Query 037542
Match_columns 129
No_of_seqs 230 out of 1203
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 13:18:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037542hhsearch_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 2E-21 4.4E-26 160.5 11.2 99 1-103 486-592 (592)
2 PRK10783 mltD membrane-bound l 99.9 7.7E-21 1.7E-25 153.6 12.1 98 1-106 350-450 (456)
3 PRK06347 autolysin; Reviewed 99.8 2E-19 4.3E-24 148.7 13.4 103 1-107 412-528 (592)
4 PRK13914 invasion associated s 99.7 4.5E-17 9.8E-22 131.2 13.6 46 62-107 200-248 (481)
5 PF01476 LysM: LysM domain; I 99.6 5.5E-15 1.2E-19 82.9 4.3 40 64-103 1-44 (44)
6 COG1388 LytE FOG: LysM repeat 99.5 5.7E-14 1.2E-18 95.1 8.0 94 8-104 1-112 (124)
7 PRK10783 mltD membrane-bound l 99.5 1.6E-13 3.5E-18 111.2 10.8 102 2-106 271-391 (456)
8 PRK14125 cell division suppres 99.3 9.6E-12 2.1E-16 82.2 6.8 48 61-108 36-94 (103)
9 TIGR02899 spore_safA spore coa 99.2 1.8E-11 3.9E-16 67.9 4.5 39 66-104 1-44 (44)
10 cd00118 LysM Lysin domain, fou 99.2 4.5E-11 9.9E-16 65.5 5.5 41 63-103 2-46 (46)
11 PF01476 LysM: LysM domain; I 99.2 2.3E-11 4.9E-16 68.0 3.1 40 1-43 5-44 (44)
12 TIGR02907 spore_VI_D stage VI 99.1 2E-10 4.4E-15 88.9 5.9 44 60-103 292-338 (338)
13 PRK10871 nlpD lipoprotein NlpD 99.1 1.6E-10 3.4E-15 89.8 5.1 45 62-106 61-109 (319)
14 COG3858 Predicted glycosyl hyd 99.1 1.6E-10 3.4E-15 91.7 5.0 89 1-108 8-100 (423)
15 TIGR02899 spore_safA spore coa 99.0 6.3E-10 1.4E-14 61.5 4.8 41 1-44 3-44 (44)
16 PRK13914 invasion associated s 99.0 1.2E-09 2.5E-14 88.7 5.7 44 62-105 28-74 (481)
17 smart00257 LysM Lysin motif. 98.9 2.9E-09 6.2E-14 57.4 4.8 40 63-102 1-44 (44)
18 PRK14125 cell division suppres 98.8 1E-08 2.2E-13 67.8 5.5 45 1-46 43-92 (103)
19 cd00118 LysM Lysin domain, fou 98.8 1.4E-08 3E-13 55.3 4.9 40 1-43 7-46 (46)
20 PRK10871 nlpD lipoprotein NlpD 98.7 2.1E-08 4.6E-13 77.9 4.9 42 1-45 67-108 (319)
21 PRK11198 LysM domain/BON super 98.7 2.9E-08 6.4E-13 69.4 5.1 43 61-103 95-146 (147)
22 smart00257 LysM Lysin motif. 98.4 5.5E-07 1.2E-11 48.2 4.8 39 1-42 6-44 (44)
23 PRK11198 LysM domain/BON super 98.4 3.5E-07 7.7E-12 64.0 4.6 43 1-43 102-146 (147)
24 COG1388 LytE FOG: LysM repeat 98.2 1.8E-06 3.9E-11 58.2 4.3 40 1-44 73-112 (124)
25 PF04225 OapA: Opacity-associa 98.2 2.1E-06 4.7E-11 54.8 3.5 45 62-106 3-55 (85)
26 TIGR03505 FimV_core FimV N-ter 98.1 3.5E-06 7.5E-11 52.5 3.7 37 70-106 1-53 (74)
27 TIGR03505 FimV_core FimV N-ter 98.0 7.7E-06 1.7E-10 50.9 3.5 42 3-44 1-51 (74)
28 PRK10190 L,D-transpeptidase; P 97.7 8.1E-05 1.8E-09 57.8 6.2 48 59-106 35-88 (310)
29 PRK10260 L,D-transpeptidase; P 97.7 8E-05 1.7E-09 57.7 6.1 48 59-106 38-91 (306)
30 COG1652 XkdP Uncharacterized p 97.6 1.8E-05 4E-10 60.2 0.8 45 62-106 211-265 (269)
31 PF05489 Phage_tail_X: Phage T 97.5 0.00014 3E-09 43.5 3.1 44 1-44 7-53 (60)
32 COG1652 XkdP Uncharacterized p 97.3 6E-05 1.3E-09 57.3 0.7 44 1-44 217-263 (269)
33 PRK10260 L,D-transpeptidase; P 97.2 0.00063 1.4E-08 52.8 5.0 40 3-45 51-90 (306)
34 PRK10190 L,D-transpeptidase; P 97.2 0.00066 1.4E-08 52.8 5.1 40 3-45 48-87 (310)
35 COG3170 FimV Tfp pilus assembl 97.0 0.0005 1.1E-08 58.4 3.1 48 61-108 188-251 (755)
36 PF05489 Phage_tail_X: Phage T 97.0 0.0019 4.1E-08 38.5 4.5 42 63-105 3-54 (60)
37 PRK11649 putative peptidase; P 96.8 0.0031 6.8E-08 51.4 5.5 46 61-106 95-145 (439)
38 COG3061 OapA Cell envelope opa 96.5 0.0083 1.8E-07 44.5 5.6 47 60-106 158-212 (242)
39 PF04225 OapA: Opacity-associa 96.1 0.0028 6E-08 40.4 1.2 45 1-45 9-54 (85)
40 PRK11649 putative peptidase; P 95.6 0.13 2.8E-06 42.1 9.3 101 1-104 102-235 (439)
41 COG3858 Predicted glycosyl hyd 95.4 0.0076 1.6E-07 48.6 1.5 43 62-104 2-47 (423)
42 COG0739 NlpD Membrane proteins 91.8 0.37 8E-06 36.0 4.8 45 62-106 2-50 (277)
43 COG4784 Putative Zn-dependent 90.8 0.57 1.2E-05 37.5 5.0 43 61-103 428-477 (479)
44 PF13518 HTH_28: Helix-turn-he 90.6 0.31 6.7E-06 27.1 2.6 25 67-91 10-34 (52)
45 COG4254 Uncharacterized protei 89.3 0.34 7.3E-06 37.7 2.6 46 62-107 6-58 (339)
46 COG3170 FimV Tfp pilus assembl 89.3 0.42 9.2E-06 41.2 3.4 45 1-45 195-248 (755)
47 KOG2850 Predicted peptidoglyca 89.0 0.3 6.5E-06 35.5 2.0 45 62-106 10-58 (186)
48 PF02796 HTH_7: Helix-turn-hel 88.8 0.53 1.1E-05 26.0 2.6 23 67-89 19-41 (45)
49 COG5004 P2-like prophage tail 87.3 1.8 3.9E-05 26.1 4.3 43 62-104 3-55 (70)
50 COG3061 OapA Cell envelope opa 85.8 1.2 2.6E-05 33.3 3.7 46 1-46 166-212 (242)
51 PF01527 HTH_Tnp_1: Transposas 84.4 0.66 1.4E-05 27.9 1.5 24 66-89 20-43 (76)
52 COG2963 Transposase and inacti 81.5 1.7 3.7E-05 28.5 2.8 25 65-89 20-45 (116)
53 PF13384 HTH_23: Homeodomain-l 81.4 2 4.3E-05 23.7 2.7 23 67-89 15-37 (50)
54 COG5004 P2-like prophage tail 80.8 2 4.4E-05 25.9 2.6 46 1-46 9-57 (70)
55 PF04218 CENP-B_N: CENP-B N-te 80.2 0.97 2.1E-05 25.9 1.1 24 66-89 19-42 (53)
56 PRK09413 IS2 repressor TnpA; R 80.0 2.2 4.9E-05 28.4 3.0 28 64-91 24-51 (121)
57 PHA00675 hypothetical protein 78.0 2.8 6.1E-05 26.2 2.7 24 67-90 37-60 (78)
58 COG4254 Uncharacterized protei 77.8 1.9 4.1E-05 33.7 2.3 46 1-46 12-57 (339)
59 PF13936 HTH_38: Helix-turn-he 75.5 4 8.6E-05 22.3 2.7 23 66-88 17-39 (44)
60 cd00569 HTH_Hin_like Helix-tur 75.3 5.2 0.00011 19.1 3.0 23 67-89 19-41 (42)
61 COG0739 NlpD Membrane proteins 75.3 4.3 9.4E-05 30.2 3.7 42 1-45 8-49 (277)
62 COG4784 Putative Zn-dependent 74.6 5.2 0.00011 32.2 4.0 42 1-43 435-477 (479)
63 PF05225 HTH_psq: helix-turn-h 73.4 3.8 8.2E-05 22.6 2.2 24 66-89 12-36 (45)
64 PF13542 HTH_Tnp_ISL3: Helix-t 72.4 5.2 0.00011 22.1 2.7 21 69-89 27-47 (52)
65 PF04545 Sigma70_r4: Sigma-70, 71.4 6.8 0.00015 21.6 3.1 23 67-89 18-40 (50)
66 PF00376 MerR: MerR family reg 68.9 5.6 0.00012 21.1 2.2 21 71-91 1-21 (38)
67 PF10668 Phage_terminase: Phag 68.6 6.8 0.00015 23.3 2.7 22 70-91 23-44 (60)
68 PF01710 HTH_Tnp_IS630: Transp 67.0 4.4 9.6E-05 26.9 1.9 25 66-90 15-39 (119)
69 PF04255 DUF433: Protein of un 65.8 7.1 0.00015 22.4 2.4 23 67-89 29-52 (56)
70 cd04762 HTH_MerR-trunc Helix-T 65.5 9 0.0002 20.2 2.7 21 71-91 2-22 (49)
71 PF08765 Mor: Mor transcriptio 65.4 7.2 0.00016 25.5 2.6 21 69-89 72-92 (108)
72 PF12471 GTP_CH_N: GTP cyclohy 64.8 4.8 0.0001 29.3 1.8 19 71-89 172-190 (194)
73 KOG2850 Predicted peptidoglyca 64.7 4.4 9.5E-05 29.5 1.6 42 1-45 16-57 (186)
74 PF14451 Ub-Mut7C: Mut7-C ubiq 63.5 12 0.00026 23.5 3.2 42 62-103 25-74 (81)
75 cd04761 HTH_MerR-SF Helix-Turn 62.5 11 0.00023 20.3 2.7 21 71-91 2-22 (49)
76 cd01104 HTH_MlrA-CarA Helix-Tu 60.7 11 0.00024 21.9 2.7 19 71-89 2-20 (68)
77 PF00356 LacI: Bacterial regul 60.3 14 0.0003 20.5 2.8 19 71-89 1-19 (46)
78 smart00351 PAX Paired Box doma 60.0 10 0.00023 25.4 2.7 25 67-91 31-55 (125)
79 PF13613 HTH_Tnp_4: Helix-turn 59.5 8.9 0.00019 21.7 2.0 23 66-88 16-38 (53)
80 COG3415 Transposase and inacti 59.1 10 0.00022 26.3 2.5 28 64-91 16-43 (138)
81 PF13693 HTH_35: Winged helix- 59.1 12 0.00027 23.3 2.7 23 67-89 13-35 (78)
82 COG3721 HugX Putative heme iro 58.9 17 0.00038 25.8 3.7 25 67-91 25-49 (176)
83 smart00421 HTH_LUXR helix_turn 57.0 18 0.0004 19.5 3.1 24 66-89 15-38 (58)
84 TIGR02531 yecD_yerC TrpR-relat 56.9 13 0.00028 23.6 2.6 26 66-91 47-72 (88)
85 PF13411 MerR_1: MerR HTH fami 56.7 12 0.00026 21.8 2.3 21 71-91 2-22 (69)
86 TIGR03595 Obg_CgtA_exten Obg f 56.5 34 0.00073 20.6 4.3 40 63-103 10-63 (69)
87 PF11268 DUF3071: Protein of u 56.4 11 0.00024 27.0 2.4 29 63-91 63-91 (170)
88 PRK09570 rpoH DNA-directed RNA 55.9 12 0.00027 23.4 2.3 43 63-105 14-63 (79)
89 PF13011 LZ_Tnp_IS481: leucine 55.8 15 0.00032 23.4 2.7 27 65-91 21-47 (85)
90 PHA01976 helix-turn-helix prot 54.9 8.5 0.00018 22.4 1.4 19 69-87 44-62 (67)
91 PF09012 FeoC: FeoC like trans 54.8 12 0.00026 22.3 2.1 19 71-89 16-34 (69)
92 TIGR01764 excise DNA binding d 53.9 19 0.00042 18.9 2.7 21 71-91 3-23 (49)
93 smart00422 HTH_MERR helix_turn 53.9 17 0.00037 21.1 2.7 21 71-91 2-22 (70)
94 cd04764 HTH_MlrA-like_sg1 Heli 53.3 18 0.00039 21.1 2.7 20 71-90 2-21 (67)
95 PF13551 HTH_29: Winged helix- 53.1 16 0.00034 23.1 2.6 26 66-91 8-34 (112)
96 PF12964 DUF3853: Protein of u 52.2 11 0.00024 24.5 1.7 38 5-43 48-85 (96)
97 PF01710 HTH_Tnp_IS630: Transp 51.2 21 0.00046 23.6 3.1 23 67-89 69-91 (119)
98 PF08281 Sigma70_r4_2: Sigma-7 50.7 19 0.00041 19.9 2.4 23 67-89 24-46 (54)
99 PF08220 HTH_DeoR: DeoR-like h 49.3 19 0.0004 20.6 2.3 18 71-88 16-33 (57)
100 smart00760 Bac_DnaA_C Bacteria 49.3 18 0.00039 20.8 2.2 22 70-91 4-25 (60)
101 PF01371 Trp_repressor: Trp re 49.2 17 0.00037 23.1 2.2 25 67-91 47-71 (87)
102 smart00345 HTH_GNTR helix_turn 48.4 31 0.00068 18.9 3.2 19 71-89 22-40 (60)
103 cd04763 HTH_MlrA-like Helix-Tu 47.9 24 0.00052 20.6 2.7 21 71-91 2-22 (68)
104 cd06170 LuxR_C_like C-terminal 47.8 32 0.00069 18.6 3.1 23 67-89 13-35 (57)
105 PF11242 DUF2774: Protein of u 47.6 30 0.00066 20.6 2.9 22 67-88 11-32 (63)
106 COG1102 Cmk Cytidylate kinase 46.9 20 0.00043 25.9 2.5 26 64-89 27-52 (179)
107 PF04760 IF2_N: Translation in 46.6 15 0.00033 20.7 1.6 19 71-89 5-23 (54)
108 cd00131 PAX Paired Box domain 46.4 23 0.0005 23.9 2.7 25 67-91 31-55 (128)
109 COG2442 Uncharacterized conser 46.1 25 0.00054 22.0 2.6 26 64-89 38-64 (79)
110 PF14502 HTH_41: Helix-turn-he 45.8 28 0.00061 19.7 2.5 19 71-89 8-26 (48)
111 PF06056 Terminase_5: Putative 44.9 36 0.00077 19.8 3.0 24 68-91 12-35 (58)
112 TIGR03028 EpsE polysaccharide 43.9 1.3E+02 0.0029 22.3 6.9 69 32-104 149-236 (239)
113 PF04967 HTH_10: HTH DNA bindi 43.8 27 0.00058 20.1 2.3 25 63-87 17-41 (53)
114 PF08299 Bac_DnaA_C: Bacterial 43.1 25 0.00054 21.1 2.2 19 71-89 5-23 (70)
115 PF12244 DUF3606: Protein of u 42.3 23 0.0005 20.5 1.9 19 71-89 22-40 (57)
116 cd04768 HTH_BmrR-like Helix-Tu 41.7 32 0.00068 21.8 2.7 21 71-91 2-22 (96)
117 PF15508 NAAA-beta: beta subun 41.5 29 0.00063 22.0 2.5 23 69-91 69-91 (95)
118 TIGR02844 spore_III_D sporulat 41.5 34 0.00074 21.4 2.7 20 70-89 20-39 (80)
119 PHA02591 hypothetical protein; 41.1 36 0.00078 21.4 2.7 28 62-89 38-68 (83)
120 TIGR02937 sigma70-ECF RNA poly 41.1 35 0.00076 22.1 3.0 23 67-89 124-146 (158)
121 PF13510 Fer2_4: 2Fe-2S iron-s 40.8 27 0.00058 21.6 2.2 22 62-83 11-32 (82)
122 PRK10344 DNA-binding transcrip 40.7 38 0.00081 21.8 2.8 23 67-89 19-41 (92)
123 cd04775 HTH_Cfa-like Helix-Tur 40.6 33 0.00072 22.0 2.7 21 71-91 3-23 (102)
124 cd04766 HTH_HspR Helix-Turn-He 40.3 35 0.00075 21.3 2.7 21 71-91 3-23 (91)
125 cd01279 HTH_HspR-like Helix-Tu 40.2 34 0.00075 21.8 2.7 20 71-90 3-22 (98)
126 PF09607 BrkDBD: Brinker DNA-b 39.8 38 0.00083 19.9 2.5 20 71-90 27-46 (58)
127 PF07789 DUF1627: Protein of u 39.6 55 0.0012 23.1 3.7 47 70-116 7-63 (155)
128 PF00165 HTH_AraC: Bacterial r 38.9 42 0.00092 17.5 2.5 21 69-89 8-28 (42)
129 smart00342 HTH_ARAC helix_turn 38.9 40 0.00088 19.5 2.7 18 71-88 3-20 (84)
130 PF14493 HTH_40: Helix-turn-he 38.7 38 0.00082 21.2 2.7 22 67-88 11-32 (91)
131 PF00392 GntR: Bacterial regul 38.6 39 0.00084 19.5 2.5 19 71-89 26-44 (64)
132 COG3753 Uncharacterized protei 38.6 30 0.00065 24.0 2.2 20 69-88 90-109 (143)
133 cd06171 Sigma70_r4 Sigma70, re 38.4 55 0.0012 17.0 3.0 22 68-89 25-46 (55)
134 cd01109 HTH_YyaN Helix-Turn-He 38.0 38 0.00082 22.0 2.7 21 71-91 2-22 (113)
135 PF12116 SpoIIID: Stage III sp 37.9 9.5 0.00021 24.0 -0.2 23 63-85 13-35 (82)
136 cd01105 HTH_GlnR-like Helix-Tu 37.6 41 0.00089 21.0 2.7 21 71-91 3-23 (88)
137 PF12728 HTH_17: Helix-turn-he 37.5 47 0.001 18.0 2.7 33 71-103 3-39 (51)
138 cd04774 HTH_YfmP Helix-Turn-He 37.4 41 0.00088 21.4 2.7 21 71-91 2-22 (96)
139 PF06627 DUF1153: Protein of u 37.2 33 0.00071 22.0 2.1 26 66-91 45-71 (90)
140 cd04788 HTH_NolA-AlbR Helix-Tu 37.1 41 0.0009 21.3 2.7 21 71-91 2-22 (96)
141 PF12298 Bot1p: Eukaryotic mit 36.7 24 0.00052 25.3 1.6 39 2-41 33-71 (172)
142 PF12298 Bot1p: Eukaryotic mit 36.5 45 0.00098 23.9 3.0 25 67-91 31-58 (172)
143 cd01107 HTH_BmrR Helix-Turn-He 36.4 42 0.0009 21.7 2.7 21 71-91 2-22 (108)
144 COG2739 Uncharacterized protei 36.0 41 0.00088 22.2 2.5 18 71-88 35-52 (105)
145 TIGR03879 near_KaiC_dom probab 35.9 59 0.0013 20.0 3.1 23 67-89 30-52 (73)
146 PRK06437 hypothetical protein; 35.9 38 0.00082 20.1 2.2 41 62-102 13-60 (67)
147 PF07022 Phage_CI_repr: Bacter 35.8 20 0.00043 21.2 0.9 19 69-87 41-59 (66)
148 cd04782 HTH_BltR Helix-Turn-He 35.8 45 0.00097 21.2 2.7 21 71-91 2-22 (97)
149 PF12844 HTH_19: Helix-turn-he 35.7 20 0.00044 20.4 1.0 19 70-88 42-60 (64)
150 TIGR00270 conserved hypothetic 35.4 40 0.00086 23.7 2.6 18 70-87 112-129 (154)
151 cd04772 HTH_TioE_rpt1 First He 35.4 46 0.00099 21.3 2.7 21 71-91 2-22 (99)
152 KOG3309 Ferredoxin [Energy pro 34.9 36 0.00077 24.1 2.2 24 61-84 55-78 (159)
153 PRK01777 hypothetical protein; 34.8 54 0.0012 21.1 2.9 41 62-102 19-73 (95)
154 cd04789 HTH_Cfa Helix-Turn-Hel 34.7 48 0.001 21.3 2.7 21 71-91 3-23 (102)
155 TIGR03826 YvyF flagellar opero 34.6 70 0.0015 22.1 3.6 31 67-101 42-74 (137)
156 PHA03253 UL35; Provisional 34.6 1E+02 0.0022 26.3 5.1 20 72-91 441-461 (609)
157 cd04770 HTH_HMRTR Helix-Turn-H 34.4 46 0.001 21.8 2.7 21 71-91 2-22 (123)
158 cd01282 HTH_MerR-like_sg3 Heli 33.9 49 0.0011 21.6 2.7 21 71-91 2-22 (112)
159 PRK12845 3-ketosteroid-delta-1 33.9 40 0.00087 28.5 2.8 25 67-91 422-450 (564)
160 cd01108 HTH_CueR Helix-Turn-He 33.6 48 0.001 22.1 2.7 21 71-91 2-22 (127)
161 cd04769 HTH_MerR2 Helix-Turn-H 33.4 50 0.0011 21.6 2.7 21 71-91 2-22 (116)
162 PRK12837 3-ketosteroid-delta-1 33.1 43 0.00094 27.7 2.8 25 67-91 373-401 (513)
163 PF08279 HTH_11: HTH domain; 32.9 41 0.00089 18.6 1.9 17 71-87 17-33 (55)
164 TIGR02044 CueR Cu(I)-responsiv 32.3 52 0.0011 21.9 2.7 21 71-91 2-22 (127)
165 TIGR00247 conserved hypothetic 32.1 74 0.0016 25.1 3.9 77 1-79 46-128 (342)
166 TIGR02008 fdx_plant ferredoxin 32.1 56 0.0012 20.7 2.7 23 62-84 15-37 (97)
167 cd01106 HTH_TipAL-Mta Helix-Tu 32.1 55 0.0012 20.8 2.7 21 71-91 2-22 (103)
168 cd00093 HTH_XRE Helix-turn-hel 31.9 75 0.0016 16.2 2.9 25 67-91 10-34 (58)
169 PF02618 YceG: YceG-like famil 31.7 14 0.00031 28.5 -0.2 77 1-79 7-88 (297)
170 cd04785 HTH_CadR-PbrR-like Hel 31.7 54 0.0012 21.8 2.7 21 71-91 2-22 (126)
171 PF14453 ThiS-like: ThiS-like 31.7 55 0.0012 19.1 2.3 40 62-102 8-53 (57)
172 cd04765 HTH_MlrA-like_sg2 Heli 31.4 57 0.0012 20.9 2.7 19 71-89 2-20 (99)
173 cd04767 HTH_HspR-like_MBC Heli 31.3 57 0.0012 22.0 2.7 21 71-91 3-23 (120)
174 PRK00118 putative DNA-binding 31.2 66 0.0014 21.1 2.9 23 67-89 31-53 (104)
175 TIGR00370 conserved hypothetic 31.2 1.2E+02 0.0025 22.3 4.5 29 63-91 84-112 (202)
176 PF00196 GerE: Bacterial regul 30.9 52 0.0011 18.5 2.2 23 66-88 15-37 (58)
177 PRK10270 putative aminodeoxych 30.8 1.1E+02 0.0024 24.2 4.7 77 1-79 46-127 (340)
178 COG5484 Uncharacterized conser 30.8 48 0.001 25.5 2.5 23 69-91 19-41 (279)
179 PF13404 HTH_AsnC-type: AsnC-t 30.5 67 0.0014 17.2 2.4 18 70-87 18-35 (42)
180 PRK12839 hypothetical protein; 30.4 49 0.0011 28.0 2.8 24 68-91 426-453 (572)
181 cd04780 HTH_MerR-like_sg5 Heli 30.2 63 0.0014 20.5 2.7 21 71-91 2-22 (95)
182 cd04777 HTH_MerR-like_sg1 Heli 30.1 56 0.0012 21.0 2.5 21 71-91 2-22 (107)
183 TIGR02051 MerR Hg(II)-responsi 30.0 59 0.0013 21.6 2.6 21 71-91 1-21 (124)
184 PRK07121 hypothetical protein; 29.8 70 0.0015 26.2 3.5 26 66-91 358-387 (492)
185 cd04773 HTH_TioE_rpt2 Second H 29.8 62 0.0014 20.9 2.7 21 71-91 2-22 (108)
186 TIGR02007 fdx_isc ferredoxin, 29.6 61 0.0013 21.1 2.6 23 62-84 16-38 (110)
187 COG3784 Uncharacterized protei 28.9 84 0.0018 20.7 3.0 31 71-101 66-100 (109)
188 cd07377 WHTH_GntR Winged helix 28.7 79 0.0017 17.5 2.7 19 71-89 27-45 (66)
189 PF13443 HTH_26: Cro/C1-type H 28.7 69 0.0015 18.0 2.5 22 68-89 9-30 (63)
190 cd01111 HTH_MerD Helix-Turn-He 28.7 68 0.0015 20.8 2.7 21 71-91 2-22 (107)
191 PF08984 DUF1858: Domain of un 28.5 61 0.0013 18.6 2.2 22 66-87 38-59 (59)
192 cd04784 HTH_CadR-PbrR Helix-Tu 28.5 66 0.0014 21.3 2.7 21 71-91 2-22 (127)
193 cd01110 HTH_SoxR Helix-Turn-He 28.4 65 0.0014 22.0 2.7 21 71-91 3-23 (139)
194 PRK05659 sulfur carrier protei 28.3 42 0.00091 19.4 1.5 41 62-102 8-59 (66)
195 TIGR02054 MerD mercuric resist 28.3 69 0.0015 21.4 2.7 21 71-91 5-25 (120)
196 PF01381 HTH_3: Helix-turn-hel 28.2 81 0.0018 17.1 2.7 23 67-89 7-29 (55)
197 PRK13182 racA polar chromosome 28.0 65 0.0014 23.1 2.7 21 71-91 2-22 (175)
198 PF01402 RHH_1: Ribbon-helix-h 28.0 84 0.0018 16.0 2.5 19 70-88 12-30 (39)
199 smart00530 HTH_XRE Helix-turn- 28.0 91 0.002 15.7 2.9 25 67-91 8-32 (56)
200 cd00592 HTH_MerR-like Helix-Tu 27.9 73 0.0016 19.9 2.7 21 71-91 2-22 (100)
201 TIGR02043 ZntR Zn(II)-responsi 27.9 69 0.0015 21.5 2.7 21 71-91 3-23 (131)
202 PF09048 Cro: Cro; InterPro: 27.7 80 0.0017 18.7 2.5 28 73-104 16-43 (59)
203 TIGR02047 CadR-PbrR Cd(II)/Pb( 27.3 71 0.0015 21.3 2.7 21 71-91 2-22 (127)
204 cd04783 HTH_MerR1 Helix-Turn-H 27.2 71 0.0015 21.2 2.6 21 71-91 2-22 (126)
205 PF04297 UPF0122: Putative hel 26.9 69 0.0015 21.0 2.4 22 67-88 31-52 (101)
206 PRK13413 mpi multiple promoter 26.9 78 0.0017 22.6 3.0 24 67-90 170-193 (200)
207 PF11834 DUF3354: Domain of un 26.8 19 0.00042 21.9 -0.2 31 72-102 31-68 (69)
208 COG2771 CsgD DNA-binding HTH d 26.6 80 0.0017 17.5 2.5 23 65-87 15-37 (65)
209 cd00207 fer2 2Fe-2S iron-sulfu 26.6 91 0.002 18.4 2.9 22 62-83 10-31 (84)
210 cd00086 homeodomain Homeodomai 26.6 54 0.0012 18.0 1.7 21 69-89 27-47 (59)
211 PRK03837 transcriptional regul 26.4 85 0.0018 22.8 3.2 27 63-89 28-57 (241)
212 PRK07198 hypothetical protein; 26.4 41 0.00088 27.5 1.5 19 71-89 176-194 (418)
213 PF07027 DUF1318: Protein of u 26.2 98 0.0021 19.9 3.0 33 71-103 52-88 (95)
214 TIGR03070 couple_hipB transcri 26.1 1E+02 0.0023 16.5 2.9 24 67-90 13-36 (58)
215 PF14549 P22_Cro: DNA-binding 26.0 91 0.002 18.3 2.6 21 71-91 11-31 (60)
216 PRK13749 transcriptional regul 25.9 73 0.0016 21.4 2.5 21 71-91 5-25 (121)
217 cd04781 HTH_MerR-like_sg6 Heli 25.8 80 0.0017 20.7 2.7 21 71-91 2-22 (120)
218 PF08769 Spo0A_C: Sporulation 25.7 66 0.0014 21.1 2.2 20 69-88 40-59 (106)
219 PF13412 HTH_24: Winged helix- 25.6 1.2E+02 0.0025 16.2 3.0 22 67-88 15-36 (48)
220 PRK06134 putative FAD-binding 25.6 68 0.0015 27.1 2.8 25 67-91 427-455 (581)
221 PF00111 Fer2: 2Fe-2S iron-sul 25.6 86 0.0019 18.4 2.6 22 62-83 8-31 (78)
222 PRK07843 3-ketosteroid-delta-1 25.6 70 0.0015 26.9 2.8 25 67-91 414-442 (557)
223 PF04921 XAP5: XAP5, circadian 25.4 62 0.0013 24.5 2.2 44 60-103 111-159 (239)
224 cd06571 Bac_DnaA_C C-terminal 25.3 98 0.0021 19.2 2.9 56 4-86 4-62 (90)
225 PF00440 TetR_N: Bacterial reg 25.3 1E+02 0.0022 16.4 2.7 20 69-88 16-35 (47)
226 TIGR02950 SigM_subfam RNA poly 25.2 90 0.002 20.7 2.9 23 67-89 119-141 (154)
227 COG0193 Pth Peptidyl-tRNA hydr 25.1 47 0.001 24.3 1.5 36 62-97 64-100 (190)
228 PRK09514 zntR zinc-responsive 24.9 81 0.0018 21.5 2.6 21 71-91 3-23 (140)
229 PRK04217 hypothetical protein; 24.7 1E+02 0.0023 20.4 3.0 22 68-89 57-78 (110)
230 PF01191 RNA_pol_Rpb5_C: RNA p 24.6 17 0.00037 22.5 -0.7 42 63-104 11-59 (74)
231 PRK12843 putative FAD-binding 24.6 74 0.0016 26.9 2.8 25 67-91 429-457 (578)
232 cd04776 HTH_GnyR Helix-Turn-He 24.4 89 0.0019 20.6 2.7 21 71-91 2-22 (118)
233 PF10543 ORF6N: ORF6N domain; 24.3 81 0.0018 19.7 2.4 28 70-97 13-43 (88)
234 PLN03111 DNA-directed RNA poly 24.1 70 0.0015 23.7 2.3 44 63-106 143-193 (206)
235 PF08356 EF_assoc_2: EF hand a 24.1 36 0.00079 21.7 0.7 17 66-82 42-60 (89)
236 smart00796 AHS1 Allophanate hy 24.0 2.9E+02 0.0062 20.1 6.0 25 67-91 98-122 (201)
237 PF07836 DmpG_comm: DmpG-like 23.8 84 0.0018 19.0 2.2 27 72-98 25-52 (66)
238 PRK06944 sulfur carrier protei 23.8 68 0.0015 18.4 1.8 41 62-102 8-58 (65)
239 cd04779 HTH_MerR-like_sg4 Heli 23.8 88 0.0019 21.3 2.6 21 71-91 2-22 (134)
240 PRK15002 redox-sensitivie tran 23.8 88 0.0019 21.9 2.7 21 71-91 13-33 (154)
241 cd00565 ThiS ThiaminS ubiquiti 23.7 69 0.0015 18.5 1.9 41 62-102 7-58 (65)
242 PF02682 AHS1: Allophanate hyd 23.6 1.7E+02 0.0036 21.3 4.2 43 63-105 93-143 (202)
243 PRK06481 fumarate reductase fl 23.6 80 0.0017 26.1 2.8 25 67-91 376-404 (506)
244 COG2012 RPB5 DNA-directed RNA 23.5 90 0.0019 19.6 2.3 42 63-104 17-65 (80)
245 PF01418 HTH_6: Helix-turn-hel 23.4 91 0.002 18.8 2.4 21 69-89 34-54 (77)
246 PRK10014 DNA-binding transcrip 23.4 82 0.0018 23.8 2.7 21 71-91 8-29 (342)
247 cd04786 HTH_MerR-like_sg7 Heli 23.4 94 0.002 21.0 2.7 21 71-91 2-22 (131)
248 TIGR02885 spore_sigF RNA polym 23.3 99 0.0022 22.4 3.0 23 67-89 197-219 (231)
249 PRK08364 sulfur carrier protei 23.3 91 0.002 18.5 2.4 41 62-102 16-63 (70)
250 TIGR01950 SoxR redox-sensitive 23.3 92 0.002 21.4 2.7 21 71-91 3-23 (142)
251 PRK07569 bidirectional hydroge 23.3 79 0.0017 23.4 2.5 24 62-85 11-34 (234)
252 PF00046 Homeobox: Homeobox do 23.0 1.1E+02 0.0024 16.8 2.6 20 70-89 28-47 (57)
253 PRK12842 putative succinate de 22.9 79 0.0017 26.6 2.7 25 67-91 424-452 (574)
254 PRK06083 sulfur carrier protei 22.8 74 0.0016 19.9 1.9 41 62-102 26-77 (84)
255 COG0789 SoxR Predicted transcr 22.6 1E+02 0.0022 19.9 2.7 21 71-91 2-22 (124)
256 PF06413 Neugrin: Neugrin; In 22.6 82 0.0018 23.6 2.4 24 66-89 25-49 (225)
257 PF11020 DUF2610: Domain of un 22.5 99 0.0022 19.4 2.4 19 4-25 56-74 (82)
258 TIGR03643 conserved hypothetic 22.5 1.2E+02 0.0026 18.6 2.7 22 70-91 14-35 (72)
259 PRK09652 RNA polymerase sigma 22.5 1.1E+02 0.0024 20.7 3.0 22 67-88 142-163 (182)
260 cd04790 HTH_Cfa-like_unk Helix 22.4 96 0.0021 21.9 2.7 21 71-91 3-23 (172)
261 PF13730 HTH_36: Helix-turn-he 22.3 1.2E+02 0.0027 16.5 2.7 19 71-89 27-45 (55)
262 PRK12537 RNA polymerase sigma 22.2 1E+02 0.0022 21.4 2.8 23 66-88 146-168 (182)
263 PHA00542 putative Cro-like pro 22.1 1.2E+02 0.0027 18.5 2.9 24 66-89 28-51 (82)
264 PRK09744 DNA-binding transcrip 22.1 1.2E+02 0.0026 18.8 2.7 20 71-90 12-31 (75)
265 PLN03148 Blue copper-like prot 22.1 1.2E+02 0.0027 21.6 3.1 14 93-106 106-119 (167)
266 PRK12514 RNA polymerase sigma 22.0 1.1E+02 0.0024 21.0 2.9 22 67-88 143-164 (179)
267 cd04787 HTH_HMRTR_unk Helix-Tu 21.9 1.1E+02 0.0023 20.6 2.7 21 71-91 2-22 (133)
268 PF09035 Tn916-Xis: Excisionas 21.6 47 0.001 20.1 0.8 39 4-43 15-53 (67)
269 TIGR02985 Sig70_bacteroi1 RNA 21.6 1.2E+02 0.0026 20.0 3.0 22 67-88 127-148 (161)
270 PRK12835 3-ketosteroid-delta-1 21.6 91 0.002 26.4 2.8 25 67-91 428-456 (584)
271 PRK06759 RNA polymerase factor 21.3 1.2E+02 0.0027 20.1 3.0 23 67-89 120-142 (154)
272 COG1356 tfx Transcriptional re 21.3 27 0.00058 24.1 -0.4 60 1-78 22-84 (143)
273 TIGR01813 flavo_cyto_c flavocy 21.2 93 0.002 24.9 2.7 25 67-91 318-346 (439)
274 TIGR02405 trehalos_R_Ecol treh 21.2 98 0.0021 23.2 2.7 19 71-89 3-21 (311)
275 PRK13752 putative transcriptio 21.0 1.1E+02 0.0023 21.1 2.6 21 71-91 9-29 (144)
276 PF10985 DUF2805: Protein of u 20.8 1.4E+02 0.0029 18.5 2.7 21 70-90 13-33 (73)
277 PRK08274 tricarballylate dehyd 20.7 1.1E+02 0.0023 24.8 2.9 26 66-91 321-350 (466)
278 PF07638 Sigma70_ECF: ECF sigm 20.6 1.2E+02 0.0026 21.4 2.9 22 67-88 149-170 (185)
279 PRK11426 hypothetical protein; 20.5 75 0.0016 21.9 1.7 20 69-88 72-91 (132)
280 PRK12844 3-ketosteroid-delta-1 20.4 1E+02 0.0022 25.9 2.8 25 67-91 407-435 (557)
281 PRK10227 DNA-binding transcrip 20.3 1.2E+02 0.0026 20.6 2.7 21 71-91 2-22 (135)
282 smart00420 HTH_DEOR helix_turn 20.3 1.5E+02 0.0032 15.4 2.7 19 69-87 14-32 (53)
283 smart00418 HTH_ARSR helix_turn 20.0 1.4E+02 0.003 16.0 2.7 21 68-88 9-29 (66)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.86 E-value=2e-21 Score=160.45 Aligned_cols=99 Identities=13% Similarity=0.176 Sum_probs=81.0
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCCCCCCCccc-----ccccccceEEEEecCCCCHHHH
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVFCKCPDQTQ-----LRNRVNYLVSYVLQPSENLSSV 75 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~~~~~~-----~~~~~~~~~~y~V~~GDTl~~I 75 (129)
+|||||.||++|++ ++++|+++|++. .+.|++||.|+||.......... ..........|+|++|||||+|
T Consensus 486 ~GDTL~sIAkkygV---Sv~~L~~~N~l~-s~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDTL~sI 561 (592)
T PRK06347 486 KGDSLWRIANNNKV---TIANLKSWNNLK-SDFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDSLWAI 561 (592)
T ss_pred CCCCHHHHHHHHCC---CHHHHHHhcCCC-cccccCCcEEEEecCcccccccccCCccCCccCccceeeecCCCCcHHHH
Confidence 59999999999999 999999999985 57899999999997542211000 0011122468999999999999
Q ss_pred HHHhCCCHHHHHhhcC---CCCCCCCEEEEc
Q 037542 76 ASRFGIETQAIIDVNG---NNIRPFDTLFVP 103 (129)
Q Consensus 76 A~~~~vs~~~l~~~N~---~~l~~Gq~L~IP 103 (129)
|++||+++++|++||+ +.|++||+|+|+
T Consensus 562 A~KygvSv~~L~~~N~L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 562 SRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK 592 (592)
T ss_pred HHHhCCCHHHHHHhcCCCcccCCCCCEEecC
Confidence 9999999999999999 779999999985
No 2
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.85 E-value=7.7e-21 Score=153.56 Aligned_cols=98 Identities=22% Similarity=0.330 Sum_probs=84.3
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCCCCCCCcccccccccceEEEEecCCCCHHHHHHHhC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVFCKCPDQTQLRNRVNYLVSYVLQPSENLSSVASRFG 80 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~IA~~~~ 80 (129)
+||||+.||++|++ ++.+|+++|++.. +.|.+||.|.||..+.+.... ......+|+|++|||||+||++||
T Consensus 350 ~GDTL~sIA~r~gv---s~~~L~~~N~l~~-~~L~~Gq~L~Ip~~~~~~~~~----~~~~~~~Y~Vr~GDTL~sIA~kyg 421 (456)
T PRK10783 350 SGDTLSGIASRLNV---STKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRLA----NNSDSITYRVRKGDSLSSIAKRHG 421 (456)
T ss_pred CCCcHHHHHHHHCc---CHHHHHHHcCCCc-ccCCCCCEEEecCCccccccc----ccccceeEEeCCCCCHHHHHHHhC
Confidence 59999999999999 9999999999854 789999999999766543211 112246899999999999999999
Q ss_pred CCHHHHHhhcC---CCCCCCCEEEEcCCC
Q 037542 81 IETQAIIDVNG---NNIRPFDTLFVPVAR 106 (129)
Q Consensus 81 vs~~~l~~~N~---~~l~~Gq~L~IP~~~ 106 (129)
|++++|++||+ ..|++||+|.|++..
T Consensus 422 Vtv~~L~~~N~l~~~~L~pGq~L~l~v~~ 450 (456)
T PRK10783 422 VNIKDVMRWNSDTAKNLQPGDKLTLFVKN 450 (456)
T ss_pred CCHHHHHHhcCCCCCcCCCCCEEEEecCC
Confidence 99999999999 579999999998865
No 3
>PRK06347 autolysin; Reviewed
Probab=99.82 E-value=2e-19 Score=148.69 Aligned_cols=103 Identities=16% Similarity=0.174 Sum_probs=82.9
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCCCCC------CCcc-----cccccccceEEEEecCC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVFCKC------PDQT-----QLRNRVNYLVSYVLQPS 69 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~------~~~~-----~~~~~~~~~~~y~V~~G 69 (129)
+||||+.||++|++ ++++|+++|++. .+.|.+||.|+||..... +... ...........|+|++|
T Consensus 412 ~GDTL~sIA~kygV---Sv~~L~~~N~l~-s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~G 487 (592)
T PRK06347 412 KGDSLWRIANNNKV---TIANLKSWNNLK-SDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKG 487 (592)
T ss_pred CCCCHHHHHHHhCC---CHHHHHHHhCCC-cceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCC
Confidence 49999999999999 999999999984 578999999999964221 0000 00001122468999999
Q ss_pred CCHHHHHHHhCCCHHHHHhhcC---CCCCCCCEEEEcCCCC
Q 037542 70 ENLSSVASRFGIETQAIIDVNG---NNIRPFDTLFVPVARL 107 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~N~---~~l~~Gq~L~IP~~~~ 107 (129)
||||+||++||+++++|++||+ +.|++||.|.||....
T Consensus 488 DTL~sIAkkygVSv~~L~~~N~l~s~~L~~GQ~L~Ip~~~~ 528 (592)
T PRK06347 488 DSLWRIANNNKVTIANLKSWNNLKSDFIYPGQKLKVSAGST 528 (592)
T ss_pred CCHHHHHHHHCCCHHHHHHhcCCCcccccCCcEEEEecCcc
Confidence 9999999999999999999999 7899999999998653
No 4
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.74 E-value=4.5e-17 Score=131.21 Aligned_cols=46 Identities=13% Similarity=0.260 Sum_probs=42.9
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC---CCCCCCCEEEEcCCCC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG---NNIRPFDTLFVPVARL 107 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~---~~l~~Gq~L~IP~~~~ 107 (129)
..|+|++|||||.||++|++++++|++||+ ..|++||+|.||....
T Consensus 200 ~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s~~L~pGQ~L~Ip~sa~ 248 (481)
T PRK13914 200 TTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAIKQTAN 248 (481)
T ss_pred eEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCccccCCCCEEEecCCCC
Confidence 579999999999999999999999999999 6899999999997654
No 5
>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=99.55 E-value=5.5e-15 Score=82.94 Aligned_cols=40 Identities=35% Similarity=0.776 Sum_probs=34.2
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEEEc
Q 037542 64 YVLQPSENLSSVASRFGIETQAIIDVNG----NNIRPFDTLFVP 103 (129)
Q Consensus 64 y~V~~GDTl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~IP 103 (129)
|+|++|||+|+||++|++++++|+++|+ ..|.+||+|+||
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 8999999999999999999999999994 569999999998
No 6
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.52 E-value=5.7e-14 Score=95.13 Aligned_cols=94 Identities=17% Similarity=0.291 Sum_probs=73.9
Q ss_pred HHHhhCCCCCCHHHHHHhCCCCC-CCCCCCCCEEEECCCCCCCC--cccccccc------------cceEEEEecCCCCH
Q 037542 8 VSTNKYQNLTTYQSVEVVNPAFV-PTKLEVGDVFIFPVFCKCPD--QTQLRNRV------------NYLVSYVLQPSENL 72 (129)
Q Consensus 8 IA~~~~~~lts~~~l~~~N~~~~-~~~l~~Gq~L~IP~~~~~~~--~~~~~~~~------------~~~~~y~V~~GDTl 72 (129)
||.+|++ ++++|+++|.+.. .+.+.+||+|.++....... ........ ....+|+|++||||
T Consensus 1 ia~~~~~---~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL 77 (124)
T COG1388 1 IASKYGV---SVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTL 77 (124)
T ss_pred Ccccccc---cHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCH
Confidence 6788998 9999999998843 78899999999996321111 00000000 11358999999999
Q ss_pred HHHHHHhCCCHHHHHhhcC---CCCCCCCEEEEcC
Q 037542 73 SSVASRFGIETQAIIDVNG---NNIRPFDTLFVPV 104 (129)
Q Consensus 73 ~~IA~~~~vs~~~l~~~N~---~~l~~Gq~L~IP~ 104 (129)
+.||++|++++.+|+++|. +.+++||.|.++.
T Consensus 78 ~~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~~ 112 (124)
T COG1388 78 SKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLPV 112 (124)
T ss_pred HHHHHHhCCCHHHHHHHhccCCCceecCcEEEEec
Confidence 9999999999999999999 7899999999997
No 7
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.51 E-value=1.6e-13 Score=111.16 Aligned_cols=102 Identities=15% Similarity=0.177 Sum_probs=77.5
Q ss_pred CCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCC-CC-CEEEECCCCCCC------Ccc-------ccc-ccccceEEEE
Q 037542 2 GDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLE-VG-DVFIFPVFCKCP------DQT-------QLR-NRVNYLVSYV 65 (129)
Q Consensus 2 GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~-~G-q~L~IP~~~~~~------~~~-------~~~-~~~~~~~~y~ 65 (129)
+.+|..||+++++ ++++|+++|+......+. .| +.|+||...... ... ... .......+|+
T Consensus 271 ~i~L~~iA~~~gv---s~~eL~~LNP~~kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p~~~~~~~~~~~~~y~ 347 (456)
T PRK10783 271 QIELAQAAEMAGM---SLTKLKTFNAGYKRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQSTLVADNTPLNSRSYK 347 (456)
T ss_pred CcCHHHHHHHcCC---CHHHHHHhCccccCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhcccccccccCcCCceEEE
Confidence 5689999999999 999999999976555443 34 788899743210 000 000 0001235899
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhhcC---CCCCCCCEEEEcCCC
Q 037542 66 LQPSENLSSVASRFGIETQAIIDVNG---NNIRPFDTLFVPVAR 106 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~N~---~~l~~Gq~L~IP~~~ 106 (129)
|++||||++||++||+++.+|.+||+ +.|++||.|.||...
T Consensus 348 Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~ 391 (456)
T PRK10783 348 VRSGDTLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTIGAGS 391 (456)
T ss_pred ECCCCcHHHHHHHHCcCHHHHHHHcCCCcccCCCCCEEEecCCc
Confidence 99999999999999999999999999 679999999999754
No 8
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.30 E-value=9.6e-12 Score=82.19 Aligned_cols=48 Identities=25% Similarity=0.391 Sum_probs=41.8
Q ss_pred eEEEEecCCCCHHHHHHHhCCC--------HHHHHhhcC---CCCCCCCEEEEcCCCCC
Q 037542 61 LVSYVLQPSENLSSVASRFGIE--------TQAIIDVNG---NNIRPFDTLFVPVARLP 108 (129)
Q Consensus 61 ~~~y~V~~GDTl~~IA~~~~vs--------~~~l~~~N~---~~l~~Gq~L~IP~~~~p 108 (129)
+..|+|++|||||+||++|+.+ ++.|++.|+ +.|++||+|.||....-
T Consensus 36 ~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~~~ 94 (103)
T PRK14125 36 YVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLKSK 94 (103)
T ss_pred cEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCCCC
Confidence 4689999999999999999865 577888897 78999999999987754
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=99.23 E-value=1.8e-11 Score=67.89 Aligned_cols=39 Identities=26% Similarity=0.467 Sum_probs=35.8
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhhcC-----CCCCCCCEEEEcC
Q 037542 66 LQPSENLSSVASRFGIETQAIIDVNG-----NNIRPFDTLFVPV 104 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~N~-----~~l~~Gq~L~IP~ 104 (129)
|++|||||+||++|++++++|.++|+ ..+.+||+|.||.
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 68999999999999999999999996 3599999999983
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=99.21 E-value=4.5e-11 Score=65.46 Aligned_cols=41 Identities=32% Similarity=0.699 Sum_probs=39.0
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEEEc
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG----NNIRPFDTLFVP 103 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~IP 103 (129)
.|+|++|||++.||++|+++..+|.++|+ ..+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 69999999999999999999999999999 579999999987
No 11
>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=99.17 E-value=2.3e-11 Score=68.03 Aligned_cols=40 Identities=23% Similarity=0.417 Sum_probs=33.0
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEEC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFP 43 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP 43 (129)
+||||+.||++|++ +.++|+++|+..+.+.|.+||+|+||
T Consensus 5 ~gDtl~~IA~~~~~---~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 5 PGDTLWSIAKRYGI---SVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp TT--HHHHHHHTTS----HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred cCCcHHHHHhhhhh---hHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 69999999999998 99999999955455569999999998
No 12
>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=99.08 E-value=2e-10 Score=88.92 Aligned_cols=44 Identities=20% Similarity=0.418 Sum_probs=41.5
Q ss_pred ceEEEEecCCCCHHHHHHHhCCCHHHHHhhcC---CCCCCCCEEEEc
Q 037542 60 YLVSYVLQPSENLSSVASRFGIETQAIIDVNG---NNIRPFDTLFVP 103 (129)
Q Consensus 60 ~~~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~---~~l~~Gq~L~IP 103 (129)
....|+|++|||||.||++||++++.|+++|+ +.|++||+|+||
T Consensus 292 ~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 292 KLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred ccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 34689999999999999999999999999998 789999999998
No 13
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=99.07 E-value=1.6e-10 Score=89.75 Aligned_cols=45 Identities=20% Similarity=0.182 Sum_probs=41.7
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEEEcCCC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG----NNIRPFDTLFVPVAR 106 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~IP~~~ 106 (129)
.+|+|++|||||.||++||+++.+|++||+ +.|++||+|.||...
T Consensus 61 ~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 61 STYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred CceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 489999999999999999999999999999 679999999997543
No 14
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=99.07 E-value=1.6e-10 Score=91.70 Aligned_cols=89 Identities=21% Similarity=0.225 Sum_probs=79.9
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCCCCCCCcccccccccceEEEEecCCCCHHHHHHHhC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVFCKCPDQTQLRNRVNYLVSYVLQPSENLSSVASRFG 80 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~IA~~~~ 80 (129)
+||+++.|+++|.. +...|...|.... +.|.+||.+.||.. ...|.|++|||+++||++|+
T Consensus 8 pg~~~~~i~~~~~~---~~~~i~~~~~~~~-d~~~~~q~~~v~~~---------------~~~y~~~~~d~~~Sia~~~~ 68 (423)
T COG3858 8 PGDSRLIIAVYFPY---TNNRIVNGNDYTN-DDLVDGQTFVVPPS---------------GHFYDVGPGDTLTSIARTVG 68 (423)
T ss_pred CCceeeeehhhccc---ccccccccccccc-ccccCceeEEECCc---------------ceEEEecCCcchhhhhhhhc
Confidence 69999999999998 8889988888866 88999999999952 26899999999999999999
Q ss_pred CCHHHHHhhcC----CCCCCCCEEEEcCCCCC
Q 037542 81 IETQAIIDVNG----NNIRPFDTLFVPVARLP 108 (129)
Q Consensus 81 vs~~~l~~~N~----~~l~~Gq~L~IP~~~~p 108 (129)
++.+.+..+|. ..|+.|-.|.+|....-
T Consensus 69 vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~~~ 100 (423)
T COG3858 69 VTQDSAAIMNFVICPGYLQYGLNLYIPSARKT 100 (423)
T ss_pred CCHHHHHhhcccccccceeeeeEEeccCCCCC
Confidence 99999999997 58999999999977654
No 15
>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=99.02 E-value=6.3e-10 Score=61.54 Aligned_cols=41 Identities=20% Similarity=0.369 Sum_probs=36.3
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCC-CCCCCCCCCEEEECC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAF-VPTKLEVGDVFIFPV 44 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~-~~~~l~~Gq~L~IP~ 44 (129)
+|||||.||++|++ ++++|+++|+.. +++.+.+||.|.||.
T Consensus 3 ~gdtl~~IA~~~~~---~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 3 KGDTLWKIAKKYGV---DFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 59999999999998 999999999843 456899999999983
No 16
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.95 E-value=1.2e-09 Score=88.70 Aligned_cols=44 Identities=25% Similarity=0.304 Sum_probs=41.4
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC---CCCCCCCEEEEcCC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG---NNIRPFDTLFVPVA 105 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~---~~l~~Gq~L~IP~~ 105 (129)
.+|+|++|||||.||++|++++++|+++|+ +.|++||.|+||..
T Consensus 28 ~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~~~I~~Gq~L~Ip~~ 74 (481)
T PRK13914 28 STVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKIVPGQKLQVNEV 74 (481)
T ss_pred ceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCcccccCCCEEEeCCC
Confidence 479999999999999999999999999998 68999999999954
No 17
>smart00257 LysM Lysin motif.
Probab=98.92 E-value=2.9e-09 Score=57.43 Aligned_cols=40 Identities=28% Similarity=0.602 Sum_probs=36.7
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEEE
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG----NNIRPFDTLFV 102 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~I 102 (129)
.|+|++|||++.||++|+++..+|.++|+ ..+.+|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 38999999999999999999999999999 57999998874
No 18
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.82 E-value=1e-08 Score=67.80 Aligned_cols=45 Identities=24% Similarity=0.422 Sum_probs=35.8
Q ss_pred CCCcHHHHHHhhCCC--CCC---HHHHHHhCCCCCCCCCCCCCEEEECCCC
Q 037542 1 SGDTFYSVSTNKYQN--LTT---YQSVEVVNPAFVPTKLEVGDVFIFPVFC 46 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~--lts---~~~l~~~N~~~~~~~l~~Gq~L~IP~~~ 46 (129)
+|||||+||++|+.. ++. ++.|++.|++. .+.|.+||+|+||...
T Consensus 43 ~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~-~~~I~~Gq~L~IP~~~ 92 (103)
T PRK14125 43 EGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLP-SGHIKAGDKLVIPVLK 92 (103)
T ss_pred CCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCC-CCcCCCCCEEEEecCC
Confidence 699999999999762 111 57788889984 5689999999999754
No 19
>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=98.80 E-value=1.4e-08 Score=55.29 Aligned_cols=40 Identities=25% Similarity=0.345 Sum_probs=36.9
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEEC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFP 43 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP 43 (129)
+|||++.||++|++ +..+|+++|+......+.+|+.|.||
T Consensus 7 ~gdt~~~ia~~~~~---~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 7 KGDTLSSIAQRYGI---SVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred CCCCHHHHHHHHCc---CHHHHHHHcCCCCccccCCCCEEecC
Confidence 59999999999998 99999999998667789999999987
No 20
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.70 E-value=2.1e-08 Score=77.94 Aligned_cols=42 Identities=19% Similarity=0.275 Sum_probs=39.5
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVF 45 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~ 45 (129)
+|||||.||++|+. ++.+|+++|++.+++.|.+||+|+||..
T Consensus 67 ~GDTL~~IA~~~g~---~~~~La~~N~l~~p~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 67 KGDTLFYIAWITGN---DFRDLAQRNNIQAPYSLNVGQTLQVGNA 108 (319)
T ss_pred CCCHHHHHHHHHCc---CHHHHHHhcCCCCCccccCCCEEEeCCC
Confidence 69999999999999 9999999999988999999999999854
No 21
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.69 E-value=2.9e-08 Score=69.43 Aligned_cols=43 Identities=23% Similarity=0.371 Sum_probs=37.7
Q ss_pred eEEEEecCCCCHHHHHHHhC---CCHHHHHhhcC------CCCCCCCEEEEc
Q 037542 61 LVSYVLQPSENLSSVASRFG---IETQAIIDVNG------NNIRPFDTLFVP 103 (129)
Q Consensus 61 ~~~y~V~~GDTl~~IA~~~~---vs~~~l~~~N~------~~l~~Gq~L~IP 103 (129)
...|+|++|||||.||++|+ ..+..|.++|+ +.|++||+|.||
T Consensus 95 ~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 35899999999999999985 35789999995 569999999998
No 22
>smart00257 LysM Lysin motif.
Probab=98.44 E-value=5.5e-07 Score=48.16 Aligned_cols=39 Identities=23% Similarity=0.325 Sum_probs=34.6
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEE
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIF 42 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~I 42 (129)
+|||++.||++|++ +..+|.++|+..+...+.+|+.|+|
T Consensus 6 ~gdt~~~ia~~~~~---~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 6 KGDTLSSIARRYGI---SVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CCCCHHHHHHHhCC---CHHHHHHHcCCCCccccCCCCEEeC
Confidence 59999999999998 8899999999656678999998875
No 23
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.42 E-value=3.5e-07 Score=63.96 Aligned_cols=43 Identities=30% Similarity=0.485 Sum_probs=37.1
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCC--CCCCCCCCCCCEEEEC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNP--AFVPTKLEVGDVFIFP 43 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~--~~~~~~l~~Gq~L~IP 43 (129)
+|||||.||++|+.+...+.+|+++|+ +.+++.|.+||+|.||
T Consensus 102 ~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 102 SGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 599999999999754346889999998 6677889999999998
No 24
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.23 E-value=1.8e-06 Score=58.21 Aligned_cols=40 Identities=25% Similarity=0.373 Sum_probs=37.0
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPV 44 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~ 44 (129)
+||||+.||++|++ ++.+|+++|++. .+.+.+||.|.++.
T Consensus 73 ~gdtL~~Ia~~~~~---tv~~l~~~n~l~-~~~i~~gq~l~~~~ 112 (124)
T COG1388 73 KGDTLSKIARKYGV---TVAELKQLNNLS-SDKIKVGQKLKLPV 112 (124)
T ss_pred cCCCHHHHHHHhCC---CHHHHHHHhccC-CCceecCcEEEEec
Confidence 59999999999999 999999999995 45999999999986
No 25
>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=98.17 E-value=2.1e-06 Score=54.77 Aligned_cols=45 Identities=22% Similarity=0.465 Sum_probs=27.7
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhh---cC-----CCCCCCCEEEEcCCC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDV---NG-----NNIRPFDTLFVPVAR 106 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~---N~-----~~l~~Gq~L~IP~~~ 106 (129)
..|+|++||||+.|=+++|++..+|.++ .. ..|+|||.|.+-...
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-T
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEECC
Confidence 4799999999999999999988776554 32 689999999886544
No 26
>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=98.12 E-value=3.5e-06 Score=52.48 Aligned_cols=37 Identities=22% Similarity=0.324 Sum_probs=31.3
Q ss_pred CCHHHHHHHh---C-CCHH----HHHhhcC--------CCCCCCCEEEEcCCC
Q 037542 70 ENLSSVASRF---G-IETQ----AIIDVNG--------NNIRPFDTLFVPVAR 106 (129)
Q Consensus 70 DTl~~IA~~~---~-vs~~----~l~~~N~--------~~l~~Gq~L~IP~~~ 106 (129)
||||+||++| + +++. .|.++|+ +.|++|++|.||...
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~~ 53 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSEE 53 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCHH
Confidence 8999999999 3 6775 6788887 679999999999754
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=98.00 E-value=7.7e-06 Score=50.91 Aligned_cols=42 Identities=19% Similarity=0.362 Sum_probs=33.2
Q ss_pred CcHHHHHHhhCCCC-CCHH----HHHHhCCCC----CCCCCCCCCEEEECC
Q 037542 3 DTFYSVSTNKYQNL-TTYQ----SVEVVNPAF----VPTKLEVGDVFIFPV 44 (129)
Q Consensus 3 DTl~~IA~~~~~~l-ts~~----~l~~~N~~~----~~~~l~~Gq~L~IP~ 44 (129)
||||.||++|..+. .++. +|.++|+.. +.+.|++|+.|.||.
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~ 51 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPS 51 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCC
Confidence 89999999996432 3555 677899843 457899999999996
No 28
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.75 E-value=8.1e-05 Score=57.82 Aligned_cols=48 Identities=13% Similarity=0.228 Sum_probs=41.1
Q ss_pred cceEEEEecCCC--CHHHHHHHhCCCHHHHHhhcC--CC--CCCCCEEEEcCCC
Q 037542 59 NYLVSYVLQPSE--NLSSVASRFGIETQAIIDVNG--NN--IRPFDTLFVPVAR 106 (129)
Q Consensus 59 ~~~~~y~V~~GD--Tl~~IA~~~~vs~~~l~~~N~--~~--l~~Gq~L~IP~~~ 106 (129)
+....|+|+.+| +|..||++|++...+|.++|+ +. .++|+.|.||..-
T Consensus 35 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~~ 88 (310)
T PRK10190 35 GQSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQL 88 (310)
T ss_pred cceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecCcc
Confidence 345689999976 599999999999999999999 43 6899999999743
No 29
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.75 E-value=8e-05 Score=57.74 Aligned_cols=48 Identities=10% Similarity=0.122 Sum_probs=41.1
Q ss_pred cceEEEEecCCCC--HHHHHHHhCCCHHHHHhhcC--C--CCCCCCEEEEcCCC
Q 037542 59 NYLVSYVLQPSEN--LSSVASRFGIETQAIIDVNG--N--NIRPFDTLFVPVAR 106 (129)
Q Consensus 59 ~~~~~y~V~~GDT--l~~IA~~~~vs~~~l~~~N~--~--~l~~Gq~L~IP~~~ 106 (129)
+....|+|+.||| |..||++|++...+|+++|+ + ..++|++|.||..-
T Consensus 38 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~~ 91 (306)
T PRK10260 38 GQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQL 91 (306)
T ss_pred cccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCCcc
Confidence 3346899999765 99999999999999999999 4 55799999999743
No 30
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.61 E-value=1.8e-05 Score=60.15 Aligned_cols=45 Identities=20% Similarity=0.391 Sum_probs=37.9
Q ss_pred EEEEecCCCCHHHHHHH-hCC--CHHHHHhhcC-------CCCCCCCEEEEcCCC
Q 037542 62 VSYVLQPSENLSSVASR-FGI--ETQAIIDVNG-------NNIRPFDTLFVPVAR 106 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~-~~v--s~~~l~~~N~-------~~l~~Gq~L~IP~~~ 106 (129)
.+|+|++|||||.||++ ||. .+..|..+|+ +.|++||+|.||-..
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~~ 265 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQL 265 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCcc
Confidence 38999999999999986 554 5677888887 689999999999644
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=97.46 E-value=0.00014 Score=43.45 Aligned_cols=44 Identities=25% Similarity=0.381 Sum_probs=35.1
Q ss_pred CCCcHHHHHHhhCCCCCCH-HHHHHhCCCC-CC-CCCCCCCEEEECC
Q 037542 1 SGDTFYSVSTNKYQNLTTY-QSVEVVNPAF-VP-TKLEVGDVFIFPV 44 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~-~~l~~~N~~~-~~-~~l~~Gq~L~IP~ 44 (129)
.||||..||.|++.....+ +.|.++|+.. +. ..|..|..|.+|.
T Consensus 7 ~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~ 53 (60)
T PF05489_consen 7 QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPD 53 (60)
T ss_pred CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCC
Confidence 5999999999998643223 7889999964 33 5799999999995
No 32
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.35 E-value=6e-05 Score=57.34 Aligned_cols=44 Identities=27% Similarity=0.486 Sum_probs=39.7
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCC---CCCCCCCCCCCEEEECC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNP---AFVPTKLEVGDVFIFPV 44 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~---~~~~~~l~~Gq~L~IP~ 44 (129)
.|||||.||++++.+..-+..|..+|. +.+++.|.+||+|.||.
T Consensus 217 rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~ 263 (269)
T COG1652 217 RGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPD 263 (269)
T ss_pred cCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCC
Confidence 599999999998877778889999999 66789999999999995
No 33
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.22 E-value=0.00063 Score=52.84 Aligned_cols=40 Identities=13% Similarity=0.071 Sum_probs=36.4
Q ss_pred CcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCC
Q 037542 3 DTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVF 45 (129)
Q Consensus 3 DTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~ 45 (129)
++|..||++|++ .+.+|+++|+..++....+|++|.||..
T Consensus 51 ~~le~iA~~f~~---g~~~l~~aNPgvdp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 51 QPLEYFAAEYQM---GLSNMMEANPGVDTFLPKGGTVLNIPQQ 90 (306)
T ss_pred chHHHHHHHhCC---CHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence 469999999999 8999999999988878889999999974
No 34
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.22 E-value=0.00066 Score=52.84 Aligned_cols=40 Identities=13% Similarity=0.068 Sum_probs=36.4
Q ss_pred CcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCC
Q 037542 3 DTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVF 45 (129)
Q Consensus 3 DTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~ 45 (129)
++|..||++|++ ...+|+++|+..++...++|++|.||..
T Consensus 48 ~~le~iA~~f~~---g~~~l~~aNPgvd~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 48 QPLETFAAQYGQ---GLSNMLEANPGADVFLPKSGSQLTIPQQ 87 (310)
T ss_pred ccHHHHHHHhCC---CHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence 469999999999 9999999999988877889999999974
No 35
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=97.04 E-value=0.0005 Score=58.35 Aligned_cols=48 Identities=25% Similarity=0.346 Sum_probs=38.7
Q ss_pred eEEEEecCCCCHHHHHHHh----CCCH----HHHHhhcC--------CCCCCCCEEEEcCCCCC
Q 037542 61 LVSYVLQPSENLSSVASRF----GIET----QAIIDVNG--------NNIRPFDTLFVPVARLP 108 (129)
Q Consensus 61 ~~~y~V~~GDTl~~IA~~~----~vs~----~~l~~~N~--------~~l~~Gq~L~IP~~~~p 108 (129)
..+|+|++|||||.||.+- ++++ ..|.++|+ +.|+.|++|.||.....
T Consensus 188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~~q~ 251 (755)
T COG3170 188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSAAQI 251 (755)
T ss_pred CcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccchhhh
Confidence 3689999999999999864 3455 45888898 57999999999975543
No 36
>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=96.99 E-value=0.0019 Score=38.53 Aligned_cols=42 Identities=21% Similarity=0.403 Sum_probs=33.2
Q ss_pred EEEecCCCCHHHHHHH-hCCC---HHHHHhhcC------CCCCCCCEEEEcCC
Q 037542 63 SYVLQPSENLSSVASR-FGIE---TQAIIDVNG------NNIRPFDTLFVPVA 105 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~-~~vs---~~~l~~~N~------~~l~~Gq~L~IP~~ 105 (129)
.|+. .||||..|+.| ||-. ++.|.++|+ ..|..|..|.+|.-
T Consensus 3 v~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i 54 (60)
T PF05489_consen 3 VYTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI 54 (60)
T ss_pred EEEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence 3444 99999999976 5653 378899999 47999999999943
No 37
>PRK11649 putative peptidase; Provisional
Probab=96.76 E-value=0.0031 Score=51.38 Aligned_cols=46 Identities=22% Similarity=0.392 Sum_probs=39.2
Q ss_pred eEEEEecCCCCHHHHHHHhCCCHHHHHhhc---C--CCCCCCCEEEEcCCC
Q 037542 61 LVSYVLQPSENLSSVASRFGIETQAIIDVN---G--NNIRPFDTLFVPVAR 106 (129)
Q Consensus 61 ~~~y~V~~GDTl~~IA~~~~vs~~~l~~~N---~--~~l~~Gq~L~IP~~~ 106 (129)
...|+|+.||||..|=+++|++..++.++- . ..|++||.|.+-...
T Consensus 95 ~~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~ 145 (439)
T PRK11649 95 VHEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTLTA 145 (439)
T ss_pred eEEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEECC
Confidence 358999999999999999999988877663 3 789999999987554
No 38
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=96.48 E-value=0.0083 Score=44.54 Aligned_cols=47 Identities=9% Similarity=0.160 Sum_probs=40.5
Q ss_pred ceEEEEecCCCCHHHHHHHhCCCHHHHHhhcC--------CCCCCCCEEEEcCCC
Q 037542 60 YLVSYVLQPSENLSSVASRFGIETQAIIDVNG--------NNIRPFDTLFVPVAR 106 (129)
Q Consensus 60 ~~~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~--------~~l~~Gq~L~IP~~~ 106 (129)
...+|+|+.|+||..+=|..++.+.++.++-. .+|+.||.+.|-++.
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 45799999999999999999998887766654 789999999998765
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=96.08 E-value=0.0028 Score=40.35 Aligned_cols=45 Identities=20% Similarity=0.188 Sum_probs=27.0
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCC-CCCCCCCCCEEEECCC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAF-VPTKLEVGDVFIFPVF 45 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~-~~~~l~~Gq~L~IP~~ 45 (129)
+||||..|=+++|++..++..|.++.... .-..|++||.|.+-..
T Consensus 9 ~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 9 SGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred CCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 69999999999999656666666666332 2357999999988653
No 40
>PRK11649 putative peptidase; Provisional
Probab=95.62 E-value=0.13 Score=42.06 Aligned_cols=101 Identities=14% Similarity=0.084 Sum_probs=61.4
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCC-CCCCCCCCCCCEEEECCCCCCCCcc-----------c--c-ccc--------
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNP-AFVPTKLEVGDVFIFPVFCKCPDQT-----------Q--L-RNR-------- 57 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~-~~~~~~l~~Gq~L~IP~~~~~~~~~-----------~--~-~~~-------- 57 (129)
+||||..|=+++|+ +..++.++-. ..+...|++||.|.+-......-.. . . +..
T Consensus 102 ~GDTl~~iL~r~Gi---~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg~F~~~~~~~ 178 (439)
T PRK11649 102 TGDTLSSILNQYGI---DMSDISQLAAQDKELRNLKIGQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGNGFKETSEMQ 178 (439)
T ss_pred CCCCHHHHHHHcCC---CHHHHHHHHHcChHhhcCCCCCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCCcEEEEEeec
Confidence 59999999999999 5555554411 1234679999999886432110000 0 0 000
Q ss_pred --ccceEEEEecCCCCHHHHHHHhCCCHHHHHhhcC--------CCCCCCCEEEEcC
Q 037542 58 --VNYLVSYVLQPSENLSSVASRFGIETQAIIDVNG--------NNIRPFDTLFVPV 104 (129)
Q Consensus 58 --~~~~~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~--------~~l~~Gq~L~IP~ 104 (129)
..........-..+|+.-|.+.|++...++++.. ..|+.|+.+.|=.
T Consensus 179 ~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~~~~~~idf~~lr~GD~f~v~~ 235 (439)
T PRK11649 179 QGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSVLM 235 (439)
T ss_pred ccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHHHhccCcChhhCCCCCEEEEEE
Confidence 0000111122245899999999999888777765 4699998877643
No 41
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=95.40 E-value=0.0076 Score=48.57 Aligned_cols=43 Identities=19% Similarity=0.272 Sum_probs=38.9
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC---CCCCCCCEEEEcC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG---NNIRPFDTLFVPV 104 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~---~~l~~Gq~L~IP~ 104 (129)
..|.|++||+++.|+++|+.+...|...|. +.|-+||.+.||.
T Consensus 2 ~i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~d~~~~~q~~~v~~ 47 (423)
T COG3858 2 SIHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTNDDLVDGQTFVVPP 47 (423)
T ss_pred EEEEccCCceeeeehhhccccccccccccccccccccCceeEEECC
Confidence 469999999999999999999999976666 6799999999997
No 42
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=91.77 E-value=0.37 Score=35.98 Aligned_cols=45 Identities=31% Similarity=0.475 Sum_probs=40.7
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC---C-CCCCCCEEEEcCCC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG---N-NIRPFDTLFVPVAR 106 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~---~-~l~~Gq~L~IP~~~ 106 (129)
..|.++.|++|..|++++++....+...|. . .+..|+.+.++...
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRAA 50 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecccc
Confidence 368999999999999999999999999998 3 78999999999864
No 43
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=90.82 E-value=0.57 Score=37.49 Aligned_cols=43 Identities=21% Similarity=0.392 Sum_probs=34.5
Q ss_pred eEEEEecCCCCHHHHHHHh-CC--CHHHHHhhcC----CCCCCCCEEEEc
Q 037542 61 LVSYVLQPSENLSSVASRF-GI--ETQAIIDVNG----NNIRPFDTLFVP 103 (129)
Q Consensus 61 ~~~y~V~~GDTl~~IA~~~-~v--s~~~l~~~N~----~~l~~Gq~L~IP 103 (129)
....+|++|||+.++|.+. |+ +++.+.-+|. ..+++|+.|+|=
T Consensus 428 irvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKii 477 (479)
T COG4784 428 IRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKII 477 (479)
T ss_pred EEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeeec
Confidence 3467899999999999764 65 5667777787 689999999873
No 44
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.56 E-value=0.31 Score=27.12 Aligned_cols=25 Identities=20% Similarity=0.325 Sum_probs=21.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
..|.++..||+.|||+...|..|=.
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHHH
Confidence 3688999999999999999888754
No 45
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.30 E-value=0.34 Score=37.75 Aligned_cols=46 Identities=15% Similarity=0.179 Sum_probs=39.0
Q ss_pred EEEEecCCCCHHHHHHHhCC---CHHHHHhhcC----CCCCCCCEEEEcCCCC
Q 037542 62 VSYVLQPSENLSSVASRFGI---ETQAIIDVNG----NNIRPFDTLFVPVARL 107 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~v---s~~~l~~~N~----~~l~~Gq~L~IP~~~~ 107 (129)
.+|.|+.||||-.++..|=. .+..++.+|. ..|++|..|.||....
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~~ 58 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPAS 58 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCccc
Confidence 68999999999999999843 5566888888 6899999999997664
No 46
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=89.29 E-value=0.42 Score=41.19 Aligned_cols=45 Identities=24% Similarity=0.389 Sum_probs=32.5
Q ss_pred CCCcHHHHHHhhCC-CCCCH----HHHHHhCCCC----CCCCCCCCCEEEECCC
Q 037542 1 SGDTFYSVSTNKYQ-NLTTY----QSVEVVNPAF----VPTKLEVGDVFIFPVF 45 (129)
Q Consensus 1 ~GDTl~~IA~~~~~-~lts~----~~l~~~N~~~----~~~~l~~Gq~L~IP~~ 45 (129)
+|||||.||.+.-- +-.|+ ..|.++|+.. +-+.|++|++|.||..
T Consensus 195 ~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 195 SGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred CcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 59999999988643 22233 4566889843 2358999999999973
No 47
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=88.98 E-value=0.3 Score=35.50 Aligned_cols=45 Identities=20% Similarity=0.428 Sum_probs=36.8
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEEEcCCC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG----NNIRPFDTLFVPVAR 106 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~IP~~~ 106 (129)
..-+|+.||||..||-.|...+.+|.+.|+ ..+..-..+.+|+..
T Consensus 10 l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv~~ 58 (186)
T KOG2850|consen 10 LEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPVTR 58 (186)
T ss_pred eeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecccch
Confidence 567899999999999999999999999996 445555666666544
No 48
>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=88.83 E-value=0.53 Score=25.96 Aligned_cols=23 Identities=13% Similarity=0.411 Sum_probs=17.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
+.|-++..||+.||++...|.++
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 67899999999999999998775
No 49
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=87.25 E-value=1.8 Score=26.12 Aligned_cols=43 Identities=14% Similarity=0.184 Sum_probs=33.6
Q ss_pred EEEEecCCCCHHHHHHHh-CC---CHHHHHhhcC------CCCCCCCEEEEcC
Q 037542 62 VSYVLQPSENLSSVASRF-GI---ETQAIIDVNG------NNIRPFDTLFVPV 104 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~-~v---s~~~l~~~N~------~~l~~Gq~L~IP~ 104 (129)
..|.-..|||+..|+.++ |- =.+.+.++|+ ..|..|-.|.+|-
T Consensus 3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD 55 (70)
T COG5004 3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPD 55 (70)
T ss_pred eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCC
Confidence 567788999999999874 43 2377899999 5688888888774
No 50
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=85.82 E-value=1.2 Score=33.29 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=38.4
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCC-CCCCCCCEEEECCCC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVP-TKLEVGDVFIFPVFC 46 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~-~~l~~Gq~L~IP~~~ 46 (129)
+|+||..+=+..++.++++.++.+.-+..++ ..|+.||.|+|-.+.
T Consensus 166 ~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 166 QGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred CCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 5999999999999988888888888776444 579999999998754
No 51
>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=84.37 E-value=0.66 Score=27.92 Aligned_cols=24 Identities=29% Similarity=0.552 Sum_probs=21.1
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhh
Q 037542 66 LQPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
...|.|+..||+.|||+...|..|
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W 43 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNW 43 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHH
T ss_pred HHCCCceEeeecccccccccccHH
Confidence 477999999999999999999888
No 52
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.46 E-value=1.7 Score=28.52 Aligned_cols=25 Identities=28% Similarity=0.465 Sum_probs=21.2
Q ss_pred EecCCCCHHHHHHHhCC-CHHHHHhh
Q 037542 65 VLQPSENLSSVASRFGI-ETQAIIDV 89 (129)
Q Consensus 65 ~V~~GDTl~~IA~~~~v-s~~~l~~~ 89 (129)
..+.|.|+..||++||+ ....|..|
T Consensus 20 ~~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 20 YLRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HHhcCccHHHHHHHhCCCChHHHHHH
Confidence 34689999999999995 88888876
No 53
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=81.37 E-value=2 Score=23.67 Aligned_cols=23 Identities=13% Similarity=0.336 Sum_probs=17.6
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
..|.|...||+.+|++...+.+|
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w 37 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRW 37 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 34999999999999999988877
No 54
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=80.81 E-value=2 Score=25.89 Aligned_cols=46 Identities=24% Similarity=0.305 Sum_probs=34.2
Q ss_pred CCCcHHHHHHhhCCCCC-CHHHHHHhCCCCCC--CCCCCCCEEEECCCC
Q 037542 1 SGDTFYSVSTNKYQNLT-TYQSVEVVNPAFVP--TKLEVGDVFIFPVFC 46 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lt-s~~~l~~~N~~~~~--~~l~~Gq~L~IP~~~ 46 (129)
.|||+..++.+++...+ =.+++.++|+.... -.|..|-.|.+|...
T Consensus 9 ~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~~ 57 (70)
T COG5004 9 QGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDIA 57 (70)
T ss_pred cCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCCC
Confidence 49999999999875321 24678889997633 368889999998644
No 55
>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=80.16 E-value=0.97 Score=25.93 Aligned_cols=24 Identities=21% Similarity=0.499 Sum_probs=16.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhh
Q 037542 66 LQPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
+..|.+...||+.||++...|..+
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 467899999999999977666543
No 56
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=79.99 E-value=2.2 Score=28.45 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=24.5
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 64 YVLQPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 64 y~V~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
+.+..|.++..||++|||+...|..|=.
T Consensus 24 ~~~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 24 QSFEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4467899999999999999999999944
No 57
>PHA00675 hypothetical protein
Probab=78.04 E-value=2.8 Score=26.17 Aligned_cols=24 Identities=17% Similarity=0.217 Sum_probs=21.4
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhc
Q 037542 67 QPSENLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N 90 (129)
+.|.+.+.||++||++-..|...=
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHH
Confidence 789999999999999998887763
No 58
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.83 E-value=1.9 Score=33.68 Aligned_cols=46 Identities=20% Similarity=0.203 Sum_probs=40.4
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCCC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVFC 46 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~~ 46 (129)
.||||..++..|-..+..+..+..+|...++..+++|..|.||...
T Consensus 12 ~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~ 57 (339)
T COG4254 12 FGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPA 57 (339)
T ss_pred cccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCcc
Confidence 4899999999997767778888999999888999999999999753
No 59
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=75.51 E-value=4 Score=22.30 Aligned_cols=23 Identities=17% Similarity=0.377 Sum_probs=15.1
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHh
Q 037542 66 LQPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
.+.|-++..||+.+|.+...|.+
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHH
Confidence 46899999999999998887754
No 60
>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=75.33 E-value=5.2 Score=19.09 Aligned_cols=23 Identities=17% Similarity=0.455 Sum_probs=19.6
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
..|.++..||+.||++...+..+
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 56889999999999998887654
No 61
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=75.31 E-value=4.3 Score=30.16 Aligned_cols=42 Identities=17% Similarity=0.271 Sum_probs=36.2
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVF 45 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~ 45 (129)
.|++|+.|+++++. ....+...|.......+..|+.+.++..
T Consensus 8 ~~~~l~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 8 KGDTLSAIAARLGI---SAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred CCCHHHHHHHHcCC---CHHHHHHHHhhccccccCccceeeeccc
Confidence 47899999999998 8989999998755458899999999974
No 62
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=74.64 E-value=5.2 Score=32.20 Aligned_cols=42 Identities=14% Similarity=0.164 Sum_probs=32.5
Q ss_pred CCCcHHHHHHhhCCCC-CCHHHHHHhCCCCCCCCCCCCCEEEEC
Q 037542 1 SGDTFYSVSTNKYQNL-TTYQSVEVVNPAFVPTKLEVGDVFIFP 43 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~l-ts~~~l~~~N~~~~~~~l~~Gq~L~IP 43 (129)
+|||+.++|.+.- |+ .+++.++-+|.+.....+.+|+.|+|=
T Consensus 435 ~GqT~~~lAA~m~-G~~rkldlfRllNam~~~a~~~pGd~vKii 477 (479)
T COG4784 435 PGQTMASLAARMM-GTDRKLDLFRLLNAMSPGATVRPGDKVKII 477 (479)
T ss_pred CCccHHHHHhhcc-CchhHHHHHHHHhccCCCCcCCCCCeeeec
Confidence 6999999998853 43 356666778988766789999999873
No 63
>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=73.42 E-value=3.8 Score=22.64 Aligned_cols=24 Identities=8% Similarity=0.317 Sum_probs=16.7
Q ss_pred ecCC-CCHHHHHHHhCCCHHHHHhh
Q 037542 66 LQPS-ENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 66 V~~G-DTl~~IA~~~~vs~~~l~~~ 89 (129)
|+.| -++...|+.|||+...|...
T Consensus 12 v~~g~~S~r~AA~~ygVp~sTL~~r 36 (45)
T PF05225_consen 12 VKNGKMSIRKAAKKYGVPRSTLRRR 36 (45)
T ss_dssp HHTTSS-HHHHHHHHT--HHHHHHH
T ss_pred HHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 3455 79999999999999888754
No 64
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=72.36 E-value=5.2 Score=22.11 Aligned_cols=21 Identities=19% Similarity=0.395 Sum_probs=17.8
Q ss_pred CCCHHHHHHHhCCCHHHHHhh
Q 037542 69 SENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~~ 89 (129)
.-|+..||+.+|+++..+.+.
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHH
Confidence 349999999999999888764
No 65
>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=71.43 E-value=6.8 Score=21.58 Aligned_cols=23 Identities=22% Similarity=0.388 Sum_probs=18.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
-.|-|+..||+.+|++.+.+...
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 56889999999999999887654
No 66
>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=68.86 E-value=5.6 Score=21.14 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=16.9
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|++...|..|=.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999998854
No 67
>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=68.57 E-value=6.8 Score=23.25 Aligned_cols=22 Identities=18% Similarity=0.371 Sum_probs=19.6
Q ss_pred CCHHHHHHHhCCCHHHHHhhcC
Q 037542 70 ENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~N~ 91 (129)
=+|-.||.++||+...|..|=.
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhh
Confidence 3899999999999999999854
No 68
>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=67.03 E-value=4.4 Score=26.95 Aligned_cols=25 Identities=16% Similarity=0.414 Sum_probs=22.0
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhhc
Q 037542 66 LQPSENLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~N 90 (129)
+..|.+...+|++|+|+...+..|=
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W~ 39 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRWL 39 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHHH
Confidence 4568999999999999999998883
No 69
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=65.83 E-value=7.1 Score=22.45 Aligned_cols=23 Identities=13% Similarity=0.237 Sum_probs=17.0
Q ss_pred cCCCCHHHHHHHhC-CCHHHHHhh
Q 037542 67 QPSENLSSVASRFG-IETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~-vs~~~l~~~ 89 (129)
..|.+...|++.|. ++.++|..+
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 88999999999998 899998765
No 70
>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=65.48 E-value=9 Score=20.17 Aligned_cols=21 Identities=10% Similarity=0.113 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|..|=.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~ 22 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVK 22 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999999843
No 71
>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=65.43 E-value=7.2 Score=25.50 Aligned_cols=21 Identities=19% Similarity=0.520 Sum_probs=15.7
Q ss_pred CCCHHHHHHHhCCCHHHHHhh
Q 037542 69 SENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~~ 89 (129)
|.++..||++||+|...|.+.
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 999999999999999887653
No 72
>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=64.80 E-value=4.8 Score=29.29 Aligned_cols=19 Identities=37% Similarity=0.545 Sum_probs=16.7
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
-|-.||+|||++..+|++.
T Consensus 172 yLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 172 YLPGVAERFGISEGELRRA 190 (194)
T ss_pred cchhhHHHcCCCHHHHHHH
Confidence 4779999999999999874
No 73
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=64.71 E-value=4.4 Score=29.52 Aligned_cols=42 Identities=19% Similarity=0.216 Sum_probs=34.4
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCC
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVF 45 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~ 45 (129)
.||||..||-+|.. ++.+|.+.|++.....+..=..+++|..
T Consensus 16 ~~dt~~a~al~~~~---~va~i~RvN~~~r~q~f~a~~~i~~pv~ 57 (186)
T KOG2850|consen 16 EGDTLQAIALNYES---DVADIKRVNNDDREQRFNALRSISIPVT 57 (186)
T ss_pred cCchhhhHHhhccc---chhhheeeccchhhhhhccccceecccc
Confidence 48999999999988 8999999998754556667777888764
No 74
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=63.45 E-value=12 Score=23.45 Aligned_cols=42 Identities=19% Similarity=0.282 Sum_probs=35.6
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHH--HhhcC------CCCCCCCEEEEc
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAI--IDVNG------NNIRPFDTLFVP 103 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l--~~~N~------~~l~~Gq~L~IP 103 (129)
..|.+..+-|+..+.+.+|+...++ .-.|+ ..++.|+.|.|-
T Consensus 25 ~~~~~~~~~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 25 FTHPFDGGATVKDVIESLGVPHTEVGLILVNGRPVDFDYRLKDGDRVAVY 74 (81)
T ss_pred eEEecCCCCcHHHHHHHcCCChHHeEEEEECCEECCCcccCCCCCEEEEE
Confidence 6788999999999999999988775 44687 579999998774
No 75
>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=62.48 E-value=11 Score=20.28 Aligned_cols=21 Identities=10% Similarity=0.177 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|..|-.
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999999944
No 76
>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=60.71 E-value=11 Score=21.87 Aligned_cols=19 Identities=16% Similarity=0.265 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
++..+|+.+|++...|..|
T Consensus 2 s~~eva~~~gvs~~tlr~w 20 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAW 20 (68)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5678999999999999988
No 77
>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=60.25 E-value=14 Score=20.53 Aligned_cols=19 Identities=16% Similarity=0.396 Sum_probs=16.3
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
||.+||+..|++...+-++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ 19 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRV 19 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 7889999999999887665
No 78
>smart00351 PAX Paired Box domain.
Probab=59.98 E-value=10 Score=25.41 Aligned_cols=25 Identities=8% Similarity=0.207 Sum_probs=21.3
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
..|.+...||++||++...+.+|=.
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kwi~ 55 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKILG 55 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 5799999999999999988777633
No 79
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=59.48 E-value=8.9 Score=21.66 Aligned_cols=23 Identities=26% Similarity=0.452 Sum_probs=19.1
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHh
Q 037542 66 LQPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
.+.|.+...+|.+|||+...+-+
T Consensus 16 LR~~~~~~~La~~FgIs~stvsr 38 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSR 38 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHH
Confidence 47789999999999998876554
No 80
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=59.14 E-value=10 Score=26.32 Aligned_cols=28 Identities=18% Similarity=0.230 Sum_probs=23.2
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 64 YVLQPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 64 y~V~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
..+..|.+...||++||++...+..|=+
T Consensus 16 ~~~~~G~S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 16 AVVGEGLSCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred HHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence 3456799999999999999988877744
No 81
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=59.12 E-value=12 Score=23.33 Aligned_cols=23 Identities=9% Similarity=0.341 Sum_probs=16.5
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
+.|=||..||+.+|++...+..+
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~na 35 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRNA 35 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHHT
T ss_pred HcCCCHHHHHHHcCCCHHHHHHH
Confidence 57899999999999988776544
No 82
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=58.95 E-value=17 Score=25.78 Aligned_cols=25 Identities=20% Similarity=0.409 Sum_probs=21.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
++.-++..||+.|+++..+|..+=+
T Consensus 25 qPdg~~eamA~~~~v~~~eIv~aLP 49 (176)
T COG3721 25 QPDGTLEAMAEQYNVTELEIVRALP 49 (176)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHhCc
Confidence 6777999999999999999988744
No 83
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=57.01 E-value=18 Score=19.48 Aligned_cols=24 Identities=21% Similarity=0.320 Sum_probs=20.6
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhh
Q 037542 66 LQPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
+..|.+...||+.+|++...+...
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHH
Confidence 357899999999999999887765
No 84
>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=56.95 E-value=13 Score=23.64 Aligned_cols=26 Identities=23% Similarity=0.341 Sum_probs=22.3
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 66 LQPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
+..|.|...||+.+|++...|.++..
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999988887643
No 85
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=56.69 E-value=12 Score=21.78 Aligned_cols=21 Identities=14% Similarity=0.264 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|++...|..|=.
T Consensus 2 ti~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999844
No 86
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=56.45 E-value=34 Score=20.58 Aligned_cols=40 Identities=8% Similarity=0.152 Sum_probs=31.2
Q ss_pred EEEecCCCCHHHHHHHhCC-CHHHHHhhcC-------------CCCCCCCEEEEc
Q 037542 63 SYVLQPSENLSSVASRFGI-ETQAIIDVNG-------------NNIRPFDTLFVP 103 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~v-s~~~l~~~N~-------------~~l~~Gq~L~IP 103 (129)
.|.| .|.-+..+..+++. +.+.+..++. ..++.|+++.|=
T Consensus 10 ~~~V-~g~~ier~~~~~~~~~~e~~~~f~~~L~~~Gv~~~L~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 10 VFVV-SGKKIERWVAKTPFNNDENLRRFARKLKKLGVEDALRKAGAKDGDTVRIG 63 (69)
T ss_pred eEEE-echHHHHHHHHcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEEc
Confidence 4666 68999999999987 5666666665 578999999873
No 87
>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=56.38 E-value=11 Score=27.02 Aligned_cols=29 Identities=14% Similarity=0.258 Sum_probs=25.7
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
.-.|+.|.|...||+.+|++++.|.++-.
T Consensus 63 QarIRaGas~eeVA~~~G~~~~rV~rfa~ 91 (170)
T PF11268_consen 63 QARIRAGASAEEVAEEAGVPVERVRRFAG 91 (170)
T ss_pred HHHHHCCCCHHHHHHHhCCCHHHhhhccc
Confidence 34579999999999999999999998865
No 88
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=55.91 E-value=12 Score=23.41 Aligned_cols=43 Identities=12% Similarity=0.243 Sum_probs=35.6
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC-------CCCCCCCEEEEcCC
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG-------NNIRPFDTLFVPVA 105 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~-------~~l~~Gq~L~IP~~ 105 (129)
.|.+-.-|-...+-++|++...+|-+.-. -.+++||.+.|--.
T Consensus 14 kH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~ 63 (79)
T PRK09570 14 EHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRK 63 (79)
T ss_pred CeEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEEEEC
Confidence 57888888889999999999999866654 47999999999643
No 89
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=55.78 E-value=15 Score=23.37 Aligned_cols=27 Identities=15% Similarity=0.265 Sum_probs=23.2
Q ss_pred EecCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 65 VLQPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 65 ~V~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
.|..|-++..+|+.|||+.....+|=.
T Consensus 21 vv~~g~~~a~aA~~~gVS~~Ta~kW~~ 47 (85)
T PF13011_consen 21 VVEQGWPVAHAAAEFGVSRRTAYKWLA 47 (85)
T ss_pred HHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence 456788999999999999988888855
No 90
>PHA01976 helix-turn-helix protein
Probab=54.88 E-value=8.5 Score=22.35 Aligned_cols=19 Identities=16% Similarity=0.260 Sum_probs=16.8
Q ss_pred CCCHHHHHHHhCCCHHHHH
Q 037542 69 SENLSSVASRFGIETQAII 87 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~ 87 (129)
-+++..||+.||+++++|.
T Consensus 44 ~~~l~~ia~~l~v~~~~l~ 62 (67)
T PHA01976 44 LKTLLRLADALGVTLDWLC 62 (67)
T ss_pred HHHHHHHHHHHCcCHHHHh
Confidence 3689999999999999885
No 91
>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=54.77 E-value=12 Score=22.26 Aligned_cols=19 Identities=32% Similarity=0.602 Sum_probs=14.6
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
++..||+.|+++.+.|..+
T Consensus 16 S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 16 SLAELAREFGISPEAVEAM 34 (69)
T ss_dssp EHHHHHHHTT--HHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 7899999999999887665
No 92
>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=53.92 E-value=19 Score=18.95 Aligned_cols=21 Identities=10% Similarity=0.268 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|++...|.++=.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 677899999999999998854
No 93
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=53.88 E-value=17 Score=21.10 Aligned_cols=21 Identities=14% Similarity=0.219 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|++...|..|=.
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999999944
No 94
>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=53.29 E-value=18 Score=21.07 Aligned_cols=20 Identities=10% Similarity=0.287 Sum_probs=17.7
Q ss_pred CHHHHHHHhCCCHHHHHhhc
Q 037542 71 NLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N 90 (129)
++..+|+.+|++...|..|=
T Consensus 2 ~i~evA~~~gvs~~tlR~~~ 21 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYE 21 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999983
No 95
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.15 E-value=16 Score=23.13 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=20.9
Q ss_pred ecCCC-CHHHHHHHhCCCHHHHHhhcC
Q 037542 66 LQPSE-NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 66 V~~GD-Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
+..|. |...||+.+|++...+.+|=.
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~ 34 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWLK 34 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 35677 699999999999988777733
No 96
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=52.17 E-value=11 Score=24.46 Aligned_cols=38 Identities=11% Similarity=0.094 Sum_probs=29.4
Q ss_pred HHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEEC
Q 037542 5 FYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFP 43 (129)
Q Consensus 5 l~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP 43 (129)
+..||+-|+.++.|+..|.+- +..++...+.|.++.|=
T Consensus 48 ~~GlAklfgcSv~Ta~RiK~s-G~id~AI~Q~Gr~IivD 85 (96)
T PF12964_consen 48 LKGLAKLFGCSVPTANRIKKS-GKIDPAITQIGRKIIVD 85 (96)
T ss_pred HHHHHHHhCCCchhHHHHHhc-CCccHHHHHcCCEEEEe
Confidence 468999999988888888866 55566677888888763
No 97
>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=51.19 E-value=21 Score=23.62 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=19.3
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
.++-|+..||++|||+...|..+
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~ 91 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRA 91 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHH
Confidence 56779999999999998887654
No 98
>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=50.66 E-value=19 Score=19.91 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=15.6
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
-.|-+...||+.+|++...+..+
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~ 46 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRR 46 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHH
Confidence 35789999999999999887653
No 99
>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=49.25 E-value=19 Score=20.64 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=14.7
Q ss_pred CHHHHHHHhCCCHHHHHh
Q 037542 71 NLSSVASRFGIETQAIID 88 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~ 88 (129)
++..+|+.|++|...+.+
T Consensus 16 s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRR 33 (57)
T ss_pred EHHHHHHHHCcCHHHHHH
Confidence 688999999998876543
No 100
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=49.25 E-value=18 Score=20.84 Aligned_cols=22 Identities=23% Similarity=0.424 Sum_probs=17.7
Q ss_pred CCHHHHHHHhCCCHHHHHhhcC
Q 037542 70 ENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~N~ 91 (129)
+-+..||+.||++.++|..-..
T Consensus 4 ~I~~~Va~~~~i~~~~i~s~~R 25 (60)
T smart00760 4 EIIEAVAEYFGVKPEDLKSKSR 25 (60)
T ss_pred HHHHHHHHHhCCCHHHHhcCCC
Confidence 3467889999999999977654
No 101
>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=49.19 E-value=17 Score=23.14 Aligned_cols=25 Identities=16% Similarity=0.307 Sum_probs=22.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
+.|-|...||+.+|++...|-+.|+
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 4789999999999999999988876
No 102
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=48.35 E-value=31 Score=18.88 Aligned_cols=19 Identities=11% Similarity=0.364 Sum_probs=15.4
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
+...||++|+++...+.++
T Consensus 22 s~~~la~~~~vs~~tv~~~ 40 (60)
T smart00345 22 SERELAAQLGVSRTTVREA 40 (60)
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 7889999999988766553
No 103
>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=47.87 E-value=24 Score=20.60 Aligned_cols=21 Identities=19% Similarity=0.221 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|++.||+...|..|-.
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999998843
No 104
>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=47.78 E-value=32 Score=18.57 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=19.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
..|-+...||+.++++...+..+
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~ 35 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999999887765
No 105
>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=47.59 E-value=30 Score=20.65 Aligned_cols=22 Identities=14% Similarity=0.398 Sum_probs=18.0
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
..|-++-.||+.+|++..+...
T Consensus 11 E~g~~FveIAr~~~i~a~e~a~ 32 (63)
T PF11242_consen 11 ESGLSFVEIARKIGITAKEVAK 32 (63)
T ss_pred HcCCcHHHHHHHhCCCHHHHHH
Confidence 4588999999999998877554
No 106
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=46.88 E-value=20 Score=25.88 Aligned_cols=26 Identities=8% Similarity=0.130 Sum_probs=21.5
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHhh
Q 037542 64 YVLQPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 64 y~V~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
-.|-.|+++-.+|++.|++..++-+.
T Consensus 27 ~~vsaG~iFR~~A~e~gmsl~ef~~~ 52 (179)
T COG1102 27 KLVSAGTIFREMARERGMSLEEFSRY 52 (179)
T ss_pred ceeeccHHHHHHHHHcCCCHHHHHHH
Confidence 45678999999999999998775544
No 107
>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=46.64 E-value=15 Score=20.65 Aligned_cols=19 Identities=26% Similarity=0.531 Sum_probs=14.9
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
+++.+|+.+|++..+|.+.
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 5678999999999886653
No 108
>cd00131 PAX Paired Box domain
Probab=46.43 E-value=23 Score=23.91 Aligned_cols=25 Identities=4% Similarity=0.145 Sum_probs=21.4
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
..|.+...||++|+++...+.+|=.
T Consensus 31 ~~G~s~~~iA~~~~Vs~~tV~r~i~ 55 (128)
T cd00131 31 QSGIRPCDISRQLRVSHGCVSKILN 55 (128)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 5799999999999999987777743
No 109
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=46.08 E-value=25 Score=21.95 Aligned_cols=26 Identities=12% Similarity=0.277 Sum_probs=22.4
Q ss_pred EEecCCCCHHHHHHHhC-CCHHHHHhh
Q 037542 64 YVLQPSENLSSVASRFG-IETQAIIDV 89 (129)
Q Consensus 64 y~V~~GDTl~~IA~~~~-vs~~~l~~~ 89 (129)
..++.|.|...|+..|. ++.++|.++
T Consensus 38 ~~l~~G~s~eeil~dyp~Lt~~dI~aa 64 (79)
T COG2442 38 EMLAAGESIEEILADYPDLTLEDIRAA 64 (79)
T ss_pred HHHHCCCCHHHHHHhCCCCCHHHHHHH
Confidence 44578999999999998 899998875
No 110
>PF14502 HTH_41: Helix-turn-helix domain
Probab=45.83 E-value=28 Score=19.68 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=16.0
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
|+...+++|+++...|+.+
T Consensus 8 tI~e~~~~~~vs~GtiQ~A 26 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNA 26 (48)
T ss_pred CHHHHHHHhCcchhHHHHH
Confidence 7888899999998887765
No 111
>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=44.89 E-value=36 Score=19.80 Aligned_cols=24 Identities=8% Similarity=0.266 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 68 PSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 68 ~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
.|=++..||+..|++...+..|=.
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHH
Confidence 488999999999999988888744
No 112
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=43.94 E-value=1.3e+02 Score=22.26 Aligned_cols=69 Identities=13% Similarity=0.189 Sum_probs=40.4
Q ss_pred CCCCCCCEEEECCCCCCCCcccccccccceEEEEecCCCCHHHHHHHh-CCCHHH------HHhhcC------------C
Q 037542 32 TKLEVGDVFIFPVFCKCPDQTQLRNRVNYLVSYVLQPSENLSSVASRF-GIETQA------IIDVNG------------N 92 (129)
Q Consensus 32 ~~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~IA~~~-~vs~~~------l~~~N~------------~ 92 (129)
-.|++|+.|.||..... ... ........|..+.|.||...-.+- |.+... |.+.|. +
T Consensus 149 i~L~~GD~I~V~~~~~v---~v~-G~V~~pg~~~~~~~~tl~~al~~aGG~~~~a~~~~v~i~R~~~~g~~~~~~~~~~~ 224 (239)
T TIGR03028 149 ILVAGGDIIYVDRAPVF---YIY-GEVQRPGAYRLERNMTVMQALAQGGGLTPRGTERGIRVMRRDDKGAVEEVSGELGD 224 (239)
T ss_pred cEEcCCCEEEEcCCccE---EEE-eEccCCeEEEeCCCCCHHHHHHhcCCCCcccCcceEEEEEECCCCcEEEEecCCCc
Confidence 46999999999964210 000 011222478889999987655443 443321 222221 3
Q ss_pred CCCCCCEEEEcC
Q 037542 93 NIRPFDTLFVPV 104 (129)
Q Consensus 93 ~l~~Gq~L~IP~ 104 (129)
.|++|+.|+||-
T Consensus 225 ~l~~gDii~V~~ 236 (239)
T TIGR03028 225 LVQPDDVIYVRE 236 (239)
T ss_pred ccCCCCEEEEeC
Confidence 489999999984
No 113
>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=43.80 E-value=27 Score=20.06 Aligned_cols=25 Identities=16% Similarity=0.305 Sum_probs=21.1
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHH
Q 037542 63 SYVLQPSENLSSVASRFGIETQAII 87 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~ 87 (129)
.|-+-++=|+..||+.+|++...+.
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 5777888999999999999876654
No 114
>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=43.14 E-value=25 Score=21.10 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=13.7
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
-+..||+.||++.++|..-
T Consensus 5 Ii~~Va~~~~v~~~~i~s~ 23 (70)
T PF08299_consen 5 IIEAVAEYFGVSVEDIRSK 23 (70)
T ss_dssp HHHHHHHHTT--HHHHHSS
T ss_pred HHHHHHHHHCCCHHHHhCC
Confidence 4677899999999998754
No 115
>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=42.32 E-value=23 Score=20.53 Aligned_cols=19 Identities=21% Similarity=0.464 Sum_probs=15.2
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
.+.-.|++||+|.++|.++
T Consensus 22 ev~ywa~~~gvt~~~L~~A 40 (57)
T PF12244_consen 22 EVRYWAKRFGVTEEQLREA 40 (57)
T ss_pred HHHHHHHHHCcCHHHHHHH
Confidence 3556789999999998876
No 116
>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=41.69 E-value=32 Score=21.83 Aligned_cols=21 Identities=10% Similarity=0.246 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|++...|.-|=.
T Consensus 2 ti~eva~~~gvs~~tLRyye~ 22 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDD 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999998854
No 117
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=41.51 E-value=29 Score=22.05 Aligned_cols=23 Identities=26% Similarity=0.336 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhCCCHHHHHhhcC
Q 037542 69 SENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
.|-+.+||+..|++..+|..+|-
T Consensus 69 ~~EirGIA~~~gi~l~~iv~lN~ 91 (95)
T PF15508_consen 69 AEEIRGIAKAAGIPLGDIVLLNL 91 (95)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Confidence 46789999999999999999984
No 118
>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=41.49 E-value=34 Score=21.36 Aligned_cols=20 Identities=15% Similarity=0.320 Sum_probs=17.0
Q ss_pred CCHHHHHHHhCCCHHHHHhh
Q 037542 70 ENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~ 89 (129)
-|+.+||+.+|++...+.+.
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~ 39 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKD 39 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHH
Confidence 38999999999999887664
No 119
>PHA02591 hypothetical protein; Provisional
Probab=41.12 E-value=36 Score=21.37 Aligned_cols=28 Identities=21% Similarity=0.433 Sum_probs=18.1
Q ss_pred EEEEecCCCCHHHHHHH---hCCCHHHHHhh
Q 037542 62 VSYVLQPSENLSSVASR---FGIETQAIIDV 89 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~---~~vs~~~l~~~ 89 (129)
..|-|...|.+-++|+. -|.+.++|++.
T Consensus 38 ~ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~ 68 (83)
T PHA02591 38 TRYFVESEDDLISVTHELARKGFTVEKIASL 68 (83)
T ss_pred EEEEEeccchHHHHHHHHHHcCCCHHHHHHH
Confidence 46777777777777753 36666666654
No 120
>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=41.11 E-value=35 Score=22.06 Aligned_cols=23 Identities=13% Similarity=0.163 Sum_probs=20.0
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
..|-++..||+.+|++...+...
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 46999999999999999887764
No 121
>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=40.81 E-value=27 Score=21.58 Aligned_cols=22 Identities=18% Similarity=0.258 Sum_probs=16.9
Q ss_pred EEEEecCCCCHHHHHHHhCCCH
Q 037542 62 VSYVLQPSENLSSVASRFGIET 83 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~ 83 (129)
..|.+.+|+||...+.+.|+.+
T Consensus 11 ~~v~~~~G~til~al~~~gi~i 32 (82)
T PF13510_consen 11 KPVEVPPGETILEALLAAGIDI 32 (82)
T ss_dssp EEEEEEET-BHHHHHHHTT--B
T ss_pred EEEEEcCCCHHHHHHHHCCCeE
Confidence 5799999999999999988753
No 122
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=40.69 E-value=38 Score=21.84 Aligned_cols=23 Identities=9% Similarity=0.348 Sum_probs=19.1
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
++|-||..|++..|++...|..+
T Consensus 19 KrG~sLa~lsr~~Gls~~TL~nA 41 (92)
T PRK10344 19 KKGTSMAAESRRNGLSSSTLANA 41 (92)
T ss_pred HcCCcHHHHHHHcCCChHHHHHH
Confidence 57889999999999988776544
No 123
>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=40.64 E-value=33 Score=21.98 Aligned_cols=21 Identities=10% Similarity=0.471 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|-.
T Consensus 3 ~i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999988854
No 124
>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=40.29 E-value=35 Score=21.31 Aligned_cols=21 Identities=19% Similarity=0.123 Sum_probs=18.8
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|++...|..|-.
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999999965
No 125
>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=40.15 E-value=34 Score=21.80 Aligned_cols=20 Identities=25% Similarity=0.311 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHhhc
Q 037542 71 NLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N 90 (129)
++..+|+.+|++...|..|=
T Consensus 3 ~i~eva~~~gVs~~tLR~ye 22 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYD 22 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 67899999999999999983
No 126
>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=39.83 E-value=38 Score=19.94 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=15.6
Q ss_pred CHHHHHHHhCCCHHHHHhhc
Q 037542 71 NLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N 90 (129)
..-+.|++|||+...|.+|=
T Consensus 27 ~~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 27 NQRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp -HHHHHHHTTS-HHHHHHHH
T ss_pred hHHHHHHHhCccHHHHHHHH
Confidence 46788999999999999883
No 127
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=39.61 E-value=55 Score=23.10 Aligned_cols=47 Identities=23% Similarity=0.374 Sum_probs=30.4
Q ss_pred CCHHHHHHHhCCCHHH----HHhhcC--CCCCCCC----EEEEcCCCCCCCCCCCCC
Q 037542 70 ENLSSVASRFGIETQA----IIDVNG--NNIRPFD----TLFVPVARLPELKQPAVA 116 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~----l~~~N~--~~l~~Gq----~L~IP~~~~p~~~~~~~~ 116 (129)
-|...||-+||++... |.-+-. ..++.+| .-.||..+.|.+++....
T Consensus 7 ~T~eELA~~FGvttRkvaStLa~~ta~Grl~Rv~q~gkfRy~iPg~~lpAepk~~sv 63 (155)
T PF07789_consen 7 KTAEELAGKFGVTTRKVASTLAMVTATGRLIRVNQNGKFRYCIPGGNLPAEPKAASV 63 (155)
T ss_pred ccHHHHHHHhCcchhhhHHHHHHHHhcceeEEecCCCceEEeCCCCCCCCCcccccc
Confidence 3888999999997533 322222 3444444 667888888877766543
No 128
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=38.90 E-value=42 Score=17.53 Aligned_cols=21 Identities=14% Similarity=0.224 Sum_probs=14.2
Q ss_pred CCCHHHHHHHhCCCHHHHHhh
Q 037542 69 SENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~~ 89 (129)
+-+|.+||...|++..-+.+.
T Consensus 8 ~~~l~~iA~~~g~S~~~f~r~ 28 (42)
T PF00165_consen 8 KLTLEDIAEQAGFSPSYFSRL 28 (42)
T ss_dssp S--HHHHHHHHTS-HHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHH
Confidence 458899999999988776553
No 129
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=38.88 E-value=40 Score=19.48 Aligned_cols=18 Identities=17% Similarity=0.403 Sum_probs=14.2
Q ss_pred CHHHHHHHhCCCHHHHHh
Q 037542 71 NLSSVASRFGIETQAIID 88 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~ 88 (129)
++..||+.+|++...|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~ 20 (84)
T smart00342 3 TLEDLAEALGMSPRHLQR 20 (84)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 678899999988877654
No 130
>PF14493 HTH_40: Helix-turn-helix domain
Probab=38.72 E-value=38 Score=21.15 Aligned_cols=22 Identities=18% Similarity=0.282 Sum_probs=18.6
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
+.|-|+..||+.-+++...|..
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~~ 32 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIYG 32 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHHH
Confidence 6799999999999998877643
No 131
>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=38.64 E-value=39 Score=19.48 Aligned_cols=19 Identities=16% Similarity=0.459 Sum_probs=13.4
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
+...||++|+++...+.++
T Consensus 26 s~~~la~~~~vsr~tvr~a 44 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREA 44 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHH
Confidence 4578999999988776654
No 132
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.62 E-value=30 Score=23.98 Aligned_cols=20 Identities=25% Similarity=0.614 Sum_probs=17.1
Q ss_pred CCCHHHHHHHhCCCHHHHHh
Q 037542 69 SENLSSVASRFGIETQAIID 88 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~ 88 (129)
-|+|..||.++|++..++.+
T Consensus 90 ~~~l~~la~~~Gld~~El~~ 109 (143)
T COG3753 90 TDTLSQLAQKTGLDEQELLK 109 (143)
T ss_pred hhHHHHHHHHhCCCHHHHHH
Confidence 47999999999999877654
No 133
>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=38.35 E-value=55 Score=16.99 Aligned_cols=22 Identities=14% Similarity=0.225 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHhh
Q 037542 68 PSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 68 ~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
.|-+...||+.+|++...+..+
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6789999999999999888765
No 134
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; 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 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=38.01 E-value=38 Score=22.03 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|.-|=.
T Consensus 2 ~i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999998854
No 135
>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=37.90 E-value=9.5 Score=24.04 Aligned_cols=23 Identities=17% Similarity=0.540 Sum_probs=16.1
Q ss_pred EEEecCCCCHHHHHHHhCCCHHH
Q 037542 63 SYVLQPSENLSSVASRFGIETQA 85 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~ 85 (129)
.|.+..+.|+-..|+.||+|-+.
T Consensus 13 ~yIi~~~aTVR~~Ak~FGvSKST 35 (82)
T PF12116_consen 13 NYIIETKATVRQAAKVFGVSKST 35 (82)
T ss_dssp HHHHHH---HHHHHHHHTS-HHH
T ss_pred HHHHHcccHHHHHHHHHCCcHHH
Confidence 57788899999999999997654
No 136
>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=37.56 E-value=41 Score=20.96 Aligned_cols=21 Identities=10% Similarity=0.167 Sum_probs=19.0
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|..|-.
T Consensus 3 ti~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999999965
No 137
>PF12728 HTH_17: Helix-turn-helix domain
Probab=37.48 E-value=47 Score=18.03 Aligned_cols=33 Identities=12% Similarity=0.132 Sum_probs=23.8
Q ss_pred CHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEEEc
Q 037542 71 NLSSVASRFGIETQAIIDVNG----NNIRPFDTLFVP 103 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~IP 103 (129)
|...+|+.+|++...|.+|=. ..+..|-...++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g~i~~~~~g~~~~~~ 39 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQGKIPPFKIGRKWRIP 39 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCeEEeCCEEEEe
Confidence 567899999999999998833 334555555554
No 138
>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=37.44 E-value=41 Score=21.43 Aligned_cols=21 Identities=19% Similarity=0.387 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|..|-.
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999999954
No 139
>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=37.18 E-value=33 Score=22.03 Aligned_cols=26 Identities=8% Similarity=0.254 Sum_probs=19.2
Q ss_pred ecCCC-CHHHHHHHhCCCHHHHHhhcC
Q 037542 66 LQPSE-NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 66 V~~GD-Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|.-|- |+..-.++|+++.+++..|=.
T Consensus 45 V~~Glis~~EA~~rY~Ls~eEf~~W~~ 71 (90)
T PF06627_consen 45 VRGGLISVEEACRRYGLSEEEFESWQR 71 (90)
T ss_dssp HHCTTS-HHHHHHCTTSSHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34454 566777899999999999854
No 140
>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=37.10 E-value=41 Score=21.27 Aligned_cols=21 Identities=14% Similarity=0.368 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|.-|-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 2 KIGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998855
No 141
>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=36.71 E-value=24 Score=25.33 Aligned_cols=39 Identities=10% Similarity=0.075 Sum_probs=27.2
Q ss_pred CCcHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEE
Q 037542 2 GDTFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFI 41 (129)
Q Consensus 2 GDTl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~ 41 (129)
|.++-.||++||+++..+++|.++-.+ .......|..|.
T Consensus 33 ~~sv~~vS~~ygi~~~RV~AIvrLkei-E~~~~~~~k~l~ 71 (172)
T PF12298_consen 33 GKSVREVSQKYGIKIQRVEAIVRLKEI-EKRWKNKGKPLA 71 (172)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH-HHHHhcccChhh
Confidence 678999999999988888888877654 222334444443
No 142
>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=36.52 E-value=45 Score=23.90 Aligned_cols=25 Identities=24% Similarity=0.570 Sum_probs=19.1
Q ss_pred cCCCCHHHHHHHhCCCH---HHHHhhcC
Q 037542 67 QPSENLSSVASRFGIET---QAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~---~~l~~~N~ 91 (129)
+.|.++-.||++|||.. ++|.++-.
T Consensus 31 ~~~~sv~~vS~~ygi~~~RV~AIvrLke 58 (172)
T PF12298_consen 31 QDGKSVREVSQKYGIKIQRVEAIVRLKE 58 (172)
T ss_pred hCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 66789999999999965 55555543
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=36.44 E-value=42 Score=21.73 Aligned_cols=21 Identities=10% Similarity=0.094 Sum_probs=18.1
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 2 ~i~eva~~~gis~~tlR~ye~ 22 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYDK 22 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998844
No 144
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.98 E-value=41 Score=22.18 Aligned_cols=18 Identities=44% Similarity=0.685 Sum_probs=15.2
Q ss_pred CHHHHHHHhCCCHHHHHh
Q 037542 71 NLSSVASRFGIETQAIID 88 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~ 88 (129)
+|..||+.|+|+-++|..
T Consensus 35 Sl~EIAee~~VSRqAIyD 52 (105)
T COG2739 35 SLSEIAEEFNVSRQAIYD 52 (105)
T ss_pred cHHHHHHHhCccHHHHHH
Confidence 789999999999877643
No 145
>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=35.89 E-value=59 Score=19.98 Aligned_cols=23 Identities=17% Similarity=0.315 Sum_probs=19.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
..|-|...||+..|++...+..+
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~ 52 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNH 52 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999999887765
No 146
>PRK06437 hypothetical protein; Provisional
Probab=35.85 E-value=38 Score=20.11 Aligned_cols=41 Identities=15% Similarity=0.400 Sum_probs=30.8
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHH-hhcC------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAII-DVNG------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~-~~N~------~~l~~Gq~L~I 102 (129)
..+.+..+-|+..+.+.++++.+.+. ..|. ..|+.|+.|.|
T Consensus 13 ~~~~i~~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~~~~~L~dgD~Vei 60 (67)
T PRK06437 13 KTIEIDHELTVNDIIKDLGLDEEEYVVIVNGSPVLEDHNVKKEDDVLI 60 (67)
T ss_pred eEEEcCCCCcHHHHHHHcCCCCccEEEEECCEECCCceEcCCCCEEEE
Confidence 46788888999999999998765543 3466 46888887754
No 147
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=35.85 E-value=20 Score=21.16 Aligned_cols=19 Identities=21% Similarity=0.291 Sum_probs=13.5
Q ss_pred CCCHHHHHHHhCCCHHHHH
Q 037542 69 SENLSSVASRFGIETQAII 87 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~ 87 (129)
-|.+..||+.+|++++.|.
T Consensus 41 ~~~l~~ia~~~gvsl~WLl 59 (66)
T PF07022_consen 41 AEWLIKIALETGVSLDWLL 59 (66)
T ss_dssp HHHHHHHHHHH---HHHHH
T ss_pred HHHHHHHHHHHCcCHHHHH
Confidence 4678899999999999886
No 148
>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=35.76 E-value=45 Score=21.16 Aligned_cols=21 Identities=19% Similarity=0.284 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|.-|-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998854
No 149
>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=35.73 E-value=20 Score=20.44 Aligned_cols=19 Identities=21% Similarity=0.527 Sum_probs=15.4
Q ss_pred CCHHHHHHHhCCCHHHHHh
Q 037542 70 ENLSSVASRFGIETQAIID 88 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~ 88 (129)
+++..||+.||++.++|..
T Consensus 42 ~~l~~i~~~~~v~~~~l~~ 60 (64)
T PF12844_consen 42 STLKKIAEALGVSLDELFD 60 (64)
T ss_dssp HHHHHHHHHHTS-HHHHCC
T ss_pred HHHHHHHHHhCCCHHHHhc
Confidence 5789999999999998864
No 150
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=35.42 E-value=40 Score=23.67 Aligned_cols=18 Identities=6% Similarity=0.156 Sum_probs=12.4
Q ss_pred CCHHHHHHHhCCCHHHHH
Q 037542 70 ENLSSVASRFGIETQAII 87 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~ 87 (129)
|++..||+.||+++.++.
T Consensus 112 ~~l~kLa~~Lgvsl~el~ 129 (154)
T TIGR00270 112 KVVEKLEKLLKIKLREQV 129 (154)
T ss_pred HHHHHHHHHhCCCHHHHc
Confidence 467777777777776654
No 151
>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=35.37 E-value=46 Score=21.25 Aligned_cols=21 Identities=14% Similarity=0.303 Sum_probs=18.7
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|.-|-.
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~ 22 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999998865
No 152
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=34.88 E-value=36 Score=24.14 Aligned_cols=24 Identities=8% Similarity=0.075 Sum_probs=20.9
Q ss_pred eEEEEecCCCCHHHHHHHhCCCHH
Q 037542 61 LVSYVLQPSENLSSVASRFGIETQ 84 (129)
Q Consensus 61 ~~~y~V~~GDTl~~IA~~~~vs~~ 84 (129)
...+.++.||||-.+|.++|+..+
T Consensus 55 ~~~i~g~vGdtlLd~ah~n~idle 78 (159)
T KOG3309|consen 55 EIKIKGKVGDTLLDAAHENNLDLE 78 (159)
T ss_pred EEEeeeecchHHHHHHHHcCCCcc
Confidence 468899999999999999998654
No 153
>PRK01777 hypothetical protein; Validated
Probab=34.78 E-value=54 Score=21.08 Aligned_cols=41 Identities=15% Similarity=0.199 Sum_probs=32.9
Q ss_pred EEEEecCCCCHHHHHHHhCCCHH--HH------HhhcC------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQ--AI------IDVNG------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~--~l------~~~N~------~~l~~Gq~L~I 102 (129)
....|..|-|+..+.+..|+..+ +| ...|+ ..|+.|+.|-|
T Consensus 19 ~~l~vp~GtTv~dal~~sgi~~~~pei~~~~~~vgI~Gk~v~~d~~L~dGDRVeI 73 (95)
T PRK01777 19 QRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEI 73 (95)
T ss_pred EEEEcCCCCcHHHHHHHcCCCccCcccccccceEEEeCeECCCCCcCCCCCEEEE
Confidence 56788999999999999999776 55 33455 57999998866
No 154
>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=34.68 E-value=48 Score=21.27 Aligned_cols=21 Identities=19% Similarity=0.373 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 3 ~i~eva~~~gvs~~tlR~ye~ 23 (102)
T cd04789 3 TISELAEKAGISRSTLLYYEK 23 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678899999999999998754
No 155
>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=34.64 E-value=70 Score=22.09 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=25.0
Q ss_pred cCC--CCHHHHHHHhCCCHHHHHhhcCCCCCCCCEEE
Q 037542 67 QPS--ENLSSVASRFGIETQAIIDVNGNNIRPFDTLF 101 (129)
Q Consensus 67 ~~G--DTl~~IA~~~~vs~~~l~~~N~~~l~~Gq~L~ 101 (129)
.++ =|+..||+..||++..|.+| |+.|-..+
T Consensus 42 ~p~~~ati~eV~e~tgVs~~~I~~~----IreGRL~~ 74 (137)
T TIGR03826 42 HENRQATVSEIVEETGVSEKLILKF----IREGRLQL 74 (137)
T ss_pred CCCCCCCHHHHHHHHCcCHHHHHHH----HHcCCeec
Confidence 355 79999999999999999999 55554443
No 156
>PHA03253 UL35; Provisional
Probab=34.59 E-value=1e+02 Score=26.33 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=15.9
Q ss_pred HHHHHHHhCCCHHH-HHhhcC
Q 037542 72 LSSVASRFGIETQA-IIDVNG 91 (129)
Q Consensus 72 l~~IA~~~~vs~~~-l~~~N~ 91 (129)
...||++||++..+ |.++|.
T Consensus 441 ~~~~~~~~~~~~~~~~~~~~~ 461 (609)
T PHA03253 441 YGAVAQKYGLSLKQVIERLNV 461 (609)
T ss_pred HHHHHHhcCCCHHHHHHHhcc
Confidence 56899999999866 566776
No 157
>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=34.44 E-value=46 Score=21.85 Aligned_cols=21 Identities=14% Similarity=0.235 Sum_probs=18.6
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|-.
T Consensus 2 ~I~eva~~~gvs~~tLRyYe~ 22 (123)
T cd04770 2 KIGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999988865
No 158
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=33.92 E-value=49 Score=21.56 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 2 ~i~eva~~~gvs~~tlR~Ye~ 22 (112)
T cd01282 2 RIGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999999998855
No 159
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=33.91 E-value=40 Score=28.46 Aligned_cols=25 Identities=16% Similarity=0.426 Sum_probs=20.9
Q ss_pred cCCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
.++|||..+|++.|+..+ .|.++|.
T Consensus 422 ~kadTleELA~k~gid~~~L~~TV~~yN~ 450 (564)
T PRK12845 422 HRADSLADLARKIGVPVDTFVATMRRFNE 450 (564)
T ss_pred EecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 478999999999999864 4677886
No 160
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. 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=33.65 E-value=48 Score=22.13 Aligned_cols=21 Identities=19% Similarity=0.227 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++||+...|.-|=.
T Consensus 2 ~I~e~a~~~gvs~~tlRyYe~ 22 (127)
T cd01108 2 NIGEAAKLTGLSAKMIRYYEE 22 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999987754
No 161
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=33.35 E-value=50 Score=21.61 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=18.7
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|+|...|.-|-.
T Consensus 2 ~ige~a~~~gvs~~tLryYe~ 22 (116)
T cd04769 2 YIGELAQQTGVTIKAIRLYEE 22 (116)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999998866
No 162
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=33.15 E-value=43 Score=27.71 Aligned_cols=25 Identities=20% Similarity=0.575 Sum_probs=20.5
Q ss_pred cCCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
.++|||..+|++.|+..+ .|.++|.
T Consensus 373 ~kaDTleELA~k~gid~~~L~~Tv~~yN~ 401 (513)
T PRK12837 373 RTADTLEELAAKIGVPADALTATVARFNG 401 (513)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 368999999999999764 4667786
No 163
>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=32.95 E-value=41 Score=18.56 Aligned_cols=17 Identities=18% Similarity=0.389 Sum_probs=13.3
Q ss_pred CHHHHHHHhCCCHHHHH
Q 037542 71 NLSSVASRFGIETQAII 87 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~ 87 (129)
|...||+.+++|...|.
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 78899999999886654
No 164
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper 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-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=32.31 E-value=52 Score=21.93 Aligned_cols=21 Identities=24% Similarity=0.294 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 2 ~I~e~a~~~gvs~~tlRyYe~ 22 (127)
T TIGR02044 2 NIGQVAKLTGLSSKMIRYYEE 22 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999987754
No 165
>TIGR00247 conserved hypothetical protein, YceG family. This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC.
Probab=32.12 E-value=74 Score=25.13 Aligned_cols=77 Identities=9% Similarity=0.092 Sum_probs=43.3
Q ss_pred CCCcHHHHHHhhCC-CC-CCH---HHHHHhCCCCCCCCCCCCCEEEECCCCCCCCccccccccc-ceEEEEecCCCCHHH
Q 037542 1 SGDTFYSVSTNKYQ-NL-TTY---QSVEVVNPAFVPTKLEVGDVFIFPVFCKCPDQTQLRNRVN-YLVSYVLQPSENLSS 74 (129)
Q Consensus 1 ~GDTl~~IA~~~~~-~l-ts~---~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~-~~~~y~V~~GDTl~~ 74 (129)
+|+|...||+.... |+ .+. ..++++++. ...|++|.-..-+......--.....+.. .....+|..|.|++.
T Consensus 46 ~G~s~~~Ia~~L~~~GvI~s~~~F~~~ak~~~~--~~~lkaG~Y~l~~~ms~~~il~~L~~g~~~~~~~vti~eG~t~~~ 123 (342)
T TIGR00247 46 KGTGVSKIAKELKKQKLIKSEKLLQYLLKIKGS--LKQFKAGTYLLNGDMTVFEILKLLLSGKENVQFDVTIPEGYTLRD 123 (342)
T ss_pred CCCCHHHHHHHHHHCCCCCCHHHHHHHHHhcCC--cCcccceEEEECCCCCHHHHHHHHHcCCcceeEEEEEcCCCcHHH
Confidence 58899999987632 11 232 233344544 35699998776553210000000000111 235788999999999
Q ss_pred HHHHh
Q 037542 75 VASRF 79 (129)
Q Consensus 75 IA~~~ 79 (129)
||++.
T Consensus 124 ia~~l 128 (342)
T TIGR00247 124 IAKKL 128 (342)
T ss_pred HHHHH
Confidence 99876
No 166
>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=32.12 E-value=56 Score=20.68 Aligned_cols=23 Identities=13% Similarity=0.135 Sum_probs=20.2
Q ss_pred EEEEecCCCCHHHHHHHhCCCHH
Q 037542 62 VSYVLQPSENLSSVASRFGIETQ 84 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~ 84 (129)
..+.+.+|+||-..+.+.|+.+.
T Consensus 15 ~~~~~~~g~tLLda~~~~Gi~i~ 37 (97)
T TIGR02008 15 ETIECPDDQYILDAAEEAGIDLP 37 (97)
T ss_pred EEEEECCCCcHHHHHHHcCCCCC
Confidence 57899999999999999998653
No 167
>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=32.12 E-value=55 Score=20.85 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+.+|++...|..|=.
T Consensus 2 ti~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998833
No 168
>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=31.86 E-value=75 Score=16.19 Aligned_cols=25 Identities=12% Similarity=0.320 Sum_probs=20.0
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
+.|-+...+|+..|++...+.++-.
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 3477889999999999888877744
No 169
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=31.74 E-value=14 Score=28.51 Aligned_cols=77 Identities=14% Similarity=0.067 Sum_probs=18.1
Q ss_pred CCCcHHHHHHhhCCCC--CCH---HHHHHhCCCCCCCCCCCCCEEEECCCCCCCCcccccccccceEEEEecCCCCHHHH
Q 037542 1 SGDTFYSVSTNKYQNL--TTY---QSVEVVNPAFVPTKLEVGDVFIFPVFCKCPDQTQLRNRVNYLVSYVLQPSENLSSV 75 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~l--ts~---~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~I 75 (129)
+|+|+..||+...... .+. ..+.+.++. ...|++|.-..-+......--.....+.......+|.+|.|++.|
T Consensus 7 ~G~s~~~Ia~~L~~~gvI~s~~~F~~~~~~~~~--~~~lkaG~Y~l~~~mS~~eil~~L~~g~~~~~~vTIpEG~t~~~i 84 (297)
T PF02618_consen 7 PGASASQIADILEEAGVIKSARAFKLYAKLNGY--DSKLKAGTYELNPGMSYKEILSILTSGKVAQVRVTIPEGFTLEQI 84 (297)
T ss_dssp -----------------------------------------EEEEE-TT--HHHHHHHHHH-----EEEEE-TT--HHHH
T ss_pred CCCCHHHHHHHHHHCCCCCCHHHHHHHHHhCCC--CCceeeeEEEeCCCCCHHHHHHHHHhcccceeEEEecCCCcHHHH
Confidence 4788888887754311 111 122233332 256888876654431100000000011122357899999999999
Q ss_pred HHHh
Q 037542 76 ASRF 79 (129)
Q Consensus 76 A~~~ 79 (129)
|++.
T Consensus 85 ~~~l 88 (297)
T PF02618_consen 85 AQRL 88 (297)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 9886
No 170
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=31.71 E-value=54 Score=21.83 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|+++..|.-|=.
T Consensus 2 ~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04785 2 SIGELARRTGVNVETIRYYES 22 (126)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999998754
No 171
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=31.70 E-value=55 Score=19.13 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=31.8
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~------~~l~~Gq~L~I 102 (129)
..+.++.+-||+.+.+.+.-..+ |.-+|+ ..|+.|+.|++
T Consensus 8 k~~~~~~~~tl~~lr~~~k~~~D-I~I~NGF~~~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 8 KEIETEENTTLFELRKESKPDAD-IVILNGFPTKEDIELKEGDEVFL 53 (57)
T ss_pred EEEEcCCCcCHHHHHHhhCCCCC-EEEEcCcccCCccccCCCCEEEE
Confidence 46788888899999999877544 778888 47899988764
No 172
>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=31.41 E-value=57 Score=20.88 Aligned_cols=19 Identities=16% Similarity=0.268 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
++..+|+.+|++...|..|
T Consensus 2 ti~EvA~~~gVs~~tLR~y 20 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYW 20 (99)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5678999999999999988
No 173
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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 spe
Probab=31.26 E-value=57 Score=21.98 Aligned_cols=21 Identities=14% Similarity=0.132 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|..|=.
T Consensus 3 sI~eVA~~~GVs~~TLR~wE~ 23 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWER 23 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999998844
No 174
>PRK00118 putative DNA-binding protein; Validated
Probab=31.22 E-value=66 Score=21.09 Aligned_cols=23 Identities=26% Similarity=0.401 Sum_probs=19.2
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
..|-|...||+.+|++...+...
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r~ 53 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDN 53 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 45889999999999999887654
No 175
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=31.20 E-value=1.2e+02 Score=22.28 Aligned_cols=29 Identities=21% Similarity=0.292 Sum_probs=24.0
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
.|-=.-|.-|..||+..|++.+++.+.=-
T Consensus 84 ~Y~~~~g~DL~~vA~~~gLs~eevi~~Hs 112 (202)
T TIGR00370 84 CYGGEFGPDLEEVAKINQLSPEEVIDIHS 112 (202)
T ss_pred EeCCCCCCCHHHHHHHhCcCHHHHHHHHh
Confidence 45445678999999999999999998854
No 176
>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=30.94 E-value=52 Score=18.48 Aligned_cols=23 Identities=17% Similarity=0.329 Sum_probs=17.9
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHh
Q 037542 66 LQPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
+-.|-+...||+..+++...+..
T Consensus 15 l~~G~~~~eIA~~l~is~~tV~~ 37 (58)
T PF00196_consen 15 LAQGMSNKEIAEELGISEKTVKS 37 (58)
T ss_dssp HHTTS-HHHHHHHHTSHHHHHHH
T ss_pred HHhcCCcchhHHhcCcchhhHHH
Confidence 45689999999999998877653
No 177
>PRK10270 putative aminodeoxychorismate lyase; Provisional
Probab=30.84 E-value=1.1e+02 Score=24.22 Aligned_cols=77 Identities=13% Similarity=0.131 Sum_probs=42.8
Q ss_pred CCCcHHHHHHhhCCC-C-CCH---HHHHHhCCCCCCCCCCCCCEEEECCCCCCCCcccccccccceEEEEecCCCCHHHH
Q 037542 1 SGDTFYSVSTNKYQN-L-TTY---QSVEVVNPAFVPTKLEVGDVFIFPVFCKCPDQTQLRNRVNYLVSYVLQPSENLSSV 75 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~-l-ts~---~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~I 75 (129)
+|+|...||+..... + .+. ....++++. ...|++|.-..=+......--.....+.......+|..|-|+..|
T Consensus 46 ~G~t~~~Ia~~L~~~gvI~s~~~F~~~~~~~~~--~~~ikaG~Y~l~~~ms~~~il~~L~~g~~~~~~vtIpEG~t~~~i 123 (340)
T PRK10270 46 PGTGRLALGEQLYADKIINRPRVFQWLLRIEPD--LSHFKAGTYRFTPQMTVREMLKLLESGKEAQFPLRLVEGMRLSDY 123 (340)
T ss_pred CCCCHHHHHHHHHHCCCCCCHHHHHHHHHhCCC--CCCccceEEEeCCCCCHHHHHHHHHcCCceeEEEEEcCCCcHHHH
Confidence 588999999875432 2 222 233444544 356999987765532100000000011112246788999999999
Q ss_pred HHHh
Q 037542 76 ASRF 79 (129)
Q Consensus 76 A~~~ 79 (129)
+++.
T Consensus 124 ~~~l 127 (340)
T PRK10270 124 LKQL 127 (340)
T ss_pred HHHH
Confidence 9765
No 178
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=30.84 E-value=48 Score=25.51 Aligned_cols=23 Identities=17% Similarity=0.365 Sum_probs=19.9
Q ss_pred CCCHHHHHHHhCCCHHHHHhhcC
Q 037542 69 SENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
|--+-.||++||+++..|..|=.
T Consensus 19 gmk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHH
Confidence 45677999999999999999866
No 179
>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=30.48 E-value=67 Score=17.24 Aligned_cols=18 Identities=11% Similarity=0.379 Sum_probs=13.3
Q ss_pred CCHHHHHHHhCCCHHHHH
Q 037542 70 ENLSSVASRFGIETQAII 87 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~ 87 (129)
-++..||+..|++...+.
T Consensus 18 ~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVR 35 (42)
T ss_dssp S-HHHHHHHHTS-HHHHH
T ss_pred ccHHHHHHHHCcCHHHHH
Confidence 378899999999987764
No 180
>PRK12839 hypothetical protein; Provisional
Probab=30.37 E-value=49 Score=27.95 Aligned_cols=24 Identities=17% Similarity=0.443 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 68 PSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 68 ~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
++|||..+|++.|++.+ .|.++|.
T Consensus 426 kadTleELA~k~gid~~~L~~TV~~yN~ 453 (572)
T PRK12839 426 RGRTIEELAEKCGIDPAGLEATVAEFNE 453 (572)
T ss_pred ECCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 58999999999999864 4677887
No 181
>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=30.23 E-value=63 Score=20.53 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|.-|=.
T Consensus 2 ~I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 2 RMSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998844
No 182
>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=30.13 E-value=56 Score=20.98 Aligned_cols=21 Identities=10% Similarity=0.142 Sum_probs=17.7
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.=+=.
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe~ 22 (107)
T cd04777 2 KIGKFAKKNNITIDTVRHYID 22 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999987754
No 183
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. 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-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=30.03 E-value=59 Score=21.58 Aligned_cols=21 Identities=14% Similarity=0.253 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+++|++...|.-|-.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~ 21 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYER 21 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999988855
No 184
>PRK07121 hypothetical protein; Validated
Probab=29.85 E-value=70 Score=26.21 Aligned_cols=26 Identities=19% Similarity=0.285 Sum_probs=21.6
Q ss_pred ecCCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 66 LQPSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
+.+.|||..+|++.|+..+ .+.++|.
T Consensus 358 ~~kadtleeLA~~~gid~~~l~~tv~~yN~ 387 (492)
T PRK07121 358 AWKAETVEELARKLGIPPGGLQATVDAYNR 387 (492)
T ss_pred ccccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3468999999999999876 6778886
No 185
>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=29.82 E-value=62 Score=20.94 Aligned_cols=21 Identities=10% Similarity=0.252 Sum_probs=18.6
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|..|-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 2 TIGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999999855
No 186
>TIGR02007 fdx_isc ferredoxin, 2Fe-2S type, ISC system. This family consists of proteobacterial ferredoxins associated with and essential to the ISC system of 2Fe-2S cluster assembly. This family is closely related to (but excludes) eukaryotic (mitochondrial) adrenodoxins, which are ferredoxins involved in electron transfer to P450 cytochromes.
Probab=29.64 E-value=61 Score=21.11 Aligned_cols=23 Identities=30% Similarity=0.368 Sum_probs=20.0
Q ss_pred EEEEecCCCCHHHHHHHhCCCHH
Q 037542 62 VSYVLQPSENLSSVASRFGIETQ 84 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~ 84 (129)
.++.+..|+||..++++.|+.+.
T Consensus 16 ~~~~~~~g~tLL~a~~~~gi~i~ 38 (110)
T TIGR02007 16 AVVEAKPGETILDVALDNGIEIE 38 (110)
T ss_pred eEEEECCCChHHHHHHHcCCCcc
Confidence 57889999999999999998753
No 187
>COG3784 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.90 E-value=84 Score=20.68 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=25.6
Q ss_pred CHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEE
Q 037542 71 NLSSVASRFGIETQAIIDVNG----NNIRPFDTLF 101 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~ 101 (129)
....||++-|++++++.++-. ....+||-+.
T Consensus 66 ~Yq~lA~~n~~s~~~vak~agqklv~Ra~~GqYvq 100 (109)
T COG3784 66 SYQQLAKKNGASTEEVAKLAGQKLVARAAPGQYVQ 100 (109)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCeee
Confidence 467788888999999999887 6788888765
No 188
>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=28.72 E-value=79 Score=17.54 Aligned_cols=19 Identities=11% Similarity=0.330 Sum_probs=15.1
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
+...||+.|+++...+.++
T Consensus 27 ~~~~la~~~~is~~~v~~~ 45 (66)
T cd07377 27 SERELAEELGVSRTTVREA 45 (66)
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 5789999999988766553
No 189
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.70 E-value=69 Score=18.03 Aligned_cols=22 Identities=14% Similarity=0.244 Sum_probs=11.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHhh
Q 037542 68 PSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 68 ~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
.|=|...+|++.|++...|.++
T Consensus 9 ~~it~~~La~~~gis~~tl~~~ 30 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRI 30 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 4556667777777766666655
No 190
>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=28.69 E-value=68 Score=20.83 Aligned_cols=21 Identities=19% Similarity=0.205 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|+++..|.-|=.
T Consensus 2 ~Ige~A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 2 SISQLALDAGVSVHIVRDYLL 22 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998854
No 191
>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=28.47 E-value=61 Score=18.56 Aligned_cols=22 Identities=27% Similarity=0.434 Sum_probs=16.4
Q ss_pred ecCCCCHHHHHHHhCCCHHHHH
Q 037542 66 LQPSENLSSVASRFGIETQAII 87 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~ 87 (129)
+-+-.||...|+..|++++.|.
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 4456799999999999998874
No 192
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=28.46 E-value=66 Score=21.32 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-+=.
T Consensus 2 ~IgevA~~~gvs~~tLRyYe~ 22 (127)
T cd04784 2 KIGELAKKTGCSVETIRYYEK 22 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999988744
No 193
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=28.40 E-value=65 Score=21.96 Aligned_cols=21 Identities=24% Similarity=0.292 Sum_probs=18.8
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|-.
T Consensus 3 ~I~EvA~~~Gvs~~tLRyYE~ 23 (139)
T cd01110 3 SVGEVAKRSGVAVSALHFYEQ 23 (139)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999998865
No 194
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=28.31 E-value=42 Score=19.42 Aligned_cols=41 Identities=22% Similarity=0.367 Sum_probs=29.9
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHH-HHhhcC----------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQA-IIDVNG----------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~-l~~~N~----------~~l~~Gq~L~I 102 (129)
..|.+..|.|+..+-..+++..+. ..+.|. ..|+.|+.|-|
T Consensus 8 ~~~~~~~~~tl~~lL~~l~~~~~~vav~vNg~iv~r~~~~~~~l~~gD~vei 59 (66)
T PRK05659 8 EPRELPDGESVAALLAREGLAGRRVAVEVNGEIVPRSQHASTALREGDVVEI 59 (66)
T ss_pred eEEEcCCCCCHHHHHHhcCCCCCeEEEEECCeEeCHHHcCcccCCCCCEEEE
Confidence 367888899999999988875433 233565 46888888765
No 195
>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=28.30 E-value=69 Score=21.44 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=18.7
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+++|+++..|.-|=.
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 688999999999999998854
No 196
>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=28.25 E-value=81 Score=17.11 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=16.1
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
+.|=|...+|++.|++...|.++
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 45677788888888888877776
No 197
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=28.03 E-value=65 Score=23.12 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=18.6
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|..|-.
T Consensus 2 ti~evA~~lGVS~~TLRrw~k 22 (175)
T PRK13182 2 KTPFVAKKLGVSPKTVQRWVK 22 (175)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999999954
No 198
>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=28.01 E-value=84 Score=15.98 Aligned_cols=19 Identities=26% Similarity=0.461 Sum_probs=15.2
Q ss_pred CCHHHHHHHhCCCHHHHHh
Q 037542 70 ENLSSVASRFGIETQAIID 88 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~ 88 (129)
+-|..+|++.|.+.+++.+
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 3577899999999988764
No 199
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=27.96 E-value=91 Score=15.67 Aligned_cols=25 Identities=8% Similarity=0.304 Sum_probs=19.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
+.|-+...+|+..|++...|..+-.
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3466888999999999888877744
No 200
>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=27.90 E-value=73 Score=19.93 Aligned_cols=21 Identities=14% Similarity=0.290 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|..|-.
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999999944
No 201
>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=27.88 E-value=69 Score=21.51 Aligned_cols=21 Identities=10% Similarity=0.202 Sum_probs=18.7
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|-.
T Consensus 3 ~I~e~a~~~gvs~~tlR~Ye~ 23 (131)
T TIGR02043 3 QIGELAKLCGVTSDTLRFYEK 23 (131)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999998866
No 202
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=27.65 E-value=80 Score=18.65 Aligned_cols=28 Identities=25% Similarity=0.466 Sum_probs=21.7
Q ss_pred HHHHHHhCCCHHHHHhhcCCCCCCCCEEEEcC
Q 037542 73 SSVASRFGIETQAIIDVNGNNIRPFDTLFVPV 104 (129)
Q Consensus 73 ~~IA~~~~vs~~~l~~~N~~~l~~Gq~L~IP~ 104 (129)
...|+.+|++...|-++ |+.|..|+|-.
T Consensus 16 ~kaA~~lGV~Q~AIsKA----lr~gR~I~v~~ 43 (59)
T PF09048_consen 16 AKAARALGVTQSAISKA----LRAGRNIFVTI 43 (59)
T ss_dssp HHHHHHHTS-HHHHHHH----HHCT-EEEEEE
T ss_pred HHHHHHcCCcHHHHHHH----HHcCCcEEEEE
Confidence 56789999999999998 88888888753
No 203
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal 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-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=27.29 E-value=71 Score=21.31 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 2 ~I~e~a~~~gvs~~tlR~Ye~ 22 (127)
T TIGR02047 2 KIGELAQKTGVSVETIRFYEK 22 (127)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999998854
No 204
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. 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=27.20 E-value=71 Score=21.17 Aligned_cols=21 Identities=14% Similarity=0.249 Sum_probs=17.9
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|+++..|.-+=.
T Consensus 2 ~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04783 2 TIGELAKAAGVNVETIRYYQR 22 (126)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999987744
No 205
>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=26.90 E-value=69 Score=20.96 Aligned_cols=22 Identities=36% Similarity=0.563 Sum_probs=14.2
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
..+=+|..||+.+|+|-..+..
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 3455899999999998876543
No 206
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=26.87 E-value=78 Score=22.61 Aligned_cols=24 Identities=13% Similarity=0.292 Sum_probs=20.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhc
Q 037542 67 QPSENLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N 90 (129)
..|-|+..||+.+|++...+.++-
T Consensus 170 ~~g~s~~~iak~lgis~~Tv~r~~ 193 (200)
T PRK13413 170 DKGTSKSEIARKLGVSRTTLARFL 193 (200)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Confidence 568999999999999999887763
No 207
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=26.81 E-value=19 Score=21.86 Aligned_cols=31 Identities=29% Similarity=0.629 Sum_probs=21.9
Q ss_pred HHHHH-HHhCCCHHHHHhhcC------CCCCCCCEEEE
Q 037542 72 LSSVA-SRFGIETQAIIDVNG------NNIRPFDTLFV 102 (129)
Q Consensus 72 l~~IA-~~~~vs~~~l~~~N~------~~l~~Gq~L~I 102 (129)
|-.|| ++||.....+...++ +.|+-|+.|++
T Consensus 31 Ll~ia~~kfg~~~~~v~~~dgaeIdDI~~IRDgD~L~~ 68 (69)
T PF11834_consen 31 LLKIASEKFGFSATKVLNEDGAEIDDIDVIRDGDHLYL 68 (69)
T ss_pred HHHHHHHHhCCCceEEEcCCCCEEeEEEEEEcCCEEEE
Confidence 34444 689988666666666 67888988876
No 208
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=26.60 E-value=80 Score=17.54 Aligned_cols=23 Identities=13% Similarity=0.319 Sum_probs=18.8
Q ss_pred EecCCCCHHHHHHHhCCCHHHHH
Q 037542 65 VLQPSENLSSVASRFGIETQAII 87 (129)
Q Consensus 65 ~V~~GDTl~~IA~~~~vs~~~l~ 87 (129)
.+..|.+...||...+++...+.
T Consensus 15 l~~~G~s~~eia~~l~is~~tV~ 37 (65)
T COG2771 15 LVAQGKSNKEIARILGISEETVK 37 (65)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHH
Confidence 45679999999999999886643
No 209
>cd00207 fer2 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin.
Probab=26.60 E-value=91 Score=18.43 Aligned_cols=22 Identities=27% Similarity=0.330 Sum_probs=19.2
Q ss_pred EEEEecCCCCHHHHHHHhCCCH
Q 037542 62 VSYVLQPSENLSSVASRFGIET 83 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~ 83 (129)
.++.+.+|+||...+++.|+.+
T Consensus 10 ~~~~~~~g~~ll~al~~~g~~~ 31 (84)
T cd00207 10 VEVEVPEGETLLDAAREAGIDI 31 (84)
T ss_pred EEEEECCCCcHHHHHHHcCCCc
Confidence 5789999999999999988764
No 210
>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=26.58 E-value=54 Score=18.01 Aligned_cols=21 Identities=14% Similarity=0.229 Sum_probs=18.1
Q ss_pred CCCHHHHHHHhCCCHHHHHhh
Q 037542 69 SENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~~ 89 (129)
.+.+..||...|++...|..|
T Consensus 27 ~~~~~~la~~~~l~~~qV~~W 47 (59)
T cd00086 27 REEREELAKELGLTERQVKIW 47 (59)
T ss_pred HHHHHHHHHHHCcCHHHHHHH
Confidence 356889999999999999886
No 211
>PRK03837 transcriptional regulator NanR; Provisional
Probab=26.38 E-value=85 Score=22.82 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=19.8
Q ss_pred EEEecCCCCH---HHHHHHhCCCHHHHHhh
Q 037542 63 SYVLQPSENL---SSVASRFGIETQAIIDV 89 (129)
Q Consensus 63 ~y~V~~GDTl---~~IA~~~~vs~~~l~~~ 89 (129)
.-..++||-| ..||++||||-.-+.++
T Consensus 28 ~g~l~pG~~Lp~E~~Lae~~gVSRt~VREA 57 (241)
T PRK03837 28 SGEFGPGDQLPSERELMAFFGVGRPAVREA 57 (241)
T ss_pred hCCCCCCCCCCCHHHHHHHhCCCHHHHHHH
Confidence 4456889955 68999999987555444
No 212
>PRK07198 hypothetical protein; Validated
Probab=26.38 E-value=41 Score=27.55 Aligned_cols=19 Identities=32% Similarity=0.539 Sum_probs=16.1
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
-|-.||+|||++..+|++.
T Consensus 176 ylpgva~rfg~~e~~lrr~ 194 (418)
T PRK07198 176 YLPGVAERFGVSETDLRRT 194 (418)
T ss_pred cccchHHHcCCCHHHHHHH
Confidence 4678999999999888765
No 213
>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=26.19 E-value=98 Score=19.94 Aligned_cols=33 Identities=12% Similarity=0.147 Sum_probs=26.8
Q ss_pred CHHHHHHHhCCCHHHHHhhcC----CCCCCCCEEEEc
Q 037542 71 NLSSVASRFGIETQAIIDVNG----NNIRPFDTLFVP 103 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~----~~l~~Gq~L~IP 103 (129)
-+..||++-|++++++...-. ....+|+-+..+
T Consensus 52 ~Y~~iA~~ng~t~~~V~~~~a~k~~~~a~~G~~vq~~ 88 (95)
T PF07027_consen 52 LYQEIAKKNGITVEQVAATAAQKWIERAPPGQYVQDA 88 (95)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHhCCCCcEEECC
Confidence 467899999999999888776 677888888765
No 214
>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=26.07 E-value=1e+02 Score=16.50 Aligned_cols=24 Identities=21% Similarity=0.185 Sum_probs=20.0
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhc
Q 037542 67 QPSENLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N 90 (129)
+.|=|...+|++.|++...|.+|=
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 457788899999999998888873
No 215
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=26.05 E-value=91 Score=18.26 Aligned_cols=21 Identities=24% Similarity=0.336 Sum_probs=17.1
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
+...+|+.+||+...+..|..
T Consensus 11 ~~~~lAkalGVs~~aVs~W~~ 31 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQWGE 31 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHhcC
Confidence 567899999999999999943
No 216
>PRK13749 transcriptional regulator MerD; Provisional
Probab=25.92 E-value=73 Score=21.41 Aligned_cols=21 Identities=19% Similarity=0.176 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+++|+++..|.-+=.
T Consensus 5 tIgelA~~~gvS~~tiR~YE~ 25 (121)
T PRK13749 5 TVSRLALDAGVSVHIVRDYLL 25 (121)
T ss_pred cHHHHHHHHCCCHHHHHHHHH
Confidence 678999999999999987744
No 217
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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, an
Probab=25.79 E-value=80 Score=20.75 Aligned_cols=21 Identities=14% Similarity=0.279 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 2 ~IgevA~~~gvs~~tlRyYe~ 22 (120)
T cd04781 2 DIAEVARQSGLPASTLRYYEE 22 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999998754
No 218
>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=25.73 E-value=66 Score=21.07 Aligned_cols=20 Identities=15% Similarity=0.346 Sum_probs=14.9
Q ss_pred CCCHHHHHHHhCCCHHHHHh
Q 037542 69 SENLSSVASRFGIETQAIID 88 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~ 88 (129)
.+-.-.||++|+++...+.+
T Consensus 40 K~LYp~IA~k~~TT~s~VER 59 (106)
T PF08769_consen 40 KELYPDIAKKYGTTPSRVER 59 (106)
T ss_dssp TTHHHHHHHHTTS-HHHHHH
T ss_pred hhHHHHHHHHHCCCHHHHHH
Confidence 35577999999999977654
No 219
>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=25.63 E-value=1.2e+02 Score=16.15 Aligned_cols=22 Identities=18% Similarity=0.382 Sum_probs=15.3
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
.++-|...||++.|++...+.+
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 3456889999999998876543
No 220
>PRK06134 putative FAD-binding dehydrogenase; Reviewed
Probab=25.60 E-value=68 Score=27.09 Aligned_cols=25 Identities=20% Similarity=0.368 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
.++|||..+|++.|++.+ .+.++|.
T Consensus 427 ~kadTleELA~~~gid~~~L~~Tv~~yN~ 455 (581)
T PRK06134 427 KRGASLEELARACGIDPDGLEATVARYNR 455 (581)
T ss_pred EecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 368999999999999864 4567786
No 221
>PF00111 Fer2: 2Fe-2S iron-sulfur cluster binding domain; InterPro: IPR001041 The ferredoxin protein family are electron carrier proteins with an iron-sulphur cofactor that act in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s) and according to sequence similarities. This entry represents members of the 2Fe-2S ferredoxin family that have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin and terpredoxin, and adrenodoxin [, , , ]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron-sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3 1JQ4_A 1DOX_A 1DOY_A 2KAJ_A ....
Probab=25.57 E-value=86 Score=18.44 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=18.2
Q ss_pred EEEEecCCCC-HHHHHHHh-CCCH
Q 037542 62 VSYVLQPSEN-LSSVASRF-GIET 83 (129)
Q Consensus 62 ~~y~V~~GDT-l~~IA~~~-~vs~ 83 (129)
.++.+.+|++ |...+++. ++.+
T Consensus 8 ~~~~~~~~~~~ll~~~~~~~gi~i 31 (78)
T PF00111_consen 8 VTVEVPPGETLLLDALERAGGIGI 31 (78)
T ss_dssp EEEEEETTSBBHHHHHHHTTTTTS
T ss_pred EEEEeCCCccHHHHHHHHcCCCCc
Confidence 5788899999 99999987 6643
No 222
>PRK07843 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=25.57 E-value=70 Score=26.86 Aligned_cols=25 Identities=20% Similarity=0.523 Sum_probs=20.8
Q ss_pred cCCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
.++|||..+|++.|+..+ .+.++|.
T Consensus 414 ~kadTleELA~~~gid~~~L~aTV~~yN~ 442 (557)
T PRK07843 414 VKADTLAELAAKIGVPADALTATVQRFNG 442 (557)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 468999999999999764 5678887
No 223
>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=25.36 E-value=62 Score=24.55 Aligned_cols=44 Identities=9% Similarity=0.101 Sum_probs=25.7
Q ss_pred ceEEEEecCCCCHHHHHHHhCC----CHHHHHhhcC-CCCCCCCEEEEc
Q 037542 60 YLVSYVLQPSENLSSVASRFGI----ETQAIIDVNG-NNIRPFDTLFVP 103 (129)
Q Consensus 60 ~~~~y~V~~GDTl~~IA~~~~v----s~~~l~~~N~-~~l~~Gq~L~IP 103 (129)
...+-+|+.|||+|..-++.-- ...+|..+.. +.+.+-.-|+||
T Consensus 111 hrr~v~vKKGdtI~~FL~~~r~~l~~~f~el~~vsvd~LM~VkedlIiP 159 (239)
T PF04921_consen 111 HRRTVRVKKGDTIWQFLEKCRKQLAKEFRELRRVSVDDLMYVKEDLIIP 159 (239)
T ss_pred CcceEEEcCCCCHHHHHHHHHHHHHHHhHHHHhcCHhheeeeccceecc
Confidence 3347789999999987654321 1334444443 444445556666
No 224
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=25.34 E-value=98 Score=19.24 Aligned_cols=56 Identities=11% Similarity=0.185 Sum_probs=33.7
Q ss_pred cHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEECCCCCCCCcccccccccceEEEEec--CCCCHHHHHHHhC-
Q 037542 4 TFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFPVFCKCPDQTQLRNRVNYLVSYVLQ--PSENLSSVASRFG- 80 (129)
Q Consensus 4 Tl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~~y~V~--~GDTl~~IA~~~~- 80 (129)
-+..+|+.|++ +.++|..-.... + +..+ .+ ...|..+ -|.|+..|++.||
T Consensus 4 Ii~~Va~~~~v---~~~~i~~~~R~~--~-------~~~a--------R~-------ia~yl~~~~~~~s~~~Ig~~fg~ 56 (90)
T cd06571 4 IIEAVAEYFGI---SVEDLRSKSRKK--E-------IALA--------RQ-------IAMYLARELTGLSLPEIGRAFGG 56 (90)
T ss_pred HHHHHHHHhCC---CHHHHhcCCCCc--C-------cchH--------HH-------HHHHHHHHHhCCCHHHHHHHhCC
Confidence 35678999988 898886544331 1 1111 00 1123332 2899999999999
Q ss_pred CCHHHH
Q 037542 81 IETQAI 86 (129)
Q Consensus 81 vs~~~l 86 (129)
.+...+
T Consensus 57 r~hStV 62 (90)
T cd06571 57 RDHSTV 62 (90)
T ss_pred CCHhHH
Confidence 665544
No 225
>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=25.30 E-value=1e+02 Score=16.44 Aligned_cols=20 Identities=15% Similarity=0.351 Sum_probs=16.0
Q ss_pred CCCHHHHHHHhCCCHHHHHh
Q 037542 69 SENLSSVASRFGIETQAIID 88 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~ 88 (129)
+=|+..||++-|++...|..
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~ 35 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYR 35 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHH
T ss_pred hCCHHHHHHHHccchhhHHH
Confidence 34788999999998887764
No 226
>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=25.19 E-value=90 Score=20.70 Aligned_cols=23 Identities=4% Similarity=0.011 Sum_probs=19.5
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
-.|-++..||+.+|++...+...
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~ 141 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSN 141 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHH
Confidence 36899999999999999887643
No 227
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=25.06 E-value=47 Score=24.33 Aligned_cols=36 Identities=17% Similarity=0.255 Sum_probs=27.9
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC-CCCCCC
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG-NNIRPF 97 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~-~~l~~G 97 (129)
.||.=..|..+..+++.|++..++|.-.=. -.|..|
T Consensus 64 ~TyMNlSG~~V~~~~~fy~i~~~~ilVvhDdLdl~~G 100 (190)
T COG0193 64 TTYMNLSGKAVGALASFYKIKPEDILVVHDELDLPLG 100 (190)
T ss_pred ccceeCcHHHHHHHHHHhCCCHHHEEEEeeccCCCCc
Confidence 478889999999999999999988765544 334444
No 228
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=24.90 E-value=81 Score=21.48 Aligned_cols=21 Identities=5% Similarity=0.033 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 3 ~I~e~a~~~gvs~~tlR~Ye~ 23 (140)
T PRK09514 3 RIGELAKLAEVTPDTLRFYEK 23 (140)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999998854
No 229
>PRK04217 hypothetical protein; Provisional
Probab=24.73 E-value=1e+02 Score=20.37 Aligned_cols=22 Identities=9% Similarity=0.211 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHhh
Q 037542 68 PSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 68 ~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
.|=|+..||+.+|++...+...
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~ 78 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRA 78 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 5779999999999999887665
No 230
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=24.57 E-value=17 Score=22.45 Aligned_cols=42 Identities=10% Similarity=0.167 Sum_probs=28.4
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC-------CCCCCCCEEEEcC
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG-------NNIRPFDTLFVPV 104 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~-------~~l~~Gq~L~IP~ 104 (129)
.|.+-.-+-...+-++|++..++|-+.-. -.+++||.+.|--
T Consensus 11 kH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R 59 (74)
T PF01191_consen 11 KHEILSEEEKKELLKKYNIKPEQLPKILSSDPVARYLGAKPGDVVKIIR 59 (74)
T ss_dssp EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHHHHHTT--TTSEEEEEE
T ss_pred CeEEcCHHHHHHHHHHhCCChhhCCcccccChhhhhcCCCCCCEEEEEe
Confidence 57777777778888899988777666544 5899999999853
No 231
>PRK12843 putative FAD-binding dehydrogenase; Reviewed
Probab=24.56 E-value=74 Score=26.85 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=20.5
Q ss_pred cCCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
...|||..+|++.|+..+ .|.++|.
T Consensus 429 ~kadTleELA~~~gid~~~L~~Tv~~yN~ 457 (578)
T PRK12843 429 TVASTLDELAPKLGIDPAALAATVQRHNQ 457 (578)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 467999999999999764 4677786
No 232
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=24.36 E-value=89 Score=20.61 Aligned_cols=21 Identities=14% Similarity=0.290 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|.-|=.
T Consensus 2 ~Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 2 TISELAREFDVTPRTLRFYED 22 (118)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998855
No 233
>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=24.34 E-value=81 Score=19.71 Aligned_cols=28 Identities=21% Similarity=0.207 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHhh---cCCCCCCC
Q 037542 70 ENLSSVASRFGIETQAIIDV---NGNNIRPF 97 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~---N~~~l~~G 97 (129)
=|.+.||+-||+....|.+. |.+.+..|
T Consensus 13 ~t~~~lA~~yg~~~~~i~~~~~rN~~rF~eg 43 (88)
T PF10543_consen 13 MTDEDLAELYGVETKTINRNFKRNKDRFIEG 43 (88)
T ss_pred EEHHHHHHHhCcCHHHHHHHHHHHHHhCCCC
Confidence 38999999999988777665 33444434
No 234
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=24.12 E-value=70 Score=23.71 Aligned_cols=44 Identities=5% Similarity=0.089 Sum_probs=35.3
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC-------CCCCCCCEEEEcCCC
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG-------NNIRPFDTLFVPVAR 106 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~-------~~l~~Gq~L~IP~~~ 106 (129)
.|.+-..|-...+-++|++...+|-+.-. -.+++||++.|--..
T Consensus 143 kH~~ls~eEk~~lL~~y~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R~S 193 (206)
T PLN03111 143 KHQVLTDEEKKTLLKRYTVKETQLPRIQVSDPIARYYGLKRGQVVKIIRPS 193 (206)
T ss_pred CeEEcCHHHHHHHHHHcCCCHHHCCcccccChhhHhcCCCCCCEEEEEECC
Confidence 47777778888899999999999866654 579999999996433
No 235
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=24.07 E-value=36 Score=21.74 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=13.2
Q ss_pred ecCC--CCHHHHHHHhCCC
Q 037542 66 LQPS--ENLSSVASRFGIE 82 (129)
Q Consensus 66 V~~G--DTl~~IA~~~~vs 82 (129)
+++| ||.|.|=|+||=+
T Consensus 42 ierGR~ETtW~vLR~FgY~ 60 (89)
T PF08356_consen 42 IERGRHETTWTVLRKFGYD 60 (89)
T ss_pred HHhCcchHHHHHHHHcCCC
Confidence 3555 8999999998853
No 236
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=24.05 E-value=2.9e+02 Score=20.09 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=21.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~N~ 91 (129)
.-|--|..+|+..|++.+++.+.--
T Consensus 98 ~~gpDL~~vA~~~gLs~~evi~~Hs 122 (201)
T smart00796 98 EFGPDLEFVARHNGLSVDEVIRLHS 122 (201)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHHh
Confidence 3366899999999999999999876
No 237
>PF07836 DmpG_comm: DmpG-like communication domain; InterPro: IPR012425 This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain []. The communication domain is thought to play an important role in the heterodimerisation of the enzyme []. Members of this entry heterodimerise with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase [].; GO: 0016833 oxo-acid-lyase activity, 0019439 aromatic compound catabolic process; PDB: 1NVM_E.
Probab=23.85 E-value=84 Score=18.98 Aligned_cols=27 Identities=15% Similarity=0.324 Sum_probs=13.4
Q ss_pred HHHHHHHhCCCHHHHHh-hcCCCCCCCC
Q 037542 72 LSSVASRFGIETQAIID-VNGNNIRPFD 98 (129)
Q Consensus 72 l~~IA~~~~vs~~~l~~-~N~~~l~~Gq 98 (129)
...+|++||++..+|.. +-...+-.||
T Consensus 25 a~raa~~ygVd~r~il~elgrR~~VgGQ 52 (66)
T PF07836_consen 25 AERAAERYGVDPRDILVELGRRKLVGGQ 52 (66)
T ss_dssp HHHHHHHHT--HHHHHHHHHHCT--TT-
T ss_pred HHHHHHHhCcCHHHHHHHHhcccccCch
Confidence 35688999998876543 3223344444
No 238
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=23.85 E-value=68 Score=18.38 Aligned_cols=41 Identities=17% Similarity=0.275 Sum_probs=28.1
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHhhcC----------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAIIDVNG----------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~----------~~l~~Gq~L~I 102 (129)
..+.+..|-|+..+-+.+++...-....|. ..|+.|+.|-|
T Consensus 8 ~~~~~~~~~tl~~ll~~l~~~~~~~v~vN~~~v~~~~~~~~~L~~gD~vei 58 (65)
T PRK06944 8 QTLSLPDGATVADALAAYGARPPFAVAVNGDFVARTQHAARALAAGDRLDL 58 (65)
T ss_pred EEEECCCCCcHHHHHHhhCCCCCeEEEECCEEcCchhcccccCCCCCEEEE
Confidence 357777888888888888775333345566 25888887754
No 239
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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=23.82 E-value=88 Score=21.31 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+|++...|.-|=.
T Consensus 2 ~I~e~a~~~gvs~~TLR~Ye~ 22 (134)
T cd04779 2 RIGQLAHLAGVSKRTIDYYTN 22 (134)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999999854
No 240
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=23.81 E-value=88 Score=21.86 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=18.7
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 13 ~IgevAk~~gvs~~TlRyYE~ 33 (154)
T PRK15002 13 TPGEVAKRSGVAVSALHFYES 33 (154)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999998855
No 241
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=23.74 E-value=69 Score=18.55 Aligned_cols=41 Identities=12% Similarity=0.327 Sum_probs=29.4
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHH-hhcC----------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAII-DVNG----------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~-~~N~----------~~l~~Gq~L~I 102 (129)
..|.+..+-|+..+-++++...+.++ ..|. ..|+.|+.|.|
T Consensus 7 ~~~~~~~~~tv~~ll~~l~~~~~~i~V~vNg~~v~~~~~~~~~L~~gD~V~i 58 (65)
T cd00565 7 EPREVEEGATLAELLEELGLDPRGVAVALNGEIVPRSEWASTPLQDGDRIEI 58 (65)
T ss_pred eEEEcCCCCCHHHHHHHcCCCCCcEEEEECCEEcCHHHcCceecCCCCEEEE
Confidence 46788888899999999887654432 3466 35888887654
No 242
>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=23.63 E-value=1.7e+02 Score=21.35 Aligned_cols=43 Identities=16% Similarity=0.193 Sum_probs=30.9
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC--------CCCCCCCEEEEcCC
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG--------NNIRPFDTLFVPVA 105 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~--------~~l~~Gq~L~IP~~ 105 (129)
.|-=.-|.-|..+|+..|++.+++.+.=- -...||--...++.
T Consensus 93 ~Y~~~~g~DL~~vA~~~gls~~evi~~H~~~~y~V~~iGF~PGfpYL~gld 143 (202)
T PF02682_consen 93 CYDGEFGPDLEEVAEHNGLSVEEVIRLHSSAEYRVYMIGFAPGFPYLGGLD 143 (202)
T ss_dssp EESTTTHTTHHHHHHHHTS-HHHHHHHHHTS-EEEEEECSSTTEEEEECSS
T ss_pred EECCCCCCCHHHHHHHhCcCHHHHHHHHHcCchHhhccCcccCcHhhcccC
Confidence 45556688999999999999999988743 24667766555543
No 243
>PRK06481 fumarate reductase flavoprotein subunit; Validated
Probab=23.56 E-value=80 Score=26.10 Aligned_cols=25 Identities=8% Similarity=0.266 Sum_probs=20.4
Q ss_pred cCCCCHHHHHHHhCCCHHH----HHhhcC
Q 037542 67 QPSENLSSVASRFGIETQA----IIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~----l~~~N~ 91 (129)
.++|||..+|++.|+..+. +.++|.
T Consensus 376 ~kadTleeLA~~~gid~~~L~~tv~~yN~ 404 (506)
T PRK06481 376 EEGKTIDELAKKINVPAETLTKTLDTWNK 404 (506)
T ss_pred EEcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4679999999999998765 556776
No 244
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=23.51 E-value=90 Score=19.56 Aligned_cols=42 Identities=17% Similarity=0.242 Sum_probs=34.6
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHhhcC-------CCCCCCCEEEEcC
Q 037542 63 SYVLQPSENLSSVASRFGIETQAIIDVNG-------NNIRPFDTLFVPV 104 (129)
Q Consensus 63 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~-------~~l~~Gq~L~IP~ 104 (129)
.|.|-.-|....|-++|++..++|=+.-. ...++|+.+.|--
T Consensus 17 eH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPva~~lgak~GdvVkIvR 65 (80)
T COG2012 17 EHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKALGAKPGDVVKIVR 65 (80)
T ss_pred ceEEcCHHHHHHHHHHhCCCHHHCCcccccChhHHHccCCCCcEEEEEe
Confidence 58888899999999999999988755433 5789999998863
No 245
>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=23.44 E-value=91 Score=18.76 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=15.6
Q ss_pred CCCHHHHHHHhCCCHHHHHhh
Q 037542 69 SENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~~ 89 (129)
.-|+..||+..+++...|.++
T Consensus 34 ~~si~elA~~~~vS~sti~Rf 54 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRF 54 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHH
Confidence 468999999999999888775
No 246
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=23.41 E-value=82 Score=23.82 Aligned_cols=21 Identities=24% Similarity=0.371 Sum_probs=17.2
Q ss_pred CHHHHHHHhCCCHHHHHhh-cC
Q 037542 71 NLSSVASRFGIETQAIIDV-NG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~-N~ 91 (129)
|+.+||+++|+|...+-++ |+
T Consensus 8 Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 8 TIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHHCC
Confidence 8999999999988776555 44
No 247
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. 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 su
Probab=23.40 E-value=94 Score=20.98 Aligned_cols=21 Identities=19% Similarity=0.273 Sum_probs=18.2
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 2 ~Ige~a~~~gvs~~tLRyYE~ 22 (131)
T cd04786 2 KIGELAKRSGMAASRIRFYEA 22 (131)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998854
No 248
>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=23.29 E-value=99 Score=22.43 Aligned_cols=23 Identities=17% Similarity=0.263 Sum_probs=20.0
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
-.|-|+..||+.+|++...+..+
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999999888765
No 249
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=23.28 E-value=91 Score=18.47 Aligned_cols=41 Identities=20% Similarity=0.298 Sum_probs=29.9
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHH-HHhhcC------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQA-IIDVNG------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~-l~~~N~------~~l~~Gq~L~I 102 (129)
..+.+..|-|+..+.+..++..+. ....|. ..|+.|+.|.|
T Consensus 16 ~~~~~~~~~tv~~ll~~l~~~~~~v~v~vNg~iv~~~~~l~~gD~Vei 63 (70)
T PRK08364 16 KEIEWRKGMKVADILRAVGFNTESAIAKVNGKVALEDDPVKDGDYVEV 63 (70)
T ss_pred eEEEcCCCCcHHHHHHHcCCCCccEEEEECCEECCCCcCcCCCCEEEE
Confidence 356778888999999999886544 334576 46888887754
No 250
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=23.28 E-value=92 Score=21.36 Aligned_cols=21 Identities=19% Similarity=0.283 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|=.
T Consensus 3 ~IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 3 TVGELAKRSGVAVSALHFYES 23 (142)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678899999999999988855
No 251
>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated
Probab=23.25 E-value=79 Score=23.41 Aligned_cols=24 Identities=21% Similarity=0.155 Sum_probs=20.3
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHH
Q 037542 62 VSYVLQPSENLSSVASRFGIETQA 85 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~ 85 (129)
..|.+.+|+||...|.+.|+.+-.
T Consensus 11 ~~~~~~~g~til~a~~~~gi~ip~ 34 (234)
T PRK07569 11 QLVSAREGETLLEAAREAGIPIPT 34 (234)
T ss_pred EEEEeCCCCHHHHHHHHcCCCCCc
Confidence 469999999999999998876533
No 252
>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=23.04 E-value=1.1e+02 Score=16.77 Aligned_cols=20 Identities=15% Similarity=0.343 Sum_probs=16.9
Q ss_pred CCHHHHHHHhCCCHHHHHhh
Q 037542 70 ENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~ 89 (129)
+....||...|++...|..|
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 45778999999999998876
No 253
>PRK12842 putative succinate dehydrogenase; Reviewed
Probab=22.91 E-value=79 Score=26.61 Aligned_cols=25 Identities=20% Similarity=0.375 Sum_probs=20.4
Q ss_pred cCCCCHHHHHHHhCCCH----HHHHhhcC
Q 037542 67 QPSENLSSVASRFGIET----QAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~----~~l~~~N~ 91 (129)
.++|||..+|++.|+.. +.+.++|.
T Consensus 424 ~kadTleELA~~~gid~~~L~~Tv~~yN~ 452 (574)
T PRK12842 424 IKGDTLAELAGKAGIDAAGLEATVRRYNE 452 (574)
T ss_pred EEcCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 46799999999999975 45677886
No 254
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=22.77 E-value=74 Score=19.92 Aligned_cols=41 Identities=12% Similarity=0.228 Sum_probs=32.2
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHH-hhcC----------CCCCCCCEEEE
Q 037542 62 VSYVLQPSENLSSVASRFGIETQAII-DVNG----------NNIRPFDTLFV 102 (129)
Q Consensus 62 ~~y~V~~GDTl~~IA~~~~vs~~~l~-~~N~----------~~l~~Gq~L~I 102 (129)
..|.+..+-||..+-+.+++....++ +.|. ..|+.|+.|-|
T Consensus 26 ~~~~~~~~~tl~~LL~~l~~~~~~vAVevNg~iVpr~~w~~t~L~egD~IEI 77 (84)
T PRK06083 26 QSIQVDISSSLAQIIAQLSLPELGCVFAINNQVVPRSEWQSTVLSSGDAISL 77 (84)
T ss_pred eEEEcCCCCcHHHHHHHcCCCCceEEEEECCEEeCHHHcCcccCCCCCEEEE
Confidence 46888888899999898888766554 7787 46899988865
No 255
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=22.63 E-value=1e+02 Score=19.92 Aligned_cols=21 Identities=14% Similarity=0.194 Sum_probs=17.9
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+.+||+...|.-|=.
T Consensus 2 ~I~eva~~~gvs~~tLRyYE~ 22 (124)
T COG0789 2 TIGEVAKLTGVSVRTLRFYER 22 (124)
T ss_pred cHHHHHHHhCCCHHHHHHHHH
Confidence 567899999999999988754
No 256
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=22.60 E-value=82 Score=23.59 Aligned_cols=24 Identities=25% Similarity=0.470 Sum_probs=18.5
Q ss_pred ecCCC-CHHHHHHHhCCCHHHHHhh
Q 037542 66 LQPSE-NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 66 V~~GD-Tl~~IA~~~~vs~~~l~~~ 89 (129)
--+.. |+..+|+.|.|+.+.|.+.
T Consensus 25 ~~p~~~t~~~Lae~F~vspe~irrI 49 (225)
T PF06413_consen 25 EDPEEWTVERLAESFKVSPEAIRRI 49 (225)
T ss_pred hCccccCHHHHHhhCCCCHHHHHHH
Confidence 33443 7889999999999887765
No 257
>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=22.53 E-value=99 Score=19.44 Aligned_cols=19 Identities=11% Similarity=0.377 Sum_probs=14.7
Q ss_pred cHHHHHHhhCCCCCCHHHHHHh
Q 037542 4 TFYSVSTNKYQNLTTYQSVEVV 25 (129)
Q Consensus 4 Tl~~IA~~~~~~lts~~~l~~~ 25 (129)
.|+.+|++.++ +.++|-.+
T Consensus 56 kL~~La~~N~v---~feeLc~Y 74 (82)
T PF11020_consen 56 KLYKLAKENNV---SFEELCVY 74 (82)
T ss_pred HHHHHHHHcCC---CHHHHHHH
Confidence 47888988888 88887653
No 258
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=22.52 E-value=1.2e+02 Score=18.65 Aligned_cols=22 Identities=14% Similarity=0.475 Sum_probs=17.3
Q ss_pred CCHHHHHHHhCCCHHHHHhhcC
Q 037542 70 ENLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~N~ 91 (129)
-++..|...||++..++.++=.
T Consensus 14 tpFeaI~~~fGL~E~eVi~lMR 35 (72)
T TIGR03643 14 TPFEAIEQQFGLSEKEVIKLMR 35 (72)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 3688999999999888766533
No 259
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=22.46 E-value=1.1e+02 Score=20.68 Aligned_cols=22 Identities=9% Similarity=0.102 Sum_probs=18.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
-.|-++..||+.+|++...+..
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~~ 163 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVRS 163 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 4688999999999999988754
No 260
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=22.39 E-value=96 Score=21.93 Aligned_cols=21 Identities=19% Similarity=0.477 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
|+..+|+++|++...|.-+=.
T Consensus 3 ~I~evA~~~gvs~~tLRyYe~ 23 (172)
T cd04790 3 TISQLARQFGLSRSTLLYYER 23 (172)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678899999999999988855
No 261
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.31 E-value=1.2e+02 Score=16.49 Aligned_cols=19 Identities=11% Similarity=0.349 Sum_probs=16.4
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
+...||+..|++...+.++
T Consensus 27 S~~~la~~~g~s~~Tv~~~ 45 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRA 45 (55)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 7889999999998887765
No 262
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.20 E-value=1e+02 Score=21.36 Aligned_cols=23 Identities=13% Similarity=0.179 Sum_probs=19.4
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHh
Q 037542 66 LQPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
.-.|-+...||+.+|++...+..
T Consensus 146 ~~~~~s~~eIA~~lgis~~tV~~ 168 (182)
T PRK12537 146 YVDGCSHAEIAQRLGAPLGTVKA 168 (182)
T ss_pred HHcCCCHHHHHHHHCCChhhHHH
Confidence 45799999999999999887654
No 263
>PHA00542 putative Cro-like protein
Probab=22.11 E-value=1.2e+02 Score=18.53 Aligned_cols=24 Identities=8% Similarity=0.184 Sum_probs=20.9
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHhh
Q 037542 66 LQPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
...|=|...+|+..|++...|.+|
T Consensus 28 ~~~glTq~elA~~lgIs~~tIsr~ 51 (82)
T PHA00542 28 IRAGWSQEQIADATDVSQPTICRI 51 (82)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHH
Confidence 356789999999999999999887
No 264
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=22.08 E-value=1.2e+02 Score=18.78 Aligned_cols=20 Identities=10% Similarity=0.204 Sum_probs=17.4
Q ss_pred CHHHHHHHhCCCHHHHHhhc
Q 037542 71 NLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N 90 (129)
+...+|+.+||+...+..|-
T Consensus 12 s~~kvA~aLGIs~~AVsQWG 31 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAWG 31 (75)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 56789999999999999993
No 265
>PLN03148 Blue copper-like protein; Provisional
Probab=22.06 E-value=1.2e+02 Score=21.64 Aligned_cols=14 Identities=7% Similarity=-0.247 Sum_probs=10.4
Q ss_pred CCCCCCEEEEcCCC
Q 037542 93 NIRPFDTLFVPVAR 106 (129)
Q Consensus 93 ~l~~Gq~L~IP~~~ 106 (129)
.=..||+|.|-+..
T Consensus 106 hC~~GmKl~I~V~~ 119 (167)
T PLN03148 106 QCFNGMKVTILVHP 119 (167)
T ss_pred ccccCCEEEEEEcC
Confidence 44569999998754
No 266
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.01 E-value=1.1e+02 Score=21.03 Aligned_cols=22 Identities=9% Similarity=0.131 Sum_probs=18.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
-.|-+...||+.+|++...+..
T Consensus 143 ~~g~s~~eIA~~lgis~~tV~~ 164 (179)
T PRK12514 143 LEGLSYKELAERHDVPLNTMRT 164 (179)
T ss_pred HcCCCHHHHHHHHCCChHHHHH
Confidence 4689999999999999987754
No 267
>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=21.86 E-value=1.1e+02 Score=20.60 Aligned_cols=21 Identities=10% Similarity=0.175 Sum_probs=17.8
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-+=.
T Consensus 2 ~IgE~A~~~gvs~~TLRyYE~ 22 (133)
T cd04787 2 KVKELANAAGVTPDTVRFYTR 22 (133)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 577899999999999987744
No 268
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=21.65 E-value=47 Score=20.06 Aligned_cols=39 Identities=15% Similarity=0.110 Sum_probs=24.2
Q ss_pred cHHHHHHhhCCCCCCHHHHHHhCCCCCCCCCCCCCEEEEC
Q 037542 4 TFYSVSTNKYQNLTTYQSVEVVNPAFVPTKLEVGDVFIFP 43 (129)
Q Consensus 4 Tl~~IA~~~~~~lts~~~l~~~N~~~~~~~l~~Gq~L~IP 43 (129)
|+..-|.=||+|.....+|...|+.. +-.+..|.+++|-
T Consensus 15 Ti~EAa~Y~gIG~~klr~l~~~~~~~-~f~~~~G~r~lIk 53 (67)
T PF09035_consen 15 TIEEAAEYFGIGEKKLRELAEENPDC-PFVLWIGNRRLIK 53 (67)
T ss_dssp EHHHHHHHT-S-HHHHHHHHHH-TT--SSEEEETTEEEEE
T ss_pred CHHHHHHHhCccHHHHHHHHHhCCCC-CEEEEECCEEEEe
Confidence 45566777888666677777555552 3368899988874
No 269
>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=21.62 E-value=1.2e+02 Score=19.97 Aligned_cols=22 Identities=14% Similarity=0.279 Sum_probs=18.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
-.|-+...||+.+|++...+..
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~ 148 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEY 148 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3688999999999999988654
No 270
>PRK12835 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=21.61 E-value=91 Score=26.43 Aligned_cols=25 Identities=16% Similarity=0.416 Sum_probs=20.6
Q ss_pred cCCCCHHHHHHHhCCCH----HHHHhhcC
Q 037542 67 QPSENLSSVASRFGIET----QAIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~----~~l~~~N~ 91 (129)
.+.|||..+|++.|+.. +.|.++|.
T Consensus 428 ~kAdTleeLA~~~gida~~L~aTV~~yN~ 456 (584)
T PRK12835 428 KKADTWDELAAKIGVPAENLRATAERFNG 456 (584)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 46799999999999975 45677886
No 271
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=21.31 E-value=1.2e+02 Score=20.06 Aligned_cols=23 Identities=4% Similarity=-0.010 Sum_probs=19.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHhh
Q 037542 67 QPSENLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~~ 89 (129)
-.|-+...||+.+|++...+...
T Consensus 120 ~~~~s~~EIA~~l~is~~tV~~~ 142 (154)
T PRK06759 120 FVGKTMGEIALETEMTYYQVRWI 142 (154)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999999887654
No 272
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=21.29 E-value=27 Score=24.07 Aligned_cols=60 Identities=15% Similarity=0.143 Sum_probs=34.1
Q ss_pred CCCcHHHHHHhhCCCCCCHHHHHHh--CCCC-CCCCCCCCCEEEECCCCCCCCcccccccccceEEEEecCCCCHHHHHH
Q 037542 1 SGDTFYSVSTNKYQNLTTYQSVEVV--NPAF-VPTKLEVGDVFIFPVFCKCPDQTQLRNRVNYLVSYVLQPSENLSSVAS 77 (129)
Q Consensus 1 ~GDTl~~IA~~~~~~lts~~~l~~~--N~~~-~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~IA~ 77 (129)
+|+|=..||++.+..-..+..|-+. -++- ..+.|.--..|.-| +...|++||++..|-+
T Consensus 22 kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnTL~l~~~i~sp------------------v~i~v~aGe~~dei~e 83 (143)
T COG1356 22 KGLTQSEIARILKTTRANVSAIEKRALENIEKARNTLLLWEQINSP------------------VSITVKAGEDIDEIPE 83 (143)
T ss_pred ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHHHHHHHhCCC------------------eEEEecCCCcHHHHHH
Confidence 5888899999988622223333221 1110 01223222223323 5789999999999987
Q ss_pred H
Q 037542 78 R 78 (129)
Q Consensus 78 ~ 78 (129)
+
T Consensus 84 ~ 84 (143)
T COG1356 84 R 84 (143)
T ss_pred H
Confidence 5
No 273
>TIGR01813 flavo_cyto_c flavocytochrome c. This model describes a family of redox proteins related to the succinate dehydrogenases and fumarate reductases of E. coli, mitochondria, and other well-characterized systems. A member of this family from Shewanella frigidimarina NCIMB400 is characterized as a water-soluble periplasmic protein with four heme groups, a non-covalently bound FAD, and essentially unidirectional fumarate reductase activity. At least seven distinct members of this family are found in Shewanella oneidensis, a species able to use a wide variety of pathways for respiraton.
Probab=21.19 E-value=93 Score=24.88 Aligned_cols=25 Identities=32% Similarity=0.526 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHhCCCHHH----HHhhcC
Q 037542 67 QPSENLSSVASRFGIETQA----IIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~----l~~~N~ 91 (129)
.+.|||..+|++.|+..+. +.++|.
T Consensus 318 ~~adtleeLa~~~g~~~~~l~~tv~~yN~ 346 (439)
T TIGR01813 318 YKGDSLEELAKQFGIPAAALKKTVKDYNE 346 (439)
T ss_pred EEeCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4689999999999997654 568885
No 274
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=21.19 E-value=98 Score=23.21 Aligned_cols=19 Identities=16% Similarity=0.333 Sum_probs=15.9
Q ss_pred CHHHHHHHhCCCHHHHHhh
Q 037542 71 NLSSVASRFGIETQAIIDV 89 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~ 89 (129)
|+.+||+++|+|...+-++
T Consensus 3 ti~dIA~~agVS~sTVSr~ 21 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRV 21 (311)
T ss_pred cHHHHHHHhCCCHHHHHHH
Confidence 7899999999988776655
No 275
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=21.01 E-value=1.1e+02 Score=21.12 Aligned_cols=21 Identities=14% Similarity=0.177 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|+++..|.-+=.
T Consensus 9 ~IgevAk~~Gvs~~TLRyYE~ 29 (144)
T PRK13752 9 TIGVFAKAAGVNVETIRFYQR 29 (144)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999987744
No 276
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=20.78 E-value=1.4e+02 Score=18.47 Aligned_cols=21 Identities=14% Similarity=0.507 Sum_probs=16.9
Q ss_pred CCHHHHHHHhCCCHHHHHhhc
Q 037542 70 ENLSSVASRFGIETQAIIDVN 90 (129)
Q Consensus 70 DTl~~IA~~~~vs~~~l~~~N 90 (129)
-++..|...||++..++.++=
T Consensus 13 tpFeaI~~qfGl~E~eVi~lM 33 (73)
T PF10985_consen 13 TPFEAIERQFGLSEKEVIKLM 33 (73)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 368899999999988876653
No 277
>PRK08274 tricarballylate dehydrogenase; Validated
Probab=20.73 E-value=1.1e+02 Score=24.82 Aligned_cols=26 Identities=19% Similarity=0.440 Sum_probs=21.1
Q ss_pred ecCCCCHHHHHHHhCCCHHH----HHhhcC
Q 037542 66 LQPSENLSSVASRFGIETQA----IIDVNG 91 (129)
Q Consensus 66 V~~GDTl~~IA~~~~vs~~~----l~~~N~ 91 (129)
+.+.|||..+|++.|+..+. |.++|.
T Consensus 321 ~~~adtleeLA~~~gi~~~~l~~tv~~yN~ 350 (466)
T PRK08274 321 PIQADTLEELAEKLGLDPAAFLRTVAAFNA 350 (466)
T ss_pred ccccCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 45789999999999997744 667787
No 278
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.64 E-value=1.2e+02 Score=21.38 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=18.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHh
Q 037542 67 QPSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~~l~~ 88 (129)
-.|-|...||+..|++...+.+
T Consensus 149 ~~Gls~~EIA~~lgiS~~tV~r 170 (185)
T PF07638_consen 149 FEGLSVEEIAERLGISERTVRR 170 (185)
T ss_pred HCCCCHHHHHHHHCcCHHHHHH
Confidence 4799999999999999887654
No 279
>PRK11426 hypothetical protein; Provisional
Probab=20.55 E-value=75 Score=21.86 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=17.1
Q ss_pred CCCHHHHHHHhCCCHHHHHh
Q 037542 69 SENLSSVASRFGIETQAIID 88 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~~ 88 (129)
.|++..+|+++|++.+++..
T Consensus 72 ~d~i~~lA~q~Gl~~~~~~~ 91 (132)
T PRK11426 72 TNAVSDLGQKLGVDTSTASS 91 (132)
T ss_pred hHHHHHHHHHHCcCHHHHHH
Confidence 58999999999999887554
No 280
>PRK12844 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=20.45 E-value=1e+02 Score=25.94 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=20.2
Q ss_pred cCCCCHHHHHHHhCCCHH----HHHhhcC
Q 037542 67 QPSENLSSVASRFGIETQ----AIIDVNG 91 (129)
Q Consensus 67 ~~GDTl~~IA~~~~vs~~----~l~~~N~ 91 (129)
.++|||..+|++.|+..+ .+.++|.
T Consensus 407 ~kadTleELA~k~gid~~~L~atv~~yN~ 435 (557)
T PRK12844 407 KRADTIEELAGKTGIDPAGLAATVERFNG 435 (557)
T ss_pred EecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 368999999999999764 4667786
No 281
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=20.34 E-value=1.2e+02 Score=20.61 Aligned_cols=21 Identities=33% Similarity=0.341 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHhhcC
Q 037542 71 NLSSVASRFGIETQAIIDVNG 91 (129)
Q Consensus 71 Tl~~IA~~~~vs~~~l~~~N~ 91 (129)
++..+|+++|++...|.-|-.
T Consensus 2 ~Ige~a~~~gvs~~tlRyYE~ 22 (135)
T PRK10227 2 NISDVAKITGLTSKAIRFYEE 22 (135)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998865
No 282
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=20.30 E-value=1.5e+02 Score=15.42 Aligned_cols=19 Identities=16% Similarity=0.291 Sum_probs=14.9
Q ss_pred CCCHHHHHHHhCCCHHHHH
Q 037542 69 SENLSSVASRFGIETQAII 87 (129)
Q Consensus 69 GDTl~~IA~~~~vs~~~l~ 87 (129)
+-++..||+.++++...+.
T Consensus 14 ~~s~~~l~~~l~~s~~tv~ 32 (53)
T smart00420 14 KVSVEELAELLGVSEMTIR 32 (53)
T ss_pred CcCHHHHHHHHCCCHHHHH
Confidence 4588999999999776653
No 283
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.02 E-value=1.4e+02 Score=15.98 Aligned_cols=21 Identities=10% Similarity=0.196 Sum_probs=15.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHh
Q 037542 68 PSENLSSVASRFGIETQAIID 88 (129)
Q Consensus 68 ~GDTl~~IA~~~~vs~~~l~~ 88 (129)
..-++..|++.++++...+.+
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~ 29 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSH 29 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHH
Confidence 344788999999997765443
Done!