
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.46 E-value=7.2e-14 Score=100.83 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=50.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHHHhcCCcccchhhchhhhhH
Q 022944 104 ARQRWTPTPVQLQILESIFDQGTGT----PSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (289)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~~~y----Ps~~~r~~LA~~L~~~~gLs~~qV~vWFQNRR 160 (289)
||.||.||.+|+..||..|+. ++| |+..+|.+||..| ||++.+|+|||||-+
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 999 9999999999999 999999999999965
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.44 E-value=6.2e-14 Score=130.07 Aligned_cols=68 Identities=32% Similarity=0.424 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhcc
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (289)
+.+|+||.|+.|+..||..||..|.+ |+||+...|++||.-. +|++.+|+|||+|||+||||..+...
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 45588999999999999999999999 9999999999999999 99999999999999999999887655
No 22
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.43 E-value=8e-14 Score=126.50 Aligned_cols=59 Identities=34% Similarity=0.509 Sum_probs=56.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
+|+||.||.+||..|...|+. |+|.+..+|.+||.+| +|.+.||+|||||+|+|-||..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~e-nRYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQE-NRYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhh-hhhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhcc
Confidence 578999999999999999999 9999999999999999 9999999999999999988844
No 23
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.42 E-value=1.2e-13 Score=122.57 Aligned_cols=69 Identities=29% Similarity=0.373 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhccccc
Q 022944 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSAN 174 (289)
Q Consensus 101 ~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~~~ 174 (289)
.+++..|.+|+-.|+..||+.|++ .+|+-.++|.+||..| |+++.+|+|||||||.||||+........
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq-tkylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmasa 233 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ-TKYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMASA 233 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh-hhcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhhc
Confidence 456667899999999999999999 9999999999999999 99999999999999999999887654433
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.40 E-value=7.6e-14 Score=119.04 Aligned_cols=67 Identities=31% Similarity=0.400 Sum_probs=61.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhcccc
Q 022944 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSSSA 173 (289)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~~~ 173 (289)
++++.|+.|+..|+..||+.|+. .+|.+.++|.+||..| +|+++||+.||||||+|.||.++.....
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~-QrYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p~ 165 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFER-QRYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQPK 165 (194)
T ss_pred HhhhhcccccCccccccHHHHhh-hhhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 46677999999999999999999 9999999999999999 9999999999999999999988874433
No 25
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.38 E-value=2.2e-13 Score=120.86 Aligned_cols=63 Identities=33% Similarity=0.467 Sum_probs=57.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhc
Q 022944 103 SARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVS 170 (289)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~ 170 (289)
..+++.+|+.+|+..||+.|+. +.|..+.++..||..| ||.++||.|||||||||||.++...
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~-~~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES-EKKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccccccccHHHHHHhHHhhcc-ccccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhh
Confidence 3445667999999999999999 8999999999999999 9999999999999999999988763
No 26
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.37 E-value=6.8e-13 Score=113.81 Aligned_cols=64 Identities=30% Similarity=0.421 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 101 KISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 101 ~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
...++.|.+.+..|+.+|++.|+. ++||+...|..|+..| +|+++.|+|||||||++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i-~p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI-NPYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc-CCCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhccc
Confidence 346667788899999999999999 8999999999999999 999999999999999999997765
No 27
>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=99.36 E-value=1.1e-13 Score=104.44 Aligned_cols=70 Identities=13% Similarity=0.134 Sum_probs=64.9
Q ss_pred hHHHHHHHHHHhhhhhhcccCCcCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 022944 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSA 74 (289)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~l~~~~k~l~~ 74 (289)
...+|+++||+.||++||+||.+|+||+.+.|.+||.+||+++|++|+++..+++++|+.++.+.+|+..
T Consensus 4 ~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~e 73 (75)
T PF00157_consen 4 PDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEE 73 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999999999999999999999999999999999999999999999999999853
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.22 E-value=1.1e-11 Score=110.64 Aligned_cols=105 Identities=24% Similarity=0.278 Sum_probs=76.8
Q ss_pred HHHHHHHHHHHHHhhhhhcchhhhhhcCCCCCCccCCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHH
Q 022944 55 IAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKI 134 (289)
Q Consensus 55 i~~~~~ic~~l~~~~k~l~~~~~~~~sg~~~~~~~~~p~~~~~g~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r 134 (289)
...++.-|-.+..+...+...... ....|..+|...... ....+.||.|+.|+..|+.+||+.|+. ++||+...|
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~g~~~~~~d~~~-~~~~~~rr~rt~~~~~ql~~ler~f~~-~h~Pd~~~r 90 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGDTC---FSKDGSIYCKRDYQR-EFKFSKRCARCKFTISQLDELERAFEK-VHLPCFACR 90 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCCCc---ccCCCcccccccchh-hhhccccccCCCCCcCHHHHHHHhhcC-CCcCccchH
Confidence 344455555565555555411111 112444444433222 124568889999999999999999999 899999999
Q ss_pred HHHHHHHHhcCCcccchhhchhhhhHHHHHHHhh
Q 022944 135 KEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (289)
Q Consensus 135 ~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (289)
+.||..+ .+++..|+|||||||+||++...
T Consensus 91 ~~la~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 91 ECLALLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred HHHhhcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 9999999 99999999999999999999875
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.98 E-value=4.2e-10 Score=108.33 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 99 GHKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 99 ~~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
..++.+|.|++|++.|+..||+.|+. ++||++..|++||.++ ++++..|+|||+|||+|++|....
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 45567788999999999999999999 8999999999999999 999999999999999999998854
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.82 E-value=1.3e-08 Score=93.33 Aligned_cols=49 Identities=29% Similarity=0.487 Sum_probs=45.4
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHH
Q 022944 111 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (289)
Q Consensus 111 t~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (289)
...-+..|..+|.+ ++||+..++.+||+.. ||+..||-+||+|||+|+|
T Consensus 184 KekSR~~LrewY~~-~~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 184 KEKSRSLLREWYLQ-NPYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hHhhHHHHHHHHhc-CCCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhh
Confidence 33446799999999 8999999999999999 9999999999999999999
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.63 E-value=5.2e-09 Score=95.45 Aligned_cols=63 Identities=27% Similarity=0.414 Sum_probs=57.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh--cCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 103 SARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~--~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
.||+|..|+..-.++|..+|.. .|+||+.+.+++||.++ +++..||-+||.|+|-+.||....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhhh
Confidence 6778889999999999999965 58999999999999999 999999999999999999985543
No 32
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.55 E-value=3.6e-08 Score=74.52 Aligned_cols=69 Identities=12% Similarity=0.133 Sum_probs=65.9
Q ss_pred hHHHHHHHHHHhhhhhhcccCCcCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Q 022944 5 NIREAAQQETQTQNQNQNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLS 73 (289)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~l~~~~k~l~ 73 (289)
....|+|.|+++|+++|+++|-+|.+++.++|++||..+|+.+|++|+....+++++|+..+.+.+|+.
T Consensus 4 ~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~ 72 (75)
T smart00352 4 TDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLE 72 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHH
Confidence 446799999999999999999999999999999999999999999999999999999999999999985
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=98.28 E-value=5e-07 Score=60.52 Aligned_cols=33 Identities=33% Similarity=0.598 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHH
Q 022944 126 TGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (289)
Q Consensus 126 ~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK 162 (289)
++||+..++.+||... ||+..||.+||-|.|.|
T Consensus 8 nPYPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 8 NPYPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp SGS--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 7999999999999999 99999999999999975
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.03 E-value=1.1e-05 Score=80.70 Aligned_cols=57 Identities=30% Similarity=0.483 Sum_probs=53.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHH
Q 022944 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (289)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~ 163 (289)
..+|+|.+||..|+..|..+|+. +++|+.+..+.|+.+| +|..+.|.+||-|-|.|.
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 46778999999999999999999 9999999999999999 999999999999988775
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.98 E-value=5.8e-06 Score=73.72 Aligned_cols=64 Identities=34% Similarity=0.525 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhh
Q 022944 100 HKISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (289)
Q Consensus 100 ~~~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (289)
..+.++.|+.+...|+..|+..|.. +++|+...+..|+..+ ++++..|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRA-TPKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccC-CCCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 3467888999999999999999999 8999999999999999 99999999999999999998766
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.48 E-value=0.00013 Score=79.09 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=58.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
.+|+.|+.++..||..|..+|.. ..||...+.+.|-..+ ++..+.|+|||||-|+|.|+....
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 36778999999999999999999 8999999999999999 999999999999999999987774
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=96.28 E-value=0.019 Score=59.63 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=47.3
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhhcc
Q 022944 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLVSS 171 (289)
Q Consensus 115 l~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~~~ 171 (289)
+.+|..+|.. |..|+..+...||.++ ||..+.|++||++++++..+..+...
T Consensus 568 ~sllkayyal-n~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYAL-NGLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7789999999 9999999999999999 99999999999999999888775533
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.19 E-value=0.0031 Score=45.20 Aligned_cols=42 Identities=21% Similarity=0.405 Sum_probs=31.1
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHH
Q 022944 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (289)
Q Consensus 115 l~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRa 161 (289)
+..|+++|.. .+++...+...|+.+. +|+..+|+.||--|+.
T Consensus 10 ~~pL~~Yy~~-h~~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLK-HKQLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHH-T----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHH-cCCccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 4569999999 8999999999999999 9999999999976543
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.43 E-value=0.012 Score=56.35 Aligned_cols=63 Identities=21% Similarity=0.228 Sum_probs=50.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh--cCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 103 SARQRWTPTPVQLQILESIFDQ--GTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 103 ~rR~Rt~ft~~Ql~~LE~~F~~--~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
..|++..+......+|+.+... ..+||+..++..||.++ ||+..||.+||-|.|.|..+-...
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 4455567888888899877333 24799999999999999 999999999999999886654443
No 40
>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=89.93 E-value=0.41 Score=31.46 Aligned_cols=23 Identities=35% Similarity=0.489 Sum_probs=20.5
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHH
Q 022944 42 VMTDEQLETLRKQIAVYATICEQ 64 (289)
Q Consensus 42 ~~t~~q~~~lr~qi~~~~~ic~~ 64 (289)
.||.+|+..||+||.+|+-+...
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~~ 24 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLARN 24 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHcC
Confidence 58999999999999999988653
No 41
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=88.44 E-value=1.2 Score=31.35 Aligned_cols=47 Identities=17% Similarity=0.217 Sum_probs=34.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhH
Q 022944 104 ARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRR 160 (289)
Q Consensus 104 rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRR 160 (289)
+|.|..+|-++...+-..++. .. ....||..+ |++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~-g~-----s~~~ia~~f----gv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE-GE-----SKRDIAREF----GVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC-TT------HHHHHHHH----T--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc-CC-----CHHHHHHHh----CCCHHHHHHHHHhHH
Confidence 467889999887777777777 32 456899999 999999999999853
No 42
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=61.06 E-value=6.5 Score=40.74 Aligned_cols=46 Identities=26% Similarity=0.291 Sum_probs=32.9
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHHHhcCCc-------ccchhhchhhhhHHHHHHHhhh
Q 022944 119 ESIFDQGTGTPSKQKIKEITVELSQHGQI-------SETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 119 E~~F~~~~~yPs~~~r~~LA~~L~~~~gL-------s~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
+.+|.+ +..+....+.+..+.+ .+ ..+.|+.||.|||+++|+.+-.
T Consensus 708 ~~w~~k-~~s~s~~~v~eYkee~----~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLK-TRSGSWVDVAEYKEEE----LLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheec-ccCchhHHHHHhhHHh----hcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 444555 6677777776666555 33 4568999999999999986644
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=60.24 E-value=42 Score=35.88 Aligned_cols=106 Identities=18% Similarity=0.282 Sum_probs=60.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhhhhcchhhhhhcCCCCCCccCCCCccCCCCCCCCCCCCCCCCHHHHHHHHHHHh
Q 022944 44 TDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTPVQLQILESIFD 123 (289)
Q Consensus 44 t~~q~~~lr~qi~~~~~ic~~l~~~~k~l~~~~~~~~sg~~~~~~~~~p~~~~~g~~~~~rR~Rt~ft~~Ql~~LE~~F~ 123 (289)
+.+.+..+..|+.+-....+.|.+-.+.- ..+... .|..+++ ...-+.|+....++-..|...++
T Consensus 582 s~eelskia~qvglp~~vvk~wfE~~~a~----e~sv~r--------sps~psg---~~p~kv~sp~k~~dq~ql~~a~e 646 (1007)
T KOG3623|consen 582 SEEELSKIAQQVGLPFAVVKAWFEDEEAE----EMSVER--------SPSQPSG---ERPVKVRSPIKEEDQQQLKQAYE 646 (1007)
T ss_pred CHHHHHHHHHHhcccHHHHHHHHHhhhhh----hhhhcc--------CccCCCC---CCCccccCCCCccchhhhHhhhh
Confidence 56666666667666655555555443221 111000 0111111 11223345555566666777777
Q ss_pred hcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 124 QGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 124 ~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
. +--++..+-..++.+| ...+.+|.|||++|+..-+.....
T Consensus 647 l-q~s~~n~~~pl~~t~~----~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 647 L-QASPSNDEFPLIATRL----QNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred c-ccCccCcccchhhhhc----cCCCcchhhcccCCCCCCCCCccc
Confidence 7 5555555555566667 888899999999999887665554
No 44
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=59.79 E-value=20 Score=24.14 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (289)
.+++.+..+|...|.. . + .-.++|..+ |++...|+.+...-..|-|
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 4678899999999865 2 2 245899999 9999999888765555443
No 45
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=58.50 E-value=11 Score=27.28 Aligned_cols=43 Identities=23% Similarity=0.407 Sum_probs=27.3
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhh
Q 022944 105 RQRWTPTPVQLQILESIF-DQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (289)
Q Consensus 105 R~Rt~ft~~Ql~~LE~~F-~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (289)
+.|..|++++...+-..+ .. ...+.++|..+ ||++..|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~------g~sv~~va~~~----gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES------GESVSEVAREY----GISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH------HCHHHHHHHHH----TS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC------CCceEeeeccc----ccccccccHHHH
Confidence 456789998866555554 33 24567899999 999999999974
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=58.24 E-value=12 Score=24.13 Aligned_cols=44 Identities=16% Similarity=0.162 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRAR 162 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK 162 (289)
.+++.+..+++..|.. . + ...++|..+ |++...|+.|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~-~-~----~~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGE-G-L----SYEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhc-C-C----CHHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 3567778888777755 2 2 245789999 99999999998765544
No 47
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=52.82 E-value=20 Score=24.35 Aligned_cols=42 Identities=29% Similarity=0.240 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHH
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRa 161 (289)
+++.+..++.-.|..+ ....++|..+ |+++..|++|...-|.
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHHHHh
Confidence 4566667776666552 3355889999 9999999999975444
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=49.81 E-value=38 Score=19.22 Aligned_cols=38 Identities=24% Similarity=0.496 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWF 156 (289)
.++......+...|.. .+ ...++|..+ +++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~--~~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA--GE----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHhC
Confidence 3566666666666655 22 344788899 99999888884
No 49
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=43.49 E-value=37 Score=38.44 Aligned_cols=61 Identities=26% Similarity=0.346 Sum_probs=53.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 102 ISARQRWTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 102 ~~rR~Rt~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
+.++.|..+-.+++..|-++|-. +.-|+...+.-|.... ..+.+++.+||+|-|.|.++..
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 35567788888999999999999 6789999988898888 8999999999999999998877
No 50
>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=42.45 E-value=39 Score=23.38 Aligned_cols=45 Identities=27% Similarity=0.228 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (289)
.+|+.++.+|.-...- + ...++|..+ ++++..|+.+..+=+.|..
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 5788888888776544 2 245899999 9999999999887666643
No 51
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=41.86 E-value=43 Score=28.40 Aligned_cols=51 Identities=22% Similarity=0.178 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
..+++.|+.+|... .. .+. ..+||..| |++...|..|-.+.+.+.|+....
T Consensus 5 ~~Lt~rqreVL~lr-~~--GlT----q~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLR-ER--GLT----QQEIADIL----GTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHH-Hc--CCC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999874 34 222 34899999 999999999999888877765544
No 52
>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=41.00 E-value=41 Score=23.71 Aligned_cols=38 Identities=32% Similarity=0.483 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCC---CCHHHHHHHHHHHHhcCCcccchhh
Q 022944 110 PTPVQLQILESIFDQGTGT---PSKQKIKEITVELSQHGQISETNVY 153 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~y---Ps~~~r~~LA~~L~~~~gLs~~qV~ 153 (289)
+|+.|+.+|...|+. .| |-.....+||..| |++..-|.
T Consensus 1 LT~~Q~e~L~~A~~~--GYfd~PR~~tl~elA~~l----gis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYEL--GYFDVPRRITLEELAEEL----GISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHc--CCCCCCCcCCHHHHHHHh----CCCHHHHH
Confidence 578899999999988 35 4455567899999 99987654
No 53
>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=38.43 E-value=18 Score=26.32 Aligned_cols=20 Identities=30% Similarity=0.662 Sum_probs=17.1
Q ss_pred HHHHHHHHHhcCCcccchhhchhh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQ 157 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQ 157 (289)
-.+||.+| |+++.+|+.|=.
T Consensus 25 lkdIA~~L----gvs~~tIr~WK~ 44 (60)
T PF10668_consen 25 LKDIAEKL----GVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHH----CCCHHHHHHHhh
Confidence 45789999 999999999953
No 54
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.91 E-value=56 Score=27.03 Aligned_cols=48 Identities=13% Similarity=-0.008 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
.+++.+..+|.-.|-. .++ ..+||..| |+++..|+.|...-|.+.|+.
T Consensus 128 ~L~~~~r~vl~l~~~~--~~s----~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIE--GLS----YEEIAEIM----GCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHc--CCC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3566666666665544 122 34789999 999999999998655555543
No 55
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=35.75 E-value=52 Score=29.20 Aligned_cols=49 Identities=29% Similarity=0.309 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCC---HHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPS---KQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs---~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
.+|+.|+.+|..+|.. .|-+ .....+||+.| |++..- +|..=|||..|-
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 7999999999999988 3544 44556788999 999865 455556666543
No 56
>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=35.48 E-value=61 Score=25.35 Aligned_cols=47 Identities=21% Similarity=0.211 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
.+++.+..++...|.. .+ ...+||..+ |+++..|+.|...-+.|-|+
T Consensus 110 ~L~~~~~~ii~~~~~~--g~----s~~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE--GL----SYKEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 3456666666555433 22 344789999 99999999998766665554
No 57
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=35.41 E-value=63 Score=27.73 Aligned_cols=48 Identities=15% Similarity=0.133 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
+++.+..+|.-.|..+ ....+||..| |++...|+++...-|.+.|+.-
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 4555555665544331 2345889999 9999999999976666665543
No 58
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.87 E-value=53 Score=26.68 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
.+++.+..++.-.|-.+ ....+||..| |++...|++|...-|.+-|+
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 34555666665554441 2255889999 99999999998765555443
No 59
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=34.82 E-value=70 Score=25.80 Aligned_cols=41 Identities=15% Similarity=0.375 Sum_probs=27.3
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhh
Q 022944 107 RWTPTPVQLQ-ILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (289)
Q Consensus 107 Rt~ft~~Ql~-~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (289)
|..|+.+... ++...+.. .++ ..++|..+ ||++..|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~--g~s----v~evA~e~----gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEP--GMT----VSLVARQH----GVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcC--CCC----HHHHHHHH----CcCHHHHHHHHH
Confidence 4457776644 44444443 332 34789999 999999999953
No 60
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.13 E-value=29 Score=23.12 Aligned_cols=40 Identities=28% Similarity=0.365 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhh
Q 022944 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (289)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (289)
..+|.++...++..+..+ .-..+||..| |.+...|..|.+
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 467888889999887762 2345799999 999999887764
No 61
>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=32.94 E-value=51 Score=25.99 Aligned_cols=36 Identities=22% Similarity=0.373 Sum_probs=20.0
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 115 l~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
+.+..-.|+. |+||...- -+..= .|||.+||+.+.+
T Consensus 14 vRiIk~Lyqs-nPyP~~~G---Tr~aR---------------RnRRRRWR~rq~Q 49 (91)
T PF00424_consen 14 VRIIKILYQS-NPYPSPEG---TRQAR---------------RNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHHT-S-S--S-S----HHHH---------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHcc-ccCCCCCC---ccccc---------------cchhhhHHHHHHH
Confidence 3445556888 89997431 11121 5899999988765
No 62
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=32.67 E-value=33 Score=35.95 Aligned_cols=63 Identities=21% Similarity=0.273 Sum_probs=46.6
Q ss_pred cchhHHHHHHHHHHhhhhh--hcccCCcCCCCcccCcccccccCCHHHHHHHHHHHHHHHHHHHHHH
Q 022944 2 EWDNIREAAQQETQTQNQN--QNQRGGENDNNNVVNGVMYVKVMTDEQLETLRKQIAVYATICEQLV 66 (289)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~l~ 66 (289)
+|+---|+..+--+-=..+ .|-+|..-|||++ +.|-+-..|++|+++|+..+++|++.-..-+
T Consensus 386 ~WeIp~~ev~l~~rIGsGsFGtV~Rg~whGdVAV--K~Lnv~~pt~~qlqaFKnEVa~lkkTRH~NI 450 (678)
T KOG0193|consen 386 EWEIPPEEVLLGERIGSGSFGTVYRGRWHGDVAV--KLLNVDDPTPEQLQAFKNEVAVLKKTRHENI 450 (678)
T ss_pred ccccCHHHhhccceeccccccceeecccccceEE--EEEecCCCCHHHHHHHHHHHHHHhhcchhhh
Confidence 5666666665544333333 5667778888888 8899999999999999999999987744433
No 63
>cd00131 PAX Paired Box domain
Probab=32.29 E-value=2.7e+02 Score=22.78 Aligned_cols=46 Identities=17% Similarity=0.171 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCc-------ccchhhchhhhh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQI-------SETNVYNWFQNR 159 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gL-------s~~qV~vWFQNR 159 (289)
..+..+...++.+... ++..+..+. +..|... ++ +...|-.||+++
T Consensus 75 ~~~~~~~~~i~~~v~~-~p~~Tl~El---~~~L~~~-gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQE-NPGMFAWEI---RDRLLQE-GVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHH-CCCCCHHHH---HHHHHHc-CCcccCCCCCHHHHHHHHHhc
Confidence 3455666666666666 666665544 4444322 44 777888887653
No 64
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=30.99 E-value=74 Score=27.71 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=23.7
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
..+||..| |+++..|+++...-|.+.|+..
T Consensus 172 ~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 172 QEQLAQQL----NVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45889999 9999999999876666666544
No 65
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.70 E-value=60 Score=27.67 Aligned_cols=30 Identities=17% Similarity=0.066 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 133 KIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
...+||..+ |++...|++|+..-|.+.|+.
T Consensus 159 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 159 SQSEIAKRL----GIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 345889999 999999999997766666654
No 66
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.07 E-value=87 Score=25.77 Aligned_cols=30 Identities=17% Similarity=0.139 Sum_probs=24.0
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
..+||..| |+++..|+.|...-|.+.|+.-
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 35789999 9999999999987666666543
No 67
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=30.00 E-value=95 Score=23.63 Aligned_cols=46 Identities=22% Similarity=0.367 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHhh----cCCCCCHHHHHHHHHHHHhcCCcccchhhchhh
Q 022944 108 WTPTPVQLQILESIFDQ----GTGTPSKQKIKEITVELSQHGQISETNVYNWFQ 157 (289)
Q Consensus 108 t~ft~~Ql~~LE~~F~~----~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQ 157 (289)
|-++.+++..|...|.. .+.+.+..+...+-..+ ++++..|..+|.
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 24567777666666666 888877777764
No 68
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.57 E-value=1e+02 Score=25.19 Aligned_cols=48 Identities=13% Similarity=0.066 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
+++.+..++.-.|..+ + ...+||..| |+++..|+++...-|.+-|+.-
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 4445555555444431 2 234789999 9999999999986666666543
No 69
>PRK04217 hypothetical protein; Provisional
Probab=29.34 E-value=1.2e+02 Score=24.69 Aligned_cols=51 Identities=12% Similarity=0.082 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhh
Q 022944 108 WTPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (289)
Q Consensus 108 t~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (289)
..++.+++.++...|.. . + ...+||+.+ +++...|+..+..-|.+.|..-.
T Consensus 41 ~~Lt~eereai~l~~~e-G-l----S~~EIAk~L----GIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 41 IFMTYEEFEALRLVDYE-G-L----TQEEAGKRM----GVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred ccCCHHHHHHHHHHHHc-C-C----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788888888877765 2 2 345799999 99999999999877776665443
No 70
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=28.90 E-value=98 Score=20.09 Aligned_cols=40 Identities=33% Similarity=0.406 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNR 159 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNR 159 (289)
.+++.+..++..+ .. .+ ...++|..+ +++...|+.|...-
T Consensus 3 ~l~~~e~~i~~~~-~~--g~----s~~eia~~l----~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLL-AE--GL----TNKEIAERL----GISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHH-Hc--CC----CHHHHHHHH----CCCHHHHHHHHHHH
Confidence 3577777777653 33 22 345889999 99999999888743
No 71
>PRK00118 putative DNA-binding protein; Validated
Probab=28.45 E-value=1e+02 Score=24.80 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
+++.|..++.-.|..+ + ...+||..+ |+++..|+.|...-|.+.|..
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 244789999 999999999998776666653
No 72
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.03 E-value=99 Score=26.04 Aligned_cols=49 Identities=27% Similarity=0.198 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhh
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (289)
+++.+..++.-.|-. .....+||..| |++...|++++..-|.+.|+.-.
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 444455555554433 12234789999 99999999999877777776544
No 73
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=27.69 E-value=90 Score=26.16 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=23.0
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
..++|..| |+++..|+++...-|.+-|..
T Consensus 155 ~~eIA~~l----gis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 155 LKEISEIL----DLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 45789999 999999999997666665553
No 74
>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=27.40 E-value=1.2e+02 Score=24.36 Aligned_cols=46 Identities=22% Similarity=0.105 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
+++.+..+|.-.|-. .+ ...+||..+ |+++..|+++...-|.|.|+
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 22 234789999 99999999888755555443
No 75
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=27.40 E-value=1e+02 Score=25.78 Aligned_cols=29 Identities=10% Similarity=0.281 Sum_probs=23.1
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
..+||..| |+++..|+++...-|.+.|+.
T Consensus 148 ~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 148 YKELAERH----DVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HHHHHHHH----CCChHHHHHHHHHHHHHHHHH
Confidence 45889999 999999999988666665553
No 76
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=27.08 E-value=1.2e+02 Score=25.19 Aligned_cols=50 Identities=12% Similarity=-0.023 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
+++.+..++.-.|-. .....+||..| |+++..|++|...-|.+.|+.-..
T Consensus 109 L~~~~r~v~~l~~~~------g~s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 109 LPVIEAQAILLCDVH------ELTYEEAASVL----DLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CCHHHHHHHHhHHHh------cCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 455555555544333 12245789999 999999999998767666665443
No 77
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=26.84 E-value=3e+02 Score=27.93 Aligned_cols=82 Identities=16% Similarity=0.165 Sum_probs=51.3
Q ss_pred cCcccccccCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhcchhhhhhcCCCCCCccCCCCccCCCCCCCCCCCCCCCCHH
Q 022944 34 VNGVMYVKVMTDEQLETLRKQIAVYATICEQLVEMHKSLSAHQDLAAAGGRLGNIYCDPLMTSGGGHKISARQRWTPTPV 113 (289)
Q Consensus 34 ~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~~l~~~~k~l~~~~~~~~sg~~~~~~~~~p~~~~~g~~~~~rR~Rt~ft~~ 113 (289)
+.+.+....-+-.+|+.|.+|+.... ++.-++.+.+.+++..++.+...+.....+.... ....++.+|++
T Consensus 13 al~~~a~a~a~a~~i~~L~~ql~aLq---~~v~eL~~~laa~~~aa~~gA~~~~~~~a~~~aP------~~~a~~~~T~d 83 (514)
T PF11336_consen 13 ALPGAAMAAATADQIKALQAQLQALQ---DQVNELRAKLAAKPAAAPGGAAIGPAATAAAAAP------SSDAQAGLTND 83 (514)
T ss_pred hccccccccCCHHHHHHHHHHHHHHH---HHHHHHHHHHhcCCCCCCccccccccccccccCC------CcccccccChH
Confidence 45666677788899999999987644 5556677777666665433443333322222111 11157899999
Q ss_pred HHHHHHHHHhh
Q 022944 114 QLQILESIFDQ 124 (289)
Q Consensus 114 Ql~~LE~~F~~ 124 (289)
++..+...+..
T Consensus 84 ~~~~~~qqiAn 94 (514)
T PF11336_consen 84 DATEMRQQIAN 94 (514)
T ss_pred HHHHHHHHHHh
Confidence 99777666555
No 78
>PRK09480 slmA division inhibitor protein; Provisional
Probab=26.75 E-value=60 Score=27.29 Aligned_cols=41 Identities=17% Similarity=0.395 Sum_probs=31.2
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHH
Q 022944 115 LQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (289)
Q Consensus 115 l~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRa 161 (289)
+......|.. .+. .......||.+. |++...++.+|.|+-.
T Consensus 16 l~aa~~l~~~-~~G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLES-PPG-ERITTAKLAARV----GVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHh-cCC-CccCHHHHHHHh----CCCHhHHHHHCCCHHH
Confidence 3444445655 445 677788999999 9999999999999763
No 79
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.29 E-value=42 Score=21.86 Aligned_cols=21 Identities=14% Similarity=0.120 Sum_probs=17.5
Q ss_pred HHHHHHHHHhcCCcccchhhchhhh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQN 158 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQN 158 (289)
..++|+.+ |+++..|+.|.++
T Consensus 3 ~~e~a~~~----gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLT----GVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHHC
Confidence 35788899 9999999999654
No 80
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.21 E-value=1.3e+02 Score=25.53 Aligned_cols=51 Identities=14% Similarity=0.231 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
.+++.+..+|+-.|-.+ ....+||..| |+++..|++-...-|.+.|+.-..
T Consensus 131 ~L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE------KSVEEVGEIV----GIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555544331 2234788999 999999999988777776665443
No 81
>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=25.69 E-value=44 Score=23.84 Aligned_cols=20 Identities=45% Similarity=0.831 Sum_probs=17.6
Q ss_pred HHHHHHHHHhcCCcccchhhchhh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQ 157 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQ 157 (289)
..+||..| |++...|+.|-+
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 82
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=25.59 E-value=43 Score=23.25 Aligned_cols=28 Identities=11% Similarity=0.219 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhcCCcccchhhchhhhhHHHHH
Q 022944 133 KIKEITVELSQHGQISETNVYNWFQNRRARSK 164 (289)
Q Consensus 133 ~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (289)
....||..+ |++...|..|+.++..+..
T Consensus 12 t~~~La~~~----gis~~tl~~~~~~~~~~~~ 39 (63)
T PF13443_consen 12 TQKDLARKT----GISRSTLSRILNGKPSNPS 39 (63)
T ss_dssp -HHHHHHHH----T--HHHHHHHHTTT-----
T ss_pred CHHHHHHHH----CcCHHHHHHHHhccccccc
Confidence 355899999 9999999999998854443
No 83
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.48 E-value=45 Score=22.11 Aligned_cols=21 Identities=38% Similarity=0.838 Sum_probs=16.8
Q ss_pred HHHHHHHHHhcCCcccchhhchhhh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQN 158 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQN 158 (289)
..++|..| |++...|..|.+.
T Consensus 20 ~~~ia~~l----gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 20 IREIAKRL----GVSRSTVYRWIKR 40 (50)
T ss_dssp HHHHHHHH----TS-HHHHHHHHT-
T ss_pred HHHHHHHH----CcCHHHHHHHHHH
Confidence 45889999 9999999999754
No 84
>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=25.39 E-value=1.2e+02 Score=25.38 Aligned_cols=50 Identities=16% Similarity=0.052 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (289)
.+++.+..+|.-.|-. .+ ...+||..| |+++..|+++-..-|.+.|+.-.
T Consensus 100 ~L~~~~r~v~~l~~~~--g~----s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELE--GL----SQQEIAEKL----GLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHc--CC----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666665544 12 244889999 99999999998766666666544
No 85
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=25.12 E-value=1.3e+02 Score=24.72 Aligned_cols=48 Identities=23% Similarity=0.223 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
.+++.+..+|.-.| .+ + ...+||..| |++...|+++...-|.+.|+.-
T Consensus 112 ~L~~~~r~il~l~~-~g--~----s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG--Y----SYKEIAEAL----GIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-cC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 35566666666666 51 2 345889999 9999999999976666666544
No 86
>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=25.06 E-value=1.1e+02 Score=25.56 Aligned_cols=46 Identities=26% Similarity=0.240 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
+++.+..++.-.|..+ ....+||..| |+++..|++....-|.+-|+
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 2244789999 99999999999866666554
No 87
>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=24.75 E-value=1.3e+02 Score=24.60 Aligned_cols=47 Identities=15% Similarity=0.087 Sum_probs=31.5
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 111 TPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 111 t~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
++.+..+|.-.|.. .+ ...+||..| |++...|+++-..-|.+-|+.-
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 22 234789999 9999999999887777766543
No 88
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.36 E-value=1.2e+02 Score=25.79 Aligned_cols=47 Identities=19% Similarity=0.014 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
.+++.+..++.-.|-.+ ....+||..| |++...|+++...-|.+-|+
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 34555555555544441 2345889999 99999999998655555444
No 89
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=24.32 E-value=1.1e+02 Score=25.06 Aligned_cols=46 Identities=20% Similarity=0.026 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
+++.|..+|.-.|-. .++ ..+||..+ |++...|+++...-|.+-|+
T Consensus 113 L~~~~r~v~~l~~~~--~~s----~~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYY--GFS----YKEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhc--CCC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 555566666555544 122 34789999 99999999988765555554
No 90
>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=23.97 E-value=68 Score=21.24 Aligned_cols=38 Identities=21% Similarity=0.518 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWF 156 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWF 156 (289)
.++++++..+-..+..+ + .+.+||..+ |++...|+.++
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 46666677777777772 3 356889999 99999988776
No 91
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.59 E-value=1.3e+02 Score=25.64 Aligned_cols=48 Identities=19% Similarity=0.052 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
+++.+..+|.-.|-. .....+||..+ |++...|+..+..-|.+.|+.-
T Consensus 107 L~~~~r~i~~l~~~~------g~~~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 107 LPEKYAEALRLTELE------GLSQKEIAEKL----GLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CCHHHHHHHHHHHhc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHH
Confidence 444455555444333 12345789999 9999999999976666555533
No 92
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.93 E-value=1.3e+02 Score=25.91 Aligned_cols=31 Identities=16% Similarity=0.027 Sum_probs=24.8
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (289)
..++|..| |++...|+++...-|.+-|+.-.
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 45789999 99999999999877777666443
No 93
>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=22.71 E-value=32 Score=25.95 Aligned_cols=23 Identities=30% Similarity=0.371 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHhcCCcccchhhchhhh
Q 022944 132 QKIKEITVELSQHGQISETNVYNWFQN 158 (289)
Q Consensus 132 ~~r~~LA~~L~~~~gLs~~qV~vWFQN 158 (289)
....+||..| ++++..|++|+.+
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 94
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.56 E-value=1.6e+02 Score=24.86 Aligned_cols=32 Identities=13% Similarity=0.045 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
..+||..| |++...|+++...-|.+-|+.-..
T Consensus 147 ~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 147 NIEAAAVM----DISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred HHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHHh
Confidence 34789999 999999999997666666654443
No 95
>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=22.54 E-value=1.4e+02 Score=24.23 Aligned_cols=45 Identities=16% Similarity=0.218 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARS 163 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~ 163 (289)
.+++.+..++.-.|-. .....+||..+ |++...|+++...-|.+-
T Consensus 111 ~L~~~~r~v~~l~~~~------g~~~~eIA~~l----~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 111 KLPERQRELLQLRYQR------GVSLTALAEQL----GRTVNAVYKALSRLRVRL 155 (159)
T ss_pred HCCHHHHHHHHHHHhc------CCCHHHHHHHh----CCCHHHHHHHHHHHHHHH
Confidence 3556666666654433 12345889999 999999998865444443
No 96
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.33 E-value=1.6e+02 Score=23.88 Aligned_cols=48 Identities=10% Similarity=0.028 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
.+++.+..++.-.|-. .++ ..+||..| |++...|++....-|.+.|+.
T Consensus 106 ~Lp~~~r~v~~l~~~~--g~s----~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWE--DMD----VAETAAAM----GCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHh--cCC----HHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3445555555554444 122 45889999 999999998887666555543
No 97
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.23 E-value=70 Score=21.06 Aligned_cols=23 Identities=39% Similarity=0.820 Sum_probs=18.9
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhH
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRR 160 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRR 160 (289)
..++|..+ ||+...|..|.+.-+
T Consensus 15 ~~~~a~~~----gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 15 VREIAREF----GISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHH----CCCHhHHHHHHHHHH
Confidence 34689999 999999999986543
No 98
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.19 E-value=1.8e+02 Score=25.91 Aligned_cols=32 Identities=16% Similarity=0.071 Sum_probs=25.0
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
.++||..| |+++..|+++...-|.+.|+.-..
T Consensus 153 ~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 153 YREIAAIA----DVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHcc
Confidence 34789999 999999999988766666665543
No 99
>PRK06930 positive control sigma-like factor; Validated
Probab=22.13 E-value=1.6e+02 Score=25.51 Aligned_cols=51 Identities=16% Similarity=0.093 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhhh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQLV 169 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~~ 169 (289)
.+++.+..++.-.|..+ ....+||..| |++...|+++...-|.|.++.-..
T Consensus 114 ~L~~rer~V~~L~~~eg------~s~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG------LSYSEIADYL----NIKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666544441 1234789999 999999999998877777765443
No 100
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.72 E-value=1.5e+02 Score=25.02 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=22.1
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
..+||..+ |++...|++|-..-|.+-|+
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 45789999 99999999998765555544
No 101
>PRK10072 putative transcriptional regulator; Provisional
Probab=21.29 E-value=51 Score=26.05 Aligned_cols=41 Identities=20% Similarity=0.207 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHH
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRA 161 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRa 161 (289)
..+...+..|...-.. + ..+||..+ |++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-----T---Q~elA~~l----GvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-----K---IDDFARVL----GVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-----C---HHHHHHHh----CCCHHHHHHHHcCCCC
Confidence 3466666666432221 2 45899999 9999999999988764
No 102
>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=21.23 E-value=1.7e+02 Score=23.97 Aligned_cols=27 Identities=19% Similarity=0.009 Sum_probs=19.7
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHH
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSK 164 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~K 164 (289)
..+||..| |+++..|++...--|.+.|
T Consensus 141 ~~eIA~~l----~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 141 IAEVARIL----GKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 44789999 9999999887754444443
No 103
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.15 E-value=1.4e+02 Score=25.44 Aligned_cols=29 Identities=21% Similarity=0.177 Sum_probs=23.1
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHH
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRK 166 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~ 166 (289)
..+||..| |+++..|+++...-|.+.|+.
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 999999999987666655554
No 104
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.12 E-value=1.2e+02 Score=23.97 Aligned_cols=38 Identities=18% Similarity=0.107 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchh
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNV 152 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV 152 (289)
++++|...-...|+. |--.+.-..+++|..| ++++..|
T Consensus 3 Ln~eq~~~Tk~elqa-n~el~~LS~~~iA~~L----n~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQA-NFELCPLSDEEIATAL----NWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHH-hhhhccccHHHHHHHh----CCCHHHH
Confidence 567777766666666 5555556677899999 8887544
No 105
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.95 E-value=1.4e+02 Score=28.42 Aligned_cols=54 Identities=11% Similarity=0.076 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHhh
Q 022944 109 TPTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQL 168 (289)
Q Consensus 109 ~ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~~ 168 (289)
.+++.+..+|+..|.- .|-.....++||..| |++...|+.+...-+.|-|+.-.
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 5667777777766632 122334456899999 99999999999877777766543
No 106
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.93 E-value=1.5e+02 Score=24.21 Aligned_cols=46 Identities=20% Similarity=0.153 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHH
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKR 165 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr 165 (289)
+++.+..+|.-.|-. . ....+||..| |++...|+.....-|.+.|+
T Consensus 110 L~~~~r~v~~l~~~~--~----~s~~EIA~~l----gis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 110 LPARTRYAFEMYRLH--G----ETQKDIAREL----GVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCHHHHHHHHHHHHc--C----CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 444555555544433 1 2245889999 99999999987655555554
No 107
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.90 E-value=1.8e+02 Score=24.28 Aligned_cols=48 Identities=13% Similarity=0.000 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 110 PTPVQLQILESIFDQGTGTPSKQKIKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 110 ft~~Ql~~LE~~F~~~~~yPs~~~r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
+++.+..++.-.|-.+ ....+||..| |+++..|+++...-+.+++..-
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 4445555555444331 2234789999 9999999999987777776543
No 108
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.87 E-value=2.4e+02 Score=24.08 Aligned_cols=30 Identities=13% Similarity=0.004 Sum_probs=23.7
Q ss_pred HHHHHHHHHhcCCcccchhhchhhhhHHHHHHHh
Q 022944 134 IKEITVELSQHGQISETNVYNWFQNRRARSKRKQ 167 (289)
Q Consensus 134 r~~LA~~L~~~~gLs~~qV~vWFQNRRaK~Kr~~ 167 (289)
..+||..| |++...|+++..--|.+.|+.-
T Consensus 155 ~~eIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 155 NPEIAEVM----EIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred HHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 44789999 9999999999986666665543
Done!