Query 027068
Match_columns 229
No_of_seqs 296 out of 1477
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 04:30:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027068.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027068hhsearch_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 8.7E-37 1.9E-41 277.4 4.9 141 7-156 214-354 (398)
2 KOG1168 Transcription factor A 99.8 2.1E-20 4.5E-25 164.3 0.3 143 7-157 225-370 (385)
3 KOG0484 Transcription factor P 99.8 3.6E-19 7.9E-24 135.3 4.2 66 88-158 14-79 (125)
4 KOG0488 Transcription factor B 99.8 1E-18 2.2E-23 157.7 6.5 71 85-160 166-236 (309)
5 KOG2251 Homeobox transcription 99.7 3.2E-18 6.9E-23 145.6 8.6 68 86-158 32-99 (228)
6 KOG0489 Transcription factor z 99.7 1.7E-18 3.6E-23 153.2 6.8 69 88-161 156-224 (261)
7 KOG4577 Transcription factor L 99.7 3.6E-18 7.9E-23 150.1 3.0 119 35-159 103-230 (383)
8 KOG0843 Transcription factor E 99.7 1.6E-17 3.5E-22 137.4 6.3 64 90-158 101-164 (197)
9 KOG0850 Transcription factor D 99.7 3.3E-17 7.2E-22 140.1 6.1 67 86-157 117-183 (245)
10 KOG0487 Transcription factor A 99.7 6.2E-17 1.3E-21 145.0 6.1 65 88-157 232-296 (308)
11 KOG0842 Transcription factor t 99.7 4.3E-17 9.3E-22 146.0 4.9 67 88-159 150-216 (307)
12 PF00046 Homeobox: Homeobox do 99.6 1.8E-16 3.9E-21 108.4 5.2 57 92-153 1-57 (57)
13 KOG0492 Transcription factor M 99.6 1.7E-16 3.7E-21 134.0 5.4 68 86-158 139-206 (246)
14 KOG0485 Transcription factor N 99.6 2.1E-16 4.6E-21 134.3 5.2 66 88-158 101-166 (268)
15 KOG0494 Transcription factor C 99.6 1.1E-15 2.3E-20 133.0 5.8 64 90-158 140-203 (332)
16 KOG0848 Transcription factor C 99.6 1.1E-15 2.3E-20 133.4 2.3 61 93-158 201-261 (317)
17 KOG0491 Transcription factor B 99.5 5.3E-15 1.2E-19 121.0 3.5 66 90-160 99-164 (194)
18 smart00389 HOX Homeodomain. DN 99.5 1.9E-14 4.2E-19 97.5 4.8 55 93-152 2-56 (56)
19 TIGR01565 homeo_ZF_HD homeobox 99.5 2.5E-14 5.4E-19 99.0 5.0 52 92-148 2-57 (58)
20 KOG0493 Transcription factor E 99.5 1E-14 2.3E-19 126.9 3.8 62 91-157 246-307 (342)
21 cd00086 homeodomain Homeodomai 99.5 3.3E-14 7.2E-19 97.0 5.5 57 93-154 2-58 (59)
22 COG5576 Homeodomain-containing 99.4 1.4E-13 3E-18 113.2 5.8 65 90-159 50-114 (156)
23 KOG0490 Transcription factor, 99.4 4E-13 8.8E-18 115.0 8.2 105 46-156 16-120 (235)
24 KOG0844 Transcription factor E 99.4 7.4E-14 1.6E-18 123.9 3.1 64 89-157 179-242 (408)
25 KOG0847 Transcription factor, 99.4 3.3E-13 7.2E-18 115.1 5.7 66 89-159 165-230 (288)
26 KOG0486 Transcription factor P 99.4 1.9E-13 4.2E-18 121.6 4.4 65 89-158 110-174 (351)
27 KOG0483 Transcription factor H 99.4 1.5E-13 3.2E-18 116.8 3.4 63 91-158 50-112 (198)
28 PF00157 Pou: Pou domain - N-t 99.2 4.6E-13 1E-17 96.8 -2.4 60 7-66 15-74 (75)
29 KOG0849 Transcription factor P 99.0 3E-10 6.5E-15 104.7 5.0 65 88-157 173-237 (354)
30 KOG0775 Transcription factor S 98.7 2.5E-08 5.5E-13 87.8 7.5 50 99-153 184-233 (304)
31 smart00352 POU Found in Pit-Oc 98.5 2.7E-08 5.8E-13 72.1 -0.0 60 7-66 15-74 (75)
32 PF05920 Homeobox_KN: Homeobox 98.3 3.1E-07 6.6E-12 59.0 2.1 33 114-150 8-40 (40)
33 KOG0774 Transcription factor P 98.3 1.3E-06 2.8E-11 76.7 6.2 62 91-156 188-251 (334)
34 KOG0490 Transcription factor, 98.1 2.6E-06 5.7E-11 72.8 4.3 64 88-156 150-213 (235)
35 KOG2252 CCAAT displacement pro 98.0 7.2E-06 1.6E-10 78.4 4.6 57 90-151 419-475 (558)
36 KOG1146 Homeobox protein [Gene 97.6 6.1E-05 1.3E-09 78.3 4.6 63 91-158 903-965 (1406)
37 PF11569 Homez: Homeodomain le 96.0 0.0037 8.1E-08 42.9 1.6 42 103-149 10-51 (56)
38 KOG0773 Transcription factor M 95.8 0.0075 1.6E-07 55.1 3.3 61 91-155 239-301 (342)
39 KOG3623 Homeobox transcription 94.3 0.059 1.3E-06 53.9 4.8 50 103-157 568-617 (1007)
40 PF04218 CENP-B_N: CENP-B N-te 90.9 0.44 9.5E-06 32.0 4.0 47 92-148 1-47 (53)
41 PF08880 QLQ: QLQ; InterPro: 89.6 0.43 9.4E-06 30.0 2.9 22 33-54 2-23 (37)
42 PF01527 HTH_Tnp_1: Transposas 66.7 6.6 0.00014 27.3 2.9 45 93-147 2-47 (76)
43 PF04967 HTH_10: HTH DNA bindi 66.5 8 0.00017 26.1 3.1 39 98-141 1-41 (53)
44 PF04545 Sigma70_r4: Sigma-70, 64.2 14 0.0003 23.7 3.9 44 97-150 4-47 (50)
45 cd06171 Sigma70_r4 Sigma70, re 63.3 8 0.00017 23.9 2.6 44 97-150 10-53 (55)
46 PF08281 Sigma70_r4_2: Sigma-7 55.8 14 0.00031 23.9 2.9 42 98-149 11-52 (54)
47 cd00569 HTH_Hin_like Helix-tur 52.6 30 0.00064 18.8 3.6 37 98-144 6-42 (42)
48 KOG3755 SATB1 matrix attachmen 45.8 10 0.00022 37.7 1.2 48 107-157 708-760 (769)
49 PRK03975 tfx putative transcri 44.0 37 0.0008 27.5 4.0 49 96-155 5-53 (141)
50 PRK09413 IS2 repressor TnpA; R 41.5 41 0.0009 26.0 3.9 42 95-146 10-52 (121)
51 PF13936 HTH_38: Helix-turn-he 40.9 17 0.00037 23.1 1.3 40 96-145 3-42 (44)
52 PF10668 Phage_terminase: Phag 40.6 14 0.00031 25.6 0.9 20 121-144 24-43 (60)
53 PRK06759 RNA polymerase factor 40.5 35 0.00076 26.6 3.4 46 97-152 106-151 (154)
54 PRK09644 RNA polymerase sigma 40.4 44 0.00095 26.5 4.0 33 121-157 126-158 (165)
55 PRK09652 RNA polymerase sigma 39.7 43 0.00092 26.5 3.8 48 97-154 128-175 (182)
56 PRK09646 RNA polymerase sigma 39.2 45 0.00098 27.4 4.0 47 98-154 143-189 (194)
57 PF00196 GerE: Bacterial regul 38.6 51 0.0011 21.7 3.5 44 97-151 3-46 (58)
58 COG3413 Predicted DNA binding 38.3 34 0.00073 29.0 3.1 49 97-152 155-205 (215)
59 PRK12526 RNA polymerase sigma 35.1 62 0.0014 26.9 4.3 31 121-155 171-201 (206)
60 TIGR02937 sigma70-ECF RNA poly 35.0 54 0.0012 24.5 3.6 46 98-153 111-156 (158)
61 PRK12512 RNA polymerase sigma 33.8 72 0.0016 25.7 4.3 50 98-157 132-181 (184)
62 PF02796 HTH_7: Helix-turn-hel 32.7 41 0.0009 21.3 2.2 38 97-144 5-42 (45)
63 PRK00118 putative DNA-binding 32.2 72 0.0016 24.5 3.8 46 98-153 18-63 (104)
64 PRK12541 RNA polymerase sigma 32.1 59 0.0013 25.6 3.5 46 98-153 113-158 (161)
65 PRK12514 RNA polymerase sigma 31.8 79 0.0017 25.3 4.2 29 121-153 147-175 (179)
66 PRK09642 RNA polymerase sigma 31.5 73 0.0016 25.0 3.9 48 98-155 107-154 (160)
67 PRK12519 RNA polymerase sigma 30.9 55 0.0012 26.7 3.2 30 120-153 158-187 (194)
68 PRK04217 hypothetical protein; 30.9 80 0.0017 24.5 3.9 52 96-157 41-92 (110)
69 PRK09480 slmA division inhibit 30.8 43 0.00092 26.9 2.5 36 108-149 21-56 (194)
70 TIGR02999 Sig-70_X6 RNA polyme 30.6 71 0.0015 25.6 3.8 46 98-153 135-180 (183)
71 PRK11924 RNA polymerase sigma 30.6 67 0.0015 25.2 3.6 30 121-154 143-172 (179)
72 PRK12516 RNA polymerase sigma 30.4 88 0.0019 25.7 4.4 31 122-156 135-165 (187)
73 TIGR02948 SigW_bacill RNA poly 29.2 69 0.0015 25.7 3.5 29 121-153 154-182 (187)
74 PRK05602 RNA polymerase sigma 28.8 89 0.0019 25.3 4.1 31 122-156 147-177 (186)
75 TIGR03879 near_KaiC_dom probab 28.4 23 0.0005 25.5 0.4 34 108-146 22-55 (73)
76 TIGR02989 Sig-70_gvs1 RNA poly 28.0 79 0.0017 24.6 3.5 44 97-150 111-154 (159)
77 PF06056 Terminase_5: Putative 28.0 34 0.00073 23.3 1.2 20 122-145 16-35 (58)
78 TIGR02985 Sig70_bacteroi1 RNA 27.9 95 0.0021 23.8 4.0 45 98-152 114-158 (161)
79 PRK12533 RNA polymerase sigma 27.2 1E+02 0.0022 26.2 4.3 32 122-157 153-184 (216)
80 PRK09648 RNA polymerase sigma 27.2 88 0.0019 25.4 3.8 46 98-153 140-185 (189)
81 PRK09639 RNA polymerase sigma 27.1 96 0.0021 24.3 3.9 47 98-155 113-159 (166)
82 cd04761 HTH_MerR-SF Helix-Turn 27.0 35 0.00076 21.2 1.1 22 122-147 3-24 (49)
83 COG4367 Uncharacterized protei 26.9 79 0.0017 23.8 3.0 39 98-141 3-41 (97)
84 KOG1146 Homeobox protein [Gene 26.9 1E+02 0.0022 33.7 4.8 61 90-155 704-764 (1406)
85 TIGR02959 SigZ RNA polymerase 26.7 89 0.0019 25.0 3.7 49 97-155 100-148 (170)
86 PRK12515 RNA polymerase sigma 26.6 94 0.002 25.2 3.9 48 98-155 132-179 (189)
87 smart00421 HTH_LUXR helix_turn 25.9 1.4E+02 0.003 18.4 3.9 39 97-146 3-41 (58)
88 PRK09047 RNA polymerase factor 25.1 1.2E+02 0.0026 23.6 4.1 46 98-153 107-152 (161)
89 PRK06930 positive control sigm 25.0 1E+02 0.0022 25.5 3.8 49 97-155 114-162 (170)
90 PF13518 HTH_28: Helix-turn-he 25.0 52 0.0011 20.7 1.6 24 122-149 15-38 (52)
91 PRK09637 RNA polymerase sigma 24.9 1E+02 0.0022 25.1 3.8 31 121-155 124-154 (181)
92 TIGR02983 SigE-fam_strep RNA p 24.8 1.3E+02 0.0028 23.5 4.3 46 99-154 112-157 (162)
93 PF12720 DUF3807: Protein of u 24.6 49 0.0011 27.8 1.8 14 32-45 48-61 (172)
94 PF13384 HTH_23: Homeodomain-l 24.0 43 0.00093 21.2 1.1 22 121-146 19-40 (50)
95 PRK12537 RNA polymerase sigma 23.8 1.2E+02 0.0026 24.4 4.0 28 121-152 151-178 (182)
96 PRK12530 RNA polymerase sigma 23.4 1.1E+02 0.0024 24.9 3.8 29 121-153 152-180 (189)
97 PRK12546 RNA polymerase sigma 23.3 1.1E+02 0.0024 25.2 3.7 32 121-156 131-162 (188)
98 TIGR02952 Sig70_famx2 RNA poly 23.3 1.2E+02 0.0027 23.7 3.9 26 121-150 140-165 (170)
99 TIGR02939 RpoE_Sigma70 RNA pol 23.2 89 0.0019 25.1 3.1 31 120-154 155-185 (190)
100 PRK12547 RNA polymerase sigma 23.1 1.2E+02 0.0026 24.1 3.7 46 98-153 113-158 (164)
101 PRK07037 extracytoplasmic-func 22.8 1.3E+02 0.0027 23.6 3.8 46 98-153 110-155 (163)
102 PRK10072 putative transcriptio 22.6 90 0.002 23.5 2.7 24 122-149 49-72 (96)
103 TIGR02954 Sig70_famx3 RNA poly 22.3 1.4E+02 0.003 23.6 4.0 46 98-153 120-165 (169)
104 PRK12543 RNA polymerase sigma 21.7 1.4E+02 0.0029 24.1 3.9 32 121-156 135-166 (179)
105 PRK06811 RNA polymerase factor 21.7 1.2E+02 0.0027 24.6 3.7 48 98-155 132-179 (189)
106 PRK12524 RNA polymerase sigma 21.5 1.4E+02 0.003 24.5 3.9 29 122-154 155-183 (196)
107 PRK12536 RNA polymerase sigma 20.8 1.4E+02 0.003 24.1 3.8 30 120-153 146-175 (181)
108 PF08280 HTH_Mga: M protein tr 20.7 86 0.0019 21.0 2.1 35 101-144 6-40 (59)
109 PRK05657 RNA polymerase sigma 20.5 1.4E+02 0.0029 27.3 4.0 53 97-155 262-314 (325)
110 PRK06986 fliA flagellar biosyn 20.5 1.4E+02 0.0031 25.3 3.9 46 99-154 186-231 (236)
111 cd02413 40S_S3_KH K homology R 20.3 77 0.0017 23.0 1.9 25 121-145 51-75 (81)
112 PRK12539 RNA polymerase sigma 20.2 1.7E+02 0.0036 23.6 4.2 47 98-154 132-178 (184)
113 PRK12538 RNA polymerase sigma 20.2 1.2E+02 0.0025 26.2 3.3 31 121-155 189-219 (233)
114 smart00027 EH Eps15 homology d 20.1 1.7E+02 0.0036 21.2 3.8 45 96-144 2-50 (96)
115 PRK09645 RNA polymerase sigma 20.1 1.7E+02 0.0037 23.2 4.1 46 98-153 119-164 (173)
No 1
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=100.00 E-value=8.7e-37 Score=277.43 Aligned_cols=141 Identities=19% Similarity=0.199 Sum_probs=123.9
Q ss_pred CcccCCchhhhhcccccCcCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcchhhhcCCCCCCCCCCCccCC
Q 027068 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASG 86 (229)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~q~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~ 86 (229)
.|||++|+++|+|+|||+|+|+|||+|||||+||||+++.++|+|||+..+++.||+.+++.... ..+....+.+..
T Consensus 214 ~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~-~~~~~~~e~i~a-- 290 (398)
T KOG3802|consen 214 TFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRES-TGSPNSIEKIGA-- 290 (398)
T ss_pred HHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccc-cCCCCCHHHhhc--
Confidence 59999999999999999999999999999999999999999999999999999999999875311 112222222222
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 87 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 87 ~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
..++|++||.|....+..||+.|.+| ++|+..+|..||.+| +|+..+|+|||||||.|+||...
T Consensus 291 -~~RkRKKRTSie~~vr~aLE~~F~~n-pKPt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 -QSRKRKKRTSIEVNVRGALEKHFLKN-PKPTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred -cccccccccceeHHHHHHHHHHHHhC-CCCCHHHHHHHHHHh----ccccceEEEEeeccccccccCCC
Confidence 22688899999999999999999999 899999999999999 99999999999999999998665
No 2
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.78 E-value=2.1e-20 Score=164.26 Aligned_cols=143 Identities=17% Similarity=0.212 Sum_probs=120.1
Q ss_pred CcccCCchhhhhcccccCcCCCc---ccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcchhhhcCCCCCCCCCCCc
Q 027068 7 NFQQGGEMERQFQQDGGDTSNGL---CVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFV 83 (229)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~---~~~~~t~~q~~~lr~qi~~~~~ic~q~~~~~~~~~~~~~~~~~~~~~~~~~p~~ 83 (229)
.|+|++|+++-+|+|||-|+-.| .|..+||.+||+|+-+-++-.||--..+.++.|+..+..........+....+.
T Consensus 225 rFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~keK~~~pd~~~l~ 304 (385)
T KOG1168|consen 225 RFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAMKEKDTKPDINELL 304 (385)
T ss_pred HHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHHHhhccCCchhhcc
Confidence 59999999999999999998877 899999999999999999999999999999999998765322111111111111
Q ss_pred cCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 84 ASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 84 ~~~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
.++ .++|+||.+..-....||.+|... +.|+.+.|..||++| .|...+|+|||||.|+|.||.+..
T Consensus 305 -~~~--ekKRKRTSIAAPEKRsLEayFavQ-PRPS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 305 -PGG--EKKRKRTSIAAPEKRSLEAYFAVQ-PRPSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred -Ccc--ccccccccccCcccccHHHHhccC-CCCchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhhhh
Confidence 222 367889999999999999999999 889999999999999 999999999999999999986554
No 3
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.76 E-value=3.6e-19 Score=135.26 Aligned_cols=66 Identities=32% Similarity=0.532 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
.++.||-||+||..||.+||+.|... |||++-.|++||..| .|++.+|+|||||||+|.+|+.+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ET-HYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAET-HYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhh-cCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 45678899999999999999999999 999999999999999 9999999999999999999987653
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=1e-18 Score=157.68 Aligned_cols=71 Identities=24% Similarity=0.329 Sum_probs=65.9
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCCCC
Q 027068 85 SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 160 (229)
Q Consensus 85 ~~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~~~ 160 (229)
...++|+|+.||.||..||..||+.|++. +|.+..+|.+||..| ||+..||++||||||+||||.......
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 44568899999999999999999999999 999999999999999 999999999999999999998887443
No 5
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.75 E-value=3.2e-18 Score=145.64 Aligned_cols=68 Identities=29% Similarity=0.488 Sum_probs=65.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 86 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
+++++.||.||+|+..||.+||.+|.+. .||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kT-qYPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKT-QYPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhh-cCccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 6778899999999999999999999999 999999999999999 9999999999999999999988864
No 6
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=1.7e-18 Score=153.16 Aligned_cols=69 Identities=23% Similarity=0.322 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCCCCC
Q 027068 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPN 161 (229)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~~~~ 161 (229)
..+.||.||.||..||.+||+.|+.| +|.++..|.+||..| .|+|+||||||||||+||||..+.....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN-~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFN-KYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccc-cccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34578999999999999999999999 999999999999999 9999999999999999999988775443
No 7
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.71 E-value=3.6e-18 Score=150.12 Aligned_cols=119 Identities=23% Similarity=0.281 Sum_probs=101.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcchhhhcCCCCCCCCCCCccCC---------CCCCCCCCCCCCCHHHHHH
Q 027068 35 TDEQMELLRKQIAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASG---------SQKLTARQRWTPTPAQLQI 105 (229)
Q Consensus 35 t~~q~~~lr~qi~~~~~ic~q~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~---------~~~~~rr~Rt~~t~~Ql~~ 105 (229)
-.+|+- -++|..||+..|.+++.+.+.|.+.++++-|..+...|.-.+... +....+|+||++|..||+.
T Consensus 103 pPtqVV-RkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLET 181 (383)
T KOG4577|consen 103 PPTQVV-RKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLET 181 (383)
T ss_pred ChHHHH-HHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHH
Confidence 344433 389999999999999999999999999988888776665444322 3345789999999999999
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCCC
Q 027068 106 LEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (229)
Q Consensus 106 Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~~ 159 (229)
|..+|... +.|.+..|++|+.+. ||..++|||||||||||+||.++...
T Consensus 182 LK~AYn~S-pKPARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 182 LKQAYNTS-PKPARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred HHHHhcCC-CchhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhcc
Confidence 99999999 899999999999999 99999999999999999999887643
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.70 E-value=1.6e-17 Score=137.43 Aligned_cols=64 Identities=36% Similarity=0.450 Sum_probs=61.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
+.+|.||.|+.+||..||.+|+.+ +|....+|+.||..| +|++.||+|||||||.|.||.+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~-~Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN-QYVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC-CeeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 788999999999999999999999 999999999999999 9999999999999999999988774
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.68 E-value=3.3e-17 Score=140.12 Aligned_cols=67 Identities=27% Similarity=0.416 Sum_probs=63.6
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 86 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
++.+|.|+.||.|+.-||..|.+.|+++ .|+-.+||.+||..| ||+..||||||||||.|.||..+.
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkT-QYLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQT-QYLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhc-chhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhc
Confidence 4567888999999999999999999999 999999999999999 999999999999999999998884
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.67 E-value=6.2e-17 Score=145.01 Aligned_cols=65 Identities=26% Similarity=0.296 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
.+..|++|-.+|..|+.+||+.|..| .|.+++.|.+|++.| +|+++||+|||||||+|.||..++
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN-~YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFN-MYITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHH-HHHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhh
Confidence 46788999999999999999999999 999999999999999 999999999999999999998864
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.67 E-value=4.3e-17 Score=145.95 Aligned_cols=67 Identities=25% Similarity=0.372 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCCC
Q 027068 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (229)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~~ 159 (229)
..++||.|..|+..|..+||+.|..+ +|.+.+||++||..| +||+.||||||||||-|.||++....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhh
Confidence 45677889999999999999999999 999999999999999 99999999999999999999887754
No 12
>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=99.65 E-value=1.8e-16 Score=108.38 Aligned_cols=57 Identities=39% Similarity=0.634 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 92 rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
|++|+.||.+|+.+|+.+|..+ +||+..++..||..| ||+..+|++||+|||++.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~-~~p~~~~~~~la~~l----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN-PYPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS-SSCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh-ccccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 5789999999999999999999 999999999999999 99999999999999999986
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.64 E-value=1.7e-16 Score=133.95 Aligned_cols=68 Identities=32% Similarity=0.401 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 86 ~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
.+++..|++||.||..||..||+.|... .|.++.+|.+++..| .|++.||+|||||||+|.||.++..
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrek-qYLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREK-QYLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHh-hhhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHH
Confidence 3466788999999999999999999999 999999999999999 9999999999999999999987653
No 14
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.63 E-value=2.1e-16 Score=134.26 Aligned_cols=66 Identities=29% Similarity=0.367 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
..++++.||+|+..|+..||..|+.. +|.+..+|..||..| .|+|.||||||||||.||||+-...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 34678899999999999999999999 999999999999999 9999999999999999999987653
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.59 E-value=1.1e-15 Score=132.96 Aligned_cols=64 Identities=25% Similarity=0.361 Sum_probs=59.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
++|+-||.||..|+..||+.|+.. +||+...|+-||..+ .|.+.+|+|||||||+||||..+.-
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhhc
Confidence 344459999999999999999999 999999999999999 9999999999999999999987763
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.56 E-value=1.1e-15 Score=133.39 Aligned_cols=61 Identities=28% Similarity=0.361 Sum_probs=57.3
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
+-|.++|..|+.+||+.|..+ +|.++..+.+||..| ||+|+||||||||||+|+||..+..
T Consensus 201 KYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHH
Confidence 558899999999999999999 999999999999999 9999999999999999999876654
No 17
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.52 E-value=5.3e-15 Score=120.96 Aligned_cols=66 Identities=30% Similarity=0.422 Sum_probs=62.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCCCC
Q 027068 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 160 (229)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~~~ 160 (229)
++++.||+|+..|+..||+.|+.. +|.+.++|.+||..| +|++.||+.||||||+|.||.++...+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 567789999999999999999999 999999999999999 999999999999999999998887654
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.51 E-value=1.9e-14 Score=97.54 Aligned_cols=55 Identities=40% Similarity=0.649 Sum_probs=51.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHH
Q 027068 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (229)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~K 152 (229)
+.|+.|+..++.+|+..|..+ +||+..++..||..| ||+..+|++||+|||++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~-~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKN-PYPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 567889999999999999999 999999999999999 9999999999999998853
No 19
>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=99.50 E-value=2.5e-14 Score=98.96 Aligned_cols=52 Identities=17% Similarity=0.381 Sum_probs=50.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHHHhhCCCcccchhehhhhhh
Q 027068 92 ARQRWTPTPAQLQILEHVYDECKGT----PRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (229)
Q Consensus 92 rr~Rt~~t~~Ql~~Le~~F~~~~~y----P~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR 148 (229)
+|.||.||++|+..||..|+.+ +| |+..+|.+||..| ||++.+|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~-~y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKL-GWKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 7899999999999999999999 99 9999999999999 999999999999964
No 20
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.50 E-value=1e-14 Score=126.91 Aligned_cols=62 Identities=32% Similarity=0.504 Sum_probs=57.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
-+|+||.||.+||..|...|..+ +|.+...|.+||.+| +|.+.||+|||||+|+|-||-...
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhccCC
Confidence 46889999999999999999999 999999999999999 999999999999999999885433
No 21
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.50 E-value=3.3e-14 Score=97.02 Aligned_cols=57 Identities=40% Similarity=0.672 Sum_probs=53.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
+.|+.++..++.+||.+|..+ +||+..++..||..| ||++.+|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~-~~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN-PYPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 567899999999999999999 999999999999999 999999999999999998763
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.44 E-value=1.4e-13 Score=113.18 Aligned_cols=65 Identities=31% Similarity=0.443 Sum_probs=59.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCCC
Q 027068 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (229)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~~ 159 (229)
..+++|++-+..|+.+|++.|+.+ +||+...|..|+..| +|+++.|+|||||||++.|+......
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~-p~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEIN-PYPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred cCcccceechHHHHHHHHHHhccC-CCCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccch
Confidence 356677778999999999999999 999999999999999 99999999999999999998776643
No 23
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.43 E-value=4e-13 Score=114.98 Aligned_cols=105 Identities=19% Similarity=0.187 Sum_probs=76.8
Q ss_pred HHHHHHHHHHHHHHhhhhhcchhhhcCCCCCCCCCCCccCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHH
Q 027068 46 IAVYAMICEQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDM 125 (229)
Q Consensus 46 i~~~~~ic~q~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~L 125 (229)
...++.-|-.+..+...+......... .|..++..........+.|+.|+.|+..|+.+||+.|+.. |||+...|+.|
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~l 93 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECL 93 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHH
Confidence 334445555555554444421122222 4444444433322244678999999999999999999999 99999999999
Q ss_pred HHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 126 TAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 126 A~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
|..+ ++++..|+|||||||+|++++.+
T Consensus 94 a~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 94 ALLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hhcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 9999 99999999999999999998775
No 24
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.42 E-value=7.4e-14 Score=123.91 Aligned_cols=64 Identities=28% Similarity=0.378 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 89 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
..-||-||.||.+|+..||+.|-+. -|.+++.|.+||..| +|.+..|||||||||+|+||++..
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrE-NYVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRE-NYVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHh-ccccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhh
Confidence 3467889999999999999999888 699999999999999 999999999999999999998765
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.40 E-value=3.3e-13 Score=115.08 Aligned_cols=66 Identities=26% Similarity=0.391 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCCC
Q 027068 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159 (229)
Q Consensus 89 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~~ 159 (229)
.+++..|.+|+..|+..||..|+.. +|+-.++|.+||..| |+++.+|+|||||||.||||+.....
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqt-kylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEm 230 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQT-KYLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEM 230 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhh-hcccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccch
Confidence 4667789999999999999999999 999999999999999 99999999999999999999876643
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.40 E-value=1.9e-13 Score=121.64 Aligned_cols=65 Identities=28% Similarity=0.428 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 89 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 89 ~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
.|.||.||.|+..||.+||..|..+ +||+...|++||.-. +|++.+|+|||+|||+||+|.++..
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhH
Confidence 3788999999999999999999999 999999999999999 9999999999999999999877654
No 27
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.39 E-value=1.5e-13 Score=116.83 Aligned_cols=63 Identities=29% Similarity=0.424 Sum_probs=57.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
..+++.+++.+|+..||..|+.. .|....++..||+.| ||.++||.|||||||||||.++...
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~-~~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE-KKLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccccccccHHHHHHhHHhhccc-cccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhh
Confidence 34455679999999999999999 899999999999999 9999999999999999999987764
No 28
>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=99.23 E-value=4.6e-13 Score=96.83 Aligned_cols=60 Identities=15% Similarity=0.123 Sum_probs=55.6
Q ss_pred CcccCCchhhhhcccccCcCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 027068 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (229)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~q~~~~~~~~~~~ 66 (229)
.|+++++.+++.|+|||.++|.+||++||+++||+|+++..+++++|+..|.+.+|+.+.
T Consensus 15 ~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~ea 74 (75)
T PF00157_consen 15 EFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhc
Confidence 488999999999999999999999999999999999999999999999999999999764
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.01 E-value=3e-10 Score=104.68 Aligned_cols=65 Identities=31% Similarity=0.494 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
.++.+|.||+|+..|+..||+.|+.+ +||++..|++||.++ ++++..|+|||+|||++++|....
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt-~yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRT-PYPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccchHHHHHHHhcCC-CCCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 45677889999999999999999999 899999999999999 999999999999999999998843
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.75 E-value=2.5e-08 Score=87.80 Aligned_cols=50 Identities=24% Similarity=0.427 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 99 t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
...-+..|..+|..+ +||+..++.+||+.+ ||+..||-+||+|||+|+|-
T Consensus 184 KekSR~~LrewY~~~-~YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 184 KEKSRSLLREWYLQN-PYPSPREKRELAEAT----GLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hHhhHHHHHHHHhcC-CCCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhhh
Confidence 344467999999999 999999999999999 99999999999999999983
No 31
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.47 E-value=2.7e-08 Score=72.06 Aligned_cols=60 Identities=13% Similarity=0.077 Sum_probs=56.9
Q ss_pred CcccCCchhhhhcccccCcCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Q 027068 7 NFQQGGEMERQFQQDGGDTSNGLCVKVMTDEQMELLRKQIAVYAMICEQLVQMHKVFSAQ 66 (229)
Q Consensus 7 ~~~~~~~~~~~~q~~~~~~~~~~~~~~~t~~q~~~lr~qi~~~~~ic~q~~~~~~~~~~~ 66 (229)
.|++.+...+.+|+|+|.++|.+||..+|+.+|++|+....+++++|+..|.+.+|+.+.
T Consensus 15 ~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~ 74 (75)
T smart00352 15 TFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 74 (75)
T ss_pred HHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhc
Confidence 577888999999999999999999999999999999999999999999999999999764
No 32
>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=98.32 E-value=3.1e-07 Score=58.96 Aligned_cols=33 Identities=27% Similarity=0.586 Sum_probs=28.1
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhH
Q 027068 114 KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (229)
Q Consensus 114 ~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak 150 (229)
+|||+..++..||... ||+..||..||-|.|.|
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 4999999999999999 99999999999999875
No 33
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.30 E-value=1.3e-06 Score=76.75 Aligned_cols=62 Identities=23% Similarity=0.450 Sum_probs=56.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh--cCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 91 TARQRWTPTPAQLQILEHVYDE--CKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~--~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
.||+|..|+..-..+|..+|.. +++||+.+.+++||+++ +|+..||-+||.|+|-+.||...
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhh
Confidence 5788889999999999999964 36999999999999999 99999999999999999987543
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.12 E-value=2.6e-06 Score=72.77 Aligned_cols=64 Identities=34% Similarity=0.545 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 88 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 88 ~~~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
..+.++.|+.+...|+..|+..|..+ ++|+...+..|+..+ |+++..|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRAT-PKPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCC-CCCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 34678889999999999999999999 999999999999999 99999999999999999998766
No 35
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.97 E-value=7.2e-06 Score=78.45 Aligned_cols=57 Identities=25% Similarity=0.401 Sum_probs=53.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHH
Q 027068 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151 (229)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~ 151 (229)
..+++|.+||..|+..|..+|+.+ ++|+.+..+.|+.+| +|....|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~-~RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN-KRPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC-CCCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 467789999999999999999999 999999999999999 999999999999988885
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.60 E-value=6.1e-05 Score=78.25 Aligned_cols=63 Identities=24% Similarity=0.381 Sum_probs=58.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhCC
Q 027068 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 158 (229)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~~ 158 (229)
+|+.|+.++..||.+|...|... .||...+.+.|...+ +++.+.|++||||-|+|.|+.....
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhhcc
Confidence 66789999999999999999999 999999999999999 9999999999999999999877743
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.99 E-value=0.0037 Score=42.87 Aligned_cols=42 Identities=21% Similarity=0.439 Sum_probs=30.5
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhh
Q 027068 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (229)
Q Consensus 103 l~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRa 149 (229)
+..|+.+|... +++...+...|..+. +|+..+|+.||--|+.
T Consensus 10 ~~pL~~Yy~~h-~~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKH-KQLQEEDLDELCDKS----RMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHT----T--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHc-CCccHhhHHHHHHHH----CCCHHHHHHHHHHhcc
Confidence 45699999998 899999999999998 9999999999976543
No 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.81 E-value=0.0075 Score=55.14 Aligned_cols=61 Identities=23% Similarity=0.272 Sum_probs=49.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 91 TARQRWTPTPAQLQILEHVYDEC--KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 91 ~rr~Rt~~t~~Ql~~Le~~F~~~--~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
..|++..+......+|+.+.... ++||+..++..||.++ ||+..||.+||.|.|-|..+-.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc----CCCcccCCchhhhcccccCCch
Confidence 34555678888899998774432 3799999999999999 9999999999999998866533
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.33 E-value=0.059 Score=53.93 Aligned_cols=50 Identities=16% Similarity=0.380 Sum_probs=45.9
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 103 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 103 l~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
+..|..+|..| ..|+..+...+|.++ ||+.+.|+.||+++++......+.
T Consensus 568 ~sllkayyaln-~~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 568 TSLLKAYYALN-GLPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccC
Confidence 67889999999 899999999999999 999999999999999998876644
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=90.87 E-value=0.44 Score=32.02 Aligned_cols=47 Identities=19% Similarity=0.234 Sum_probs=35.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhh
Q 027068 92 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 148 (229)
Q Consensus 92 rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRR 148 (229)
+|+|..+|-++...+-..++.+ . ...+||..+ |++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-~-----s~~~ia~~f----gv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-E-----SKRDIAREF----GVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-T------HHHHHHHH----T--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-C-----CHHHHHHHh----CCCHHHHHHHHHhHH
Confidence 4788899999988888888888 3 466899999 999999999998853
No 41
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=89.62 E-value=0.43 Score=29.97 Aligned_cols=22 Identities=32% Similarity=0.468 Sum_probs=19.6
Q ss_pred cCCHHHHHHHHHHHHHHHHHHH
Q 027068 33 VMTDEQMELLRKQIAVYAMICE 54 (229)
Q Consensus 33 ~~t~~q~~~lr~qi~~~~~ic~ 54 (229)
.||.+|+..||+||..|.-+.+
T Consensus 2 ~FT~~Ql~~L~~Qi~ayK~l~~ 23 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAYKYLAR 23 (37)
T ss_pred CCCHHHHHHHHHHHHHHHHHHc
Confidence 5899999999999999987665
No 42
>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=66.70 E-value=6.6 Score=27.25 Aligned_cols=45 Identities=22% Similarity=0.414 Sum_probs=29.3
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhh
Q 027068 93 RQRWTPTPAQLQILEHVY-DECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNR 147 (229)
Q Consensus 93 r~Rt~~t~~Ql~~Le~~F-~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNR 147 (229)
++|..||+++...+-..+ ..+ ..+.++|..+ ||++..+..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~----gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREY----GISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHH----TS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeeccc----ccccccccHHHHHH
Confidence 456789998877776666 333 4577899999 99999999997543
No 43
>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=66.50 E-value=8 Score=26.10 Aligned_cols=39 Identities=31% Similarity=0.451 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCC--CCCHHHHHHHHHHHHhhCCCcccchh
Q 027068 98 PTPAQLQILEHVYDECKG--TPRKQKIQDMTAELAKHGQISETNVY 141 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~--yP~~~~r~~LA~~L~~~~gls~~qV~ 141 (229)
+|+.|+.+|..+|+.. - +|-.....+||..| |++..-|-
T Consensus 1 LT~~Q~e~L~~A~~~G-Yfd~PR~~tl~elA~~l----gis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELG-YFDVPRRITLEELAEEL----GISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcC-CCCCCCcCCHHHHHHHh----CCCHHHHH
Confidence 4788999999999887 2 25566778899999 99987654
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=64.20 E-value=14 Score=23.73 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhH
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak 150 (229)
.+++.+..+|...|-.+ ..-.++|..+ |++...|+.+...-..|
T Consensus 4 ~L~~~er~vi~~~y~~~------~t~~eIa~~l----g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG------LTLEEIAERL----GISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHH----TSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC------CCHHHHHHHH----CCcHHHHHHHHHHHHHH
Confidence 46788899999988555 2355899999 99999998877544444
No 45
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=63.35 E-value=8 Score=23.93 Aligned_cols=44 Identities=11% Similarity=0.170 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhH
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak 150 (229)
.+++.+..+++..|..+ + ...++|..+ |++...|+.|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--~----~~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG--L----SYEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC--C----CHHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 35677778887777544 1 345788999 99999999998755443
No 46
>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=55.79 E-value=14 Score=23.88 Aligned_cols=42 Identities=21% Similarity=0.199 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhh
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRa 149 (229)
+++.+..++.-.|-.+ ....++|..+ |+++..|+.|...-|.
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 4566677777666555 3456889999 9999999999875443
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=52.63 E-value=30 Score=18.82 Aligned_cols=37 Identities=16% Similarity=0.423 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehh
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWF 144 (229)
++......+...|... + ...++|..+ |++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~--~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG--E----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHhC
Confidence 5566666666666543 2 345788888 99998888773
No 48
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=45.76 E-value=10 Score=37.72 Aligned_cols=48 Identities=21% Similarity=0.275 Sum_probs=33.2
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHH-----HhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 107 EHVYDECKGTPRKQKIQDMTAEL-----AKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 107 e~~F~~~~~yP~~~~r~~LA~~L-----~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
+.+|.++ +.+....+.+..+.+ .+ ..+...|+.||.|||+++|+.+..
T Consensus 708 ~~w~~k~-~s~s~~~v~eYkee~~~~~~~e--~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKT-RSGSWVDVAEYKEEELLMPYEE--KFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecc-cCchhHHHHHhhHHhhcchhhh--hhhhcchHHHHHHHHHHHhhhhcc
Confidence 5556666 667777766665554 11 135578999999999999986654
No 49
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.98 E-value=37 Score=27.53 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 96 t~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
..+++.|+.+|.. +..+ + ...+||..| |++...|..|-.+.+.+.++..
T Consensus 5 ~~Lt~rqreVL~l-r~~G--l----Tq~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG--L----TQQEIADIL----GTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHcC--C----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 5678999999987 4344 1 345899999 9999999999987777766544
No 50
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=41.55 E-value=41 Score=25.95 Aligned_cols=42 Identities=10% Similarity=0.302 Sum_probs=28.0
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhh
Q 027068 95 RWTPTPAQLQ-ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (229)
Q Consensus 95 Rt~~t~~Ql~-~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQN 146 (229)
|..|+.+... ++...+..+ + ...++|..+ ||++..|..|.+-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g--~----sv~evA~e~----gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG--M----TVSLVARQH----GVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC--C----CHHHHHHHH----CcCHHHHHHHHHH
Confidence 4557777654 334444433 2 244789999 9999999999643
No 51
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=40.94 E-value=17 Score=23.13 Aligned_cols=40 Identities=18% Similarity=0.241 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhh
Q 027068 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145 (229)
Q Consensus 96 t~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQ 145 (229)
..+|.+++..++.+++.+ ....+||..| |.+...|..+..
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 457888899999888766 2345799999 999988877653
No 52
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=40.55 E-value=14 Score=25.64 Aligned_cols=20 Identities=30% Similarity=0.723 Sum_probs=17.0
Q ss_pred HHHHHHHHHHhhCCCcccchhehh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWF 144 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWF 144 (229)
.-.+||.+| |+++.+|..|=
T Consensus 24 ~lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHH----CCCHHHHHHHh
Confidence 345789999 99999999984
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.47 E-value=35 Score=26.56 Aligned_cols=46 Identities=7% Similarity=0.099 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHH
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~K 152 (229)
.+++.+..++...|-.+ ....+||..| |++...|+.|...-|.+.|
T Consensus 106 ~L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHh
Confidence 34555566665554444 2356889999 9999999998865444443
No 54
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=40.35 E-value=44 Score=26.53 Aligned_cols=33 Identities=15% Similarity=0.161 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
...+||..| |+++..|++|...-|.+.|+.-..
T Consensus 126 s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 126 TYEEAASVL----DLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 355888899 999999999998766666665443
No 55
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=39.69 E-value=43 Score=26.51 Aligned_cols=48 Identities=10% Similarity=0.009 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
.+++.+..+|...|-.+ ....+||..| |+++..|+.|...-+.+.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG------LSYEEIAEIM----GCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666554433 1344888999 999999999998555555543
No 56
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=39.17 E-value=45 Score=27.38 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
+++.+..+|...|-.+ ....+||+.| |++...|+++...-|.+.|+.
T Consensus 143 L~~~~r~vl~l~~~~~------~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 143 LTDTQRESVTLAYYGG------LTYREVAERL----AVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCChHhHHHHHHHHHHHHHHH
Confidence 4555555555444333 2455888999 999999999987655555543
No 57
>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=38.58 E-value=51 Score=21.74 Aligned_cols=44 Identities=23% Similarity=0.276 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHH
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~ 151 (229)
.+|+.++.+|.-...-. ...++|..| ++++..|+.+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~-------~~~eIA~~l----~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM-------SNKEIAEEL----GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH----TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC-------CcchhHHhc----CcchhhHHHHHHHHHHHh
Confidence 57888888887666443 355899999 999999999887665554
No 58
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=38.34 E-value=34 Score=29.05 Aligned_cols=49 Identities=33% Similarity=0.370 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHH
Q 027068 97 TPTPAQLQILEHVYDECKG--TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~--yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~K 152 (229)
.+|+.|+.+|..+|+.+ = ||-.....+||+.| |+++.- ++.-=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~G-YFd~PR~~~l~dLA~~l----GISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG-YFDYPRRVSLKDLAKEL----GISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHh----CCCHHH--HHHHHHHHHHH
Confidence 69999999999999887 2 35556677899999 999875 34444555544
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=35.13 E-value=62 Score=26.94 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
...+||..| |+++..|+++...-+.+.++..
T Consensus 171 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQL----NVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 456888999 9999999998876666655543
No 60
>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=34.99 E-value=54 Score=24.52 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..++...|-.+ ....+||..+ |+++..|+.+...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~~~g------~s~~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLEG------LSYKEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 4566666665544333 2345889999 99999999998766555443
No 61
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=33.75 E-value=72 Score=25.69 Aligned_cols=50 Identities=24% Similarity=0.248 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
+++.+..+|...|-.+ ..-.+||..| |++...|+.++..-|.+.|..-..
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 132 LPPRQRDVVQSISVEG------ASIKETAAKL----SMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhhc
Confidence 3444444554443333 2345888999 999999999998777776665443
No 62
>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=32.73 E-value=41 Score=21.29 Aligned_cols=38 Identities=18% Similarity=0.482 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehh
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWF 144 (229)
.++.++...+..++... ..+.+||+.+ |++...|+-++
T Consensus 5 ~~~~~~~~~i~~l~~~G------~si~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG------MSIAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC------CCHHHHHHHH----CcCHHHHHHHH
Confidence 46666777777777666 2366899999 99999888765
No 63
>PRK00118 putative DNA-binding protein; Validated
Probab=32.18 E-value=72 Score=24.47 Aligned_cols=46 Identities=20% Similarity=0.286 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..++...|..+ ....+||..+ |+++..|+.|...-|.+.+.
T Consensus 18 L~ekqRevl~L~y~eg------~S~~EIAe~l----GIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDD------YSLGEIAEEF----NVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 4566777776666555 2345799999 99999999999766666554
No 64
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=32.11 E-value=59 Score=25.60 Aligned_cols=46 Identities=11% Similarity=-0.054 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.|..+|.-.|-.+ ....++|..| |++...|+++...-|.+.++
T Consensus 113 L~~~~r~v~~l~~~~~------~s~~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG------FSYKEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 5555555555544333 2345888999 99999999988755555544
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.82 E-value=79 Score=25.34 Aligned_cols=29 Identities=7% Similarity=0.376 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
..++||..| |+++..|+++...-|.+.|+
T Consensus 147 s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERH----DVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHH----CCChHHHHHHHHHHHHHHHH
Confidence 356888999 99999999998766665554
No 66
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.45 E-value=73 Score=24.96 Aligned_cols=48 Identities=15% Similarity=0.096 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
+++.+..++.-.|-.+ ....+||..| |+++..|++....-|.+.|+.-
T Consensus 107 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE------KSYQEIALQE----KIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 3444555555444333 2345888999 9999999999876666655543
No 67
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.93 E-value=55 Score=26.67 Aligned_cols=30 Identities=13% Similarity=0.128 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 120 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 120 ~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
....+||..| |++...|+.|+..-|.+.++
T Consensus 158 ~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 158 LSQSEIAKRL----GIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4456889999 99999999999766666554
No 68
>PRK04217 hypothetical protein; Provisional
Probab=30.87 E-value=80 Score=24.46 Aligned_cols=52 Identities=13% Similarity=0.095 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 96 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 96 t~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
..++.+++.++...|... . ...+||+.| |++...|+..+..-+.+.+..-..
T Consensus 41 ~~Lt~eereai~l~~~eG-l-----S~~EIAk~L----GIS~sTV~r~L~RArkkLre~L~~ 92 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG-L-----TQEEAGKRM----GVSRGTVWRALTSARKKVAQMLVE 92 (110)
T ss_pred ccCCHHHHHHHHHHHHcC-C-----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHHh
Confidence 457888888887777655 2 456899999 999999999998777776654433
No 69
>PRK09480 slmA division inhibitor protein; Provisional
Probab=30.79 E-value=43 Score=26.94 Aligned_cols=36 Identities=14% Similarity=0.329 Sum_probs=29.1
Q ss_pred HHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhh
Q 027068 108 HVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 149 (229)
Q Consensus 108 ~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRa 149 (229)
..|... +. .......||+.. |++...++.+|.|+-.
T Consensus 21 ~l~~~~-~G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 21 QMLESP-PG-ERITTAKLAARV----GVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHhc-CC-CccCHHHHHHHh----CCCHhHHHHHCCCHHH
Confidence 345444 45 777888999999 9999999999999774
No 70
>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=30.64 E-value=71 Score=25.61 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..++.-.|-.+ ....++|..| |+++..|++....-|.+.++
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 5555555555554444 2345888999 99999999988766655544
No 71
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.64 E-value=67 Score=25.25 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
.-.+||..| |+++..|+.|...=|.+.|+.
T Consensus 143 ~~~eIA~~l----gis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEIL----GVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 345888999 999999999998666665543
No 72
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=30.37 E-value=88 Score=25.66 Aligned_cols=31 Identities=10% Similarity=0.092 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
..+||..| |+++..|++....-|.+.++.-.
T Consensus 135 ~~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 135 YEEAAEIC----GCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45888999 99999999998766666665444
No 73
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=29.22 E-value=69 Score=25.69 Aligned_cols=29 Identities=14% Similarity=0.337 Sum_probs=23.0
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
...++|..| |+++..|+++...-|.+.+.
T Consensus 154 s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 154 SLKEISEIL----DLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 456888999 99999999999766666554
No 74
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.77 E-value=89 Score=25.25 Aligned_cols=31 Identities=16% Similarity=0.186 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
..+||..| |++...|+.+...-|.+.|+.-.
T Consensus 147 ~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 147 NIEAAAVM----DISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788899 99999999998766666655444
No 75
>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=28.36 E-value=23 Score=25.53 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=24.5
Q ss_pred HHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhh
Q 027068 108 HVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (229)
Q Consensus 108 ~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQN 146 (229)
..|... +|-......+||..| |+++..|+.|+.+
T Consensus 22 ~af~L~-R~~eGlS~kEIAe~L----GIS~~TVk~~l~~ 55 (73)
T TIGR03879 22 AAAALA-REEAGKTASEIAEEL----GRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHH-HHHcCCCHHHHHHHH----CcCHHHHHHHHhc
Confidence 334444 344444567999999 9999999999864
No 76
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=28.00 E-value=79 Score=24.59 Aligned_cols=44 Identities=18% Similarity=0.271 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhH
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak 150 (229)
.+++.+..++...|-.+ ....+||..| |++...|+++...-|.+
T Consensus 111 ~L~~~~r~v~~l~~~~g------~~~~eIA~~l----~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG------VSLTALAEQL----GRTVNAVYKALSRLRVR 154 (159)
T ss_pred HCCHHHHHHHHHHHhcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHH
Confidence 35555555655544333 2456889999 99999999876543333
No 77
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=27.98 E-value=34 Score=23.34 Aligned_cols=20 Identities=30% Similarity=0.795 Sum_probs=17.4
Q ss_pred HHHHHHHHHhhCCCcccchhehhh
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQ 145 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQ 145 (229)
..+||..| |++...|+.|-+
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 999999999964
No 78
>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=27.87 E-value=95 Score=23.82 Aligned_cols=45 Identities=18% Similarity=0.104 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~K 152 (229)
+++.+..+|.-.|-.+ ....+||..| |+++..|+.+...-|.+.|
T Consensus 114 L~~~~r~il~l~~~~~------~~~~eIA~~l----gis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG------KSYKEIAEEL----GISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 3444455555433322 2345788899 9999999988765444443
No 79
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=27.20 E-value=1e+02 Score=26.24 Aligned_cols=32 Identities=19% Similarity=0.274 Sum_probs=24.5
Q ss_pred HHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhhC
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 157 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~~ 157 (229)
..+||..| |+++..|++....-|.+.++.-..
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 45888999 999999999887666666655433
No 80
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=27.19 E-value=88 Score=25.35 Aligned_cols=46 Identities=15% Similarity=-0.009 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..++...|-.+ ....+||..| |++...|+.+...-|.+.|+
T Consensus 140 L~~~~r~i~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 140 LPEKQREILILRVVVG------LSAEETAEAV----GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4445555555444333 3456889999 99999999988654444443
No 81
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=27.13 E-value=96 Score=24.33 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
+++.+..+|.-.| .+ ....+||..| |+++..|+.+...-|.+.|+.-
T Consensus 113 L~~~~r~il~l~~-~g------~s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-SG------YSYKEIAEAL----GIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-cC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 5566666666666 43 2345889999 9999999999876666655543
No 82
>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=27.01 E-value=35 Score=21.24 Aligned_cols=22 Identities=9% Similarity=0.107 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhCCCcccchhehhhhh
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQNR 147 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNR 147 (229)
..++|+.+ |+++..|+.|.++.
T Consensus 3 ~~e~a~~~----gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLT----GVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHHCC
Confidence 45788888 99999999997543
No 83
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.88 E-value=79 Score=23.83 Aligned_cols=39 Identities=13% Similarity=0.048 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchh
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVY 141 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~ 141 (229)
++++|...-...|..+ --.+.-..+++|..| ++++..|.
T Consensus 3 Ln~eq~~~Tk~elqan-~el~~LS~~~iA~~L----n~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQAN-FELCPLSDEEIATAL----NWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHh-hhhccccHHHHHHHh----CCCHHHHH
Confidence 5667766655555555 445556677899999 98886543
No 84
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=26.86 E-value=1e+02 Score=33.75 Aligned_cols=61 Identities=21% Similarity=0.315 Sum_probs=53.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 90 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 90 ~~rr~Rt~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
+.++-|++.-.+++.+|-.+|-.+ --|+...+..|.... ..+.+.+.+||+|-|.|.++..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~-~sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQD-NSPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCC-CCHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 355677888889999999999999 579999999998888 8999999999999999988766
No 85
>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=26.68 E-value=89 Score=25.03 Aligned_cols=49 Identities=16% Similarity=0.097 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
.+++.+..+|.-.|-.+ ....+||..| |+++..|+++-..-|.+.++.-
T Consensus 100 ~L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG------LSQQEIAEKL----GLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 45556666666555444 2345889999 9999999998876555555543
No 86
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.63 E-value=94 Score=25.23 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
+++.+..+|+-.|-.+ ....+||..| |+++..|++-...-|.+.++.-
T Consensus 132 L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 132 LSPAHREIIDLVYYHE------KSVEEVGEIV----GIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 4444555554444333 2345788899 9999999998876666665543
No 87
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=25.85 E-value=1.4e+02 Score=18.41 Aligned_cols=39 Identities=26% Similarity=0.351 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhh
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 146 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQN 146 (229)
.+++.+..++.. +..+ + ...++|..+ |++...|+.|...
T Consensus 3 ~l~~~e~~i~~~-~~~g--~----s~~eia~~l----~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRL-LAEG--L----TNKEIAERL----GISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHH-HHcC--C----CHHHHHHHH----CCCHHHHHHHHHH
Confidence 357777777755 3333 2 346889999 9999999988764
No 88
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=25.08 E-value=1.2e+02 Score=23.61 Aligned_cols=46 Identities=17% Similarity=0.117 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..++.-.|-.+ ....+||..| |++...|++....-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 107 LPARQREAFLLRYWED------MDVAETAAAM----GCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CCHHHHHHHHHHHHhc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4455555555544333 2245889999 99999999987755555544
No 89
>PRK06930 positive control sigma-like factor; Validated
Probab=25.04 E-value=1e+02 Score=25.45 Aligned_cols=49 Identities=10% Similarity=0.119 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
.+++.+..++.-.|..+ ....++|..| |++...|+.+...-+.+.++.-
T Consensus 114 ~L~~rer~V~~L~~~eg------~s~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG------LSYSEIADYL----NIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 46666666666655444 1345889999 9999999999987777666543
No 90
>PF13518 HTH_28: Helix-turn-helix domain
Probab=24.96 E-value=52 Score=20.72 Aligned_cols=24 Identities=29% Similarity=0.755 Sum_probs=19.6
Q ss_pred HHHHHHHHHhhCCCcccchhehhhhhhh
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQNRRA 149 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRRa 149 (229)
..++|..+ ||+...|..|.+.-+.
T Consensus 15 ~~~~a~~~----gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREF----GISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHH----CCCHhHHHHHHHHHHh
Confidence 44789999 9999999999975443
No 91
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=24.95 E-value=1e+02 Score=25.11 Aligned_cols=31 Identities=19% Similarity=0.266 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
...+||..| |++...|+..+..-|.+.++.-
T Consensus 124 ~~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 124 SQKEIAEKL----GLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHH
Confidence 355888999 9999999998876555555433
No 92
>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=24.78 E-value=1.3e+02 Score=23.52 Aligned_cols=46 Identities=22% Similarity=0.164 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 99 t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
++.+..+|.-.|-.+ ....++|..| |++...|+++-..-|.+.++.
T Consensus 112 ~~~~r~i~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 112 PARQRAVVVLRYYED------LSEAQVAEAL----GISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHhhhHHHhc------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 445555555444333 2345888899 999999999887666666553
No 93
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=24.56 E-value=49 Score=27.75 Aligned_cols=14 Identities=43% Similarity=0.843 Sum_probs=12.3
Q ss_pred ccCCHHHHHHHHHH
Q 027068 32 KVMTDEQMELLRKQ 45 (229)
Q Consensus 32 ~~~t~~q~~~lr~q 45 (229)
..||++||+.||.-
T Consensus 48 RTLTDEQI~IFRHS 61 (172)
T PF12720_consen 48 RTLTDEQIEIFRHS 61 (172)
T ss_pred ccccHHHHHHHHHH
Confidence 57999999999874
No 94
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.02 E-value=43 Score=21.17 Aligned_cols=22 Identities=27% Similarity=0.767 Sum_probs=16.8
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQN 146 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQN 146 (229)
...++|..| |++...|..|.+.
T Consensus 19 s~~~ia~~l----gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRL----GVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHH----TS-HHHHHHHHT-
T ss_pred CHHHHHHHH----CcCHHHHHHHHHH
Confidence 355899999 9999999999754
No 95
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=23.85 E-value=1.2e+02 Score=24.44 Aligned_cols=28 Identities=14% Similarity=0.290 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHH
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLK 152 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~K 152 (229)
...+||..| |++...|+++-..-|.+.|
T Consensus 151 s~~eIA~~l----gis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 151 SHAEIAQRL----GAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CHHHHHHHH----CCChhhHHHHHHHHHHHHH
Confidence 355888999 9999999998865444443
No 96
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.36 E-value=1.1e+02 Score=24.94 Aligned_cols=29 Identities=21% Similarity=0.274 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
...+||..| |+++..|+++...-|.+.|+
T Consensus 152 s~~EIA~~l----gis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 152 SSEQICQEC----DISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 356888999 99999999998755555544
No 97
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.27 E-value=1.1e+02 Score=25.21 Aligned_cols=32 Identities=16% Similarity=0.126 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
...++|..| |++...|+++...-|.+.|+.-.
T Consensus 131 s~~EIA~~L----giS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMC----GVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHh
Confidence 345888899 99999999999876666665443
No 98
>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=23.27 E-value=1.2e+02 Score=23.65 Aligned_cols=26 Identities=15% Similarity=0.023 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhH
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRAR 150 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak 150 (229)
...+||..| |+++..|+....--|.+
T Consensus 140 s~~eIA~~l----~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 140 PIAEVARIL----GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHH
Confidence 345888899 99999998876433333
No 99
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=23.16 E-value=89 Score=25.08 Aligned_cols=31 Identities=10% Similarity=0.113 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 120 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 120 ~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
..-.+||..| |+++..|+++...-|.+-|+.
T Consensus 155 ~s~~EIA~~l----gis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 155 LSYEDIARIM----DCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 3456889999 999999999986555555443
No 100
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.09 E-value=1.2e+02 Score=24.06 Aligned_cols=46 Identities=13% Similarity=0.067 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..++.-.|-.+ ....+||..| |+++..|+++...-|.+.|.
T Consensus 113 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 113 LSADQREAIILIGASG------FSYEDAAAIC----GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 3444555554443333 2456889999 99999999988755555443
No 101
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=22.82 E-value=1.3e+02 Score=23.60 Aligned_cols=46 Identities=15% Similarity=0.093 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..+|.-.|-.+ ....++|+.| |++...|+.....-+.+.++
T Consensus 110 L~~~~r~v~~l~~~~~------~s~~EIA~~l----gis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 110 LPARTRYAFEMYRLHG------ETQKDIAREL----GVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4444555555444333 2355888999 99999999986655555444
No 102
>PRK10072 putative transcriptional regulator; Provisional
Probab=22.62 E-value=90 Score=23.50 Aligned_cols=24 Identities=29% Similarity=0.410 Sum_probs=20.9
Q ss_pred HHHHHHHHHhhCCCcccchhehhhhhhh
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQNRRA 149 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRRa 149 (229)
..+||..+ |++...|..|...+|.
T Consensus 49 Q~elA~~l----GvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 49 IDDFARVL----GVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHh----CCCHHHHHHHHcCCCC
Confidence 56899999 9999999999987764
No 103
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=22.33 E-value=1.4e+02 Score=23.64 Aligned_cols=46 Identities=13% Similarity=0.168 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..++...|-.+ ....++|..| |+++..|+++...-|.+.++
T Consensus 120 L~~~~r~i~~l~~~~g------~s~~eiA~~l----gis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD------LTIKEIAEVM----NKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 3444444444443333 2456889999 99999999887655555444
No 104
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.69 E-value=1.4e+02 Score=24.09 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHhh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 156 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~~ 156 (229)
...+||..| |++...|++....-|.+.|+.-.
T Consensus 135 s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLL----QIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 355888899 99999999998877777766443
No 105
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.67 E-value=1.2e+02 Score=24.61 Aligned_cols=48 Identities=17% Similarity=0.312 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
+++.+..++.-.|-.+ ....+||+.| |++...|++..+.-|.+-|++.
T Consensus 132 L~~~~r~i~~l~~~~g------~s~~EIAe~l----gis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 132 LEKLDREIFIRRYLLG------EKIEEIAKKL----GLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CCHHHHHHHHHHHHcc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHcc
Confidence 4444555554433222 2345888899 9999999988765555555433
No 106
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=21.51 E-value=1.4e+02 Score=24.49 Aligned_cols=29 Identities=10% Similarity=0.091 Sum_probs=23.0
Q ss_pred HHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 122 IQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 122 r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
-.+||..| |++...|+++..--|.+.|+.
T Consensus 155 ~~eIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 155 NPEIAEVM----EIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred HHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 45888999 999999999997666665554
No 107
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.82 E-value=1.4e+02 Score=24.06 Aligned_cols=30 Identities=13% Similarity=0.058 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 120 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 120 ~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
....++|..| |+++..|++....-|.+.|+
T Consensus 146 ~s~~EIA~~l----~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 146 LSVAETAQLT----GLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 3456888999 99999999998766666555
No 108
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=20.73 E-value=86 Score=20.99 Aligned_cols=35 Identities=26% Similarity=0.296 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehh
Q 027068 101 AQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (229)
Q Consensus 101 ~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWF 144 (229)
.|+..|+-.+. + ...+.. +||..| |++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~-~~~~~~---ela~~l----~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-N-KWITLK---ELAKKL----NISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-H-TSBBHH---HHHHHC----TS-HHHHHHHH
T ss_pred HHHHHHHHHHc-C-CCCcHH---HHHHHH----CCCHHHHHHHH
Confidence 57888888898 5 445554 889999 99999887544
No 109
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.54 E-value=1.4e+02 Score=27.27 Aligned_cols=53 Identities=13% Similarity=0.157 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 97 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 97 ~~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
.+++.+..+|...|-.. |-......+||..| |++...|+.+...-+.+.|+.-
T Consensus 262 ~L~~~~R~vl~lrygL~--~~e~~s~~EIA~~L----gis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLL--GYEAATLEDVAREI----GLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccC--CCCCcCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 56777777777766322 23334567899999 9999999999887666666544
No 110
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.53 E-value=1.4e+02 Score=25.32 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=31.7
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 99 t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
++.+..++...|-.. ....+||..| |++...|+.+...-+.+.|+.
T Consensus 186 ~~~~r~vl~l~~~~g------~s~~EIA~~l----gis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 186 PEREQLVLSLYYQEE------LNLKEIGAVL----GVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHhHhccC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 444444444444333 3456889999 999999999998777776654
No 111
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.28 E-value=77 Score=23.01 Aligned_cols=25 Identities=20% Similarity=0.287 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhhCCCcccchhehhh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQ 145 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQ 145 (229)
.+.+|...|....+|.+.+|.+|+.
T Consensus 51 ~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 51 RIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred hHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 4455555555555999999999984
No 112
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.20 E-value=1.7e+02 Score=23.63 Aligned_cols=47 Identities=13% Similarity=-0.002 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~ 154 (229)
+++.+..+++-.|-.+ ....+||..| |++...|+.+...-|.+.|+.
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 132 LPEKMRLAIQAVKLEG------LSVAEAATRS----GMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CCHHHHHHHHHHHHcC------CcHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 4455555555433323 3456889999 999999999886555555543
No 113
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.18 E-value=1.2e+02 Score=26.15 Aligned_cols=31 Identities=10% Similarity=0.170 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhhCCCcccchhehhhhhhhHHHHHh
Q 027068 121 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155 (229)
Q Consensus 121 ~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr~~ 155 (229)
...+||..| |+++..|++....-|.+.|+.-
T Consensus 189 s~~EIA~~L----gis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 189 SNGEIAEVM----DTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 345888899 9999999999876666666543
No 114
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.12 E-value=1.7e+02 Score=21.19 Aligned_cols=45 Identities=13% Similarity=0.310 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHHhhc----CCCCCHHHHHHHHHHHHhhCCCcccchhehh
Q 027068 96 WTPTPAQLQILEHVYDEC----KGTPRKQKIQDMTAELAKHGQISETNVYNWF 144 (229)
Q Consensus 96 t~~t~~Ql~~Le~~F~~~----~~yP~~~~r~~LA~~L~~~~gls~~qV~vWF 144 (229)
+-++.+++..|...|..- ..+.+..+...+-..+ |+++..|.-.|
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~----~~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKS----GLPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHc----CCCHHHHHHHH
Confidence 457889999999998763 2356666555555555 77776666655
No 115
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=20.07 E-value=1.7e+02 Score=23.16 Aligned_cols=46 Identities=20% Similarity=0.239 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhCCCcccchhehhhhhhhHHHH
Q 027068 98 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153 (229)
Q Consensus 98 ~t~~Ql~~Le~~F~~~~~yP~~~~r~~LA~~L~~~~gls~~qV~vWFQNRRak~Kr 153 (229)
+++.+..+|.-.|-.+ ....+||..| |+++..|+.....-|.+.|+
T Consensus 119 L~~~~r~vl~L~~~~g------~s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG------WSTAQIAADL----GIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 4445555555544333 2345888999 99999999987655554444
Done!