Query 040221
Match_columns 142
No_of_seqs 121 out of 1267
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 06:17:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040221hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06347 autolysin; Reviewed 99.9 3E-22 6.6E-27 166.4 13.4 115 13-142 478-592 (592)
2 PRK10783 mltD membrane-bound l 99.8 2.7E-20 5.9E-25 151.5 12.7 106 13-142 342-447 (456)
3 PRK06347 autolysin; Reviewed 99.8 7.2E-20 1.6E-24 152.3 13.2 120 14-142 405-524 (592)
4 PRK13914 invasion associated s 99.7 2.7E-17 5.8E-22 133.2 12.6 122 15-142 28-244 (481)
5 COG1388 LytE FOG: LysM repeat 99.6 9.6E-15 2.1E-19 99.7 8.9 107 28-142 1-111 (124)
6 PF01476 LysM: LysM domain; I 99.6 1.3E-15 2.8E-20 85.9 3.4 43 100-142 1-44 (44)
7 PRK10783 mltD membrane-bound l 99.5 1E-13 2.2E-18 113.2 11.0 117 18-142 267-388 (456)
8 PRK14125 cell division suppres 99.3 2.8E-12 6E-17 85.1 6.5 48 95-142 34-89 (103)
9 TIGR02899 spore_safA spore coa 99.3 9.4E-12 2E-16 69.4 5.0 41 102-142 1-43 (44)
10 cd00118 LysM Lysin domain, fou 99.3 1.9E-11 4E-16 67.6 6.1 44 99-142 2-46 (46)
11 TIGR02907 spore_VI_D stage VI 99.3 1.2E-11 2.6E-16 96.1 6.4 49 94-142 290-338 (338)
12 PRK10871 nlpD lipoprotein NlpD 99.2 2.7E-11 5.8E-16 94.5 5.4 46 97-142 60-106 (319)
13 PRK13914 invasion associated s 99.1 1.6E-10 3.5E-15 94.1 6.3 47 96-142 26-72 (481)
14 smart00257 LysM Lysin motif. 99.0 2E-09 4.4E-14 58.6 5.5 43 99-141 1-44 (44)
15 PF01476 LysM: LysM domain; I 99.0 2.7E-10 6E-15 63.9 2.0 43 17-65 1-44 (44)
16 PRK11198 LysM domain/BON super 98.9 4.6E-09 1E-13 73.9 5.9 47 96-142 94-146 (147)
17 COG3858 Predicted glycosyl hyd 98.6 2.8E-08 6.1E-13 79.4 4.2 89 19-142 6-95 (423)
18 PRK14125 cell division suppres 98.5 3E-07 6.5E-12 61.0 5.8 52 11-68 33-92 (103)
19 TIGR02899 spore_safA spore coa 98.5 4.5E-07 9.8E-12 50.1 4.8 41 20-66 2-44 (44)
20 cd00118 LysM Lysin domain, fou 98.5 3.5E-07 7.5E-12 50.0 4.3 44 16-65 2-46 (46)
21 TIGR02907 spore_VI_D stage VI 98.2 1.1E-06 2.5E-11 68.6 4.2 45 15-65 294-338 (338)
22 PRK10871 nlpD lipoprotein NlpD 98.2 1.4E-06 3.1E-11 68.2 4.6 48 14-67 60-108 (319)
23 PF04225 OapA: Opacity-associa 98.1 4.4E-06 9.6E-11 53.5 3.9 45 97-141 2-51 (85)
24 smart00257 LysM Lysin motif. 98.0 1.9E-05 4.2E-10 42.3 4.5 42 17-64 2-44 (44)
25 COG1388 LytE FOG: LysM repeat 98.0 1.1E-05 2.5E-10 54.7 4.2 48 14-67 66-113 (124)
26 COG1652 XkdP Uncharacterized p 97.9 3.9E-06 8.5E-11 64.4 1.3 45 98-142 211-262 (269)
27 TIGR03505 FimV_core FimV N-ter 97.8 3.6E-05 7.7E-10 48.0 4.5 37 106-142 1-50 (74)
28 PRK11198 LysM domain/BON super 97.6 0.00011 2.5E-09 51.6 4.5 51 13-66 94-147 (147)
29 PRK10190 L,D-transpeptidase; P 97.5 0.00034 7.5E-09 54.7 6.3 48 95-142 35-85 (310)
30 PRK10260 L,D-transpeptidase; P 97.5 0.00037 7.9E-09 54.4 6.4 48 95-142 38-88 (306)
31 PF05489 Phage_tail_X: Phage T 96.8 0.0038 8.2E-08 37.3 4.8 40 103-142 6-52 (60)
32 PRK11649 putative peptidase; P 96.7 0.0035 7.6E-08 51.5 5.7 48 94-141 92-141 (439)
33 COG3170 FimV Tfp pilus assembl 96.7 0.0019 4.1E-08 55.3 3.9 49 94-142 185-246 (755)
34 TIGR03505 FimV_core FimV N-ter 95.9 0.019 4.2E-07 35.7 4.4 43 23-67 1-52 (74)
35 COG3061 OapA Cell envelope opa 95.9 0.039 8.5E-07 41.1 6.5 47 95-141 157-208 (242)
36 PRK10190 L,D-transpeptidase; P 95.7 0.019 4.1E-07 45.1 4.6 47 15-67 38-87 (310)
37 PRK10260 L,D-transpeptidase; P 95.4 0.03 6.4E-07 43.9 4.7 47 15-67 41-90 (306)
38 PRK11649 putative peptidase; P 93.9 0.47 1E-05 39.1 8.6 120 16-141 97-233 (439)
39 PF04225 OapA: Opacity-associa 93.8 0.057 1.2E-06 34.4 2.4 47 16-68 4-55 (85)
40 COG4784 Putative Zn-dependent 93.4 0.16 3.5E-06 40.6 4.7 48 94-141 425-476 (479)
41 COG1652 XkdP Uncharacterized p 92.7 0.033 7.1E-07 42.7 0.0 50 16-68 212-265 (269)
42 KOG2850 Predicted peptidoglyca 92.6 0.08 1.7E-06 38.6 1.9 46 97-142 9-55 (186)
43 PF13518 HTH_28: Helix-turn-he 91.7 0.2 4.3E-06 28.1 2.5 24 103-126 10-33 (52)
44 PF02796 HTH_7: Helix-turn-hel 90.3 0.36 7.7E-06 26.7 2.7 23 103-125 19-41 (45)
45 PF01527 HTH_Tnp_1: Transposas 89.1 0.24 5.1E-06 30.2 1.4 25 102-126 20-44 (76)
46 PF05489 Phage_tail_X: Phage T 87.9 1.1 2.5E-05 26.5 3.8 44 21-68 7-55 (60)
47 PF13384 HTH_23: Homeodomain-l 85.9 1.1 2.3E-05 24.9 2.8 24 103-126 15-38 (50)
48 COG4254 Uncharacterized protei 85.5 0.93 2E-05 35.5 3.1 45 98-142 6-54 (339)
49 PF04218 CENP-B_N: CENP-B N-te 83.8 0.52 1.1E-05 27.2 0.8 24 102-125 19-42 (53)
50 PRK09413 IS2 repressor TnpA; R 83.1 1.5 3.3E-05 29.5 3.0 25 102-126 26-50 (121)
51 COG2963 Transposase and inacti 81.2 1.8 4E-05 28.6 2.9 25 102-126 21-46 (116)
52 cd00569 HTH_Hin_like Helix-tur 80.3 3.1 6.7E-05 20.2 3.1 23 103-125 19-41 (42)
53 PF13936 HTH_38: Helix-turn-he 80.2 2.6 5.6E-05 23.1 2.8 24 102-125 17-40 (44)
54 COG5004 P2-like prophage tail 80.2 6.5 0.00014 23.7 4.6 45 98-142 3-54 (70)
55 PF05225 HTH_psq: helix-turn-h 78.3 2.5 5.4E-05 23.5 2.3 23 103-125 13-36 (45)
56 PHA00675 hypothetical protein 78.1 3.2 7E-05 25.9 3.0 24 103-126 37-60 (78)
57 TIGR01764 excise DNA binding d 78.1 4.3 9.3E-05 21.8 3.3 35 107-141 3-38 (49)
58 PF10668 Phage_terminase: Phag 77.9 3.1 6.7E-05 24.8 2.8 23 105-127 22-44 (60)
59 PF04967 HTH_10: HTH DNA bindi 77.6 5.1 0.00011 23.1 3.6 27 15-47 16-42 (53)
60 COG3170 FimV Tfp pilus assembl 75.2 6.9 0.00015 34.3 5.2 56 11-68 185-249 (755)
61 PF04545 Sigma70_r4: Sigma-70, 73.7 5.9 0.00013 21.9 3.2 23 103-125 18-40 (50)
62 COG3858 Predicted glycosyl hyd 72.1 3.3 7.3E-05 33.9 2.5 48 15-68 50-98 (423)
63 PF10668 Phage_terminase: Phag 71.9 4.3 9.3E-05 24.1 2.3 29 17-51 17-45 (60)
64 PF01710 HTH_Tnp_IS630: Transp 71.4 3.2 6.9E-05 27.8 1.9 25 102-126 15-39 (119)
65 cd04762 HTH_MerR-trunc Helix-T 71.2 6.1 0.00013 21.0 2.8 20 107-126 2-21 (49)
66 PF13542 HTH_Tnp_ISL3: Helix-t 70.6 6.3 0.00014 21.9 2.8 20 106-125 28-47 (52)
67 PF00376 MerR: MerR family reg 70.2 6.3 0.00014 21.0 2.6 20 107-126 1-20 (38)
68 COG3415 Transposase and inacti 69.4 4.9 0.00011 28.0 2.5 25 102-126 18-42 (138)
69 PF13518 HTH_28: Helix-turn-he 69.3 7.5 0.00016 21.4 3.0 24 21-50 11-34 (52)
70 cd04761 HTH_MerR-SF Helix-Turn 67.5 7.9 0.00017 20.9 2.8 20 107-126 2-21 (49)
71 cd01104 HTH_MlrA-CarA Helix-Tu 65.8 8.2 0.00018 22.6 2.8 20 107-126 2-21 (68)
72 PF08765 Mor: Mor transcriptio 65.3 7.7 0.00017 25.5 2.8 21 105-125 72-92 (108)
73 PF06056 Terminase_5: Putative 64.1 12 0.00025 22.0 3.1 25 104-128 12-36 (58)
74 smart00351 PAX Paired Box doma 63.7 8 0.00017 26.2 2.7 23 103-125 31-53 (125)
75 smart00421 HTH_LUXR helix_turn 63.2 13 0.00028 20.3 3.2 24 103-126 16-39 (58)
76 COG4784 Putative Zn-dependent 62.7 8 0.00017 31.3 2.8 59 4-65 418-477 (479)
77 PF13411 MerR_1: MerR HTH fami 62.6 9.8 0.00021 22.3 2.7 20 107-126 2-21 (69)
78 PF12728 HTH_17: Helix-turn-he 61.3 16 0.00034 20.1 3.3 35 107-141 3-38 (51)
79 TIGR02531 yecD_yerC TrpR-relat 60.0 11 0.00023 24.2 2.6 26 102-127 47-72 (88)
80 PF08281 Sigma70_r4_2: Sigma-7 59.4 12 0.00026 20.9 2.5 22 104-125 25-46 (54)
81 PF13011 LZ_Tnp_IS481: leucine 59.3 12 0.00026 23.9 2.7 25 102-126 22-46 (85)
82 smart00422 HTH_MERR helix_turn 59.0 13 0.00028 21.8 2.8 20 107-126 2-21 (70)
83 PF04255 DUF433: Protein of un 59.0 12 0.00025 21.6 2.5 23 103-125 29-52 (56)
84 PF01527 HTH_Tnp_1: Transposas 58.7 7.7 0.00017 23.2 1.8 24 21-50 22-45 (76)
85 PF13693 HTH_35: Winged helix- 58.6 13 0.00029 23.2 2.8 21 103-123 13-33 (78)
86 PF13613 HTH_Tnp_4: Helix-turn 57.9 10 0.00022 21.5 2.1 24 102-125 16-39 (53)
87 cd04764 HTH_MlrA-like_sg1 Heli 57.4 15 0.00032 21.6 2.8 20 107-126 2-21 (67)
88 PF09012 FeoC: FeoC like trans 54.3 15 0.00031 22.0 2.4 20 106-125 15-34 (69)
89 PF01710 HTH_Tnp_IS630: Transp 53.8 19 0.00041 24.0 3.2 75 21-125 17-91 (119)
90 PHA02591 hypothetical protein; 53.6 47 0.001 20.9 4.6 35 95-129 35-72 (83)
91 cd00131 PAX Paired Box domain 53.2 15 0.00033 25.0 2.6 23 103-125 31-53 (128)
92 PF13551 HTH_29: Winged helix- 52.8 16 0.00034 23.3 2.6 23 103-125 9-32 (112)
93 cd06170 LuxR_C_like C-terminal 52.4 25 0.00055 19.1 3.2 24 103-126 13-36 (57)
94 cd06171 Sigma70_r4 Sigma70, re 52.4 25 0.00055 18.6 3.1 22 104-125 25-46 (55)
95 PF11268 DUF3071: Protein of u 51.7 14 0.00029 26.7 2.3 27 100-126 64-90 (170)
96 COG3061 OapA Cell envelope opa 51.5 18 0.0004 27.2 3.0 47 16-68 161-212 (242)
97 cd04763 HTH_MlrA-like Helix-Tu 51.4 21 0.00045 21.0 2.8 20 107-126 2-21 (68)
98 PF12471 GTP_CH_N: GTP cyclohy 51.1 11 0.00024 27.5 1.7 20 106-125 171-190 (194)
99 PF04760 IF2_N: Translation in 50.3 14 0.0003 20.9 1.8 19 107-125 5-23 (54)
100 PF01371 Trp_repressor: Trp re 49.7 19 0.0004 23.0 2.4 25 103-127 47-71 (87)
101 PF08220 HTH_DeoR: DeoR-like h 49.5 20 0.00044 20.6 2.5 18 107-124 16-33 (57)
102 PRK10344 DNA-binding transcrip 47.9 26 0.00056 22.6 2.9 21 103-123 19-39 (92)
103 PF00356 LacI: Bacterial regul 46.5 32 0.00069 19.1 2.8 21 24-50 1-22 (46)
104 COG5484 Uncharacterized conser 45.5 21 0.00046 27.5 2.6 22 105-126 19-40 (279)
105 TIGR02937 sigma70-ECF RNA poly 45.1 29 0.00062 22.8 3.1 23 103-125 124-146 (158)
106 TIGR03879 near_KaiC_dom probab 44.3 38 0.00083 20.9 3.2 23 103-125 30-52 (73)
107 PRK09413 IS2 repressor TnpA; R 43.1 34 0.00074 22.8 3.1 25 20-50 27-51 (121)
108 COG0739 NlpD Membrane proteins 43.0 34 0.00073 25.6 3.5 45 17-67 4-49 (277)
109 PF06627 DUF1153: Protein of u 43.0 22 0.00049 22.8 2.0 22 106-127 50-71 (90)
110 PF00165 HTH_AraC: Bacterial r 42.7 37 0.0008 17.8 2.7 21 104-124 7-27 (42)
111 cd01279 HTH_HspR-like Helix-Tu 42.1 32 0.0007 22.1 2.8 20 107-126 3-22 (98)
112 cd04768 HTH_BmrR-like Helix-Tu 41.9 33 0.00071 21.9 2.8 20 107-126 2-21 (96)
113 cd01105 HTH_GlnR-like Helix-Tu 41.0 35 0.00076 21.4 2.8 20 107-126 3-22 (88)
114 PF00196 GerE: Bacterial regul 40.8 35 0.00075 19.4 2.5 23 103-125 16-38 (58)
115 cd00086 homeodomain Homeodomai 40.7 27 0.00058 19.5 2.0 21 105-125 27-47 (59)
116 PRK00118 putative DNA-binding 40.5 40 0.00087 22.2 3.0 23 103-125 31-53 (104)
117 cd04774 HTH_YfmP Helix-Turn-He 40.4 36 0.00077 21.8 2.8 20 107-126 2-21 (96)
118 TIGR00370 conserved hypothetic 40.4 30 0.00065 25.6 2.7 33 12-50 80-112 (202)
119 cd04766 HTH_HspR Helix-Turn-He 40.1 37 0.0008 21.3 2.8 21 107-127 3-23 (91)
120 cd00093 HTH_XRE Helix-turn-hel 40.0 47 0.001 17.2 3.0 23 104-126 11-33 (58)
121 PF09607 BrkDBD: Brinker DNA-b 39.9 41 0.00088 19.8 2.7 21 107-127 27-47 (58)
122 cd04775 HTH_Cfa-like Helix-Tur 39.9 36 0.00079 21.9 2.8 20 107-126 3-22 (102)
123 PF01381 HTH_3: Helix-turn-hel 38.7 45 0.00098 18.3 2.8 23 103-125 7-29 (55)
124 cd04788 HTH_NolA-AlbR Helix-Tu 38.2 41 0.00088 21.4 2.8 20 107-126 2-21 (96)
125 COG2963 Transposase and inacti 38.1 38 0.00082 22.2 2.7 23 20-48 22-45 (116)
126 smart00342 HTH_ARAC helix_turn 38.1 44 0.00095 19.5 2.8 18 107-124 3-20 (84)
127 PHA01976 helix-turn-helix prot 37.8 52 0.0011 19.0 3.1 23 103-125 13-35 (67)
128 PF13443 HTH_26: Cro/C1-type H 37.6 42 0.00091 19.1 2.6 24 103-126 8-31 (63)
129 PF13022 HTH_Tnp_1_2: Helix-tu 37.4 39 0.00084 23.7 2.7 21 106-126 35-55 (142)
130 COG2739 Uncharacterized protei 37.4 39 0.00084 22.3 2.5 18 107-124 35-52 (105)
131 smart00345 HTH_GNTR helix_turn 37.3 50 0.0011 18.1 2.8 23 107-129 22-45 (60)
132 smart00760 Bac_DnaA_C Bacteria 37.2 38 0.00083 19.5 2.4 21 107-127 5-25 (60)
133 COG3413 Predicted DNA binding 37.2 51 0.0011 24.2 3.5 28 14-47 170-197 (215)
134 PF00046 Homeobox: Homeobox do 36.9 51 0.0011 18.4 2.8 20 106-125 28-47 (57)
135 PF08279 HTH_11: HTH domain; 36.8 38 0.00082 18.8 2.2 17 107-123 17-33 (55)
136 cd04789 HTH_Cfa Helix-Turn-Hel 36.5 45 0.00097 21.5 2.8 20 107-126 3-22 (102)
137 cd04787 HTH_HMRTR_unk Helix-Tu 36.1 62 0.0013 21.9 3.6 65 24-127 2-68 (133)
138 cd04772 HTH_TioE_rpt1 First He 36.1 46 0.001 21.4 2.8 21 107-127 2-22 (99)
139 cd04770 HTH_HMRTR Helix-Turn-H 36.1 57 0.0012 21.6 3.4 21 24-50 2-22 (123)
140 cd04782 HTH_BltR Helix-Turn-He 35.1 49 0.0011 21.1 2.8 20 107-126 2-21 (97)
141 PF00392 GntR: Bacterial regul 35.1 51 0.0011 19.1 2.7 18 107-124 26-43 (64)
142 smart00530 HTH_XRE Helix-turn- 35.0 63 0.0014 16.5 3.0 23 104-126 9-31 (56)
143 cd01107 HTH_BmrR Helix-Turn-He 34.5 49 0.0011 21.5 2.8 24 107-130 2-27 (108)
144 TIGR02844 spore_III_D sporulat 34.5 50 0.0011 20.7 2.6 20 106-125 20-39 (80)
145 cd00592 HTH_MerR-like Helix-Tu 34.1 52 0.0011 20.8 2.8 20 107-126 2-21 (100)
146 cd01106 HTH_TipAL-Mta Helix-Tu 34.0 51 0.0011 21.1 2.8 20 107-126 2-21 (103)
147 PF12116 SpoIIID: Stage III sp 33.8 15 0.00032 23.2 0.1 22 100-121 14-35 (82)
148 PRK13413 mpi multiple promoter 32.7 55 0.0012 23.6 3.1 24 103-126 170-193 (200)
149 COG2771 CsgD DNA-binding HTH d 32.6 60 0.0013 18.2 2.7 23 102-124 16-38 (65)
150 PRK12845 3-ketosteroid-delta-1 32.6 44 0.00095 28.5 2.8 26 102-127 421-450 (564)
151 COG3784 Uncharacterized protei 32.6 35 0.00075 22.5 1.7 36 105-140 64-100 (109)
152 PF08299 Bac_DnaA_C: Bacterial 32.3 47 0.001 19.9 2.2 18 107-124 5-22 (70)
153 PF05263 DUF722: Protein of un 32.3 56 0.0012 22.5 2.8 27 100-126 94-120 (130)
154 PF12298 Bot1p: Eukaryotic mit 32.2 61 0.0013 23.4 3.1 20 103-122 31-50 (172)
155 PF11020 DUF2610: Domain of un 32.2 59 0.0013 20.5 2.6 20 106-125 55-74 (82)
156 cd04765 HTH_MlrA-like_sg2 Heli 32.0 58 0.0012 21.0 2.8 19 107-125 2-20 (99)
157 TIGR03070 couple_hipB transcri 31.9 73 0.0016 17.3 2.9 24 103-126 13-36 (58)
158 TIGR03826 YvyF flagellar opero 31.8 69 0.0015 22.2 3.2 23 104-126 43-67 (137)
159 PRK12837 3-ketosteroid-delta-1 31.6 48 0.001 27.7 2.9 26 102-127 372-401 (513)
160 cd04773 HTH_TioE_rpt2 Second H 31.6 58 0.0013 21.2 2.8 20 107-126 2-21 (108)
161 PF15145 DUF4577: Domain of un 31.5 48 0.001 22.3 2.3 29 100-128 84-115 (128)
162 smart00389 HOX Homeodomain. DN 31.5 44 0.00096 18.4 2.0 21 105-125 27-47 (56)
163 PF04297 UPF0122: Putative hel 31.5 54 0.0012 21.5 2.5 22 103-124 31-52 (101)
164 COG0193 Pth Peptidyl-tRNA hydr 31.3 31 0.00068 25.3 1.5 63 25-123 27-89 (190)
165 PF13404 HTH_AsnC-type: AsnC-t 31.3 67 0.0015 17.3 2.5 20 105-124 17-36 (42)
166 PF14549 P22_Cro: DNA-binding 31.3 71 0.0015 18.8 2.8 20 107-126 11-30 (60)
167 PF13510 Fer2_4: 2Fe-2S iron-s 31.3 58 0.0013 20.1 2.6 24 97-120 10-33 (82)
168 PF12244 DUF3606: Protein of u 31.0 52 0.0011 19.1 2.2 29 14-48 12-40 (57)
169 PF01402 RHH_1: Ribbon-helix-h 30.7 76 0.0016 16.2 2.7 19 106-124 12-30 (39)
170 TIGR02043 ZntR Zn(II)-responsi 30.7 98 0.0021 20.9 3.9 22 24-51 3-24 (131)
171 PRK04217 hypothetical protein; 30.4 75 0.0016 21.2 3.1 22 104-125 57-78 (110)
172 COG2442 Uncharacterized conser 30.2 61 0.0013 20.2 2.5 24 102-125 40-64 (79)
173 cd07377 WHTH_GntR Winged helix 29.1 79 0.0017 17.7 2.8 24 107-130 27-51 (66)
174 KOG2850 Predicted peptidoglyca 29.0 41 0.00089 24.6 1.8 45 17-67 12-57 (186)
175 cd04780 HTH_MerR-like_sg5 Heli 28.9 71 0.0015 20.4 2.8 20 107-126 2-21 (95)
176 PF08984 DUF1858: Domain of un 28.6 69 0.0015 18.4 2.4 22 102-123 38-59 (59)
177 PF10543 ORF6N: ORF6N domain; 28.6 40 0.00086 21.3 1.5 30 13-48 3-32 (88)
178 PRK12839 hypothetical protein; 28.6 56 0.0012 27.9 2.8 25 103-127 425-453 (572)
179 PHA00542 putative Cro-like pro 28.6 81 0.0018 19.5 2.9 23 103-125 29-51 (82)
180 PF00440 TetR_N: Bacterial reg 28.4 95 0.0021 16.7 2.9 21 105-125 16-36 (47)
181 PF14493 HTH_40: Helix-turn-he 28.0 72 0.0016 20.0 2.7 22 103-124 11-32 (91)
182 PF11242 DUF2774: Protein of u 27.9 1E+02 0.0023 18.4 3.0 21 103-123 11-31 (63)
183 PF13412 HTH_24: Winged helix- 27.7 1.1E+02 0.0023 16.4 3.1 22 103-124 15-36 (48)
184 PF05052 MerE: MerE protein; 27.6 33 0.00071 21.2 0.9 17 1-17 1-17 (75)
185 COG3721 HugX Putative heme iro 27.4 1.2E+02 0.0026 21.7 3.8 23 103-125 25-47 (176)
186 cd01111 HTH_MerD Helix-Turn-He 27.4 78 0.0017 20.7 2.8 20 107-126 2-21 (107)
187 PRK07121 hypothetical protein; 27.2 69 0.0015 26.5 3.1 26 102-127 358-387 (492)
188 PF12844 HTH_19: Helix-turn-he 27.2 84 0.0018 17.8 2.7 23 103-125 10-32 (64)
189 TIGR02950 SigM_subfam RNA poly 27.2 82 0.0018 21.1 3.0 23 103-125 119-141 (154)
190 TIGR02985 Sig70_bacteroi1 RNA 27.0 84 0.0018 21.0 3.1 23 103-125 127-149 (161)
191 PF14451 Ub-Mut7C: Mut7-C ubiq 26.8 1.1E+02 0.0023 19.2 3.2 46 96-141 23-73 (81)
192 PF08671 SinI: Anti-repressor 26.5 69 0.0015 16.2 1.9 16 110-125 10-25 (30)
193 PRK09652 RNA polymerase sigma 26.5 86 0.0019 21.5 3.1 23 103-125 142-164 (182)
194 TIGR00270 conserved hypothetic 26.4 85 0.0018 22.1 3.0 36 106-141 112-152 (154)
195 PF08822 DUF1804: Protein of u 26.4 79 0.0017 22.7 2.8 27 100-126 14-40 (165)
196 PRK06759 RNA polymerase factor 25.8 91 0.002 20.9 3.1 23 103-125 120-142 (154)
197 PRK06437 hypothetical protein; 25.8 48 0.001 19.7 1.4 45 97-141 12-60 (67)
198 PF02682 AHS1: Allophanate hyd 25.7 57 0.0012 24.0 2.1 50 11-66 88-142 (202)
199 PF05920 Homeobox_KN: Homeobox 25.4 90 0.0019 16.7 2.3 19 107-125 15-33 (40)
200 TIGR02054 MerD mercuric resist 24.8 92 0.002 21.0 2.8 24 107-130 5-30 (120)
201 PRK09570 rpoH DNA-directed RNA 24.5 56 0.0012 20.5 1.6 42 100-141 15-60 (79)
202 PRK15002 redox-sensitivie tran 24.3 89 0.0019 22.0 2.8 20 107-126 13-32 (154)
203 PRK10072 putative transcriptio 24.3 1.1E+02 0.0023 19.8 3.0 25 102-126 43-67 (96)
204 COG3753 Uncharacterized protei 24.1 80 0.0017 22.0 2.4 20 105-124 90-109 (143)
205 PF10654 DUF2481: Protein of u 23.7 78 0.0017 21.4 2.2 23 103-125 78-100 (126)
206 TIGR02885 spore_sigF RNA polym 23.7 99 0.0021 22.7 3.1 24 103-126 197-220 (231)
207 COG3423 Nlp Predicted transcri 23.7 1.1E+02 0.0023 19.2 2.7 22 103-124 19-40 (82)
208 PRK06134 putative FAD-binding 23.6 79 0.0017 27.0 2.8 26 102-127 426-455 (581)
209 smart00796 AHS1 Allophanate hy 23.6 85 0.0018 23.1 2.7 34 12-51 90-123 (201)
210 PRK07843 3-ketosteroid-delta-1 23.4 82 0.0018 26.7 2.9 26 102-127 413-442 (557)
211 PRK12514 RNA polymerase sigma 23.3 1E+02 0.0022 21.4 3.0 22 103-124 143-164 (179)
212 PF07027 DUF1318: Protein of u 23.2 80 0.0017 20.4 2.2 36 106-141 51-87 (95)
213 PRK12537 RNA polymerase sigma 23.1 99 0.0021 21.7 2.9 24 102-125 146-169 (182)
214 PF04921 XAP5: XAP5, circadian 23.1 85 0.0018 24.0 2.6 45 98-142 113-159 (239)
215 PF04539 Sigma70_r3: Sigma-70 23.0 1E+02 0.0022 18.3 2.6 22 23-50 21-42 (78)
216 PF15508 NAAA-beta: beta subun 22.9 1E+02 0.0023 19.5 2.7 23 105-127 69-91 (95)
217 PF09339 HTH_IclR: IclR helix- 22.9 1.1E+02 0.0024 16.8 2.6 19 107-125 20-38 (52)
218 COG1102 Cmk Cytidylate kinase 22.9 87 0.0019 22.8 2.5 25 101-125 28-52 (179)
219 cd04777 HTH_MerR-like_sg1 Heli 22.8 1.1E+02 0.0023 19.8 2.8 20 107-126 2-21 (107)
220 TIGR01321 TrpR trp operon repr 22.7 88 0.0019 20.3 2.3 27 103-129 53-80 (94)
221 PRK12843 putative FAD-binding 22.5 86 0.0019 26.7 2.9 25 103-127 429-457 (578)
222 PF13730 HTH_36: Helix-turn-he 22.5 1.3E+02 0.0028 16.5 2.8 19 107-125 27-45 (55)
223 PRK11924 RNA polymerase sigma 22.4 1.1E+02 0.0024 20.8 3.0 23 103-125 139-161 (179)
224 PF07638 Sigma70_ECF: ECF sigm 22.3 1.1E+02 0.0023 21.8 2.9 22 103-124 149-170 (185)
225 COG5566 Uncharacterized conser 22.3 1.1E+02 0.0024 21.1 2.8 21 105-125 102-122 (137)
226 PRK06481 fumarate reductase fl 21.8 93 0.002 26.0 2.9 25 103-127 376-404 (506)
227 PRK12842 putative succinate de 21.8 87 0.0019 26.6 2.7 26 102-127 423-452 (574)
228 PF14502 HTH_41: Helix-turn-he 21.6 1.4E+02 0.0029 16.9 2.6 18 107-124 8-25 (48)
229 PF01418 HTH_6: Helix-turn-hel 21.6 1.1E+02 0.0024 18.5 2.5 22 105-126 34-55 (77)
230 PF08280 HTH_Mga: M protein tr 21.6 1.1E+02 0.0024 17.5 2.5 19 106-124 20-38 (59)
231 TIGR02008 fdx_plant ferredoxin 21.5 1.1E+02 0.0024 19.4 2.7 24 97-120 14-37 (97)
232 PF08769 Spo0A_C: Sporulation 21.0 90 0.002 20.5 2.2 18 106-123 41-58 (106)
233 PF13413 HTH_25: Helix-turn-he 20.9 1.3E+02 0.0029 17.5 2.7 23 103-125 8-30 (62)
234 PRK05572 sporulation sigma fac 20.8 1.2E+02 0.0027 22.6 3.2 24 103-126 216-239 (252)
235 PRK12835 3-ketosteroid-delta-1 20.5 1E+02 0.0022 26.5 2.9 25 103-127 428-456 (584)
236 PRK09638 RNA polymerase sigma 20.2 1.3E+02 0.0028 20.8 3.0 23 103-125 140-162 (176)
237 TIGR00721 tfx DNA-binding prot 20.2 1.5E+02 0.0032 20.5 3.2 23 103-125 19-41 (137)
238 TIGR02989 Sig-70_gvs1 RNA poly 20.0 1.4E+02 0.003 20.1 3.1 23 103-125 125-147 (159)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.88 E-value=3e-22 Score=166.44 Aligned_cols=115 Identities=23% Similarity=0.340 Sum_probs=92.8
Q ss_pred CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCC
Q 040221 13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEP 92 (142)
Q Consensus 13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (142)
....|.+..||+++.||++| ||++++|++||++..+.|++||.|+||........... . ......
T Consensus 478 ~~~~YtVk~GDTL~sIAkky------gVSv~~L~~~N~l~s~~L~~GQ~L~Ip~~~~~s~~~t~--~-------~s~~~~ 542 (592)
T PRK06347 478 NAKVYTVAKGDSLWRIANNN------KVTIANLKSWNNLKSDFIYPGQKLKVSAGSTTNNTNTA--K-------PSTNKP 542 (592)
T ss_pred cceeeeecCCCCHHHHHHHH------CCCHHHHHHhcCCCcccccCCcEEEEecCccccccccc--C-------CccCCc
Confidence 34578999999999999999 99999999999998888999999999976422110000 0 000111
Q ss_pred CCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 93 EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 93 ~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
......+|+|++|||||.||++||+++++|++||+|..+.|++||.|.|+
T Consensus 543 ~~~~~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 543 SNSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK 592 (592)
T ss_pred cCccceeeecCCCCcHHHHHHHhCCCHHHHHHhcCCCcccCCCCCEEecC
Confidence 12346789999999999999999999999999999998889999999986
No 2
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.84 E-value=2.7e-20 Score=151.51 Aligned_cols=106 Identities=16% Similarity=0.224 Sum_probs=89.7
Q ss_pred CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCC
Q 040221 13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEP 92 (142)
Q Consensus 13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (142)
....|.++.||+++.||++| |+++.+|++||++..+.|.+||.|+||..+.... ..
T Consensus 342 ~~~~y~Vk~GDTL~sIA~r~------gvs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~~~~~------------------~~ 397 (456)
T PRK10783 342 NSRSYKVRSGDTLSGIASRL------NVSTKDLQQWNNLRGSKLKVGQTLTIGAGSSAQR------------------LA 397 (456)
T ss_pred CceEEEECCCCcHHHHHHHH------CcCHHHHHHHcCCCcccCCCCCEEEecCCccccc------------------cc
Confidence 34568899999999999999 9999999999999778899999999997542200 01
Q ss_pred CCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 93 EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 93 ~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
......+|+|++||||++||++|||++++|++||++..+.|++||+|.|+
T Consensus 398 ~~~~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~~L~pGq~L~l~ 447 (456)
T PRK10783 398 NNSDSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAKNLQPGDKLTLF 447 (456)
T ss_pred ccccceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCCcCCCCCEEEEe
Confidence 12345689999999999999999999999999999866699999999874
No 3
>PRK06347 autolysin; Reviewed
Probab=99.83 E-value=7.2e-20 Score=152.33 Aligned_cols=120 Identities=20% Similarity=0.307 Sum_probs=91.2
Q ss_pred CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCCC
Q 040221 14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPE 93 (142)
Q Consensus 14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (142)
...|.+..||+++.||++| ||++.+|++||++..+.|.+|+.|+||....... ......... . ........
T Consensus 405 ~~~ytVk~GDTL~sIA~ky------gVSv~~L~~~N~l~s~~L~~Gq~L~IP~~~~~~~-~t~~~s~~~-~-~~k~~s~~ 475 (592)
T PRK06347 405 AKVYTVVKGDSLWRIANNN------KVTIANLKSWNNLKSDFIYPGQKLKVSAGSTSNT-NTSKPSTNT-N-TSKPSTNT 475 (592)
T ss_pred ceeEEecCCCCHHHHHHHh------CCCHHHHHHHhCCCcceeccCcEEEEecCCcccc-ccccccccc-c-cccccccc
Confidence 4578899999999999999 9999999999999878899999999997532100 000000000 0 00000011
Q ss_pred CCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 94 PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 94 ~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
......|+|++|||||+||++||+++++|++||++..+.|++||.|.||
T Consensus 476 ~~~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s~~L~~GQ~L~Ip 524 (592)
T PRK06347 476 NTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQKLKVS 524 (592)
T ss_pred cccceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCcccccCCcEEEEe
Confidence 2335689999999999999999999999999999988889999999997
No 4
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.74 E-value=2.7e-17 Score=133.25 Aligned_cols=122 Identities=25% Similarity=0.343 Sum_probs=89.9
Q ss_pred ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCC---------------CC-----
Q 040221 15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQ---------------PP----- 74 (142)
Q Consensus 15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~---------------~~----- 74 (142)
.++.++.||+++.||++| |+++++|+++|++..+.|.+||.|.||....... .+
T Consensus 28 ~tytVq~GDTLw~IA~~y------gvtv~~I~~~N~l~~~~I~~Gq~L~Ip~~~~~~~~~~~Vta~~LNVRsgps~s~~I 101 (481)
T PRK13914 28 STVVVEAGDTLWGIAQSK------GTTVDAIKKANNLTTDKIVPGQKLQVNEVAAAEKTEKSVSATWLNVRSGAGVDNSI 101 (481)
T ss_pred ceEEECCCCCHHHHHHHH------CCCHHHHHHHhCCCcccccCCCEEEeCCCCcccccceeEecceEEEecCCCCCcce
Confidence 357899999999999999 9999999999999888999999999994321000 00
Q ss_pred --------------------------------------------CCCCc---cC-----CCC----ccc-----------
Q 040221 75 --------------------------------------------PQQPI---VT-----KPS----ICT----------- 87 (142)
Q Consensus 75 --------------------------------------------~~~~~---~~-----~~~----~~~----------- 87 (142)
.++.. .. ++. +..
T Consensus 102 Igsl~~G~~V~Vl~~~~ngW~kI~~~~GktGwV~~~YLs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 181 (481)
T PRK13914 102 ITSIKGGTKVTVETTESNGWHKITYNDGKTGFVNGKYLTDKVTSTPVAPTQEVKKETTTQQAAPAAETKTEVKQTTQATT 181 (481)
T ss_pred eeeecCCCEEEEeecccCCeEEEEcCCCCEEEEecccccCCCccCccccchhhhhccccccccchhcccchhccCCcccC
Confidence 00000 00 000 000
Q ss_pred -C----CCC---CCCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 88 -E----KSE---PEPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 88 -~----~~~---~~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
+ ... ........|+|++|||||.||++|++++++|++||++....|++||.|.||
T Consensus 182 ~~~~~~~~~~~~~~~~~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s~~L~pGQ~L~Ip 244 (481)
T PRK13914 182 PAPKVAETKETPVVDQNATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAIK 244 (481)
T ss_pred CcccccccccCccccCCCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCccccCCCCEEEec
Confidence 0 000 012346789999999999999999999999999999988889999999997
No 5
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.59 E-value=9.6e-15 Score=99.70 Aligned_cols=107 Identities=29% Similarity=0.427 Sum_probs=77.6
Q ss_pred HHHHhcccccCCCCHHHHHHhCCCC--CCCCCCCCcEEecCCCCCCCCCC--CCCccCCCCcccCCCCCCCCCceEEEec
Q 040221 28 VAKTAGFVVFSGIAISILKALNPLN--KNRNETTQPQPIAESTQPIQPPP--QQPIVTKPSICTEKSEPEPASCRTVEIV 103 (142)
Q Consensus 28 iA~~~~~~~~~gvs~~~L~~~N~l~--~~~l~~Gq~l~vp~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~y~V~ 103 (142)
||.+| ++++..|+++|.+. .+.+.+|+.+.++.......... ......+.. ............+|+|+
T Consensus 1 ia~~~------~~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~V~ 72 (124)
T COG1388 1 IASKY------GVSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVS--DSSSASKAPPVVTYTVK 72 (124)
T ss_pred Ccccc------cccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceee--ccccccccCCCceEEEe
Confidence 56788 99999999999998 67899999999997421100000 000000000 00001112345789999
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 104 RGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
+||+|+.||++|++++.+|+++|.+..+.+++||.|.+|
T Consensus 73 ~gdtL~~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~ 111 (124)
T COG1388 73 KGDTLSKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLP 111 (124)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHhccCCCceecCcEEEEe
Confidence 999999999999999999999999999999999999875
No 6
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=99.58 E-value=1.3e-15 Score=85.93 Aligned_cols=43 Identities=40% Similarity=0.874 Sum_probs=37.2
Q ss_pred EEecCCCcHHHHHHHhCCCHHHHHHHh-CCCCCCCCCCCEEecC
Q 040221 100 VEIVRGDTLWGLSRKYGVSIDAIKEAN-GLSGDTIYAGKKLIIP 142 (142)
Q Consensus 100 y~V~~GDTl~~IA~rygvs~~~L~~~N-~l~~~~l~~Gq~L~IP 142 (142)
|+|++||||++||++|++++++|++|| ++....|.+||.|+||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 899999999999999999999999999 8888669999999998
No 7
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.52 E-value=1e-13 Score=113.22 Aligned_cols=117 Identities=23% Similarity=0.302 Sum_probs=79.9
Q ss_pred CCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCC-CC-CcEEecCCCCCC-CCCCC-CCccCCCCcccCCCCC
Q 040221 18 DGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNE-TT-QPQPIAESTQPI-QPPPQ-QPIVTKPSICTEKSEP 92 (142)
Q Consensus 18 ~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~-~G-q~l~vp~~~~~~-~~~~~-~~~~~~~~~~~~~~~~ 92 (142)
...++.++..||+++ |+++++|.++|+... ..+. .| +.|+||...... ..... ........ ......
T Consensus 267 ~v~~~i~L~~iA~~~------gvs~~eL~~LNP~~kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p--~~~~~~ 338 (456)
T PRK10783 267 DLGQQIELAQAAEMA------GMSLTKLKTFNAGYKRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQS--TLVADN 338 (456)
T ss_pred ecCCCcCHHHHHHHc------CCCHHHHHHhCccccCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhccc--cccccc
Confidence 344566899999999 999999999998533 3222 33 677888753210 00000 00000000 000001
Q ss_pred CCCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 93 EPASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 93 ~~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
......+|+|++||||++||++||+++.+|++||++..+.|++||.|+||
T Consensus 339 ~~~~~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~~~L~~Gq~L~Ip 388 (456)
T PRK10783 339 TPLNSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTIG 388 (456)
T ss_pred CcCCceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCcccCCCCCEEEec
Confidence 12346789999999999999999999999999999888889999999987
No 8
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.35 E-value=2.8e-12 Score=85.06 Aligned_cols=48 Identities=35% Similarity=0.684 Sum_probs=43.2
Q ss_pred CCceEEEecCCCcHHHHHHHhCCC--------HHHHHHHhCCCCCCCCCCCEEecC
Q 040221 95 ASCRTVEIVRGDTLWGLSRKYGVS--------IDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 95 ~~~~~y~V~~GDTl~~IA~rygvs--------~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
..+..|+|++|||||+||++|+++ +..|++.|++.++.|++||.|+||
T Consensus 34 ~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP 89 (103)
T PRK14125 34 NQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIP 89 (103)
T ss_pred CCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEe
Confidence 467789999999999999999765 577888899999889999999998
No 9
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=99.27 E-value=9.4e-12 Score=69.45 Aligned_cols=41 Identities=49% Similarity=0.945 Sum_probs=37.6
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHhC-CCC-CCCCCCCEEecC
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEANG-LSG-DTIYAGKKLIIP 142 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N~-l~~-~~l~~Gq~L~IP 142 (142)
|++|||||+||++|++++.+|+++|+ +.+ ..+.+||.|.||
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip 43 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIP 43 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecC
Confidence 58999999999999999999999996 655 789999999998
No 10
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=99.27 E-value=1.9e-11 Score=67.62 Aligned_cols=44 Identities=41% Similarity=0.776 Sum_probs=41.5
Q ss_pred EEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221 99 TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP 142 (142)
Q Consensus 99 ~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP 142 (142)
+|+|++|||+++||++|+++..+|+++|+... ..+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 69999999999999999999999999999855 889999999998
No 11
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=99.26 E-value=1.2e-11 Score=96.10 Aligned_cols=49 Identities=24% Similarity=0.396 Sum_probs=46.6
Q ss_pred CCCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 94 PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 94 ~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
...|.+|+|++|||||.||+|||+++.+|++||++..+.|++||.|+||
T Consensus 290 ~~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 290 FTKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred ccccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 3678999999999999999999999999999999988899999999998
No 12
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=99.19 E-value=2.7e-11 Score=94.52 Aligned_cols=46 Identities=20% Similarity=0.345 Sum_probs=43.7
Q ss_pred ceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221 97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP 142 (142)
Q Consensus 97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP 142 (142)
..+|+|++|||||.||.+||+++.+|.+||+|.+ ..|++||+|+||
T Consensus 60 ~~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~ 106 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVG 106 (319)
T ss_pred CCceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeC
Confidence 4689999999999999999999999999999988 899999999986
No 13
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.10 E-value=1.6e-10 Score=94.10 Aligned_cols=47 Identities=47% Similarity=0.783 Sum_probs=44.3
Q ss_pred CceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCCCCCCCCCEEecC
Q 040221 96 SCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSGDTIYAGKKLIIP 142 (142)
Q Consensus 96 ~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~~~l~~Gq~L~IP 142 (142)
.+..|+|++|||||.||++||+++++|+++|+|..+.|++||.|+||
T Consensus 26 sa~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~~~I~~Gq~L~Ip 72 (481)
T PRK13914 26 SASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKIVPGQKLQVN 72 (481)
T ss_pred cCceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCcccccCCCEEEeC
Confidence 44579999999999999999999999999999988899999999997
No 14
>smart00257 LysM Lysin motif.
Probab=98.97 E-value=2e-09 Score=58.56 Aligned_cols=43 Identities=37% Similarity=0.669 Sum_probs=38.9
Q ss_pred EEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEec
Q 040221 99 TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLII 141 (142)
Q Consensus 99 ~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~I 141 (142)
+|+|++|||+++||++|+++..+|.++|+... ..+++|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 48899999999999999999999999998544 88999999875
No 15
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=98.97 E-value=2.7e-10 Score=63.86 Aligned_cols=43 Identities=21% Similarity=0.188 Sum_probs=34.9
Q ss_pred CCCCCCCCHHHHHHHhcccccCCCCHHHHHHhC-CCCCCCCCCCCcEEec
Q 040221 17 NDGSGDGREAAVAKTAGFVVFSGIAISILKALN-PLNKNRNETTQPQPIA 65 (142)
Q Consensus 17 ~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N-~l~~~~l~~Gq~l~vp 65 (142)
|++..|||++.||++| |+++++|+++| ++....|.+||.|+||
T Consensus 1 y~V~~gDtl~~IA~~~------~~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRY------GISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHT------TS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhh------hhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 4567899999999999 99999999999 6766569999999998
No 16
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.88 E-value=4.6e-09 Score=73.92 Aligned_cols=47 Identities=36% Similarity=0.488 Sum_probs=41.8
Q ss_pred CceEEEecCCCcHHHHHHHhC---CCHHHHHHHhC--CCC-CCCCCCCEEecC
Q 040221 96 SCRTVEIVRGDTLWGLSRKYG---VSIDAIKEANG--LSG-DTIYAGKKLIIP 142 (142)
Q Consensus 96 ~~~~y~V~~GDTl~~IA~ryg---vs~~~L~~~N~--l~~-~~l~~Gq~L~IP 142 (142)
...+|+|++|||||+||++|+ ..+.+|+++|+ +.+ +.|++||+|.||
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 567899999999999999985 45789999997 777 889999999998
No 17
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.64 E-value=2.8e-08 Score=79.43 Aligned_cols=89 Identities=19% Similarity=0.121 Sum_probs=77.3
Q ss_pred CCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCCCCCCce
Q 040221 19 GSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCR 98 (142)
Q Consensus 19 ~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 98 (142)
+..|+....|+++| +.+...|...|.+.++.+-.||.++||.. ..
T Consensus 6 ~~pg~~~~~i~~~~------~~~~~~i~~~~~~~~d~~~~~q~~~v~~~-----------------------------~~ 50 (423)
T COG3858 6 VGPGDSRLIIAVYF------PYTNNRIVNGNDYTNDDLVDGQTFVVPPS-----------------------------GH 50 (423)
T ss_pred ccCCceeeeehhhc------cccccccccccccccccccCceeEEECCc-----------------------------ce
Confidence 45688899999999 99999997777776678999999999952 45
Q ss_pred EEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221 99 TVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP 142 (142)
Q Consensus 99 ~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP 142 (142)
+|.|++||++++||++++++.+.+..+|.+.. ..+.+|-.|.+|
T Consensus 51 ~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P 95 (423)
T COG3858 51 FYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIP 95 (423)
T ss_pred EEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEecc
Confidence 89999999999999999999999999996554 788888888877
No 18
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.52 E-value=3e-07 Score=60.98 Aligned_cols=52 Identities=13% Similarity=-0.027 Sum_probs=45.5
Q ss_pred CCCCccCCCCCCCCHHHHHHHhcccccCCCC--------HHHHHHhCCCCCCCCCCCCcEEecCCC
Q 040221 11 PRVPAENDGSGDGREAAVAKTAGFVVFSGIA--------ISILKALNPLNKNRNETTQPQPIAEST 68 (142)
Q Consensus 11 ~~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs--------~~~L~~~N~l~~~~l~~Gq~l~vp~~~ 68 (142)
......++++.|||++.||++| +.+ +..|++.|++.++.|.+||.|+||...
T Consensus 33 ~~~~~~~tV~~GDTLW~IA~~y------~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~ 92 (103)
T PRK14125 33 KNQYVEITVQEGDTLWALADQY------AGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLK 92 (103)
T ss_pred CCCcEEEEECCCCCHHHHHHHh------CCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCC
Confidence 4567788999999999999999 765 678889999988889999999999764
No 19
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=98.46 E-value=4.5e-07 Score=50.09 Aligned_cols=41 Identities=22% Similarity=0.166 Sum_probs=35.9
Q ss_pred CCCCCHHHHHHHhcccccCCCCHHHHHHhCC-CCC-CCCCCCCcEEecC
Q 040221 20 SGDGREAAVAKTAGFVVFSGIAISILKALNP-LNK-NRNETTQPQPIAE 66 (142)
Q Consensus 20 ~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~-l~~-~~l~~Gq~l~vp~ 66 (142)
..||+++.||++| |+++.+|.++|+ +.+ ..+.+|+.|.||.
T Consensus 2 ~~gdtl~~IA~~~------~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 2 QKGDTLWKIAKKY------GVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCHHHHHHHH------CcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 4689999999999 999999999997 433 5799999999983
No 20
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=98.46 E-value=3.5e-07 Score=49.97 Aligned_cols=44 Identities=20% Similarity=0.205 Sum_probs=39.0
Q ss_pred cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCC-CCCCCCCCcEEec
Q 040221 16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLN-KNRNETTQPQPIA 65 (142)
Q Consensus 16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~-~~~l~~Gq~l~vp 65 (142)
++....||+++.||++| +++..+|.++|+.. ...+.+|+.++||
T Consensus 2 ~~~v~~gdt~~~ia~~~------~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRY------GISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHH------CcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 35667899999999999 99999999999984 4789999999886
No 21
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=98.25 E-value=1.1e-06 Score=68.63 Aligned_cols=45 Identities=18% Similarity=0.008 Sum_probs=41.7
Q ss_pred ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEec
Q 040221 15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIA 65 (142)
Q Consensus 15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp 65 (142)
..+.++.|||++.||+|| |+++..|+++|++..+.|.+|+.|+||
T Consensus 294 ~~YiVq~GDTL~sIAkRY------GVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 294 RMCIVQEGDTIETIAERY------EISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred EEEEECCCCCHHHHHHHH------CcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 356789999999999999 999999999999987899999999997
No 22
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.24 E-value=1.4e-06 Score=68.24 Aligned_cols=48 Identities=10% Similarity=-0.012 Sum_probs=44.0
Q ss_pred CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCC
Q 040221 14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAES 67 (142)
Q Consensus 14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~ 67 (142)
+.+|++..|||++.||.+| |+++.+|.+||+|.+ +.|.+||.|.||..
T Consensus 60 ~~~y~Vk~GDTL~~IA~~~------g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAWIT------GNDFRDLAQRNNIQAPYSLNVGQTLQVGNA 108 (319)
T ss_pred CCceEECCCCHHHHHHHHH------CcCHHHHHHhcCCCCCccccCCCEEEeCCC
Confidence 5679999999999999999 999999999999966 78999999999754
No 23
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=98.09 E-value=4.4e-06 Score=53.52 Aligned_cols=45 Identities=20% Similarity=0.258 Sum_probs=26.6
Q ss_pred ceEEEecCCCcHHHHHHHhCCCHHHHHHHh----CCCC-CCCCCCCEEec
Q 040221 97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEAN----GLSG-DTIYAGKKLII 141 (142)
Q Consensus 97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N----~l~~-~~l~~Gq~L~I 141 (142)
|..|+|++||||..|-+++|++..++.++= .-.. ..|+|||.|.+
T Consensus 2 W~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f 51 (85)
T PF04225_consen 2 WQEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEF 51 (85)
T ss_dssp --EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEE
T ss_pred CcEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEE
Confidence 789999999999999999999988877763 2234 78999999863
No 24
>smart00257 LysM Lysin motif.
Probab=97.97 E-value=1.9e-05 Score=42.26 Aligned_cols=42 Identities=21% Similarity=0.239 Sum_probs=35.7
Q ss_pred CCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCC-CCCCCCCCCcEEe
Q 040221 17 NDGSGDGREAAVAKTAGFVVFSGIAISILKALNPL-NKNRNETTQPQPI 64 (142)
Q Consensus 17 ~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l-~~~~l~~Gq~l~v 64 (142)
+....||+++.||++| +++..+|.++|+. ....+.+|+.++|
T Consensus 2 ~~v~~gdt~~~ia~~~------~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 2 YTVKKGDTLSSIARRY------GISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred eEeCCCCCHHHHHHHh------CCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 4567899999999999 9999999999995 3467889988764
No 25
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=97.96 E-value=1.1e-05 Score=54.68 Aligned_cols=48 Identities=19% Similarity=0.229 Sum_probs=44.7
Q ss_pred CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCC
Q 040221 14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAES 67 (142)
Q Consensus 14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~ 67 (142)
...|.+..||+++.||++| ++++.+|+++|.+.++.+.+||.|.++..
T Consensus 66 ~~~~~V~~gdtL~~Ia~~~------~~tv~~l~~~n~l~~~~i~~gq~l~~~~~ 113 (124)
T COG1388 66 VVTYTVKKGDTLSKIARKY------GVTVAELKQLNNLSSDKIKVGQKLKLPVS 113 (124)
T ss_pred CceEEEecCCCHHHHHHHh------CCCHHHHHHHhccCCCceecCcEEEEecc
Confidence 4578899999999999999 99999999999999889999999999963
No 26
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.91 E-value=3.9e-06 Score=64.41 Aligned_cols=45 Identities=49% Similarity=0.737 Sum_probs=39.9
Q ss_pred eEEEecCCCcHHHHHHHh-C--CCHHHHHHHhC---CCC-CCCCCCCEEecC
Q 040221 98 RTVEIVRGDTLWGLSRKY-G--VSIDAIKEANG---LSG-DTIYAGKKLIIP 142 (142)
Q Consensus 98 ~~y~V~~GDTl~~IA~ry-g--vs~~~L~~~N~---l~~-~~l~~Gq~L~IP 142 (142)
.+|+|++|||||.||+++ | +.+..|...|+ +.+ +.|++||+|.||
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP 262 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIP 262 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCC
Confidence 489999999999999775 4 56788999998 777 999999999998
No 27
>TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Probab=97.84 E-value=3.6e-05 Score=48.04 Aligned_cols=37 Identities=38% Similarity=0.644 Sum_probs=30.3
Q ss_pred CcHHHHHHHh---C-CCHH----HHHHHhC----CCC-CCCCCCCEEecC
Q 040221 106 DTLWGLSRKY---G-VSID----AIKEANG----LSG-DTIYAGKKLIIP 142 (142)
Q Consensus 106 DTl~~IA~ry---g-vs~~----~L~~~N~----l~~-~~l~~Gq~L~IP 142 (142)
||||+||++| + +++. .|.+.|. -.+ +.|++|+.|.||
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP 50 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIP 50 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCC
Confidence 8999999999 3 6765 6778883 234 889999999998
No 28
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=97.59 E-value=0.00011 Score=51.62 Aligned_cols=51 Identities=16% Similarity=0.008 Sum_probs=41.0
Q ss_pred CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCC--CCC-CCCCCCCcEEecC
Q 040221 13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP--LNK-NRNETTQPQPIAE 66 (142)
Q Consensus 13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~--l~~-~~l~~Gq~l~vp~ 66 (142)
...+|....||+++.||++| +..+..+..|.++|+ +.+ +.|.+||.|.||.
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~---~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP~ 147 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKV---YGNANKYNKIFEANKPMLKSPDKIYPGQVLRIPE 147 (147)
T ss_pred CCeEEEECCCCCHHHHHHHH---cCChhhHHHHHHhhhhcCCCcCCcCcCCEEecCC
Confidence 34678899999999999998 112256889999998 655 6899999999983
No 29
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.48 E-value=0.00034 Score=54.68 Aligned_cols=48 Identities=25% Similarity=0.304 Sum_probs=40.8
Q ss_pred CCceEEEecCCC--cHHHHHHHhCCCHHHHHHHhC-CCCCCCCCCCEEecC
Q 040221 95 ASCRTVEIVRGD--TLWGLSRKYGVSIDAIKEANG-LSGDTIYAGKKLIIP 142 (142)
Q Consensus 95 ~~~~~y~V~~GD--Tl~~IA~rygvs~~~L~~~N~-l~~~~l~~Gq~L~IP 142 (142)
.....|+|+.+| +|.+||++|++....|.++|. +.....++|++|.||
T Consensus 35 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP 85 (310)
T PRK10190 35 GQSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIP 85 (310)
T ss_pred cceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEec
Confidence 456789999966 699999999999999999995 444567899999998
No 30
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.48 E-value=0.00037 Score=54.40 Aligned_cols=48 Identities=23% Similarity=0.310 Sum_probs=40.8
Q ss_pred CCceEEEecCCC--cHHHHHHHhCCCHHHHHHHhC-CCCCCCCCCCEEecC
Q 040221 95 ASCRTVEIVRGD--TLWGLSRKYGVSIDAIKEANG-LSGDTIYAGKKLIIP 142 (142)
Q Consensus 95 ~~~~~y~V~~GD--Tl~~IA~rygvs~~~L~~~N~-l~~~~l~~Gq~L~IP 142 (142)
.....|+|++|+ +|..||++|++....|+++|. +.....++|++|.||
T Consensus 38 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP 88 (306)
T PRK10260 38 GQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIP 88 (306)
T ss_pred cccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeC
Confidence 456689999966 599999999999999999995 444667899999997
No 31
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=96.82 E-value=0.0038 Score=37.31 Aligned_cols=40 Identities=40% Similarity=0.677 Sum_probs=32.1
Q ss_pred cCCCcHHHHHHH-hCCC---HHHHHHHh-CCCC--CCCCCCCEEecC
Q 040221 103 VRGDTLWGLSRK-YGVS---IDAIKEAN-GLSG--DTIYAGKKLIIP 142 (142)
Q Consensus 103 ~~GDTl~~IA~r-ygvs---~~~L~~~N-~l~~--~~l~~Gq~L~IP 142 (142)
+.||+|..|+.| ||-. ++++.+.| +|.. ..|..|..|.||
T Consensus 6 ~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP 52 (60)
T PF05489_consen 6 TQGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILP 52 (60)
T ss_pred eCcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECC
Confidence 499999999955 5654 37889999 6665 468899999998
No 32
>PRK11649 putative peptidase; Provisional
Probab=96.74 E-value=0.0035 Score=51.53 Aligned_cols=48 Identities=21% Similarity=0.338 Sum_probs=40.4
Q ss_pred CCCceEEEecCCCcHHHHHHHhCCCHHHHHHHh-CCCC-CCCCCCCEEec
Q 040221 94 PASCRTVEIVRGDTLWGLSRKYGVSIDAIKEAN-GLSG-DTIYAGKKLII 141 (142)
Q Consensus 94 ~~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N-~l~~-~~l~~Gq~L~I 141 (142)
...|..|+|++||||.+|=+++|++..++.++- ...+ ..|++||.|.+
T Consensus 92 ~~~~~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~ 141 (439)
T PRK11649 92 EAGVHEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSW 141 (439)
T ss_pred CCceEEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEE
Confidence 356789999999999999999999999988873 3344 78999999864
No 33
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=96.69 E-value=0.0019 Score=55.28 Aligned_cols=49 Identities=31% Similarity=0.520 Sum_probs=39.1
Q ss_pred CCCceEEEecCCCcHHHHHHHh----CCCH----HHHHHHhC--C--CC-CCCCCCCEEecC
Q 040221 94 PASCRTVEIVRGDTLWGLSRKY----GVSI----DAIKEANG--L--SG-DTIYAGKKLIIP 142 (142)
Q Consensus 94 ~~~~~~y~V~~GDTl~~IA~ry----gvs~----~~L~~~N~--l--~~-~~l~~Gq~L~IP 142 (142)
.....+|+|++|||||+||.+. ++++ ..|++.|. + .+ ++|+.|++|.||
T Consensus 185 ~a~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP 246 (755)
T COG3170 185 AAPGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIP 246 (755)
T ss_pred CCCCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeecc
Confidence 3667899999999999999887 3554 45788883 2 23 689999999998
No 34
>TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Probab=95.90 E-value=0.019 Score=35.69 Aligned_cols=43 Identities=19% Similarity=0.117 Sum_probs=32.9
Q ss_pred CCHHHHHHHhcccccCCCCHH----HHHHhCCC---C-C-CCCCCCCcEEecCC
Q 040221 23 GREAAVAKTAGFVVFSGIAIS----ILKALNPL---N-K-NRNETTQPQPIAES 67 (142)
Q Consensus 23 ~~~~~iA~~~~~~~~~gvs~~----~L~~~N~l---~-~-~~l~~Gq~l~vp~~ 67 (142)
||++.||+++ .....+++. .|.+.|+- . + +.|+.|+.|.||..
T Consensus 1 DTLw~IA~~~--~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~ 52 (74)
T TIGR03505 1 DTLWGIAQRV--RPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE 52 (74)
T ss_pred CcHHHHHHHH--ccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence 7999999999 233337777 66788873 2 2 68999999999974
No 35
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=95.86 E-value=0.039 Score=41.13 Aligned_cols=47 Identities=21% Similarity=0.337 Sum_probs=40.4
Q ss_pred CCceEEEecCCCcHHHHHHHhCCCHHHHHHHhCC---CC--CCCCCCCEEec
Q 040221 95 ASCRTVEIVRGDTLWGLSRKYGVSIDAIKEANGL---SG--DTIYAGKKLII 141 (142)
Q Consensus 95 ~~~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l---~~--~~l~~Gq~L~I 141 (142)
..|.+|+|..|+||..+=+.+++.+.++..+-.. .. +.|+.||.+.|
T Consensus 157 g~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki 208 (242)
T COG3061 157 GNWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKI 208 (242)
T ss_pred ccceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEE
Confidence 4899999999999999999999999998888743 22 67999999876
No 36
>PRK10190 L,D-transpeptidase; Provisional
Probab=95.70 E-value=0.019 Score=45.10 Aligned_cols=47 Identities=13% Similarity=0.041 Sum_probs=38.4
Q ss_pred ccCCCCCCC--CHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCC
Q 040221 15 AENDGSGDG--REAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAES 67 (142)
Q Consensus 15 ~~~~~~~~~--~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~ 67 (142)
.++...++| .+..||++| ++...+|+++|+-.+ ...++|+.|.||..
T Consensus 38 ~~~~v~~~~~~~le~iA~~f------~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 38 LTVTVPDHNTQPLETFAAQY------GQGLSNMLEANPGADVFLPKSGSQLTIPQQ 87 (310)
T ss_pred EEEEecCCCCccHHHHHHHh------CCCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence 345566655 599999999 999999999999755 45679999999974
No 37
>PRK10260 L,D-transpeptidase; Provisional
Probab=95.40 E-value=0.03 Score=43.90 Aligned_cols=47 Identities=11% Similarity=-0.075 Sum_probs=38.5
Q ss_pred ccCCCCCCC--CHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCC
Q 040221 15 AENDGSGDG--REAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAES 67 (142)
Q Consensus 15 ~~~~~~~~~--~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~ 67 (142)
.+++..+++ ++..||++| ++....|+++|+..+ ...+.|+.|.||..
T Consensus 41 ~~~~v~~~~~~~le~iA~~f------~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 41 QVITIPEGNTQPLEYFAAEY------QMGLSNMMEANPGVDTFLPKGGTVLNIPQQ 90 (306)
T ss_pred EEEEeCCCCCchHHHHHHHh------CCCHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence 455666655 599999999 999999999999655 45679999999974
No 38
>PRK11649 putative peptidase; Provisional
Probab=93.93 E-value=0.47 Score=39.14 Aligned_cols=120 Identities=13% Similarity=0.076 Sum_probs=70.5
Q ss_pred cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCC-CC-CCCCCCCcEEecCCCCC-CC-CCCCCCccC------CCCc
Q 040221 16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPL-NK-NRNETTQPQPIAESTQP-IQ-PPPQQPIVT------KPSI 85 (142)
Q Consensus 16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l-~~-~~l~~Gq~l~vp~~~~~-~~-~~~~~~~~~------~~~~ 85 (142)
++..+.|||++.|=+++ |++..++.++-.. .+ ..|++||.+.+-..... .. ..+...... ....
T Consensus 97 ~~~Vk~GDTl~~iL~r~------Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg~ 170 (439)
T PRK11649 97 EYVVSTGDTLSSILNQY------GIDMSDISQLAAQDKELRNLKIGQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGNG 170 (439)
T ss_pred EEEeCCCCCHHHHHHHc------CCCHHHHHHHHHcChHhhcCCCCCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCCc
Confidence 67889999999999999 9999999877332 22 58999999988644321 10 001100000 0000
Q ss_pred ccCCCCCCCCCceEE--EecCCCcHHHHHHHhCCCHHHHHHHhC-----CCCCCCCCCCEEec
Q 040221 86 CTEKSEPEPASCRTV--EIVRGDTLWGLSRKYGVSIDAIKEANG-----LSGDTIYAGKKLII 141 (142)
Q Consensus 86 ~~~~~~~~~~~~~~y--~V~~GDTl~~IA~rygvs~~~L~~~N~-----l~~~~l~~Gq~L~I 141 (142)
+..........+... ...-..+|+.-|.+-|++...+.++.. +.-..|+.|++..|
T Consensus 171 F~~~~~~~~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~~~~~~idf~~lr~GD~f~v 233 (439)
T PRK11649 171 FKETSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSV 233 (439)
T ss_pred EEEEEeecccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHHHhccCcChhhCCCCCEEEE
Confidence 110001111111111 112247999999999999877776653 22255899988654
No 39
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=93.81 E-value=0.057 Score=34.44 Aligned_cols=47 Identities=17% Similarity=0.076 Sum_probs=28.1
Q ss_pred cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCC---C--CCCCCCCCCcEEecCCC
Q 040221 16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP---L--NKNRNETTQPQPIAEST 68 (142)
Q Consensus 16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~---l--~~~~l~~Gq~l~vp~~~ 68 (142)
+++++.||+++.|-+++ |++..++.++=. . .-..|++||.|.+-...
T Consensus 4 ~~~V~~GDtLs~iF~~~------gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 4 EYTVKSGDTLSTIFRRA------GLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp EEE--TT--HHHHHHHT------T--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-T
T ss_pred EEEECCCCcHHHHHHHc------CCCHHHHHHHHhccCccchHhhCCCCCEEEEEECC
Confidence 56788999999999999 999998865432 2 22689999999988653
No 40
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=93.36 E-value=0.16 Score=40.62 Aligned_cols=48 Identities=29% Similarity=0.479 Sum_probs=39.3
Q ss_pred CCCceEEEecCCCcHHHHHHHh-CCC--HHHHHHHhCCCC-CCCCCCCEEec
Q 040221 94 PASCRTVEIVRGDTLWGLSRKY-GVS--IDAIKEANGLSG-DTIYAGKKLII 141 (142)
Q Consensus 94 ~~~~~~y~V~~GDTl~~IA~ry-gvs--~~~L~~~N~l~~-~~l~~Gq~L~I 141 (142)
+-.....+|++|||+.++|.+. |++ ++-++-+|.+.. ..+++|+.++|
T Consensus 425 PlrirvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi 476 (479)
T COG4784 425 PLRIRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI 476 (479)
T ss_pred ceEEEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence 4455667899999999999776 544 667888899988 89999999986
No 41
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=92.71 E-value=0.033 Score=42.75 Aligned_cols=50 Identities=14% Similarity=0.131 Sum_probs=44.5
Q ss_pred cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCC---CCC-CCCCCCCcEEecCCC
Q 040221 16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP---LNK-NRNETTQPQPIAEST 68 (142)
Q Consensus 16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~---l~~-~~l~~Gq~l~vp~~~ 68 (142)
.|++..|||++.|++++ |..++-+..|..+|+ +.+ +.|.+||.+.||...
T Consensus 212 ~~~v~rgDTl~~is~~~---Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~~ 265 (269)
T COG1652 212 TNTVKRGDTLWQISKKV---YGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQL 265 (269)
T ss_pred EEEeccCCcccccchhh---cCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCcc
Confidence 68899999999999999 888999999999999 544 799999999999753
No 42
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=92.58 E-value=0.08 Score=38.63 Aligned_cols=46 Identities=28% Similarity=0.357 Sum_probs=35.9
Q ss_pred ceEEEecCCCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221 97 CRTVEIVRGDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLIIP 142 (142)
Q Consensus 97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~IP 142 (142)
...-+++.||||..||-+|...+.+|++.|++.. ..+.+-+.+.+|
T Consensus 9 ~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~p 55 (186)
T KOG2850|consen 9 ELEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIP 55 (186)
T ss_pred heeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecc
Confidence 3457899999999999999999999999997655 555544444443
No 43
>PF13518 HTH_28: Helix-turn-helix domain
Probab=91.72 E-value=0.2 Score=28.10 Aligned_cols=24 Identities=17% Similarity=0.458 Sum_probs=21.5
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
..|.|+..+|++||++...+..|-
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 368899999999999999999885
No 44
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=90.34 E-value=0.36 Score=26.74 Aligned_cols=23 Identities=17% Similarity=0.397 Sum_probs=18.1
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|-+..+||+.||++...|+++
T Consensus 19 ~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HTT--HHHHHHHTTS-HHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 57889999999999999999875
No 45
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=89.10 E-value=0.24 Score=30.17 Aligned_cols=25 Identities=20% Similarity=0.461 Sum_probs=21.7
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
...|.|+..||++||++...|..|=
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHH
Confidence 3678999999999999999999994
No 46
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=87.93 E-value=1.1 Score=26.52 Aligned_cols=44 Identities=9% Similarity=0.002 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHhcccccCCCC--HHHHHHhCCC-CC--CCCCCCCcEEecCCC
Q 040221 21 GDGREAAVAKTAGFVVFSGIA--ISILKALNPL-NK--NRNETTQPQPIAEST 68 (142)
Q Consensus 21 ~~~~~~~iA~~~~~~~~~gvs--~~~L~~~N~l-~~--~~l~~Gq~l~vp~~~ 68 (142)
+|||+..||-|+ ++... ++.+.++|+- .. ..|..|..|.+|...
T Consensus 7 ~GDtlD~I~~r~----yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i~ 55 (60)
T PF05489_consen 7 QGDTLDLIAYRH----YGREDGAVEALLEANPGLADTGPVLPAGTVIILPDIP 55 (60)
T ss_pred CcCcHHHHHHHH----hCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCCC
Confidence 799999999998 33332 3788999984 22 478999999999654
No 47
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=85.89 E-value=1.1 Score=24.93 Aligned_cols=24 Identities=17% Similarity=0.237 Sum_probs=18.6
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
..|.|...||+.+|++...+.+|=
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w~ 38 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRWI 38 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHH
Confidence 349999999999999999999884
No 48
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.48 E-value=0.93 Score=35.50 Aligned_cols=45 Identities=31% Similarity=0.235 Sum_probs=38.3
Q ss_pred eEEEecCCCcHHHHHHHhC---CCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221 98 RTVEIVRGDTLWGLSRKYG---VSIDAIKEANGLSG-DTIYAGKKLIIP 142 (142)
Q Consensus 98 ~~y~V~~GDTl~~IA~ryg---vs~~~L~~~N~l~~-~~l~~Gq~L~IP 142 (142)
.+|+|+.||||-.++..|= -.+..++..|.+.+ ..+++|..|.||
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip 54 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIP 54 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCC
Confidence 6899999999999999994 33566778898888 889999999887
No 49
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=83.77 E-value=0.52 Score=27.16 Aligned_cols=24 Identities=21% Similarity=0.509 Sum_probs=17.6
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
+..|.+..+||+.||++..++..|
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 467889999999999998887765
No 50
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=83.07 E-value=1.5 Score=29.48 Aligned_cols=25 Identities=20% Similarity=0.126 Sum_probs=22.9
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
+..|.++..||++||++...|..|=
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 5678999999999999999999994
No 51
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.21 E-value=1.8 Score=28.59 Aligned_cols=25 Identities=24% Similarity=0.464 Sum_probs=21.5
Q ss_pred ecCCCcHHHHHHHhCC-CHHHHHHHh
Q 040221 102 IVRGDTLWGLSRKYGV-SIDAIKEAN 126 (142)
Q Consensus 102 V~~GDTl~~IA~rygv-s~~~L~~~N 126 (142)
.+.|.|+..||++||+ +...|..|=
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHHH
Confidence 4678999999999995 999999773
No 52
>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=80.33 E-value=3.1 Score=20.19 Aligned_cols=23 Identities=22% Similarity=0.419 Sum_probs=19.9
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|.++..||+.||++...+..|
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 46789999999999999988765
No 53
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=80.16 E-value=2.6 Score=23.13 Aligned_cols=24 Identities=13% Similarity=0.367 Sum_probs=15.8
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.+.|-++..||+++|.+...+.++
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHH
Confidence 368999999999999999887653
No 54
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=80.16 E-value=6.5 Score=23.72 Aligned_cols=45 Identities=31% Similarity=0.471 Sum_probs=32.8
Q ss_pred eEEEecCCCcHHHHHHHh-CCC---HHHHHHHh-CCCC--CCCCCCCEEecC
Q 040221 98 RTVEIVRGDTLWGLSRKY-GVS---IDAIKEAN-GLSG--DTIYAGKKLIIP 142 (142)
Q Consensus 98 ~~y~V~~GDTl~~IA~ry-gvs---~~~L~~~N-~l~~--~~l~~Gq~L~IP 142 (142)
..++...|||+..|+.|+ |-+ .+++.+.| +|.+ ..|..|-.|.+|
T Consensus 3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lP 54 (70)
T COG5004 3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLP 54 (70)
T ss_pred eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecC
Confidence 356677899999999665 533 46777888 7776 557777777665
No 55
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=78.25 E-value=2.5 Score=23.45 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=16.8
Q ss_pred cCC-CcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRG-DTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~G-DTl~~IA~rygvs~~~L~~~ 125 (142)
+.| -++...|+.|||+...|...
T Consensus 13 ~~g~~S~r~AA~~ygVp~sTL~~r 36 (45)
T PF05225_consen 13 KNGKMSIRKAAKKYGVPRSTLRRR 36 (45)
T ss_dssp HTTSS-HHHHHHHHT--HHHHHHH
T ss_pred HhCCCCHHHHHHHHCcCHHHHHHH
Confidence 345 89999999999999999865
No 56
>PHA00675 hypothetical protein
Probab=78.09 E-value=3.2 Score=25.93 Aligned_cols=24 Identities=29% Similarity=0.256 Sum_probs=21.3
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
+.|.+.+.||++||++...+...=
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHH
Confidence 689999999999999998888763
No 57
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model 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 model 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 (pfam00376).
Probab=78.07 E-value=4.3 Score=21.81 Aligned_cols=35 Identities=20% Similarity=0.141 Sum_probs=23.7
Q ss_pred cHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEec
Q 040221 107 TLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLII 141 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~I 141 (142)
|+.++|+.+|++...|.+|-+-.. ...+.|...++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~ 38 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEGELPAYRVGRHYRI 38 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcCCCCeEEeCCeEEE
Confidence 577899999999999999863322 22333555443
No 58
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=77.89 E-value=3.1 Score=24.75 Aligned_cols=23 Identities=26% Similarity=0.283 Sum_probs=20.2
Q ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Q 040221 105 GDTLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~N~ 127 (142)
+=+|-+||.++|++..+|..|-.
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhh
Confidence 45889999999999999999963
No 59
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=77.59 E-value=5.1 Score=23.13 Aligned_cols=27 Identities=19% Similarity=0.063 Sum_probs=24.1
Q ss_pred ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHH
Q 040221 15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKA 47 (142)
Q Consensus 15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~ 47 (142)
.|++.+++-++.+||+.+ ||+-+.+.+
T Consensus 16 GYfd~PR~~tl~elA~~l------gis~st~~~ 42 (53)
T PF04967_consen 16 GYFDVPRRITLEELAEEL------GISKSTVSE 42 (53)
T ss_pred CCCCCCCcCCHHHHHHHh------CCCHHHHHH
Confidence 588999999999999999 999888753
No 60
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=75.22 E-value=6.9 Score=34.28 Aligned_cols=56 Identities=13% Similarity=0.045 Sum_probs=42.5
Q ss_pred CCCCccCCCCCCCCHHHHHHHhcccccCCCCHHHH----HHhCCC--CC---CCCCCCCcEEecCCC
Q 040221 11 PRVPAENDGSGDGREAAVAKTAGFVVFSGIAISIL----KALNPL--NK---NRNETTQPQPIAEST 68 (142)
Q Consensus 11 ~~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L----~~~N~l--~~---~~l~~Gq~l~vp~~~ 68 (142)
+-++-.|+.+.+||+|.||.+. .=..++++++. -++|+- .+ +.|+.|+.|.||...
T Consensus 185 ~a~g~tyt~~~~Dtl~dIAs~~--rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~~ 249 (755)
T COG3170 185 AAPGDTYTVRSGDTLWDIASRL--RPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSAA 249 (755)
T ss_pred CCCCcccccCCcchHHHHHHhh--cCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccchh
Confidence 4456678999999999999998 22466777665 478874 22 589999999999753
No 61
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.73 E-value=5.9 Score=21.94 Aligned_cols=23 Identities=22% Similarity=0.400 Sum_probs=19.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-|+.+||+.+|++...+..+
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 56789999999999999887764
No 62
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=72.06 E-value=3.3 Score=33.91 Aligned_cols=48 Identities=13% Similarity=0.003 Sum_probs=41.3
Q ss_pred ccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCCC
Q 040221 15 AENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAEST 68 (142)
Q Consensus 15 ~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~~ 68 (142)
..++...+|++++||.++ +++.+.++.+|.+.. ..+..|-.+.+|...
T Consensus 50 ~~y~~~~~d~~~Sia~~~------~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~ 98 (423)
T COG3858 50 HFYDVGPGDTLTSIARTV------GVTQDSAAIMNFVICPGYLQYGLNLYIPSAR 98 (423)
T ss_pred eEEEecCCcchhhhhhhh------cCCHHHHHhhcccccccceeeeeEEeccCCC
Confidence 357888999999999999 999999999998754 578888888888754
No 63
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=71.91 E-value=4.3 Score=24.15 Aligned_cols=29 Identities=14% Similarity=0.292 Sum_probs=24.2
Q ss_pred CCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCC
Q 040221 17 NDGSGDGREAAVAKTAGFVVFSGIAISILKALNPL 51 (142)
Q Consensus 17 ~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l 51 (142)
..+.+.-++-.||+++ ||+...|..|=..
T Consensus 17 ~~~~g~i~lkdIA~~L------gvs~~tIr~WK~~ 45 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKL------GVSESTIRKWKSR 45 (60)
T ss_pred HHhCCCccHHHHHHHH------CCCHHHHHHHhhh
Confidence 3455678999999999 9999999988654
No 64
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=71.35 E-value=3.2 Score=27.84 Aligned_cols=25 Identities=20% Similarity=0.423 Sum_probs=22.5
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
+..|.+...+|++|+|+...+..|=
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W~ 39 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRWL 39 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHHH
Confidence 4578899999999999999999994
No 65
>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=71.20 E-value=6.1 Score=21.02 Aligned_cols=20 Identities=20% Similarity=0.101 Sum_probs=17.9
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++.++|+.+|++...|..|=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999994
No 66
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=70.57 E-value=6.3 Score=21.87 Aligned_cols=20 Identities=20% Similarity=0.426 Sum_probs=17.6
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~ 125 (142)
-|+..||+.+|+++..+.++
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHH
Confidence 48999999999999988764
No 67
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=70.19 E-value=6.3 Score=20.97 Aligned_cols=20 Identities=20% Similarity=0.258 Sum_probs=16.6
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
|..++|+.+|+++..|+.|=
T Consensus 1 ti~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 35689999999999999996
No 68
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=69.37 E-value=4.9 Score=27.99 Aligned_cols=25 Identities=20% Similarity=0.318 Sum_probs=22.6
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
+..|.+...||++||++...+..|=
T Consensus 18 ~~~G~S~re~Ak~~gvs~sTvy~wv 42 (138)
T COG3415 18 VGEGLSCREAAKRFGVSISTVYRWV 42 (138)
T ss_pred HHcCccHHHHHHHhCccHHHHHHHH
Confidence 4689999999999999999999884
No 69
>PF13518 HTH_28: Helix-turn-helix domain
Probab=69.33 E-value=7.5 Score=21.36 Aligned_cols=24 Identities=17% Similarity=0.106 Sum_probs=20.2
Q ss_pred CCCCHHHHHHHhcccccCCCCHHHHHHhCC
Q 040221 21 GDGREAAVAKTAGFVVFSGIAISILKALNP 50 (142)
Q Consensus 21 ~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~ 50 (142)
+|.+...+|+.| ||+...|..|-.
T Consensus 11 ~g~s~~~~a~~~------gis~~tv~~w~~ 34 (52)
T PF13518_consen 11 EGESVREIAREF------GISRSTVYRWIK 34 (52)
T ss_pred cCCCHHHHHHHH------CCCHhHHHHHHH
Confidence 356999999999 999999987754
No 70
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=67.50 E-value=7.9 Score=20.95 Aligned_cols=20 Identities=25% Similarity=0.277 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+.+|++...|..|-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999995
No 71
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), 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- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=65.76 E-value=8.2 Score=22.60 Aligned_cols=20 Identities=30% Similarity=0.386 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++.++|+.+|++...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999884
No 72
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=65.29 E-value=7.7 Score=25.51 Aligned_cols=21 Identities=38% Similarity=0.528 Sum_probs=15.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~ 125 (142)
|.+...||++||+|...+++.
T Consensus 72 G~n~~eLA~kyglS~r~I~~I 92 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRI 92 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 999999999999998877653
No 73
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=64.09 E-value=12 Score=21.97 Aligned_cols=25 Identities=12% Similarity=0.186 Sum_probs=21.9
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHhCC
Q 040221 104 RGDTLWGLSRKYGVSIDAIKEANGL 128 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~~N~l 128 (142)
.|=++..||+.+|++...+..|=..
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 5789999999999999999998643
No 74
>smart00351 PAX Paired Box domain.
Probab=63.70 E-value=8 Score=26.16 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=20.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|.+...||++||++...+.+|
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kw 53 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKI 53 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 57899999999999999888877
No 75
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=63.19 E-value=13 Score=20.32 Aligned_cols=24 Identities=21% Similarity=0.252 Sum_probs=20.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
..|.+...||+.+|++...+..+-
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 578899999999999998887763
No 76
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=62.72 E-value=8 Score=31.29 Aligned_cols=59 Identities=12% Similarity=0.066 Sum_probs=41.6
Q ss_pred CCCCCCCCCCCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEec
Q 040221 4 PEDSVPTPRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIA 65 (142)
Q Consensus 4 ~~~~~~~~~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp 65 (142)
.|-+.-+|..=---++..|+|+.++|.+- ..-.-.++.|+-+|.+.. ..+.+|++++|-
T Consensus 418 ~E~a~lkPlrirvvtVk~GqT~~~lAA~m---~G~~rkldlfRllNam~~~a~~~pGd~vKii 477 (479)
T COG4784 418 AERAALKPLRIRVVTVKPGQTMASLAARM---MGTDRKLDLFRLLNAMSPGATVRPGDKVKII 477 (479)
T ss_pred hHHhccCceEEEEEEecCCccHHHHHhhc---cCchhHHHHHHHHhccCCCCcCCCCCeeeec
Confidence 34444444444445678899999999886 222335677888999866 689999998874
No 77
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=62.57 E-value=9.8 Score=22.32 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
|+.++|+.+|++...|+.|=
T Consensus 2 ti~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999995
No 78
>PF12728 HTH_17: Helix-turn-helix domain
Probab=61.25 E-value=16 Score=20.15 Aligned_cols=35 Identities=17% Similarity=0.111 Sum_probs=24.1
Q ss_pred cHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEec
Q 040221 107 TLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLII 141 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~I 141 (142)
|..++|+.+|++...+.+|=.-.. ..++.|-..++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g~i~~~~~g~~~~~ 38 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQGKIPPFKIGRKWRI 38 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCeEEeCCEEEE
Confidence 567899999999999999842222 33346655544
No 79
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=60.04 E-value=11 Score=24.18 Aligned_cols=26 Identities=19% Similarity=0.305 Sum_probs=23.1
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHhC
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N~ 127 (142)
+..|.|...||+.+|++...+.++.+
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46889999999999999999998763
No 80
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=59.36 E-value=12 Score=20.90 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=15.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHH
Q 040221 104 RGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.|-+..+||+.+|++...+..+
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~ 46 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRR 46 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHH
Confidence 5778999999999999988764
No 81
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=59.26 E-value=12 Score=23.88 Aligned_cols=25 Identities=16% Similarity=0.114 Sum_probs=21.9
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
|..|-++..+|+.|||+.....+|=
T Consensus 22 v~~g~~~a~aA~~~gVS~~Ta~kW~ 46 (85)
T PF13011_consen 22 VEQGWPVAHAAAEFGVSRRTAYKWL 46 (85)
T ss_pred HHcCCcHHHHHHHhCCCHHHHHHHH
Confidence 4578899999999999999988884
No 82
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=59.03 E-value=13 Score=21.77 Aligned_cols=20 Identities=20% Similarity=0.316 Sum_probs=17.9
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+.+|++...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999994
No 83
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=59.01 E-value=12 Score=21.63 Aligned_cols=23 Identities=17% Similarity=0.458 Sum_probs=16.4
Q ss_pred cCCCcHHHHHHHhC-CCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYG-VSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~ryg-vs~~~L~~~ 125 (142)
..|.+...|++.|. ++.+++...
T Consensus 29 ~~G~s~eeI~~~yp~Lt~~~i~aA 52 (56)
T PF04255_consen 29 AAGESPEEIAEDYPSLTLEDIRAA 52 (56)
T ss_dssp HTT--HHHHHHHSTT--HHHHHHH
T ss_pred HcCCCHHHHHHHCCCCCHHHHHHH
Confidence 78999999999997 999988763
No 84
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=58.71 E-value=7.7 Score=23.23 Aligned_cols=24 Identities=25% Similarity=0.227 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhcccccCCCCHHHHHHhCC
Q 040221 21 GDGREAAVAKTAGFVVFSGIAISILKALNP 50 (142)
Q Consensus 21 ~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~ 50 (142)
.|.++..+|+.| ||+...|..|=.
T Consensus 22 ~g~sv~~va~~~------gi~~~~l~~W~~ 45 (76)
T PF01527_consen 22 SGESVSEVAREY------GISPSTLYNWRK 45 (76)
T ss_dssp HHCHHHHHHHHH------TS-HHHHHHHHH
T ss_pred CCCceEeeeccc------ccccccccHHHH
Confidence 467889999999 999999988743
No 85
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=58.58 E-value=13 Score=23.24 Aligned_cols=21 Identities=38% Similarity=0.593 Sum_probs=15.9
Q ss_pred cCCCcHHHHHHHhCCCHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIK 123 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~ 123 (142)
++|-||..||+.+|++...+.
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~ 33 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLR 33 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHH
T ss_pred HcCCCHHHHHHHcCCCHHHHH
Confidence 578999999999999988876
No 86
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=57.95 E-value=10 Score=21.50 Aligned_cols=24 Identities=17% Similarity=0.306 Sum_probs=19.6
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.+.|.+...||.+||++.....++
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri 39 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRI 39 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHH
Confidence 467889999999999998776553
No 87
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). 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. 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 in the N-terminal domains of typical MerR-like proteins.
Probab=57.40 E-value=15 Score=21.59 Aligned_cols=20 Identities=20% Similarity=0.212 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+..++|+.+|++...|+.|=
T Consensus 2 ~i~evA~~~gvs~~tlR~~~ 21 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYE 21 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999993
No 88
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=54.30 E-value=15 Score=21.97 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=14.9
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~ 125 (142)
=++.+||++|+++.+.+...
T Consensus 15 ~S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 15 VSLAELAREFGISPEAVEAM 34 (69)
T ss_dssp EEHHHHHHHTT--HHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHH
Confidence 37899999999999887654
No 89
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=53.84 E-value=19 Score=24.04 Aligned_cols=75 Identities=21% Similarity=0.132 Sum_probs=44.3
Q ss_pred CCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCCCCCCceEE
Q 040221 21 GDGREAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTV 100 (142)
Q Consensus 21 ~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y 100 (142)
.|.....+|++| +|+...+..|=.- ...|+.- +..... . .+ ....-....
T Consensus 17 ~g~s~~eaa~~F------~VS~~Tv~~W~k~----~~~G~~~--~k~r~~-----~-Ki------------d~~~L~~~v 66 (119)
T PF01710_consen 17 KGKSIREAAKRF------GVSRNTVYRWLKR----KETGDLE--PKPRGR-----K-KI------------DRDELKALV 66 (119)
T ss_pred ccchHHHHHHHh------CcHHHHHHHHHHh----ccccccc--cccccc-----c-cc------------cHHHHHHHH
Confidence 367889999999 9999999988541 1233210 000000 0 00 000000111
Q ss_pred EecCCCcHHHHHHHhCCCHHHHHHH
Q 040221 101 EIVRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 101 ~V~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.-.+.-|+.+||++|||+...|..+
T Consensus 67 ~~~pd~tl~Ela~~l~Vs~~ti~~~ 91 (119)
T PF01710_consen 67 EENPDATLRELAERLGVSPSTIWRA 91 (119)
T ss_pred HHCCCcCHHHHHHHcCCCHHHHHHH
Confidence 2257889999999999999887765
No 90
>PHA02591 hypothetical protein; Provisional
Probab=53.63 E-value=47 Score=20.91 Aligned_cols=35 Identities=17% Similarity=0.279 Sum_probs=25.8
Q ss_pred CCceEEEecCCCcHHHHHHHh---CCCHHHHHHHhCCC
Q 040221 95 ASCRTVEIVRGDTLWGLSRKY---GVSIDAIKEANGLS 129 (142)
Q Consensus 95 ~~~~~y~V~~GDTl~~IA~ry---gvs~~~L~~~N~l~ 129 (142)
.....|.|...|-+-++|++. |.++.+|.+.=++.
T Consensus 35 v~~~ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~LGVs 72 (83)
T PHA02591 35 VGQTRYFVESEDDLISVTHELARKGFTVEKIASLLGVS 72 (83)
T ss_pred eCCEEEEEeccchHHHHHHHHHHcCCCHHHHHHHhCCC
Confidence 345678888888888888665 78888887765543
No 91
>cd00131 PAX Paired Box domain
Probab=53.17 E-value=15 Score=24.95 Aligned_cols=23 Identities=22% Similarity=0.226 Sum_probs=20.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|.+...||++||++...+.+|
T Consensus 31 ~~G~s~~~iA~~~~Vs~~tV~r~ 53 (128)
T cd00131 31 QSGIRPCDISRQLRVSHGCVSKI 53 (128)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 58999999999999999887777
No 92
>PF13551 HTH_29: Winged helix-turn helix
Probab=52.80 E-value=16 Score=23.33 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=20.1
Q ss_pred cCCC-cHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGD-TLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GD-Tl~~IA~rygvs~~~L~~~ 125 (142)
..|. |...||+.+|++...+.+|
T Consensus 9 ~~g~~~~~~ia~~lg~s~~Tv~r~ 32 (112)
T PF13551_consen 9 AEGVSTIAEIARRLGISRRTVYRW 32 (112)
T ss_pred HcCCCcHHHHHHHHCcCHHHHHHH
Confidence 4677 5999999999999998877
No 93
>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=52.41 E-value=25 Score=19.14 Aligned_cols=24 Identities=21% Similarity=0.238 Sum_probs=20.2
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
..|-+...||+.++++...+..+-
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~ 36 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHL 36 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 367899999999999998887663
No 94
>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=52.39 E-value=25 Score=18.56 Aligned_cols=22 Identities=14% Similarity=0.291 Sum_probs=19.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHH
Q 040221 104 RGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.|-+...||+.+|++...+..+
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6779999999999999998876
No 95
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=51.74 E-value=14 Score=26.71 Aligned_cols=27 Identities=15% Similarity=0.309 Sum_probs=23.9
Q ss_pred EEecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 100 VEIVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 100 y~V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
-.|+.|.|...||..+|++++.+.++-
T Consensus 64 arIRaGas~eeVA~~~G~~~~rV~rfa 90 (170)
T PF11268_consen 64 ARIRAGASAEEVAEEAGVPVERVRRFA 90 (170)
T ss_pred HHHHCCCCHHHHHHHhCCCHHHhhhcc
Confidence 357899999999999999999988764
No 96
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=51.49 E-value=18 Score=27.24 Aligned_cols=47 Identities=11% Similarity=0.083 Sum_probs=37.3
Q ss_pred cCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-----CCCCCCCcEEecCCC
Q 040221 16 ENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-----NRNETTQPQPIAEST 68 (142)
Q Consensus 16 ~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-----~~l~~Gq~l~vp~~~ 68 (142)
+++++.|+|+.-+=+.+ ++.+.++-++-.... +.|+.||.+.|....
T Consensus 161 sy~V~~G~TLaQlFRdn------~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 161 SYTVPQGKTLAQLFRDN------NLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred eEEecCCccHHHHHhcc------CCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 56788889999998889 888888876665421 578999999999764
No 97
>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=51.38 E-value=21 Score=21.03 Aligned_cols=20 Identities=10% Similarity=0.130 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+..|++...|+.|-
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye 21 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999995
No 98
>PF12471 GTP_CH_N: GTP cyclohydrolase N terminal ; InterPro: IPR022163 This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N-terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.
Probab=51.05 E-value=11 Score=27.52 Aligned_cols=20 Identities=25% Similarity=0.454 Sum_probs=16.8
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~ 125 (142)
=-|..||+|||++...|++.
T Consensus 171 WyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 171 WYLPGVAERFGISEGELRRA 190 (194)
T ss_pred ccchhhHHHcCCCHHHHHHH
Confidence 35678999999999999873
No 99
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=50.27 E-value=14 Score=20.95 Aligned_cols=19 Identities=21% Similarity=0.322 Sum_probs=15.2
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~ 125 (142)
+++++|+.+|++.++|.+.
T Consensus 5 ~V~elAk~l~v~~~~ii~~ 23 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKK 23 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHHH
Confidence 5679999999999887654
No 100
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 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.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=49.70 E-value=19 Score=23.05 Aligned_cols=25 Identities=24% Similarity=0.379 Sum_probs=22.2
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHhC
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N~ 127 (142)
..|-+...||+.+|++...|-+-|+
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3788999999999999999988773
No 101
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=49.54 E-value=20 Score=20.58 Aligned_cols=18 Identities=28% Similarity=0.464 Sum_probs=15.4
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~ 124 (142)
++..+|+.|++|...+++
T Consensus 16 s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRR 33 (57)
T ss_pred EHHHHHHHHCcCHHHHHH
Confidence 678999999999887764
No 102
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=47.94 E-value=26 Score=22.64 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=18.7
Q ss_pred cCCCcHHHHHHHhCCCHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIK 123 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~ 123 (142)
++|-||..||+.+|++...|.
T Consensus 19 KrG~sLa~lsr~~Gls~~TL~ 39 (92)
T PRK10344 19 KKGTSMAAESRRNGLSSSTLA 39 (92)
T ss_pred HcCCcHHHHHHHcCCChHHHH
Confidence 578999999999999988875
No 103
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=46.51 E-value=32 Score=19.06 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=17.7
Q ss_pred CHHHHHHHhcccccCCCCHHHH-HHhCC
Q 040221 24 REAAVAKTAGFVVFSGIAISIL-KALNP 50 (142)
Q Consensus 24 ~~~~iA~~~~~~~~~gvs~~~L-~~~N~ 50 (142)
|+.+||+.. |+|...+ +.+|+
T Consensus 1 Ti~dIA~~a------gvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREA------GVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHH------TSSHHHHHHHHTT
T ss_pred CHHHHHHHH------CcCHHHHHHHHhC
Confidence 578999999 9999999 45665
No 104
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=45.45 E-value=21 Score=27.50 Aligned_cols=22 Identities=36% Similarity=0.438 Sum_probs=19.6
Q ss_pred CCcHHHHHHHhCCCHHHHHHHh
Q 040221 105 GDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~N 126 (142)
|--+-+||.+||+++.+|+.|-
T Consensus 19 gmk~~dIAeklGvspntiksWK 40 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWK 40 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHH
Confidence 4567799999999999999997
No 105
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=45.13 E-value=29 Score=22.77 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=20.4
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-++.+||+.+|++...+..+
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 46999999999999999988765
No 106
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=44.35 E-value=38 Score=20.89 Aligned_cols=23 Identities=13% Similarity=0.264 Sum_probs=20.6
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|-|...||+..|++...++.+
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~ 52 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNH 52 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 37889999999999999999876
No 107
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=43.14 E-value=34 Score=22.79 Aligned_cols=25 Identities=24% Similarity=0.146 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHHhcccccCCCCHHHHHHhCC
Q 040221 20 SGDGREAAVAKTAGFVVFSGIAISILKALNP 50 (142)
Q Consensus 20 ~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~ 50 (142)
.+|.+...||++| ||+...|..|=.
T Consensus 27 ~~g~sv~evA~e~------gIs~~tl~~W~r 51 (121)
T PRK09413 27 EPGMTVSLVARQH------GVAASQLFLWRK 51 (121)
T ss_pred cCCCCHHHHHHHH------CcCHHHHHHHHH
Confidence 4578999999999 999999999854
No 108
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=43.02 E-value=34 Score=25.58 Aligned_cols=45 Identities=22% Similarity=0.107 Sum_probs=38.9
Q ss_pred CCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCC-CCCCCCcEEecCC
Q 040221 17 NDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKN-RNETTQPQPIAES 67 (142)
Q Consensus 17 ~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~-~l~~Gq~l~vp~~ 67 (142)
+....++++..++.++ +++...+.+.|..... .+..|+.+.++..
T Consensus 4 ~~~~~~~~l~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 4 YVVKKGDTLSAIAARL------GISAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred EEecCCCHHHHHHHHc------CCCHHHHHHHHhhccccccCccceeeeccc
Confidence 4456789999999999 9999999999987664 7889999999976
No 109
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=43.01 E-value=22 Score=22.81 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=18.0
Q ss_pred CcHHHHHHHhCCCHHHHHHHhC
Q 040221 106 DTLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~N~ 127 (142)
-|+.+..++|+++.++|.+|-.
T Consensus 50 is~~EA~~rY~Ls~eEf~~W~~ 71 (90)
T PF06627_consen 50 ISVEEACRRYGLSEEEFESWQR 71 (90)
T ss_dssp S-HHHHHHCTTSSHHHHHHHHH
T ss_pred CCHHHHHHHhCCCHHHHHHHHH
Confidence 4667778999999999999973
No 110
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=42.66 E-value=37 Score=17.85 Aligned_cols=21 Identities=19% Similarity=0.136 Sum_probs=14.3
Q ss_pred CCCcHHHHHHHhCCCHHHHHH
Q 040221 104 RGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~ 124 (142)
.+-+|.+||...|++...|.+
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r 27 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSR 27 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHH
Confidence 345889999999998877655
No 111
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.10 E-value=32 Score=22.08 Aligned_cols=20 Identities=5% Similarity=0.110 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+.+|++...|..|=
T Consensus 3 ~i~eva~~~gVs~~tLR~ye 22 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYD 22 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57789999999999999984
No 112
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.86 E-value=33 Score=21.90 Aligned_cols=20 Identities=25% Similarity=0.408 Sum_probs=17.9
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
|...+|+.+|++...|+-|=
T Consensus 2 ti~eva~~~gvs~~tLRyye 21 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYD 21 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999886
No 113
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=41.01 E-value=35 Score=21.40 Aligned_cols=20 Identities=20% Similarity=0.149 Sum_probs=18.4
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+.+|++...|+.|-
T Consensus 3 ti~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57789999999999999997
No 114
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=40.82 E-value=35 Score=19.35 Aligned_cols=23 Identities=17% Similarity=0.305 Sum_probs=18.4
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-+...||+.++++...+...
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~ 38 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSH 38 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHH
T ss_pred HhcCCcchhHHhcCcchhhHHHH
Confidence 47889999999999998877643
No 115
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=40.66 E-value=27 Score=19.47 Aligned_cols=21 Identities=14% Similarity=0.161 Sum_probs=18.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~ 125 (142)
.+.+..||...|++..++..|
T Consensus 27 ~~~~~~la~~~~l~~~qV~~W 47 (59)
T cd00086 27 REEREELAKELGLTERQVKIW 47 (59)
T ss_pred HHHHHHHHHHHCcCHHHHHHH
Confidence 356789999999999999988
No 116
>PRK00118 putative DNA-binding protein; Validated
Probab=40.51 E-value=40 Score=22.23 Aligned_cols=23 Identities=17% Similarity=0.297 Sum_probs=19.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|-|...||+.+|++...+..+
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r~ 53 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDN 53 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 46889999999999999887765
No 117
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.43 E-value=36 Score=21.82 Aligned_cols=20 Identities=10% Similarity=0.240 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+++|++...|+.|-
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye 21 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYE 21 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999995
No 118
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=40.39 E-value=30 Score=25.57 Aligned_cols=33 Identities=15% Similarity=0.139 Sum_probs=29.7
Q ss_pred CCCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCC
Q 040221 12 RVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNP 50 (142)
Q Consensus 12 ~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~ 50 (142)
+.|+.+++.-|.-+..+|+.. |++.+++.+.=-
T Consensus 80 ~iPV~Y~~~~g~DL~~vA~~~------gLs~eevi~~Hs 112 (202)
T TIGR00370 80 EIPVCYGGEFGPDLEEVAKIN------QLSPEEVIDIHS 112 (202)
T ss_pred EEeeEeCCCCCCCHHHHHHHh------CcCHHHHHHHHh
Confidence 579999999899999999999 999999987654
No 119
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.07 E-value=37 Score=21.33 Aligned_cols=21 Identities=5% Similarity=-0.001 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHHHhC
Q 040221 107 TLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N~ 127 (142)
+...+|+.+|++...|..|-.
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999999973
No 120
>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=40.03 E-value=47 Score=17.21 Aligned_cols=23 Identities=35% Similarity=0.368 Sum_probs=19.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHh
Q 040221 104 RGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~~N 126 (142)
.|-+...+|+..|++...+..|-
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~ 33 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIE 33 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHH
Confidence 56788999999999998888874
No 121
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=39.93 E-value=41 Score=19.85 Aligned_cols=21 Identities=19% Similarity=0.262 Sum_probs=16.2
Q ss_pred cHHHHHHHhCCCHHHHHHHhC
Q 040221 107 TLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N~ 127 (142)
+.-..|++|||+...+.+|=.
T Consensus 27 ~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 27 NQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -HHHHHHHTTS-HHHHHHHHT
T ss_pred hHHHHHHHhCccHHHHHHHHH
Confidence 456789999999999999953
No 122
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=39.91 E-value=36 Score=21.94 Aligned_cols=20 Identities=35% Similarity=0.433 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+++|++...|.-|=
T Consensus 3 ~i~eva~~~gvs~~tLR~ye 22 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYE 22 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999996
No 123
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=38.66 E-value=45 Score=18.32 Aligned_cols=23 Identities=26% Similarity=0.320 Sum_probs=18.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
+.|-|..++|++.|++...+.+|
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~ 29 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRI 29 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHH
Confidence 46778889999999999998887
No 124
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.17 E-value=41 Score=21.44 Aligned_cols=20 Identities=20% Similarity=0.443 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+.+|++...|.-|=
T Consensus 2 ~i~eva~~~gvs~~tlR~ye 21 (96)
T cd04788 2 KIGELARRTGLSVRTLHHYD 21 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999999996
No 125
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.12 E-value=38 Score=22.15 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=18.8
Q ss_pred CCCCCHHHHHHHhcccccCCC-CHHHHHHh
Q 040221 20 SGDGREAAVAKTAGFVVFSGI-AISILKAL 48 (142)
Q Consensus 20 ~~~~~~~~iA~~~~~~~~~gv-s~~~L~~~ 48 (142)
.+|.+...||++| || +...|..|
T Consensus 22 ~~g~sv~~vAr~~------gv~~~~~l~~W 45 (116)
T COG2963 22 RGGDTVSEVAREF------GIVSATQLYKW 45 (116)
T ss_pred hcCccHHHHHHHh------CCCChHHHHHH
Confidence 3577899999999 95 88888765
No 126
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=38.06 E-value=44 Score=19.50 Aligned_cols=18 Identities=28% Similarity=0.350 Sum_probs=14.2
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~ 124 (142)
++..||+++|++...|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~ 20 (84)
T smart00342 3 TLEDLAEALGMSPRHLQR 20 (84)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 678889999988877654
No 127
>PHA01976 helix-turn-helix protein
Probab=37.76 E-value=52 Score=18.97 Aligned_cols=23 Identities=30% Similarity=0.222 Sum_probs=17.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
+.|-|..++|++.|++...+.+|
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~ 35 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDF 35 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Confidence 45677788888888888887776
No 128
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=37.63 E-value=42 Score=19.12 Aligned_cols=24 Identities=33% Similarity=0.339 Sum_probs=15.9
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
+.|=|..++|++.|++...|.+|=
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~ 31 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRIL 31 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 356688889999999988888874
No 129
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=37.44 E-value=39 Score=23.66 Aligned_cols=21 Identities=14% Similarity=0.145 Sum_probs=17.5
Q ss_pred CcHHHHHHHhCCCHHHHHHHh
Q 040221 106 DTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~N 126 (142)
-|+..||+..|++...|++|-
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr 55 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWR 55 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHH
T ss_pred chHHHHHHHhCCCHHHHHHHH
Confidence 489999999999999999994
No 130
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.43 E-value=39 Score=22.33 Aligned_cols=18 Identities=28% Similarity=0.436 Sum_probs=15.5
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~ 124 (142)
+|..||..|+|+-+++..
T Consensus 35 Sl~EIAee~~VSRqAIyD 52 (105)
T COG2739 35 SLSEIAEEFNVSRQAIYD 52 (105)
T ss_pred cHHHHHHHhCccHHHHHH
Confidence 789999999999887654
No 131
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=37.33 E-value=50 Score=18.14 Aligned_cols=23 Identities=30% Similarity=0.416 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHHH-hCCC
Q 040221 107 TLWGLSRKYGVSIDAIKEA-NGLS 129 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~-N~l~ 129 (142)
|...||++|+++...+.+. +.|.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 7789999999998776653 3443
No 132
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=37.19 E-value=38 Score=19.51 Aligned_cols=21 Identities=14% Similarity=0.324 Sum_probs=16.8
Q ss_pred cHHHHHHHhCCCHHHHHHHhC
Q 040221 107 TLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N~ 127 (142)
-+..+|+.||++.++|..-..
T Consensus 5 I~~~Va~~~~i~~~~i~s~~R 25 (60)
T smart00760 5 IIEAVAEYFGVKPEDLKSKSR 25 (60)
T ss_pred HHHHHHHHhCCCHHHHhcCCC
Confidence 456789999999999976553
No 133
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=37.16 E-value=51 Score=24.21 Aligned_cols=28 Identities=25% Similarity=0.080 Sum_probs=24.8
Q ss_pred CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHH
Q 040221 14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKA 47 (142)
Q Consensus 14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~ 47 (142)
-.|++-+++-++.+||+.+ ||+-+.+.+
T Consensus 170 ~GYFd~PR~~~l~dLA~~l------GISkst~~e 197 (215)
T COG3413 170 MGYFDYPRRVSLKDLAKEL------GISKSTLSE 197 (215)
T ss_pred cCCCCCCccCCHHHHHHHh------CCCHHHHHH
Confidence 3688999999999999999 999988864
No 134
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=36.95 E-value=51 Score=18.37 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=17.4
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~ 125 (142)
+....||..+|++..++..|
T Consensus 28 ~~~~~la~~l~l~~~~V~~W 47 (57)
T PF00046_consen 28 EEREELAKELGLTERQVKNW 47 (57)
T ss_dssp HHHHHHHHHHTSSHHHHHHH
T ss_pred cccccccccccccccccccC
Confidence 45678999999999999887
No 135
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=36.80 E-value=38 Score=18.80 Aligned_cols=17 Identities=35% Similarity=0.403 Sum_probs=13.2
Q ss_pred cHHHHHHHhCCCHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIK 123 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~ 123 (142)
|...||+.+++|...+.
T Consensus 17 t~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIR 33 (55)
T ss_dssp EHHHHHHHCTS-HHHHH
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 78899999999976554
No 136
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.51 E-value=45 Score=21.54 Aligned_cols=20 Identities=25% Similarity=0.252 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+++|++...|+-|=
T Consensus 3 ~i~eva~~~gvs~~tlR~ye 22 (102)
T cd04789 3 TISELAEKAGISRSTLLYYE 22 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999885
No 137
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=36.15 E-value=62 Score=21.91 Aligned_cols=65 Identities=17% Similarity=0.176 Sum_probs=40.5
Q ss_pred CHHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCCCCCCceEEEec
Q 040221 24 REAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIV 103 (142)
Q Consensus 24 ~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~V~ 103 (142)
+...+|+++ ||+...|+-|=.. | +|+... ........|...
T Consensus 2 ~IgE~A~~~------gvs~~TLRyYE~~-------G---Ll~p~r-----------------------~~~~gyR~Y~~~ 42 (133)
T cd04787 2 KVKELANAA------GVTPDTVRFYTRI-------G---LLRPTR-----------------------DPVNGYRLYSEK 42 (133)
T ss_pred CHHHHHHHH------CcCHHHHHHHHHC-------C---CCCCCc-----------------------CCCCCeeeCCHH
Confidence 467899999 9999999987532 1 111100 001334456554
Q ss_pred CCCcHHHHH--HHhCCCHHHHHHHhC
Q 040221 104 RGDTLWGLS--RKYGVSIDAIKEANG 127 (142)
Q Consensus 104 ~GDTl~~IA--~rygvs~~~L~~~N~ 127 (142)
.=+.+..|. +..|.+.++|+.+=.
T Consensus 43 ~~~~l~~I~~lr~~G~sL~eI~~~l~ 68 (133)
T cd04787 43 DLSRLRFILSARQLGFSLKDIKEILS 68 (133)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 455555553 778999999888753
No 138
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=36.11 E-value=46 Score=21.38 Aligned_cols=21 Identities=19% Similarity=0.319 Sum_probs=18.5
Q ss_pred cHHHHHHHhCCCHHHHHHHhC
Q 040221 107 TLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N~ 127 (142)
+...+|+.+|++...|+-|-.
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~ 22 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999973
No 139
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.07 E-value=57 Score=21.57 Aligned_cols=21 Identities=19% Similarity=0.355 Sum_probs=18.3
Q ss_pred CHHHHHHHhcccccCCCCHHHHHHhCC
Q 040221 24 REAAVAKTAGFVVFSGIAISILKALNP 50 (142)
Q Consensus 24 ~~~~iA~~~~~~~~~gvs~~~L~~~N~ 50 (142)
+...+|+++ ||+...|+-|-.
T Consensus 2 ~I~eva~~~------gvs~~tLRyYe~ 22 (123)
T cd04770 2 KIGELAKAA------GVSPDTIRYYER 22 (123)
T ss_pred CHHHHHHHH------CcCHHHHHHHHH
Confidence 467899999 999999998775
No 140
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=35.14 E-value=49 Score=21.12 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=17.7
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+.+|++...|+-|-
T Consensus 2 ~i~eva~~~gvs~~tlR~ye 21 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYD 21 (97)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999999995
No 141
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=35.10 E-value=51 Score=19.06 Aligned_cols=18 Identities=33% Similarity=0.595 Sum_probs=12.7
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~ 124 (142)
+...||++|+++...+++
T Consensus 26 s~~~la~~~~vsr~tvr~ 43 (64)
T PF00392_consen 26 SERELAERYGVSRTTVRE 43 (64)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHhccCCcHHHH
Confidence 447899999999776654
No 142
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=35.00 E-value=63 Score=16.50 Aligned_cols=23 Identities=30% Similarity=0.351 Sum_probs=19.6
Q ss_pred CCCcHHHHHHHhCCCHHHHHHHh
Q 040221 104 RGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~~N 126 (142)
.|-+...+|+..|++...+..|-
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHH
Confidence 46688899999999999998875
No 143
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=34.52 E-value=49 Score=21.54 Aligned_cols=24 Identities=25% Similarity=0.332 Sum_probs=19.3
Q ss_pred cHHHHHHHhCCCHHHHHHHh--CCCC
Q 040221 107 TLWGLSRKYGVSIDAIKEAN--GLSG 130 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N--~l~~ 130 (142)
+...+|+.+|++...|+-|= ||-.
T Consensus 2 ~i~eva~~~gis~~tlR~ye~~GLi~ 27 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYDKIGLLK 27 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 45789999999999999885 5443
No 144
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=34.46 E-value=50 Score=20.68 Aligned_cols=20 Identities=20% Similarity=0.390 Sum_probs=17.1
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~ 125 (142)
-|+.+||+.+|++...+.+.
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~ 39 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKD 39 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHH
Confidence 48999999999999887763
No 145
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.06 E-value=52 Score=20.79 Aligned_cols=20 Identities=20% Similarity=0.353 Sum_probs=17.9
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+.+|++...|..|-
T Consensus 2 ~~~eva~~~gi~~~tlr~~~ 21 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYE 21 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999995
No 146
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=34.05 E-value=51 Score=21.15 Aligned_cols=20 Identities=20% Similarity=0.292 Sum_probs=17.5
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+.+|++...|+.|=
T Consensus 2 ti~eva~~~gvs~~tlR~ye 21 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYD 21 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999884
No 147
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=33.81 E-value=15 Score=23.23 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=14.8
Q ss_pred EEecCCCcHHHHHHHhCCCHHH
Q 040221 100 VEIVRGDTLWGLSRKYGVSIDA 121 (142)
Q Consensus 100 y~V~~GDTl~~IA~rygvs~~~ 121 (142)
|.+..+.|+-..|+.||+|-..
T Consensus 14 yIi~~~aTVR~~Ak~FGvSKST 35 (82)
T PF12116_consen 14 YIIETKATVRQAAKVFGVSKST 35 (82)
T ss_dssp HHHHH---HHHHHHHHTS-HHH
T ss_pred HHHHcccHHHHHHHHHCCcHHH
Confidence 6677788999999999999644
No 148
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=32.65 E-value=55 Score=23.62 Aligned_cols=24 Identities=25% Similarity=0.299 Sum_probs=21.6
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
..|.|+..||+.+|++...++++-
T Consensus 170 ~~g~s~~~iak~lgis~~Tv~r~~ 193 (200)
T PRK13413 170 DKGTSKSEIARKLGVSRTTLARFL 193 (200)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Confidence 568999999999999999998875
No 149
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=32.61 E-value=60 Score=18.24 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=18.9
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHH
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~ 124 (142)
+..|.+...||...+++...+..
T Consensus 16 ~~~G~s~~eia~~l~is~~tV~~ 38 (65)
T COG2771 16 VAQGKSNKEIARILGISEETVKT 38 (65)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHH
Confidence 46789999999999999876543
No 150
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=32.60 E-value=44 Score=28.51 Aligned_cols=26 Identities=38% Similarity=0.597 Sum_probs=21.3
Q ss_pred ecCCCcHHHHHHHhCCCHH----HHHHHhC
Q 040221 102 IVRGDTLWGLSRKYGVSID----AIKEANG 127 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~----~L~~~N~ 127 (142)
+.++|||.++|++.|+..+ .+.+||.
T Consensus 421 ~~kadTleELA~k~gid~~~L~~TV~~yN~ 450 (564)
T PRK12845 421 AHRADSLADLARKIGVPVDTFVATMRRFNE 450 (564)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 4478999999999999964 5667884
No 151
>COG3784 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.58 E-value=35 Score=22.49 Aligned_cols=36 Identities=17% Similarity=0.228 Sum_probs=28.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEe
Q 040221 105 GDTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLI 140 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~ 140 (142)
..+...||++-|++.+++..+-+-+- .+..+||-+.
T Consensus 64 ~a~Yq~lA~~n~~s~~~vak~agqklv~Ra~~GqYvq 100 (109)
T COG3784 64 AASYQQLAKKNGASTEEVAKLAGQKLVARAAPGQYVQ 100 (109)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCeee
Confidence 34566889999999999999887665 7788888764
No 152
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=32.35 E-value=47 Score=19.95 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=12.8
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~ 124 (142)
-+..+|+.||++.++|..
T Consensus 5 Ii~~Va~~~~v~~~~i~s 22 (70)
T PF08299_consen 5 IIEAVAEYFGVSVEDIRS 22 (70)
T ss_dssp HHHHHHHHTT--HHHHHS
T ss_pred HHHHHHHHHCCCHHHHhC
Confidence 356789999999999874
No 153
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=32.25 E-value=56 Score=22.49 Aligned_cols=27 Identities=11% Similarity=0.122 Sum_probs=23.7
Q ss_pred EEecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 100 VEIVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 100 y~V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
|-=..|-|+..||.+++++..+.++|+
T Consensus 94 y~~r~~~TW~~IA~~l~i~erta~r~~ 120 (130)
T PF05263_consen 94 YDRRSRRTWYQIAQKLHISERTARRWR 120 (130)
T ss_pred HcccccchHHHHHHHhCccHHHHHHHH
Confidence 444578999999999999999999987
No 154
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=32.24 E-value=61 Score=23.39 Aligned_cols=20 Identities=30% Similarity=0.665 Sum_probs=16.8
Q ss_pred cCCCcHHHHHHHhCCCHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAI 122 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L 122 (142)
+.|.++..||.+||+.+..+
T Consensus 31 ~~~~sv~~vS~~ygi~~~RV 50 (172)
T PF12298_consen 31 QDGKSVREVSQKYGIKIQRV 50 (172)
T ss_pred hCCCCHHHHHHHhCCCHHHH
Confidence 67889999999999996543
No 155
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=32.20 E-value=59 Score=20.49 Aligned_cols=20 Identities=20% Similarity=0.348 Sum_probs=16.5
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~ 125 (142)
..|+.+|+..|++.++|..+
T Consensus 55 ~kL~~La~~N~v~feeLc~Y 74 (82)
T PF11020_consen 55 SKLYKLAKENNVSFEELCVY 74 (82)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 45778899999999998765
No 156
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=32.00 E-value=58 Score=20.99 Aligned_cols=19 Identities=5% Similarity=0.118 Sum_probs=17.3
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~ 125 (142)
++..+|+.+|++...|+.|
T Consensus 2 ti~EvA~~~gVs~~tLR~y 20 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYW 20 (99)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4678999999999999999
No 157
>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=31.92 E-value=73 Score=17.30 Aligned_cols=24 Identities=25% Similarity=0.271 Sum_probs=20.3
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
+.|=|..++|++.|++...+.+|=
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 457788899999999999998883
No 158
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=31.76 E-value=69 Score=22.23 Aligned_cols=23 Identities=22% Similarity=0.133 Sum_probs=20.8
Q ss_pred CC--CcHHHHHHHhCCCHHHHHHHh
Q 040221 104 RG--DTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 104 ~G--DTl~~IA~rygvs~~~L~~~N 126 (142)
++ -|+..|+...||++..|..|=
T Consensus 43 p~~~ati~eV~e~tgVs~~~I~~~I 67 (137)
T TIGR03826 43 ENRQATVSEIVEETGVSEKLILKFI 67 (137)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 55 799999999999999999984
No 159
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=31.58 E-value=48 Score=27.74 Aligned_cols=26 Identities=38% Similarity=0.459 Sum_probs=21.0
Q ss_pred ecCCCcHHHHHHHhCCCHH----HHHHHhC
Q 040221 102 IVRGDTLWGLSRKYGVSID----AIKEANG 127 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~----~L~~~N~ 127 (142)
+.+.|||.++|++.|+..+ ++.+||.
T Consensus 372 ~~kaDTleELA~k~gid~~~L~~Tv~~yN~ 401 (513)
T PRK12837 372 WRTADTLEELAAKIGVPADALTATVARFNG 401 (513)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 3478999999999999864 5667884
No 160
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=31.57 E-value=58 Score=21.22 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=17.9
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+.+|++...|..|-
T Consensus 2 ~i~eva~~~gvs~~tlR~ye 21 (108)
T cd04773 2 TIGELAHLLGVPPSTLRHWE 21 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999996
No 161
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=31.55 E-value=48 Score=22.31 Aligned_cols=29 Identities=31% Similarity=0.540 Sum_probs=25.4
Q ss_pred EEecCCCcHHHHHHHh---CCCHHHHHHHhCC
Q 040221 100 VEIVRGDTLWGLSRKY---GVSIDAIKEANGL 128 (142)
Q Consensus 100 y~V~~GDTl~~IA~ry---gvs~~~L~~~N~l 128 (142)
-.+|.|.-+.++++|. |-.+++|++.|++
T Consensus 84 LiiQTgnkMddvSrRL~aEgKdIdeLKKiN~m 115 (128)
T PF15145_consen 84 LIIQTGNKMDDVSRRLTAEGKDIDELKKINSM 115 (128)
T ss_pred heeeccchHHHHHHHHHhccCCHHHHHHHHHH
Confidence 4689999999999998 7889999999863
No 162
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=31.46 E-value=44 Score=18.39 Aligned_cols=21 Identities=24% Similarity=0.164 Sum_probs=18.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~ 125 (142)
.+....||+..|++..++..|
T Consensus 27 ~~~~~~la~~~~l~~~qV~~W 47 (56)
T smart00389 27 REEREELAAKLGLSERQVKVW 47 (56)
T ss_pred HHHHHHHHHHHCcCHHHHHHh
Confidence 356889999999999999987
No 163
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). 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 [].; PDB: 1S7O_A 1XSV_B.
Probab=31.45 E-value=54 Score=21.54 Aligned_cols=22 Identities=18% Similarity=0.274 Sum_probs=14.3
Q ss_pred cCCCcHHHHHHHhCCCHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~ 124 (142)
...=|+..||..+|+|.+.+..
T Consensus 31 ~eDlSlsEIAe~~~iSRqaV~d 52 (101)
T PF04297_consen 31 EEDLSLSEIAEELGISRQAVYD 52 (101)
T ss_dssp TS---HHHHHHHCTS-HHHHHH
T ss_pred ccCCCHHHHHHHHCCCHHHHHH
Confidence 3455899999999999776554
No 164
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=31.33 E-value=31 Score=25.33 Aligned_cols=63 Identities=14% Similarity=0.112 Sum_probs=40.8
Q ss_pred HHHHHHHhcccccCCCCHHHHHHhCCCCCCCCCCCCcEEecCCCCCCCCCCCCCccCCCCcccCCCCCCCCCceEEEecC
Q 040221 25 EAAVAKTAGFVVFSGIAISILKALNPLNKNRNETTQPQPIAESTQPIQPPPQQPIVTKPSICTEKSEPEPASCRTVEIVR 104 (142)
Q Consensus 25 ~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~~l~~Gq~l~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~V~~ 104 (142)
+..||+++ ++++..=..++.........|+.+++-. ..+|-=.+
T Consensus 27 vD~La~~~------~~~~~~~~kf~~~~~~~~i~g~kv~l~k------------------------------P~TyMNlS 70 (190)
T COG0193 27 VDLLARRL------NLSFKEEKKFNGLVAKGTIEGEKVILLK------------------------------PTTYMNLS 70 (190)
T ss_pred HHHHHHHh------CCCCccccccCceeEEEEeCCcEEEEec------------------------------CccceeCc
Confidence 45677777 7777666666654332223444332221 22566679
Q ss_pred CCcHHHHHHHhCCCHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIK 123 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~ 123 (142)
|..+..+++-|.+..++|.
T Consensus 71 G~~V~~~~~fy~i~~~~il 89 (190)
T COG0193 71 GKAVGALASFYKIKPEDIL 89 (190)
T ss_pred HHHHHHHHHHhCCCHHHEE
Confidence 9999999999999988764
No 165
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=31.31 E-value=67 Score=17.28 Aligned_cols=20 Identities=15% Similarity=0.297 Sum_probs=14.2
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~ 124 (142)
.-++..||+..|++.....+
T Consensus 17 r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHH
Confidence 34788999999999877653
No 166
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=31.30 E-value=71 Score=18.80 Aligned_cols=20 Identities=25% Similarity=0.250 Sum_probs=16.6
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+.+|++...+..|.
T Consensus 11 ~~~~lAkalGVs~~aVs~W~ 30 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQWG 30 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHhc
Confidence 45689999999999999994
No 167
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=31.28 E-value=58 Score=20.14 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=17.2
Q ss_pred ceEEEecCCCcHHHHHHHhCCCHH
Q 040221 97 CRTVEIVRGDTLWGLSRKYGVSID 120 (142)
Q Consensus 97 ~~~y~V~~GDTl~~IA~rygvs~~ 120 (142)
...|.+.+|+|+.+.+.+.|+.+-
T Consensus 10 G~~v~~~~G~til~al~~~gi~ip 33 (82)
T PF13510_consen 10 GKPVEVPPGETILEALLAAGIDIP 33 (82)
T ss_dssp TEEEEEEET-BHHHHHHHTT--B-
T ss_pred CEEEEEcCCCHHHHHHHHCCCeEE
Confidence 456899999999999999886643
No 168
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=31.02 E-value=52 Score=19.07 Aligned_cols=29 Identities=21% Similarity=0.014 Sum_probs=22.9
Q ss_pred CccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHh
Q 040221 14 PAENDGSGDGREAAVAKTAGFVVFSGIAISILKAL 48 (142)
Q Consensus 14 p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~ 48 (142)
+...+..+...+.-.|++| |++.++|.++
T Consensus 12 ~~~I~~~e~~ev~ywa~~~------gvt~~~L~~A 40 (57)
T PF12244_consen 12 RDRIDLSEPYEVRYWAKRF------GVTEEQLREA 40 (57)
T ss_pred hHhcCCCCHHHHHHHHHHH------CcCHHHHHHH
Confidence 3445566677788899999 9999999865
No 169
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=30.70 E-value=76 Score=16.21 Aligned_cols=19 Identities=21% Similarity=0.274 Sum_probs=15.4
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~ 124 (142)
+-|..+|++.|.+..++.+
T Consensus 12 ~~l~~~a~~~g~s~s~~ir 30 (39)
T PF01402_consen 12 ERLDELAKELGRSRSELIR 30 (39)
T ss_dssp HHHHHHHHHHTSSHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHH
Confidence 3577899999999988765
No 170
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=30.69 E-value=98 Score=20.91 Aligned_cols=22 Identities=18% Similarity=0.244 Sum_probs=18.9
Q ss_pred CHHHHHHHhcccccCCCCHHHHHHhCCC
Q 040221 24 REAAVAKTAGFVVFSGIAISILKALNPL 51 (142)
Q Consensus 24 ~~~~iA~~~~~~~~~gvs~~~L~~~N~l 51 (142)
+...+|+++ ||+...|+-|-..
T Consensus 3 ~I~e~a~~~------gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 3 QIGELAKLC------GVTSDTLRFYEKN 24 (131)
T ss_pred CHHHHHHHH------CcCHHHHHHHHHC
Confidence 467899999 9999999988753
No 171
>PRK04217 hypothetical protein; Provisional
Probab=30.36 E-value=75 Score=21.16 Aligned_cols=22 Identities=27% Similarity=0.246 Sum_probs=18.8
Q ss_pred CCCcHHHHHHHhCCCHHHHHHH
Q 040221 104 RGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 104 ~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.|-|..+||+.+|++...++..
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~ 78 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRA 78 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6779999999999998887654
No 172
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=30.18 E-value=61 Score=20.24 Aligned_cols=24 Identities=17% Similarity=0.490 Sum_probs=20.6
Q ss_pred ecCCCcHHHHHHHhC-CCHHHHHHH
Q 040221 102 IVRGDTLWGLSRKYG-VSIDAIKEA 125 (142)
Q Consensus 102 V~~GDTl~~IA~ryg-vs~~~L~~~ 125 (142)
.+.|.|..+|+..|. ++.++|++.
T Consensus 40 l~~G~s~eeil~dyp~Lt~~dI~aa 64 (79)
T COG2442 40 LAAGESIEEILADYPDLTLEDIRAA 64 (79)
T ss_pred HHCCCCHHHHHHhCCCCCHHHHHHH
Confidence 478999999999997 999888764
No 173
>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=29.15 E-value=79 Score=17.66 Aligned_cols=24 Identities=29% Similarity=0.410 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHH-hCCCC
Q 040221 107 TLWGLSRKYGVSIDAIKEA-NGLSG 130 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~-N~l~~ 130 (142)
+..+||+.|+++...+.+. +.|..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6889999999998776653 44443
No 174
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=29.03 E-value=41 Score=24.65 Aligned_cols=45 Identities=13% Similarity=0.070 Sum_probs=36.6
Q ss_pred CCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCC-CCCCCCCcEEecCC
Q 040221 17 NDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNK-NRNETTQPQPIAES 67 (142)
Q Consensus 17 ~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~-~~l~~Gq~l~vp~~ 67 (142)
-+...|+++-.||=.| ..++.+|...|++.. ..+-.-+.+++|..
T Consensus 12 ~~iq~~dt~~a~al~~------~~~va~i~RvN~~~r~q~f~a~~~i~~pv~ 57 (186)
T KOG2850|consen 12 VTIQEGDTLQAIALNY------ESDVADIKRVNNDDREQRFNALRSISIPVT 57 (186)
T ss_pred eeeccCchhhhHHhhc------ccchhhheeeccchhhhhhccccceecccc
Confidence 4567899999999999 999999999997755 45566667777764
No 175
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.90 E-value=71 Score=20.38 Aligned_cols=20 Identities=35% Similarity=0.386 Sum_probs=17.7
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
++..+|+.+|++...|+-|=
T Consensus 2 ~I~eva~~~gvs~~tlR~Ye 21 (95)
T cd04780 2 RMSELSKRSGVSVATIKYYL 21 (95)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999885
No 176
>PF08984 DUF1858: Domain of unknown function (DUF1858); InterPro: IPR015077 This protein has no known function. It is found in various hypothetical bacterial proteins. ; PDB: 2K53_A 2K5E_A 2FI0_A.
Probab=28.64 E-value=69 Score=18.43 Aligned_cols=22 Identities=14% Similarity=0.289 Sum_probs=16.5
Q ss_pred ecCCCcHHHHHHHhCCCHHHHH
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIK 123 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~ 123 (142)
+.+..|+...|+.+|++++.|.
T Consensus 38 ~~~~~Tl~~aa~~~gid~~~li 59 (59)
T PF08984_consen 38 MAKFETLEQAAKMHGIDLEKLI 59 (59)
T ss_dssp HHHHSBHHHHHHHHT--HHHHH
T ss_pred hcccCCHHHHHHHcCCCHHHhC
Confidence 3566799999999999998873
No 177
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=28.61 E-value=40 Score=21.28 Aligned_cols=30 Identities=13% Similarity=0.103 Sum_probs=25.9
Q ss_pred CCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHh
Q 040221 13 VPAENDGSGDGREAAVAKTAGFVVFSGIAISILKAL 48 (142)
Q Consensus 13 ~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~ 48 (142)
+|.++++.+=-|...||+.| |+....|.+.
T Consensus 3 ~i~e~rg~rV~t~~~lA~~y------g~~~~~i~~~ 32 (88)
T PF10543_consen 3 QIIEYRGQRVMTDEDLAELY------GVETKTINRN 32 (88)
T ss_pred ccEEEcCEEEEEHHHHHHHh------CcCHHHHHHH
Confidence 57788888888999999999 9999999643
No 178
>PRK12839 hypothetical protein; Provisional
Probab=28.60 E-value=56 Score=27.91 Aligned_cols=25 Identities=32% Similarity=0.458 Sum_probs=20.7
Q ss_pred cCCCcHHHHHHHhCCCH----HHHHHHhC
Q 040221 103 VRGDTLWGLSRKYGVSI----DAIKEANG 127 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~----~~L~~~N~ 127 (142)
.++|||.++|++.|++. +.+.+||.
T Consensus 425 ~kadTleELA~k~gid~~~L~~TV~~yN~ 453 (572)
T PRK12839 425 TRGRTIEELAEKCGIDPAGLEATVAEFNE 453 (572)
T ss_pred EECCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 46899999999999995 45678884
No 179
>PHA00542 putative Cro-like protein
Probab=28.59 E-value=81 Score=19.48 Aligned_cols=23 Identities=17% Similarity=-0.009 Sum_probs=21.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|=|...+|+.+|++...|.+|
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~ 51 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRI 51 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 56789999999999999999998
No 180
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=28.41 E-value=95 Score=16.67 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=16.9
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~ 125 (142)
+=|+..||++-|++...|...
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHHH
T ss_pred hCCHHHHHHHHccchhhHHHH
Confidence 448889999999998887753
No 181
>PF14493 HTH_40: Helix-turn-helix domain
Probab=28.02 E-value=72 Score=19.97 Aligned_cols=22 Identities=14% Similarity=0.210 Sum_probs=18.7
Q ss_pred cCCCcHHHHHHHhCCCHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~ 124 (142)
+.|-|+..||++-+++...|..
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~ 32 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYG 32 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHH
Confidence 5799999999999999877654
No 182
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=27.89 E-value=1e+02 Score=18.40 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=17.1
Q ss_pred cCCCcHHHHHHHhCCCHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIK 123 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~ 123 (142)
..|-+.-+||+.+|++..+..
T Consensus 11 E~g~~FveIAr~~~i~a~e~a 31 (63)
T PF11242_consen 11 ESGLSFVEIARKIGITAKEVA 31 (63)
T ss_pred HcCCcHHHHHHHhCCCHHHHH
Confidence 368899999999999976644
No 183
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=27.73 E-value=1.1e+02 Score=16.40 Aligned_cols=22 Identities=23% Similarity=0.188 Sum_probs=15.5
Q ss_pred cCCCcHHHHHHHhCCCHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~ 124 (142)
.++-|...||++.|++...+.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~ 36 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNR 36 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHH
Confidence 3556888999999999877654
No 184
>PF05052 MerE: MerE protein; InterPro: IPR007746 The prokaryotic MerE (or URF-1) protein is part of the mercury resistance operon often located on plasmids or transposons [, ]. It has been suggested that MerE is a broad mercury transporter mediating transport across the bacterial membrane [].
Probab=27.59 E-value=33 Score=21.21 Aligned_cols=17 Identities=41% Similarity=0.626 Sum_probs=13.4
Q ss_pred CCCCCCCCCCCCCCccC
Q 040221 1 MQSPEDSVPTPRVPAEN 17 (142)
Q Consensus 1 ~~~~~~~~~~~~~p~~~ 17 (142)
|.|||-..++.++|+.-
T Consensus 1 m~~p~~~p~e~~k~i~g 17 (75)
T PF05052_consen 1 MNSPERLPPETRKPITG 17 (75)
T ss_pred CCCcccCChhhcCcchh
Confidence 78888888888877653
No 185
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=27.45 E-value=1.2e+02 Score=21.73 Aligned_cols=23 Identities=26% Similarity=0.260 Sum_probs=19.3
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
++.-++..||.+|+++.-+|...
T Consensus 25 qPdg~~eamA~~~~v~~~eIv~a 47 (176)
T COG3721 25 QPDGTLEAMAEQYNVTELEIVRA 47 (176)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHh
Confidence 56679999999999999888763
No 186
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=27.40 E-value=78 Score=20.69 Aligned_cols=20 Identities=20% Similarity=0.325 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+.+|+++..|+-|=
T Consensus 2 ~Ige~A~~~gvs~~tlR~ye 21 (107)
T cd01111 2 SISQLALDAGVSVHIVRDYL 21 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999999985
No 187
>PRK07121 hypothetical protein; Validated
Probab=27.24 E-value=69 Score=26.52 Aligned_cols=26 Identities=23% Similarity=0.349 Sum_probs=21.7
Q ss_pred ecCCCcHHHHHHHhCCCHH----HHHHHhC
Q 040221 102 IVRGDTLWGLSRKYGVSID----AIKEANG 127 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~----~L~~~N~ 127 (142)
+.+.|||.++|++.|+..+ .+.+||.
T Consensus 358 ~~kadtleeLA~~~gid~~~l~~tv~~yN~ 387 (492)
T PRK07121 358 AWKAETVEELARKLGIPPGGLQATVDAYNR 387 (492)
T ss_pred ccccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3468999999999999976 6778884
No 188
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=27.16 E-value=84 Score=17.84 Aligned_cols=23 Identities=30% Similarity=0.359 Sum_probs=14.6
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
+.|-|...+|+..|++...|..|
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~ 32 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKI 32 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 34667777888888877777766
No 189
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=27.15 E-value=82 Score=21.12 Aligned_cols=23 Identities=9% Similarity=0.141 Sum_probs=20.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-+..+||+.+|++...+...
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~ 141 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSN 141 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHH
Confidence 37999999999999999888754
No 190
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=27.01 E-value=84 Score=20.98 Aligned_cols=23 Identities=13% Similarity=0.396 Sum_probs=19.4
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-+..+||+.+|++...++..
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~~ 149 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEYH 149 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 36889999999999999887653
No 191
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=26.78 E-value=1.1e+02 Score=19.18 Aligned_cols=46 Identities=17% Similarity=0.155 Sum_probs=35.8
Q ss_pred CceEEEecCCCcHHHHHHHhCCCHHHHHH--HhCCC--C-CCCCCCCEEec
Q 040221 96 SCRTVEIVRGDTLWGLSRKYGVSIDAIKE--ANGLS--G-DTIYAGKKLII 141 (142)
Q Consensus 96 ~~~~y~V~~GDTl~~IA~rygvs~~~L~~--~N~l~--~-~~l~~Gq~L~I 141 (142)
....+....+.|+..+-+.+|++..++.. .|+.. - ..++.|++|.|
T Consensus 23 ~~~~~~~~~~~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V 73 (81)
T PF14451_consen 23 GPFTHPFDGGATVKDVIESLGVPHTEVGLILVNGRPVDFDYRLKDGDRVAV 73 (81)
T ss_pred CceEEecCCCCcHHHHHHHcCCChHHeEEEEECCEECCCcccCCCCCEEEE
Confidence 45578889999999999999999888644 47532 2 56888998865
No 192
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=26.53 E-value=69 Score=16.18 Aligned_cols=16 Identities=25% Similarity=0.385 Sum_probs=10.9
Q ss_pred HHHHHhCCCHHHHHHH
Q 040221 110 GLSRKYGVSIDAIKEA 125 (142)
Q Consensus 110 ~IA~rygvs~~~L~~~ 125 (142)
.=|+.-|++.++++++
T Consensus 10 ~eA~~~Gls~eeir~F 25 (30)
T PF08671_consen 10 KEAKESGLSKEEIREF 25 (30)
T ss_dssp HHHHHTT--HHHHHHH
T ss_pred HHHHHcCCCHHHHHHH
Confidence 3478889999998875
No 193
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=26.51 E-value=86 Score=21.49 Aligned_cols=23 Identities=13% Similarity=0.315 Sum_probs=19.7
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-++.+||+.+|++...+..+
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~~~ 164 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVRSR 164 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 47899999999999999887643
No 194
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=26.44 E-value=85 Score=22.12 Aligned_cols=36 Identities=8% Similarity=-0.040 Sum_probs=26.3
Q ss_pred CcHHHHHHHhCCCHHHHHH----HhCCCC-CCCCCCCEEec
Q 040221 106 DTLWGLSRKYGVSIDAIKE----ANGLSG-DTIYAGKKLII 141 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~----~N~l~~-~~l~~Gq~L~I 141 (142)
+++..||+.||+++.+|.. |+.-.. ..+..|+.+.|
T Consensus 112 ~~l~kLa~~Lgvsl~el~~e~~~~~~~~~~~~~TlGd~v~i 152 (154)
T TIGR00270 112 KVVEKLEKLLKIKLREQVPEIKIEKSGRKSLGPTLGDFIKI 152 (154)
T ss_pred HHHHHHHHHhCCCHHHHccchhhccccCccCCCCCcceeEe
Confidence 5889999999999988652 334222 55778888776
No 195
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.37 E-value=79 Score=22.73 Aligned_cols=27 Identities=19% Similarity=0.111 Sum_probs=23.4
Q ss_pred EEecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 100 VEIVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 100 y~V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
+.|-.+-+|..+|..+||+....++|-
T Consensus 14 ~YV~~~~sLe~aA~~~gVs~~TarrWK 40 (165)
T PF08822_consen 14 AYVFDRLSLEQAAAKCGVSYATARRWK 40 (165)
T ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHH
Confidence 345677899999999999999999996
No 196
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.84 E-value=91 Score=20.92 Aligned_cols=23 Identities=9% Similarity=0.089 Sum_probs=20.3
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-+..+||+.+|++...++.+
T Consensus 120 ~~~~s~~EIA~~l~is~~tV~~~ 142 (154)
T PRK06759 120 FVGKTMGEIALETEMTYYQVRWI 142 (154)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 47889999999999999988765
No 197
>PRK06437 hypothetical protein; Provisional
Probab=25.77 E-value=48 Score=19.75 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=31.8
Q ss_pred ceEEEecCCCcHHHHHHHhCCCHHHHHH-HhC--CCC-CCCCCCCEEec
Q 040221 97 CRTVEIVRGDTLWGLSRKYGVSIDAIKE-ANG--LSG-DTIYAGKKLII 141 (142)
Q Consensus 97 ~~~y~V~~GDTl~~IA~rygvs~~~L~~-~N~--l~~-~~l~~Gq~L~I 141 (142)
...+.+..+-|+.++.+++|++.+.+.- .|+ +.. ..|+.|++|-|
T Consensus 12 ~~~~~i~~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~~~~~L~dgD~Vei 60 (67)
T PRK06437 12 NKTIEIDHELTVNDIIKDLGLDEEEYVVIVNGSPVLEDHNVKKEDDVLI 60 (67)
T ss_pred ceEEEcCCCCcHHHHHHHcCCCCccEEEEECCEECCCceEcCCCCEEEE
Confidence 3467778889999999999987655432 364 334 56888888754
No 198
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=25.70 E-value=57 Score=24.01 Aligned_cols=50 Identities=16% Similarity=0.100 Sum_probs=35.2
Q ss_pred CCCCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCCCCC-----CCCCCCcEEecC
Q 040221 11 PRVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPLNKN-----RNETTQPQPIAE 66 (142)
Q Consensus 11 ~~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l~~~-----~l~~Gq~l~vp~ 66 (142)
-+.|+.|++.-|.-+..+|+.. |++.+++.+.=--... -+.+|.......
T Consensus 88 ~~iPV~Y~~~~g~DL~~vA~~~------gls~~evi~~H~~~~y~V~~iGF~PGfpYL~gl 142 (202)
T PF02682_consen 88 IEIPVCYDGEFGPDLEEVAEHN------GLSVEEVIRLHSSAEYRVYMIGFAPGFPYLGGL 142 (202)
T ss_dssp EEEEEEESTTTHTTHHHHHHHH------TS-HHHHHHHHHTS-EEEEEECSSTTEEEEECS
T ss_pred EEEEEEECCCCCCCHHHHHHHh------CcCHHHHHHHHHcCchHhhccCcccCcHhhccc
Confidence 3568999999999999999999 9999999876532221 234555555443
No 199
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=25.43 E-value=90 Score=16.66 Aligned_cols=19 Identities=21% Similarity=0.178 Sum_probs=14.8
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~ 125 (142)
-...||+..|++..+|..|
T Consensus 15 ek~~L~~~tgls~~Qi~~W 33 (40)
T PF05920_consen 15 EKEELAKQTGLSRKQISNW 33 (40)
T ss_dssp HHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 3457899999999999877
No 200
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=24.76 E-value=92 Score=20.96 Aligned_cols=24 Identities=29% Similarity=0.432 Sum_probs=19.9
Q ss_pred cHHHHHHHhCCCHHHHHHHh--CCCC
Q 040221 107 TLWGLSRKYGVSIDAIKEAN--GLSG 130 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N--~l~~ 130 (142)
+...+|+++|+++..|+-|= +|-.
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~~GLL~ 30 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLLRGLLH 30 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 67889999999999999884 5543
No 201
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=24.47 E-value=56 Score=20.51 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=31.4
Q ss_pred EEecCCCcHHHHHHHhCCCHHHHHHHh---CCCC-CCCCCCCEEec
Q 040221 100 VEIVRGDTLWGLSRKYGVSIDAIKEAN---GLSG-DTIYAGKKLII 141 (142)
Q Consensus 100 y~V~~GDTl~~IA~rygvs~~~L~~~N---~l~~-~~l~~Gq~L~I 141 (142)
|.+-.-+-...+-++|++...+|-+.- .+-. -.+++||.+.|
T Consensus 15 H~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI 60 (79)
T PRK09570 15 HEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKI 60 (79)
T ss_pred eEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEE
Confidence 666667777888999999999986654 2333 46888998876
No 202
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=24.34 E-value=89 Score=21.99 Aligned_cols=20 Identities=20% Similarity=0.286 Sum_probs=18.4
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+++|++...|+-|=
T Consensus 13 ~IgevAk~~gvs~~TlRyYE 32 (154)
T PRK15002 13 TPGEVAKRSGVAVSALHFYE 32 (154)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 77899999999999999886
No 203
>PRK10072 putative transcriptional regulator; Provisional
Probab=24.32 E-value=1.1e+02 Score=19.82 Aligned_cols=25 Identities=28% Similarity=0.300 Sum_probs=21.7
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
-+.|-|-..+|+.+|++...+..|=
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE 67 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWE 67 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3568888999999999999999994
No 204
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.06 E-value=80 Score=21.95 Aligned_cols=20 Identities=30% Similarity=0.380 Sum_probs=17.3
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~ 124 (142)
-++|.+||.++|++..++..
T Consensus 90 ~~~l~~la~~~Gld~~El~~ 109 (143)
T COG3753 90 TDTLSQLAQKTGLDEQELLK 109 (143)
T ss_pred hhHHHHHHHHhCCCHHHHHH
Confidence 57999999999999887654
No 205
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.74 E-value=78 Score=21.40 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=19.2
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|=|+++||..|+++-+.+..+
T Consensus 78 ~AGlt~~aIAd~F~iS~s~~~nf 100 (126)
T PF10654_consen 78 HAGLTCYAIADYFKISKSTVFNF 100 (126)
T ss_pred hcCCChHHHHHHHhHHHHHHHHH
Confidence 37889999999999998776654
No 206
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=23.72 E-value=99 Score=22.67 Aligned_cols=24 Identities=13% Similarity=0.169 Sum_probs=20.7
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
-.|-|+..||+.+|++...+..+-
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~~ 220 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRLE 220 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 368899999999999998887763
No 207
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=23.68 E-value=1.1e+02 Score=19.23 Aligned_cols=22 Identities=32% Similarity=0.502 Sum_probs=18.6
Q ss_pred cCCCcHHHHHHHhCCCHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~ 124 (142)
++|-||.+++++-|++...|..
T Consensus 19 k~G~Sl~~LS~~agls~~tL~n 40 (82)
T COG3423 19 KKGTSLAALSREAGLSSSTLAN 40 (82)
T ss_pred HccccHHHHHHHcCCCHHHHHH
Confidence 5788999999999999888874
No 208
>PRK06134 putative FAD-binding dehydrogenase; Reviewed
Probab=23.64 E-value=79 Score=27.00 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=20.8
Q ss_pred ecCCCcHHHHHHHhCCCH----HHHHHHhC
Q 040221 102 IVRGDTLWGLSRKYGVSI----DAIKEANG 127 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~----~~L~~~N~ 127 (142)
+.++|||.++|++.|++. +++.+||.
T Consensus 426 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 455 (581)
T PRK06134 426 LKRGASLEELARACGIDPDGLEATVARYNR 455 (581)
T ss_pred EEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 347899999999999995 45577883
No 209
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=23.59 E-value=85 Score=23.06 Aligned_cols=34 Identities=18% Similarity=0.241 Sum_probs=29.5
Q ss_pred CCCccCCCCCCCCHHHHHHHhcccccCCCCHHHHHHhCCC
Q 040221 12 RVPAENDGSGDGREAAVAKTAGFVVFSGIAISILKALNPL 51 (142)
Q Consensus 12 ~~p~~~~~~~~~~~~~iA~~~~~~~~~gvs~~~L~~~N~l 51 (142)
+.|+.|++.-|--+..+|+.. |++.+++.+.---
T Consensus 90 ~IPV~Y~~~~gpDL~~vA~~~------gLs~~evi~~Hs~ 123 (201)
T smart00796 90 EIPVCYGGEFGPDLEFVARHN------GLSVDEVIRLHSA 123 (201)
T ss_pred EEeeEeCCCCCCCHHHHHHHh------CcCHHHHHHHHhC
Confidence 579999988777899999999 9999999987753
No 210
>PRK07843 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=23.43 E-value=82 Score=26.74 Aligned_cols=26 Identities=42% Similarity=0.608 Sum_probs=21.1
Q ss_pred ecCCCcHHHHHHHhCCCH----HHHHHHhC
Q 040221 102 IVRGDTLWGLSRKYGVSI----DAIKEANG 127 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~----~~L~~~N~ 127 (142)
+.++|||..+|++.|+.. +.+.+||.
T Consensus 413 ~~kadTleELA~~~gid~~~L~aTV~~yN~ 442 (557)
T PRK07843 413 IVKADTLAELAAKIGVPADALTATVQRFNG 442 (557)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 347899999999999985 45668884
No 211
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.33 E-value=1e+02 Score=21.41 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=19.2
Q ss_pred cCCCcHHHHHHHhCCCHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~ 124 (142)
-.|-+...||+.+|+++..++.
T Consensus 143 ~~g~s~~eIA~~lgis~~tV~~ 164 (179)
T PRK12514 143 LEGLSYKELAERHDVPLNTMRT 164 (179)
T ss_pred HcCCCHHHHHHHHCCChHHHHH
Confidence 4788999999999999988764
No 212
>PF07027 DUF1318: Protein of unknown function (DUF1318); InterPro: IPR008309 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.23 E-value=80 Score=20.45 Aligned_cols=36 Identities=8% Similarity=0.179 Sum_probs=25.9
Q ss_pred CcHHHHHHHhCCCHHHHHHHhCCCC-CCCCCCCEEec
Q 040221 106 DTLWGLSRKYGVSIDAIKEANGLSG-DTIYAGKKLII 141 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~~N~l~~-~~l~~Gq~L~I 141 (142)
.-...||++.|++++++...-.-.- ....+|+-+..
T Consensus 51 ~~Y~~iA~~ng~t~~~V~~~~a~k~~~~a~~G~~vq~ 87 (95)
T PF07027_consen 51 ALYQEIAKKNGITVEQVAATAAQKWIERAPPGQYVQD 87 (95)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhCCCCcEEEC
Confidence 3455899999999999888775443 56667776654
No 213
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=23.11 E-value=99 Score=21.65 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=20.0
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 040221 102 IVRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.-.|-+..+||+.+|+++..++.+
T Consensus 146 ~~~~~s~~eIA~~lgis~~tV~~~ 169 (182)
T PRK12537 146 YVDGCSHAEIAQRLGAPLGTVKAW 169 (182)
T ss_pred HHcCCCHHHHHHHHCCChhhHHHH
Confidence 358899999999999998877653
No 214
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=23.05 E-value=85 Score=23.95 Aligned_cols=45 Identities=36% Similarity=0.616 Sum_probs=25.5
Q ss_pred eEEEecCCCcHHHHHHHhC-CCHHHHHHHhCCCC-CCCCCCCEEecC
Q 040221 98 RTVEIVRGDTLWGLSRKYG-VSIDAIKEANGLSG-DTIYAGKKLIIP 142 (142)
Q Consensus 98 ~~y~V~~GDTl~~IA~ryg-vs~~~L~~~N~l~~-~~l~~Gq~L~IP 142 (142)
...+|++|||+|..=.+.. .-..++.+|-.+.. +.+++-.-|+||
T Consensus 113 r~v~vKKGdtI~~FL~~~r~~l~~~f~el~~vsvd~LM~VkedlIiP 159 (239)
T PF04921_consen 113 RTVRVKKGDTIWQFLEKCRKQLAKEFRELRRVSVDDLMYVKEDLIIP 159 (239)
T ss_pred ceEEEcCCCCHHHHHHHHHHHHHHHhHHHHhcCHhheeeeccceecc
Confidence 3778999999997754431 11233555555544 444444445554
No 215
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=23.04 E-value=1e+02 Score=18.29 Aligned_cols=22 Identities=18% Similarity=0.363 Sum_probs=16.9
Q ss_pred CCHHHHHHHhcccccCCCCHHHHHHhCC
Q 040221 23 GREAAVAKTAGFVVFSGIAISILKALNP 50 (142)
Q Consensus 23 ~~~~~iA~~~~~~~~~gvs~~~L~~~N~ 50 (142)
=+...||+.. |+++.++..+-.
T Consensus 21 Pt~eEiA~~l------gis~~~v~~~l~ 42 (78)
T PF04539_consen 21 PTDEEIAEEL------GISVEEVRELLQ 42 (78)
T ss_dssp -BHHHHHHHH------TS-HHHHHHHHH
T ss_pred CCHHHHHHHH------cccHHHHHHHHH
Confidence 3678999999 999999986654
No 216
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=22.92 E-value=1e+02 Score=19.54 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=20.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Q 040221 105 GDTLWGLSRKYGVSIDAIKEANG 127 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~N~ 127 (142)
.|=+..||+..|++..+|..+|-
T Consensus 69 ~~EirGIA~~~gi~l~~iv~lN~ 91 (95)
T PF15508_consen 69 AEEIRGIAKAAGIPLGDIVLLNL 91 (95)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Confidence 36688999999999999999993
No 217
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=22.91 E-value=1.1e+02 Score=16.80 Aligned_cols=19 Identities=21% Similarity=0.375 Sum_probs=15.2
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~ 125 (142)
++.+||++.|++...+.++
T Consensus 20 t~~eia~~~gl~~stv~r~ 38 (52)
T PF09339_consen 20 TLSEIARALGLPKSTVHRL 38 (52)
T ss_dssp EHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 8999999999998776654
No 218
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=22.85 E-value=87 Score=22.76 Aligned_cols=25 Identities=16% Similarity=0.368 Sum_probs=21.8
Q ss_pred EecCCCcHHHHHHHhCCCHHHHHHH
Q 040221 101 EIVRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 101 ~V~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
.|..|+.+-.+|+..|++..++-+.
T Consensus 28 ~vsaG~iFR~~A~e~gmsl~ef~~~ 52 (179)
T COG1102 28 LVSAGTIFREMARERGMSLEEFSRY 52 (179)
T ss_pred eeeccHHHHHHHHHcCCCHHHHHHH
Confidence 4679999999999999998887664
No 219
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.78 E-value=1.1e+02 Score=19.77 Aligned_cols=20 Identities=15% Similarity=0.350 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 040221 107 TLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~N 126 (142)
+...+|+++|++...|+-+=
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe 21 (107)
T cd04777 2 KIGKFAKKNNITIDTVRHYI 21 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999998775
No 220
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=22.67 E-value=88 Score=20.29 Aligned_cols=27 Identities=26% Similarity=0.316 Sum_probs=22.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh-CCC
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN-GLS 129 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N-~l~ 129 (142)
+.|-|-..||++.|++...|-++. .++
T Consensus 53 ~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 53 NGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred hCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 357799999999999999999985 455
No 221
>PRK12843 putative FAD-binding dehydrogenase; Reviewed
Probab=22.51 E-value=86 Score=26.74 Aligned_cols=25 Identities=24% Similarity=0.292 Sum_probs=20.6
Q ss_pred cCCCcHHHHHHHhCCCH----HHHHHHhC
Q 040221 103 VRGDTLWGLSRKYGVSI----DAIKEANG 127 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~----~~L~~~N~ 127 (142)
.+.|||.++|++.|+.. +++.+||.
T Consensus 429 ~kadTleELA~~~gid~~~L~~Tv~~yN~ 457 (578)
T PRK12843 429 TVASTLDELAPKLGIDPAALAATVQRHNQ 457 (578)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 47899999999999985 45677884
No 222
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.48 E-value=1.3e+02 Score=16.53 Aligned_cols=19 Identities=26% Similarity=0.358 Sum_probs=16.5
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~~ 125 (142)
+...||+..|++...+.++
T Consensus 27 S~~~la~~~g~s~~Tv~~~ 45 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRA 45 (55)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 6789999999998888765
No 223
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=22.40 E-value=1.1e+02 Score=20.83 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=19.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-+...||+.+|++...+..+
T Consensus 139 ~~~~~~~eIA~~lgis~~tv~~~ 161 (179)
T PRK11924 139 VEGLSYREIAEILGVPVGTVKSR 161 (179)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 36889999999999999887764
No 224
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.34 E-value=1.1e+02 Score=21.85 Aligned_cols=22 Identities=14% Similarity=0.365 Sum_probs=19.1
Q ss_pred cCCCcHHHHHHHhCCCHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~ 124 (142)
-.|-|...||+.+|++...+.+
T Consensus 149 ~~Gls~~EIA~~lgiS~~tV~r 170 (185)
T PF07638_consen 149 FEGLSVEEIAERLGISERTVRR 170 (185)
T ss_pred HCCCCHHHHHHHHCcCHHHHHH
Confidence 4799999999999999888764
No 225
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=22.30 E-value=1.1e+02 Score=21.10 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=18.4
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 040221 105 GDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~ 125 (142)
|.+..++|++|..|...|.+.
T Consensus 102 G~n~~eLaKkYrlS~~~Iy~V 122 (137)
T COG5566 102 GSNYVELAKKYRLSENHIYRV 122 (137)
T ss_pred CccHHHHHHHhcccHHHHHHH
Confidence 889999999999998888764
No 226
>PRK06481 fumarate reductase flavoprotein subunit; Validated
Probab=21.81 E-value=93 Score=26.00 Aligned_cols=25 Identities=24% Similarity=0.324 Sum_probs=20.3
Q ss_pred cCCCcHHHHHHHhCCCHHH----HHHHhC
Q 040221 103 VRGDTLWGLSRKYGVSIDA----IKEANG 127 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~----L~~~N~ 127 (142)
.++|||.++|++.|+..+. +.+||.
T Consensus 376 ~kadTleeLA~~~gid~~~L~~tv~~yN~ 404 (506)
T PRK06481 376 EEGKTIDELAKKINVPAETLTKTLDTWNK 404 (506)
T ss_pred EEcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4689999999999999765 556783
No 227
>PRK12842 putative succinate dehydrogenase; Reviewed
Probab=21.79 E-value=87 Score=26.64 Aligned_cols=26 Identities=31% Similarity=0.562 Sum_probs=21.0
Q ss_pred ecCCCcHHHHHHHhCCCH----HHHHHHhC
Q 040221 102 IVRGDTLWGLSRKYGVSI----DAIKEANG 127 (142)
Q Consensus 102 V~~GDTl~~IA~rygvs~----~~L~~~N~ 127 (142)
+.++|||.++|++.|+.. +.+.+||.
T Consensus 423 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 452 (574)
T PRK12842 423 LIKGDTLAELAGKAGIDAAGLEATVRRYNE 452 (574)
T ss_pred EEEcCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 447899999999999985 45678884
No 228
>PF14502 HTH_41: Helix-turn-helix domain
Probab=21.64 E-value=1.4e+02 Score=16.93 Aligned_cols=18 Identities=39% Similarity=0.538 Sum_probs=14.4
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040221 107 TLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 107 Tl~~IA~rygvs~~~L~~ 124 (142)
|..+.+++|+++...++.
T Consensus 8 tI~e~~~~~~vs~GtiQ~ 25 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQN 25 (48)
T ss_pred CHHHHHHHhCcchhHHHH
Confidence 677889999999776654
No 229
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.59 E-value=1.1e+02 Score=18.50 Aligned_cols=22 Identities=27% Similarity=0.120 Sum_probs=16.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHh
Q 040221 105 GDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 105 GDTl~~IA~rygvs~~~L~~~N 126 (142)
.-|..+||+..+++...+.++=
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~ 55 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFC 55 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHH
Confidence 4588899999999999988874
No 230
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=21.56 E-value=1.1e+02 Score=17.45 Aligned_cols=19 Identities=37% Similarity=0.366 Sum_probs=14.3
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIKE 124 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~~ 124 (142)
=++..||+++|++...|+.
T Consensus 20 ~~~~ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 20 ITLKELAKKLNISERTIKN 38 (59)
T ss_dssp BBHHHHHHHCTS-HHHHHH
T ss_pred CcHHHHHHHHCCCHHHHHH
Confidence 4788999999999766553
No 231
>TIGR02008 fdx_plant ferredoxin [2Fe-2S]. This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins.
Probab=21.54 E-value=1.1e+02 Score=19.39 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=20.7
Q ss_pred ceEEEecCCCcHHHHHHHhCCCHH
Q 040221 97 CRTVEIVRGDTLWGLSRKYGVSID 120 (142)
Q Consensus 97 ~~~y~V~~GDTl~~IA~rygvs~~ 120 (142)
...+.+.+|++|-+.+.+.|+.+.
T Consensus 14 ~~~~~~~~g~tLLda~~~~Gi~i~ 37 (97)
T TIGR02008 14 EETIECPDDQYILDAAEEAGIDLP 37 (97)
T ss_pred EEEEEECCCCcHHHHHHHcCCCCC
Confidence 467889999999999999998753
No 232
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=21.02 E-value=90 Score=20.51 Aligned_cols=18 Identities=17% Similarity=0.442 Sum_probs=13.1
Q ss_pred CcHHHHHHHhCCCHHHHH
Q 040221 106 DTLWGLSRKYGVSIDAIK 123 (142)
Q Consensus 106 DTl~~IA~rygvs~~~L~ 123 (142)
+-...||++|+++++...
T Consensus 41 ~LYp~IA~k~~TT~s~VE 58 (106)
T PF08769_consen 41 ELYPDIAKKYGTTPSRVE 58 (106)
T ss_dssp THHHHHHHHTTS-HHHHH
T ss_pred hHHHHHHHHHCCCHHHHH
Confidence 456699999999986654
No 233
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=20.93 E-value=1.3e+02 Score=17.51 Aligned_cols=23 Identities=13% Similarity=0.264 Sum_probs=17.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
+.|=|+.++|++.+++...|..+
T Consensus 8 ~~glsl~~va~~t~I~~~~l~ai 30 (62)
T PF13413_consen 8 AKGLSLEDVAEETKISVSYLEAI 30 (62)
T ss_dssp CTT--HHHHHHHCS--HHHHHHH
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Confidence 57889999999999999999876
No 234
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.78 E-value=1.2e+02 Score=22.62 Aligned_cols=24 Identities=13% Similarity=0.261 Sum_probs=21.1
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEAN 126 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~N 126 (142)
..|-|+..||+.+|++...+..+-
T Consensus 216 ~~~~s~~eIA~~lgis~~~V~~~~ 239 (252)
T PRK05572 216 FKDKTQSEVAKRLGISQVQVSRLE 239 (252)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHH
Confidence 478899999999999999888764
No 235
>PRK12835 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=20.54 E-value=1e+02 Score=26.46 Aligned_cols=25 Identities=32% Similarity=0.372 Sum_probs=20.8
Q ss_pred cCCCcHHHHHHHhCCCH----HHHHHHhC
Q 040221 103 VRGDTLWGLSRKYGVSI----DAIKEANG 127 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~----~~L~~~N~ 127 (142)
.+.|||.++|++.|+.. +.+.+||.
T Consensus 428 ~kAdTleeLA~~~gida~~L~aTV~~yN~ 456 (584)
T PRK12835 428 KKADTWDELAAKIGVPAENLRATAERFNG 456 (584)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 47899999999999984 56678884
No 236
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.18 E-value=1.3e+02 Score=20.75 Aligned_cols=23 Identities=13% Similarity=0.166 Sum_probs=19.7
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-+..+||+.+|++...+...
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~ 162 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSR 162 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHH
Confidence 47999999999999999877543
No 237
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=20.17 E-value=1.5e+02 Score=20.54 Aligned_cols=23 Identities=4% Similarity=0.098 Sum_probs=19.7
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
..|-|...||+++|++...+..+
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~ 41 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAI 41 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 47889999999999998877654
No 238
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=20.02 E-value=1.4e+02 Score=20.09 Aligned_cols=23 Identities=30% Similarity=0.505 Sum_probs=20.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 040221 103 VRGDTLWGLSRKYGVSIDAIKEA 125 (142)
Q Consensus 103 ~~GDTl~~IA~rygvs~~~L~~~ 125 (142)
-.|-+...||+.+|++...+...
T Consensus 125 ~~g~~~~eIA~~l~is~~tv~~~ 147 (159)
T TIGR02989 125 QRGVSLTALAEQLGRTVNAVYKA 147 (159)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHH
Confidence 47899999999999999888764
Done!