Query gi|254780431|ref|YP_003064844.1| hypothetical protein CLIBASIA_01580 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 178
No_of_seqs 118 out of 521
Neff 6.3
Searched_HMMs 39220
Date Sun May 29 16:09:03 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780431.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam07750 GcrA GcrA cell cycle 100.0 0 0 431.7 10.9 162 1-174 1-162 (162)
2 COG5352 Uncharacterized protei 100.0 0 0 387.9 8.5 169 1-174 1-169 (169)
3 cd00569 HTH_Hin_like Helix-tur 95.8 0.015 3.8E-07 38.4 4.3 33 3-36 6-38 (42)
4 COG3415 Transposase and inacti 94.2 0.14 3.6E-06 32.0 5.6 40 4-44 7-46 (138)
5 pfam02796 HTH_7 Helix-turn-hel 93.8 0.091 2.3E-06 33.3 4.1 34 3-37 6-39 (45)
6 pfam04297 UPF0122 Putative hel 92.7 0.24 6.2E-06 30.5 4.8 38 4-42 19-56 (101)
7 PRK02277 orotate phosphoribosy 91.4 0.24 6E-06 30.5 3.5 38 1-39 1-38 (201)
8 PRK00118 putative DNA-binding 91.1 0.49 1.2E-05 28.5 4.9 38 4-42 19-56 (105)
9 PRK03975 tfx putative transcri 91.0 0.3 7.7E-06 29.9 3.7 41 3-45 5-47 (139)
10 COG2522 Predicted transcriptio 90.9 0.33 8.5E-06 29.6 3.9 34 7-41 11-44 (119)
11 cd06170 LuxR_C_like C-terminal 90.7 0.55 1.4E-05 28.1 4.9 42 5-48 3-48 (57)
12 cd00090 HTH_ARSR Arsenical Res 90.2 0.68 1.7E-05 27.5 5.0 45 4-49 6-53 (78)
13 PRK06930 positive control sigm 90.1 0.3 7.5E-06 29.9 3.0 28 15-43 127-154 (170)
14 cd06171 Sigma70_r4 Sigma70, re 89.4 0.88 2.2E-05 26.8 5.0 38 4-42 12-49 (55)
15 PRK09637 RNA polymerase sigma 89.2 0.91 2.3E-05 26.7 5.0 37 5-42 109-145 (181)
16 PRK12527 RNA polymerase sigma 88.5 1.1 2.7E-05 26.3 4.9 31 11-42 114-144 (159)
17 PRK12516 RNA polymerase sigma 88.4 1.1 2.9E-05 26.1 5.0 38 5-43 122-159 (190)
18 PRK10188 DNA-binding transcrip 88.1 0.73 1.9E-05 27.3 3.9 12 17-28 193-204 (240)
19 PRK12520 RNA polymerase sigma 88.0 1.1 2.8E-05 26.2 4.7 26 17-43 146-171 (191)
20 PRK11886 biotin--protein ligas 88.0 1.1 2.9E-05 26.1 4.8 39 4-43 2-42 (319)
21 pfam08281 Sigma70_r4_2 Sigma-7 87.9 1.2 3E-05 26.0 4.8 33 9-42 17-49 (54)
22 PRK12544 RNA polymerase sigma 87.5 1.4 3.6E-05 25.4 5.0 27 16-43 163-189 (207)
23 pfam00196 GerE Bacterial regul 86.7 1.5 3.7E-05 25.3 4.8 39 9-48 9-51 (58)
24 COG0856 Orotate phosphoribosyl 86.5 0.92 2.4E-05 26.7 3.7 38 4-42 4-41 (203)
25 pfam09329 zf-primase Primase z 86.4 0.31 7.9E-06 29.8 1.2 32 140-171 4-46 (46)
26 PRK12546 RNA polymerase sigma 86.4 1.6 4.2E-05 25.0 4.9 32 11-43 122-153 (188)
27 pfam01047 MarR MarR family. Th 85.8 1.7 4.4E-05 24.9 4.7 46 4-50 2-51 (59)
28 PRK12515 RNA polymerase sigma 85.7 2.1 5.3E-05 24.3 5.1 40 3-43 132-171 (189)
29 PRK05602 RNA polymerase sigma 85.6 1.9 4.9E-05 24.6 4.9 34 8-42 134-167 (186)
30 PRK09047 RNA polymerase factor 85.5 2 5E-05 24.5 4.9 27 15-42 119-145 (161)
31 PRK12517 RNA polymerase sigma 85.4 2.1 5.4E-05 24.3 5.0 31 11-42 137-167 (188)
32 PRK09647 RNA polymerase sigma 85.2 2.1 5.2E-05 24.4 4.9 27 16-43 171-197 (222)
33 PRK12511 RNA polymerase sigma 85.2 0.85 2.2E-05 26.9 3.0 28 15-43 124-151 (182)
34 pfam01527 Transposase_8 Transp 85.1 1.2 3.1E-05 25.8 3.7 40 3-43 7-47 (75)
35 PRK07037 extracytoplasmic-func 85.0 2.2 5.6E-05 24.2 5.0 27 15-42 136-162 (183)
36 PRK11922 RNA polymerase sigma 84.9 2.3 5.9E-05 24.1 5.0 31 11-42 158-188 (231)
37 PRK12543 RNA polymerase sigma 84.6 2.4 6.2E-05 23.9 5.0 33 9-42 136-168 (190)
38 PRK09643 RNA polymerase sigma 84.6 2.3 6E-05 24.0 5.0 37 6-43 135-171 (197)
39 PRK09644 RNA polymerase sigma 84.2 2.4 6.2E-05 23.9 4.9 33 9-42 115-147 (165)
40 TIGR02607 antidote_HigA addict 84.2 0.95 2.4E-05 26.6 2.8 32 9-41 9-42 (81)
41 PRK12538 RNA polymerase sigma 83.8 2.7 7E-05 23.6 5.0 31 11-42 180-210 (233)
42 smart00421 HTH_LUXR helix_turn 83.6 2.6 6.6E-05 23.7 4.9 43 4-48 5-51 (58)
43 PRK10403 transcriptional regul 83.5 2.7 6.9E-05 23.6 4.9 43 4-48 155-201 (215)
44 PRK12524 RNA polymerase sigma 83.4 2.9 7.3E-05 23.4 5.0 32 10-42 144-175 (196)
45 PRK12533 RNA polymerase sigma 83.3 2.8 7.2E-05 23.5 4.9 28 14-42 149-176 (217)
46 PRK11512 DNA-binding transcrip 83.3 3.2 8.2E-05 23.1 5.2 45 4-49 39-87 (144)
47 PRK12532 RNA polymerase sigma 82.7 3.2 8.2E-05 23.1 5.0 28 15-43 149-176 (195)
48 PRK09639 RNA polymerase sigma 82.6 2.9 7.5E-05 23.4 4.8 35 6-42 116-150 (166)
49 PRK12540 RNA polymerase sigma 82.2 3.3 8.4E-05 23.0 5.0 38 5-43 114-151 (181)
50 pfam04545 Sigma70_r4 Sigma-70, 82.2 2.5 6.3E-05 23.8 4.3 38 4-42 6-43 (50)
51 PRK09645 RNA polymerase sigma 81.8 3.8 9.7E-05 22.6 5.1 39 3-42 117-155 (171)
52 PRK09642 RNA polymerase sigma 81.7 3.6 9.1E-05 22.8 5.0 34 8-42 112-145 (160)
53 PHA00675 hypothetical protein 81.5 2.8 7E-05 23.5 4.3 35 3-38 23-58 (78)
54 PHA01976 helix-turn-helix prot 81.5 1.9 4.9E-05 24.6 3.5 29 6-37 5-33 (67)
55 TIGR00721 tfx DNA-binding prot 81.4 1.7 4.4E-05 24.9 3.3 32 3-36 7-38 (142)
56 COG2390 DeoR Transcriptional r 81.3 3.6 9.1E-05 22.8 4.8 36 10-46 17-56 (321)
57 COG2771 CsgD DNA-binding HTH d 81.2 3.5 8.9E-05 22.9 4.8 36 6-42 7-42 (65)
58 COG1356 tfx Transcriptional re 80.8 0.54 1.4E-05 28.2 0.5 32 3-36 9-40 (143)
59 PRK12545 RNA polymerase sigma 80.8 1.6 4.1E-05 25.1 2.9 27 16-43 153-179 (201)
60 COG2739 Uncharacterized protei 80.6 3.4 8.6E-05 23.0 4.5 39 4-43 19-57 (105)
61 PRK11179 DNA-binding transcrip 79.7 5.4 0.00014 21.6 5.3 41 7-48 11-52 (153)
62 pfam08069 Ribosomal_S13_N Ribo 79.0 2.3 5.9E-05 24.1 3.3 26 4-29 30-55 (60)
63 pfam04645 DUF603 Protein of un 78.9 1.6 4.2E-05 25.0 2.5 34 12-47 12-46 (181)
64 smart00344 HTH_ASNC helix_turn 78.5 3.9 1E-04 22.6 4.3 38 9-47 7-45 (108)
65 pfam08279 HTH_11 HTH domain. T 78.1 4.3 0.00011 22.3 4.4 37 9-46 4-42 (55)
66 pfam05029 TIMELESS_C Timeless 77.9 4.1 0.0001 22.4 4.3 52 2-53 168-224 (507)
67 COG5484 Uncharacterized conser 77.6 2.5 6.3E-05 23.8 3.1 41 5-46 6-46 (279)
68 pfam01371 Trp_repressor Trp re 76.9 4.6 0.00012 22.1 4.3 35 6-42 37-71 (88)
69 PRK09958 DNA-binding transcrip 76.4 6.2 0.00016 21.3 4.8 44 4-49 145-192 (204)
70 KOG0048 consensus 76.2 4.8 0.00012 21.9 4.3 39 2-42 64-103 (238)
71 smart00347 HTH_MARR helix_turn 75.7 6.4 0.00016 21.1 4.8 45 4-49 9-57 (101)
72 PRK12542 RNA polymerase sigma 75.3 6.9 0.00018 20.9 4.9 27 15-42 135-161 (185)
73 COG3093 VapI Plasmid maintenan 75.3 3.6 9.1E-05 22.8 3.4 32 9-41 12-45 (104)
74 TIGR01122 ilvE_I branched-chai 75.2 1.5 3.8E-05 25.3 1.4 29 26-54 209-238 (302)
75 PRK09483 response regulator; P 74.6 7.7 0.0002 20.6 4.9 44 4-49 150-197 (216)
76 PRK09706 transcriptional repre 74.4 4.5 0.00011 22.1 3.7 34 5-42 7-40 (135)
77 PRK03573 transcriptional regul 74.2 7.6 0.00019 20.7 4.8 44 6-50 32-80 (144)
78 PRK11169 leucine-responsive tr 74.0 3.2 8.1E-05 23.1 2.8 39 8-47 17-56 (164)
79 PRK10840 transcriptional regul 73.0 6.1 0.00016 21.3 4.1 44 4-49 152-199 (216)
80 COG2345 Predicted transcriptio 73.0 6.1 0.00016 21.3 4.1 38 11-49 17-58 (218)
81 PRK10360 DNA-binding transcrip 72.6 8.7 0.00022 20.3 4.8 38 4-43 139-176 (196)
82 COG2197 CitB Response regulato 72.2 6.9 0.00018 20.9 4.2 45 3-49 149-197 (211)
83 KOG3056 consensus 72.0 2.2 5.5E-05 24.2 1.6 36 140-175 279-325 (578)
84 PRK09935 transcriptional regul 71.8 9.6 0.00025 20.0 4.9 44 4-49 151-198 (210)
85 PRK12535 RNA polymerase sigma 71.6 10 0.00025 19.9 5.0 31 11-42 141-171 (195)
86 PRK11475 DNA-binding transcrip 70.9 4.1 0.00011 22.4 2.9 35 7-45 139-173 (205)
87 pfam01710 Transposase_14 Trans 69.9 9.7 0.00025 19.9 4.6 41 1-42 1-41 (120)
88 COG2826 Tra8 Transposase and i 69.2 6.8 0.00017 21.0 3.7 33 5-38 11-51 (318)
89 PRK08561 rps15p 30S ribosomal 67.2 4.5 0.00011 22.1 2.4 25 5-29 31-55 (151)
90 PRK10651 transcriptional regul 66.3 13 0.00033 19.2 4.9 44 4-49 157-204 (216)
91 PRK08241 RNA polymerase factor 65.9 6.4 0.00016 21.1 3.0 26 17-43 171-196 (341)
92 PRK13870 transcriptional regul 65.7 8.4 0.00021 20.4 3.5 23 14-37 183-206 (234)
93 PTZ00072 40S ribosomal protein 63.3 4.9 0.00013 21.9 2.0 25 5-29 28-52 (148)
94 KOG0991 consensus 62.8 8.8 0.00023 20.2 3.2 25 15-39 17-44 (333)
95 pfam01418 HTH_6 Helix-turn-hel 62.7 8.4 0.00021 20.4 3.1 31 17-48 33-63 (106)
96 PRK10430 DNA-binding transcrip 62.6 9.6 0.00025 20.0 3.4 19 17-36 177-195 (239)
97 pfam01022 HTH_5 Bacterial regu 62.1 13 0.00034 19.1 4.0 32 5-37 2-33 (47)
98 PRK09954 hypothetical protein; 61.7 8 0.0002 20.5 2.8 40 4-44 2-42 (362)
99 TIGR03020 EpsA transcriptional 61.3 14 0.00035 18.9 4.0 20 16-36 203-222 (247)
100 PRK10100 DNA-binding transcrip 61.0 16 0.00041 18.5 4.9 44 4-49 157-204 (216)
101 KOG0400 consensus 60.8 8.1 0.00021 20.5 2.7 43 4-46 30-81 (151)
102 pfam08879 WRC WRC. The WRC dom 60.4 4 0.0001 22.5 1.1 21 143-163 15-35 (46)
103 COG2963 Transposase and inacti 60.3 16 0.0004 18.6 4.1 37 1-37 6-43 (116)
104 PRK09636 RNA polymerase sigma 60.0 9.2 0.00023 20.1 2.9 26 16-42 125-150 (289)
105 pfam01381 HTH_3 Helix-turn-hel 59.6 8.7 0.00022 20.3 2.7 24 10-36 3-26 (55)
106 COG2856 Predicted Zn peptidase 59.6 12 0.00032 19.2 3.5 38 9-47 121-162 (213)
107 pfam11722 zf-TRM13_CCCH CCCH z 59.1 3 7.7E-05 23.3 0.3 18 143-160 13-30 (31)
108 TIGR02612 mob_myst_A mobile my 58.9 6.2 0.00016 21.2 1.9 21 17-38 37-57 (150)
109 PRK04140 hypothetical protein; 57.5 14 0.00035 19.0 3.4 28 9-37 128-156 (319)
110 COG1476 Predicted transcriptio 57.4 13 0.00032 19.2 3.2 30 7-39 5-34 (68)
111 cd00915 MD-1_MD-2 MD-1 and MD- 57.2 4.7 0.00012 22.0 1.0 21 129-149 67-87 (130)
112 TIGR01884 cas_HTH CRISPR locus 57.1 19 0.00047 18.1 4.5 45 3-48 167-216 (231)
113 pfam02001 DUF134 Protein of un 56.4 18 0.00045 18.3 3.8 41 4-49 38-78 (100)
114 PRK10870 transcriptional repre 55.4 12 0.0003 19.4 2.8 43 6-49 56-104 (176)
115 PRK01381 Trp operon repressor; 55.0 15 0.00038 18.7 3.3 32 6-37 43-78 (99)
116 pfam08222 HTH_CodY CodY helix- 54.8 9.2 0.00023 20.1 2.2 24 19-44 4-27 (60)
117 PRK11302 DNA-binding transcrip 54.7 14 0.00036 18.9 3.1 32 16-48 32-63 (284)
118 pfam06056 Terminase_5 Putative 54.6 14 0.00037 18.8 3.2 33 9-42 4-36 (58)
119 TIGR02787 codY_Gpos GTP-sensin 54.5 2.1 5.5E-05 24.3 -1.1 24 19-44 203-226 (255)
120 PRK07500 rpoH2 RNA polymerase 54.0 11 0.00027 19.7 2.4 15 21-36 151-165 (289)
121 pfam04967 HTH_10 HTH DNA bindi 53.2 11 0.00028 19.6 2.4 38 4-42 2-46 (53)
122 pfam01325 Fe_dep_repress Iron 52.8 22 0.00055 17.7 4.4 36 8-44 8-45 (58)
123 PRK10046 dpiA two-component re 52.3 13 0.00033 19.1 2.6 19 16-35 175-193 (225)
124 COG1395 Predicted transcriptio 52.3 18 0.00045 18.3 3.3 28 9-37 128-156 (313)
125 pfam01475 FUR Ferric uptake re 50.4 24 0.0006 17.4 4.2 36 1-36 4-45 (120)
126 PRK09413 insertion sequence 2 50.4 22 0.00057 17.6 3.6 45 4-50 15-59 (121)
127 cd00093 HTH_XRE Helix-turn-hel 49.6 18 0.00047 18.1 3.1 31 10-42 3-34 (58)
128 PRK09635 sigI RNA polymerase s 49.1 18 0.00046 18.2 2.9 29 11-42 129-157 (290)
129 PRK09390 fixJ response regulat 47.5 26 0.00067 17.1 4.1 33 3-37 142-174 (202)
130 COG1737 RpiR Transcriptional r 47.0 21 0.00052 17.8 3.0 30 18-48 36-65 (281)
131 PRK11557 putative DNA-binding 46.5 23 0.00058 17.5 3.1 30 18-48 34-63 (282)
132 PHA00542 putative Cro-like pro 46.5 25 0.00063 17.3 3.3 30 4-34 17-46 (82)
133 pfam07900 DUF1670 Protein of u 46.2 19 0.00049 18.0 2.7 25 12-37 157-181 (220)
134 COG5606 Uncharacterized conser 46.2 12 0.00031 19.3 1.7 31 12-43 33-69 (91)
135 PRK13719 conjugal transfer tra 45.7 20 0.00051 17.9 2.8 36 14-49 156-194 (220)
136 PRK04217 hypothetical protein; 45.7 28 0.00071 16.9 3.8 41 4-49 44-84 (110)
137 pfam11972 HTH_13 HTH DNA bindi 45.1 21 0.00052 17.8 2.7 26 19-45 14-39 (54)
138 PRK03902 manganese transport t 45.1 28 0.00073 16.9 4.6 43 6-49 8-55 (142)
139 PRK04158 transcriptional repre 44.4 8.9 0.00023 20.2 0.8 24 19-44 202-225 (256)
140 pfam04218 CENP-B_N CENP-B N-te 44.4 29 0.00074 16.8 4.0 32 5-38 10-41 (53)
141 PRK09464 pdhR transcriptional 44.1 30 0.00075 16.8 4.0 42 5-47 13-65 (254)
142 pfam09958 DUF2192 Uncharacteri 43.9 25 0.00064 17.2 3.0 47 5-58 7-53 (231)
143 COG1654 BirA Biotin operon rep 42.8 31 0.00079 16.7 4.4 39 6-45 6-45 (79)
144 COG1321 TroR Mn-dependent tran 42.7 31 0.00079 16.7 3.8 33 16-49 22-57 (154)
145 smart00418 HTH_ARSR helix_turn 42.5 26 0.00065 17.2 2.9 37 10-47 2-41 (66)
146 pfam10654 DUF2481 Protein of u 42.3 27 0.00069 17.0 3.0 36 2-38 64-99 (126)
147 pfam01978 TrmB Sugar-specific 42.2 27 0.00069 17.1 3.0 44 4-48 7-54 (68)
148 COG1318 Predicted transcriptio 42.2 18 0.00046 18.2 2.1 34 15-48 58-94 (182)
149 smart00530 HTH_XRE Helix-turn- 42.0 25 0.00064 17.3 2.8 21 16-37 8-28 (56)
150 pfam08535 KorB KorB domain. Th 41.8 18 0.00045 18.3 2.0 20 16-36 1-20 (93)
151 pfam09339 HTH_IclR IclR helix- 41.8 20 0.0005 18.0 2.2 28 9-37 7-36 (52)
152 pfam10053 DUF2290 Uncharacteri 41.2 14 0.00035 18.9 1.3 27 115-141 123-150 (196)
153 cd00167 SANT 'SWI3, ADA2, N-Co 40.2 34 0.00086 16.4 4.8 41 2-42 1-43 (45)
154 PRK11337 DNA-binding transcrip 40.0 33 0.00083 16.5 3.1 32 17-49 46-77 (293)
155 COG1535 EntB Isochorismate hyd 39.8 13 0.00034 19.1 1.1 19 4-22 84-102 (218)
156 COG4189 Predicted transcriptio 39.6 34 0.00088 16.3 4.0 43 5-47 23-68 (308)
157 smart00529 HTH_DTXR Helix-turn 39.4 25 0.00064 17.2 2.5 27 21-48 2-31 (96)
158 COG1846 MarR Transcriptional r 39.2 35 0.00089 16.3 4.6 45 5-50 22-70 (126)
159 pfam10668 Phage_terminase Phag 39.1 34 0.00087 16.4 3.1 29 6-35 7-38 (60)
160 pfam02992 Transposase_21 Trans 38.9 17 0.00042 18.4 1.5 14 8-21 108-121 (226)
161 PRK11569 transcriptional repre 37.9 28 0.0007 17.0 2.5 30 8-38 31-62 (274)
162 pfam03811 Ins_element1 Inserti 37.8 37 0.00093 16.2 3.1 32 8-40 53-84 (88)
163 cd06571 Bac_DnaA_C C-terminal 36.9 28 0.00071 17.0 2.3 27 17-43 43-69 (90)
164 COG5619 Uncharacterized conser 36.8 12 0.00031 19.3 0.5 29 114-142 146-175 (224)
165 TIGR02573 LcrG_PcrG type III s 36.3 39 0.00099 16.0 3.4 30 4-33 18-48 (93)
166 pfam06242 DUF1013 Protein of u 35.8 23 0.00059 17.5 1.8 28 8-37 74-101 (141)
167 pfam02954 HTH_8 Bacterial regu 34.6 41 0.0011 15.8 4.7 36 6-42 6-41 (42)
168 COG2508 Regulator of polyketid 34.4 42 0.0011 15.8 4.5 37 6-43 354-390 (421)
169 pfam00249 Myb_DNA-binding Myb- 34.2 42 0.0011 15.8 4.6 39 1-39 2-42 (47)
170 TIGR01764 excise DNA binding d 34.2 36 0.00091 16.3 2.5 28 19-47 2-29 (49)
171 pfam08542 Rep_fac_C Replicatio 33.7 43 0.0011 15.7 3.6 28 6-33 22-50 (90)
172 PRK11534 DNA-binding transcrip 33.6 42 0.0011 15.8 2.8 41 5-46 10-57 (224)
173 COG1522 Lrp Transcriptional re 32.3 45 0.0011 15.6 5.2 40 4-44 7-47 (154)
174 PRK06393 rpoE DNA-directed RNA 32.1 21 0.00053 17.8 1.1 13 21-34 43-55 (64)
175 TIGR01321 TrpR trp operon repr 32.0 45 0.0011 15.6 2.8 30 6-35 44-77 (95)
176 PRK10421 DNA-binding transcrip 32.0 45 0.0012 15.6 3.8 42 4-46 4-56 (253)
177 pfam00440 TetR_N Bacterial reg 32.0 34 0.00086 16.4 2.1 21 16-37 14-34 (47)
178 COG3369 Zinc finger domain con 31.9 16 0.00042 18.5 0.5 27 139-165 28-55 (78)
179 PRK12400 D-amino acid aminotra 31.6 21 0.00053 17.8 1.0 24 5-28 51-79 (290)
180 PRK01119 hypothetical protein; 31.4 25 0.00063 17.3 1.4 27 5-41 56-82 (106)
181 pfam08104 Antimicrobial_9 Pone 31.4 28 0.00072 16.9 1.6 23 10-43 1-23 (26)
182 COG4465 CodY Pleiotropic trans 31.2 29 0.00073 16.9 1.7 23 19-43 205-227 (261)
183 PRK12856 hypothetical protein; 30.7 26 0.00066 17.1 1.4 25 5-39 56-80 (103)
184 COG1510 Predicted transcriptio 30.6 31 0.0008 16.6 1.8 34 16-50 39-75 (177)
185 pfam04760 IF2_N Translation in 30.4 48 0.0012 15.4 3.1 30 17-47 2-31 (52)
186 COG3355 Predicted transcriptio 30.3 48 0.0012 15.4 4.6 48 4-52 26-78 (126)
187 TIGR00589 ogt methylated-DNA-[ 30.2 25 0.00065 17.2 1.2 15 16-30 17-31 (80)
188 PRK10668 DNA-binding transcrip 29.8 39 0.00098 16.0 2.1 28 9-37 18-49 (216)
189 TIGR03070 couple_hipB transcri 29.7 42 0.0011 15.8 2.3 26 8-36 7-32 (58)
190 PRK09975 DNA-binding transcrip 29.7 40 0.001 15.9 2.2 25 12-37 22-49 (213)
191 COG2150 Predicted regulator of 29.3 50 0.0013 15.3 4.2 36 7-43 15-65 (167)
192 pfam00500 Late_protein_L1 L1 ( 29.3 19 0.00049 18.0 0.5 29 122-150 221-254 (503)
193 TIGR00235 udk uridine kinase; 29.0 14 0.00036 18.9 -0.2 14 1-14 128-141 (220)
194 COG2186 FadR Transcriptional r 29.0 36 0.00093 16.2 1.9 42 4-46 12-64 (241)
195 COG2973 TrpR Trp operon repres 28.3 52 0.0013 15.2 3.2 24 6-29 48-71 (103)
196 KOG1416 consensus 28.2 53 0.0013 15.1 3.0 22 4-28 116-137 (475)
197 cd04762 HTH_MerR-trunc Helix-T 28.1 42 0.0011 15.8 2.1 23 19-42 1-23 (49)
198 PRK09480 slmA nucleoid occlusi 27.7 40 0.001 15.9 1.9 28 8-36 16-47 (194)
199 TIGR02980 SigBFG RNA polymeras 27.3 43 0.0011 15.7 2.0 29 9-38 98-126 (229)
200 smart00550 Zalpha Z-DNA-bindin 27.1 55 0.0014 15.0 4.6 37 11-48 12-54 (68)
201 PRK08351 DNA-directed RNA poly 27.1 29 0.00074 16.8 1.1 12 21-33 41-52 (61)
202 smart00351 PAX Paired Box doma 27.0 55 0.0014 15.0 5.5 46 5-51 20-65 (125)
203 COG0350 Ada Methylated DNA-pro 27.0 37 0.00093 16.2 1.6 26 15-41 102-128 (168)
204 COG2944 Predicted transcriptio 26.3 57 0.0014 14.9 3.9 30 4-36 45-74 (104)
205 PRK12855 hypothetical protein; 26.0 35 0.00089 16.3 1.3 25 5-39 56-80 (103)
206 smart00419 HTH_CRP helix_turn_ 25.9 58 0.0015 14.9 2.9 29 19-48 9-40 (48)
207 KOG1035 consensus 25.8 48 0.0012 15.4 2.0 10 125-134 432-441 (1351)
208 cd07377 WHTH_GntR Winged helix 25.6 58 0.0015 14.8 2.9 26 18-44 24-50 (66)
209 PRK00967 hypothetical protein; 25.5 36 0.00092 16.2 1.3 24 6-39 57-80 (105)
210 cd02421 Peptidase_C39_likeD A 25.4 59 0.0015 14.8 3.6 45 6-50 10-58 (124)
211 PRK02877 hypothetical protein; 24.8 38 0.00098 16.0 1.4 25 5-39 56-80 (107)
212 pfam09862 DUF2089 Protein of u 24.7 61 0.0015 14.7 4.9 40 3-43 34-73 (113)
213 TIGR03338 phnR_burk phosphonat 24.5 61 0.0016 14.7 2.9 42 4-46 13-64 (212)
214 cd01667 TGS_ThrRS_N TGS _ThrRS 24.4 19 0.00049 18.0 -0.2 26 16-41 14-40 (61)
215 TIGR01927 menC_gamma/gm+ o-suc 24.3 37 0.00093 16.2 1.2 41 11-51 250-293 (336)
216 cd04763 HTH_MlrA-like Helix-Tu 24.2 62 0.0016 14.7 3.3 23 6-28 45-67 (68)
217 pfam04035 consensus 24.1 38 0.00098 16.0 1.3 12 21-33 40-51 (60)
218 TIGR01908 cas_CXXC_CXXC CRISPR 24.0 50 0.0013 15.3 1.8 29 133-165 33-63 (339)
219 pfam00392 GntR Bacterial regul 23.8 63 0.0016 14.6 2.6 27 18-45 23-50 (64)
220 PRK10225 DNA-binding transcrip 23.2 65 0.0016 14.6 4.9 42 5-47 12-64 (257)
221 pfam06610 DUF1144 Protein of u 23.0 45 0.0011 15.6 1.4 23 13-38 100-122 (143)
222 pfam01906 DUF74 Domain of unkn 22.8 44 0.0011 15.7 1.3 22 7-38 55-76 (101)
223 smart00717 SANT SANT SWI3, AD 22.6 67 0.0017 14.5 4.9 42 2-43 3-46 (49)
224 pfam05427 FIBP Acidic fibrobla 22.3 67 0.0017 14.5 2.2 35 121-155 177-211 (361)
225 TIGR00642 mmCoA_mut_beta methy 22.2 68 0.0017 14.4 2.4 44 7-50 245-294 (642)
226 TIGR03612 RutA pyrimidine util 22.2 53 0.0013 15.1 1.7 17 4-20 144-160 (355)
227 smart00346 HTH_ICLR helix_turn 22.0 68 0.0017 14.4 3.5 30 8-38 8-39 (91)
228 pfam07592 Transposase_36 Rhodo 21.8 69 0.0018 14.4 2.4 34 15-49 22-59 (311)
229 PRK09834 DNA-binding transcrip 21.8 69 0.0018 14.4 2.7 31 8-43 14-46 (264)
230 PRK11523 DNA-binding transcrip 21.4 70 0.0018 14.3 4.8 45 4-49 10-62 (258)
231 pfam01729 QRPTase_C Quinolinat 21.3 36 0.00093 16.2 0.7 20 23-49 34-53 (169)
232 pfam03965 Pencillinase_R Penic 21.3 70 0.0018 14.3 4.9 48 4-51 2-56 (115)
233 pfam09976 DUF2133 Uncharacteri 21.3 44 0.0011 15.7 1.1 12 6-17 1-12 (43)
234 PRK03772 threonyl-tRNA synthet 20.7 30 0.00076 16.8 0.1 27 15-41 14-41 (642)
235 KOG3121 consensus 20.5 15 0.00039 18.6 -1.4 22 143-164 145-168 (184)
236 PRK01217 hypothetical protein; 20.5 52 0.0013 15.2 1.3 24 6-39 64-87 (114)
237 PRK11050 manganese transport r 20.2 74 0.0019 14.2 3.1 43 5-48 39-86 (155)
238 smart00345 HTH_GNTR helix_turn 20.0 75 0.0019 14.1 2.7 24 20-44 22-45 (60)
No 1
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
Probab=100.00 E-value=0 Score=431.66 Aligned_cols=162 Identities=44% Similarity=0.789 Sum_probs=129.6
Q ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 97778999999999981865889999967854346666777514554455544444432233322234454322222223
Q gi|254780431|r 1 MVWTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRVKVNENKQSDGNRKNVTLGSTSPKTRQSSNVY 80 (178)
Q Consensus 1 MsWTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (178)
||||||||++||+||.+|+||||||++||||||||||||||||||++|+++.+.+..+............+.
T Consensus 1 MsWTdErve~LkkLW~eGlSaSqIA~~LGgvTRNAVIGKaHRLgLs~R~~~~~~~~~~~~~~~~~~~~~~~~-------- 72 (162)
T pfam07750 1 MNWTDERVELLKKLWLEGLSASQIAAQLGGVSRNAVIGKVHRLGLSGRAKPMSPTAAPARPKRAGPPAAAPR-------- 72 (162)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCEEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--------
T ss_conf 988889999999999853659999999765540000002242255656677766667776566677544445--------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHHH
Q ss_conf 33443211100000124544556223444334453111563333684320055789986450047878768887716888
Q gi|254780431|r 81 ICEPVLKGQLPVVRSKRKSKSMEKNNTISSGIVLPISRCLRLMELTDNTCKWPLGDPFGKDFSFCGSDVCNDSPYCDYHK 160 (178)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sLl~Lte~tCkWPiGDP~~~dF~FCG~~~~~g~PYC~~H~ 160 (178)
...+..............+...++....+.+....++||+|++++||||||||+++||||||+++.+|+|||.+|+
T Consensus 73 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~CrWPiGdP~~~dF~FCG~~~~~g~pYC~~H~ 148 (162)
T pfam07750 73 ----PSAGRTALQLELPAEVALEPAAPVVERIVVPMPRRLQLLELGEATCRWPIGDPLSEDFAFCGNKSSEGSPYCAPHA 148 (162)
T ss_pred ----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf ----5666542233445454446444532111254454444300676766188889898886542888989895339999
Q ss_pred HHHCCCCCCHHHHH
Q ss_conf 88705775102344
Q gi|254780431|r 161 KLAYQRVNDRRKVQ 174 (178)
Q Consensus 161 ~iAYQP~~~rr~~~ 174 (178)
.|||||+++||+++
T Consensus 149 ~~AyqP~~~rr~~r 162 (162)
T pfam07750 149 RLAYQPGAERRRMR 162 (162)
T ss_pred HHHCCCCCHHHCCC
T ss_conf 98648864000049
No 2
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=0 Score=387.88 Aligned_cols=169 Identities=43% Similarity=0.772 Sum_probs=131.0
Q ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 97778999999999981865889999967854346666777514554455544444432233322234454322222223
Q gi|254780431|r 1 MVWTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRVKVNENKQSDGNRKNVTLGSTSPKTRQSSNVY 80 (178)
Q Consensus 1 MsWTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (178)
|+||||||++|||||.|||||||||+|||||||||||||||||||++|.++......+. .....+- .........
T Consensus 1 MnWtdERve~LkKLWseGLSASQIAaQLGGVsRnAVIGKVHRL~lsgR~~~~a~~aR~k---~~~sapr--~~~~~a~s~ 75 (169)
T COG5352 1 MNWTDERVETLKKLWSEGLSASQIAAQLGGVSRNAVIGKVHRLGLSGRAKPTAAPARQK---KTTSAPR--APVRAAQSV 75 (169)
T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHEEEEECCCCCCCCCCCCCCCCC---CCCCCCC--CCHHHHHCC
T ss_conf 97418999999999983047999999965840422100123414566577676655532---1235778--730555125
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHHH
Q ss_conf 33443211100000124544556223444334453111563333684320055789986450047878768887716888
Q gi|254780431|r 81 ICEPVLKGQLPVVRSKRKSKSMEKNNTISSGIVLPISRCLRLMELTDNTCKWPLGDPFGKDFSFCGSDVCNDSPYCDYHK 160 (178)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sLl~Lte~tCkWPiGDP~~~dF~FCG~~~~~g~PYC~~H~ 160 (178)
...+...+.++.......+...+....+..+.++|+++.++|++|+++|||||||||..+||+|||.++....|||.+|+
T Consensus 76 ~~~~tr~gatal~~~~a~~~va~~~~~p~~~~v~P~Sr~l~ll~L~ertCkWPiGdPl~edF~FCGn~s~eagpYC~~Ha 155 (169)
T COG5352 76 RHTPTRTGATALQAEVATPVVAPRYIRPAENVVLPISRHLTLLELGERTCKWPIGDPLNEDFHFCGNESAEAGPYCEYHA 155 (169)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf 66654346532224225654443335523311034432000100010113687899644555433788655584156766
Q ss_pred HHHCCCCCCHHHHH
Q ss_conf 88705775102344
Q gi|254780431|r 161 KLAYQRVNDRRKVQ 174 (178)
Q Consensus 161 ~iAYQP~~~rr~~~ 174 (178)
++||||..+||+.|
T Consensus 156 r~Afqp~aerrr~R 169 (169)
T COG5352 156 RVAFQPAAERRRAR 169 (169)
T ss_pred HHHCCHHHHHHHCC
T ss_conf 65234577776229
No 3
>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=95.77 E-value=0.015 Score=38.42 Aligned_cols=33 Identities=33% Similarity=0.585 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH
Q ss_conf 7789999999999818658899999678543466
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAV 36 (178)
-|+|.++.+++|-.+|.|-++||+.+| |||-.|
T Consensus 6 lt~~q~~~ar~l~~~G~~~~~iA~~~G-Vsr~Ti 38 (42)
T cd00569 6 LTPEQIEEARRLLAAGESVAEIARRLG-VSRSTL 38 (42)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHH
T ss_conf 999999999999997898999999979-799999
No 4
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=94.19 E-value=0.14 Score=32.04 Aligned_cols=40 Identities=25% Similarity=0.244 Sum_probs=36.8
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 78999999999981865889999967854346666777514
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
-|+|...+..+-.+|+|..|||+++| ||.+-|+.=++|..
T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~g-vs~sTvy~wv~r~~ 46 (138)
T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFG-VSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHC
T ss_conf 89999999999976854999999969-22999999998733
No 5
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=93.84 E-value=0.091 Score=33.25 Aligned_cols=34 Identities=32% Similarity=0.511 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 77899999999998186588999996785434666
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAVI 37 (178)
-+++.++.++.|-.+|.|..|||+++| |||.-|-
T Consensus 6 l~~~~~~~v~~L~~~G~~i~~IA~~~~-vsrsTvY 39 (45)
T pfam02796 6 LNEEDINEVITLLEEGISIKQIAKIFG-ISRSTVY 39 (45)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHC-CHHHHHH
T ss_conf 389999999999987994999999986-0088887
No 6
>pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.
Probab=92.70 E-value=0.24 Score=30.46 Aligned_cols=38 Identities=29% Similarity=0.468 Sum_probs=33.1
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 789999999999818658899999678543466667775
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
|+.--+.+.-...+.+|-|+||..+| |||.||---++|
T Consensus 19 T~KQ~~~~~lyy~eDlSL~EIAe~~~-iSRQaV~D~ikR 56 (101)
T pfam04297 19 TDKQKNYFELYYLDDLSLSEIAEEFN-VSRQAVYDNIKR 56 (101)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 59999999999876398999998819-859999999999
No 7
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=91.41 E-value=0.24 Score=30.54 Aligned_cols=38 Identities=37% Similarity=0.388 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 977789999999999818658899999678543466667
Q gi|254780431|r 1 MVWTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 1 MsWTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK 39 (178)
|+=-||=+++.++|=.+|||.-|||.+|. |||+-|-=-
T Consensus 1 Mk~i~eLi~kA~eL~~~Gls~geIAdELn-vS~eT~~WL 38 (201)
T PRK02277 1 MKMIEELIEKALELRSEGLSTGEIADELN-VSRETATWL 38 (201)
T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHHH-HHHHHHHHH
T ss_conf 98689999999999986997666355540-269999999
No 8
>PRK00118 putative DNA-binding protein; Validated
Probab=91.15 E-value=0.49 Score=28.47 Aligned_cols=38 Identities=24% Similarity=0.430 Sum_probs=32.2
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 789999999999818658899999678543466667775
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
|+---+.+.-...+-+|-++||..+| |||.||---++|
T Consensus 19 T~kQ~~~~~lyy~~DlSl~EIAe~~~-iSRQaV~D~ikr 56 (105)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEFN-VSRQAVYDNIKR 56 (105)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 59999999999885499999989969-859999999999
No 9
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=90.99 E-value=0.3 Score=29.85 Aligned_cols=41 Identities=32% Similarity=0.441 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH--HHHHHHHCC
Q ss_conf 7789999999999818658899999678543466--667775145
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAV--IGKLHRLFL 45 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAV--IGK~hRLgL 45 (178)
-||--++.| +|-..|++.+|||+.|| .||-.| |-|.-|-+.
T Consensus 5 Lt~~q~~vL-~lR~~G~tQ~eIA~~lg-TSraNvs~iEk~A~eNI 47 (139)
T PRK03975 5 LTERQIEVL-RLRKRGLTQQEIADILG-TSRANISIIEKRARENI 47 (139)
T ss_pred HHHHHHHHH-HHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHH
T ss_conf 689999999-99982897999999977-32889999999999999
No 10
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=90.85 E-value=0.33 Score=29.55 Aligned_cols=34 Identities=41% Similarity=0.404 Sum_probs=28.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 99999999981865889999967854346666777
Q gi|254780431|r 7 RIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLH 41 (178)
Q Consensus 7 rve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~h 41 (178)
|...-+.|=.+|+|..+||+.|| +|.-||=-=++
T Consensus 11 Ra~lA~~L~eeG~Sq~~iA~LLG-ltqaAVS~Yls 44 (119)
T COG2522 11 RALLAKELIEEGLSQYRIAKLLG-LTQAAVSQYLS 44 (119)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHC
T ss_conf 99999999995886999999968-88999999973
No 11
>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=90.74 E-value=0.55 Score=28.12 Aligned_cols=42 Identities=24% Similarity=0.376 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH----CCCCC
Q ss_conf 899999999998186588999996785434666677751----45544
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL----FLSNR 48 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL----gLs~R 48 (178)
+--.+.| .|+.+|+|..|||.+|| +|-+.|-.-..++ |..+|
T Consensus 3 ~rE~~il-~~~~~G~s~~eIA~~L~-is~~TV~~~~~~i~~Kl~~~~r 48 (57)
T cd06170 3 PREREVL-RLLAEGKTNKEIADILG-ISEKTVKTHLRNIMRKLGVKSR 48 (57)
T ss_pred HHHHHHH-HHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCH
T ss_conf 8999999-99980799999999989-7899999999999998689999
No 12
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=90.18 E-value=0.68 Score=27.52 Aligned_cols=45 Identities=24% Similarity=0.350 Sum_probs=36.2
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCC
Q ss_conf 7899999999998186588999996785434666677751---455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~ 49 (178)
.+-|...|.-|...+++++|||+.+| +|+++|---...| ||-...
T Consensus 6 ~~~r~~Il~~L~~~~~~~~eia~~l~-is~~~vs~hL~~L~~~Gli~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGPLTVSELAERLG-LSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEE
T ss_conf 99999999999848906999987778-4878999999999988986899
No 13
>PRK06930 positive control sigma-like factor; Validated
Probab=90.11 E-value=0.3 Score=29.91 Aligned_cols=28 Identities=32% Similarity=0.411 Sum_probs=25.5
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 98186588999996785434666677751
Q gi|254780431|r 15 WSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 15 W~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
-.+|+|.++||..|| ||+++|---++|-
T Consensus 127 ~~~glsy~EIA~~L~-Is~~tV~~~l~RA 154 (170)
T PRK06930 127 RGYGLSYSEIAAYLN-IKKSTVQSMIERA 154 (170)
T ss_pred HHHCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 761888999999979-8899999999999
No 14
>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=89.39 E-value=0.88 Score=26.81 Aligned_cols=38 Identities=34% Similarity=0.479 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 789999999999818658899999678543466667775
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+|+--+.|.--+-+|+|..|||..|| +|.++|=...||
T Consensus 12 ~~~~r~vl~l~y~~~~s~~EIa~~lg-is~~tVk~~l~r 49 (55)
T cd06171 12 PEREREVILLRFGEGLSYEEIAEILG-ISRSTVRQRLHR 49 (55)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 99998989999980999999999989-599999999999
No 15
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=89.20 E-value=0.91 Score=26.70 Aligned_cols=37 Identities=27% Similarity=0.370 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 89999999999818658899999678543466667775
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
++.-+.+.-..-+|+|..|||..|| +|-|+|=-.+||
T Consensus 109 ~~~R~v~~L~~~eg~s~~EIA~~L~-is~~tVksrl~R 145 (181)
T PRK09637 109 EKYAEALRLTELEGLSQKEIAEKLG-LSLSGAKSRVQR 145 (181)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9998997999885999999999989-499999999999
No 16
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=88.52 E-value=1.1 Score=26.27 Aligned_cols=31 Identities=35% Similarity=0.368 Sum_probs=25.2
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999818658899999678543466667775
Q gi|254780431|r 11 LKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 11 LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+.--.-+|+|..|||..|| +|.++|-.-++|
T Consensus 114 ~~L~~~egls~~EIA~~lg-is~~tVk~~l~r 144 (159)
T PRK12527 114 FLLRKLEGLSHQQIAEHLG-ISRSLVEKHIVN 144 (159)
T ss_pred HHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9889873979999999989-199999999999
No 17
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=88.38 E-value=1.1 Score=26.08 Aligned_cols=38 Identities=11% Similarity=0.170 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 899999999998186588999996785434666677751
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
++--+.+--.+-+|+|..|||..|| +|-|.|--.+||-
T Consensus 122 ~~~R~vl~L~~~egls~~EIAe~Lg-is~~TVksrl~RA 159 (190)
T PRK12516 122 DDQREAIILIGASGFAYEEAAEICG-CAVGTIKSRVSRA 159 (190)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 9998999989982999999999989-4999999999999
No 18
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=88.06 E-value=0.73 Score=27.31 Aligned_cols=12 Identities=42% Similarity=0.656 Sum_probs=4.0
Q ss_pred CCCCHHHHHHHH
Q ss_conf 186588999996
Q gi|254780431|r 17 EGLSASQIAVQL 28 (178)
Q Consensus 17 eG~SasqIA~~l 28 (178)
+|.|+.|||..|
T Consensus 193 ~GKTs~EIa~IL 204 (240)
T PRK10188 193 EGKTSAEIAMIL 204 (240)
T ss_pred CCCCHHHHHHHH
T ss_conf 799999999883
No 19
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=88.02 E-value=1.1 Score=26.17 Aligned_cols=26 Identities=23% Similarity=0.212 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 186588999996785434666677751
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
+|+|..|||..|| +|.|+|=-..||-
T Consensus 146 ~~ls~~EIA~~l~-~s~~tVk~~l~RA 171 (191)
T PRK12520 146 LELETEEICKELQ-ITATNLWVMLYRA 171 (191)
T ss_pred HCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 3899999999989-4999999999999
No 20
>PRK11886 biotin--protein ligase; Provisional
Probab=87.98 E-value=1.1 Score=26.07 Aligned_cols=39 Identities=31% Similarity=0.520 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 789999999999818--6588999996785434666677751
Q gi|254780431|r 4 TVERIDKLKKFWSEG--LSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 4 Tderve~LkkLW~eG--~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
|-|++-+|=++=.+| +|.-+||.+|| |||+||=--+..|
T Consensus 2 ~~~~~~~lL~~L~~g~~~SGe~la~~Lg-vSR~aVwK~i~~L 42 (319)
T PRK11886 2 TYEKMLQLLSLLADGDFHSGEQLAEELG-ISRAAIWKHIQTL 42 (319)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 1789999999973799296999999879-8899999999999
No 21
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=87.85 E-value=1.2 Score=25.99 Aligned_cols=33 Identities=33% Similarity=0.476 Sum_probs=27.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999818658899999678543466667775
Q gi|254780431|r 9 DKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 9 e~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+.+---.-+|+|..|||+.|| +|-|+|=..+||
T Consensus 17 ~~~~l~~~~~~s~~eIA~~lg-~s~~tVk~~l~R 49 (54)
T pfam08281 17 EVFLLRYLEGLSYAEIAELLG-ISEGTVKSRLSR 49 (54)
T ss_pred HHHHHHHHHCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 896879987859999999989-499999999999
No 22
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=87.46 E-value=1.4 Score=25.44 Aligned_cols=27 Identities=19% Similarity=0.036 Sum_probs=25.1
Q ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 8186588999996785434666677751
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
-+|+|..|||..|| +|-++|--..||-
T Consensus 163 ~eglS~~EIAe~Lg-is~~tVks~L~RA 189 (207)
T PRK12544 163 FIELETPEICHNED-LTVSNLNVMLYRS 189 (207)
T ss_pred HCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 81999999999979-7999999999999
No 23
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=86.74 E-value=1.5 Score=25.35 Aligned_cols=39 Identities=23% Similarity=0.319 Sum_probs=28.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH----HCCCCC
Q ss_conf 9999999818658899999678543466667775----145544
Q gi|254780431|r 9 DKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR----LFLSNR 48 (178)
Q Consensus 9 e~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR----LgLs~R 48 (178)
-..=.|+.+|+|..|||.+|| +|-+.|=--..+ ||..+|
T Consensus 9 ~~il~~l~~G~s~~eIA~~L~-is~~TV~~h~~~i~~Kl~v~nr 51 (58)
T pfam00196 9 REVLRLLAAGKSNKEIADILG-ISEKTVKVHRSNIMRKLNVHSR 51 (58)
T ss_pred HHHHHHHHHCCCHHHHHHHHC-CCHHHHHHHHHHHHHHCCCCCH
T ss_conf 999999980799999999978-8899999999999998099999
No 24
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=86.53 E-value=0.92 Score=26.66 Aligned_cols=38 Identities=34% Similarity=0.427 Sum_probs=33.2
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 789999999999818658899999678543466667775
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
-+|=|++..+|=..|||.-|||.+|+ |||+-+-=-+-|
T Consensus 4 IeeLi~kA~eLk~~Glt~gEIAdELN-vSreTa~WL~~r 41 (203)
T COG0856 4 IEELIKKARELKSKGLTTGEIADELN-VSRETATWLLTR 41 (203)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHC-CHHHHHHHHHHH
T ss_conf 89999999999877985777676641-048778888754
No 25
>pfam09329 zf-primase Primase zinc finger. This zinc finger is found in yeast Mcm10 proteins and DnaG-type primases.
Probab=86.44 E-value=0.31 Score=29.79 Aligned_cols=32 Identities=25% Similarity=0.697 Sum_probs=23.5
Q ss_pred CCCEECCCCCCCCC-----------CCCHHHHHHHCCCCCCHH
Q ss_conf 45004787876888-----------771688888705775102
Q gi|254780431|r 140 KDFSFCGSDVCNDS-----------PYCDYHKKLAYQRVNDRR 171 (178)
Q Consensus 140 ~dF~FCG~~~~~g~-----------PYC~~H~~iAYQP~~~rr 171 (178)
.||.||-...-+|. -||.+|..++|+..+.+|
T Consensus 4 ~DlG~Ck~~kkdG~~C~~~VN~~~~e~C~yHv~~~~rk~~s~R 46 (46)
T pfam09329 4 RDLGTCKAVRKDGKRCTSWVNKRKTEFCEYHVEAAYRKSSSKR 46 (46)
T ss_pred CCCCCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHHCCC
T ss_conf 6363460513699916681627868640767999997875279
No 26
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=86.40 E-value=1.6 Score=25.03 Aligned_cols=32 Identities=25% Similarity=0.235 Sum_probs=26.9
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 999998186588999996785434666677751
Q gi|254780431|r 11 LKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 11 LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
|.--.-+|+|..|||..|| ++-|+|-..+||-
T Consensus 122 l~L~~~egls~~EIAe~Lg-is~gTVKsRL~RA 153 (188)
T PRK12546 122 LILVGASGFSYEEAAEMCG-VAVGTVKSRANRA 153 (188)
T ss_pred HHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 5879982989999999989-3999999999999
No 27
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=85.84 E-value=1.7 Score=24.91 Aligned_cols=46 Identities=33% Similarity=0.473 Sum_probs=37.6
Q ss_pred CHHHHHHHHHHH-HCCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCCC
Q ss_conf 789999999999-8186588999996785434666677751---4554455
Q gi|254780431|r 4 TVERIDKLKKFW-SEGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNRVK 50 (178)
Q Consensus 4 Tderve~LkkLW-~eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~~ 50 (178)
|-.....|..|| ..|+|.++||+.++ +++.+|-.-+.|| ||-.|..
T Consensus 2 T~~Q~~vL~~l~~~~~~s~~~la~~~~-~~~~~vs~~i~~Le~~glv~R~~ 51 (59)
T pfam01047 2 TLTQFHILRILYEHGPLTVSELAEKLG-VDRSTVTRVLDRLEKKGLIERSR 51 (59)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEECC
T ss_conf 899999999999469929999999988-58654999999998897988627
No 28
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=85.71 E-value=2.1 Score=24.34 Aligned_cols=40 Identities=8% Similarity=0.159 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 77899999999998186588999996785434666677751
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
.+++--+.|.-..-+|+|..|||..|| +|-|+|=...||-
T Consensus 132 L~~~~R~vi~l~~~e~~s~~EIA~~lg-is~~tV~~~l~RA 171 (189)
T PRK12515 132 LSPAHREIIDLVYYHEKSVEEVGEIVG-IPESTVKTRMFYA 171 (189)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 999999999999984999999999989-2999999999999
No 29
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=85.62 E-value=1.9 Score=24.59 Aligned_cols=34 Identities=24% Similarity=0.308 Sum_probs=25.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999999818658899999678543466667775
Q gi|254780431|r 8 IDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 8 ve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
-+.+.-..-+|+|..+||..|| +|-|+|=...||
T Consensus 134 R~v~~L~~~~g~s~~EIA~~l~-is~~tVk~~l~R 167 (186)
T PRK05602 134 REAIVLQYYQGLSNIEAARVMG-LSVDALESLLAR 167 (186)
T ss_pred HHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 8999999863899999999989-399999999999
No 30
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=85.46 E-value=2 Score=24.50 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=24.2
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9818658899999678543466667775
Q gi|254780431|r 15 WSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 15 W~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
--+|+|..|||+.|| +|-++|-...||
T Consensus 119 ~~egls~~EIA~~l~-is~~tVk~~l~R 145 (161)
T PRK09047 119 YWEDMDVAETAAAMG-CSEGSVKTHCSR 145 (161)
T ss_pred HHHCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 998779999999989-699999999999
No 31
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=85.41 E-value=2.1 Score=24.32 Aligned_cols=31 Identities=32% Similarity=0.403 Sum_probs=26.4
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999818658899999678543466667775
Q gi|254780431|r 11 LKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 11 LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
|--..-+|+|..|||..|| +|-|+|=..+||
T Consensus 137 i~L~~~eg~s~~EIA~~Lg-is~~tVksrl~R 167 (188)
T PRK12517 137 LLLQVIGGFSGEEIAEILD-LNKNTVMTRLFR 167 (188)
T ss_pred HHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9999983999999999989-399999999999
No 32
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=85.25 E-value=2.1 Score=24.38 Aligned_cols=27 Identities=44% Similarity=0.580 Sum_probs=24.4
Q ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 8186588999996785434666677751
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
-+|+|..|||+.|| +|-++|-...||-
T Consensus 171 ~eglS~~EIAe~Lg-is~gTVKsrl~RA 197 (222)
T PRK09647 171 IEGLSYEEIAATLG-VKLGTVRSRIHRG 197 (222)
T ss_pred HCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 63999999999989-3999999999999
No 33
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=85.24 E-value=0.85 Score=26.89 Aligned_cols=28 Identities=29% Similarity=0.398 Sum_probs=24.9
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 98186588999996785434666677751
Q gi|254780431|r 15 WSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 15 W~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
.-+|+|..|||..|| +|-|+|=-.+||-
T Consensus 124 ~~egls~~EIAe~Lg-is~gTVKsrl~RA 151 (182)
T PRK12511 124 AIEGLSYQEAANVLG-IPIGTLMSRIGRA 151 (182)
T ss_pred EECCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 007999999999989-3999999999999
No 34
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=85.11 E-value=1.2 Score=25.83 Aligned_cols=40 Identities=20% Similarity=0.285 Sum_probs=30.6
Q ss_pred CCHH-HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 7789-9999999998186588999996785434666677751
Q gi|254780431|r 3 WTVE-RIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 3 WTde-rve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
||+| +++.++.....|.|.++||+++| |+-|.+-.=+...
T Consensus 7 ys~efK~~~V~~~~~~g~sv~~var~~g-i~~~~l~~W~k~~ 47 (75)
T pfam01527 7 YSEEFKARAVKESLEPGASVSELAREHG-VSPATLYKWRKKY 47 (75)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 9999999999999809984999999989-5999999999998
No 35
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=84.95 E-value=2.2 Score=24.19 Aligned_cols=27 Identities=22% Similarity=0.190 Sum_probs=23.9
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9818658899999678543466667775
Q gi|254780431|r 15 WSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 15 W~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
--+|+|..|||++|| +|-|+|=--+||
T Consensus 136 ~~eg~s~~EIAe~Lg-iS~~tVk~~l~r 162 (183)
T PRK07037 136 RLRGETLQDIARELN-VSQTLVNFMIRD 162 (183)
T ss_pred HHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 873989999999989-299999999999
No 36
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=84.91 E-value=2.3 Score=24.06 Aligned_cols=31 Identities=32% Similarity=0.372 Sum_probs=26.2
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999818658899999678543466667775
Q gi|254780431|r 11 LKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 11 LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+.-..-+|+|..|||..|| +|-|+|=-.+||
T Consensus 158 ~~L~~~eglS~~EIA~~Lg-is~~TVKsrL~R 188 (231)
T PRK11922 158 FVLRVVEELSVEETAQALG-LPEETVKTRLHR 188 (231)
T ss_pred HHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9999993999999999989-399999999999
No 37
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=84.58 E-value=2.4 Score=23.92 Aligned_cols=33 Identities=15% Similarity=0.205 Sum_probs=27.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999818658899999678543466667775
Q gi|254780431|r 9 DKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 9 e~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+.+.-..-+|+|..+||..|| +|.|+|=...||
T Consensus 136 ~vi~L~~~~g~s~~EIA~~l~-is~~tVk~rl~r 168 (190)
T PRK12543 136 QVIILRYLHDYSQEEVAQILH-IPIGTVKSRIHA 168 (190)
T ss_pred HHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 999999985999999999989-399999999999
No 38
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=84.56 E-value=2.3 Score=24.00 Aligned_cols=37 Identities=27% Similarity=0.247 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 99999999998186588999996785434666677751
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
+--+.|.-..-+|+|..|||..|| +|-|+|=-..||-
T Consensus 135 ~~R~vl~L~~~eg~s~~EIA~~lg-is~~tVKsrl~RA 171 (197)
T PRK09643 135 EQRAALVAVDMQGYSVADTARMLG-VAEGTVKSRCARG 171 (197)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 887999999981999999999989-3999999999999
No 39
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=84.24 E-value=2.4 Score=23.90 Aligned_cols=33 Identities=18% Similarity=0.136 Sum_probs=26.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999818658899999678543466667775
Q gi|254780431|r 9 DKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 9 e~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+.+.--.-+|+|..|||..|| +|-|+|=...||
T Consensus 115 ~v~~L~~~~~~s~~EIA~~l~-is~~tVk~rl~R 147 (165)
T PRK09644 115 QAILLCDVHELTYEEAASVLD-LKENTYKSHLFR 147 (165)
T ss_pred HHHHHHHHHCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 999999998889999999989-399999999999
No 40
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=84.20 E-value=0.95 Score=26.56 Aligned_cols=32 Identities=31% Similarity=0.442 Sum_probs=26.4
Q ss_pred HHHHHHHHC--CCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 999999981--865889999967854346666777
Q gi|254780431|r 9 DKLKKFWSE--GLSASQIAVQLGGVTRNAVIGKLH 41 (178)
Q Consensus 9 e~LkkLW~e--G~SasqIA~~lGgvtRNAVIGK~h 41 (178)
|.|++=+.+ |+|++++|+.|| |||+.|=.-||
T Consensus 9 E~L~eEfL~PLg~s~~~LA~~Lg-Vsr~~~sriv~ 42 (81)
T TIGR02607 9 EILLEEFLEPLGLSVRALAKALG-VSRSTLSRIVN 42 (81)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC-CCHHHHHHHHH
T ss_conf 13287752104706899998709-99788888874
No 41
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=83.77 E-value=2.7 Score=23.57 Aligned_cols=31 Identities=29% Similarity=0.284 Sum_probs=23.9
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999818658899999678543466667775
Q gi|254780431|r 11 LKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 11 LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+.-..-+|+|..|||..|| +|-|+|=-.+||
T Consensus 180 l~L~~~egls~~EIA~~Lg-is~~TVKsrL~R 210 (233)
T PRK12538 180 VILSYHENMSNGEIAEVMD-TTVAAVESLLKR 210 (233)
T ss_pred HHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9999984999999999989-299999999999
No 42
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=83.58 E-value=2.6 Score=23.71 Aligned_cols=43 Identities=30% Similarity=0.468 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH----HCCCCC
Q ss_conf 789999999999818658899999678543466667775----145544
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR----LFLSNR 48 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR----LgLs~R 48 (178)
|+--.+.|. |-.+|+|..|||.+|| +|.+.|=.-+.+ ||..+|
T Consensus 5 T~rE~~il~-~l~~G~s~~eIA~~L~-is~~TV~~~~~~i~~Kl~v~~r 51 (58)
T smart00421 5 TPREREVLR-LLAEGLTNKEIAERLG-ISEKTVKTHLSNIMRKLGVRSR 51 (58)
T ss_pred CHHHHHHHH-HHHHCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCH
T ss_conf 899999999-9981799999998989-7898999999999998489999
No 43
>PRK10403 transcriptional regulator NarP; Provisional
Probab=83.48 E-value=2.7 Score=23.61 Aligned_cols=43 Identities=30% Similarity=0.391 Sum_probs=31.4
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH----CCCCC
Q ss_conf 7899999999998186588999996785434666677751----45544
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL----FLSNR 48 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL----gLs~R 48 (178)
|+--.+.| +|..+|+|-.|||.+|| +|.+.|=--++|+ |+.+|
T Consensus 155 T~RE~eVL-~lla~G~snkeIA~~L~-iS~~TV~~h~~~I~~KLgv~nR 201 (215)
T PRK10403 155 TERELDVL-HELAQGLSNKQIASVLN-ISEQTVKVHIRNLLRKLNVRSR 201 (215)
T ss_pred CHHHHHHH-HHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCH
T ss_conf 99999999-99986999999999979-8299999999999998689989
No 44
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=83.39 E-value=2.9 Score=23.44 Aligned_cols=32 Identities=28% Similarity=0.207 Sum_probs=20.9
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 999999818658899999678543466667775
Q gi|254780431|r 10 KLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 10 ~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
.+.-..-+|+|..|||..|| +|-++|=-.+||
T Consensus 144 vi~L~~~eg~s~~EIA~~lg-is~~tVk~~l~R 175 (196)
T PRK12524 144 AVVLRHIEGLSNPEIAEVMQ-IGVEAVESLTAR 175 (196)
T ss_pred HHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 98999980899999999989-299999999999
No 45
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=83.32 E-value=2.8 Score=23.49 Aligned_cols=28 Identities=29% Similarity=0.255 Sum_probs=25.5
Q ss_pred HHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99818658899999678543466667775
Q gi|254780431|r 14 FWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 14 LW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
-.-+|+|..|||..|| ++-+.|--..||
T Consensus 149 r~~eglS~~EIAeiLg-ip~gTVKSRL~R 176 (217)
T PRK12533 149 RELEDMSYREIAAIAD-VPVGTVMSRLAR 176 (217)
T ss_pred HHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9980999999999989-499999999999
No 46
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=83.26 E-value=3.2 Score=23.11 Aligned_cols=45 Identities=20% Similarity=0.217 Sum_probs=37.1
Q ss_pred CHHHHHHHHHHH-HCCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCC
Q ss_conf 789999999999-8186588999996785434666677751---455445
Q gi|254780431|r 4 TVERIDKLKKFW-SEGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW-~eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~ 49 (178)
|-..-..|..|| ..|+|.++||+.|| +++.+|-+-+.|| ||-.|.
T Consensus 39 t~~Q~~vL~~L~~~~~~t~~eLa~~l~-id~~tvt~~ldrLe~~GlI~R~ 87 (144)
T PRK11512 39 TAAQFKVLCSIRCAACITPVELKKVLS-VDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEC
T ss_conf 999999999999869979999999978-8887899999999978796635
No 47
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=82.70 E-value=3.2 Score=23.12 Aligned_cols=28 Identities=21% Similarity=0.268 Sum_probs=24.5
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 98186588999996785434666677751
Q gi|254780431|r 15 WSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 15 W~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
--+|+|..+||..|| +|-|+|=...||-
T Consensus 149 ~~egls~~EIA~~lg-is~~tVks~l~RA 176 (195)
T PRK12532 149 EILGFSSDEIQQMCG-ISTSNYHTIMHRA 176 (195)
T ss_pred HHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 981999999999989-5999999999999
No 48
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=82.61 E-value=2.9 Score=23.35 Aligned_cols=35 Identities=31% Similarity=0.359 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999999818658899999678543466667775
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
..-+.+ -|.-+|+|..|||+.|| +|-++|=-..||
T Consensus 116 ~~r~v~-~l~~~g~s~~EIA~~l~-is~~tVk~~l~R 150 (166)
T PRK09639 116 RDRTVL-LLRFSGYSYKEIAQALG-IDESSVGTTLHR 150 (166)
T ss_pred HHHHHH-HHHHHCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 999999-99993899999999989-199999999999
No 49
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=82.21 E-value=3.3 Score=23.02 Aligned_cols=38 Identities=16% Similarity=0.218 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 899999999998186588999996785434666677751
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
++--+.|---.-+|+|..|||+.|| ++-++|=-..||-
T Consensus 114 ~~~R~vl~L~~~egls~~EIA~iL~-is~gTVKsRL~RA 151 (181)
T PRK12540 114 QDQREALILVGASGFSYEDAAAICG-CAVGTIKSRVNRA 151 (181)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 9998998879980999999999989-4999999999999
No 50
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are 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.
Probab=82.17 E-value=2.5 Score=23.84 Aligned_cols=38 Identities=26% Similarity=0.350 Sum_probs=28.7
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 789999999999818658899999678543466667775
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+++--+.+.--+-+|+|..|||..|| +|+.+|=-..||
T Consensus 6 ~~~~r~ii~l~y~~~~t~~EIA~~lg-is~~~V~~~~~r 43 (50)
T pfam04545 6 PPREREVLVLRFGEGLTLEEIGERLG-ISRERVRQIEKR 43 (50)
T ss_pred CHHHHHHHHHHCCCCCHHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 99999999987068824999999989-799999999999
No 51
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=81.81 E-value=3.8 Score=22.63 Aligned_cols=39 Identities=31% Similarity=0.440 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 7789999999999818658899999678543466667775
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
.+++.-+.+.----+|+|..+||..|| +|-|+|=-..||
T Consensus 117 L~~~~r~v~~l~~~~g~s~~EIA~~l~-is~~tVk~~l~r 155 (171)
T PRK09645 117 LSPEHRAVLVRSYYRGWSTAQIAADLG-IPEGTVKSRLHY 155 (171)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 999988798999986999999999989-299999999999
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=81.74 E-value=3.6 Score=22.80 Aligned_cols=34 Identities=29% Similarity=0.219 Sum_probs=27.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999999818658899999678543466667775
Q gi|254780431|r 8 IDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 8 ve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
-+.|.--.-+|+|..+||..|| +|-|+|=-..||
T Consensus 112 R~v~~L~~~e~~s~~EIA~~l~-is~~tVk~~l~R 145 (160)
T PRK09642 112 RDVVLAHYLEEKSYQEIALQEN-IEVKTVEMKLYR 145 (160)
T ss_pred HHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9997999982999999999989-199999999999
No 53
>PHA00675 hypothetical protein
Probab=81.51 E-value=2.8 Score=23.55 Aligned_cols=35 Identities=17% Similarity=0.394 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHH-CCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 77899999999998-1865889999967854346666
Q gi|254780431|r 3 WTVERIDKLKKFWS-EGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 3 WTderve~LkkLW~-eG~SasqIA~~lGgvtRNAVIG 38 (178)
-||+-||..+.|-+ +|||..++|..+. ++|.+|-+
T Consensus 23 ltd~~Vd~IR~LrE~~gl~Yg~La~~f~-~pkgtIAk 58 (78)
T PHA00675 23 LTDAEVERIRELHEVEGMSYAVLAEKFE-QSKGAIAK 58 (78)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHH
T ss_conf 7789999999999872843899999972-75689999
No 54
>PHA01976 helix-turn-helix protein
Probab=81.49 E-value=1.9 Score=24.58 Aligned_cols=29 Identities=17% Similarity=0.300 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 99999999998186588999996785434666
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVI 37 (178)
+|+..|++ ..|+|..|.|+.+| |||.+|-
T Consensus 5 ~RL~~lR~--~~g~sQ~eLA~~lG-Vs~~~is 33 (67)
T PHA01976 5 IQLIKARN--ARAWSAPELSRRAG-VRHSLIY 33 (67)
T ss_pred HHHHHHHH--HCCCCHHHHHHHHC-CCHHHHH
T ss_conf 99999999--86999999999949-9899999
No 55
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=81.39 E-value=1.7 Score=24.88 Aligned_cols=32 Identities=34% Similarity=0.414 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH
Q ss_conf 7789999999999818658899999678543466
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAV 36 (178)
-||.-+..| +|=..|++.++||+.|| .||-=|
T Consensus 7 LTe~Q~kVL-~lR~kGl~Q~eIAk~Lk-TtRaNv 38 (142)
T TIGR00721 7 LTERQIKVL-ELREKGLKQKEIAKILK-TTRANV 38 (142)
T ss_pred CHHHHHHHH-HHHHCCCCHHHHHHHHC-CCCHHH
T ss_conf 406568999-98633888788987726-720137
No 56
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=81.29 E-value=3.6 Score=22.81 Aligned_cols=36 Identities=31% Similarity=0.424 Sum_probs=23.9
Q ss_pred HHHHH-HHCCCCHHHHHHHHCCCCHHHHHH---HHHHHCCC
Q ss_conf 99999-981865889999967854346666---77751455
Q gi|254780431|r 10 KLKKF-WSEGLSASQIAVQLGGVTRNAVIG---KLHRLFLS 46 (178)
Q Consensus 10 ~LkkL-W~eG~SasqIA~~lGgvtRNAVIG---K~hRLgLs 46 (178)
++.-| ..+|++.+|||++|| +||--|.. +++..|+-
T Consensus 17 ~~A~lYY~~gltQ~eIA~~Lg-iSR~~v~rlL~~Ar~~GiV 56 (321)
T COG2390 17 RAAWLYYVEGLTQSEIAERLG-ISRATVSRLLAKAREEGIV 56 (321)
T ss_pred HHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCEE
T ss_conf 999999846887999998839-8899999999999987938
No 57
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=81.25 E-value=3.5 Score=22.86 Aligned_cols=36 Identities=25% Similarity=0.386 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999999818658899999678543466667775
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
.|-..+.+|+.+|+|..|||..|| +|.+.|---..+
T Consensus 7 ~rE~~~~~l~~~G~s~~eia~~l~-is~~tV~~h~~~ 42 (65)
T COG2771 7 PREREILRLVAQGKSNKEIARILG-ISEETVKTHLRN 42 (65)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 889999999986998999999987-799999999999
No 58
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=80.84 E-value=0.54 Score=28.21 Aligned_cols=32 Identities=38% Similarity=0.430 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH
Q ss_conf 7789999999999818658899999678543466
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAV 36 (178)
-||.-|+.| .|-.+|++.++||++|| .||--|
T Consensus 9 lte~qikvl-~lRekG~tQ~eIA~~L~-TTraNv 40 (143)
T COG1356 9 LTEQQIKVL-VLREKGLTQSEIARILK-TTRANV 40 (143)
T ss_pred EEHHHEEEE-EHHHCCCCHHHHHHHHC-CCCCCH
T ss_conf 002302356-52640564899999975-451017
No 59
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=80.78 E-value=1.6 Score=25.07 Aligned_cols=27 Identities=22% Similarity=0.140 Sum_probs=23.2
Q ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 8186588999996785434666677751
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
-+|+|..+||..|| +|-|+|=...||-
T Consensus 153 ~egls~~EIA~~L~-is~~tVksrL~RA 179 (201)
T PRK12545 153 FLDFEIDDICTELT-LTANHCSVLLYRA 179 (201)
T ss_pred HHCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 92898999999989-6999999999999
No 60
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.60 E-value=3.4 Score=22.97 Aligned_cols=39 Identities=28% Similarity=0.469 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 7899999999998186588999996785434666677751
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
|+--..-+.-...+.+|-++||.+.+ |||.||---+.|-
T Consensus 19 T~KQ~~Y~~lyy~dDlSl~EIAee~~-VSRqAIyDnIKr~ 57 (105)
T COG2739 19 TKKQKNYLELYYLDDLSLSEIAEEFN-VSRQAIYDNIKRT 57 (105)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 68899999999981166999999957-5099999999999
No 61
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=79.71 E-value=5.4 Score=21.62 Aligned_cols=41 Identities=12% Similarity=0.188 Sum_probs=32.5
Q ss_pred HHHHHHHHHHC-CCCHHHHHHHHCCCCHHHHHHHHHHHCCCCC
Q ss_conf 99999999981-8658899999678543466667775145544
Q gi|254780431|r 7 RIDKLKKFWSE-GLSASQIAVQLGGVTRNAVIGKLHRLFLSNR 48 (178)
Q Consensus 7 rve~LkkLW~e-G~SasqIA~~lGgvtRNAVIGK~hRLgLs~R 48 (178)
-...|+.|=.+ -+|.++||++|| +|+.+|--.+.||--.|=
T Consensus 11 D~~IL~~Lq~d~R~s~~eiA~~lg-lS~stv~~Ri~rLe~~Gv 52 (153)
T PRK11179 11 DRGILEALMENARTPYAELAKQFG-VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCC
T ss_conf 999999999848999999999989-299999999999997996
No 62
>pfam08069 Ribosomal_S13_N Ribosomal S13/S15 N-terminal domain. This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021.
Probab=78.99 E-value=2.3 Score=24.06 Aligned_cols=26 Identities=35% Similarity=0.360 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 78999999999981865889999967
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLG 29 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lG 29 (178)
.||-.++.-+|..+|+|.|||+-.|=
T Consensus 30 ~~eve~~I~klakkG~~pSqIG~iLR 55 (60)
T pfam08069 30 PEEVEELIVKLAKKGLTPSQIGVILR 55 (60)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 99999999999987998889735653
No 63
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=78.95 E-value=1.6 Score=25.02 Aligned_cols=34 Identities=35% Similarity=0.569 Sum_probs=25.2
Q ss_pred HHHHHCC-CCHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 9999818-65889999967854346666777514554
Q gi|254780431|r 12 KKFWSEG-LSASQIAVQLGGVTRNAVIGKLHRLFLSN 47 (178)
Q Consensus 12 kkLW~eG-~SasqIA~~lGgvtRNAVIGK~hRLgLs~ 47 (178)
--++.+| |+-.|||.+|| |||--| .|+.+-=-++
T Consensus 12 v~yF~eG~L~D~eIA~~LG-Vsr~nV-~kmRqKwes~ 46 (181)
T pfam04645 12 VAYFKEGSLSDAEIAKELG-VSRVNV-WRMRQKWESG 46 (181)
T ss_pred HHHHHCCCCCHHHHHHHHC-CHHHHH-HHHHHHHHHC
T ss_conf 9999617875799999978-309999-9999999812
No 64
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=78.47 E-value=3.9 Score=22.55 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=29.9
Q ss_pred HHHHHHHHC-CCCHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 999999981-865889999967854346666777514554
Q gi|254780431|r 9 DKLKKFWSE-GLSASQIAVQLGGVTRNAVIGKLHRLFLSN 47 (178)
Q Consensus 9 e~LkkLW~e-G~SasqIA~~lGgvtRNAVIGK~hRLgLs~ 47 (178)
..|+.|=.+ -+|.++||++|| +|+.+|--.+.||-=++
T Consensus 7 ~Il~~L~~n~R~s~~~iA~~lg-~S~~tv~~Ri~~L~~~G 45 (108)
T smart00344 7 KILEELQKDARISLAELAKKVG-LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCC
T ss_conf 9999999828999999999989-39999999999996089
No 65
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=78.06 E-value=4.3 Score=22.28 Aligned_cols=37 Identities=22% Similarity=0.335 Sum_probs=27.9
Q ss_pred HHHHHHH-HCC-CCHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf 9999999-818-6588999996785434666677751455
Q gi|254780431|r 9 DKLKKFW-SEG-LSASQIAVQLGGVTRNAVIGKLHRLFLS 46 (178)
Q Consensus 9 e~LkkLW-~eG-~SasqIA~~lGgvtRNAVIGK~hRLgLs 46 (178)
..|..|= .++ +|+.+||++|| |||-+|.--+.-|.-.
T Consensus 4 ~il~~L~~~~~~vt~~~La~~l~-VSr~TV~rdi~~L~~~ 42 (55)
T pfam08279 4 QILELLLQAREPISGQELAEKLG-VSRRTIRRDIKALEAL 42 (55)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHC
T ss_conf 99999997699918999999969-8899999999999988
No 66
>pfam05029 TIMELESS_C Timeless protein C terminal region. The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologues of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, but is the likely orthologue of a fly gene, timeout (also called tim-2). mTim has been shown to be essential for embryonic development, but does not have substantiated circadian function. Some family members contain a SANT domain in this region.
Probab=77.92 E-value=4.1 Score=22.44 Aligned_cols=52 Identities=23% Similarity=0.326 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHHCCCC----HHHHHHHH-CCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 7778999999999981865----88999996-7854346666777514554455544
Q gi|254780431|r 2 VWTVERIDKLKKFWSEGLS----ASQIAVQL-GGVTRNAVIGKLHRLFLSNRVKVNE 53 (178)
Q Consensus 2 sWTderve~LkkLW~eG~S----asqIA~~l-GgvtRNAVIGK~hRLgLs~R~~~~~ 53 (178)
-||+|-...|+.|+.+=-. -..|...| |..||+.||.|.--|||....+-..
T Consensus 168 LwTeeeeleL~~Lyee~kd~~d~L~~I~~~~t~kRsr~qVi~KLl~LGLv~DrreL~ 224 (507)
T pfam05029 168 LWTGDEDLELQRLYEEFRDSDDVLGHIMKNITGKRSRAQVVDKLLQLGLVSEKRELR 224 (507)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHC
T ss_conf 368889999999887515775248899887424620888999998703643355544
No 67
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=77.64 E-value=2.5 Score=23.84 Aligned_cols=41 Identities=27% Similarity=0.217 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf 899999999998186588999996785434666677751455
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLS 46 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs 46 (178)
+++-...|++|.+|+--..||..|| |+-|.|=-=-.|-|-+
T Consensus 6 ~~~r~~Akk~yl~gmk~~dIAeklG-vspntiksWKrr~gWs 46 (279)
T COG5484 6 NDKRIIAKKDYLKGMKLKDIAEKLG-VSPNTIKSWKRRDGWS 46 (279)
T ss_pred CCHHHHHHHHHHHHCCHHHHHHHHC-CCHHHHHHHHHHCCCC
T ss_conf 5218899999984341999999968-9868888778740888
No 68
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=76.94 E-value=4.6 Score=22.09 Aligned_cols=35 Identities=29% Similarity=0.351 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999999818658899999678543466667775
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+|++..+.|-.+|+|..||++++| || -|.|..+.|
T Consensus 37 ~R~~va~~LL~~~~syreI~~~~g-~S-~aTItRvsr 71 (88)
T pfam01371 37 QRLRIAKELLRGELSQREIAQELG-AS-IATITRGSN 71 (88)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHC-CC-HHHHHHHHH
T ss_conf 999999999978998999999859-85-231478899
No 69
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=76.35 E-value=6.2 Score=21.25 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=29.9
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH----HCCCCCC
Q ss_conf 789999999999818658899999678543466667775----1455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR----LFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR----LgLs~R~ 49 (178)
|+--.+.|+ |..+|+|-.|||++|+ +|-+.|=--..| ||+.+|.
T Consensus 145 t~RE~eVL~-ll~~G~snkeIA~~L~-iS~~TV~~h~~~i~~KL~v~~r~ 192 (204)
T PRK09958 145 SKQEISVMR-YILDGKDNNDIAEKMF-ISNKTVSTYKSRLMEKLECKSLM 192 (204)
T ss_pred CHHHHHHHH-HHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCHH
T ss_conf 999999999-9986999999998978-89999999999999984899999
No 70
>KOG0048 consensus
Probab=76.24 E-value=4.8 Score=21.95 Aligned_cols=39 Identities=36% Similarity=0.259 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHH-HCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 77789999999999-818658899999678543466667775
Q gi|254780431|r 2 VWTVERIDKLKKFW-SEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 2 sWTderve~LkkLW-~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
+||+|-.+++=+|. .=|..=|+||+.|-|-|=|+| |-|-
T Consensus 64 ~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeI--KN~W 103 (238)
T KOG0048 64 NFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEV--KNHW 103 (238)
T ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHH--HHHH
T ss_conf 898899999999999975189999876788568999--8998
No 71
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=75.71 E-value=6.4 Score=21.15 Aligned_cols=45 Identities=33% Similarity=0.403 Sum_probs=36.1
Q ss_pred CHHHHHHHHHHH-HCCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCC
Q ss_conf 789999999999-8186588999996785434666677751---455445
Q gi|254780431|r 4 TVERIDKLKKFW-SEGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW-~eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~ 49 (178)
|-.....|.-|+ ..|+|.++||+.|+ +++.+|-.-+.+| ||-.|.
T Consensus 9 t~~q~~vL~~l~~~~~~t~~~la~~l~-~~~~~vs~~v~~L~~~glv~r~ 57 (101)
T smart00347 9 TPTQFLVLRILYEEGPLSVSELAKRLG-VSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHCCCCEEEE
T ss_conf 999999999999769979999999989-6887999999999458938982
No 72
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=75.33 E-value=6.9 Score=20.91 Aligned_cols=27 Identities=22% Similarity=0.290 Sum_probs=19.3
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9818658899999678543466667775
Q gi|254780431|r 15 WSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 15 W~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
.-+|+|..|||..|| +|-++|=-..||
T Consensus 135 ~~~gls~~EIA~~L~-is~~tVk~rl~R 161 (185)
T PRK12542 135 VFYNLTYQEISSVMG-ITEANVRKQFER 161 (185)
T ss_pred HHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 983999999999989-299999999999
No 73
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=75.28 E-value=3.6 Score=22.81 Aligned_cols=32 Identities=34% Similarity=0.583 Sum_probs=25.7
Q ss_pred HHHHHHHHC--CCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 999999981--865889999967854346666777
Q gi|254780431|r 9 DKLKKFWSE--GLSASQIAVQLGGVTRNAVIGKLH 41 (178)
Q Consensus 9 e~LkkLW~e--G~SasqIA~~lGgvtRNAVIGK~h 41 (178)
|.|+.=..| |+|....|+.|| |+||.|=--++
T Consensus 12 EiL~eeflep~glt~~~lA~~lg-V~r~~is~lin 45 (104)
T COG3093 12 EILREEFLEPLGLTQTELAEALG-VTRNTISELIN 45 (104)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHHHHC
T ss_conf 88999984521698999999939-98999999983
No 74
>TIGR01122 ilvE_I branched-chain amino acid aminotransferase; InterPro: IPR005785 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies. One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C-terminus side of the PlP-lysine. Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE) (2.6.1.42 from EC). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family. ; GO: 0004084 branched-chain-amino-acid transaminase activity, 0009081 branched chain family amino acid metabolic process.
Probab=75.18 E-value=1.5 Score=25.31 Aligned_cols=29 Identities=24% Similarity=0.193 Sum_probs=22.9
Q ss_pred HHHCCCCHHHHHHHHH-HHCCCCCCCCCCC
Q ss_conf 9967854346666777-5145544555444
Q gi|254780431|r 26 VQLGGVTRNAVIGKLH-RLFLSNRVKVNEN 54 (178)
Q Consensus 26 ~~lGgvtRNAVIGK~h-RLgLs~R~~~~~~ 54 (178)
..|-|+|||+||=-++ .||+.=+-.+.+.
T Consensus 209 s~L~GITRd~VitlA~ke~G~~V~E~~I~R 238 (302)
T TIGR01122 209 SILKGITRDTVITLAKKELGIEVVEQRISR 238 (302)
T ss_pred HHCCCCCHHHHHHHHHHCCCEEEEECCCCH
T ss_conf 224888888999998510862688233572
No 75
>PRK09483 response regulator; Provisional
Probab=74.58 E-value=7.7 Score=20.62 Aligned_cols=44 Identities=20% Similarity=0.272 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH----HCCCCCC
Q ss_conf 789999999999818658899999678543466667775----1455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR----LFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR----LgLs~R~ 49 (178)
|+--.+.|+ |..+|+|-.|||.+|+ +|.+.|=--..| ||+.+|.
T Consensus 150 T~RE~eVl~-ll~~G~snkeIA~~L~-iS~~TV~~h~~~i~~KL~v~~r~ 197 (216)
T PRK09483 150 SERELQIML-MITKGQKVNEISEQLN-LSPKTVNSYRYRMFSKLNISGDV 197 (216)
T ss_pred CHHHHHHHH-HHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCHH
T ss_conf 999999999-9987999999999969-89999999999999980999999
No 76
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=74.43 E-value=4.5 Score=22.14 Aligned_cols=34 Identities=29% Similarity=0.334 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 89999999999818658899999678543466667775
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
-+||..+++- .|+|.+++|+.+| ||+.+ |++--+
T Consensus 7 G~Ri~~~R~~--~glTQ~eLA~~~G-vs~~t-Vs~wE~ 40 (135)
T PRK09706 7 GQRIRYRRKQ--LKLSQRALAKAVG-VSHVS-ISQWER 40 (135)
T ss_pred HHHHHHHHHH--CCCCHHHHHHHHC-CCHHH-HHHHHC
T ss_conf 9999999998--5999999999969-88999-999982
No 77
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=74.24 E-value=7.6 Score=20.65 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=35.0
Q ss_pred HHHHHHHHHHH--CCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCCC
Q ss_conf 99999999998--186588999996785434666677751---4554455
Q gi|254780431|r 6 ERIDKLKKFWS--EGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNRVK 50 (178)
Q Consensus 6 erve~LkkLW~--eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~~ 50 (178)
..-..|..||. .|+|.++||+.|| |++.+|-+-+.|| ||-.|..
T Consensus 32 ~q~~~L~~L~~~~~g~tq~eLa~~l~-v~~~t~tr~ld~LE~~GlI~R~~ 80 (144)
T PRK03573 32 THWVTLHNIHQLPPDQSQIQLAKAIG-IEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEEC
T ss_conf 59999999997398989999999979-87836999999999888978622
No 78
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=73.98 E-value=3.2 Score=23.15 Aligned_cols=39 Identities=15% Similarity=0.372 Sum_probs=31.1
Q ss_pred HHHHHHHHHCC-CCHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 99999999818-65889999967854346666777514554
Q gi|254780431|r 8 IDKLKKFWSEG-LSASQIAVQLGGVTRNAVIGKLHRLFLSN 47 (178)
Q Consensus 8 ve~LkkLW~eG-~SasqIA~~lGgvtRNAVIGK~hRLgLs~ 47 (178)
...|..|=.+| +|.++||+++| +|+.+|--.+.||--.|
T Consensus 17 ~~IL~~Lq~daR~s~~eLA~~vg-lS~stv~~RikrLe~~G 56 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVG-LSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCC
T ss_conf 99999999848999999999989-29999999999999789
No 79
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=73.00 E-value=6.1 Score=21.26 Aligned_cols=44 Identities=18% Similarity=0.352 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH----HHHCCCCCC
Q ss_conf 7899999999998186588999996785434666677----751455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKL----HRLFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~----hRLgLs~R~ 49 (178)
|+--.|.| +|-.+|+|-.|||++|+ +|.+.|=--. ..||+.+|.
T Consensus 152 T~RE~eVL-~lla~G~snkeIA~~L~-iS~~TV~~h~~~i~~KLgv~n~~ 199 (216)
T PRK10840 152 SPKESEVL-RLFAEGFLVTEIAKKLN-RSIKTISSQKKSAMMKLGVENDI 199 (216)
T ss_pred CHHHHHHH-HHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 98999999-99986999999998969-89999999999999982999899
No 80
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=72.99 E-value=6.1 Score=21.27 Aligned_cols=38 Identities=32% Similarity=0.291 Sum_probs=28.8
Q ss_pred HHHHH-HCCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCC
Q ss_conf 99999-8186588999996785434666677751---455445
Q gi|254780431|r 11 LKKFW-SEGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNRV 49 (178)
Q Consensus 11 LkkLW-~eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~ 49 (178)
|--|= ..+.|+.|||++|| +|.|||-.-.-.| ||....
T Consensus 17 l~lL~~~g~~sa~elA~~Lg-is~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 17 LELLKKSGPVSADELAEELG-ISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEE
T ss_conf 99983169824999998859-9989999999999868666876
No 81
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=72.55 E-value=8.7 Score=20.27 Aligned_cols=38 Identities=21% Similarity=0.282 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 7899999999998186588999996785434666677751
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
|+--.+.|+ |..+|+|..|||.+|+ +|-+.|=--..++
T Consensus 139 T~RE~eVL~-lia~G~snkeIA~~L~-IS~~TVk~h~~~i 176 (196)
T PRK10360 139 TKRERQVAE-KLAQGMAVKEIAAELG-LSPKTVHVHRANL 176 (196)
T ss_pred CHHHHHHHH-HHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 979999999-9987999999999969-9999999999999
No 82
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=72.22 E-value=6.9 Score=20.93 Aligned_cols=45 Identities=31% Similarity=0.471 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH----HHHHHHHCCCCCC
Q ss_conf 7789999999999818658899999678543466----6677751455445
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAV----IGKLHRLFLSNRV 49 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAV----IGK~hRLgLs~R~ 49 (178)
-|+..++.|+ |-.+|+|-.|||.+|+ +|-+-| -.-..+||+.+|.
T Consensus 149 LT~RE~eVl~-lla~G~snkeIA~~L~-iS~~TVk~h~~~i~~KL~v~~Rt 197 (211)
T COG2197 149 LTPRELEVLR-LLAEGLSNKEIAEELN-LSEKTVKTHVSNILRKLGVRNRT 197 (211)
T ss_pred CCHHHHHHHH-HHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHCCCCCHH
T ss_conf 9989999999-9987998899999978-78989999999999983999899
No 83
>KOG3056 consensus
Probab=71.99 E-value=2.2 Score=24.22 Aligned_cols=36 Identities=28% Similarity=0.625 Sum_probs=26.4
Q ss_pred CCCEECCCCCCCCC-----------CCCHHHHHHHCCCCCCHHHHHH
Q ss_conf 45004787876888-----------7716888887057751023443
Q gi|254780431|r 140 KDFSFCGSDVCNDS-----------PYCDYHKKLAYQRVNDRRKVQA 175 (178)
Q Consensus 140 ~dF~FCG~~~~~g~-----------PYC~~H~~iAYQP~~~rr~~~~ 175 (178)
-||..|-....+|. -||.+|...+|+.++.+|..-+
T Consensus 279 ~dlGtC~a~rK~G~~Cts~VN~~l~~~C~yHv~~~~~k~sakR~el~ 325 (578)
T KOG3056 279 ADLGTCKAKRKDGEKCTSVVNKSLCDYCDYHVEQAYRKLSAKRIELN 325 (578)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHC
T ss_conf 55530311136898345401341788999999988741252045533
No 84
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=71.76 E-value=9.6 Score=19.98 Aligned_cols=44 Identities=25% Similarity=0.347 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH----HCCCCCC
Q ss_conf 789999999999818658899999678543466667775----1455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR----LFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR----LgLs~R~ 49 (178)
|+--.+.|+ |..+|+|..|||.+|+ +|.+.|=.-..+ ||+++|.
T Consensus 151 t~RE~eVL~-ll~~G~snkeIA~~L~-iS~~TV~~h~~~I~~KL~v~nr~ 198 (210)
T PRK09935 151 SNREVTVLR-YLANGLSNKEIAEQLL-LSNKTISAHKSNIYGKLGLHSIV 198 (210)
T ss_pred CHHHHHHHH-HHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCHH
T ss_conf 989999999-9986999999998949-88999999999999981999999
No 85
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=71.61 E-value=10 Score=19.88 Aligned_cols=31 Identities=16% Similarity=0.083 Sum_probs=23.7
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999818658899999678543466667775
Q gi|254780431|r 11 LKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 11 LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
|---.-+|+|..+||..|| ++-+.|=..+||
T Consensus 141 l~L~~~~g~s~~EIA~ilg-i~~gTVKsRl~R 171 (195)
T PRK12535 141 LILTQVLGYTYEEAAKIAD-VRVGTIRSRVAR 171 (195)
T ss_pred HHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 9999982998999999989-399999999999
No 86
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=70.87 E-value=4.1 Score=22.38 Aligned_cols=35 Identities=31% Similarity=0.449 Sum_probs=24.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 999999999818658899999678543466667775145
Q gi|254780431|r 7 RIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFL 45 (178)
Q Consensus 7 rve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgL 45 (178)
-.|.| +|..+|+|..|||.+|+ +|..-| ..||-++
T Consensus 139 E~eVl-~l~a~G~s~~eIA~~L~-~S~kTv--~thr~~~ 173 (205)
T PRK11475 139 EREIL-RFMSRGYSMPQIAEQLE-RNIKTI--RAHKFNV 173 (205)
T ss_pred HHHHH-HHHHCCCCHHHHHHHHC-CCHHHH--HHHHHHH
T ss_conf 99999-99976999999999978-888899--9999999
No 87
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=69.88 E-value=9.7 Score=19.94 Aligned_cols=41 Identities=17% Similarity=0.299 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 977789999999999818658899999678543466667775
Q gi|254780431|r 1 MVWTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 1 MsWTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
|+..-+=-++.=+.=.+|.|..|.|+.+| ||+|.|..=..|
T Consensus 1 MaYS~DlR~rVl~~ve~G~S~~eaA~~F~-Is~~Tv~rWlkr 41 (120)
T pfam01710 1 MAYSLDLRKKVIDYIESGGSITEASKVFQ-IGRATIYRWLKR 41 (120)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHC
T ss_conf 98768999999999986999999999937-029999999855
No 88
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=69.20 E-value=6.8 Score=20.97 Aligned_cols=33 Identities=27% Similarity=0.419 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCC--------CCHHHHHH
Q ss_conf 89999999999818658899999678--------54346666
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGG--------VTRNAVIG 38 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGg--------vtRNAVIG 38 (178)
+||.+ +..|-.+|+|..|||++||- +-||-+.+
T Consensus 11 ~eR~~-I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~ 51 (318)
T COG2826 11 FERYE-IERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRD 51 (318)
T ss_pred HHHHH-HHHHHHCCCCHHHHHHHHCCCCCHHHHHHHCCCCCC
T ss_conf 88999-999998599899999985768620427986687521
No 89
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=67.22 E-value=4.5 Score=22.15 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 8999999999981865889999967
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLG 29 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lG 29 (178)
||-.++.-+|..+|+|.|||+-.|-
T Consensus 31 ~eve~~I~klaKkG~spS~IG~~LR 55 (151)
T PRK08561 31 EEIEELVVELAKQGYSPSMIGIILR 55 (151)
T ss_pred HHHHHHHHHHHHCCCCHHHHHCEEC
T ss_conf 9999999999967998878610122
No 90
>PRK10651 transcriptional regulator NarL; Provisional
Probab=66.27 E-value=13 Score=19.16 Aligned_cols=44 Identities=34% Similarity=0.388 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH----CCCCCC
Q ss_conf 7899999999998186588999996785434666677751----455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL----FLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL----gLs~R~ 49 (178)
|+--.+.|+- ..+|+|..|||.+|| +|-+.|=.-++|+ |+.+|.
T Consensus 157 T~RE~eVL~l-l~~G~snkeIA~~L~-iS~~TV~~h~~~i~~KLgv~nr~ 204 (216)
T PRK10651 157 TPRERDILKL-IAQGLSNKMIARRLD-ITESTVKVHVKHMLKKMKLKSRV 204 (216)
T ss_pred CHHHHHHHHH-HHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCHH
T ss_conf 9899999999-985999999999969-78999999999999984899999
No 91
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=65.86 E-value=6.4 Score=21.15 Aligned_cols=26 Identities=38% Similarity=0.478 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 186588999996785434666677751
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
.|+|++|||..|| +|-.||=.-.||-
T Consensus 171 ~g~s~~EiAe~Lg-~S~aAVks~L~RA 196 (341)
T PRK08241 171 LGWSAAEVAEALG-TSTAAVNSALQRA 196 (341)
T ss_pred CCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 2998899999978-9999999999999
No 92
>PRK13870 transcriptional regulator TraR; Provisional
Probab=65.68 E-value=8.4 Score=20.38 Aligned_cols=23 Identities=35% Similarity=0.518 Sum_probs=13.9
Q ss_pred HH-HCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 99-8186588999996785434666
Q gi|254780431|r 14 FW-SEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 14 LW-~eG~SasqIA~~lGgvtRNAVI 37 (178)
.| ++|.|+.|||..|| +|-+-|.
T Consensus 183 ~W~A~GKT~~EIA~ILg-ISe~TV~ 206 (234)
T PRK13870 183 RWIAVGMTMEEIADVEG-VKYNSVR 206 (234)
T ss_pred HHHHCCCCHHHHHHHHC-CCHHHHH
T ss_conf 99978998999999979-8899999
No 93
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=63.26 E-value=4.9 Score=21.89 Aligned_cols=25 Identities=36% Similarity=0.500 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 8999999999981865889999967
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLG 29 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lG 29 (178)
||-.++.-+|..+|+|.|||+-.|-
T Consensus 28 ~eve~~I~klakkG~t~SqIG~~LR 52 (148)
T PTZ00072 28 RDVVDQICKLAKKGLTPSQIGVYLR 52 (148)
T ss_pred HHHHHHHHHHHHCCCCHHHCCCEEC
T ss_conf 9999999999977999877120133
No 94
>KOG0991 consensus
Probab=62.75 E-value=8.8 Score=20.22 Aligned_cols=25 Identities=36% Similarity=0.538 Sum_probs=11.4
Q ss_pred HHCCCCHHHHHHHHCC---CCHHHHHHH
Q ss_conf 9818658899999678---543466667
Q gi|254780431|r 15 WSEGLSASQIAVQLGG---VTRNAVIGK 39 (178)
Q Consensus 15 W~eG~SasqIA~~lGg---vtRNAVIGK 39 (178)
|-|-+--+.+....|+ |.|=.||++
T Consensus 17 wVeKYrP~~l~dIVGNe~tv~rl~via~ 44 (333)
T KOG0991 17 WVEKYRPSVLQDIVGNEDTVERLSVIAK 44 (333)
T ss_pred HHHHHCCHHHHHHHCCHHHHHHHHHHHH
T ss_conf 7886085299882177989999999997
No 95
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=62.73 E-value=8.4 Score=20.38 Aligned_cols=31 Identities=26% Similarity=0.250 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCC
Q ss_conf 18658899999678543466667775145544
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAVIGKLHRLFLSNR 48 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R 48 (178)
..+|..+||++.| ||-.+|+==++.||++|=
T Consensus 33 ~~~si~~lA~~~~-vS~atv~Rf~kklG~~Gf 63 (106)
T pfam01418 33 IHLSIAELAKAAG-VSEASVVRFCRKLGFSGF 63 (106)
T ss_pred HHCCHHHHHHHHC-CCHHHHHHHHHHHCCCCH
T ss_conf 8833999998969-989999999999589989
No 96
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=62.64 E-value=9.6 Score=19.98 Aligned_cols=19 Identities=16% Similarity=0.328 Sum_probs=11.2
Q ss_pred CCCCHHHHHHHHCCCCHHHH
Q ss_conf 18658899999678543466
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAV 36 (178)
.++||.+||+.+| +||-.+
T Consensus 177 ~~~sa~eva~~~g-iSRvTa 195 (239)
T PRK10430 177 YEFSTDELANEVN-ISRVSC 195 (239)
T ss_pred CCCCHHHHHHHHC-CCHHHH
T ss_conf 9846999998858-529889
No 97
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=62.06 E-value=13 Score=19.08 Aligned_cols=32 Identities=22% Similarity=0.283 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 899999999998186588999996785434666
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVI 37 (178)
+-|+..|.-|=.+-++.+||+..+| ++.-+|-
T Consensus 2 p~Rl~Il~~L~~~~~~v~el~~~l~-~sq~~vS 33 (47)
T pfam01022 2 PTRLKILYLLSEGELCVCELAEILG-LSQSTVS 33 (47)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHH
T ss_conf 5899999999808996999999989-5886999
No 98
>PRK09954 hypothetical protein; Provisional
Probab=61.66 E-value=8 Score=20.50 Aligned_cols=40 Identities=18% Similarity=0.241 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHHHCC-CCHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 789999999999818-65889999967854346666777514
Q gi|254780431|r 4 TVERIDKLKKFWSEG-LSASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 4 Tderve~LkkLW~eG-~SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
|+-.-+.|+-+=... .|..+||++|| +||.+|-+-+..|-
T Consensus 2 t~re~~il~~i~~~p~i~q~ela~~lg-isrs~va~hi~~l~ 42 (362)
T PRK09954 2 NNREKEILAILRRNPLIQQNEIADILQ-ISRSRVAAHIMDLM 42 (362)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHH
T ss_conf 868999999998789958999999979-87999999999887
No 99
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=61.30 E-value=14 Score=18.93 Aligned_cols=20 Identities=30% Similarity=0.513 Sum_probs=7.2
Q ss_pred HCCCCHHHHHHHHCCCCHHHH
Q ss_conf 818658899999678543466
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAV 36 (178)
.+|+|-.|||.+|| +|-+.|
T Consensus 203 a~G~sn~eIA~~L~-iS~~TV 222 (247)
T TIGR03020 203 RDGKTNEEIAAILG-ISSLTV 222 (247)
T ss_pred HCCCCHHHHHHHHC-CCHHHH
T ss_conf 87999999999949-799999
No 100
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=61.05 E-value=16 Score=18.54 Aligned_cols=44 Identities=30% Similarity=0.330 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH----HCCCCCC
Q ss_conf 789999999999818658899999678543466667775----1455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR----LFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR----LgLs~R~ 49 (178)
|+--.|.|+-+ .+|+|-.|||.+|+ +|-+-|=--+++ ||+..|.
T Consensus 157 T~RE~eIL~ll-a~G~sNkEIA~~L~-iSe~TVk~H~~~I~~KL~v~~R~ 204 (216)
T PRK10100 157 THREKEILNKL-RIGASNNEIARSLF-ISENTVKTHLYNLFKKIAVKNRT 204 (216)
T ss_pred CHHHHHHHHHH-HCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCHH
T ss_conf 98999999999-87999999998949-88989999999999980999999
No 101
>KOG0400 consensus
Probab=60.82 E-value=8.1 Score=20.48 Aligned_cols=43 Identities=33% Similarity=0.384 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHC---C------CCHHHHHHHHHHHCCC
Q ss_conf 78999999999981865889999967---8------5434666677751455
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLG---G------VTRNAVIGKLHRLFLS 46 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lG---g------vtRNAVIGK~hRLgLs 46 (178)
.||-.|+..||=.+|++.|||+..|- | |+-|-++--..+-||.
T Consensus 30 ~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~ 81 (151)
T KOG0400 30 ADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLA 81 (151)
T ss_pred HHHHHHHHHHHHHCCCCHHHCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 8999999999986699865812665322475444410006999999976998
No 102
>pfam08879 WRC WRC. The WRC domain, named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that the WRC domain functions in DNA binding.
Probab=60.39 E-value=4 Score=22.50 Aligned_cols=21 Identities=19% Similarity=0.330 Sum_probs=18.5
Q ss_pred EECCCCCCCCCCCCHHHHHHH
Q ss_conf 047878768887716888887
Q gi|254780431|r 143 SFCGSDVCNDSPYCDYHKKLA 163 (178)
Q Consensus 143 ~FCG~~~~~g~PYC~~H~~iA 163 (178)
|=|-..+.+|..||+.|..-.
T Consensus 15 WrC~~~~~~~~~~Ce~H~~~~ 35 (46)
T pfam08879 15 WRCSRRVLPGKKLCERHLHRG 35 (46)
T ss_pred CCCCCCCCCCCCHHHHHHHHC
T ss_conf 644886678701889988601
No 103
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=60.33 E-value=16 Score=18.57 Aligned_cols=37 Identities=16% Similarity=0.343 Sum_probs=26.7
Q ss_pred CCCCHH-HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 977789-9999999998186588999996785434666
Q gi|254780431|r 1 MVWTVE-RIDKLKKFWSEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 1 MsWTde-rve~LkkLW~eG~SasqIA~~lGgvtRNAVI 37 (178)
|.||+| +++.....-..|.|-++||+++|-++.|..=
T Consensus 6 r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~ 43 (116)
T COG2963 6 KKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLY 43 (116)
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHH
T ss_conf 64899999999999981783599999994877537899
No 104
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=60.01 E-value=9.2 Score=20.12 Aligned_cols=26 Identities=27% Similarity=0.253 Sum_probs=24.0
Q ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 818658899999678543466667775
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
-+|+|..|||..|| +|-.+|=.-.||
T Consensus 125 v~g~s~~EIA~iLg-~s~~avR~~l~R 150 (289)
T PRK09636 125 VFGVPFDEIASTLG-RSEAACRQLASR 150 (289)
T ss_pred HHCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 60999999999981-799999999999
No 105
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=59.62 E-value=8.7 Score=20.26 Aligned_cols=24 Identities=38% Similarity=0.703 Sum_probs=19.8
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCCHHHH
Q ss_conf 999999818658899999678543466
Q gi|254780431|r 10 KLKKFWSEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 10 ~LkkLW~eG~SasqIA~~lGgvtRNAV 36 (178)
.+++ ..|+|..++|+.+| ||+..|
T Consensus 3 ~~R~--~~g~tq~~lA~~~g-is~~~i 26 (55)
T pfam01381 3 ELRE--ELGLSQEELAEKLG-VSRSTI 26 (55)
T ss_pred HHHH--HCCCCHHHHHHHHC-CCHHHH
T ss_conf 9897--82998999999989-699999
No 106
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=59.60 E-value=12 Score=19.24 Aligned_cols=38 Identities=18% Similarity=0.232 Sum_probs=31.3
Q ss_pred HHHHHHHHCCC----CHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 99999998186----5889999967854346666777514554
Q gi|254780431|r 9 DKLKKFWSEGL----SASQIAVQLGGVTRNAVIGKLHRLFLSN 47 (178)
Q Consensus 9 e~LkkLW~eG~----SasqIA~~lGgvtRNAVIGK~hRLgLs~ 47 (178)
+.|.++|.... +..+|++.+| ||.+++.=|.+.+||-.
T Consensus 121 ~~l~~~~~~~~~~~~~l~~la~~~g-Vs~e~i~~rl~~~~l~~ 162 (213)
T COG2856 121 EVLRERLEQIQGDPENLAELAKYFG-VSIEAILYRLSDIGLLP 162 (213)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHC-CCHHHHHHHHHHCCCCC
T ss_conf 9998632004587889999999969-77999999997526876
No 107
>pfam11722 zf-TRM13_CCCH CCCH zinc finger in TRM13 protein. This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain.
Probab=59.06 E-value=3 Score=23.29 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=16.8
Q ss_pred EECCCCCCCCCCCCHHHH
Q ss_conf 047878768887716888
Q gi|254780431|r 143 SFCGSDVCNDSPYCDYHK 160 (178)
Q Consensus 143 ~FCG~~~~~g~PYC~~H~ 160 (178)
+||+-.+..|+-||.+|.
T Consensus 13 R~C~m~~~~g~~~C~~H~ 30 (31)
T pfam11722 13 RFCKMERKAGSKYCGEHA 30 (31)
T ss_pred EEEECEECCCCCCCCCCC
T ss_conf 005032368771200469
No 108
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=58.85 E-value=6.2 Score=21.24 Aligned_cols=21 Identities=43% Similarity=0.585 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 1865889999967854346666
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAVIG 38 (178)
=|+|..|.|.+|| |++.-|.+
T Consensus 37 LGms~~QLA~RlG-V~p~Rv~~ 57 (150)
T TIGR02612 37 LGMSGAQLAARLG-VTPQRVEA 57 (150)
T ss_pred HCCCHHHHHHHCC-CCHHHHHH
T ss_conf 2515788766528-97377999
No 109
>PRK04140 hypothetical protein; Provisional
Probab=57.54 E-value=14 Score=18.97 Aligned_cols=28 Identities=36% Similarity=0.598 Sum_probs=22.8
Q ss_pred HHHHHHH-HCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 9999999-8186588999996785434666
Q gi|254780431|r 9 DKLKKFW-SEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 9 e~LkkLW-~eG~SasqIA~~lGgvtRNAVI 37 (178)
++||++= ..|+|--++|..|| |||-+|-
T Consensus 128 ~~Lr~~Re~~g~SlG~LA~~LG-VSRrtv~ 156 (319)
T PRK04140 128 DLLRELREKLGLSLGELASELG-VSRRTIS 156 (319)
T ss_pred HHHHHHHHHCCCCHHHHHHHHC-CCHHHHH
T ss_conf 9999999981988889999849-8699999
No 110
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=57.41 E-value=13 Score=19.20 Aligned_cols=30 Identities=27% Similarity=0.526 Sum_probs=22.9
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 999999999818658899999678543466667
Q gi|254780431|r 7 RIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 7 rve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK 39 (178)
|+..|++. -|+|.++.|+.+| |||-.++-.
T Consensus 5 k~k~~R~~--~~ltQ~elA~~vg-VsRQTi~~i 34 (68)
T COG1476 5 KLKELRAE--LGLTQEELAKLVG-VSRQTIIAI 34 (68)
T ss_pred HHHHHHHH--HCCCHHHHHHHCC-CCHHHHHHH
T ss_conf 99999998--2858999999919-579999999
No 111
>cd00915 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family.
Probab=57.21 E-value=4.7 Score=22.02 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCCCCEECCCCC
Q ss_conf 200557899864500478787
Q gi|254780431|r 129 TCKWPLGDPFGKDFSFCGSDV 149 (178)
Q Consensus 129 tCkWPiGDP~~~dF~FCG~~~ 149 (178)
+=+.||=+++.++|.|||+.-
T Consensus 67 ~~ke~iC~~~~~~ySFCg~lK 87 (130)
T cd00915 67 TRSEIICHGYLDKYSFCGALK 87 (130)
T ss_pred CCCCCEECCCCCCCEEECCCC
T ss_conf 212321358998616514446
No 112
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity..
Probab=57.15 E-value=19 Score=18.11 Aligned_cols=45 Identities=27% Similarity=0.319 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHHHHC-C-CCHHHHHHHHCCCCHHHHHHHHHHH---CCCCC
Q ss_conf 778999999999981-8-6588999996785434666677751---45544
Q gi|254780431|r 3 WTVERIDKLKKFWSE-G-LSASQIAVQLGGVTRNAVIGKLHRL---FLSNR 48 (178)
Q Consensus 3 WTderve~LkkLW~e-G-~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R 48 (178)
-+++.++.|..|-++ | .+-..||+.|| +|+.-+.-.+.-| ||-..
T Consensus 167 ~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg-~s~~T~~~~~~~Lek~gLv~~ 216 (231)
T TIGR01884 167 LSREELKVLEALKAEKGEKSVKNIAKKLG-KSLSTISRHLAELEKKGLVES 216 (231)
T ss_pred CCHHHHHHHHHHHCCCCEECHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEE
T ss_conf 88999999999850788052877998857-888799999998874475456
No 113
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=56.35 E-value=18 Score=18.26 Aligned_cols=41 Identities=24% Similarity=0.398 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 7899999999998186588999996785434666677751455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~ 49 (178)
|-|-.|.|+-.=.|||+..+-|.+|| |||-.| +|+=-++|.
T Consensus 38 ~~dE~EAiRL~D~egl~QeeaA~~Mg-VSR~Tf----~ril~~ARk 78 (100)
T pfam02001 38 TLDEFEAIRLVDYEDYTQEEAAKLMG-ISRRTV----WRLLTSARK 78 (100)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHCC-CCHHHH----HHHHHHHHH
T ss_conf 49999999987360798999998849-769999----999999999
No 114
>PRK10870 transcriptional repressor MprA; Provisional
Probab=55.41 E-value=12 Score=19.43 Aligned_cols=43 Identities=19% Similarity=0.163 Sum_probs=32.7
Q ss_pred HHHHHHHHHHH---CCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCC
Q ss_conf 99999999998---186588999996785434666677751---455445
Q gi|254780431|r 6 ERIDKLKKFWS---EGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNRV 49 (178)
Q Consensus 6 erve~LkkLW~---eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~ 49 (178)
-+-..|.-|-. .+++-||||+.+| +||-.+-+-+.+| ||-.|.
T Consensus 56 ~~f~vL~~L~~~~~~~l~PseLa~~l~-~s~a~iTr~vD~LEkkGlV~R~ 104 (176)
T PRK10870 56 TLFMALITLESQENHSIQPSELSCALG-SSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEE
T ss_conf 899999999718999859899999977-8710199999999988997872
No 115
>PRK01381 Trp operon repressor; Provisional
Probab=55.03 E-value=15 Score=18.75 Aligned_cols=32 Identities=25% Similarity=0.393 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHC----CCCHHHHH
Q ss_conf 999999999981865889999967----85434666
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLG----GVTRNAVI 37 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lG----gvtRNAVI 37 (178)
.|+...+.|=...+|..+||..|| -|||-+-.
T Consensus 43 ~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITRGSn~ 78 (99)
T PRK01381 43 TRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCEECCCCHHH
T ss_conf 999999999948764999999849740200002698
No 116
>pfam08222 HTH_CodY CodY helix-turn-helix domain. This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk.
Probab=54.81 E-value=9.2 Score=20.12 Aligned_cols=24 Identities=38% Similarity=0.631 Sum_probs=17.8
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 65889999967854346666777514
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
+.||+||.+.| +||.-++. +-|.-
T Consensus 4 lvASkiAd~~g-iTRSVIVN-AlRKl 27 (60)
T pfam08222 4 LTASKIADRIG-ITRSVIVN-ALRKL 27 (60)
T ss_pred EEHHHHHHHHC-CHHHHHHH-HHHHH
T ss_conf 40556667629-61899999-99876
No 117
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=54.71 E-value=14 Score=18.91 Aligned_cols=32 Identities=16% Similarity=-0.052 Sum_probs=28.7
Q ss_pred HCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCC
Q ss_conf 818658899999678543466667775145544
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNR 48 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R 48 (178)
.-.+|.+|||++.| ||-..|+==+++||+.|=
T Consensus 32 v~~~si~eLA~~~~-vS~aTV~Rf~kkLGf~Gf 63 (284)
T PRK11302 32 AIHSSIATLAKMAN-VSEPTVNRFCRSLDTKGF 63 (284)
T ss_pred HHHCCHHHHHHHHC-CCHHHHHHHHHHHCCCCH
T ss_conf 97666999998969-988899999999578978
No 118
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). 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.
Probab=54.65 E-value=14 Score=18.83 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=23.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999818658899999678543466667775
Q gi|254780431|r 9 DKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 9 e~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
...+.|.-+|.+-++||++|| +...-|-.=..|
T Consensus 4 ~~Ar~LY~qg~~~~eIA~~Lg-~~~~tVysWk~r 36 (58)
T pfam06056 4 RQARTLYWQGYRPAEIAQELG-LKARTVYSWKDR 36 (58)
T ss_pred HHHHHHHHCCCCHHHHHHHHC-CCCCHHHHHHHH
T ss_conf 999999996898999999978-993145658652
No 119
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154 This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region..
Probab=54.47 E-value=2.1 Score=24.26 Aligned_cols=24 Identities=46% Similarity=0.558 Sum_probs=17.4
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 65889999967854346666777514
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
|.||.||.++| +||. ||==|-|.-
T Consensus 203 LvAS~IAD~vG-ITRS-VIVNALRKl 226 (255)
T TIGR02787 203 LVASKIADRVG-ITRS-VIVNALRKL 226 (255)
T ss_pred EEEEEECCCCC-CCHH-HHHHHHHHH
T ss_conf 77530207126-6033-554543444
No 120
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=54.04 E-value=11 Score=19.71 Aligned_cols=15 Identities=40% Similarity=0.538 Sum_probs=8.4
Q ss_pred HHHHHHHHCCCCHHHH
Q ss_conf 8899999678543466
Q gi|254780431|r 21 ASQIAVQLGGVTRNAV 36 (178)
Q Consensus 21 asqIA~~lGgvtRNAV 36 (178)
..+||.+|| ++..-|
T Consensus 151 ~~eiA~~l~-~~~~~v 165 (289)
T PRK07500 151 HREIATALG-VSLSDV 165 (289)
T ss_pred HHHHHHHHC-CCHHHH
T ss_conf 999998809-999999
No 121
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=53.21 E-value=11 Score=19.61 Aligned_cols=38 Identities=18% Similarity=0.373 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHH-------CCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 7899999999998-------18658899999678543466667775
Q gi|254780431|r 4 TVERIDKLKKFWS-------EGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 4 Tderve~LkkLW~-------eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
||.-.+.|+.-.. .+.|..+||++|| +|++++---.+|
T Consensus 2 T~rQ~evl~~A~~~GYfd~PR~~~l~elA~~lg-is~sT~~~hLr~ 46 (53)
T pfam04967 2 TDRQREILRLAYKMGYFDYPRRVTLKDLAKELG-ISKSTLSEHLRR 46 (53)
T ss_pred CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 889999999999868977887688999999969-899999999999
No 122
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=52.82 E-value=22 Score=17.66 Aligned_cols=36 Identities=19% Similarity=0.285 Sum_probs=24.2
Q ss_pred HHHHHHHHHC--CCCHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 9999999981--865889999967854346666777514
Q gi|254780431|r 8 IDKLKKFWSE--GLSASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 8 ve~LkkLW~e--G~SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
++..-.|..+ -.+.++||+.|| |+.-.|-.-+.||.
T Consensus 8 Lk~Iy~l~~~~~~v~~~~iA~~L~-Vs~~SVt~mlkkL~ 45 (58)
T pfam01325 8 LETIYTLSEEKGVVKTKDLAERLN-VSPSTVSEMLKKLE 45 (58)
T ss_pred HHHHHHHHCCCCCEEHHHHHHHHC-CCCHHHHHHHHHHH
T ss_conf 999999882699612999999959-99252999999999
No 123
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=52.29 E-value=13 Score=19.13 Aligned_cols=19 Identities=21% Similarity=0.296 Sum_probs=8.9
Q ss_pred HCCCCHHHHHHHHCCCCHHH
Q ss_conf 81865889999967854346
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNA 35 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNA 35 (178)
.+++||.+||+.+| +||-.
T Consensus 175 ~~~~ta~eva~~~g-iSrvT 193 (225)
T PRK10046 175 GVQHTAETVAQALT-ISRTT 193 (225)
T ss_pred CCCCCHHHHHHHHC-CCHHH
T ss_conf 99868999999858-51999
No 124
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=52.27 E-value=18 Score=18.26 Aligned_cols=28 Identities=39% Similarity=0.578 Sum_probs=23.4
Q ss_pred HHHHHHH-HCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 9999999-8186588999996785434666
Q gi|254780431|r 9 DKLKKFW-SEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 9 e~LkkLW-~eG~SasqIA~~lGgvtRNAVI 37 (178)
++||++= ..|+|-.++|..|| |||-+|=
T Consensus 128 e~Lre~Ree~glSlG~lA~~lg-VSRktV~ 156 (313)
T COG1395 128 EKLREKREEMGLSLGDLATMLG-VSRKTVY 156 (313)
T ss_pred HHHHHHHHHCCCCHHHHHHHHC-CCHHHHH
T ss_conf 9999999980867878898838-4688898
No 125
>pfam01475 FUR Ferric uptake regulator family. This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.
Probab=50.42 E-value=24 Score=17.42 Aligned_cols=36 Identities=25% Similarity=0.255 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHHHHHHCC--CCHHHHHHHHC----CCCHHHH
Q ss_conf 977789999999999818--65889999967----8543466
Q gi|254780431|r 1 MVWTVERIDKLKKFWSEG--LSASQIAVQLG----GVTRNAV 36 (178)
Q Consensus 1 MsWTderve~LkkLW~eG--~SasqIA~~lG----gvtRNAV 36 (178)
|-+|..|...|.-|+..+ +||.+|-.+|. .|++..|
T Consensus 4 lR~T~qR~~Il~~l~~~~~~~ta~~i~~~l~~~~~~i~~~TV 45 (120)
T pfam01475 4 LKITPQRLKILEVLEKSDEHLSAEEIYRELLEEDPNISLATV 45 (120)
T ss_pred CCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHH
T ss_conf 988889999999998279998999999999965899878999
No 126
>PRK09413 insertion sequence 2 OrfA protein; Reviewed
Probab=50.41 E-value=22 Score=17.59 Aligned_cols=45 Identities=20% Similarity=0.342 Sum_probs=34.8
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf 78999999999981865889999967854346666777514554455
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRVK 50 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~~ 50 (178)
++|++....+=..-|.|-|++|++-| |+.|-+-- =.||-+.+...
T Consensus 15 ~~EK~~IV~es~ePG~sVs~VARrHG-i~~~qlf~-WRr~~~eG~~~ 59 (121)
T PRK09413 15 TQEKIAIVQQSFEPGMTVSLVARQHG-VAASQLFL-WRKQYQEGSLT 59 (121)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHH-HHHHHHHCCCC
T ss_conf 89999999999569984999999949-98999999-99998621211
No 127
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=49.62 E-value=18 Score=18.13 Aligned_cols=31 Identities=32% Similarity=0.681 Sum_probs=20.7
Q ss_pred HHHHHHH-CCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999998-18658899999678543466667775
Q gi|254780431|r 10 KLKKFWS-EGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 10 ~LkkLW~-eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
.|+.+=. .|+|..|+|+.+| +|. +.|.+.-+
T Consensus 3 ~l~~~r~~~~ls~~~lA~~~g-is~-~~l~~~e~ 34 (58)
T cd00093 3 RLKELRKEKGLTQEELAEKLG-VSR-STISRIEN 34 (58)
T ss_pred HHHHHHHHCCCCHHHHHHHCC-CCH-HHHHHHHC
T ss_conf 999999975999999957149-999-99999987
No 128
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=49.05 E-value=18 Score=18.18 Aligned_cols=29 Identities=31% Similarity=0.395 Sum_probs=25.3
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99999818658899999678543466667775
Q gi|254780431|r 11 LKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 11 LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
|++. .|+|..|||..|| .|-.||=.-+||
T Consensus 129 Lrdv--fg~~~~EIA~~Lg-~s~~a~Rqll~R 157 (290)
T PRK09635 129 LHEI--FGLPYQQIATTIG-SQASTCRQLAHR 157 (290)
T ss_pred HHHH--CCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 6986--0898899999968-998999999999
No 129
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=47.51 E-value=26 Score=17.13 Aligned_cols=33 Identities=21% Similarity=0.259 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 77899999999998186588999996785434666
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAVI 37 (178)
-|+--.+.|+.| .+|+|..|||.+|+ +|-+.|=
T Consensus 142 LT~RE~eVL~ll-~~G~snkeIA~~L~-iS~~TV~ 174 (202)
T PRK09390 142 LSERERQVMDGL-VAGLSNKVIARDLD-ISPRTVE 174 (202)
T ss_pred CCHHHHHHHHHH-HCCCCHHHHHHHHC-CCHHHHH
T ss_conf 998999999999-83896899999979-8788999
No 130
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=46.98 E-value=21 Score=17.82 Aligned_cols=30 Identities=23% Similarity=0.233 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHCCCCHHHHHHHHHHHCCCCC
Q ss_conf 8658899999678543466667775145544
Q gi|254780431|r 18 GLSASQIAVQLGGVTRNAVIGKLHRLFLSNR 48 (178)
Q Consensus 18 G~SasqIA~~lGgvtRNAVIGK~hRLgLs~R 48 (178)
=+|..+||++.| ||.-+|+==+++||..|=
T Consensus 36 ~~si~elA~~a~-VS~aTv~Rf~~kLGf~Gf 65 (281)
T COG1737 36 LLSIAELAERAG-VSPATVVRFARKLGFEGF 65 (281)
T ss_pred HCCHHHHHHHHC-CCHHHHHHHHHHCCCCCH
T ss_conf 614999998819-988899999998599988
No 131
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=46.54 E-value=23 Score=17.54 Aligned_cols=30 Identities=27% Similarity=0.315 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHCCCCHHHHHHHHHHHCCCCC
Q ss_conf 8658899999678543466667775145544
Q gi|254780431|r 18 GLSASQIAVQLGGVTRNAVIGKLHRLFLSNR 48 (178)
Q Consensus 18 G~SasqIA~~lGgvtRNAVIGK~hRLgLs~R 48 (178)
-+|..|||++.| ||-..|+==++.||++|=
T Consensus 34 ~~si~eLA~~~~-vS~aTVvRf~kkLGf~Gf 63 (282)
T PRK11557 34 HLSSQQLANEAG-VSQSSVVKFAQKLGYKGF 63 (282)
T ss_pred HCCHHHHHHHHC-CCHHHHHHHHHHHCCCCH
T ss_conf 656999998969-998899999999389989
No 132
>PHA00542 putative Cro-like protein
Probab=46.50 E-value=25 Score=17.30 Aligned_cols=30 Identities=23% Similarity=0.161 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHH
Q ss_conf 7899999999998186588999996785434
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRN 34 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRN 34 (178)
+.--+|+.+.|-..|++.+||+..-| |+-.
T Consensus 17 ~k~P~E~V~aLi~~G~tQ~qI~~~tg-v~Qp 46 (82)
T PHA00542 17 TQRPDELVCALIRAGWSQEQIADATD-VSQP 46 (82)
T ss_pred HCCHHHHHHHHHHCCCCHHHHHHHHC-CCCH
T ss_conf 32989999999982256999998608-7703
No 133
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=46.22 E-value=19 Score=18.00 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=19.6
Q ss_pred HHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 99998186588999996785434666
Q gi|254780431|r 12 KKFWSEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 12 kkLW~eG~SasqIA~~lGgvtRNAVI 37 (178)
-+||-+|.+.+|||++.- -|=+||-
T Consensus 157 v~~~lkg~~t~eiaR~t~-HS~~Avd 181 (220)
T pfam07900 157 VELYLKGYQTSEIARLTN-HSPESID 181 (220)
T ss_pred HHHHHCCCCHHHHHHHHC-CCHHHHH
T ss_conf 999982688889999853-7989999
No 134
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=46.19 E-value=12 Score=19.35 Aligned_cols=31 Identities=45% Similarity=0.636 Sum_probs=23.1
Q ss_pred HHHH--HCCCCHHHHHHHHCCCCHHHH----HHHHHHH
Q ss_conf 9999--818658899999678543466----6677751
Q gi|254780431|r 12 KKFW--SEGLSASQIAVQLGGVTRNAV----IGKLHRL 43 (178)
Q Consensus 12 kkLW--~eG~SasqIA~~lGgvtRNAV----IGK~hRL 43 (178)
-++| ..+++.+|||.-|| |||.-| =||.|+.
T Consensus 33 i~~~i~q~~l~Q~qiae~lg-V~qprvS~l~~gk~~~f 69 (91)
T COG5606 33 IKQWIEQAALSQAQIAELLG-VTQPRVSDLARGKIQDF 69 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHCCHHHH
T ss_conf 99999997877999999838-88731889983614576
No 135
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=45.72 E-value=20 Score=17.88 Aligned_cols=36 Identities=31% Similarity=0.383 Sum_probs=30.7
Q ss_pred HHHCCCCHHHHHHHHC---CCCHHHHHHHHHHHCCCCCC
Q ss_conf 9981865889999967---85434666677751455445
Q gi|254780431|r 14 FWSEGLSASQIAVQLG---GVTRNAVIGKLHRLFLSNRV 49 (178)
Q Consensus 14 LW~eG~SasqIA~~lG---gvtRNAVIGK~hRLgLs~R~ 49 (178)
|..=|.|--+||+.|| |-|||++.---.++|.+.|.
T Consensus 156 ~Ys~G~SH~~ia~~L~It~~sSkn~~s~i~k~~gissrd 194 (220)
T PRK13719 156 LYSFGFSHNSIASLLNITNGSSKNKISEILKFFGISSRD 194 (220)
T ss_pred EEECCCCHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHH
T ss_conf 875242468899884741354077999999972988599
No 136
>PRK04217 hypothetical protein; Provisional
Probab=45.69 E-value=28 Score=16.95 Aligned_cols=41 Identities=32% Similarity=0.447 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 7899999999998186588999996785434666677751455445
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~ 49 (178)
|-|-.|.|+-.=.+||+..+-|.+|| |||-.+ +|+--++|.
T Consensus 44 tvdE~EaiRL~D~egl~qeeaA~~M~-VSR~Tf----~ril~~AR~ 84 (110)
T PRK04217 44 TYEEFEALRLVDYEGLTQEEAGKRMG-VSRGTV----WRALTSARK 84 (110)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHCC-CCHHHH----HHHHHHHHH
T ss_conf 19999999987360798999998849-769999----999999999
No 137
>pfam11972 HTH_13 HTH DNA binding domain. This is a helix-turn-helix DNA binding domain.
Probab=45.10 E-value=21 Score=17.83 Aligned_cols=26 Identities=38% Similarity=0.363 Sum_probs=23.9
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 658899999678543466667775145
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAVIGKLHRLFL 45 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAVIGK~hRLgL 45 (178)
.|+.-||++|+ ||--++..-+.-|||
T Consensus 14 Vsa~miak~L~-vT~~~a~~lv~eLgl 39 (54)
T pfam11972 14 VSAGMIAKELK-VTPRAALRLVKELGL 39 (54)
T ss_pred CCHHHHHHHHC-CCHHHHHHHHHHCCC
T ss_conf 00999999958-787999999987281
No 138
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=45.10 E-value=28 Score=16.89 Aligned_cols=43 Identities=21% Similarity=0.179 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHHHHHHH---CCCCCC
Q ss_conf 9999999999818--6588999996785434666677751---455445
Q gi|254780431|r 6 ERIDKLKKFWSEG--LSASQIAVQLGGVTRNAVIGKLHRL---FLSNRV 49 (178)
Q Consensus 6 erve~LkkLW~eG--~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R~ 49 (178)
+=++..-.|+.++ .+.++||+.|| ||.-+|-.-+.|| ||-...
T Consensus 8 dYLe~Iy~L~~~~~~vr~~dIA~~L~-Vs~~SVs~mikkL~~~Glv~~~ 55 (142)
T PRK03902 8 DYIEQIYLLIEEKGYARVSDIAEALS-VHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHC-CCCHHHHHHHHHHHHCCCCEEC
T ss_conf 99999999982589712999999978-9953399999999987992455
No 139
>PRK04158 transcriptional repressor CodY; Validated
Probab=44.39 E-value=8.9 Score=20.20 Aligned_cols=24 Identities=46% Similarity=0.558 Sum_probs=13.1
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 65889999967854346666777514
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
+.||.||.+.| +||. ||=-|-|..
T Consensus 202 LVASkIADrvG-ITRS-VIVNALRKl 225 (256)
T PRK04158 202 LVASKIADRVG-ITRS-VIVNALRKL 225 (256)
T ss_pred EEEHHHHHHHC-CCHH-HHHHHHHHH
T ss_conf 75433344308-7156-778777765
No 140
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
Probab=44.39 E-value=29 Score=16.82 Aligned_cols=32 Identities=25% Similarity=0.376 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 8999999999981865889999967854346666
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIG 38 (178)
+|+++.+.++- +|.|-+.||+++| |..+.|=+
T Consensus 10 ~eKi~iI~~~e-~G~s~~~lar~~g-i~~STl~~ 41 (53)
T pfam04218 10 REKIEVIQRSE-EGESKASLARRFN-VPRSTLRD 41 (53)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHHC-CCHHHHHH
T ss_conf 99999999998-5896889999969-87979999
No 141
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=44.05 E-value=30 Score=16.79 Aligned_cols=42 Identities=26% Similarity=0.250 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHCC-------C-CHHHHHHHHCCCCHHHHHHHHHHH---CCCC
Q ss_conf 89999999999818-------6-588999996785434666677751---4554
Q gi|254780431|r 5 VERIDKLKKFWSEG-------L-SASQIAVQLGGVTRNAVIGKLHRL---FLSN 47 (178)
Q Consensus 5 derve~LkkLW~eG-------~-SasqIA~~lGgvtRNAVIGK~hRL---gLs~ 47 (178)
|.=.+.|++.=.+| | |-.++|++|| |||+.|=-=..+| ||-.
T Consensus 13 e~V~~~L~~~I~~G~l~pGd~LPsE~eLA~~lg-VSR~~VREAL~~L~~~GlV~ 65 (254)
T PRK09464 13 DVIEQQLEFLILEGTLRPGEKLPPERELAKQFD-VSRPSLREAIQRLEAKGLLL 65 (254)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC-CCCHHHHHHHHHHHHCCCEE
T ss_conf 999999999998499999396936999999868-99559999999999889989
No 142
>pfam09958 DUF2192 Uncharacterized protein conserved in archaea (DUF2192). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=43.86 E-value=25 Score=17.24 Aligned_cols=47 Identities=21% Similarity=0.253 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 899999999998186588999996785434666677751455445554444443
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRVKVNENKQSD 58 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~~~~~~~~~~ 58 (178)
-+||+.|..||++ |-+. .++||+++|+-....=...+.+|.++-+++
T Consensus 7 r~RI~v~~~ll~~------vL~~-~~~sR~~lv~~L~~~Y~e~~I~P~RG~s~~ 53 (231)
T pfam09958 7 RERIEVLTDLLSR------LLEG-EILTREDLIELLQEVYEEKGIKPFRGLSPP 53 (231)
T ss_pred HHHHHHHHHHHHH------HHHH-CCCCHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 9999999999999------9871-567899999999999997598867799986
No 143
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=42.80 E-value=31 Score=16.66 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=27.4
Q ss_pred HHHHHH-HHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 999999-9999818658899999678543466667775145
Q gi|254780431|r 6 ERIDKL-KKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFL 45 (178)
Q Consensus 6 erve~L-kkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgL 45 (178)
+.+-+| ..+=..=+|.-+||.+|| +||-||---+..|--
T Consensus 6 ~~~~~ll~~~~~~~~SGe~La~~Lg-iSRtaVwK~Iq~Lr~ 45 (79)
T COG1654 6 QMLLLLLLLLTGNFVSGEKLAEELG-ISRTAVWKHIQQLRE 45 (79)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHH
T ss_conf 9999999973799666899999978-659999999999998
No 144
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=42.74 E-value=31 Score=16.66 Aligned_cols=33 Identities=27% Similarity=0.237 Sum_probs=26.9
Q ss_pred HCCCCHHHHHHHHCCCCHHHH---HHHHHHHCCCCCC
Q ss_conf 818658899999678543466---6677751455445
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAV---IGKLHRLFLSNRV 49 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAV---IGK~hRLgLs~R~ 49 (178)
..-...++||+.|+ |+.-.| +.|..++||-...
T Consensus 22 ~~~~~~~diA~~L~-Vsp~sVt~ml~rL~~~GlV~~~ 57 (154)
T COG1321 22 KGFARTKDIAERLK-VSPPSVTEMLKRLERLGLVEYE 57 (154)
T ss_pred CCCCCHHHHHHHHC-CCCHHHHHHHHHHHHCCCEEEE
T ss_conf 68751999999858-9927899999999878997884
No 145
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=42.49 E-value=26 Score=17.19 Aligned_cols=37 Identities=27% Similarity=0.318 Sum_probs=26.7
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCC
Q ss_conf 9999998186588999996785434666677751---4554
Q gi|254780431|r 10 KLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL---FLSN 47 (178)
Q Consensus 10 ~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~ 47 (178)
.|.-|=...++++||++.+| +++.+|---...| ||-.
T Consensus 2 Il~~L~~~~~~~~ela~~l~-is~~tvs~HL~~L~~~Glv~ 41 (66)
T smart00418 2 ILKLLAEGELCVCELAEILG-LSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred HHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEE
T ss_conf 58897739966999999988-29888879999999889268
No 146
>pfam10654 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.
Probab=42.26 E-value=27 Score=17.02 Aligned_cols=36 Identities=22% Similarity=0.369 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 7778999999999981865889999967854346666
Q gi|254780431|r 2 VWTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 2 sWTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIG 38 (178)
.|-+=.|..+-+|=-.|||.+.||..++ |||.-|-.
T Consensus 64 ~we~iti~Efv~LRhAGlt~~aIAD~F~-iS~s~~~n 99 (126)
T pfam10654 64 NWEEITIIEFVELRHAGLTGYAIADHFK-VSKSVVFN 99 (126)
T ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHH-HHHHHHHH
T ss_conf 6546019999998855886079999974-77999999
No 147
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=42.25 E-value=27 Score=17.05 Aligned_cols=44 Identities=25% Similarity=0.198 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHH-HCCCCHHHHHHHHCCCCHHHHHHHHHHH---CCCCC
Q ss_conf 789999999999-8186588999996785434666677751---45544
Q gi|254780431|r 4 TVERIDKLKKFW-SEGLSASQIAVQLGGVTRNAVIGKLHRL---FLSNR 48 (178)
Q Consensus 4 Tderve~LkkLW-~eG~SasqIA~~lGgvtRNAVIGK~hRL---gLs~R 48 (178)
|+--+.....|= ....++++||+.+| ++|..|---..+| ||..+
T Consensus 7 s~~E~~vY~~Ll~~g~~t~~eia~~~~-i~r~~vY~~L~~L~~kGlv~~ 54 (68)
T pfam01978 7 SEYEAKVYLALLKLGPATADEIAEESG-VPRSKVYEVLRSLEKKGLVER 54 (68)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEE
T ss_conf 999999999999819988999999959-889899999999998898898
No 148
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=42.23 E-value=18 Score=18.17 Aligned_cols=34 Identities=29% Similarity=0.356 Sum_probs=24.0
Q ss_pred HHCCCCHHHHHHHHCC---CCHHHHHHHHHHHCCCCC
Q ss_conf 9818658899999678---543466667775145544
Q gi|254780431|r 15 WSEGLSASQIAVQLGG---VTRNAVIGKLHRLFLSNR 48 (178)
Q Consensus 15 W~eG~SasqIA~~lGg---vtRNAVIGK~hRLgLs~R 48 (178)
=.-|++.|+||.+||. .-||-+-|..|-.+|...
T Consensus 58 ekag~Ti~EIAeelG~TeqTir~hlkgetkAG~lv~e 94 (182)
T COG1318 58 EKAGMTISEIAEELGRTEQTVRNHLKGETKAGQLVRE 94 (182)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHH
T ss_conf 8703749999999687799999997514033169999
No 149
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=41.97 E-value=25 Score=17.26 Aligned_cols=21 Identities=33% Similarity=0.662 Sum_probs=17.5
Q ss_pred HCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 8186588999996785434666
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAVI 37 (178)
..|+|..|+|+.+| ||...|-
T Consensus 8 ~~glsq~~lA~~~g-is~~~is 28 (56)
T smart00530 8 EKGLTQEELAEKLG-VSRSTLS 28 (56)
T ss_pred HCCCCHHHHHHHHC-CCHHHHH
T ss_conf 72999999999989-5999999
No 150
>pfam08535 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif.
Probab=41.83 E-value=18 Score=18.27 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=14.9
Q ss_pred HCCCCHHHHHHHHCCCCHHHH
Q ss_conf 818658899999678543466
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAV 36 (178)
.+|.+-++||+.|| -+..-|
T Consensus 1 ~~G~kk~~IAk~LG-ks~s~V 20 (93)
T pfam08535 1 AKGVKQAEIAKKLG-KSKSFV 20 (93)
T ss_pred CCCCCHHHHHHHHC-CCHHHH
T ss_conf 99877999999978-898899
No 151
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=41.82 E-value=20 Score=17.95 Aligned_cols=28 Identities=25% Similarity=0.363 Sum_probs=20.1
Q ss_pred HHHHHHH--HCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 9999999--8186588999996785434666
Q gi|254780431|r 9 DKLKKFW--SEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 9 e~LkkLW--~eG~SasqIA~~lGgvtRNAVI 37 (178)
+.|.-|= ..+++.+|||+.+| ++++.|-
T Consensus 7 ~iL~~~~~~~~~~~l~eia~~~g-l~kstv~ 36 (52)
T pfam09339 7 AILEALAEAPGGLSLTEIARRTG-LPKSTAH 36 (52)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHC-CCHHHHH
T ss_conf 99999862899989999999989-1999999
No 152
>pfam10053 DUF2290 Uncharacterized conserved protein (DUF2290). Members of this family of hypothetical bacterial proteins have no known function.
Probab=41.17 E-value=14 Score=18.94 Aligned_cols=27 Identities=11% Similarity=0.263 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCCC-CCCCCCCCCCCCCC
Q ss_conf 3111563333684-32005578998645
Q gi|254780431|r 115 PISRCLRLMELTD-NTCKWPLGDPFGKD 141 (178)
Q Consensus 115 ~~~~~~sLl~Lte-~tCkWPiGDP~~~d 141 (178)
+.+-+.+=++|.+ ..||||+..|.++.
T Consensus 123 ~~~HP~sHltlG~~~~CRIpv~~pltp~ 150 (196)
T pfam10053 123 DGAHPASHLTIGDVSGCRIPVSAALTPR 150 (196)
T ss_pred CCCCCCEEEEECCCCCCEEECCCCCCHH
T ss_conf 7779860166247788500236887889
No 153
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=40.21 E-value=34 Score=16.40 Aligned_cols=41 Identities=24% Similarity=0.224 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHH-CC-CCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 777899999999998-18-658899999678543466667775
Q gi|254780431|r 2 VWTVERIDKLKKFWS-EG-LSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 2 sWTderve~LkkLW~-eG-~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
.||+|-.++|.++=. -| ..=..||..||+=|.+.|.-+...
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~W~~Ia~~~~~Rt~~q~~~~~~~ 43 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRN 43 (45)
T ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf 9499999999999998888949979945299997999999986
No 154
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=40.04 E-value=33 Score=16.51 Aligned_cols=32 Identities=16% Similarity=0.087 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 186588999996785434666677751455445
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRV 49 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~ 49 (178)
--+|.++||+..| ||-..|+==++.||++|=.
T Consensus 46 ~~~si~eLA~~~~-vS~aTVvRf~kkLGf~Gf~ 77 (293)
T PRK11337 46 CATALKDVAEALA-VSEAMIVKVAKLLGFSGFR 77 (293)
T ss_pred HHCCHHHHHHHHC-CCHHHHHHHHHHHCCCCHH
T ss_conf 7666999998959-9888999999995789789
No 155
>COG1535 EntB Isochorismate hydrolase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=39.78 E-value=13 Score=19.05 Aligned_cols=19 Identities=47% Similarity=0.767 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHCCCCHH
Q ss_conf 7899999999998186588
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSAS 22 (178)
Q Consensus 4 Tderve~LkkLW~eG~Sas 22 (178)
++|--.+|+++|+-|+++|
T Consensus 84 s~~draLL~d~WGpgl~~~ 102 (218)
T COG1535 84 SPEDRALLKDFWGPGLTAS 102 (218)
T ss_pred CHHHHHHHHHHCCCCCCCC
T ss_conf 9789899997328988888
No 156
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=39.62 E-value=34 Score=16.34 Aligned_cols=43 Identities=30% Similarity=0.318 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHCC-CCHHHHHHHHC--CCCHHHHHHHHHHHCCCC
Q ss_conf 89999999999818-65889999967--854346666777514554
Q gi|254780431|r 5 VERIDKLKKFWSEG-LSASQIAVQLG--GVTRNAVIGKLHRLFLSN 47 (178)
Q Consensus 5 derve~LkkLW~eG-~SasqIA~~lG--gvtRNAVIGK~hRLgLs~ 47 (178)
.-||+.|+-|..+| +---|||..|| --|-.|-|-+.-+-||-.
T Consensus 23 ~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlir 68 (308)
T COG4189 23 KVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIR 68 (308)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf 8999999999871798789999885886566665578888647246
No 157
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=39.43 E-value=25 Score=17.23 Aligned_cols=27 Identities=33% Similarity=0.337 Sum_probs=21.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHH---CCCCC
Q ss_conf 88999996785434666677751---45544
Q gi|254780431|r 21 ASQIAVQLGGVTRNAVIGKLHRL---FLSNR 48 (178)
Q Consensus 21 asqIA~~lGgvtRNAVIGK~hRL---gLs~R 48 (178)
.++||+.|| |++-.|..-+.|| ||-..
T Consensus 2 ~~diA~~L~-vs~~sVs~~l~~L~~~Gli~~ 31 (96)
T smart00529 2 TSEIAERLN-VSPPTVTQMLKKLEKDGLVEY 31 (96)
T ss_pred HHHHHHHHC-CCCHHHHHHHHHHHHCCCEEE
T ss_conf 788998849-991679999999998889887
No 158
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=39.24 E-value=35 Score=16.31 Aligned_cols=45 Identities=27% Similarity=0.385 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHCCCCH-HHHHHHHCCCCHHHHHHHHHHH---CCCCCCC
Q ss_conf 89999999999818658-8999996785434666677751---4554455
Q gi|254780431|r 5 VERIDKLKKFWSEGLSA-SQIAVQLGGVTRNAVIGKLHRL---FLSNRVK 50 (178)
Q Consensus 5 derve~LkkLW~eG~Sa-sqIA~~lGgvtRNAVIGK~hRL---gLs~R~~ 50 (178)
-.....|.-|+..|-.. ++||+.|+ +++.+|-.-+.+| ||-.|..
T Consensus 22 ~~q~~~L~~l~~~~~~~~~~la~~l~-~~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 22 PPQYQVLLALYEAGGITVKELAERLG-LDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEEC
T ss_conf 89999999999848999999999978-78888999999999889936743
No 159
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=39.11 E-value=34 Score=16.37 Aligned_cols=29 Identities=31% Similarity=0.536 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHCC---CCHHHHHHHHCCCCHHH
Q ss_conf 9999999999818---65889999967854346
Q gi|254780431|r 6 ERIDKLKKFWSEG---LSASQIAVQLGGVTRNA 35 (178)
Q Consensus 6 erve~LkkLW~eG---~SasqIA~~lGgvtRNA 35 (178)
-+-++.++||.+. +.--+||.+|| |+-..
T Consensus 7 P~RDkA~eiy~~s~G~~~l~~IA~~L~-vs~~~ 38 (60)
T pfam10668 7 PDRDKAKEMWKESGGTMKLKDIANKLN-VSESQ 38 (60)
T ss_pred CCHHHHHHHHHHCCCCEEHHHHHHHHC-CCHHH
T ss_conf 578899999998289644999999968-79888
No 160
>pfam02992 Transposase_21 Transposase family tnp2.
Probab=38.86 E-value=17 Score=18.42 Aligned_cols=14 Identities=43% Similarity=1.066 Sum_probs=8.1
Q ss_pred HHHHHHHHHCCCCH
Q ss_conf 99999999818658
Q gi|254780431|r 8 IDKLKKFWSEGLSA 21 (178)
Q Consensus 8 ve~LkkLW~eG~Sa 21 (178)
||.|++||.+|..+
T Consensus 108 ieeL~~LW~~Gv~t 121 (226)
T pfam02992 108 IEELKDLWEEGVET 121 (226)
T ss_pred HHHHHHHHHCCCEE
T ss_conf 99999998669541
No 161
>PRK11569 transcriptional repressor IclR; Provisional
Probab=37.94 E-value=28 Score=16.98 Aligned_cols=30 Identities=13% Similarity=0.202 Sum_probs=21.5
Q ss_pred HHHHHHHH--HCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 99999999--81865889999967854346666
Q gi|254780431|r 8 IDKLKKFW--SEGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 8 ve~LkkLW--~eG~SasqIA~~lGgvtRNAVIG 38 (178)
++.|.-|= ..++|.++||+++| ++|..|-.
T Consensus 31 l~IL~~la~~~~~lsl~eia~~lg-lpksT~~R 62 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAG-LPNSTTHR 62 (274)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHH
T ss_conf 999999963899989999999879-19999999
No 162
>pfam03811 Ins_element1 Insertion element protein.
Probab=37.75 E-value=37 Score=16.18 Aligned_cols=32 Identities=22% Similarity=0.239 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH
Q ss_conf 999999998186588999996785434666677
Q gi|254780431|r 8 IDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKL 40 (178)
Q Consensus 8 ve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~ 40 (178)
-++.-+|-.+|..-..||+-|+ |+-|.||-..
T Consensus 53 keqiv~m~~nG~GiRdtaRvl~-Is~nTVlrtL 84 (88)
T pfam03811 53 KEQIVDMAMNGAGCRYTARTLK-IGINTVIRTL 84 (88)
T ss_pred HHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHH
T ss_conf 8999999767985404478737-5689999987
No 163
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=36.93 E-value=28 Score=16.97 Aligned_cols=27 Identities=26% Similarity=0.538 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 186588999996785434666677751
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
-|+|.++||+.||+-....|+--+.+.
T Consensus 43 ~~~s~~~Ig~~fg~rdHsTV~~a~~kv 69 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKI 69 (90)
T ss_pred HCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 788999999995899714999999999
No 164
>COG5619 Uncharacterized conserved protein [Function unknown]
Probab=36.84 E-value=12 Score=19.29 Aligned_cols=29 Identities=14% Similarity=0.380 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCCCC-CCCCCCCCCCCCC
Q ss_conf 5311156333368432-0055789986450
Q gi|254780431|r 114 LPISRCLRLMELTDNT-CKWPLGDPFGKDF 142 (178)
Q Consensus 114 ~~~~~~~sLl~Lte~t-CkWPiGDP~~~dF 142 (178)
.+-+-+.+-+.+...+ ||||+--|.+++-
T Consensus 146 ~~gaHP~sH~hiG~~S~cRiPv~~pltp~~ 175 (224)
T COG5619 146 VDGAHPKSHLHIGDVSGCRIPVSAPLTPRW 175 (224)
T ss_pred CCCCCCCCEEEEECCCCCCCEEECCCCHHH
T ss_conf 888898743675025675011205678899
No 165
>TIGR02573 LcrG_PcrG type III secretion protein LcrG; InterPro: IPR009863 This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops . This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the prot ein is believed to make a 1:1 complex with PcrV (LcrV) . Mutations in LcrG cause premature secretion of effector proteins into the medium ..
Probab=36.35 E-value=39 Score=16.01 Aligned_cols=30 Identities=27% Similarity=0.500 Sum_probs=20.5
Q ss_pred CHHHHHHHHHHHH-CCCCHHHHHHHHCCCCH
Q ss_conf 7899999999998-18658899999678543
Q gi|254780431|r 4 TVERIDKLKKFWS-EGLSASQIAVQLGGVTR 33 (178)
Q Consensus 4 Tderve~LkkLW~-eG~SasqIA~~lGgvtR 33 (178)
.|||-.+|.+||. =|+.+----..|||.++
T Consensus 18 sd~R~~LL~Em~~~LG~~p~ag~~Lf~~~~~ 48 (93)
T TIGR02573 18 SDERAKLLQEMWQGLGLAPEAGEKLFGGLEA 48 (93)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCCC
T ss_conf 7889999999986169866889998646897
No 166
>pfam06242 DUF1013 Protein of unknown function (DUF1013). Family of uncharacterized proteins found in Proteobacteria.
Probab=35.80 E-value=23 Score=17.49 Aligned_cols=28 Identities=32% Similarity=0.388 Sum_probs=18.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 999999998186588999996785434666
Q gi|254780431|r 8 IDKLKKFWSEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 8 ve~LkkLW~eG~SasqIA~~lGgvtRNAVI 37 (178)
|.=|-+..-| |+-+||++.+| .|+|-|-
T Consensus 74 I~WLiknhPe-L~D~QI~kLiG-TTK~TI~ 101 (141)
T pfam06242 74 IAWLLRNHPE-LSDAQISKLIG-TTKTTIE 101 (141)
T ss_pred HHHHHHCCCC-CCHHHHHHHHC-CCHHHHH
T ss_conf 9999971670-24878888747-7578899
No 167
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=34.62 E-value=41 Score=15.84 Aligned_cols=36 Identities=25% Similarity=0.253 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 9999999999818658899999678543466667775
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
||-..+..|=.-|-.-++-|+.|| +||..+-=|+.+
T Consensus 6 Er~~I~~aL~~~~gn~~~aA~~LG-isr~tL~~kmkk 41 (42)
T pfam02954 6 EKELIEAALERTGGNKSKAARLLG-ISRRTLYRKLKK 41 (42)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHC-CCHHHHHHHHHH
T ss_conf 999999999994997999999979-699999999973
No 168
>COG2508 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=34.39 E-value=42 Score=15.81 Aligned_cols=37 Identities=24% Similarity=0.340 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 99999999998186588999996785434666677751
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
|=++.|.-+|.+....++=|++|. |.||.++=++-|.
T Consensus 354 eLl~TL~~yl~~~~ni~~tAk~L~-iHRNTL~YRi~ki 390 (421)
T COG2508 354 ELLETLRAYLKNNGNISATAKRLF-VHRNTLRYRLKKI 390 (421)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 799999999984897999999837-4542399999999
No 169
>pfam00249 Myb_DNA-binding Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.
Probab=34.25 E-value=42 Score=15.80 Aligned_cols=39 Identities=28% Similarity=0.248 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHHHHHHC-CCC-HHHHHHHHCCCCHHHHHHH
Q ss_conf 97778999999999981-865-8899999678543466667
Q gi|254780431|r 1 MVWTVERIDKLKKFWSE-GLS-ASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 1 MsWTderve~LkkLW~e-G~S-asqIA~~lGgvtRNAVIGK 39 (178)
+.||.|--++|.++=.+ |.. =+.||..||+=|.+.|.-.
T Consensus 2 ~~Wt~eEd~~l~~~v~~~G~~~W~~Ia~~~~~rs~~qc~~r 42 (47)
T pfam00249 2 GPWTPEEDELLIEAVKKHGNGNWKKIAKLLPGRTDNQCKNR 42 (47)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHH
T ss_conf 89999999999999999887939999988299988999999
No 170
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=34.16 E-value=36 Score=16.26 Aligned_cols=28 Identities=25% Similarity=0.290 Sum_probs=23.3
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 65889999967854346666777514554
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAVIGKLHRLFLSN 47 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAVIGK~hRLgLs~ 47 (178)
||..|+|+.|| ||+.-|-=.+|.=.|..
T Consensus 2 lTv~EaA~yLg-v~~~t~~~l~~~g~l~~ 29 (49)
T TIGR01764 2 LTVEEAAEYLG-VSKSTVYRLIEEGELPA 29 (49)
T ss_pred CCHHHHHHHCC-CCHHHHHHHHHCCCCCE
T ss_conf 87788997719-99057899997189850
No 171
>pfam08542 Rep_fac_C Replication factor C. This family includes several subunits of DNA replication factor C.
Probab=33.72 E-value=43 Score=15.74 Aligned_cols=28 Identities=32% Similarity=0.402 Sum_probs=20.9
Q ss_pred HHHHHHH-HHHHCCCCHHHHHHHHCCCCH
Q ss_conf 9999999-999818658899999678543
Q gi|254780431|r 6 ERIDKLK-KFWSEGLSASQIAVQLGGVTR 33 (178)
Q Consensus 6 erve~Lk-kLW~eG~SasqIA~~lGgvtR 33 (178)
+-.+.+. .+|.+|+|+.+|-.+|-.+-.
T Consensus 22 ~a~~~i~~~~~~~G~s~~Dii~~l~~~i~ 50 (90)
T pfam08542 22 EAYKTLRELLIEKGYSAEDIITQLHRVLK 50 (90)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 99999999999859999999999999998
No 172
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=33.60 E-value=42 Score=15.77 Aligned_cols=41 Identities=17% Similarity=0.128 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHH-------CCCCHHHHHHHHCCCCHHHHHHHHHHHCCC
Q ss_conf 899999999998-------186588999996785434666677751455
Q gi|254780431|r 5 VERIDKLKKFWS-------EGLSASQIAVQLGGVTRNAVIGKLHRLFLS 46 (178)
Q Consensus 5 derve~LkkLW~-------eG~SasqIA~~lGgvtRNAVIGK~hRLgLs 46 (178)
++--+.||+.=- +-++-.+||++|| |||+-|--=..||--.
T Consensus 10 ~~AY~~Lr~~Il~G~l~PG~~L~e~~Lae~lg-VSRtPVREAL~rL~~e 57 (224)
T PRK11534 10 LDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYA-LGVGPLREALSQLVAE 57 (224)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHC
T ss_conf 99999999999869989939558999999979-8858999999999987
No 173
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=32.27 E-value=45 Score=15.59 Aligned_cols=40 Identities=18% Similarity=0.312 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHHCC-CCHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 789999999999818-65889999967854346666777514
Q gi|254780431|r 4 TVERIDKLKKFWSEG-LSASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 4 Tderve~LkkLW~eG-~SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
+|--...|+.|=.+| .|-++||++|| +|..+|.-.+-||-
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg-lS~~~v~~Ri~~L~ 47 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG-LSPSTVLRRIKRLE 47 (154)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHH
T ss_conf 799999999999727657999999979-79899999999999
No 174
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=32.09 E-value=21 Score=17.78 Aligned_cols=13 Identities=38% Similarity=0.493 Sum_probs=9.1
Q ss_pred HHHHHHHHCCCCHH
Q ss_conf 88999996785434
Q gi|254780431|r 21 ASQIAVQLGGVTRN 34 (178)
Q Consensus 21 asqIA~~lGgvtRN 34 (178)
-|+||++|| |+..
T Consensus 43 ~SeIAk~lg-I~~p 55 (64)
T PRK06393 43 GSAIAKRAG-ITEP 55 (64)
T ss_pred HHHHHHHHC-CCCC
T ss_conf 608999829-9988
No 175
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=32.04 E-value=45 Score=15.58 Aligned_cols=30 Identities=27% Similarity=0.482 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHC----CCCHHH
Q ss_conf 999999999981865889999967----854346
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLG----GVTRNA 35 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lG----gvtRNA 35 (178)
.||....+|=..-+|..||+..|| -+||-|
T Consensus 44 ~R~~I~~~LL~~~~~QREi~~~lG~SiA~ITRGS 77 (95)
T TIGR01321 44 SRVRIVEELLEGEMSQREIAEKLGVSIATITRGS 77 (95)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 7999999996148974788886376166787878
No 176
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=31.98 E-value=45 Score=15.56 Aligned_cols=42 Identities=33% Similarity=0.466 Sum_probs=32.1
Q ss_pred CHHHHHHHHHHHHCC-------C-CHHHHHHHHCCCCHHHHHHHHHHH---CCC
Q ss_conf 789999999999818-------6-588999996785434666677751---455
Q gi|254780431|r 4 TVERIDKLKKFWSEG-------L-SASQIAVQLGGVTRNAVIGKLHRL---FLS 46 (178)
Q Consensus 4 Tderve~LkkLW~eG-------~-SasqIA~~lGgvtRNAVIGK~hRL---gLs 46 (178)
+|+=++.|+++=..| | |=.+++++|| |||+.|=-=..+| ||-
T Consensus 4 ~e~V~e~Lr~~I~~g~l~pG~~LP~E~eLae~~G-VSRt~VREAL~~L~~eGlV 56 (253)
T PRK10421 4 SDEVADRVRALIEEKNLEAGMKLPAERQLAMQLG-VSRNSLREALAKLVSEGVL 56 (253)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCE
T ss_conf 9999999999998199998595933999999979-6989999999999988987
No 177
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=31.95 E-value=34 Score=16.42 Aligned_cols=21 Identities=24% Similarity=0.420 Sum_probs=16.7
Q ss_pred HCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 8186588999996785434666
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRNAVI 37 (178)
-++.|-.+||++.| ||+.++-
T Consensus 14 ~~~~s~~~Ia~~ag-vs~~~iy 34 (47)
T pfam00440 14 YDATTVREIAKEAG-VSKGALY 34 (47)
T ss_pred CCCCCHHHHHHHHC-CCHHHHH
T ss_conf 15077999999979-6988999
No 178
>COG3369 Zinc finger domain containing protein (CDGSH-type) [Function unknown]
Probab=31.88 E-value=16 Score=18.47 Aligned_cols=27 Identities=26% Similarity=0.736 Sum_probs=21.7
Q ss_pred CCCCEECCCCCCCCCCCCH-HHHHHHCC
Q ss_conf 6450047878768887716-88888705
Q gi|254780431|r 139 GKDFSFCGSDVCNDSPYCD-YHKKLAYQ 165 (178)
Q Consensus 139 ~~dF~FCG~~~~~g~PYC~-~H~~iAYQ 165 (178)
....+.|++-....+|||. .|..+.|+
T Consensus 28 ~~~~~LCrCG~S~NKPfCDGtH~k~gf~ 55 (78)
T COG3369 28 DEQAALCRCGHSENKPFCDGTHKKTGFD 55 (78)
T ss_pred CEEEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf 3279997236757888667744340236
No 179
>PRK12400 D-amino acid aminotransferase; Reviewed
Probab=31.59 E-value=21 Score=17.81 Aligned_cols=24 Identities=17% Similarity=0.162 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHH-----CCCCHHHHHHHH
Q ss_conf 899999999998-----186588999996
Q gi|254780431|r 5 VERIDKLKKFWS-----EGLSASQIAVQL 28 (178)
Q Consensus 5 derve~LkkLW~-----eG~SasqIA~~l 28 (178)
|++.++|.+=-. -.+|..+|-..+
T Consensus 51 d~Hl~RL~~Sa~~l~i~~p~s~~el~~~~ 79 (290)
T PRK12400 51 DPHITRLYRSMEEIELTLPFSKAELITLL 79 (290)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 99999999999986768988999999999
No 180
>PRK01119 hypothetical protein; Provisional
Probab=31.44 E-value=25 Score=17.28 Aligned_cols=27 Identities=26% Similarity=0.367 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 8999999999981865889999967854346666777
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLH 41 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~h 41 (178)
+-|-+.|.+|..+ |++||. |||||--.
T Consensus 56 ~aR~~A~~rm~~~-------A~~lGA---NAVVgv~~ 82 (106)
T PRK01119 56 NAREEAIREMEQR-------AKDIGA---NAVVGVDI 82 (106)
T ss_pred HHHHHHHHHHHHH-------HHHCCC---CEEEEEEE
T ss_conf 9999999999999-------997499---98999988
No 181
>pfam08104 Antimicrobial_9 Ponericin L family. This family consists of the ponericin L family of antimicrobial peptides that are isolated from the venom of the predatory ant Pachycondyla goeldii. Ponericin L family shares similarities with dermaseptins. Ponericin L may adopt an amphipathic alpha-helical structure in polar environments and these peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion.
Probab=31.35 E-value=28 Score=16.92 Aligned_cols=23 Identities=39% Similarity=0.850 Sum_probs=15.2
Q ss_pred HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 9999998186588999996785434666677751
Q gi|254780431|r 10 KLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 10 ~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
.||+||.+ +-| .-.||+||+.-|
T Consensus 1 llkelwtk----------ikg-agkavlgkikgl 23 (26)
T pfam08104 1 LLKELWTK----------IKG-AGKAVLGKIKGL 23 (26)
T ss_pred CHHHHHHH----------HCC-CHHHHHHHHHHH
T ss_conf 95899999----------315-128899886666
No 182
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=31.22 E-value=29 Score=16.87 Aligned_cols=23 Identities=39% Similarity=0.492 Sum_probs=16.1
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 6588999996785434666677751
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
+.||.||.++| +||.-+ =-+-|.
T Consensus 205 lvASkiADrvG-ITRSVI-VNALRK 227 (261)
T COG4465 205 LVASKIADRVG-ITRSVI-VNALRK 227 (261)
T ss_pred EEEHHHHHHHC-CHHHHH-HHHHHH
T ss_conf 63024556517-339999-999987
No 183
>PRK12856 hypothetical protein; Provisional
Probab=30.67 E-value=26 Score=17.14 Aligned_cols=25 Identities=28% Similarity=0.275 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 89999999999818658899999678543466667
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK 39 (178)
+-|-+.|.+|..+ |++||. |||||-
T Consensus 56 ~aR~~A~~~m~~~-------A~~lGA---nAVVgv 80 (103)
T PRK12856 56 EARDIAMDEMKEL-------AKQKGA---NAIVGV 80 (103)
T ss_pred HHHHHHHHHHHHH-------HHHCCC---CEEEEE
T ss_conf 9999999999999-------997499---989999
No 184
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=30.65 E-value=31 Score=16.62 Aligned_cols=34 Identities=26% Similarity=0.355 Sum_probs=26.3
Q ss_pred HCCCCHHHHHHHHCCCCHH---HHHHHHHHHCCCCCCC
Q ss_conf 8186588999996785434---6666777514554455
Q gi|254780431|r 16 SEGLSASQIAVQLGGVTRN---AVIGKLHRLFLSNRVK 50 (178)
Q Consensus 16 ~eG~SasqIA~~lGgvtRN---AVIGK~hRLgLs~R~~ 50 (178)
.+-+++++|+++|| +||. .++-|...+||..+..
T Consensus 39 ~~Pmtl~Ei~E~lg-~Sks~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 39 RKPLTLDEIAEALG-MSKSNVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred CCCCCHHHHHHHHC-CCCCHHHHHHHHHHHCCHHHHHH
T ss_conf 99966999999977-78012889999998545688530
No 185
>pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
Probab=30.44 E-value=48 Score=15.39 Aligned_cols=30 Identities=30% Similarity=0.465 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 1865889999967854346666777514554
Q gi|254780431|r 17 EGLSASQIAVQLGGVTRNAVIGKLHRLFLSN 47 (178)
Q Consensus 17 eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~ 47 (178)
++++-.++|++|| ++=+-||.+...+|...
T Consensus 2 ~~itV~elA~~l~-~~~~~vi~~L~~~Gi~~ 31 (52)
T pfam04760 2 EKIRVYELAKELG-VSSKELIKKLFKLGIMK 31 (52)
T ss_pred CCEEHHHHHHHHC-CCHHHHHHHHHHCCCEE
T ss_conf 8173999999988-88999999999879855
No 186
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=30.25 E-value=48 Score=15.37 Aligned_cols=48 Identities=25% Similarity=0.284 Sum_probs=37.0
Q ss_pred CHHHHHHHHHHH--HCCCCHHHHHHHHCCCCHHHHHHHHH---HHCCCCCCCCC
Q ss_conf 789999999999--81865889999967854346666777---51455445554
Q gi|254780431|r 4 TVERIDKLKKFW--SEGLSASQIAVQLGGVTRNAVIGKLH---RLFLSNRVKVN 52 (178)
Q Consensus 4 Tderve~LkkLW--~eG~SasqIA~~lGgvtRNAVIGK~h---RLgLs~R~~~~ 52 (178)
+|--|+.+++|= ..+++.-+||+.|+ .+|..|==-+. ..||--|.+..
T Consensus 26 s~~Dv~v~~~LL~~~~~~tvdelae~ln-r~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 26 SELDVEVYKALLEENGPLTVDELAEILN-RSRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf 6889999999986469957999999978-3199999999999985886666422
No 187
>TIGR00589 ogt methylated-DNA-[protein]-cysteine S-methyltransferase; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme . This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources .; GO: 0003824 catalytic activity, 0006281 DNA repair.
Probab=30.18 E-value=25 Score=17.21 Aligned_cols=15 Identities=27% Similarity=0.395 Sum_probs=12.7
Q ss_pred HCCCCHHHHHHHHCC
Q ss_conf 818658899999678
Q gi|254780431|r 16 SEGLSASQIAVQLGG 30 (178)
Q Consensus 16 ~eG~SasqIA~~lGg 30 (178)
+|=.|++|||++||.
T Consensus 17 G~t~sY~~lA~~iG~ 31 (80)
T TIGR00589 17 GETKSYGELAKRIGN 31 (80)
T ss_pred CCCCCHHHHHHHHCC
T ss_conf 763268999997188
No 188
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=29.78 E-value=39 Score=16.02 Aligned_cols=28 Identities=36% Similarity=0.560 Sum_probs=19.5
Q ss_pred HHHHHHH-HCCC---CHHHHHHHHCCCCHHHHH
Q ss_conf 9999999-8186---588999996785434666
Q gi|254780431|r 9 DKLKKFW-SEGL---SASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 9 e~LkkLW-~eG~---SasqIA~~lGgvtRNAVI 37 (178)
+..-+|. ..|+ |-++||++-| |||-||.
T Consensus 18 ~AA~~lFaekGy~~ttl~dIA~~AG-VS~GaiY 49 (216)
T PRK10668 18 DVALRLFSQQGVSATSLADIAKAAG-VTRGAIY 49 (216)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHC-CCHHHHH
T ss_conf 9999999984935188999999968-9857999
No 189
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=29.73 E-value=42 Score=15.79 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=19.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHH
Q ss_conf 99999999818658899999678543466
Q gi|254780431|r 8 IDKLKKFWSEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 8 ve~LkkLW~eG~SasqIA~~lGgvtRNAV 36 (178)
|...+| ..|+|.++.|+..| ||++.|
T Consensus 7 Ir~~Rk--~~glTQ~~LA~~aG-vs~~~I 32 (58)
T TIGR03070 7 VRARRK--ALGLTQADLADLAG-VGLRFI 32 (58)
T ss_pred HHHHHH--HCCCCHHHHHHHHC-CCHHHH
T ss_conf 999999--94998999998819-989999
No 190
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=29.65 E-value=40 Score=15.94 Aligned_cols=25 Identities=32% Similarity=0.422 Sum_probs=17.8
Q ss_pred HHHHHCCC---CHHHHHHHHCCCCHHHHH
Q ss_conf 99998186---588999996785434666
Q gi|254780431|r 12 KKFWSEGL---SASQIAVQLGGVTRNAVI 37 (178)
Q Consensus 12 kkLW~eG~---SasqIA~~lGgvtRNAVI 37 (178)
+-+...|. |-++||++.| |||-||-
T Consensus 22 ~lFae~G~~~tTl~~IA~~AG-Vt~GaiY 49 (213)
T PRK09975 22 AQFALRGVANTTLNDIADAAN-VTRGAIY 49 (213)
T ss_pred HHHHHHCCCCCCHHHHHHHHC-CCHHHHH
T ss_conf 999985945588999999968-9848999
No 191
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=29.34 E-value=50 Score=15.27 Aligned_cols=36 Identities=28% Similarity=0.439 Sum_probs=28.4
Q ss_pred HHHHHHHHHHCCCC---------------HHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 99999999981865---------------88999996785434666677751
Q gi|254780431|r 7 RIDKLKKFWSEGLS---------------ASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 7 rve~LkkLW~eG~S---------------asqIA~~lGgvtRNAVIGK~hRL 43 (178)
+....|+||.-|+| -++||+..| |-|--|.--+.+.
T Consensus 15 q~~Vvk~l~~~GisV~~g~~~~~gdIEI~~t~iAka~g-VdRrvV~~Ti~~I 65 (167)
T COG2150 15 QKKVVKKLLESGISVKNGGKIYCGDIEIPITKIAKATG-VDRRVVYATIELI 65 (167)
T ss_pred HHHHHHHHHHHCEEECCCCCEEECCEEECHHHHHHHHC-CCHHHHHHHHHHH
T ss_conf 99999999980836726983563768855589899868-6567699999998
No 192
>pfam00500 Late_protein_L1 L1 (late) protein.
Probab=29.27 E-value=19 Score=18.03 Aligned_cols=29 Identities=24% Similarity=0.645 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCC-----CCCCCCCCEECCCCCC
Q ss_conf 3336843200557-----8998645004787876
Q gi|254780431|r 122 LMELTDNTCKWPL-----GDPFGKDFSFCGSDVC 150 (178)
Q Consensus 122 Ll~Lte~tCkWPi-----GDP~~~dF~FCG~~~~ 150 (178)
-||+-..+||||- -||-....+||++.-+
T Consensus 221 PLDIv~sicKYPD~LkM~~d~yGds~FF~~rREQ 254 (503)
T pfam00500 221 PLDIVQSICKYPDYLKMAADPYGDSMFFYARREQ 254 (503)
T ss_pred CHHHHCCCCCCCHHHHCCCCCCCCEEEEEEHHHH
T ss_conf 8266375204864551365654666589764685
No 193
>TIGR00235 udk uridine kinase; InterPro: IPR000764 Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP A cDNA for uridine kinase from mouse brain was found which encodes a protein of 277 amino acids. A truncated form of the cDNA was expressed in Escherichia coli, and shown to display uridine kinase activity and to readily form a tetramer, the most active form of the wild-type enzyme. Sequence analysis has identified three ATP-binding site consensus motifs. The predicted secondary structure, and sequence comparison with kinases of known structure, is consistent with uridine kinase having the alpha/beta core nucleotide-binding fold common to many kinases .; GO: 0005524 ATP binding, 0016773 phosphotransferase activity alcohol group as acceptor.
Probab=29.04 E-value=14 Score=18.91 Aligned_cols=14 Identities=29% Similarity=0.475 Sum_probs=9.8
Q ss_pred CCCCHHHHHHHHHH
Q ss_conf 97778999999999
Q gi|254780431|r 1 MVWTVERIDKLKKF 14 (178)
Q Consensus 1 MsWTderve~LkkL 14 (178)
|-|+|||+..|-+|
T Consensus 128 ~~l~D~Rl~~L~dl 141 (220)
T TIGR00235 128 LLLTDERLRDLMDL 141 (220)
T ss_pred HHHHHHHHHHHHCC
T ss_conf 88887999887182
No 194
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=29.02 E-value=36 Score=16.19 Aligned_cols=42 Identities=29% Similarity=0.362 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHHCCC--------CHHHHHHHHCCCCHHHHHHHHHHH---CCC
Q ss_conf 7899999999998186--------588999996785434666677751---455
Q gi|254780431|r 4 TVERIDKLKKFWSEGL--------SASQIAVQLGGVTRNAVIGKLHRL---FLS 46 (178)
Q Consensus 4 Tderve~LkkLW~eG~--------SasqIA~~lGgvtRNAVIGK~hRL---gLs 46 (178)
.|+-++.|+++=.+|- |=.+++++|| |||++|=.=.-+| ||-
T Consensus 12 ~~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fg-VSR~~vREAl~~L~a~Glv 64 (241)
T COG2186 12 ADEVAEQIGALIVSGELPPGDRLPSERELAERFG-VSRTVVREALKRLEAKGLV 64 (241)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC-CCCHHHHHHHHHHHHCCCE
T ss_conf 9999999999998399999999988999999978-9956899999999987886
No 195
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=28.29 E-value=52 Score=15.16 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 999999999981865889999967
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLG 29 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lG 29 (178)
.||....+|-..-+|..||+..||
T Consensus 48 ~Rv~Iv~eLL~ge~sQREi~~~Lg 71 (103)
T COG2973 48 TRVRIVEELLRGELSQREIAQKLG 71 (103)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf 999999999956353999999858
No 196
>KOG1416 consensus
Probab=28.19 E-value=53 Score=15.14 Aligned_cols=22 Identities=41% Similarity=0.690 Sum_probs=10.4
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 7899999999998186588999996
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQL 28 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~l 28 (178)
|.|-|+.||+ +|+++.+|-++|
T Consensus 116 t~EeI~~mr~---eg~~g~EiI~kL 137 (475)
T KOG1416 116 TQEEIEEMRQ---EGLSGEEIIEKL 137 (475)
T ss_pred CHHHHHHHHH---HCCCHHHHHHHH
T ss_conf 7999999997---266789999999
No 197
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=28.15 E-value=42 Score=15.78 Aligned_cols=23 Identities=22% Similarity=0.289 Sum_probs=18.0
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 658899999678543466667775
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAVIGKLHR 42 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAVIGK~hR 42 (178)
|+.+|.|+.|| ||.+.|.==...
T Consensus 1 lt~~e~A~~lg-Vs~~TlrrW~~~ 23 (49)
T cd04762 1 LTTKEAAELLG-VSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHC-CCHHHHHHHHHC
T ss_conf 98899999979-899999999987
No 198
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=27.74 E-value=40 Score=15.89 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=19.6
Q ss_pred HHHHHHHH----HCCCCHHHHHHHHCCCCHHHH
Q ss_conf 99999999----818658899999678543466
Q gi|254780431|r 8 IDKLKKFW----SEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 8 ve~LkkLW----~eG~SasqIA~~lGgvtRNAV 36 (178)
++.+.+|- .++.|.+.||+++| ||..|+
T Consensus 16 l~a~~~ll~~~~~~~iTt~~iA~~~g-vs~aal 47 (194)
T PRK09480 16 LQTLAQMLESPPGERITTAKLAARVG-VSEAAL 47 (194)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHC-CCHHHH
T ss_conf 99999998627976422999998909-978999
No 199
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 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 recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=27.34 E-value=43 Score=15.70 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=18.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 999999981865889999967854346666
Q gi|254780431|r 9 DKLKKFWSEGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 9 e~LkkLW~eG~SasqIA~~lGgvtRNAVIG 38 (178)
|.|.+=-+--=++++||..|| ||+--|+-
T Consensus 98 eeL~~~lgR~Pt~~EiAe~L~-~s~EEv~~ 126 (229)
T TIGR02980 98 EELTQRLGRSPTVAEIAEELG-VSEEEVVE 126 (229)
T ss_pred HHHHHHHCCCCCHHHHHHHHC-CCHHHHHH
T ss_conf 999998288988789998858-89999999
No 200
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=27.13 E-value=55 Score=15.02 Aligned_cols=37 Identities=27% Similarity=0.292 Sum_probs=23.2
Q ss_pred HHHHHHCC---CCHHHHHHHHCCCCH---HHHHHHHHHHCCCCC
Q ss_conf 99999818---658899999678543---466667775145544
Q gi|254780431|r 11 LKKFWSEG---LSASQIAVQLGGVTR---NAVIGKLHRLFLSNR 48 (178)
Q Consensus 11 LkkLW~eG---~SasqIA~~lGgvtR---NAVIGK~hRLgLs~R 48 (178)
|.-|-..| .+|-+||++|| |++ |.|+=+.-+.|...+
T Consensus 12 l~~L~~~g~~~~tA~~lak~lg-~~Kk~vN~~LY~L~k~g~v~~ 54 (68)
T smart00550 12 LEFLENSGDETSTALQLAKNLG-LPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHCCCCCCHHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEC
T ss_conf 9999974886403999999949-989999999999997488310
No 201
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=27.08 E-value=29 Score=16.83 Aligned_cols=12 Identities=33% Similarity=0.484 Sum_probs=8.6
Q ss_pred HHHHHHHHCCCCH
Q ss_conf 8899999678543
Q gi|254780431|r 21 ASQIAVQLGGVTR 33 (178)
Q Consensus 21 asqIA~~lGgvtR 33 (178)
-|+||++|| ++.
T Consensus 41 ~SeIAk~lg-i~~ 52 (61)
T PRK08351 41 NSEIAKKIG-AKV 52 (61)
T ss_pred HHHHHHHHC-CCC
T ss_conf 618999849-998
No 202
>smart00351 PAX Paired Box domain.
Probab=27.04 E-value=55 Score=15.01 Aligned_cols=46 Identities=20% Similarity=0.302 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf 89999999999818658899999678543466667775145544555
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRLFLSNRVKV 51 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRLgLs~R~~~ 51 (178)
++--.+.=+|-.+|....+|+++|. ||.-.|---.-|.-=.+..++
T Consensus 20 ~~~R~kIveLa~~G~rpcdISr~L~-VShGCVSKIL~Ry~etGsi~P 65 (125)
T smart00351 20 DEERQRIVELAQNGVRPCDISRQLC-VSHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC-CCCCHHHHHHHHHHHCCCCCC
T ss_conf 8999999999985998999875645-771069999999971388789
No 203
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=27.04 E-value=37 Score=16.17 Aligned_cols=26 Identities=31% Similarity=0.483 Sum_probs=16.4
Q ss_pred HHCCCCHHHHHHHHCCCC-HHHHHHHHH
Q ss_conf 981865889999967854-346666777
Q gi|254780431|r 15 WSEGLSASQIAVQLGGVT-RNAVIGKLH 41 (178)
Q Consensus 15 W~eG~SasqIA~~lGgvt-RNAVIGK~h 41 (178)
|++-.|.+|||++||..+ +-| +|-+.
T Consensus 102 ~Get~TY~eiA~~ig~p~a~rA-VG~A~ 128 (168)
T COG0350 102 YGETVTYGEIARRLGRPTAVRA-VGNAN 128 (168)
T ss_pred CCCCCCHHHHHHHHCCCCHHHH-HHHHH
T ss_conf 9886459999999779955889-99998
No 204
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=26.29 E-value=57 Score=14.93 Aligned_cols=30 Identities=30% Similarity=0.420 Sum_probs=23.1
Q ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH
Q ss_conf 789999999999818658899999678543466
Q gi|254780431|r 4 TVERIDKLKKFWSEGLSASQIAVQLGGVTRNAV 36 (178)
Q Consensus 4 Tderve~LkkLW~eG~SasqIA~~lGgvtRNAV 36 (178)
+-+.|..+++ ..|+|.++-|+.|| ||++-|
T Consensus 45 s~~eIk~iRe--~~~lSq~vFA~~L~-vs~~Tv 74 (104)
T COG2944 45 SPTEIKAIRE--KLGLSQPVFARYLG-VSVSTV 74 (104)
T ss_pred CHHHHHHHHH--HHCCCHHHHHHHHC-CCHHHH
T ss_conf 8899999999--82888999999988-879999
No 205
>PRK12855 hypothetical protein; Provisional
Probab=25.99 E-value=35 Score=16.30 Aligned_cols=25 Identities=24% Similarity=0.210 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 89999999999818658899999678543466667
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK 39 (178)
+-|-+.|.+|..+ |++||. |||||-
T Consensus 56 ~aR~~Ai~~m~~~-------A~~~GA---nAVVgv 80 (103)
T PRK12855 56 EARDIAMEEMKTL-------ARQKNA---NAIVGI 80 (103)
T ss_pred HHHHHHHHHHHHH-------HHHCCC---CEEEEE
T ss_conf 9999999999999-------997499---999999
No 206
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=25.89 E-value=58 Score=14.88 Aligned_cols=29 Identities=38% Similarity=0.524 Sum_probs=20.3
Q ss_pred CCHHHHHHHHCCCCHHHH---HHHHHHHCCCCC
Q ss_conf 658899999678543466---667775145544
Q gi|254780431|r 19 LSASQIAVQLGGVTRNAV---IGKLHRLFLSNR 48 (178)
Q Consensus 19 ~SasqIA~~lGgvtRNAV---IGK~hRLgLs~R 48 (178)
+|-.+||..|| +||-.| +.+-.+.||-.+
T Consensus 9 lt~~~iA~~lG-~tretvsR~l~~l~~~GlI~~ 40 (48)
T smart00419 9 LTRQEIAELLG-LTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred CCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEEE
T ss_conf 79999999979-979999999999998897997
No 207
>KOG1035 consensus
Probab=25.77 E-value=48 Score=15.40 Aligned_cols=10 Identities=30% Similarity=0.497 Sum_probs=4.9
Q ss_pred CCCCCCCCCC
Q ss_conf 6843200557
Q gi|254780431|r 125 LTDNTCKWPL 134 (178)
Q Consensus 125 Lte~tCkWPi 134 (178)
|+...|+-|.
T Consensus 432 l~~~f~~~~~ 441 (1351)
T KOG1035 432 LTHPFLRFPT 441 (1351)
T ss_pred HHCHHCCCCC
T ss_conf 1110105655
No 208
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.62 E-value=58 Score=14.85 Aligned_cols=26 Identities=38% Similarity=0.487 Sum_probs=21.3
Q ss_pred CC-CHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 86-5889999967854346666777514
Q gi|254780431|r 18 GL-SASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 18 G~-SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
-| |-.++|+++| ||||.|--=..+|-
T Consensus 24 ~LPs~~~La~~~~-vSr~tvr~Al~~L~ 50 (66)
T cd07377 24 RLPSERELAEELG-VSRTTVREALRELE 50 (66)
T ss_pred CCCCHHHHHHHHC-CCHHHHHHHHHHHH
T ss_conf 9927999999979-88899999999999
No 209
>PRK00967 hypothetical protein; Provisional
Probab=25.49 E-value=36 Score=16.21 Aligned_cols=24 Identities=33% Similarity=0.426 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 9999999999818658899999678543466667
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK 39 (178)
-|-+.|.+|..+ |+++|. |||||-
T Consensus 57 aR~~A~~rl~~~-------A~~~GA---nAVIgv 80 (105)
T PRK00967 57 ARDIAIDRMKEE-------AKQKGA---NAIVGM 80 (105)
T ss_pred HHHHHHHHHHHH-------HHHCCC---CEEEEE
T ss_conf 999999999999-------997599---999999
No 210
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=25.43 E-value=59 Score=14.82 Aligned_cols=45 Identities=18% Similarity=0.118 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHC----CCCHHHHHHHHHHHCCCCCCC
Q ss_conf 999999999981865889999967----854346666777514554455
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLG----GVTRNAVIGKLHRLFLSNRVK 50 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lG----gvtRNAVIGK~hRLgLs~R~~ 50 (178)
+=+..|.++++.-.|..+|...|+ +.|-+.++--+.|+||.+|.-
T Consensus 10 ~cL~~l~r~~g~~~s~~~L~~glpl~~~~ls~~~~~rAA~~~Gl~a~~v 58 (124)
T cd02421 10 DCLVLLARQFGKPASRDSLVAGLPLDDGRLSPALFPRAAARAGLSARVV 58 (124)
T ss_pred HHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHCCCEEEEE
T ss_conf 9999999995899999999844998778859999999999879832564
No 211
>PRK02877 hypothetical protein; Provisional
Probab=24.83 E-value=38 Score=16.05 Aligned_cols=25 Identities=28% Similarity=0.365 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 89999999999818658899999678543466667
Q gi|254780431|r 5 VERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 5 derve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK 39 (178)
+-|-+.|.+|..+ |++||. |||||-
T Consensus 56 ~aR~~A~~~m~~~-------A~~lGA---nAIVgv 80 (107)
T PRK02877 56 KAREIAFEELGEQ-------ARALGA---DAVVGI 80 (107)
T ss_pred HHHHHHHHHHHHH-------HHHCCC---CEEEEE
T ss_conf 9999999999999-------997499---989999
No 212
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=24.72 E-value=61 Score=14.74 Aligned_cols=40 Identities=18% Similarity=0.292 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 77899999999998186588999996785434666677751
Q gi|254780431|r 3 WTVERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 3 WTderve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
-|+|-.+-++.+-...=|-.++|++|| ||-+.|=++..+|
T Consensus 34 L~~E~l~Fi~~fi~~~Gnlke~~~~lg-iSYpTvR~rLd~i 73 (113)
T pfam09862 34 LTPEQLEFVELFIKCRGNIKEVEKELG-ISYPTVRNRLDEI 73 (113)
T ss_pred CCHHHHHHHHHHHHHCCCHHHHHHHHC-CCCHHHHHHHHHH
T ss_conf 899999999999991688999999978-8818899999999
No 213
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=24.52 E-value=61 Score=14.71 Aligned_cols=42 Identities=33% Similarity=0.394 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHHHCC-------CCHHHHHHHHCCCCHHHHHHHHHHH---CCC
Q ss_conf 789999999999818-------6588999996785434666677751---455
Q gi|254780431|r 4 TVERIDKLKKFWSEG-------LSASQIAVQLGGVTRNAVIGKLHRL---FLS 46 (178)
Q Consensus 4 Tderve~LkkLW~eG-------~SasqIA~~lGgvtRNAVIGK~hRL---gLs 46 (178)
+|.=.+.|++.=-.| |+-.++|++|| |||+.|=-=..|| ||-
T Consensus 13 ~~~v~~~lr~~I~~g~l~pG~~L~E~~La~~~g-VSRtpvREAL~~L~~eGlv 64 (212)
T TIGR03338 13 TTLVQDEIERAILSGELPPGAKLNESDIAARLG-VSRGPVREAFRALEEAGLV 64 (212)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCH
T ss_conf 999999999999839999909818999999889-6949999999999986963
No 214
>cd01667 TGS_ThrRS_N TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along with an adjacent N-terminal domain. The specific function of TGS is not well understood.
Probab=24.35 E-value=19 Score=18.00 Aligned_cols=26 Identities=27% Similarity=0.511 Sum_probs=22.2
Q ss_pred HCCCCHHHHHHHHC-CCCHHHHHHHHH
Q ss_conf 81865889999967-854346666777
Q gi|254780431|r 16 SEGLSASQIAVQLG-GVTRNAVIGKLH 41 (178)
Q Consensus 16 ~eG~SasqIA~~lG-gvtRNAVIGK~h 41 (178)
.+|.|.-+||+.++ +.-++||..|+.
T Consensus 14 ~~~~T~~eiA~~i~~~l~k~~vaa~vn 40 (61)
T cd01667 14 PKGTTPLDIAKSISPGLAKKAVAAKVN 40 (61)
T ss_pred CCCCCHHHHHHHHCHHHHCCEEEEEEC
T ss_conf 899899999998596634137999999
No 215
>TIGR01927 menC_gamma/gm+ o-succinylbenzoic acid (OSB) synthetase; InterPro: IPR010196 This entry describes the enzyme o-succinylbenzoic acid synthetase (MenC) that is involved in one of the steps of the menaquinone biosynthesis pathway. The biosynthesis of menaquinone has been studied most in E. colii . 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) is dehydrated by MenC to give the aromatic compound O-succinylbenzoate (OSB) . MenC, which is a member of the enolase superfamily and x-ray structure has been determined , . Many of the common names of the proteins in this family are incorrectly described as O-succinylbenzoyl-CoA synthase. Members are restricted to bacteria. ; GO: 0000287 magnesium ion binding, 0016836 hydro-lyase activity, 0009234 menaquinone biosynthetic process.
Probab=24.28 E-value=37 Score=16.18 Aligned_cols=41 Identities=20% Similarity=0.346 Sum_probs=23.2
Q ss_pred HHHHHHCCCCHHHH--HHHHCCCCH-HHHHHHHHHHCCCCCCCC
Q ss_conf 99999818658899--999678543-466667775145544555
Q gi|254780431|r 11 LKKFWSEGLSASQI--AVQLGGVTR-NAVIGKLHRLFLSNRVKV 51 (178)
Q Consensus 11 LkkLW~eG~SasqI--A~~lGgvtR-NAVIGK~hRLgLs~R~~~ 51 (178)
|-.+-.+|-+..-| +.-+|++.| |..|-|+|+|||.+=-|+
T Consensus 250 lA~~~~~G~~g~~ViKP~~~Gs~~~~~~~~~~a~~lGl~AV~SS 293 (336)
T TIGR01927 250 LAAEYEKGVRGALVIKPAIIGSPAKLRDLVQKAHRLGLQAVFSS 293 (336)
T ss_pred HHHHHCCCCCCEEEECHHHCCCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 99986289972478650122878999999998775686301688
No 216
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=24.18 E-value=62 Score=14.67 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 99999999998186588999996
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQL 28 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~l 28 (178)
+++..++.|=..|+|-++|++.|
T Consensus 45 ~~l~~I~~l~~~G~~i~~i~~lL 67 (68)
T cd04763 45 DRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 99999999999799899999972
No 217
>pfam04035 consensus
Probab=24.10 E-value=38 Score=16.04 Aligned_cols=12 Identities=42% Similarity=0.504 Sum_probs=8.1
Q ss_pred HHHHHHHHCCCCH
Q ss_conf 8899999678543
Q gi|254780431|r 21 ASQIAVQLGGVTR 33 (178)
Q Consensus 21 asqIA~~lGgvtR 33 (178)
-|+||++|| ++.
T Consensus 40 ~SeIAk~l~-i~~ 51 (60)
T pfam04035 40 KSEIAKRLG-AKI 51 (60)
T ss_pred HHHHHHHHC-CCC
T ss_conf 779999849-998
No 218
>TIGR01908 cas_CXXC_CXXC CRISPR-associated CXXC_CXXC protein Cst1; InterPro: IPR010180 CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes conserved region of about 65 amino acids from an otherwise highly divergent protein found in a minority of CRISPR-associated protein regions. This region features two motifs of CXXC..
Probab=24.02 E-value=50 Score=15.29 Aligned_cols=29 Identities=24% Similarity=0.450 Sum_probs=20.6
Q ss_pred CCC--CCCCCCCEECCCCCCCCCCCCHHHHHHHCC
Q ss_conf 578--998645004787876888771688888705
Q gi|254780431|r 133 PLG--DPFGKDFSFCGSDVCNDSPYCDYHKKLAYQ 165 (178)
Q Consensus 133 PiG--DP~~~dF~FCG~~~~~g~PYC~~H~~iAYQ 165 (178)
||| .|+.+.|.-=|. +|.|||. ||.++||
T Consensus 33 ~~~g~~~~~~N~fwng~---~k~~lC~-~Cef~~Q 63 (339)
T TIGR01908 33 LFGGLNGDVINFFWNGK---PKLPLCE-ICEFIYQ 63 (339)
T ss_pred CCCCCCCCEECCCCCCC---CCCCCCH-HHHHHHH
T ss_conf 45457878010556778---8876141-7899999
No 219
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=23.75 E-value=63 Score=14.62 Aligned_cols=27 Identities=37% Similarity=0.506 Sum_probs=21.1
Q ss_pred CC-CHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 86-58899999678543466667775145
Q gi|254780431|r 18 GL-SASQIAVQLGGVTRNAVIGKLHRLFL 45 (178)
Q Consensus 18 G~-SasqIA~~lGgvtRNAVIGK~hRLgL 45 (178)
-| |-.++|+++| ||||-|--=..+|--
T Consensus 23 ~LPs~~~La~~~~-vSr~tvr~Al~~L~~ 50 (64)
T pfam00392 23 KLPSERELAAEFG-VSRTTVREALRRLEA 50 (64)
T ss_pred CCHHHHHHHHHHC-CCHHHHHHHHHHHHH
T ss_conf 9847999999979-699999999999998
No 220
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=23.22 E-value=65 Score=14.55 Aligned_cols=42 Identities=29% Similarity=0.206 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHCC-------C-CHHHHHHHHCCCCHHHHHHHHHHH---CCCC
Q ss_conf 89999999999818-------6-588999996785434666677751---4554
Q gi|254780431|r 5 VERIDKLKKFWSEG-------L-SASQIAVQLGGVTRNAVIGKLHRL---FLSN 47 (178)
Q Consensus 5 derve~LkkLW~eG-------~-SasqIA~~lGgvtRNAVIGK~hRL---gLs~ 47 (178)
++=++.|+++=.+| | |=.++|.+|| |||+.|=-=..+| ||-.
T Consensus 12 eqV~~~Lr~~I~~G~l~PGdrLP~EreLAe~lg-VSRt~VREAL~~Le~~GLV~ 64 (257)
T PRK10225 12 QEVGAMIRDLIIKTPYNPGERLPPEREIAEMLD-VTRTVVREALIMLEIKGLVE 64 (257)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCEE
T ss_conf 999999999998289999793952999999979-88789999999999889979
No 221
>pfam06610 DUF1144 Protein of unknown function (DUF1144). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=22.99 E-value=45 Score=15.61 Aligned_cols=23 Identities=30% Similarity=0.367 Sum_probs=15.9
Q ss_pred HHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 99981865889999967854346666
Q gi|254780431|r 13 KFWSEGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 13 kLW~eG~SasqIA~~lGgvtRNAVIG 38 (178)
-||.-|-+..||.. +|+-||||-
T Consensus 100 iL~~vGA~~~qi~t---av~snavvs 122 (143)
T pfam06610 100 ILLVVGADFAQIIT---AVSSNAVVS 122 (143)
T ss_pred HHHHHCCCHHHHHH---HHHHHHHHH
T ss_conf 99997488999999---999999999
No 222
>pfam01906 DUF74 Domain of unknown function (DUF74). Members of this protein family have no known function. The domain is about 100 amino acids long and is found in prokaryotes.
Probab=22.77 E-value=44 Score=15.68 Aligned_cols=22 Identities=45% Similarity=0.690 Sum_probs=11.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 99999999981865889999967854346666
Q gi|254780431|r 7 RIDKLKKFWSEGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 7 rve~LkkLW~eG~SasqIA~~lGgvtRNAVIG 38 (178)
|-+.|.+|..+ |++||. |||||
T Consensus 55 R~eA~~rl~~~-------A~~~GA---nAIIg 76 (101)
T pfam01906 55 RDEALERMKEE-------ARELGA---NAVVG 76 (101)
T ss_pred HHHHHHHHHHH-------HHHCCC---CEEEE
T ss_conf 99999999999-------997699---99999
No 223
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=22.56 E-value=67 Score=14.47 Aligned_cols=42 Identities=26% Similarity=0.291 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHH-HCC-CCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 77789999999999-818-6588999996785434666677751
Q gi|254780431|r 2 VWTVERIDKLKKFW-SEG-LSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 2 sWTderve~LkkLW-~eG-~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
.||+|-.+.|.++= .-| ..=..||..||+=|-+.|.-+...+
T Consensus 3 ~Wt~eE~~~l~~~~~~~g~~~W~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 3 EWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHC
T ss_conf 98999999999999997879599999883999989999998863
No 224
>pfam05427 FIBP Acidic fibroblast growth factor binding (FIBP). Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF.
Probab=22.27 E-value=67 Score=14.46 Aligned_cols=35 Identities=20% Similarity=0.124 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCC
Q ss_conf 33336843200557899864500478787688877
Q gi|254780431|r 121 RLMELTDNTCKWPLGDPFGKDFSFCGSDVCNDSPY 155 (178)
Q Consensus 121 sLl~Lte~tCkWPiGDP~~~dF~FCG~~~~~g~PY 155 (178)
-+..+.-.|+|==+..-.-+||.||+..-+.-=.|
T Consensus 177 F~a~~RFEt~KkklqyLtf~D~~~ca~~~m~~WT~ 211 (361)
T pfam05427 177 FIACNRFETTKKKLQYLTFEDFATCAGALMTNWTY 211 (361)
T ss_pred EEEHHHHHCCHHHHCEECCCHHHHHHHHHHHHCCH
T ss_conf 31100202241353200353499999999864233
No 225
>TIGR00642 mmCoA_mut_beta methylmalonyl-CoA mutase, small subunit; InterPro: IPR004608 Methylmalonyl-CoA mutase (5.4.99.2 from EC) catalyses the isomerization of succinyl-CoA to methylmalonyl-CoA during the synthesis of propionate from tricarboxylic acid-cycle intermediates in propionic acid fermentation. The adenosylcobalamin-binding, catalytic chain of methylmalonyl-CoA mutase may form homodimers, as in the mitochondrion and in Escherichia coli, or heterodimers with a shorter, homologous chain that does not bind adenosylcobalamin. This family is this non-catalytic beta chain, as found in the enzyme from Propionibacterium freudenreichii, for which the 3-dimensional structure has been solved .; GO: 0004494 methylmalonyl-CoA mutase activity, 0031419 cobalamin binding, 0019652 lactate fermentation to propionate and acetate.
Probab=22.19 E-value=68 Score=14.42 Aligned_cols=44 Identities=16% Similarity=0.206 Sum_probs=32.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHC---CCCHHHHHHHHH--HH-CCCCCCC
Q ss_conf 99999999981865889999967---854346666777--51-4554455
Q gi|254780431|r 7 RIDKLKKFWSEGLSASQIAVQLG---GVTRNAVIGKLH--RL-FLSNRVK 50 (178)
Q Consensus 7 rve~LkkLW~eG~SasqIA~~lG---gvtRNAVIGK~h--RL-gLs~R~~ 50 (178)
-+|.|++|-..|+.+++|..+|. +++-|.-+--+. =| -|.+|..
T Consensus 245 gaeylr~Lte~G~~~~ea~~~I~Fr~~a~~dqFm~iAk~RAlR~lWAri~ 294 (642)
T TIGR00642 245 GAEYLRKLTEAGYKAEEALSRIKFRLAADDDQFMTIAKLRALRELWARIA 294 (642)
T ss_pred HHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHEEE
T ss_conf 99999999856883788873142110137504789999999998622041
No 226
>TIGR03612 RutA pyrimidine utilization protein A. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the luciferase family defined by pfam00296 and is likely a FMN-dependent monoxygenase.
Probab=22.17 E-value=53 Score=15.12 Aligned_cols=17 Identities=29% Similarity=0.757 Sum_probs=13.0
Q ss_pred CHHHHHHHHHHHHCCCC
Q ss_conf 78999999999981865
Q gi|254780431|r 4 TVERIDKLKKFWSEGLS 20 (178)
Q Consensus 4 Tderve~LkkLW~eG~S 20 (178)
++|=|+.+++||.++-.
T Consensus 144 a~E~~~v~~~LW~~~~~ 160 (355)
T TIGR03612 144 LAEYVQVLRELWATGVS 160 (355)
T ss_pred HHHHHHHHHHHHHCCCC
T ss_conf 99999999999607887
No 227
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=22.04 E-value=68 Score=14.40 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=21.7
Q ss_pred HHHHHHHHH--CCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 999999998--1865889999967854346666
Q gi|254780431|r 8 IDKLKKFWS--EGLSASQIAVQLGGVTRNAVIG 38 (178)
Q Consensus 8 ve~LkkLW~--eG~SasqIA~~lGgvtRNAVIG 38 (178)
++.|.-|=. .++|.++|++++| ++++.|--
T Consensus 8 l~IL~~l~~~~~~~sl~eia~~~~-l~ksT~~R 39 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLG-LSKSTAHR 39 (91)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHH
T ss_conf 999999972899989999999989-09999999
No 228
>pfam07592 Transposase_36 Rhodopirellula transposase. These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces.
Probab=21.81 E-value=69 Score=14.37 Aligned_cols=34 Identities=29% Similarity=0.379 Sum_probs=27.8
Q ss_pred HHCCCCHHHHHHHHC----CCCHHHHHHHHHHHCCCCCC
Q ss_conf 981865889999967----85434666677751455445
Q gi|254780431|r 15 WSEGLSASQIAVQLG----GVTRNAVIGKLHRLFLSNRV 49 (178)
Q Consensus 15 W~eG~SasqIA~~lG----gvtRNAVIGK~hRLgLs~R~ 49 (178)
|.- +|+.+||++|. .||++.|-.-.++||.+-+.
T Consensus 22 WT~-kS~r~la~eL~~~G~~vs~~tV~~lL~~~GysLq~ 59 (311)
T pfam07592 22 WTR-KSTRKLAEELNQRGYKVSRETVGRLLNELGYSLQA 59 (311)
T ss_pred EEH-HHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHH
T ss_conf 312-04999999999759874288999999874921132
No 229
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=21.81 E-value=69 Score=14.37 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=22.8
Q ss_pred HHHHHHHH--HCCCCHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 99999999--8186588999996785434666677751
Q gi|254780431|r 8 IDKLKKFW--SEGLSASQIAVQLGGVTRNAVIGKLHRL 43 (178)
Q Consensus 8 ve~LkkLW--~eG~SasqIA~~lGgvtRNAVIGK~hRL 43 (178)
++.|.-|= ..++|.+|||+++| +++.. +|||
T Consensus 14 l~ILe~l~~~~~~lslsela~~lg-lpksT----v~Rl 46 (264)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTG-LHRTT----VRRL 46 (264)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHC-CCHHH----HHHH
T ss_conf 999998741799979999999979-09999----9999
No 230
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=21.39 E-value=70 Score=14.32 Aligned_cols=45 Identities=24% Similarity=0.196 Sum_probs=34.1
Q ss_pred CHHHHHHHHHHHHCC-------C-CHHHHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 789999999999818-------6-588999996785434666677751455445
Q gi|254780431|r 4 TVERIDKLKKFWSEG-------L-SASQIAVQLGGVTRNAVIGKLHRLFLSNRV 49 (178)
Q Consensus 4 Tderve~LkkLW~eG-------~-SasqIA~~lGgvtRNAVIGK~hRLgLs~R~ 49 (178)
.|+=++.|+++=..| | |=.++|.+|| |||+.|=.=..+|-..|-.
T Consensus 10 ~eqV~~~L~~~I~~G~l~pGdrLPsEreLAe~fG-VSRt~VREAL~~Le~~GlV 62 (258)
T PRK11523 10 YQQLAADLKERIEQGVYLVGDKLPAERFIADEKN-VSRTVVREAIIMLEVEGYV 62 (258)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCCE
T ss_conf 9999999999998599999790966999999979-8879999999999988998
No 231
>pfam01729 QRPTase_C Quinolinate phosphoribosyl transferase, C-terminal domain. Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The C-terminal domain has a 7 beta-stranded TIM barrel-like fold.
Probab=21.32 E-value=36 Score=16.19 Aligned_cols=20 Identities=55% Similarity=0.763 Sum_probs=14.6
Q ss_pred HHHHHHCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 999996785434666677751455445
Q gi|254780431|r 23 QIAVQLGGVTRNAVIGKLHRLFLSNRV 49 (178)
Q Consensus 23 qIA~~lGgvtRNAVIGK~hRLgLs~R~ 49 (178)
.-|-..|| |..|||||+-..
T Consensus 34 k~Av~~GG-------g~~HR~gL~d~i 53 (169)
T pfam01729 34 KYAVLIGG-------GDNHRLGLSDAV 53 (169)
T ss_pred HHHHHHCC-------CCCCCCCCCHHE
T ss_conf 99998658-------312216887103
No 232
>pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
Probab=21.30 E-value=70 Score=14.31 Aligned_cols=48 Identities=19% Similarity=0.214 Sum_probs=35.2
Q ss_pred CHHHHHHHHHHHH-CCCCHHHHHHHHC---CCCHHHHHHHHHHH---CCCCCCCC
Q ss_conf 7899999999998-1865889999967---85434666677751---45544555
Q gi|254780431|r 4 TVERIDKLKKFWS-EGLSASQIAVQLG---GVTRNAVIGKLHRL---FLSNRVKV 51 (178)
Q Consensus 4 Tderve~LkkLW~-eG~SasqIA~~lG---gvtRNAVIGK~hRL---gLs~R~~~ 51 (178)
||---+.++-||. .+.|+.+|-..|. +.++|.|.=-..|| |+-.|.+.
T Consensus 2 s~~E~~IM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~~~ 56 (115)
T pfam03965 2 GDAEWEVMRILWALGPATVKEVVEELPEPRDWAYSTVKTLLTRLVKKGLLSREKD 56 (115)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEEEC
T ss_conf 8899999999980799779999998514568857289999999997786268733
No 233
>pfam09976 DUF2133 Uncharacterized protein conserved in bacteria (DUF2133). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=21.28 E-value=44 Score=15.66 Aligned_cols=12 Identities=33% Similarity=1.066 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHC
Q ss_conf 999999999981
Q gi|254780431|r 6 ERIDKLKKFWSE 17 (178)
Q Consensus 6 erve~LkkLW~e 17 (178)
|++|.||++|.+
T Consensus 1 eq~e~ik~wwk~ 12 (43)
T pfam09976 1 EQLERLKAWWKR 12 (43)
T ss_pred CHHHHHHHHHHH
T ss_conf 968899999998
No 234
>PRK03772 threonyl-tRNA synthetase; Validated
Probab=20.75 E-value=30 Score=16.77 Aligned_cols=27 Identities=19% Similarity=0.628 Sum_probs=23.8
Q ss_pred HHCCCCHHHHHHHHC-CCCHHHHHHHHH
Q ss_conf 981865889999967-854346666777
Q gi|254780431|r 15 WSEGLSASQIAVQLG-GVTRNAVIGKLH 41 (178)
Q Consensus 15 W~eG~SasqIA~~lG-gvtRNAVIGK~h 41 (178)
...|.|..+||+.|| +..++||.+|+.
T Consensus 14 ~~~~~t~~dIA~~Is~~Lak~avaa~vn 41 (642)
T PRK03772 14 FDHPVSPMDVALDIGPGLAKACIAGRVN 41 (642)
T ss_pred CCCCCCHHHHHHHHCHHHHHHHEEEEEC
T ss_conf 7899999999999786776662899989
No 235
>KOG3121 consensus
Probab=20.52 E-value=15 Score=18.63 Aligned_cols=22 Identities=14% Similarity=0.258 Sum_probs=13.1
Q ss_pred EECCCCCCC--CCCCCHHHHHHHC
Q ss_conf 047878768--8877168888870
Q gi|254780431|r 143 SFCGSDVCN--DSPYCDYHKKLAY 164 (178)
Q Consensus 143 ~FCG~~~~~--g~PYC~~H~~iAY 164 (178)
.|-|.+.+- --|-|.....|-|
T Consensus 145 ~~~g~p~~~~G~~P~ctq~lMi~~ 168 (184)
T KOG3121 145 TIGGNPAQVVGTEPRCTQNLMIEA 168 (184)
T ss_pred EECCCCCEEECCCCHHHHHHHHHH
T ss_conf 773887235315730268999999
No 236
>PRK01217 hypothetical protein; Provisional
Probab=20.50 E-value=52 Score=15.17 Aligned_cols=24 Identities=38% Similarity=0.486 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 9999999999818658899999678543466667
Q gi|254780431|r 6 ERIDKLKKFWSEGLSASQIAVQLGGVTRNAVIGK 39 (178)
Q Consensus 6 erve~LkkLW~eG~SasqIA~~lGgvtRNAVIGK 39 (178)
-|-+-|.+|..+ |++||. |||||-
T Consensus 64 aR~eA~~rm~~~-------A~~~GA---nAVIgv 87 (114)
T PRK01217 64 ARNQALERMIDH-------AKALGA---NAVISV 87 (114)
T ss_pred HHHHHHHHHHHH-------HHHCCC---CEEEEE
T ss_conf 999999999999-------997599---999999
No 237
>PRK11050 manganese transport regulator MntR; Provisional
Probab=20.24 E-value=74 Score=14.16 Aligned_cols=43 Identities=23% Similarity=0.275 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHH---HHHHHCCCCC
Q ss_conf 89999999999818--65889999967854346666---7775145544
Q gi|254780431|r 5 VERIDKLKKFWSEG--LSASQIAVQLGGVTRNAVIG---KLHRLFLSNR 48 (178)
Q Consensus 5 derve~LkkLW~eG--~SasqIA~~lGgvtRNAVIG---K~hRLgLs~R 48 (178)
++=+|+.-.|=.++ --...||..|| ||.-.|.. |..+.||-..
T Consensus 39 EDYlE~I~~L~~~~G~aR~~DIA~~Lg-Vs~pSVt~mlkrL~~~GlV~~ 86 (155)
T PRK11050 39 EDYVELIADLIAEVGEARQVDIAARLG-VSQPTVAKMLKRLARDGLVEM 86 (155)
T ss_pred HHHHHHHHHHHHCCCCEEHHHHHHHHC-CCCHHHHHHHHHHHHCCCEEE
T ss_conf 999999999998269564999998909-993319999999987899887
No 238
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.05 E-value=75 Score=14.14 Aligned_cols=24 Identities=46% Similarity=0.576 Sum_probs=19.6
Q ss_pred CHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 5889999967854346666777514
Q gi|254780431|r 20 SASQIAVQLGGVTRNAVIGKLHRLF 44 (178)
Q Consensus 20 SasqIA~~lGgvtRNAVIGK~hRLg 44 (178)
|-.++|+++| |||+.|--=...|-
T Consensus 22 s~~~la~~~~-vSr~tvr~A~~~L~ 45 (60)
T smart00345 22 SERELAAQLG-VSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHC-CCHHHHHHHHHHHH
T ss_conf 0999999989-49999999999999
Done!