Query 027928
Match_columns 217
No_of_seqs 56 out of 58
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 03:37:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027928.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027928hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00046 Homeobox: Homeobox do 99.4 6.5E-14 1.4E-18 93.6 2.7 56 79-139 2-57 (57)
2 smart00389 HOX Homeodomain. DN 99.2 8.7E-12 1.9E-16 82.1 2.3 54 80-138 3-56 (56)
3 cd00086 homeodomain Homeodomai 99.2 1.5E-11 3.3E-16 81.0 2.8 57 79-140 2-58 (59)
4 KOG0492 Transcription factor M 98.9 1.1E-09 2.4E-14 96.9 4.6 60 80-144 147-206 (246)
5 KOG0843 Transcription factor E 98.8 9.7E-09 2.1E-13 88.9 5.8 64 76-144 101-164 (197)
6 COG5576 Homeodomain-containing 98.7 1.9E-08 4.1E-13 83.3 4.7 64 75-143 49-112 (156)
7 TIGR01565 homeo_ZF_HD homeobox 98.7 4.1E-08 8.8E-13 70.3 5.0 51 79-134 3-57 (58)
8 KOG2251 Homeobox transcription 98.4 5.6E-07 1.2E-11 79.5 5.9 65 75-144 35-99 (228)
9 KOG0484 Transcription factor P 98.3 4.3E-07 9.3E-12 74.0 2.0 64 74-142 14-77 (125)
10 KOG0489 Transcription factor z 98.2 5.1E-07 1.1E-11 78.7 2.1 67 76-147 158-224 (261)
11 KOG0483 Transcription factor H 98.1 8.7E-07 1.9E-11 76.2 1.1 59 78-141 51-109 (198)
12 KOG0842 Transcription factor t 98.1 6.8E-06 1.5E-10 75.0 6.0 67 78-149 154-220 (307)
13 KOG0494 Transcription factor C 98.0 8.3E-06 1.8E-10 74.8 5.0 59 80-143 144-202 (332)
14 KOG0848 Transcription factor C 97.9 4.1E-06 8.9E-11 76.7 1.6 55 81-140 203-257 (317)
15 KOG0493 Transcription factor E 97.8 1.6E-05 3.5E-10 73.0 4.4 57 78-139 247-303 (342)
16 KOG0487 Transcription factor A 97.7 3.5E-05 7.7E-10 70.5 4.6 62 80-146 238-299 (308)
17 KOG0485 Transcription factor N 97.7 1.8E-05 4E-10 71.0 2.6 60 79-143 106-165 (268)
18 KOG0844 Transcription factor E 97.7 2.7E-05 5.9E-10 72.8 3.0 65 80-151 184-248 (408)
19 KOG0490 Transcription factor, 97.6 4.8E-05 1E-09 61.4 3.6 64 74-142 57-120 (235)
20 KOG0488 Transcription factor B 97.6 5.9E-05 1.3E-09 68.2 3.9 61 78-143 173-233 (309)
21 KOG0850 Transcription factor D 97.6 0.00013 2.8E-09 65.4 5.5 68 80-152 125-192 (245)
22 KOG0849 Transcription factor P 97.5 5.4E-05 1.2E-09 69.1 3.1 60 78-142 177-236 (354)
23 KOG4577 Transcription factor L 97.3 0.00022 4.7E-09 66.5 3.8 64 74-142 164-227 (383)
24 KOG0486 Transcription factor P 97.3 0.00018 3.9E-09 67.1 3.0 65 76-145 111-175 (351)
25 KOG0491 Transcription factor B 97.1 0.00016 3.5E-09 62.8 0.4 61 80-145 103-163 (194)
26 KOG3802 Transcription factor O 96.9 0.0014 3E-08 62.3 4.9 57 78-139 295-351 (398)
27 KOG0847 Transcription factor, 95.3 0.0069 1.5E-07 55.1 1.0 58 80-142 170-227 (288)
28 KOG2252 CCAAT displacement pro 95.2 0.011 2.3E-07 58.4 2.0 61 77-142 420-480 (558)
29 KOG0490 Transcription factor, 95.0 0.027 5.9E-07 45.6 3.7 65 73-142 149-213 (235)
30 KOG0775 Transcription factor S 93.6 0.062 1.3E-06 49.8 3.2 56 82-142 181-236 (304)
31 PF05920 Homeobox_KN: Homeobox 93.5 0.017 3.7E-07 38.4 -0.4 34 99-136 7-40 (40)
32 KOG1168 Transcription factor A 90.0 0.5 1.1E-05 44.7 4.8 56 80-144 312-367 (385)
33 cd06171 Sigma70_r4 Sigma70, re 77.0 1.3 2.9E-05 26.8 1.1 39 85-133 12-50 (55)
34 KOG1146 Homeobox protein [Gene 70.7 4.5 9.7E-05 44.2 3.7 58 80-142 906-963 (1406)
35 PF08281 Sigma70_r4_2: Sigma-7 63.7 3.2 7E-05 27.2 0.7 37 85-131 12-48 (54)
36 PRK09646 RNA polymerase sigma 62.0 13 0.00029 29.8 4.1 44 85-142 144-187 (194)
37 PRK06811 RNA polymerase factor 61.8 14 0.0003 29.6 4.1 51 85-149 133-183 (189)
38 PRK09652 RNA polymerase sigma 59.3 7.9 0.00017 29.5 2.3 38 84-131 129-166 (182)
39 KOG0774 Transcription factor P 56.7 10 0.00023 35.7 3.0 59 77-139 188-248 (334)
40 PF13936 HTH_38: Helix-turn-he 56.3 11 0.00023 24.9 2.2 26 85-116 6-31 (44)
41 PF04936 DUF658: Protein of un 55.3 4 8.6E-05 35.9 0.0 42 89-135 73-114 (186)
42 TIGR02952 Sig70_famx2 RNA poly 55.3 11 0.00023 28.9 2.3 45 84-142 123-167 (170)
43 TIGR02989 Sig-70_gvs1 RNA poly 55.0 16 0.00035 27.7 3.3 45 84-142 112-156 (159)
44 cd00569 HTH_Hin_like Helix-tur 54.4 12 0.00027 19.9 2.0 35 85-129 7-41 (42)
45 PF09179 TilS: TilS substrate 52.1 24 0.00052 23.9 3.5 33 84-116 10-43 (69)
46 PRK09637 RNA polymerase sigma 51.3 13 0.00028 29.9 2.4 38 83-130 106-143 (181)
47 PRK09639 RNA polymerase sigma 49.9 13 0.00029 28.4 2.2 35 85-130 114-148 (166)
48 COG0735 Fur Fe2+/Zn2+ uptake r 48.0 24 0.00053 28.5 3.5 31 80-111 15-45 (145)
49 TIGR02948 SigW_bacill RNA poly 47.4 16 0.00035 28.4 2.3 36 85-130 138-173 (187)
50 PRK09648 RNA polymerase sigma 46.1 18 0.00038 28.7 2.4 35 86-130 142-176 (189)
51 PF09851 SHOCT: Short C-termin 45.8 49 0.0011 20.7 3.9 28 86-115 2-29 (31)
52 PRK11924 RNA polymerase sigma 44.6 21 0.00045 27.1 2.5 38 85-132 127-164 (179)
53 PRK12531 RNA polymerase sigma 44.6 35 0.00076 27.4 3.9 43 86-142 144-186 (194)
54 TIGR02959 SigZ RNA polymerase 43.8 20 0.00043 28.3 2.3 38 83-130 100-137 (170)
55 PRK12519 RNA polymerase sigma 43.7 16 0.00035 28.9 1.8 36 85-130 143-178 (194)
56 PRK12526 RNA polymerase sigma 42.1 38 0.00083 27.7 3.8 44 85-142 155-198 (206)
57 PF01047 MarR: MarR family; I 40.3 34 0.00073 22.4 2.7 16 85-100 2-17 (59)
58 PRK05602 RNA polymerase sigma 38.8 34 0.00074 27.0 3.0 49 85-145 130-178 (186)
59 PF12323 HTH_OrfB_IS605: Helix 37.5 29 0.00063 22.7 2.0 18 81-98 8-25 (46)
60 TIGR02943 Sig70_famx1 RNA poly 37.3 48 0.001 26.7 3.6 43 86-142 134-176 (188)
61 PRK09643 RNA polymerase sigma 37.1 49 0.0011 26.7 3.7 44 85-142 136-179 (192)
62 PRK11923 algU RNA polymerase s 36.7 48 0.001 26.3 3.5 45 85-143 140-184 (193)
63 PF08863 YolD: YolD-like prote 36.6 95 0.002 22.1 4.7 47 86-132 2-53 (92)
64 TIGR02954 Sig70_famx3 RNA poly 36.3 50 0.0011 25.6 3.5 46 84-143 120-165 (169)
65 TIGR02939 RpoE_Sigma70 RNA pol 36.3 24 0.00051 27.6 1.7 35 86-130 141-175 (190)
66 TIGR02983 SigE-fam_strep RNA p 36.1 46 0.001 25.4 3.2 45 85-143 112-156 (162)
67 PRK09651 RNA polymerase sigma 36.0 30 0.00065 27.3 2.2 47 85-143 121-167 (172)
68 KOG3623 Homeobox transcription 35.5 35 0.00077 36.2 3.2 50 89-143 568-617 (1007)
69 PRK12539 RNA polymerase sigma 35.3 32 0.0007 27.3 2.3 46 83-142 131-176 (184)
70 PRK09642 RNA polymerase sigma 34.8 31 0.00068 26.4 2.1 37 85-131 108-144 (160)
71 PRK09047 RNA polymerase factor 34.5 37 0.0008 25.8 2.5 43 86-142 109-151 (161)
72 PF04545 Sigma70_r4: Sigma-70, 34.2 59 0.0013 21.1 3.1 32 85-126 6-37 (50)
73 PRK06759 RNA polymerase factor 34.0 26 0.00056 26.5 1.5 44 85-142 108-151 (154)
74 KOG0773 Transcription factor M 33.8 26 0.00057 31.2 1.8 54 81-138 243-298 (342)
75 PRK09462 fur ferric uptake reg 33.6 86 0.0019 24.8 4.5 30 82-111 13-42 (148)
76 PRK03975 tfx putative transcri 33.6 36 0.00079 28.3 2.4 49 85-146 8-56 (141)
77 PRK12514 RNA polymerase sigma 32.7 80 0.0017 24.7 4.1 35 86-130 132-166 (179)
78 PRK12515 RNA polymerase sigma 32.3 41 0.00088 26.7 2.5 36 85-130 133-168 (189)
79 PF00196 GerE: Bacterial regul 32.0 23 0.0005 23.7 0.9 38 84-132 4-41 (58)
80 smart00421 HTH_LUXR helix_turn 31.7 27 0.00058 21.6 1.1 36 85-131 5-40 (58)
81 PF13565 HTH_32: Homeodomain-l 31.6 48 0.001 22.8 2.4 48 76-129 25-76 (77)
82 COG5014 Predicted Fe-S oxidore 30.9 66 0.0014 29.2 3.7 38 87-124 173-218 (228)
83 KOG3755 SATB1 matrix attachmen 29.5 13 0.00029 38.3 -0.9 42 99-140 713-757 (769)
84 PF02787 CPSase_L_D3: Carbamoy 29.5 61 0.0013 25.9 3.0 28 83-113 7-34 (123)
85 PRK09644 RNA polymerase sigma 29.1 75 0.0016 24.6 3.4 36 85-130 110-145 (165)
86 PRK08295 RNA polymerase factor 28.6 81 0.0017 25.1 3.6 44 85-143 157-200 (208)
87 PF04967 HTH_10: HTH DNA bindi 28.6 86 0.0019 22.2 3.3 38 85-126 2-40 (53)
88 PF03461 TRCF: TRCF domain; I 28.5 37 0.00081 25.8 1.6 30 94-123 21-51 (101)
89 PRK09641 RNA polymerase sigma 28.2 81 0.0017 24.5 3.5 44 85-142 138-181 (187)
90 PF10893 DUF2724: Protein of u 26.9 51 0.0011 25.2 2.0 22 76-97 28-49 (68)
91 PRK04217 hypothetical protein; 26.9 46 0.001 26.6 1.9 39 83-131 42-80 (110)
92 COG3066 MutH DNA mismatch repa 26.8 31 0.00068 31.1 1.0 59 65-123 125-185 (229)
93 PRK09638 RNA polymerase sigma 26.3 28 0.00061 27.0 0.6 27 108-140 145-171 (176)
94 PF10925 DUF2680: Protein of u 26.1 91 0.002 22.5 3.1 33 85-122 2-34 (59)
95 PF06056 Terminase_5: Putative 25.7 24 0.00053 25.0 0.1 29 93-131 7-35 (58)
96 PF09929 DUF2161: Uncharacteri 25.6 45 0.00097 27.6 1.6 27 105-131 58-101 (118)
97 PF07040 DUF1326: Protein of u 25.5 80 0.0017 27.1 3.2 33 83-115 70-102 (184)
98 PRK08301 sporulation sigma fac 24.9 1E+02 0.0022 25.6 3.7 43 86-142 181-227 (234)
99 PRK12511 RNA polymerase sigma 24.7 75 0.0016 25.7 2.8 46 83-142 111-156 (182)
100 PRK12538 RNA polymerase sigma 24.3 37 0.00081 28.9 1.0 36 85-130 173-208 (233)
101 smart00424 STE STE like transc 24.1 39 0.00084 27.8 1.0 24 90-131 78-102 (111)
102 PRK12537 RNA polymerase sigma 24.1 66 0.0014 25.5 2.3 44 85-142 135-178 (182)
103 PRK05803 sporulation sigma fac 24.0 1.1E+02 0.0023 25.7 3.7 44 86-143 178-225 (233)
104 PRK12512 RNA polymerase sigma 23.9 59 0.0013 25.6 2.0 36 85-130 133-168 (184)
105 TIGR02984 Sig-70_plancto1 RNA 23.9 1.1E+02 0.0023 23.8 3.4 44 85-142 142-185 (189)
106 KOG1644 U2-associated snRNP A' 23.6 2E+02 0.0044 26.4 5.5 41 79-123 193-233 (233)
107 PRK12533 RNA polymerase sigma 23.6 1.1E+02 0.0025 25.7 3.8 46 85-144 136-181 (216)
108 PRK12536 RNA polymerase sigma 23.6 70 0.0015 25.3 2.4 34 87-130 133-166 (181)
109 PF14163 SieB: Superinfection 23.4 54 0.0012 26.2 1.7 38 85-122 80-117 (151)
110 PF02796 HTH_7: Helix-turn-hel 23.3 23 0.0005 23.2 -0.4 34 85-128 7-40 (45)
111 TIGR02937 sigma70-ECF RNA poly 23.0 57 0.0012 23.2 1.6 36 85-130 112-147 (158)
112 cd06170 LuxR_C_like C-terminal 23.0 60 0.0013 20.2 1.6 35 85-130 2-36 (57)
113 KOG2202 U2 snRNP splicing fact 22.9 87 0.0019 29.0 3.1 60 81-140 37-127 (260)
114 PF02200 STE: STE like transcr 22.6 43 0.00093 27.5 1.0 23 91-131 78-101 (110)
115 PRK12542 RNA polymerase sigma 22.4 97 0.0021 24.5 3.0 45 85-143 124-168 (185)
116 PRK12361 hypothetical protein; 22.2 1.5E+02 0.0034 28.3 4.7 21 80-100 218-238 (547)
117 PRK12522 RNA polymerase sigma 22.1 77 0.0017 24.7 2.3 43 86-142 122-164 (173)
118 PRK12532 RNA polymerase sigma 21.8 76 0.0016 25.3 2.3 36 85-130 138-173 (195)
119 PRK09649 RNA polymerase sigma 21.3 70 0.0015 25.6 2.0 44 85-142 132-175 (185)
120 PF04683 Proteasom_Rpn13: Prot 21.2 55 0.0012 24.7 1.3 12 122-133 74-85 (85)
121 COG1846 MarR Transcriptional r 20.9 1E+02 0.0022 21.6 2.5 19 84-102 20-38 (126)
122 PRK08583 RNA polymerase sigma 20.5 1.4E+02 0.0031 25.2 3.8 45 84-142 206-250 (257)
123 PRK12524 RNA polymerase sigma 20.4 1.5E+02 0.0032 23.9 3.7 45 85-143 138-182 (196)
124 PRK12516 RNA polymerase sigma 20.4 81 0.0018 25.5 2.2 44 85-142 118-161 (187)
125 PRK07037 extracytoplasmic-func 20.4 77 0.0017 24.2 2.0 35 85-129 111-145 (163)
126 COG1309 AcrR Transcriptional r 20.2 48 0.001 23.4 0.7 37 91-134 21-57 (201)
No 1
>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=99.43 E-value=6.5e-14 Score=93.59 Aligned_cols=56 Identities=29% Similarity=0.569 Sum_probs=52.7
Q ss_pred CCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHH
Q 027928 79 GTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQ 139 (217)
Q Consensus 79 ~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRr 139 (217)
..|+.+|++|+.+||.+|..+ .+|+.++++.|+..|+ |+...|.+||||+|+++|+
T Consensus 2 r~r~~~t~~q~~~L~~~f~~~-~~p~~~~~~~la~~l~----l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 2 RKRTRFTKEQLKVLEEYFQEN-PYPSKEEREELAKELG----LTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSHHHHHHHHHHHHHS-SSCHHHHHHHHHHHHT----SSHHHHHHHHHHHHHHHHH
T ss_pred cCCCCCCHHHHHHHHHHHHHh-cccccccccccccccc----ccccccccCHHHhHHHhCc
Confidence 579999999999999999985 6999999999999997 9999999999999999985
No 2
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.19 E-value=8.7e-12 Score=82.12 Aligned_cols=54 Identities=31% Similarity=0.510 Sum_probs=50.3
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHH
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARER 138 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReR 138 (217)
.|+..|++|+.+||..|.... +|+.++|++|+..|+ +..+.|.+||+|+|+|++
T Consensus 3 ~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKLG----LSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHhHHHHhhccC
Confidence 577899999999999999887 999999999999998 899999999999998864
No 3
>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=99.17 E-value=1.5e-11 Score=81.02 Aligned_cols=57 Identities=28% Similarity=0.480 Sum_probs=52.2
Q ss_pred CCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHH
Q 027928 79 GTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQK 140 (217)
Q Consensus 79 ~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrK 140 (217)
..|...+++|+.+||..|... .+|+.++|++|++.|+ |..+.|.+||+|+|++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~-~~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN-PYPSREEREELAKELG----LTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHC----cCHHHHHHHHHHHHHHHhcc
Confidence 357889999999999999995 5999999999999998 99999999999999998753
No 4
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.91 E-value=1.1e-09 Score=96.91 Aligned_cols=60 Identities=23% Similarity=0.335 Sum_probs=56.3
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhh
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRN 144 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~ 144 (217)
.|-.+|+.||..||.-|+... |.|+++-.++.+.|. +.++.|..||||||||+||-|+..
T Consensus 147 PRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL~----LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 147 PRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSLE----LTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred CCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhhh----hhhhheehhhhhhhHHHHHHHHHH
Confidence 699999999999999999997 999999999999998 999999999999999999977643
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.78 E-value=9.7e-09 Score=88.90 Aligned_cols=64 Identities=25% Similarity=0.396 Sum_probs=59.1
Q ss_pred CCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhh
Q 027928 76 HPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRN 144 (217)
Q Consensus 76 ~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~ 144 (217)
.|.+.|..+|++||..||+.|.+.+ |-.-.+-++++..|+ ++++-|..||||||.+-||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L~----LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSLS----LSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHcC----CChhHhhhhhhhhhHHHHHHHHHh
Confidence 5788999999999999999999987 778888899999999 999999999999999999988875
No 6
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.69 E-value=1.9e-08 Score=83.28 Aligned_cols=64 Identities=28% Similarity=0.446 Sum_probs=58.5
Q ss_pred cCCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 75 THPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 75 t~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
+.+.+.|-.=|-+|+.+|+..|...- +|+......|...|. |..++|..||||+||++|.+...
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~ln----m~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLLN----MPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhcC----CChhhhhhhhchHHHHHHHhccc
Confidence 34677899999999999999999986 999999999999998 99999999999999999998764
No 7
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.66 E-value=4.1e-08 Score=70.31 Aligned_cols=51 Identities=18% Similarity=0.209 Sum_probs=47.4
Q ss_pred CCCCCCChHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhhhcCcccCceeeEeecccH
Q 027928 79 GTRWNPTQEQIGILEMLYRGGMRT----PNAQQIEQITAQLGKYGKIEGKNVFYWFQNHK 134 (217)
Q Consensus 79 ~~RW~PTpEQL~iLE~lY~~G~rt----Ps~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrK 134 (217)
+.|-.+|++|+..||..|...- + |+.+.+++|+..|+ |++..|.+||||.|
T Consensus 3 R~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~lg----l~~~vvKVWfqN~k 57 (58)
T TIGR01565 3 RRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEIG----VTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHhC----CCHHHeeeecccCC
Confidence 5789999999999999998763 7 99999999999998 99999999999987
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.38 E-value=5.6e-07 Score=79.55 Aligned_cols=65 Identities=25% Similarity=0.433 Sum_probs=58.5
Q ss_pred cCCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhh
Q 027928 75 THPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRN 144 (217)
Q Consensus 75 t~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~ 144 (217)
+...+.|-++|-+||.+||.||+..+ +|+..--++++..|. +.+..|..||-||||+-|++++..
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkln----LpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKLN----LPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHhC----CchhhhhhhhccccchhhHhhhhh
Confidence 34566799999999999999999998 999988888888887 999999999999999999988764
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.25 E-value=4.3e-07 Score=74.00 Aligned_cols=64 Identities=23% Similarity=0.376 Sum_probs=55.0
Q ss_pred ccCCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 74 ETHPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 74 ~t~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.+-..+-|-++|..||..||.+|-..- +|..=--++|+-.+. +.+.+|..|||||||.=|++.|
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETH-YPDIYTREEiA~kid----LTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETH-YPDIYTREEIALKID----LTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhc-CCcchhHHHHHHhhh----hhHHHHHHHHHhhHHHHHHHHH
Confidence 444567799999999999999998775 999988888988887 8999999999999998765544
No 10
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.23 E-value=5.1e-07 Score=78.68 Aligned_cols=67 Identities=19% Similarity=0.211 Sum_probs=58.6
Q ss_pred CCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhhcC
Q 027928 76 HPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNSLG 147 (217)
Q Consensus 76 ~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~l~ 147 (217)
...+.|-..|.+||..||--|.--. +-+--.-.+|+..|. +.|+-|++||||||.+.|+..+...+.
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L~----LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHALN----LTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhcc----hhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 4677899999999999999998874 888888889999998 999999999999999998876655543
No 11
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.11 E-value=8.7e-07 Score=76.24 Aligned_cols=59 Identities=29% Similarity=0.517 Sum_probs=53.7
Q ss_pred CCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHH
Q 027928 78 GGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQ 141 (217)
Q Consensus 78 ~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKq 141 (217)
....=..|-+|...||.-|.... +-+.++..+++.+|+ +...-|-.||||||||=|.||
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~Lg----L~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKELG----LQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred ccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhhC----CChhHHHHHHhhccccccchh
Confidence 34566789999999999999998 999999999999988 899999999999999999885
No 12
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.07 E-value=6.8e-06 Score=75.05 Aligned_cols=67 Identities=27% Similarity=0.345 Sum_probs=61.1
Q ss_pred CCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhhcCCC
Q 027928 78 GGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNSLGLS 149 (217)
Q Consensus 78 ~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~l~~~ 149 (217)
...|.-+|+.|.-.||.=|+.- ||.|+-+-++|+..|+ +..+-|.+||||||=+-||+++...|...
T Consensus 154 RKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~Lr----LT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 154 RKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSLR----LTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhcC----CCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 4469999999999999999998 7999999999999999 99999999999999999999887777543
No 13
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=97.98 E-value=8.3e-06 Score=74.78 Aligned_cols=59 Identities=25% Similarity=0.353 Sum_probs=52.9
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
.|..+|..||..||..|+..- ||+. --.+.|..+..|.+-++..|||||||+=|++.+|
T Consensus 144 ~RTiFT~~Qle~LEkaFkeaH-YPDv----~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 144 FRTIFTSYQLEELEKAFKEAH-YPDV----YAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccchhhHHHHHHHHHHHhhcc-CccH----HHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 489999999999999999986 9998 5667788888999999999999999998887665
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=97.91 E-value=4.1e-06 Score=76.69 Aligned_cols=55 Identities=31% Similarity=0.442 Sum_probs=50.5
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHH
Q 027928 81 RWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQK 140 (217)
Q Consensus 81 RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrK 140 (217)
|.-=|--|...||-=|... |+=++....++++-|+ +.|+-|..|||||||+||+.
T Consensus 203 RvVYTDhQRLELEKEfh~S-ryITirRKSELA~~Lg----LsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHTS-RYITIRRKSELAATLG----LSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred eEEecchhhhhhhhhhccc-cceeeehhHHHHHhhC----ccHhhhhHhhhhhhHHHHHH
Confidence 5567889999999999888 6999999999999999 99999999999999999983
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=97.85 E-value=1.6e-05 Score=73.03 Aligned_cols=57 Identities=25% Similarity=0.429 Sum_probs=52.0
Q ss_pred CCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHH
Q 027928 78 GGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQ 139 (217)
Q Consensus 78 ~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRr 139 (217)
-+.|--+|-|||+.|..-|... ||-+.+.-|+++.+|+ +.+.-+..||||+||+-|+
T Consensus 247 KRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~ELg----LNEsQIKIWFQNKRAKiKK 303 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQELG----LNESQIKIWFQNKRAKIKK 303 (342)
T ss_pred cCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHhC----cCHHHhhHHhhhhhhhhhh
Confidence 5678999999999999999876 7999999999999999 8999999999999987665
No 16
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=97.73 E-value=3.5e-05 Score=70.47 Aligned_cols=62 Identities=24% Similarity=0.343 Sum_probs=53.8
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhhc
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNSL 146 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~l 146 (217)
.|=.=|..||..||.=|--.| +-+.|.--+|.+.|- +.++-|.+||||||-++|+--|++.+
T Consensus 238 KRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~lN----LTeRQVKIWFQNRRMK~KK~~re~r~ 299 (308)
T KOG0487|consen 238 KRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTLN----LTERQVKIWFQNRRMKEKKVNRENRL 299 (308)
T ss_pred ccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhcc----cchhheeeeehhhhhHHhhhhhhhhc
Confidence 488889999999999887777 889988888888887 99999999999999999987665554
No 17
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=97.72 E-value=1.8e-05 Score=71.04 Aligned_cols=60 Identities=22% Similarity=0.263 Sum_probs=54.2
Q ss_pred CCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 79 GTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 79 ~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
.+|--++..|+-.||+.|+.+ ||.|.++-..+++.|. +.++-|..||||||-+=||+-.-
T Consensus 106 ktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sLq----LTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 106 KTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASLQ----LTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhhh----hhhhhhhhhhhhhhHHHHHHHhh
Confidence 369999999999999999999 6999999999999997 99999999999999888877543
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.67 E-value=2.7e-05 Score=72.83 Aligned_cols=65 Identities=23% Similarity=0.337 Sum_probs=50.4
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhhcCCCCC
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNSLGLSHC 151 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~l~~~~s 151 (217)
-|.-+|.|||..||.=|.+.+ |=|--.-=++++.|- +.++-+..||||||-++||+ |.+|+-++.
T Consensus 184 YRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaLN----LPEtTIKVWFQNRRMKDKRQ--RlamaWPhp 248 (408)
T KOG0844|consen 184 YRTAFTREQIARLEKEFYREN-YVSRPRRCELAAALN----LPETTIKVWFQNRRMKDKRQ--RLAMAWPHP 248 (408)
T ss_pred HHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhhC----CCcceeehhhhhchhhhhhh--hhhccCCCC
Confidence 488899999999997665554 566666678888887 99999999999998877654 445655543
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.64 E-value=4.8e-05 Score=61.44 Aligned_cols=64 Identities=22% Similarity=0.243 Sum_probs=52.9
Q ss_pred ccCCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 74 ETHPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 74 ~t~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.......|-++|..|+.+||.+|..- -+|...= ...|+..=.+++..|..||||++|..|++.+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~----r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV-HLPCFAC----RECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC-CcCccch----HHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 33456679999999999999999988 5999844 4456666669999999999999999998775
No 20
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=97.59 E-value=5.9e-05 Score=68.15 Aligned_cols=61 Identities=20% Similarity=0.278 Sum_probs=53.6
Q ss_pred CCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 78 GGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 78 ~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
.-.|--+|-.||.-||-.|..-- |-|..+-.+|++.|+ +.+.-|+-||||||.+=|+....
T Consensus 173 RksRTaFT~~Ql~~LEkrF~~QK-YLS~~DR~~LA~~Lg----LTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 173 RKSRTAFSDHQLFELEKRFEKQK-YLSVADRIELAASLG----LTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred ccchhhhhHHHHHHHHHHHHHhh-cccHHHHHHHHHHcC----CchhhHHHHHhhhhHHHHHHHHh
Confidence 34588899999999999998875 999999999999999 99999999999998877776544
No 21
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=97.55 E-value=0.00013 Score=65.38 Aligned_cols=68 Identities=21% Similarity=0.280 Sum_probs=56.5
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhhcCCCCCC
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNSLGLSHCP 152 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~l~~~~sp 152 (217)
.|.--+.-||+.|-.=|.+.. +.---+-.++++.|+ +.-+-|.+||||||.+-|+..+..+.+..+.+
T Consensus 125 PRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsLG----LTQTQVKIWFQNrRSK~KKl~k~g~~~~e~~p 192 (245)
T KOG0850|consen 125 PRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASLG----LTQTQVKIWFQNRRSKFKKLKKQGSGPVEGDP 192 (245)
T ss_pred CcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHhC----CchhHhhhhhhhhHHHHHHHHhcCCCccccCc
Confidence 588889999999999998875 777778889999999 89999999999999888877775555554444
No 22
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.55 E-value=5.4e-05 Score=69.15 Aligned_cols=60 Identities=23% Similarity=0.382 Sum_probs=52.6
Q ss_pred CCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 78 GGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 78 ~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.+.|-..|++|+..||+.|...+ ||....-++++.+.. +.+.+|+.||||++|+-|+...
T Consensus 177 rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i~----l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKETG----LPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhcc----CCchHHHHHHhhhhhhhhhccc
Confidence 34577899999999999999998 999988888887766 7889999999999998888764
No 23
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.30 E-value=0.00022 Score=66.52 Aligned_cols=64 Identities=25% Similarity=0.406 Sum_probs=52.4
Q ss_pred ccCCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 74 ETHPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 74 ~t~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
....-++|-+=|.-||..|...|...- -|- ..+.++|..-.-+.=+-|..|||||||+|||-++
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~Sp-KPA----RHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSP-KPA----RHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCC-chh----HHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 344567899999999999999998763 333 4777888877778999999999999999999654
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=97.27 E-value=0.00018 Score=67.06 Aligned_cols=65 Identities=23% Similarity=0.385 Sum_probs=55.2
Q ss_pred CCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhh
Q 027928 76 HPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNS 145 (217)
Q Consensus 76 ~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~ 145 (217)
.+.++|--+|..||+.||..|.. .|+|+-+--++|+-- -.+.++||=.||-||||..|...|.+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~r-NrypdMstrEEIavw----tNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR-NRYPDMSTREEIAVW----TNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh-ccCCccchhhHHHhh----ccccchhhhhhcccchhhhhhhhhhHH
Confidence 46889999999999999999998 589999777777654 559999999999999999887666544
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=97.05 E-value=0.00016 Score=62.81 Aligned_cols=61 Identities=21% Similarity=0.375 Sum_probs=55.4
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhh
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNS 145 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~ 145 (217)
.|--++--||..||+-|..- ++.|..|.++++.-|. ++++-|.-||||+|-+.|+.+|++.
T Consensus 103 ~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L~----LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 103 ARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANALS----LSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hcccccCccccccHHHHhhh-hhcccHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHhccC
Confidence 57888889999999999876 6999999999999999 9999999999999999999888765
No 26
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=96.88 E-value=0.0014 Score=62.26 Aligned_cols=57 Identities=26% Similarity=0.405 Sum_probs=48.8
Q ss_pred CCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHH
Q 027928 78 GGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQ 139 (217)
Q Consensus 78 ~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRr 139 (217)
...|-+-+.-.+.+||..|-.-- -|+.|+|.+|+++|. +|---|=.||=|||-+|||
T Consensus 295 RKKRTSie~~vr~aLE~~F~~np-KPt~qEIt~iA~~L~----leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 295 RKKRTSIEVNVRGALEKHFLKNP-KPTSQEITHIAESLQ----LEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred cccccceeHHHHHHHHHHHHhCC-CCCHHHHHHHHHHhc----cccceEEEEeecccccccc
Confidence 34577888999999999998775 799999999999998 8888999999999844433
No 27
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=95.29 E-value=0.0069 Score=55.09 Aligned_cols=58 Identities=26% Similarity=0.314 Sum_probs=48.9
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
+|=+++-.||..||--|.+.- +|--++-.++++.|+ ..++-|-.||||||-+=|+|..
T Consensus 170 srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~lg----mteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQELN----MTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cCCCccchhhhhhhhhhhhhh-cccchhHHHhhcccc----ccHHHHHHHHhcchhhhhhhhc
Confidence 355667899999999999885 898888888988887 7899999999999977766654
No 28
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=95.19 E-value=0.011 Score=58.38 Aligned_cols=61 Identities=25% Similarity=0.323 Sum_probs=54.3
Q ss_pred CCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 77 PGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 77 P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
+-.+|--+|..|+..|--||+..- .||.|-+++|..+|+ ++-+-|-+||-|.|.|.+-|..
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~~-RPS~Emq~tIS~qL~----L~~sTV~NfFmNaRRRsl~~~~ 480 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKENK-RPSREMQETISQQLN----LELSTVINFFMNARRRSLDKKV 480 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcCC-CCCHHHHHHHHHHhC----CcHHHHHHHHHhhhhhcccccc
Confidence 344599999999999999999886 899999999999999 9999999999999988755544
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.03 E-value=0.027 Score=45.57 Aligned_cols=65 Identities=28% Similarity=0.552 Sum_probs=53.9
Q ss_pred cccCCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 73 VETHPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 73 v~t~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
+...+.+.|-..+..|+.+|+..|...- .|.....+++...++ .....|..||||++++.++.+.
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~~----~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEETG----LSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhcC----CChhhhhhhcccHHHHHHhhcc
Confidence 3344556688888999999999999986 888877777777777 7888899999999999998776
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=93.62 E-value=0.062 Score=49.80 Aligned_cols=56 Identities=18% Similarity=0.392 Sum_probs=45.2
Q ss_pred CCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 82 WNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 82 W~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
..+..-=..+|-+.|... .||+.++..+|+..-+ +.-+-|=+||.|||-|+|-...
T Consensus 181 yCFKekSR~~LrewY~~~-~YPsp~eKReLA~aTg----Lt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 181 YCFKEKSRSLLREWYLQN-PYPSPREKRELAEATG----LTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred eehhHhhHHHHHHHHhcC-CCCChHHHHHHHHHhC----Cchhhhhhhhhhhhhhhhhccc
Confidence 345555678999999965 6999999999888765 7778889999999999994433
No 31
>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=93.55 E-value=0.017 Score=38.43 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=26.2
Q ss_pred CCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHH
Q 027928 99 GMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKAR 136 (217)
Q Consensus 99 G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAR 136 (217)
..-+|+.+++++|..+-+ ++-+.|-.||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tg----ls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTG----LSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHT----S-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcC----CCHHHHHHHHHHhHcc
Confidence 345899999999988765 8999999999998876
No 32
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=89.96 E-value=0.5 Score=44.72 Aligned_cols=56 Identities=29% Similarity=0.408 Sum_probs=41.3
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhh
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRN 144 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~ 144 (217)
.|-.=-.--.+.||-.|..-- -||.|.|.-|++.|. +.-.-|-.||=|.| |||+|.
T Consensus 312 KRTSIAAPEKRsLEayFavQP-RPS~EkIAaIAekLD----LKKNVVRVWFCNQR----QKQKRm 367 (385)
T KOG1168|consen 312 KRTSIAAPEKRSLEAYFAVQP-RPSGEKIAAIAEKLD----LKKNVVRVWFCNQR----QKQKRM 367 (385)
T ss_pred ccccccCcccccHHHHhccCC-CCchhHHHHHHHhhh----hhhceEEEEeeccH----HHHHHh
Confidence 344433334567999998875 699999999999999 55555779999975 555553
No 33
>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=76.95 E-value=1.3 Score=26.82 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=28.6
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeeccc
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNH 133 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNr 133 (217)
++.|..+++++|-.|+ .+.+|++.|+ ++...|+-|.+..
T Consensus 12 ~~~~~~~~~~~~~~~~------~~~~ia~~~~----~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRFGEGL------SYEEIAEILG----ISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHHhcCC------CHHHHHHHHC----cCHHHHHHHHHHH
Confidence 5678999999998776 2557777777 7777776665443
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=70.67 E-value=4.5 Score=44.24 Aligned_cols=58 Identities=26% Similarity=0.507 Sum_probs=48.5
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.|-..+-+||++|--+|+.- +||..++|+.+-.-+. .+-..|-.||||-++.++...-
T Consensus 906 ~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~~----~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 906 YRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPIG----LPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hccchhHHHHHHHHHHHhhc-cCChHHHHHhhccccc----CCcchhHHhhhhhhhhhhhhhh
Confidence 48889999999999999987 5999999988776665 6667788999999988876543
No 35
>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=63.67 E-value=3.2 Score=27.20 Aligned_cols=37 Identities=27% Similarity=0.350 Sum_probs=26.5
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
++.|..++.+.|-.|+ ...+|++.|+ |+.++|..|.+
T Consensus 12 ~~~~r~i~~l~~~~g~------s~~eIa~~l~----~s~~~v~~~l~ 48 (54)
T PF08281_consen 12 PERQREIFLLRYFQGM------SYAEIAEILG----ISESTVKRRLR 48 (54)
T ss_dssp -HHHHHHHHHHHTS---------HHHHHHHCT----S-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCc------CHHHHHHHHC----cCHHHHHHHHH
Confidence 5788999999999998 3457888876 88888887765
No 36
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=61.99 E-value=13 Score=29.78 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=32.6
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++.|..+|.+-|-.|+ .+++|++.|+ |..++| .++..|.|++.+
T Consensus 144 ~~~~r~vl~l~~~~~~------s~~EIA~~Lg----is~~tV----k~~l~ra~~~Lr 187 (194)
T PRK09646 144 TDTQRESVTLAYYGGL------TYREVAERLA----VPLGTV----KTRMRDGLIRLR 187 (194)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHhC----CChHhH----HHHHHHHHHHHH
Confidence 4677788888887776 4678999998 899999 455556666655
No 37
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=61.81 E-value=14 Score=29.59 Aligned_cols=51 Identities=29% Similarity=0.437 Sum_probs=36.8
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhhcCCC
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNSLGLS 149 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~l~~~ 149 (217)
++.|..++...|-.|+ -+++|++.|+ |+..+| .|+..|.|++.+.+.++++
T Consensus 133 ~~~~r~i~~l~~~~g~------s~~EIAe~lg----is~~~V----~~~l~Ra~~~Lr~~~~~~~ 183 (189)
T PRK06811 133 EKLDREIFIRRYLLGE------KIEEIAKKLG----LTRSAI----DNRLSRGRKKLQKNKLNIS 183 (189)
T ss_pred CHHHHHHHHHHHHccC------CHHHHHHHHC----CCHHHH----HHHHHHHHHHHHHcccCcc
Confidence 4567788888777776 3457888887 777666 4677788888887776554
No 38
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=59.31 E-value=7.9 Score=29.50 Aligned_cols=38 Identities=16% Similarity=0.084 Sum_probs=30.1
Q ss_pred CChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 84 PTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 84 PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
=++.|..+|...|-.|+ .+.+|+..|+ |+...|..|..
T Consensus 129 L~~~~r~vl~l~~~~~~------s~~eIA~~lg----is~~tV~~~l~ 166 (182)
T PRK09652 129 LPEELRTAITLREIEGL------SYEEIAEIMG----CPIGTVRSRIF 166 (182)
T ss_pred CCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHHH
Confidence 46788889999888887 3458888888 89999976665
No 39
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=56.74 E-value=10 Score=35.70 Aligned_cols=59 Identities=22% Similarity=0.322 Sum_probs=47.4
Q ss_pred CCCCCCCCChHHHHHHHHHHh--cCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHH
Q 027928 77 PGGTRWNPTQEQIGILEMLYR--GGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQ 139 (217)
Q Consensus 77 P~~~RW~PTpEQL~iLE~lY~--~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRr 139 (217)
.++.|-|++..=-.||-+.|- ...-+||.|..++++.+ ..|.=+-|-+||-|++-|=++
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkq----CnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQ----CNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHH----cCceehhhccccccceeehhh
Confidence 477888999888899987773 46779999776665555 569999999999999988765
No 40
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=56.32 E-value=11 Score=24.92 Aligned_cols=26 Identities=38% Similarity=0.594 Sum_probs=14.7
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLG 116 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~ 116 (217)
|++|...++.+|..|+ -+.+|++.|+
T Consensus 6 t~~eR~~I~~l~~~G~------s~~~IA~~lg 31 (44)
T PF13936_consen 6 TPEERNQIEALLEQGM------SIREIAKRLG 31 (44)
T ss_dssp ------HHHHHHCS---------HHHHHHHTT
T ss_pred hhhHHHHHHHHHHcCC------CHHHHHHHHC
Confidence 7889999999999997 3567888887
No 41
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=55.33 E-value=4 Score=35.92 Aligned_cols=42 Identities=19% Similarity=0.294 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHH
Q 027928 89 IGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKA 135 (217)
Q Consensus 89 L~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKA 135 (217)
.+..=+.|..|. -|-.-+..+|+..|. |--.|||||.|--|-
T Consensus 73 p~sVy~~y~kG~-~~~TGta~eisq~~~----i~k~~Vy~yis~Gk~ 114 (186)
T PF04936_consen 73 PASVYDYYDKGI-FIMTGTAREISQFFS----IKKQNVYYYISVGKK 114 (186)
T ss_pred cHHHHHHHhccc-cccCccHHHHHhhhc----cccccEEEEEecccc
Confidence 345567788886 677777778888887 889999999997653
No 42
>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=55.28 E-value=11 Score=28.90 Aligned_cols=45 Identities=18% Similarity=0.209 Sum_probs=31.0
Q ss_pred CChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 84 PTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 84 PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
=+|.|..+|...|-.|+ .+++|++.|+ |+..+|.. +..|.|++.|
T Consensus 123 L~~~~r~vl~l~~~~g~------s~~eIA~~l~----is~~tv~~----~l~ra~~~Lr 167 (170)
T TIGR02952 123 LTPKQQHVIALRFGQNL------PIAEVARILG----KTEGAVKI----LQFRAIKKLA 167 (170)
T ss_pred CCHHHHHHHHHHHhcCC------CHHHHHHHHC----CCHHHHHH----HHHHHHHHHH
Confidence 35677788888887776 3568888888 88888853 4445555544
No 43
>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=55.01 E-value=16 Score=27.68 Aligned_cols=45 Identities=22% Similarity=0.370 Sum_probs=32.2
Q ss_pred CChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 84 PTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 84 PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
=++.|..++.+.|-.|+ .+++|++.|+ |+..+|+++ ..|-|+|.+
T Consensus 112 L~~~~r~v~~l~~~~g~------~~~eIA~~l~----is~~tv~~~----l~Rar~~Lr 156 (159)
T TIGR02989 112 LPERQRELLQLRYQRGV------SLTALAEQLG----RTVNAVYKA----LSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHHHHHhcCC------CHHHHHHHhC----CCHHHHHHH----HHHHHHHHH
Confidence 46778888888777776 4668888888 888999844 445555443
No 44
>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=54.44 E-value=12 Score=19.85 Aligned_cols=35 Identities=26% Similarity=0.461 Sum_probs=21.8
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEe
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYW 129 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyW 129 (217)
+.++..++..+|..|. .+.+|+..++ |.-+.|+.|
T Consensus 7 ~~~~~~~i~~~~~~~~------s~~~ia~~~~----is~~tv~~~ 41 (42)
T cd00569 7 TPEQIEEARRLLAAGE------SVAEIARRLG----VSRSTLYRY 41 (42)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHh
Confidence 3456666666677765 3456666665 666667666
No 45
>PF09179 TilS: TilS substrate binding domain; InterPro: IPR015262 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the substrate-binding domain of lysidine-tRNA(Ile) synthetase, which ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a PP-loop motif involved in ATP binding. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) versus AUG (Met) and UGA (stop) versus UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This domain is found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain architecture of this protein is variable; some, including characterised proteins of Escherichia coli and Bacillus subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family. It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, E. coli NtrL, and B. subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain. The HUP domain class (after HIGH-signature proteins, UspA, and PP-ATPase) groups together PP-loop ATPases, the nucleotide-binding domains of class I aminoacyl-tRNA synthetases, UspA protein (USPA domains), photolyases, and electron transport flavoproteins (ETFP). The HUP domain is a distinct class of alpha/beta domain[]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016879 ligase activity, forming carbon-nitrogen bonds, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 1NI5_A 3A2K_A.
Probab=52.07 E-value=24 Score=23.91 Aligned_cols=33 Identities=33% Similarity=0.434 Sum_probs=23.6
Q ss_pred CChHHHHHHHHHHh-cCCCCCCHHHHHHHHHHhh
Q 027928 84 PTQEQIGILEMLYR-GGMRTPNAQQIEQITAQLG 116 (217)
Q Consensus 84 PTpEQL~iLE~lY~-~G~rtPs~eqI~qIT~~L~ 116 (217)
|-+.|..+|=..+. .|...|+..++++|-.+|.
T Consensus 10 ~~~~q~~lLR~wL~~~g~~~ps~~~l~~i~~~l~ 43 (69)
T PF09179_consen 10 PPARQRRLLRRWLRQLGLPMPSQAHLEQILRQLI 43 (69)
T ss_dssp -HHHHHHHHHHHHHHTT-T--HHHHHHHHHHHCC
T ss_pred CHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHh
Confidence 34567788877774 3778999999999999986
No 46
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=51.29 E-value=13 Score=29.90 Aligned_cols=38 Identities=13% Similarity=0.145 Sum_probs=29.5
Q ss_pred CCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 83 NPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 83 ~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
.=++.|..+|.+.|-.|+ .+.+|+..|+ |+..+|...+
T Consensus 106 ~L~~~~r~i~~l~~~~g~------~~~EIA~~lg----is~~tV~~~l 143 (181)
T PRK09637 106 ALPEKYAEALRLTELEGL------SQKEIAEKLG----LSLSGAKSRV 143 (181)
T ss_pred hCCHHHHHHHHHHHhcCC------CHHHHHHHhC----CCHHHHHHHH
Confidence 346678888999888887 4568888888 8888887655
No 47
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=49.89 E-value=13 Score=28.42 Aligned_cols=35 Identities=23% Similarity=0.348 Sum_probs=27.3
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++.|..+|...| .|+ .+++|+..|+ |..+.|.++.
T Consensus 114 ~~~~r~il~l~~-~g~------s~~eIA~~lg----is~~tV~~~i 148 (166)
T PRK09639 114 TERDRTVLLLRF-SGY------SYKEIAEALG----IKESSVGTTL 148 (166)
T ss_pred CHHHHHHHHHHH-cCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 456778888888 887 3568888888 8998887766
No 48
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=48.01 E-value=24 Score=28.48 Aligned_cols=31 Identities=16% Similarity=0.268 Sum_probs=25.7
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCCHHHHHHH
Q 027928 80 TRWNPTQEQIGILEMLYRGGMRTPNAQQIEQI 111 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qI 111 (217)
.-+..|+-++.||+.|...+.. ||+++|=..
T Consensus 15 ~glr~T~qR~~vl~~L~~~~~~-~sAeei~~~ 45 (145)
T COG0735 15 AGLRLTPQRLAVLELLLEADGH-LSAEELYEE 45 (145)
T ss_pred cCCCcCHHHHHHHHHHHhcCCC-CCHHHHHHH
Confidence 3578999999999999999886 999876543
No 49
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=47.44 E-value=16 Score=28.45 Aligned_cols=36 Identities=11% Similarity=0.150 Sum_probs=26.3
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++.|..+|++.|-.|+ -+++|++.|+ |+..+|+.++
T Consensus 138 ~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~~v~~~l 173 (187)
T TIGR02948 138 PPKYRMVIVLKYMEDL------SLKEISEILD----LPVGTVKTRI 173 (187)
T ss_pred CHHHhHHhhhHHhcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 4566677777676665 3568888888 8888887766
No 50
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=46.11 E-value=18 Score=28.72 Aligned_cols=35 Identities=20% Similarity=0.118 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
+.|..|++..|-.|. .+++|++.|+ |...+|.++.
T Consensus 142 ~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l 176 (189)
T PRK09648 142 EKQREILILRVVVGL------SAEETAEAVG----STPGAVRVAQ 176 (189)
T ss_pred HHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 456777777777775 3678888887 8888887654
No 51
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=45.80 E-value=49 Score=20.74 Aligned_cols=28 Identities=29% Similarity=0.444 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQL 115 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L 115 (217)
.+||..|.++|..|. =|.++-++..+.|
T Consensus 2 ~~~L~~L~~l~~~G~--IseeEy~~~k~~l 29 (31)
T PF09851_consen 2 EDRLEKLKELYDKGE--ISEEEYEQKKARL 29 (31)
T ss_pred hHHHHHHHHHHHcCC--CCHHHHHHHHHHH
Confidence 368999999999997 6777776666554
No 52
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=44.63 E-value=21 Score=27.11 Aligned_cols=38 Identities=18% Similarity=0.270 Sum_probs=28.3
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecc
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQN 132 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQN 132 (217)
++.+..+|.+.|-.|+ ...+|+..|+ |+..+|..|..-
T Consensus 127 ~~~~r~i~~l~~~~~~------~~~eIA~~lg----is~~tv~~~~~r 164 (179)
T PRK11924 127 PVKQREVFLLRYVEGL------SYREIAEILG----VPVGTVKSRLRR 164 (179)
T ss_pred CHHHHHHhhHHHHcCC------CHHHHHHHHC----CCHHHHHHHHHH
Confidence 3456777888877776 3468999988 999999877643
No 53
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=44.61 E-value=35 Score=27.40 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++|..|+.+.|-.|+ .+++|++.|+ |+..+| .++-.|.+++.|
T Consensus 144 ~~~r~v~~l~~~eg~------s~~EIA~~lg----is~~tV----k~rl~ra~~~Lr 186 (194)
T PRK12531 144 KAQRDVLQAVYLEEL------PHQQVAEMFD----IPLGTV----KSRLRLAVEKLR 186 (194)
T ss_pred HHHHHHHHHHHHcCC------CHHHHHHHhC----cCHHHH----HHHHHHHHHHHH
Confidence 567778888887776 3568999998 899998 344445555444
No 54
>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=43.75 E-value=20 Score=28.31 Aligned_cols=38 Identities=13% Similarity=0.149 Sum_probs=30.8
Q ss_pred CCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 83 NPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 83 ~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
.=++.|..+|++.|-.|. .+++|++.|+ |+..+|..+.
T Consensus 100 ~L~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~tV~~~l 137 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL------SQQEIAEKLG----LSLSGAKSRV 137 (170)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 456788889999888887 4678999998 9999998665
No 55
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=43.73 E-value=16 Score=28.94 Aligned_cols=36 Identities=28% Similarity=0.346 Sum_probs=27.9
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
.++|..+|++.|-.|+ .+++|++.|+ |+.++|..|+
T Consensus 143 ~~~~~~v~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l 178 (194)
T PRK12519 143 PESQRQVLELAYYEGL------SQSEIAKRLG----IPLGTVKARA 178 (194)
T ss_pred CHHHhhhhhhhhhcCC------CHHHHHHHhC----CCHHHHHHHH
Confidence 4667778888776776 3568888888 8999998777
No 56
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=42.07 E-value=38 Score=27.70 Aligned_cols=44 Identities=20% Similarity=0.139 Sum_probs=30.1
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++.|..+|.+.|-.|+ .+++|++.|+ |+..+|..+ ..|.+++.+
T Consensus 155 ~~~~r~vl~l~~~~g~------s~~EIA~~lg----is~~tV~~~----l~Ra~~~Lr 198 (206)
T PRK12526 155 PEAQQTVVKGVYFQEL------SQEQLAQQLN----VPLGTVKSR----LRLALAKLK 198 (206)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHH----HHHHHHHHH
Confidence 4567778888887776 3568888888 888888443 344444443
No 57
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=40.31 E-value=34 Score=22.45 Aligned_cols=16 Identities=44% Similarity=0.663 Sum_probs=14.1
Q ss_pred ChHHHHHHHHHHhcCC
Q 027928 85 TQEQIGILEMLYRGGM 100 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~ 100 (217)
|+.|..+|..||..|.
T Consensus 2 t~~q~~iL~~l~~~~~ 17 (59)
T PF01047_consen 2 TPSQFRILRILYENGG 17 (59)
T ss_dssp THHHHHHHHHHHHHSS
T ss_pred CHHHHHHHHHHHHcCC
Confidence 6889999999998875
No 58
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=38.75 E-value=34 Score=27.02 Aligned_cols=49 Identities=12% Similarity=0.159 Sum_probs=32.1
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNS 145 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~ 145 (217)
++.|..||.+.|-.|+ .+++|+..|+ |.-.+|..+. +|||.+=++.-..
T Consensus 130 ~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l--~Rar~~Lr~~l~~ 178 (186)
T PRK05602 130 PERQREAIVLQYYQGL------SNIEAAAVMD----ISVDALESLL--ARGRRALRAQLAD 178 (186)
T ss_pred CHHHHHHhhHHHhcCC------CHHHHHHHhC----cCHHHHHHHH--HHHHHHHHHHHHh
Confidence 5667778888777776 3457777787 8888887665 4444444444333
No 59
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=37.54 E-value=29 Score=22.70 Aligned_cols=18 Identities=39% Similarity=0.459 Sum_probs=14.0
Q ss_pred CCCCChHHHHHHHHHHhc
Q 027928 81 RWNPTQEQIGILEMLYRG 98 (217)
Q Consensus 81 RW~PTpEQL~iLE~lY~~ 98 (217)
|=.||++|...|+..+..
T Consensus 8 rl~Pt~~Q~~~L~~~~~~ 25 (46)
T PF12323_consen 8 RLYPTKEQEEKLERWFGA 25 (46)
T ss_pred EEecCHHHHHHHHHHHHH
Confidence 456899999999887643
No 60
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=37.31 E-value=48 Score=26.74 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
+.|..+|.+.|-.|+ .+++|++.|+ |...+| .+|..|.|++.+
T Consensus 134 ~~~r~v~~l~~~~g~------s~~EIA~~lg----is~~tv----k~rl~Rar~~Lr 176 (188)
T TIGR02943 134 EQTARVFMMREVLGF------ESDEICQELE----ISTSNC----HVLLYRARLSLR 176 (188)
T ss_pred HHHHHHHHHHHHhCC------CHHHHHHHhC----CCHHHH----HHHHHHHHHHHH
Confidence 557778888887776 4678888888 888888 455566666554
No 61
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=37.14 E-value=49 Score=26.66 Aligned_cols=44 Identities=23% Similarity=0.275 Sum_probs=31.5
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.+.|..+|++.|-.|+ .+++|+..|+ |...+| .+|-.|.|++.+
T Consensus 136 p~~~r~i~~l~~~~g~------s~~EIA~~lg----~s~~tV----~~rl~rar~~Lr 179 (192)
T PRK09643 136 PVEQRAALVAVDMQGY------SVADAARMLG----VAEGTV----KSRCARGRARLA 179 (192)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHH----HHHHHHHHHHHH
Confidence 3778899999888886 3568888888 888888 455445555544
No 62
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=36.68 E-value=48 Score=26.26 Aligned_cols=45 Identities=16% Similarity=0.154 Sum_probs=29.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
++++..++...|-.|+ ..++|++.|+ |+.++|. ++..|.|++.|+
T Consensus 140 ~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~tv~----~~l~Rar~~Lr~ 184 (193)
T PRK11923 140 PEDLRTALTLREFDGL------SYEDIASVMQ----CPVGTVR----SRIFRAREAIDK 184 (193)
T ss_pred CHHHhHHHhhHHhcCC------CHHHHHHHHC----CCHHHHH----HHHHHHHHHHHH
Confidence 3445556666665555 3568899988 8888884 455566665543
No 63
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=36.57 E-value=95 Score=22.12 Aligned_cols=47 Identities=21% Similarity=0.326 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhh-hcCcccCceeeEeecc
Q 027928 86 QEQIGILEMLYRGGMRT----PNAQQIEQITAQLG-KYGKIEGKNVFYWFQN 132 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rt----Ps~eqI~qIT~~L~-~~G~Ie~kNVfyWFQN 132 (217)
|||...|..+++.-... -+.+++++|-..|. +|-.=..-.|-||-.+
T Consensus 2 PEH~e~L~~~~~e~~k~~kp~Lde~~leei~~~l~~a~~~~~~v~ity~~~g 53 (92)
T PF08863_consen 2 PEHKEALRELIKEQNKVEKPELDEQQLEEINEKLSEAYQENQPVTITYYEDG 53 (92)
T ss_pred ChHHHHHHHHHHHhcccCCCCCcHHHHHHHHHHHHHHhcCCCEEEEEEEECC
Confidence 79999999987654443 37889999999886 5655566677777643
No 64
>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=36.31 E-value=50 Score=25.59 Aligned_cols=46 Identities=15% Similarity=0.141 Sum_probs=33.4
Q ss_pred CChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 84 PTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 84 PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
=.+.|..++.+.|-.|+ .+++|++.|+ |+.++|. ++..|.+++.++
T Consensus 120 L~~~~r~i~~l~~~~g~------s~~eiA~~lg----is~~tv~----~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHDL------TIKEIAEVMN----KPEGTVK----TYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcCC------CHHHHHHHHC----CCHHHHH----HHHHHHHHHHHH
Confidence 34667788888888886 4568888888 8888886 455566666553
No 65
>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=36.26 E-value=24 Score=27.58 Aligned_cols=35 Identities=11% Similarity=0.066 Sum_probs=24.1
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++|..++...|-.|. ..++|++.|+ |...+|..+.
T Consensus 141 ~~~r~v~~l~~~~~~------s~~EIA~~lg----is~~tv~~~l 175 (190)
T TIGR02939 141 EDLRTAITLRELEGL------SYEDIARIMD----CPVGTVRSRI 175 (190)
T ss_pred HHHhhhhhhhhhcCC------CHHHHHHHHC----cCHHHHHHHH
Confidence 456666666665554 3568888888 8888886554
No 66
>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=36.07 E-value=46 Score=25.43 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=33.7
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
++.|..+|++.|-.|+ .+++|++.|+ |+..+|. ++..|.+++-+.
T Consensus 112 ~~~~r~i~~l~~~~g~------s~~eIA~~lg----is~~tV~----~~l~ra~~~Lr~ 156 (162)
T TIGR02983 112 PARQRAVVVLRYYEDL------SEAQVAEALG----ISVGTVK----SRLSRALARLRE 156 (162)
T ss_pred CHHHHHHhhhHHHhcC------CHHHHHHHhC----CCHHHHH----HHHHHHHHHHHH
Confidence 5788889999888887 3568888888 8888886 455566666554
No 67
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=36.03 E-value=30 Score=27.27 Aligned_cols=47 Identities=19% Similarity=0.191 Sum_probs=30.3
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
+++|..|+.+.|-.|. .+++|++.|+ |...+|..+. +||+.+=+..+
T Consensus 121 ~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l--~Ra~~~~~~~~ 167 (172)
T PRK09651 121 NGKTREAFLLSQLDGL------TYSEIAHKLG----VSVSSVKKYV--AKATEHCLLFR 167 (172)
T ss_pred CHHHhHHhhhhhccCC------CHHHHHHHhC----CCHHHHHHHH--HHHHHHHHHHH
Confidence 5567777777777776 3568888888 8888876554 34444333433
No 68
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=35.48 E-value=35 Score=36.23 Aligned_cols=50 Identities=22% Similarity=0.427 Sum_probs=40.3
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 89 IGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 89 L~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
+.+|---|..-+ -|++++...|+.+.+ +.-.-|.-||+|.+|.++.-.|.
T Consensus 568 ~sllkayyaln~-~ps~eelskia~qvg----lp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 568 TSLLKAYYALNG-LPSEEELSKIAQQVG----LPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHHHhc----ccHHHHHHHHHhhhhhhhhhccC
Confidence 556666665554 899999999999988 67777999999999988876653
No 69
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=35.26 E-value=32 Score=27.30 Aligned_cols=46 Identities=9% Similarity=0.070 Sum_probs=32.7
Q ss_pred CCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 83 NPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 83 ~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.=++.|..++++.|-.|+ .+++|++.|+ |+..+|..+ ..|-+++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~tV~~~----l~ra~~~Lr 176 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEGL------SVAEAATRSG----MSESAVKVS----VHRGLKALA 176 (184)
T ss_pred hCCHHHHHHHHHHHHcCC------cHHHHHHHHC----cCHHHHHHH----HHHHHHHHH
Confidence 346777888888887776 4678899988 888888654 445555444
No 70
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=34.82 E-value=31 Score=26.40 Aligned_cols=37 Identities=19% Similarity=0.092 Sum_probs=27.5
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
++.|..++.+.|-.|+ -+++|++.|+ |+.++|.....
T Consensus 108 p~~~r~v~~l~~~~g~------s~~EIA~~lg----is~~tV~~~l~ 144 (160)
T PRK09642 108 PENYRDVVLAHYLEEK------SYQEIALQEK----IEVKTVEMKLY 144 (160)
T ss_pred CHHHHHHHHHHHHhCC------CHHHHHHHHC----CCHHHHHHHHH
Confidence 3467788888888887 2458888888 88888876543
No 71
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=34.51 E-value=37 Score=25.76 Aligned_cols=43 Identities=19% Similarity=0.232 Sum_probs=29.8
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
+.|..++.+.|-.|+ -+++|++.|+ |+..+|.. +..|.+++.|
T Consensus 109 ~~~r~v~~l~~~~g~------s~~EIA~~lg----is~~tV~~----~l~ra~~~Lr 151 (161)
T PRK09047 109 ARQREAFLLRYWEDM------DVAETAAAMG----CSEGSVKT----HCSRATHALA 151 (161)
T ss_pred HHHHHHHHHHHHhcC------CHHHHHHHHC----CCHHHHHH----HHHHHHHHHH
Confidence 466777788787776 2568899998 88888864 4445555443
No 72
>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=34.21 E-value=59 Score=21.09 Aligned_cols=32 Identities=25% Similarity=0.531 Sum_probs=23.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCcee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNV 126 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNV 126 (217)
+++|..+|...|-.|+ -.++|++.|+ |+...|
T Consensus 6 ~~~er~vi~~~y~~~~------t~~eIa~~lg----~s~~~V 37 (50)
T PF04545_consen 6 PPREREVIRLRYFEGL------TLEEIAERLG----ISRSTV 37 (50)
T ss_dssp -HHHHHHHHHHHTST-------SHHHHHHHHT----SCHHHH
T ss_pred CHHHHHHHHHHhcCCC------CHHHHHHHHC----CcHHHH
Confidence 6889999999997776 2568888887 554444
No 73
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.03 E-value=26 Score=26.51 Aligned_cols=44 Identities=11% Similarity=0.133 Sum_probs=32.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++.|..++...|-.|+ -+++|++.|+ |+..+|..|. .|.++|.|
T Consensus 108 ~~~~r~ii~l~~~~~~------s~~EIA~~l~----is~~tV~~~~----~ra~~~Lr 151 (154)
T PRK06759 108 DEKEKYIIFERFFVGK------TMGEIALETE----MTYYQVRWIY----RQALEKMR 151 (154)
T ss_pred CHHHHHHHHHHHhcCC------CHHHHHHHHC----CCHHHHHHHH----HHHHHHHh
Confidence 4578888898888887 2678888888 8888887554 44544444
No 74
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=33.84 E-value=26 Score=31.22 Aligned_cols=54 Identities=20% Similarity=0.315 Sum_probs=36.6
Q ss_pred CCCCChHHHHHHHHHHhcCC--CCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHH
Q 027928 81 RWNPTQEQIGILEMLYRGGM--RTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARER 138 (217)
Q Consensus 81 RW~PTpEQL~iLE~lY~~G~--rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReR 138 (217)
+...-.+...||..-...-. -||+.++...+..+-+ +.-..|.+||-|.|.|.-
T Consensus 243 ~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TG----Ls~~Qv~NWFINaR~R~w 298 (342)
T KOG0773|consen 243 QRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTG----LSRPQVSNWFINARVRLW 298 (342)
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcC----CCcccCCchhhhcccccC
Confidence 34446677777775443322 4899887776665554 777779999999986643
No 75
>PRK09462 fur ferric uptake regulator; Provisional
Probab=33.65 E-value=86 Score=24.80 Aligned_cols=30 Identities=20% Similarity=0.199 Sum_probs=23.9
Q ss_pred CCCChHHHHHHHHHHhcCCCCCCHHHHHHH
Q 027928 82 WNPTQEQIGILEMLYRGGMRTPNAQQIEQI 111 (217)
Q Consensus 82 W~PTpEQL~iLE~lY~~G~rtPs~eqI~qI 111 (217)
...|+..+.||+.|+.....-||+++|-+.
T Consensus 13 lr~T~qR~~Il~~l~~~~~~h~sa~eI~~~ 42 (148)
T PRK09462 13 LKVTLPRLKILEVLQEPDNHHVSAEDLYKR 42 (148)
T ss_pred CCCCHHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence 458999999999999865458999877543
No 76
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=33.56 E-value=36 Score=28.26 Aligned_cols=49 Identities=31% Similarity=0.436 Sum_probs=36.2
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhhhc
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRNSL 146 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~~l 146 (217)
|+-|+++|.. |..|+ -.++|++.|+ |+..+|-.|-+ +|+++=++.+.-+
T Consensus 8 t~rqreVL~l-r~~Gl------Tq~EIAe~LG----iS~~tVs~ie~--ra~kkLr~~~~tl 56 (141)
T PRK03975 8 TERQIEVLRL-RERGL------TQQEIADILG----TSRANVSSIEK--RARENIEKARETL 56 (141)
T ss_pred CHHHHHHHHH-HHcCC------CHHHHHHHHC----CCHHHHHHHHH--HHHHHHHHHHHHH
Confidence 6889999988 56776 2458899998 88888888877 4566655555544
No 77
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=32.66 E-value=80 Score=24.71 Aligned_cols=35 Identities=9% Similarity=0.342 Sum_probs=26.1
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++|..+|...|-.|+ -+++|++.|+ |+..+|..+.
T Consensus 132 ~~~r~i~~l~~~~g~------s~~eIA~~lg----is~~tV~~~l 166 (179)
T PRK12514 132 KDRAAAVRRAYLEGL------SYKELAERHD----VPLNTMRTWL 166 (179)
T ss_pred HHHHHHHHHHHHcCC------CHHHHHHHHC----CChHHHHHHH
Confidence 466777888887776 2678999998 8888885443
No 78
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=32.34 E-value=41 Score=26.75 Aligned_cols=36 Identities=17% Similarity=0.320 Sum_probs=27.2
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
+++|..+|++-|-.|+ .+++|++.|+ |+.++|.+-.
T Consensus 133 ~~~~r~vl~l~~~~~~------s~~eIA~~lg----is~~tV~~~l 168 (189)
T PRK12515 133 SPAHREIIDLVYYHEK------SVEEVGEIVG----IPESTVKTRM 168 (189)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHH
Confidence 5677788888787776 3568999988 8888886544
No 79
>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=32.02 E-value=23 Score=23.74 Aligned_cols=38 Identities=26% Similarity=0.364 Sum_probs=28.7
Q ss_pred CChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecc
Q 027928 84 PTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQN 132 (217)
Q Consensus 84 PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQN 132 (217)
-|+-++.+|..+..+.. .++|++.|. |+.+.|.+...|
T Consensus 4 LT~~E~~vl~~l~~G~~-------~~eIA~~l~----is~~tV~~~~~~ 41 (58)
T PF00196_consen 4 LTERELEVLRLLAQGMS-------NKEIAEELG----ISEKTVKSHRRR 41 (58)
T ss_dssp S-HHHHHHHHHHHTTS--------HHHHHHHHT----SHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHhcCC-------cchhHHhcC----cchhhHHHHHHH
Confidence 47889999999988775 678999997 888888765443
No 80
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=31.67 E-value=27 Score=21.56 Aligned_cols=36 Identities=25% Similarity=0.399 Sum_probs=24.8
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
++.|..++.. +..|+ -.++|+..|+ |+...|+.|.+
T Consensus 5 ~~~e~~i~~~-~~~g~------s~~eia~~l~----is~~tv~~~~~ 40 (58)
T smart00421 5 TPREREVLRL-LAEGL------TNKEIAERLG----ISEKTVKTHLS 40 (58)
T ss_pred CHHHHHHHHH-HHcCC------CHHHHHHHHC----CCHHHHHHHHH
Confidence 6788889977 45665 2357777776 77788866544
No 81
>PF13565 HTH_32: Homeodomain-like domain
Probab=31.55 E-value=48 Score=22.79 Aligned_cols=48 Identities=21% Similarity=0.288 Sum_probs=27.5
Q ss_pred CCCCCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhh-hcC---cccCceeeEe
Q 027928 76 HPGGTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLG-KYG---KIEGKNVFYW 129 (217)
Q Consensus 76 ~P~~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~-~~G---~Ie~kNVfyW 129 (217)
.+|++|. +++|.+.|..+....- .=+. .+|.+.|. .|| .|+.+.|+.|
T Consensus 25 ~~Grp~~--~~e~~~~i~~~~~~~p-~wt~---~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 25 RPGRPRK--DPEQRERIIALIEEHP-RWTP---REIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred CCCCCCC--cHHHHHHHHHHHHhCC-CCCH---HHHHHHHHHHhCCCCCccHhHHHHh
Confidence 3566666 7888666666665442 2233 45666665 445 4466666544
No 82
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=30.88 E-value=66 Score=29.16 Aligned_cols=38 Identities=24% Similarity=0.239 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhcCCC-CC------CHHHHHH-HHHHhhhcCcccCc
Q 027928 87 EQIGILEMLYRGGMR-TP------NAQQIEQ-ITAQLGKYGKIEGK 124 (217)
Q Consensus 87 EQL~iLE~lY~~G~r-tP------s~eqI~q-IT~~L~~~G~Ie~k 124 (217)
-||..|+.|+..|++ .| ..|++.. ++..|+.||+|...
T Consensus 173 ~QL~aLr~L~~~g~rf~pA~~~~f~~Ed~~k~Lak~Lgehp~~P~~ 218 (228)
T COG5014 173 YQLKALRHLHGKGHRFWPAVVYDFFREDGLKELAKRLGEHPPIPCR 218 (228)
T ss_pred HHHHHHHHHHhcCceeeehhhhccchhhhHHHHHHHhccCCCCCcc
Confidence 599999999999994 33 4466655 89999999988754
No 83
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=29.54 E-value=13 Score=38.30 Aligned_cols=42 Identities=21% Similarity=0.348 Sum_probs=29.2
Q ss_pred CCCCCCHHHHHHHHHHhh---hcCcccCceeeEeecccHHHHHHH
Q 027928 99 GMRTPNAQQIEQITAQLG---KYGKIEGKNVFYWFQNHKARERQK 140 (217)
Q Consensus 99 G~rtPs~eqI~qIT~~L~---~~G~Ie~kNVfyWFQNrKAReRrK 140 (217)
-++.|+.-.|.+-++++- ---+.+.|||-+||.|+++.+++-
T Consensus 713 k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~ 757 (769)
T KOG3755|consen 713 KTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRL 757 (769)
T ss_pred cccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhh
Confidence 345666666666665543 113569999999999999888664
No 84
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=29.52 E-value=61 Score=25.92 Aligned_cols=28 Identities=25% Similarity=0.468 Sum_probs=23.1
Q ss_pred CCChHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 027928 83 NPTQEQIGILEMLYRGGMRTPNAQQIEQITA 113 (217)
Q Consensus 83 ~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~ 113 (217)
.||++-|-+|-+.++.|+ +.++|.++|.
T Consensus 7 ~Ptd~Rlf~i~eAlrrG~---sveeI~e~T~ 34 (123)
T PF02787_consen 7 HPTDERLFAIAEALRRGY---SVEEIHELTK 34 (123)
T ss_dssp STBTTHHHHHHHHHHTTB----HHHHHHHH-
T ss_pred CCCCcHHHHHHHHHHcCC---CHHHHHHHHC
Confidence 589999999999999998 7888887774
No 85
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=29.07 E-value=75 Score=24.60 Aligned_cols=36 Identities=6% Similarity=-0.034 Sum_probs=25.8
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++.|..++.+.|-.|. .+.+|+..|+ |+...|..|.
T Consensus 110 ~~~~r~v~~l~~~~g~------s~~eIA~~lg----is~~tv~~~l 145 (165)
T PRK09644 110 PVIEAQAILLCDVHEL------TYEEAASVLD----LKLNTYKSHL 145 (165)
T ss_pred CHHHHHHHHhHHHhcC------CHHHHHHHHC----CCHHHHHHHH
Confidence 4567777777776665 3568888888 7888886554
No 86
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=28.65 E-value=81 Score=25.13 Aligned_cols=44 Identities=23% Similarity=0.363 Sum_probs=28.9
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
++.+..+|.. |-.|. .+++|++.|+ |+.++|. |+..|-|++.+.
T Consensus 157 ~~~~r~vl~l-~~e~~------s~~EIA~~lg----is~~tV~----~~l~rar~~Lr~ 200 (208)
T PRK08295 157 SELEKEVLEL-YLDGK------SYQEIAEELN----RHVKSID----NALQRVKRKLEK 200 (208)
T ss_pred CHHHHHHHHH-HHccC------CHHHHHHHHC----CCHHHHH----HHHHHHHHHHHH
Confidence 3555666666 55554 3567888887 8888885 566666666554
No 87
>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=28.56 E-value=86 Score=22.16 Aligned_cols=38 Identities=32% Similarity=0.474 Sum_probs=30.8
Q ss_pred ChHHHHHHHHHHhcCCC-CCCHHHHHHHHHHhhhcCcccCcee
Q 027928 85 TQEQIGILEMLYRGGMR-TPNAQQIEQITAQLGKYGKIEGKNV 126 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~r-tPs~eqI~qIT~~L~~~G~Ie~kNV 126 (217)
|+.|..+|...|+.|-- .|-.-.+++|++.|+ |+...|
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lg----is~st~ 40 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELAEELG----ISKSTV 40 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhC----CCHHHH
Confidence 78999999999999853 477789999999998 554443
No 88
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=28.53 E-value=37 Score=25.83 Aligned_cols=30 Identities=20% Similarity=0.434 Sum_probs=20.7
Q ss_pred HHHhcCCCCCCHHHHHHHHHHhh-hcCcccC
Q 027928 94 MLYRGGMRTPNAQQIEQITAQLG-KYGKIEG 123 (217)
Q Consensus 94 ~lY~~G~rtPs~eqI~qIT~~L~-~~G~Ie~ 123 (217)
++|++=...=+.+++.+|.++|. +||++..
T Consensus 21 ~~Yrrl~~~~~~~el~~l~~El~DRFG~~P~ 51 (101)
T PF03461_consen 21 ELYRRLASAESEEELEDLREELIDRFGPLPE 51 (101)
T ss_dssp HHHHHHHC--SHHHHHHHHHHHHHHH-S--H
T ss_pred HHHHHHhhCCCHHHHHHHHHHHHHHcCCCcH
Confidence 46877666788999999999998 9998864
No 89
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.23 E-value=81 Score=24.53 Aligned_cols=44 Identities=14% Similarity=0.239 Sum_probs=28.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++.|..+|.+.|-.|. .+++|++.|+ |+-.+|. |+-.|.|+|-+
T Consensus 138 ~~~~r~il~l~~~~~~------s~~eIA~~lg----is~~~v~----~~l~Rar~~Lr 181 (187)
T PRK09641 138 PEKYRTVIVLKYIEDL------SLKEISEILD----LPVGTVK----TRIHRGREALR 181 (187)
T ss_pred CHHHHHHhhhHHhhCC------CHHHHHHHHC----CCHHHHH----HHHHHHHHHHH
Confidence 3456666666665554 3568899988 8877774 44445555544
No 90
>PF10893 DUF2724: Protein of unknown function (DUF2724); InterPro: IPR021221 This entry is represented by Bacteriophage 186, Fil. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.94 E-value=51 Score=25.17 Aligned_cols=22 Identities=36% Similarity=0.703 Sum_probs=18.4
Q ss_pred CCCCCCCCCChHHHHHHHHHHh
Q 027928 76 HPGGTRWNPTQEQIGILEMLYR 97 (217)
Q Consensus 76 ~P~~~RW~PTpEQL~iLE~lY~ 97 (217)
-|.+.||.|..-|-+.|-.+=.
T Consensus 28 l~~GkRWhP~~sq~~lL~~l~~ 49 (68)
T PF10893_consen 28 LPDGKRWHPCRSQKELLAGLST 49 (68)
T ss_pred CCCCCcCCCCccHHHHHHHhhc
Confidence 4688999999999998887753
No 91
>PRK04217 hypothetical protein; Provisional
Probab=26.90 E-value=46 Score=26.59 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=31.3
Q ss_pred CCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 83 NPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 83 ~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
.-|++|+.++..+|..|+ .+++|++.|+ |+...|+..++
T Consensus 42 ~Lt~eereai~l~~~eGl------S~~EIAk~LG----IS~sTV~r~L~ 80 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL------TQEEAGKRMG----VSRGTVWRALT 80 (110)
T ss_pred cCCHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHHHH
Confidence 357899999999998887 4677888887 88888876655
No 92
>COG3066 MutH DNA mismatch repair protein [DNA replication, recombination, and repair]
Probab=26.77 E-value=31 Score=31.07 Aligned_cols=59 Identities=22% Similarity=0.266 Sum_probs=36.1
Q ss_pred CCCCCCCCcc-cCCCCC-CCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccC
Q 027928 65 DEKRNPPQVE-THPGGT-RWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEG 123 (217)
Q Consensus 65 ~~~~~~~~v~-t~P~~~-RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~ 123 (217)
++-.++-|.. ++-|++ =|.|+.||-..|-.=+..=|-.=.--+.++||+..+.+=++--
T Consensus 125 veGeR~IPLaeRrvGsPllWsP~~eee~qLr~DWEELMd~IvLGkve~ItArhGevlQlRP 185 (229)
T COG3066 125 VEGERSIPLAERRVGSPLLWSPNEEEERQLREDWEELMDMIVLGKVEQITARHGEVLQLRP 185 (229)
T ss_pred ccCccccchHHhhcCCccccCCCHHHHHHHHhhHHHHHHHHHHhhHHHHHhhhcceeeecc
Confidence 3444443333 333443 8999999988876555544444445578899998765555433
No 93
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.29 E-value=28 Score=27.00 Aligned_cols=27 Identities=22% Similarity=0.242 Sum_probs=17.9
Q ss_pred HHHHHHHhhhcCcccCceeeEeecccHHHHHHH
Q 027928 108 IEQITAQLGKYGKIEGKNVFYWFQNHKARERQK 140 (217)
Q Consensus 108 I~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrK 140 (217)
+++|++.|+ |+.++|..+. +|||++-+
T Consensus 145 ~~eIA~~l~----is~~~V~~~l--~ra~~~l~ 171 (176)
T PRK09638 145 YEEIAKMLN----IPEGTVKSRV--HHGIKQLR 171 (176)
T ss_pred HHHHHHHHC----CChhHHHHHH--HHHHHHHH
Confidence 568888888 8999985543 44444433
No 94
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=26.05 E-value=91 Score=22.48 Aligned_cols=33 Identities=27% Similarity=0.307 Sum_probs=22.7
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCccc
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIE 122 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie 122 (217)
|.+|...|++||..=. +.-++|-+..-.+|.|.
T Consensus 2 T~~Qk~el~~l~~qm~-----e~kK~~idk~Ve~G~iT 34 (59)
T PF10925_consen 2 TDQQKKELKALYKQML-----ELKKQIIDKYVEAGVIT 34 (59)
T ss_pred CHHHHHHHHHHHHHHH-----HHHHHHHHHHHHcCCCC
Confidence 7899999999987643 34445555555666665
No 95
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=25.71 E-value=24 Score=25.00 Aligned_cols=29 Identities=31% Similarity=0.665 Sum_probs=23.1
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 93 EMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 93 E~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
-.||-.|. .+.+|++.|+ |..+-|++|-+
T Consensus 7 ~~LY~~G~------~~~eIA~~Lg----~~~~TV~~W~~ 35 (58)
T PF06056_consen 7 RSLYLQGW------SIKEIAEELG----VPRSTVYSWKD 35 (58)
T ss_pred HHHHHcCC------CHHHHHHHHC----CChHHHHHHHH
Confidence 35677776 3679999999 88999999954
No 96
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=25.56 E-value=45 Score=27.55 Aligned_cols=27 Identities=26% Similarity=0.446 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhhhcCccc-----------------CceeeEeec
Q 027928 105 AQQIEQITAQLGKYGKIE-----------------GKNVFYWFQ 131 (217)
Q Consensus 105 ~eqI~qIT~~L~~~G~Ie-----------------~kNVfyWFQ 131 (217)
-|+.-.|++.|..+|+.. -.|+|-||.
T Consensus 58 RQ~Al~~A~~L~~~Gp~~~~~l~~~~~~~~A~~IL~~N~YGWFe 101 (118)
T PF09929_consen 58 RQDALRCAAALAEHGPSRPADLRKATGVPKATSILRDNHYGWFE 101 (118)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHhcCCChHHHHHHhCccccee
Confidence 366777777777777644 368999996
No 97
>PF07040 DUF1326: Protein of unknown function (DUF1326); InterPro: IPR009758 This family consists of several hypothetical bacterial proteins, which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N terminus. The function of this family is unknown.
Probab=25.53 E-value=80 Score=27.06 Aligned_cols=33 Identities=21% Similarity=0.246 Sum_probs=24.3
Q ss_pred CCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Q 027928 83 NPTQEQIGILEMLYRGGMRTPNAQQIEQITAQL 115 (217)
Q Consensus 83 ~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L 115 (217)
+-|.+|..+|+.||.+..++|-+.=..-+.+.+
T Consensus 70 rAs~~QreAL~~I~~G~~Gg~~~~~a~lv~e~~ 102 (184)
T PF07040_consen 70 RASDAQREALEAIFTGQAGGPFAVFASLVGEVL 102 (184)
T ss_pred CCCHHHHHHHHHHhcCcccCcHHHHHHHhhhhc
Confidence 368999999999999988888774333333333
No 98
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.89 E-value=1e+02 Score=25.59 Aligned_cols=43 Identities=16% Similarity=0.256 Sum_probs=28.8
Q ss_pred hHHHHHHHHHH----hcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 86 QEQIGILEMLY----RGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 86 pEQL~iLE~lY----~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
+.|..++.+.| -.|+ -+++|++.|+ |+..+|. ++..|.++|.|
T Consensus 181 ~~~R~v~~L~y~l~~~eg~------s~~EIA~~lg----is~~tVk----~~~~rA~~~Lr 227 (234)
T PRK08301 181 DREKQIMELRFGLNGGEEK------TQKEVADMLG----ISQSYIS----RLEKRIIKRLK 227 (234)
T ss_pred HHHHHHHHHHhccCCCCCC------CHHHHHHHHC----CCHHHHH----HHHHHHHHHHH
Confidence 56777777777 4565 2568888888 8888884 44445555544
No 99
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.69 E-value=75 Score=25.71 Aligned_cols=46 Identities=22% Similarity=0.307 Sum_probs=31.5
Q ss_pred CCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 83 NPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 83 ~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.=++.|..+|++.|-.|+ -.++|++.|+ |+...|..+. .|.|++.+
T Consensus 111 ~Lp~~~R~v~~L~~~eg~------s~~EIA~~lg----is~~tV~~~l----~Rar~~Lr 156 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGL------SYQEAAAVLG----IPIGTLMSRI----GRARAALR 156 (182)
T ss_pred hCCHHHHHHHHHHHHcCC------CHHHHHHHhC----cCHHHHHHHH----HHHHHHHH
Confidence 345677778888787776 2568888888 8888887654 34444443
No 100
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.34 E-value=37 Score=28.91 Aligned_cols=36 Identities=14% Similarity=0.087 Sum_probs=27.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++.|..+|.+.|-.|+ ..++|++.|+ |+..+|....
T Consensus 173 p~~~R~v~~L~~~eg~------s~~EIA~~Lg----is~~tVk~~l 208 (233)
T PRK12538 173 PEQQRIAVILSYHENM------SNGEIAEVMD----TTVAAVESLL 208 (233)
T ss_pred CHHHHHHhhhHHhcCC------CHHHHHHHHC----cCHHHHHHHH
Confidence 3567778888887777 3568888888 9999996544
No 101
>smart00424 STE STE like transcription factors.
Probab=24.15 E-value=39 Score=27.79 Aligned_cols=24 Identities=33% Similarity=0.852 Sum_probs=16.8
Q ss_pred HHHHHHHhcCC-CCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 90 GILEMLYRGGM-RTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 90 ~iLE~lY~~G~-rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
..||.||+.+- ||-. -.+|||||.
T Consensus 78 ~fL~fL~kN~CirTQK------------------KQKVFyWfs 102 (111)
T smart00424 78 PFLDFLFKNMCLRTQK------------------KQKVFFWFS 102 (111)
T ss_pred HHHHHHHHcccceecc------------------ceEEEEEEe
Confidence 37999998864 3322 247999995
No 102
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.07 E-value=66 Score=25.49 Aligned_cols=44 Identities=18% Similarity=0.241 Sum_probs=30.9
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++.|..++.+.|-.|+ -+++|++.|+ |+..+|..+ ..|.+++-|
T Consensus 135 ~~~~r~i~~l~~~~~~------s~~eIA~~lg----is~~tV~~~----l~ra~~~Lr 178 (182)
T PRK12537 135 EPARRNCILHAYVDGC------SHAEIAQRLG----APLGTVKAW----IKRSLKALR 178 (182)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----CChhhHHHH----HHHHHHHHH
Confidence 3456667888787776 3678999998 899998754 445555544
No 103
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=23.97 E-value=1.1e+02 Score=25.66 Aligned_cols=44 Identities=23% Similarity=0.306 Sum_probs=28.0
Q ss_pred hHHHHHHHHHH----hcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 86 QEQIGILEMLY----RGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 86 pEQL~iLE~lY----~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
+.|..|+...| -.|. -+++|++.|+ |+.++| .|+.-|.++|.++
T Consensus 178 ~~~R~i~~l~y~~~~~e~~------S~~EIA~~lg----is~~tV----~~~~~rA~~kLr~ 225 (233)
T PRK05803 178 EREKEVIEMRYGLGNGKEK------TQREIAKALG----ISRSYV----SRIEKRALKKLFK 225 (233)
T ss_pred HHHHHHHHHHhCCCCCCCc------CHHHHHHHHC----cCHHHH----HHHHHHHHHHHHH
Confidence 45666777766 2332 2567777787 888888 5565566666554
No 104
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=23.93 E-value=59 Score=25.55 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=27.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++.|..+|.+.|-.|+ ..++|++.|+ |+-..|..++
T Consensus 133 ~~~~r~v~~l~~~~g~------s~~eIA~~l~----is~~tV~~~l 168 (184)
T PRK12512 133 PPRQRDVVQSISVEGA------SIKETAAKLS----MSEGAVRVAL 168 (184)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHH
Confidence 4667888888887776 3568888888 8888887554
No 105
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=23.91 E-value=1.1e+02 Score=23.79 Aligned_cols=44 Identities=7% Similarity=0.097 Sum_probs=29.4
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++.|..++...|-.|+ ..++|++.|+ |+..+|. ++..|.|++.|
T Consensus 142 ~~~~r~vi~l~~~~g~------s~~eIA~~lg----is~~~v~----~~l~Ra~~~Lr 185 (189)
T TIGR02984 142 PEDYREVILLRHLEGL------SFAEVAERMD----RSEGAVS----MLWVRGLARLR 185 (189)
T ss_pred CHHHHHHHHHHHhcCC------CHHHHHHHHC----cCHHHHH----HHHHHHHHHHH
Confidence 5667777777776665 2457888887 7777764 45556666554
No 106
>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]
Probab=23.59 E-value=2e+02 Score=26.41 Aligned_cols=41 Identities=17% Similarity=0.240 Sum_probs=31.3
Q ss_pred CCCCCCChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccC
Q 027928 79 GTRWNPTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEG 123 (217)
Q Consensus 79 ~~RW~PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~ 123 (217)
..+-.|||||...+-+.|.... |-++|+.+-..|. .|+|.+
T Consensus 193 ~~~~~~t~e~~~~iK~ai~~a~---sl~Ei~RL~~~l~-~G~~p~ 233 (233)
T KOG1644|consen 193 NSVVTPTPEDREKIKEAIKNAS---SLAEINRLEQLLQ-SGQIPK 233 (233)
T ss_pred cCCCCCCHHHHHHHHHHHHhcc---cHHHHHHHHHHHh-cCCCCC
Confidence 3468889999999999887654 5677777766665 888863
No 107
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=23.56 E-value=1.1e+02 Score=25.74 Aligned_cols=46 Identities=20% Similarity=0.133 Sum_probs=31.2
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHhh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKRN 144 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr~ 144 (217)
.+.|..+|.+.|-.|+ -.++|++.|+ |+..+|.. |-.|.|++.+..
T Consensus 136 p~~~R~v~~L~y~eg~------s~~EIAe~Lg----iS~~tVk~----~L~RAr~~Lr~~ 181 (216)
T PRK12533 136 PVEYREVLVLRELEDM------SYREIAAIAD----VPVGTVMS----RLARARRRLAAL 181 (216)
T ss_pred CHHHHhHhhhHHhcCC------CHHHHHHHHC----CCHHHHHH----HHHHHHHHHHHH
Confidence 3457777787777776 2458888888 99999954 444566655543
No 108
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.56 E-value=70 Score=25.31 Aligned_cols=34 Identities=12% Similarity=0.060 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 87 EQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 87 EQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
.|..++.+.|-.|+ .+++|+..|+ |+..+|....
T Consensus 133 ~~r~v~~l~~~~g~------s~~EIA~~l~----is~~tV~~~l 166 (181)
T PRK12536 133 RQRLPIVHVKLEGL------SVAETAQLTG----LSESAVKVGI 166 (181)
T ss_pred HHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 34455666666666 3568888888 8888887655
No 109
>PF14163 SieB: Superinfection exclusion protein B
Probab=23.42 E-value=54 Score=26.17 Aligned_cols=38 Identities=24% Similarity=0.239 Sum_probs=28.3
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCccc
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIE 122 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie 122 (217)
|++|.++|-++|..|..+=....-+.....|.+.|=|.
T Consensus 80 t~~EkavL~~~~~~~~~~~~lp~~~~~v~~L~~~gIl~ 117 (151)
T PF14163_consen 80 TPEEKAVLREFYIQGNNTLTLPYNNPAVKSLLQKGILE 117 (151)
T ss_pred CHHHHHHHHHHHHCCCCeEEecCCCHHHHHHHHCCCeE
Confidence 78999999999999976665556666666766666553
No 110
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=23.25 E-value=23 Score=23.23 Aligned_cols=34 Identities=35% Similarity=0.629 Sum_probs=21.5
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeE
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFY 128 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfy 128 (217)
+++|+..+-.||..|+ -|.+|+..++ |+-.-||.
T Consensus 7 ~~~~~~~i~~l~~~G~------si~~IA~~~g----vsr~TvyR 40 (45)
T PF02796_consen 7 SKEQIEEIKELYAEGM------SIAEIAKQFG----VSRSTVYR 40 (45)
T ss_dssp SHCCHHHHHHHHHTT--------HHHHHHHTT----S-HHHHHH
T ss_pred CHHHHHHHHHHHHCCC------CHHHHHHHHC----cCHHHHHH
Confidence 4557777778999996 3667887776 55444443
No 111
>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=22.99 E-value=57 Score=23.19 Aligned_cols=36 Identities=22% Similarity=0.329 Sum_probs=26.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++.|..+|...|-.|. .+++|+..|+ |+.+.|..+.
T Consensus 112 ~~~~~~ii~~~~~~g~------s~~eIA~~l~----~s~~~v~~~~ 147 (158)
T TIGR02937 112 PEREREVLVLRYLEGL------SYKEIAEILG----ISVGTVKRRL 147 (158)
T ss_pred CHHHHHHHhhHHhcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 5788888888877776 3457888877 7777775443
No 112
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=22.98 E-value=60 Score=20.19 Aligned_cols=35 Identities=29% Similarity=0.372 Sum_probs=22.1
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
++.|..+++.+ ..|+ .+++|+..|. |+...|++|.
T Consensus 2 ~~~e~~i~~~~-~~~~------s~~eia~~l~----~s~~tv~~~~ 36 (57)
T cd06170 2 TPREREVLRLL-AEGK------TNKEIADILG----ISEKTVKTHL 36 (57)
T ss_pred CHHHHHHHHHH-HcCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 46778888775 4665 3456666665 6666666554
No 113
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=22.94 E-value=87 Score=29.02 Aligned_cols=60 Identities=27% Similarity=0.381 Sum_probs=37.7
Q ss_pred CCCCChHHHHHHHHHHhcC-CCCCCHH---------H--------HHHHHHHhh-hcCcccCc------------eeeEe
Q 027928 81 RWNPTQEQIGILEMLYRGG-MRTPNAQ---------Q--------IEQITAQLG-KYGKIEGK------------NVFYW 129 (217)
Q Consensus 81 RW~PTpEQL~iLE~lY~~G-~rtPs~e---------q--------I~qIT~~L~-~~G~Ie~k------------NVfyW 129 (217)
-=.||--|-.+|.++|..- +-.|..+ . .+++-.+|. +||-|++- |||.=
T Consensus 37 h~kpt~s~t~ll~nmyq~P~~~~~~~d~~~~~~~de~~q~~~defyEd~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~ 116 (260)
T KOG2202|consen 37 HEKPTFSQTVLLKNMYQNPENSWERRDAQGQFLTDEELQRHEDEFYEDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVK 116 (260)
T ss_pred hcccccchHHHHHHHHhCCCCCchhhhhccccccHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhh
Confidence 3467888888899999663 4333221 1 244555555 99999997 66777
Q ss_pred ecccHHHHHHH
Q 027928 130 FQNHKARERQK 140 (217)
Q Consensus 130 FQNrKAReRrK 140 (217)
|+.--.-++-.
T Consensus 117 f~~Ee~ae~a~ 127 (260)
T KOG2202|consen 117 FRSEEDAEAAL 127 (260)
T ss_pred cccHHHHHHHH
Confidence 76554444433
No 114
>PF02200 STE: STE like transcription factor; InterPro: IPR003120 This family consists of transcription factors related to STE and is found associated with the C2H2 zinc finger in some proteins.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.60 E-value=43 Score=27.53 Aligned_cols=23 Identities=43% Similarity=1.047 Sum_probs=16.4
Q ss_pred HHHHHHhcCC-CCCCHHHHHHHHHHhhhcCcccCceeeEeec
Q 027928 91 ILEMLYRGGM-RTPNAQQIEQITAQLGKYGKIEGKNVFYWFQ 131 (217)
Q Consensus 91 iLE~lY~~G~-rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQ 131 (217)
-||.||+.+- ||-. -.+|||||.
T Consensus 78 fL~fL~kn~CirTQK------------------KQKVF~Wfs 101 (110)
T PF02200_consen 78 FLDFLYKNNCIRTQK------------------KQKVFYWFS 101 (110)
T ss_pred HHHHHHHcccceecc------------------ceeEEEEec
Confidence 7999998864 3322 247999995
No 115
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.41 E-value=97 Score=24.52 Aligned_cols=45 Identities=16% Similarity=0.240 Sum_probs=31.4
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
++.|..++.+-|-.|+ .+++|++.|+ |+..+|.. +..|.|++-+.
T Consensus 124 ~~~~r~i~~l~~~~g~------s~~EIA~~lg----is~~tVk~----~l~Rar~~Lr~ 168 (185)
T PRK12542 124 NESNRQVFKYKVFYNL------TYQEISSVMG----ITEANVRK----QFERARKRVQN 168 (185)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHH----HHHHHHHHHHH
Confidence 3567788888787776 3568888888 88888865 44555555543
No 116
>PRK12361 hypothetical protein; Provisional
Probab=22.17 E-value=1.5e+02 Score=28.25 Aligned_cols=21 Identities=19% Similarity=0.224 Sum_probs=16.0
Q ss_pred CCCCCChHHHHHHHHHHhcCC
Q 027928 80 TRWNPTQEQIGILEMLYRGGM 100 (217)
Q Consensus 80 ~RW~PTpEQL~iLE~lY~~G~ 100 (217)
+.-.|+++|++.||.+|+.|-
T Consensus 218 p~v~~n~~q~~~l~~~~~~~~ 238 (547)
T PRK12361 218 KTARLNKRQLRALEKMLEQGK 238 (547)
T ss_pred CCCCCCHHHHHHHHHHHHcCC
Confidence 345688888888888887764
No 117
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.06 E-value=77 Score=24.73 Aligned_cols=43 Identities=14% Similarity=0.241 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 86 QEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 86 pEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
+.|..++.+.|-.|+ ..++|++.|+ |+.++|.... .|.|++.+
T Consensus 122 ~~~r~i~~l~~~~~~------s~~EIA~~lg----is~~tV~~~l----~Ra~~~Lr 164 (173)
T PRK12522 122 EKYKTVLVLYYYEQY------SYKEMSEILN----IPIGTVKYRL----NYAKKQMR 164 (173)
T ss_pred HHHHHHHHHHHHcCC------CHHHHHHHhC----CCHHHHHHHH----HHHHHHHH
Confidence 456677888887776 3468888988 8888887543 45555444
No 118
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=21.79 E-value=76 Score=25.35 Aligned_cols=36 Identities=14% Similarity=0.184 Sum_probs=27.0
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEee
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWF 130 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWF 130 (217)
.+.|..+++..|-.|+ -+++|++.|+ |+..+|....
T Consensus 138 ~~~~r~i~~L~~~~g~------s~~EIA~~lg----is~~tVk~~l 173 (195)
T PRK12532 138 PENTARVFTLKEILGF------SSDEIQQMCG----ISTSNYHTIM 173 (195)
T ss_pred CHHHHHHhhhHHHhCC------CHHHHHHHHC----CCHHHHHHHH
Confidence 4567788888787787 3568888888 8888887654
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.29 E-value=70 Score=25.65 Aligned_cols=44 Identities=20% Similarity=0.105 Sum_probs=29.9
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
.+.|..++.+-|-.|+ -.++|++.|+ |+..+|.... .|.|++-|
T Consensus 132 p~~~r~v~~L~~~~g~------s~~EIA~~lg----is~~tVk~~l----~Rar~~Lr 175 (185)
T PRK09649 132 TTDQREALLLTQLLGL------SYADAAAVCG----CPVGTIRSRV----ARARDALL 175 (185)
T ss_pred CHHHhHHhhhHHHcCC------CHHHHHHHHC----CCHHHHHHHH----HHHHHHHH
Confidence 4677888888888887 2457888887 8888776544 34444444
No 120
>PF04683 Proteasom_Rpn13: Proteasome complex subunit Rpn13 ubiquitin receptor; InterPro: IPR006773 This family was thought originally to be involved in cell-adhesion [, ], but the members are now known to be proteasome subunit Rpn13, a novel ubiquitin receptor. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologues dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain []. The domain forms two contiguous anti-parallel beta-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold []. Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37 []. ; GO: 0005634 nucleus, 0005737 cytoplasm; PDB: 2Z4D_A 2KR0_A 2Z59_A 2R2Y_A.
Probab=21.22 E-value=55 Score=24.73 Aligned_cols=12 Identities=25% Similarity=0.872 Sum_probs=7.8
Q ss_pred cCceeeEeeccc
Q 027928 122 EGKNVFYWFQNH 133 (217)
Q Consensus 122 e~kNVfyWFQNr 133 (217)
++...|||.|.+
T Consensus 74 s~~~~fFWmQe~ 85 (85)
T PF04683_consen 74 SDQRYFFWMQEP 85 (85)
T ss_dssp TT-EEEEEE-SS
T ss_pred CCccEEEEecCC
Confidence 566789999974
No 121
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=20.92 E-value=1e+02 Score=21.60 Aligned_cols=19 Identities=37% Similarity=0.352 Sum_probs=15.7
Q ss_pred CChHHHHHHHHHHhcCCCC
Q 027928 84 PTQEQIGILEMLYRGGMRT 102 (217)
Q Consensus 84 PTpEQL~iLE~lY~~G~rt 102 (217)
=|+.|..+|..||..+-.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~ 38 (126)
T COG1846 20 LTPPQYQVLLALYEAGGIT 38 (126)
T ss_pred CCHHHHHHHHHHHHhCCCc
Confidence 5789999999999887533
No 122
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.46 E-value=1.4e+02 Score=25.20 Aligned_cols=45 Identities=13% Similarity=0.218 Sum_probs=31.3
Q ss_pred CChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 84 PTQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 84 PTpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
=++.|..+|.+.|-.|. -.++|++.|+ |....|.. +..|.++|.|
T Consensus 206 L~~~~r~vl~l~~~~g~------s~~eIA~~l~----is~~tV~~----~~~ra~~kLr 250 (257)
T PRK08583 206 LSDREKSIIQCTFIENL------SQKETGERLG----ISQMHVSR----LQRQAIKKLR 250 (257)
T ss_pred CCHHHHHHHHHHHhCCC------CHHHHHHHHC----CCHHHHHH----HHHHHHHHHH
Confidence 35678888999888776 2468888888 88888844 3445555544
No 123
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.44 E-value=1.5e+02 Score=23.87 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=30.4
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHHh
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQKR 143 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqrr 143 (217)
++.|..++.+.|-.|. ..++|++.|+ |....|..+ ..|.|++.+.
T Consensus 138 ~~~~r~i~~L~~~~g~------s~~eIA~~lg----is~~tV~~~----l~Ra~~~Lr~ 182 (196)
T PRK12524 138 PERQRQAVVLRHIEGL------SNPEIAEVME----IGVEAVESL----TARGKRALAA 182 (196)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----cCHHHHHHH----HHHHHHHHHH
Confidence 4566677777776665 2568888888 888888654 4455555554
No 124
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.40 E-value=81 Score=25.55 Aligned_cols=44 Identities=16% Similarity=0.189 Sum_probs=31.5
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccHHHHHHHHH
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHKARERQKQK 142 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrKAReRrKqr 142 (217)
++.|..++.+.|-.|+ .+++|++.|+ |...+|.. |-.|.|++.+
T Consensus 118 p~~~r~i~~L~~~~g~------s~~EIA~~Lg----is~~tVk~----~l~Rar~~Lr 161 (187)
T PRK12516 118 PDDQREAIILVGASGF------AYEEAAEICG----CAVGTIKS----RVNRARQRLQ 161 (187)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHH----HHHHHHHHHH
Confidence 4568888888888887 3458888888 88888864 4445555544
No 125
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.37 E-value=77 Score=24.25 Aligned_cols=35 Identities=20% Similarity=0.210 Sum_probs=26.4
Q ss_pred ChHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEe
Q 027928 85 TQEQIGILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYW 129 (217)
Q Consensus 85 TpEQL~iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyW 129 (217)
++.|..+|+..|-.|+ .+++|++.|+ |+..+|...
T Consensus 111 ~~~~r~v~~l~~~~~~------s~~EIA~~lg----is~~tV~~~ 145 (163)
T PRK07037 111 PARTRYAFEMYRLHGE------TQKDIARELG----VSPTLVNFM 145 (163)
T ss_pred CHHHHHHHHHHHHcCC------CHHHHHHHHC----CCHHHHHHH
Confidence 5566778888887776 3568888888 888888753
No 126
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=20.19 E-value=48 Score=23.40 Aligned_cols=37 Identities=14% Similarity=0.399 Sum_probs=26.3
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHHhhhcCcccCceeeEeecccH
Q 027928 91 ILEMLYRGGMRTPNAQQIEQITAQLGKYGKIEGKNVFYWFQNHK 134 (217)
Q Consensus 91 iLE~lY~~G~rtPs~eqI~qIT~~L~~~G~Ie~kNVfyWFQNrK 134 (217)
.++.+...|..- --|..|++.++ |.-..+|+.|.|+.
T Consensus 21 a~~l~~~~G~~~---~t~~~Ia~~ag----vs~~~~Y~~f~~K~ 57 (201)
T COG1309 21 ALRLFAEKGYAA---TTVDEIAKAAG----VSKGTLYRHFPSKE 57 (201)
T ss_pred HHHHHHHcCcCC---CCHHHHHHHhC----CCcchhHHHcCCHH
Confidence 344455555421 13568888886 99999999999987
Done!