Query 047095
Match_columns 188
No_of_seqs 211 out of 1444
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 07:33:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06347 autolysin; Reviewed 100.0 1.6E-28 3.6E-33 218.1 18.5 180 1-186 341-565 (592)
2 PRK06347 autolysin; Reviewed 99.9 3.9E-27 8.5E-32 209.3 16.1 153 1-159 416-592 (592)
3 PRK10783 mltD membrane-bound l 99.9 6E-26 1.3E-30 197.6 16.5 156 1-163 274-451 (456)
4 PRK13914 invasion associated s 99.7 2.2E-15 4.8E-20 130.5 13.6 109 50-162 26-247 (481)
5 PRK10783 mltD membrane-bound l 99.6 1.3E-15 2.8E-20 133.1 11.0 97 1-103 354-450 (456)
6 PRK13914 invasion associated s 99.3 1.2E-11 2.5E-16 107.6 9.9 48 51-102 199-246 (481)
7 PF01476 LysM: LysM domain; I 99.3 3E-12 6.5E-17 76.4 3.8 40 120-159 1-44 (44)
8 COG1388 LytE FOG: LysM repeat 99.3 2.4E-11 5.2E-16 88.4 8.2 92 65-160 1-112 (124)
9 COG1388 LytE FOG: LysM repeat 99.3 2.5E-11 5.4E-16 88.3 8.0 94 4-102 1-113 (124)
10 PF01476 LysM: LysM domain; I 99.2 1.2E-11 2.7E-16 73.7 4.1 43 54-100 1-44 (44)
11 PRK14125 cell division suppres 99.0 5.9E-10 1.3E-14 78.6 6.6 53 50-104 35-93 (103)
12 PRK14125 cell division suppres 99.0 1.5E-09 3.2E-14 76.6 6.5 48 117-164 36-94 (103)
13 TIGR02899 spore_safA spore coa 98.9 2.1E-09 4.6E-14 63.5 4.2 39 122-160 1-44 (44)
14 cd00118 LysM Lysin domain, fou 98.9 5.6E-09 1.2E-13 61.1 5.3 41 119-159 2-46 (46)
15 TIGR02907 spore_VI_D stage VI 98.8 8.6E-09 1.9E-13 85.6 5.8 45 115-159 291-338 (338)
16 COG3858 Predicted glycosyl hyd 98.7 1.7E-08 3.7E-13 86.0 6.0 95 52-164 2-100 (423)
17 TIGR02907 spore_VI_D stage VI 98.7 1.8E-08 3.9E-13 83.7 6.0 49 48-100 290-338 (338)
18 TIGR02899 spore_safA spore coa 98.7 2.3E-08 5.1E-13 58.9 4.3 42 56-101 1-44 (44)
19 cd00118 LysM Lysin domain, fou 98.7 4.6E-08 1E-12 57.0 5.4 44 53-100 2-46 (46)
20 PRK10871 nlpD lipoprotein NlpD 98.7 2.6E-08 5.6E-13 83.2 5.0 44 118-161 61-108 (319)
21 PRK10871 nlpD lipoprotein NlpD 98.6 4.2E-08 9.2E-13 81.9 5.2 48 51-102 60-108 (319)
22 smart00257 LysM Lysin motif. 98.5 2.8E-07 6.2E-12 52.9 4.6 39 119-157 1-43 (44)
23 PRK11198 LysM domain/BON super 98.4 4.7E-07 1E-11 67.9 5.6 50 50-100 94-146 (147)
24 smart00257 LysM Lysin motif. 98.3 1.4E-06 2.9E-11 50.0 4.9 43 53-99 1-44 (44)
25 COG3858 Predicted glycosyl hyd 98.3 1.2E-06 2.7E-11 74.8 5.2 85 2-103 13-98 (423)
26 PRK11198 LysM domain/BON super 98.2 2.9E-06 6.2E-11 63.7 4.8 42 118-159 96-146 (147)
27 PRK10190 L,D-transpeptidase; P 97.5 0.00028 6.2E-09 58.8 6.2 47 115-161 35-87 (310)
28 COG1652 XkdP Uncharacterized p 97.5 4.5E-05 9.7E-10 62.7 1.3 50 52-102 211-264 (269)
29 PRK10260 L,D-transpeptidase; P 97.5 0.00031 6.7E-09 58.4 6.2 47 115-161 38-90 (306)
30 PF04225 OapA: Opacity-associa 96.9 0.0015 3.3E-08 44.4 3.9 48 51-102 2-54 (85)
31 TIGR03505 FimV_core FimV N-ter 96.8 0.0018 3.9E-08 42.9 3.9 41 60-102 1-52 (74)
32 TIGR03505 FimV_core FimV N-ter 96.7 0.0026 5.6E-08 42.1 3.7 37 126-162 1-53 (74)
33 PF05489 Phage_tail_X: Phage T 96.5 0.0061 1.3E-07 38.7 4.4 47 54-102 4-54 (60)
34 PRK10260 L,D-transpeptidase; P 96.4 0.0086 1.9E-07 49.9 6.1 51 50-104 39-92 (306)
35 PF04225 OapA: Opacity-associa 96.4 0.0037 8E-08 42.5 3.3 44 118-161 3-54 (85)
36 PRK10190 L,D-transpeptidase; P 96.4 0.0097 2.1E-07 49.8 6.1 51 50-104 36-89 (310)
37 COG1652 XkdP Uncharacterized p 96.1 0.0025 5.4E-08 52.3 1.2 45 118-162 211-265 (269)
38 PF05489 Phage_tail_X: Phage T 95.3 0.032 7E-07 35.3 4.0 39 123-161 6-54 (60)
39 PRK11649 putative peptidase; P 94.2 0.36 7.9E-06 42.5 8.9 95 50-148 94-215 (439)
40 COG3061 OapA Cell envelope opa 94.1 0.15 3.4E-06 40.4 5.7 48 115-162 157-212 (242)
41 COG3170 FimV Tfp pilus assembl 93.8 0.063 1.4E-06 49.3 3.5 53 49-102 186-248 (755)
42 COG3061 OapA Cell envelope opa 91.5 0.75 1.6E-05 36.6 6.3 73 27-103 134-212 (242)
43 PRK11649 putative peptidase; P 90.9 0.46 1E-05 41.9 5.1 45 117-161 95-144 (439)
44 COG3170 FimV Tfp pilus assembl 90.2 0.2 4.4E-06 46.1 2.3 47 117-163 188-250 (755)
45 PF13518 HTH_28: Helix-turn-he 87.1 0.59 1.3E-05 27.8 2.3 24 123-146 10-33 (52)
46 COG5004 P2-like prophage tail 82.8 2.9 6.3E-05 26.7 3.9 50 52-102 3-56 (70)
47 COG4784 Putative Zn-dependent 82.6 2.5 5.5E-05 36.1 4.7 47 51-99 428-476 (479)
48 PF02796 HTH_7: Helix-turn-hel 81.9 1.5 3.3E-05 25.7 2.4 23 123-145 19-41 (45)
49 PF01527 HTH_Tnp_1: Transposas 81.4 0.94 2E-05 29.2 1.5 24 122-145 20-43 (76)
50 KOG2850 Predicted peptidoglyca 78.9 1.4 3.1E-05 34.2 2.0 45 118-162 10-58 (186)
51 COG0739 NlpD Membrane proteins 75.1 5.6 0.00012 32.0 4.6 44 119-162 3-50 (277)
52 PF13384 HTH_23: Homeodomain-l 74.8 3.6 7.8E-05 24.2 2.6 23 123-145 15-37 (50)
53 COG2963 Transposase and inacti 74.1 3.1 6.8E-05 29.3 2.6 24 122-145 21-45 (116)
54 PF04218 CENP-B_N: CENP-B N-te 73.5 1.5 3.2E-05 26.9 0.6 24 122-145 19-42 (53)
55 PHA00675 hypothetical protein 73.4 3.6 7.8E-05 27.3 2.4 26 123-148 37-62 (78)
56 COG4254 Uncharacterized protei 71.9 4.3 9.3E-05 33.9 3.1 51 52-104 6-58 (339)
57 PRK09413 IS2 repressor TnpA; R 70.7 4.4 9.6E-05 29.0 2.7 26 120-145 24-49 (121)
58 PF13936 HTH_38: Helix-turn-he 67.5 6.3 0.00014 22.9 2.4 22 123-144 18-39 (44)
59 COG0739 NlpD Membrane proteins 65.7 11 0.00025 30.2 4.5 46 53-102 3-49 (277)
60 COG4784 Putative Zn-dependent 64.5 9.2 0.0002 32.8 3.7 42 117-158 428-476 (479)
61 cd00569 HTH_Hin_like Helix-tur 63.5 11 0.00024 19.2 2.9 23 123-145 19-41 (42)
62 PF05225 HTH_psq: helix-turn-h 63.4 7.1 0.00015 22.9 2.1 24 122-145 12-36 (45)
63 COG5004 P2-like prophage tail 63.0 20 0.00043 23.0 4.1 44 118-161 3-56 (70)
64 PF10668 Phage_terminase: Phag 59.0 11 0.00025 23.7 2.6 21 127-147 24-44 (60)
65 PF04545 Sigma70_r4: Sigma-70, 58.3 14 0.0003 21.7 2.8 23 123-145 18-40 (50)
66 PF00376 MerR: MerR family reg 57.9 13 0.00028 21.0 2.5 21 127-147 1-21 (38)
67 PF13693 HTH_35: Winged helix- 55.3 12 0.00027 24.8 2.4 23 123-145 13-35 (78)
68 PF04255 DUF433: Protein of un 55.1 12 0.00026 22.9 2.2 23 123-145 29-52 (56)
69 PF08765 Mor: Mor transcriptio 52.1 15 0.00032 25.8 2.5 20 125-144 72-91 (108)
70 KOG2850 Predicted peptidoglyca 51.5 12 0.00026 29.2 2.1 48 51-102 9-57 (186)
71 PF13613 HTH_Tnp_4: Helix-turn 50.8 13 0.00028 22.4 1.8 23 122-144 16-38 (53)
72 cd04762 HTH_MerR-trunc Helix-T 50.7 19 0.00042 20.2 2.6 20 127-146 2-21 (49)
73 PF13443 HTH_26: Cro/C1-type H 50.4 4.9 0.00011 24.8 -0.1 22 126-147 41-62 (63)
74 cd04761 HTH_MerR-SF Helix-Turn 50.3 19 0.00042 20.6 2.5 21 127-147 2-22 (49)
75 cd01104 HTH_MlrA-CarA Helix-Tu 49.8 18 0.00039 22.5 2.5 20 127-146 2-21 (68)
76 PF13011 LZ_Tnp_IS481: leucine 49.6 17 0.00037 24.6 2.4 25 121-145 21-45 (85)
77 PF01710 HTH_Tnp_IS630: Transp 48.5 12 0.00027 26.6 1.7 24 122-145 15-38 (119)
78 PF13411 MerR_1: MerR HTH fami 48.3 21 0.00045 22.2 2.6 21 127-147 2-22 (69)
79 PF09012 FeoC: FeoC like trans 46.4 20 0.00044 22.7 2.3 19 127-145 16-34 (69)
80 PF13542 HTH_Tnp_ISL3: Helix-t 45.9 25 0.00054 20.6 2.6 20 126-145 28-47 (52)
81 PHA01976 helix-turn-helix prot 44.6 17 0.00037 22.6 1.7 19 125-143 44-62 (67)
82 COG4254 Uncharacterized protei 44.4 26 0.00056 29.4 3.1 46 118-163 6-58 (339)
83 PF06056 Terminase_5: Putative 44.1 31 0.00066 21.4 2.8 23 124-146 12-34 (58)
84 PF01381 HTH_3: Helix-turn-hel 44.1 13 0.00028 22.1 1.1 17 126-142 39-55 (55)
85 cd04764 HTH_MlrA-like_sg1 Heli 43.4 27 0.00058 21.8 2.5 20 127-146 2-21 (67)
86 PF11268 DUF3071: Protein of u 43.0 21 0.00045 27.4 2.3 28 120-147 64-91 (170)
87 smart00421 HTH_LUXR helix_turn 42.7 34 0.00074 19.7 2.9 24 122-145 15-38 (58)
88 PF00356 LacI: Bacterial regul 42.5 33 0.00071 20.2 2.6 22 127-148 1-23 (46)
89 smart00422 HTH_MERR helix_turn 42.4 28 0.00061 21.6 2.5 20 127-146 2-21 (70)
90 smart00351 PAX Paired Box doma 42.2 24 0.00052 25.4 2.4 23 123-145 31-53 (125)
91 PRK10344 DNA-binding transcrip 41.5 30 0.00064 23.7 2.6 22 123-144 19-40 (92)
92 PF08281 Sigma70_r4_2: Sigma-7 40.3 31 0.00067 20.4 2.4 21 124-144 25-45 (54)
93 TIGR02531 yecD_yerC TrpR-relat 39.7 29 0.00062 23.6 2.3 26 122-147 47-72 (88)
94 PF08220 HTH_DeoR: DeoR-like h 39.0 34 0.00074 20.9 2.5 18 127-144 16-33 (57)
95 PF12471 GTP_CH_N: GTP cyclohy 36.6 24 0.00052 27.4 1.7 25 121-145 166-190 (194)
96 PF11242 DUF2774: Protein of u 36.5 49 0.0011 21.0 2.8 22 123-144 11-32 (63)
97 cd04763 HTH_MlrA-like Helix-Tu 36.4 40 0.00086 21.1 2.5 21 127-147 2-22 (68)
98 PF12244 DUF3606: Protein of u 36.0 30 0.00065 21.4 1.8 18 128-145 23-40 (57)
99 PF04760 IF2_N: Translation in 35.9 25 0.00055 21.1 1.5 18 127-144 5-22 (54)
100 PF07022 Phage_CI_repr: Bacter 33.5 27 0.00058 22.0 1.4 19 125-143 41-59 (66)
101 smart00760 Bac_DnaA_C Bacteria 32.9 31 0.00066 21.2 1.5 18 2-19 7-24 (60)
102 PF13551 HTH_29: Winged helix- 32.7 42 0.00091 22.7 2.4 23 123-145 9-32 (112)
103 PHA02591 hypothetical protein; 32.4 49 0.0011 22.1 2.4 26 119-144 39-67 (83)
104 TIGR01764 excise DNA binding d 32.3 95 0.0021 17.2 3.8 21 127-147 3-23 (49)
105 PF08299 Bac_DnaA_C: Bacterial 31.2 29 0.00063 22.2 1.2 18 2-19 7-24 (70)
106 PF04967 HTH_10: HTH DNA bindi 30.9 48 0.001 20.2 2.1 25 119-143 17-41 (53)
107 COG2739 Uncharacterized protei 30.8 45 0.00098 23.4 2.1 17 127-143 35-51 (105)
108 cd06170 LuxR_C_like C-terminal 30.7 70 0.0015 18.4 2.9 23 123-145 13-35 (57)
109 KOG3309 Ferredoxin [Energy pro 30.6 46 0.001 25.1 2.3 26 115-140 53-78 (159)
110 PF12844 HTH_19: Helix-turn-he 30.5 34 0.00073 20.9 1.4 20 126-145 42-61 (64)
111 cd04768 HTH_BmrR-like Helix-Tu 30.3 53 0.0012 22.3 2.5 22 127-148 2-23 (96)
112 PF13510 Fer2_4: 2Fe-2S iron-s 30.2 66 0.0014 21.2 2.9 22 118-139 11-32 (82)
113 TIGR02937 sigma70-ECF RNA poly 29.4 59 0.0013 22.7 2.8 23 123-145 124-146 (158)
114 COG3753 Uncharacterized protei 29.4 52 0.0011 24.3 2.4 20 125-144 90-109 (143)
115 cd00131 PAX Paired Box domain 29.4 50 0.0011 23.8 2.4 23 123-145 31-53 (128)
116 cd04775 HTH_Cfa-like Helix-Tur 28.8 58 0.0013 22.3 2.5 22 127-148 3-24 (102)
117 PF00165 HTH_AraC: Bacterial r 28.4 76 0.0017 17.7 2.6 21 124-144 7-27 (42)
118 COG5484 Uncharacterized conser 28.1 52 0.0011 27.0 2.4 24 125-148 19-42 (279)
119 cd01279 HTH_HspR-like Helix-Tu 27.9 62 0.0013 22.1 2.5 20 127-146 3-22 (98)
120 cd01109 HTH_YyaN Helix-Turn-He 27.8 61 0.0013 22.6 2.5 21 127-147 2-22 (113)
121 cd04766 HTH_HspR Helix-Turn-He 27.8 64 0.0014 21.5 2.5 21 127-147 3-23 (91)
122 COG2442 Uncharacterized conser 27.4 69 0.0015 21.3 2.6 25 121-145 39-64 (79)
123 PF01371 Trp_repressor: Trp re 27.2 49 0.0011 22.4 1.8 26 123-148 47-72 (87)
124 PF09607 BrkDBD: Brinker DNA-b 26.8 53 0.0012 20.6 1.8 18 129-146 29-46 (58)
125 cd04772 HTH_TioE_rpt1 First He 26.8 67 0.0015 21.9 2.5 21 127-147 2-22 (99)
126 PF12116 SpoIIID: Stage III sp 26.6 24 0.00051 23.7 0.2 23 119-141 13-35 (82)
127 cd04774 HTH_YfmP Helix-Turn-He 26.6 68 0.0015 21.8 2.5 21 127-147 2-22 (96)
128 PF01402 RHH_1: Ribbon-helix-h 26.3 46 0.001 18.2 1.4 17 1-17 14-30 (39)
129 cd01107 HTH_BmrR Helix-Turn-He 26.1 69 0.0015 22.2 2.5 21 127-147 2-22 (108)
130 smart00345 HTH_GNTR helix_turn 26.0 81 0.0018 18.4 2.6 19 127-145 22-40 (60)
131 PF11020 DUF2610: Domain of un 25.9 75 0.0016 21.2 2.4 20 126-145 55-74 (82)
132 TIGR02844 spore_III_D sporulat 25.6 77 0.0017 21.1 2.5 19 127-145 21-39 (80)
133 cd04788 HTH_NolA-AlbR Helix-Tu 25.6 73 0.0016 21.6 2.5 21 127-147 2-22 (96)
134 cd04782 HTH_BltR Helix-Turn-He 25.3 74 0.0016 21.6 2.5 21 127-147 2-22 (97)
135 TIGR03879 near_KaiC_dom probab 25.2 96 0.0021 20.3 2.9 23 123-145 30-52 (73)
136 cd06171 Sigma70_r4 Sigma70, re 25.2 1E+02 0.0022 17.1 2.9 22 124-145 25-46 (55)
137 PRK12845 3-ketosteroid-delta-1 25.2 69 0.0015 29.2 3.0 27 122-148 421-451 (564)
138 COG3415 Transposase and inacti 25.1 63 0.0014 23.9 2.2 25 121-145 17-41 (138)
139 cd01105 HTH_GlnR-like Helix-Tu 25.0 77 0.0017 21.1 2.5 22 127-148 3-24 (88)
140 PRK12837 3-ketosteroid-delta-1 24.4 73 0.0016 28.5 3.0 26 123-148 373-402 (513)
141 cd04770 HTH_HMRTR Helix-Turn-H 24.3 77 0.0017 22.3 2.6 22 127-148 2-23 (123)
142 COG0350 Ada Methylated DNA-pro 24.0 1.6E+02 0.0034 22.4 4.3 44 127-176 107-155 (168)
143 PF13404 HTH_AsnC-type: AsnC-t 23.9 95 0.0021 17.7 2.4 18 126-143 18-35 (42)
144 cd01106 HTH_TipAL-Mta Helix-Tu 23.9 81 0.0018 21.5 2.5 20 127-146 2-21 (103)
145 cd04769 HTH_MerR2 Helix-Turn-H 23.5 82 0.0018 22.1 2.5 22 127-148 2-23 (116)
146 cd01108 HTH_CueR Helix-Turn-He 23.5 79 0.0017 22.6 2.5 22 127-148 2-23 (127)
147 PF00196 GerE: Bacterial regul 23.5 78 0.0017 19.0 2.1 22 123-144 16-37 (58)
148 smart00342 HTH_ARAC helix_turn 23.4 91 0.002 19.3 2.6 18 127-144 3-20 (84)
149 cd04789 HTH_Cfa Helix-Turn-Hel 23.4 85 0.0018 21.5 2.6 22 127-148 3-24 (102)
150 PF06627 DUF1153: Protein of u 23.2 65 0.0014 22.0 1.8 26 123-148 46-72 (90)
151 PF00392 GntR: Bacterial regul 23.2 91 0.002 19.1 2.5 18 128-145 27-44 (64)
152 PF02515 CoA_transf_3: CoA-tra 23.0 60 0.0013 25.0 1.9 19 4-22 32-50 (191)
153 cd01282 HTH_MerR-like_sg3 Heli 22.8 88 0.0019 21.8 2.6 22 127-148 2-23 (112)
154 TIGR02044 CueR Cu(I)-responsiv 22.5 85 0.0019 22.4 2.5 21 127-147 2-22 (127)
155 PF08279 HTH_11: HTH domain; 22.3 95 0.0021 18.2 2.3 17 127-143 17-33 (55)
156 cd04785 HTH_CadR-PbrR-like Hel 22.2 88 0.0019 22.3 2.5 22 127-148 2-23 (126)
157 PRK12839 hypothetical protein; 22.2 87 0.0019 28.6 3.0 26 123-148 425-454 (572)
158 PF14502 HTH_41: Helix-turn-he 21.9 1.1E+02 0.0023 18.4 2.4 19 127-145 8-26 (48)
159 PF08984 DUF1858: Domain of un 21.7 1E+02 0.0022 18.8 2.4 23 121-143 37-59 (59)
160 cd00086 homeodomain Homeodomai 21.7 79 0.0017 18.6 1.9 21 125-145 27-47 (59)
161 cd00093 HTH_XRE Helix-turn-hel 21.6 1.2E+02 0.0025 16.6 2.7 26 123-148 10-35 (58)
162 cd04767 HTH_HspR-like_MBC Heli 21.5 95 0.0021 22.3 2.5 21 127-147 3-23 (120)
163 cd04765 HTH_MlrA-like_sg2 Heli 21.3 98 0.0021 21.2 2.5 19 127-145 2-20 (99)
164 PRK00118 putative DNA-binding 20.8 1.2E+02 0.0025 21.3 2.8 23 123-145 31-53 (104)
165 TIGR03070 couple_hipB transcri 20.7 1.2E+02 0.0027 17.4 2.6 26 123-148 13-38 (58)
166 TIGR02051 MerR Hg(II)-responsi 20.5 99 0.0021 22.0 2.5 21 127-147 1-21 (124)
167 cd00592 HTH_MerR-like Helix-Tu 20.5 1.1E+02 0.0023 20.6 2.6 21 127-147 2-22 (100)
168 PRK14584 hmsS hemin storage sy 20.5 2.3E+02 0.0049 21.4 4.4 34 127-160 100-139 (153)
169 cd04784 HTH_CadR-PbrR Helix-Tu 20.2 1E+02 0.0022 21.9 2.5 22 127-148 2-23 (127)
170 COG1102 Cmk Cytidylate kinase 20.2 62 0.0013 24.9 1.4 28 122-149 29-59 (179)
171 PF12728 HTH_17: Helix-turn-he 20.1 1.2E+02 0.0027 17.4 2.5 34 127-160 3-40 (51)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.96 E-value=1.6e-28 Score=218.08 Aligned_cols=180 Identities=15% Similarity=0.211 Sum_probs=137.5
Q ss_pred ChhHHHHcCCCHHHHHhcCCCCCCCCCCCCCCEEEEcCccccCC--------C--------ccccCceEEEecCCCcHHH
Q 047095 1 MTFISEMFDTSIDNILSFNPQVPDKDILSVGSRIKVPFKCNCIN--------G--------QFLANNFSYKIISHDTYAK 64 (188)
Q Consensus 1 L~~IA~~~gvs~~~l~~~Np~l~~~~~l~~Gq~L~IP~~~~~~~--------~--------~~~~~~~~Y~V~~GDTL~~ 64 (188)
|+.||++|||++++|+++| ++.. +.|.+||.|+||....... . ........|+|++||||+.
T Consensus 341 L~~IA~rygvSv~eL~~~N-~l~~-d~L~~Gq~L~VP~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~ytVk~GDTL~s 418 (592)
T PRK06347 341 LWRIANNHKVTVANLKAWN-NLKS-DFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGTSTNAKVYTVVKGDSLWR 418 (592)
T ss_pred HHHHHHHhCCCHHHHHHHh-CCCc-cccccCcEEEEeccccccccccccccccccccccccccccCceeEEecCCCCHHH
Confidence 6899999999999999999 6864 7899999999997421100 0 0112356899999999999
Q ss_pred HHHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEcccCCCCCC---c---------ccCCccceEEEEeecCCcHHHHH
Q 047095 65 VAETYYANLTTVDWLRANNIFPDNNIPDVNTTINVVVNCSCGDK---K---------VSKDYGLFLTYPIELGENLSTIA 132 (188)
Q Consensus 65 IA~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP~~~~~~~~---~---------~~~~~~~~~~y~V~~GDTl~~IA 132 (188)
||+ +|++ ++++|+++|++..+.+.+ ||.|.||........ . ..........|+|++|||||+||
T Consensus 419 IA~-kygV--Sv~~L~~~N~l~s~~L~~-Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sIA 494 (592)
T PRK06347 419 IAN-NNKV--TIANLKSWNNLKSDFIYP-GQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIA 494 (592)
T ss_pred HHH-HhCC--CHHHHHHHhCCCcceecc-CcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHHH
Confidence 997 8985 999999999987778999 999999975321000 0 00011224679999999999999
Q ss_pred HHhCCCHHHHHhhcCCCC--CC-CCEEEEcCCCCCCC--------------CCCcccCCCCCcHHHhhhhh
Q 047095 133 NMSGLSPELLQSYNRGSD--FS-SGLVFIPEKDQSGK--------------YPPLQMSRDGTDFFECASLL 186 (188)
Q Consensus 133 ~~~~vs~~~l~~~N~~~~--~~-g~~l~iP~~~~~~~--------------~~p~~~~~~~~~~~~~~~~~ 186 (188)
++||+++++|++||++.+ +. ||.|.||....... ..-.+.++.|||+|.||+-.
T Consensus 495 kkygVSv~~L~~~N~l~s~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDTL~sIA~Ky 565 (592)
T PRK06347 495 NNNKVTIANLKSWNNLKSDFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDSLWAISRQY 565 (592)
T ss_pred HHHCCCHHHHHHhcCCCcccccCCcEEEEecCcccccccccCCccCCccCccceeeecCCCCcHHHHHHHh
Confidence 999999999999999865 55 99999998643211 01235678999999999853
No 2
>PRK06347 autolysin; Reviewed
Probab=99.95 E-value=3.9e-27 Score=209.31 Aligned_cols=153 Identities=16% Similarity=0.217 Sum_probs=120.4
Q ss_pred ChhHHHHcCCCHHHHHhcCCCCCCCCCCCCCCEEEEcCccccCC----------C-----ccccCceEEEecCCCcHHHH
Q 047095 1 MTFISEMFDTSIDNILSFNPQVPDKDILSVGSRIKVPFKCNCIN----------G-----QFLANNFSYKIISHDTYAKV 65 (188)
Q Consensus 1 L~~IA~~~gvs~~~l~~~Np~l~~~~~l~~Gq~L~IP~~~~~~~----------~-----~~~~~~~~Y~V~~GDTL~~I 65 (188)
|+.||++|||++++|+++| .+.. +.|.+||.|+||....... . ........|+|++|||||+|
T Consensus 416 L~sIA~kygVSv~~L~~~N-~l~s-~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sI 493 (592)
T PRK06347 416 LWRIANNNKVTIANLKSWN-NLKS-DFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRI 493 (592)
T ss_pred HHHHHHHhCCCHHHHHHHh-CCCc-ceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHH
Confidence 5789999999999999999 6864 6799999999996432100 0 00112457999999999999
Q ss_pred HHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEcccCCCCCCc------ccCCccceEEEEeecCCcHHHHHHHhCCCH
Q 047095 66 AETYYANLTTVDWLRANNIFPDNNIPDVNTTINVVVNCSCGDKK------VSKDYGLFLTYPIELGENLSTIANMSGLSP 139 (188)
Q Consensus 66 A~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP~~~~~~~~~------~~~~~~~~~~y~V~~GDTl~~IA~~~~vs~ 139 (188)
|+ +|+. ++++|++||++..+.|++ ||.|.||......... ..........|+|++|||||+||++||+++
T Consensus 494 Ak-kygV--Sv~~L~~~N~l~s~~L~~-GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDTL~sIA~KygvSv 569 (592)
T PRK06347 494 AN-NNKV--TIANLKSWNNLKSDFIYP-GQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDSLWAISRQYKTTV 569 (592)
T ss_pred HH-HHCC--CHHHHHHhcCCCcccccC-CcEEEEecCcccccccccCCccCCccCccceeeecCCCCcHHHHHHHhCCCH
Confidence 97 8985 999999999997788999 9999999754321100 000112246899999999999999999999
Q ss_pred HHHHhhcCCCC--CC-CCEEEEc
Q 047095 140 ELLQSYNRGSD--FS-SGLVFIP 159 (188)
Q Consensus 140 ~~l~~~N~~~~--~~-g~~l~iP 159 (188)
++|++||++.. ++ ||+|.|+
T Consensus 570 ~~L~~~N~L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 570 DNIKAWNKLTSNMIHVGQKLTIK 592 (592)
T ss_pred HHHHHhcCCCcccCCCCCEEecC
Confidence 99999999875 55 9999885
No 3
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.94 E-value=6e-26 Score=197.59 Aligned_cols=156 Identities=21% Similarity=0.231 Sum_probs=122.5
Q ss_pred ChhHHHHcCCCHHHHHhcCCCCCCCCCCCCC-CEEEEcCccccC------C-------Cc-----cccCceEEEecCCCc
Q 047095 1 MTFISEMFDTSIDNILSFNPQVPDKDILSVG-SRIKVPFKCNCI------N-------GQ-----FLANNFSYKIISHDT 61 (188)
Q Consensus 1 L~~IA~~~gvs~~~l~~~Np~l~~~~~l~~G-q~L~IP~~~~~~------~-------~~-----~~~~~~~Y~V~~GDT 61 (188)
|..||+++||++++|+++||+++.....+.| +.|+||...... . .. .......|+|++|||
T Consensus 274 L~~iA~~~gvs~~eL~~LNP~~kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p~~~~~~~~~~~~~y~Vk~GDT 353 (456)
T PRK10783 274 LAQAAEMAGMSLTKLKTFNAGYKRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQSTLVADNTPLNSRSYKVRSGDT 353 (456)
T ss_pred HHHHHHHcCCCHHHHHHhCccccCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhcccccccccCcCCceEEEECCCCc
Confidence 5689999999999999999998764333345 788999864310 0 00 011356899999999
Q ss_pred HHHHHHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEcccCCCCCCcccCCccceEEEEeecCCcHHHHHHHhCCCHHH
Q 047095 62 YAKVAETYYANLTTVDWLRANNIFPDNNIPDVNTTINVVVNCSCGDKKVSKDYGLFLTYPIELGENLSTIANMSGLSPEL 141 (188)
Q Consensus 62 L~~IA~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~IA~~~~vs~~~ 141 (188)
|++||+ +|+. ++++|.++|++..+.+.+ ||.|.||..+.+.... ......+|+|++|||||+||++|||++++
T Consensus 354 L~sIA~-r~gv--s~~~L~~~N~l~~~~L~~-Gq~L~Ip~~~~~~~~~---~~~~~~~Y~Vr~GDTL~sIA~kygVtv~~ 426 (456)
T PRK10783 354 LSGIAS-RLNV--STKDLQQWNNLRGSKLKV-GQTLTIGAGSSAQRLA---NNSDSITYRVRKGDSLSSIAKRHGVNIKD 426 (456)
T ss_pred HHHHHH-HHCc--CHHHHHHHcCCCcccCCC-CCEEEecCCccccccc---ccccceeEEeCCCCCHHHHHHHhCCCHHH
Confidence 999997 8985 999999999986678999 9999999876543211 11234689999999999999999999999
Q ss_pred HHhhcCCCC--CC-CCEEEEcCCCC
Q 047095 142 LQSYNRGSD--FS-SGLVFIPEKDQ 163 (188)
Q Consensus 142 l~~~N~~~~--~~-g~~l~iP~~~~ 163 (188)
|++||++.. ++ ||+|.|++...
T Consensus 427 L~~~N~l~~~~L~pGq~L~l~v~~~ 451 (456)
T PRK10783 427 VMRWNSDTAKNLQPGDKLTLFVKNN 451 (456)
T ss_pred HHHhcCCCCCcCCCCCEEEEecCCC
Confidence 999999764 55 99999887653
No 4
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.65 E-value=2.2e-15 Score=130.50 Aligned_cols=109 Identities=17% Similarity=0.147 Sum_probs=85.9
Q ss_pred CceEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEcccCCC-----------------CC-----
Q 047095 50 NNFSYKIISHDTYAKVAETYYANLTTVDWLRANNIFPDNNIPDVNTTINVVVNCSC-----------------GD----- 107 (188)
Q Consensus 50 ~~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP~~~~~-----------------~~----- 107 (188)
....|+|++|||||.||+ +|+. ++++|+++|++.++.|.+ ||.|.||..... +.
T Consensus 26 sa~tytVq~GDTLw~IA~-~ygv--tv~~I~~~N~l~~~~I~~-Gq~L~Ip~~~~~~~~~~~Vta~~LNVRsgps~s~~I 101 (481)
T PRK13914 26 SASTVVVEAGDTLWGIAQ-SKGT--TVDAIKKANNLTTDKIVP-GQKLQVNEVAAAEKTEKSVSATWLNVRSGAGVDNSI 101 (481)
T ss_pred cCceEEECCCCCHHHHHH-HHCC--CHHHHHHHhCCCcccccC-CCEEEeCCCCcccccceeEecceEEEecCCCCCcce
Confidence 346799999999999997 8985 999999999998889999 999999843100 00
Q ss_pred ---------------Cc-----------------------------ccC-------------------------------
Q 047095 108 ---------------KK-----------------------------VSK------------------------------- 112 (188)
Q Consensus 108 ---------------~~-----------------------------~~~------------------------------- 112 (188)
.+ +.+
T Consensus 102 Igsl~~G~~V~Vl~~~~ngW~kI~~~~GktGwV~~~YLs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 181 (481)
T PRK13914 102 ITSIKGGTKVTVETTESNGWHKITYNDGKTGFVNGKYLTDKVTSTPVAPTQEVKKETTTQQAAPAAETKTEVKQTTQATT 181 (481)
T ss_pred eeeecCCCEEEEeecccCCeEEEEcCCCCEEEEecccccCCCccCccccchhhhhccccccccchhcccchhccCCcccC
Confidence 00 000
Q ss_pred -------------CccceEEEEeecCCcHHHHHHHhCCCHHHHHhhcCCCC--CC-CCEEEEcCCC
Q 047095 113 -------------DYGLFLTYPIELGENLSTIANMSGLSPELLQSYNRGSD--FS-SGLVFIPEKD 162 (188)
Q Consensus 113 -------------~~~~~~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~~--~~-g~~l~iP~~~ 162 (188)
.......|+|++|||||+||++|++++++|++||++.+ +. |+.|.||...
T Consensus 182 ~~~~~~~~~~~~~~~~~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s~~L~pGQ~L~Ip~sa 247 (481)
T PRK13914 182 PAPKVAETKETPVVDQNATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAIKQTA 247 (481)
T ss_pred CcccccccccCccccCCCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCccccCCCCEEEecCCC
Confidence 00012589999999999999999999999999999875 44 9999999764
No 5
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.64 E-value=1.3e-15 Score=133.08 Aligned_cols=97 Identities=12% Similarity=0.195 Sum_probs=80.8
Q ss_pred ChhHHHHcCCCHHHHHhcCCCCCCCCCCCCCCEEEEcCccccCCCccccCceEEEecCCCcHHHHHHHHcCCCCCHHHHH
Q 047095 1 MTFISEMFDTSIDNILSFNPQVPDKDILSVGSRIKVPFKCNCINGQFLANNFSYKIISHDTYAKVAETYYANLTTVDWLR 80 (188)
Q Consensus 1 L~~IA~~~gvs~~~l~~~Np~l~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~ 80 (188)
|+.||++||+++++|+++| .+.. +.|.+||.|.||..+.+...........|+|++||||++||+ +|++ ++++|+
T Consensus 354 L~sIA~r~gvs~~~L~~~N-~l~~-~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vr~GDTL~sIA~-kygV--tv~~L~ 428 (456)
T PRK10783 354 LSGIASRLNVSTKDLQQWN-NLRG-SKLKVGQTLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAK-RHGV--NIKDVM 428 (456)
T ss_pred HHHHHHHHCcCHHHHHHHc-CCCc-ccCCCCCEEEecCCcccccccccccceeEEeCCCCCHHHHHH-HhCC--CHHHHH
Confidence 5789999999999999999 5765 789999999999876553222222456899999999999997 8985 999999
Q ss_pred HhCCCCCCCccCCCcEEEEcccC
Q 047095 81 ANNIFPDNNIPDVNTTINVVVNC 103 (188)
Q Consensus 81 ~~N~l~~~~i~~~Gq~L~IP~~~ 103 (188)
+||++..+.|++ ||+|.|+...
T Consensus 429 ~~N~l~~~~L~p-Gq~L~l~v~~ 450 (456)
T PRK10783 429 RWNSDTAKNLQP-GDKLTLFVKN 450 (456)
T ss_pred HhcCCCCCcCCC-CCEEEEecCC
Confidence 999975458999 9999998753
No 6
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.31 E-value=1.2e-11 Score=107.57 Aligned_cols=48 Identities=15% Similarity=0.086 Sum_probs=43.6
Q ss_pred ceEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEccc
Q 047095 51 NFSYKIISHDTYAKVAETYYANLTTVDWLRANNIFPDNNIPDVNTTINVVVN 102 (188)
Q Consensus 51 ~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP~~ 102 (188)
...|+|++|||||.||+ +|+. ++++|.++|++..+.|++ ||.|.||..
T Consensus 199 a~tytVq~GDTL~sIAk-rYgV--tv~eI~~~N~l~s~~L~p-GQ~L~Ip~s 246 (481)
T PRK13914 199 ATTHAVKSGDTIWALSV-KYGV--SVQDIMSWNNLSSSSIYV-GQKLAIKQT 246 (481)
T ss_pred CeEEEECCCCCHHHHHH-HHCC--CHHHHHHhcCCCccccCC-CCEEEecCC
Confidence 46899999999999997 8985 999999999997778999 999999975
No 7
>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=99.29 E-value=3e-12 Score=76.44 Aligned_cols=40 Identities=28% Similarity=0.443 Sum_probs=31.9
Q ss_pred EEeecCCcHHHHHHHhCCCHHHHHhhcCCC-C--CC-CCEEEEc
Q 047095 120 YPIELGENLSTIANMSGLSPELLQSYNRGS-D--FS-SGLVFIP 159 (188)
Q Consensus 120 y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~-~--~~-g~~l~iP 159 (188)
|+|++|||+|+||++||++.++|+++|+.. . +. |+.|.||
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 899999999999999999999999999443 2 44 9999998
No 8
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.27 E-value=2.4e-11 Score=88.42 Aligned_cols=92 Identities=22% Similarity=0.270 Sum_probs=70.6
Q ss_pred HHHHHcCCCCCHHHHHHhCCCC--CCCccCCCcEEEEcccCCCCCC--cc--cCCc-----------cceEEEEeecCCc
Q 047095 65 VAETYYANLTTVDWLRANNIFP--DNNIPDVNTTINVVVNCSCGDK--KV--SKDY-----------GLFLTYPIELGEN 127 (188)
Q Consensus 65 IA~~~y~~l~s~~~L~~~N~l~--~~~i~~~Gq~L~IP~~~~~~~~--~~--~~~~-----------~~~~~y~V~~GDT 127 (188)
||. +|+. ++++|.++|.+. .+.+.+ ||+|.+|........ .. .... ....+|+|++|||
T Consensus 1 ia~-~~~~--~v~~l~~~n~~~~~s~~i~~-gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdt 76 (124)
T COG1388 1 IAS-KYGV--SVKALKKANALTGKSDAIKP-GQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDT 76 (124)
T ss_pred Ccc-cccc--cHHHHHHHhcccCCCCcccc-CceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCC
Confidence 454 6775 899999999987 788999 999999964221111 10 0000 1135799999999
Q ss_pred HHHHHHHhCCCHHHHHhhcCCCCCC---CCEEEEcC
Q 047095 128 LSTIANMSGLSPELLQSYNRGSDFS---SGLVFIPE 160 (188)
Q Consensus 128 l~~IA~~~~vs~~~l~~~N~~~~~~---g~~l~iP~ 160 (188)
|+.||++|++++.+|+++|++.+.. ||.|.+|.
T Consensus 77 L~~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~~ 112 (124)
T COG1388 77 LSKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLPV 112 (124)
T ss_pred HHHHHHHhCCCHHHHHHHhccCCCceecCcEEEEec
Confidence 9999999999999999999998733 99999987
No 9
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.26 E-value=2.5e-11 Score=88.34 Aligned_cols=94 Identities=22% Similarity=0.338 Sum_probs=74.9
Q ss_pred HHHHcCCCHHHHHhcCCCCCC-CCCCCCCCEEEEcCcccc--CCCc----cc------------cCceEEEecCCCcHHH
Q 047095 4 ISEMFDTSIDNILSFNPQVPD-KDILSVGSRIKVPFKCNC--INGQ----FL------------ANNFSYKIISHDTYAK 64 (188)
Q Consensus 4 IA~~~gvs~~~l~~~Np~l~~-~~~l~~Gq~L~IP~~~~~--~~~~----~~------------~~~~~Y~V~~GDTL~~ 64 (188)
||.+|++++++|+++| .+.. .+.+.+||.|.+|..... ..+. .. .....|+|++||||+.
T Consensus 1 ia~~~~~~v~~l~~~n-~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~~ 79 (124)
T COG1388 1 IASKYGVSVKALKKAN-ALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLSK 79 (124)
T ss_pred CcccccccHHHHHHHh-cccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHHH
Confidence 6889999999999999 7763 578899999999963111 1110 00 1135799999999999
Q ss_pred HHHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEccc
Q 047095 65 VAETYYANLTTVDWLRANNIFPDNNIPDVNTTINVVVN 102 (188)
Q Consensus 65 IA~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP~~ 102 (188)
||+ +|+. ++.+|.++|.+..+.+++ ||.|.+|..
T Consensus 80 Ia~-~~~~--tv~~l~~~n~l~~~~i~~-gq~l~~~~~ 113 (124)
T COG1388 80 IAR-KYGV--TVAELKQLNNLSSDKIKV-GQKLKLPVS 113 (124)
T ss_pred HHH-HhCC--CHHHHHHHhccCCCceec-CcEEEEecc
Confidence 997 7885 999999999998779999 999999874
No 10
>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=99.23 E-value=1.2e-11 Score=73.74 Aligned_cols=43 Identities=23% Similarity=0.306 Sum_probs=34.5
Q ss_pred EEecCCCcHHHHHHHHcCCCCCHHHHHHhC-CCCCCCccCCCcEEEEc
Q 047095 54 YKIISHDTYAKVAETYYANLTTVDWLRANN-IFPDNNIPDVNTTINVV 100 (188)
Q Consensus 54 Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N-~l~~~~i~~~Gq~L~IP 100 (188)
|+|++|||+++||+ +|+. +.++|+++| .+..+.|.+ ||+|.||
T Consensus 1 y~V~~gDtl~~IA~-~~~~--~~~~l~~~N~~~~~~~l~~-G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAK-RYGI--SVDELMELNPNIDSDNLQP-GQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHH-HTTS---HHHHHHHCCTTHGGCGGT-TEEEEEC
T ss_pred CEECcCCcHHHHHh-hhhh--hHhHHHHhcCCCCcccCCC-CCEEEeC
Confidence 89999999999997 8975 999999999 565555999 9999998
No 11
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.05 E-value=5.9e-10 Score=78.62 Aligned_cols=53 Identities=21% Similarity=0.338 Sum_probs=43.3
Q ss_pred CceEEEecCCCcHHHHHHHHcCCC--CC----HHHHHHhCCCCCCCccCCCcEEEEcccCC
Q 047095 50 NNFSYKIISHDTYAKVAETYYANL--TT----VDWLRANNIFPDNNIPDVNTTINVVVNCS 104 (188)
Q Consensus 50 ~~~~Y~V~~GDTL~~IA~~~y~~l--~s----~~~L~~~N~l~~~~i~~~Gq~L~IP~~~~ 104 (188)
.+..|+|++|||||+||+ +|+.- ++ +++|++.|.+.++.|++ ||.|.||...+
T Consensus 35 ~~~~~tV~~GDTLW~IA~-~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~-Gq~L~IP~~~~ 93 (103)
T PRK14125 35 QYVEITVQEGDTLWALAD-QYAGKHHMAKNEFIEWVEDVNNLPSGHIKA-GDKLVIPVLKS 93 (103)
T ss_pred CcEEEEECCCCCHHHHHH-HhCCCcCCCHHHHHHHHHHhcCCCCCcCCC-CCEEEEecCCC
Confidence 567899999999999997 78741 01 57788899998778999 99999997643
No 12
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.98 E-value=1.5e-09 Score=76.58 Aligned_cols=48 Identities=15% Similarity=0.235 Sum_probs=40.1
Q ss_pred eEEEEeecCCcHHHHHHHhCCC--------HHHHHhhcCCCC--CC-CCEEEEcCCCCC
Q 047095 117 FLTYPIELGENLSTIANMSGLS--------PELLQSYNRGSD--FS-SGLVFIPEKDQS 164 (188)
Q Consensus 117 ~~~y~V~~GDTl~~IA~~~~vs--------~~~l~~~N~~~~--~~-g~~l~iP~~~~~ 164 (188)
..+|+|++|||||+||++|+.+ +++|++.|++.+ +. |+.|.||.....
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 4789999999999999999864 577788898765 45 999999987654
No 13
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=98.90 E-value=2.1e-09 Score=63.47 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=33.8
Q ss_pred eecCCcHHHHHHHhCCCHHHHHhhcCCC-C---CC-CCEEEEcC
Q 047095 122 IELGENLSTIANMSGLSPELLQSYNRGS-D---FS-SGLVFIPE 160 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~~N~~~-~---~~-g~~l~iP~ 160 (188)
|++|||||+||++|+++.++|.++|+.. + +. |++|+||.
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 6889999999999999999999999843 2 33 99999983
No 14
>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=98.87 E-value=5.6e-09 Score=61.06 Aligned_cols=41 Identities=39% Similarity=0.502 Sum_probs=36.8
Q ss_pred EEEeecCCcHHHHHHHhCCCHHHHHhhcCCCC---CC-CCEEEEc
Q 047095 119 TYPIELGENLSTIANMSGLSPELLQSYNRGSD---FS-SGLVFIP 159 (188)
Q Consensus 119 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~~---~~-g~~l~iP 159 (188)
.|+|++|||+|+||++|+++..+|.++|+..+ +. |+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 59999999999999999999999999999843 44 9998887
No 15
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=98.79 E-value=8.6e-09 Score=85.58 Aligned_cols=45 Identities=22% Similarity=0.313 Sum_probs=40.3
Q ss_pred cceEEEEeecCCcHHHHHHHhCCCHHHHHhhcCCCC--CC-CCEEEEc
Q 047095 115 GLFLTYPIELGENLSTIANMSGLSPELLQSYNRGSD--FS-SGLVFIP 159 (188)
Q Consensus 115 ~~~~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~~--~~-g~~l~iP 159 (188)
..+..|+|++|||||+||++||++++.|+++|++.. +. |++|+||
T Consensus 291 ~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 291 TKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred cccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 345789999999999999999999999999998765 44 9999998
No 16
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.74 E-value=1.7e-08 Score=85.95 Aligned_cols=95 Identities=18% Similarity=0.219 Sum_probs=78.0
Q ss_pred eEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEcccCCCCCCcccCCccceEEEEeecCCcHHHH
Q 047095 52 FSYKIISHDTYAKVAETYYANLTTVDWLRANNIFPDNNIPDVNTTINVVVNCSCGDKKVSKDYGLFLTYPIELGENLSTI 131 (188)
Q Consensus 52 ~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP~~~~~~~~~~~~~~~~~~~y~V~~GDTl~~I 131 (188)
..|.|++||++..|++ +|.. +...|...|....+.+.. ||.+.||.. ...|.|++|||+++|
T Consensus 2 ~i~~~~pg~~~~~i~~-~~~~--~~~~i~~~~~~~~d~~~~-~q~~~v~~~--------------~~~y~~~~~d~~~Si 63 (423)
T COG3858 2 SIHLVGPGDSRLIIAV-YFPY--TNNRIVNGNDYTNDDLVD-GQTFVVPPS--------------GHFYDVGPGDTLTSI 63 (423)
T ss_pred EEEEccCCceeeeehh-hccc--cccccccccccccccccC-ceeEEECCc--------------ceEEEecCCcchhhh
Confidence 3689999999999997 8986 777886666654577888 999999963 157999999999999
Q ss_pred HHHhCCCHHHHHhhcCCCC---CC-CCEEEEcCCCCC
Q 047095 132 ANMSGLSPELLQSYNRGSD---FS-SGLVFIPEKDQS 164 (188)
Q Consensus 132 A~~~~vs~~~l~~~N~~~~---~~-g~~l~iP~~~~~ 164 (188)
|++|+++++.+...|.... +. |-.+.+|-....
T Consensus 64 a~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~~~ 100 (423)
T COG3858 64 ARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSARKT 100 (423)
T ss_pred hhhhcCCHHHHHhhcccccccceeeeeEEeccCCCCC
Confidence 9999999999999998754 33 778888876544
No 17
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=98.74 E-value=1.8e-08 Score=83.69 Aligned_cols=49 Identities=18% Similarity=0.208 Sum_probs=44.6
Q ss_pred ccCceEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCCCCCCccCCCcEEEEc
Q 047095 48 LANNFSYKIISHDTYAKVAETYYANLTTVDWLRANNIFPDNNIPDVNTTINVV 100 (188)
Q Consensus 48 ~~~~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l~~~~i~~~Gq~L~IP 100 (188)
+..+..|+|++|||||+||+ +|++ +++.|+++|++.++.|.+ ||.|.||
T Consensus 290 ~~~~~~YiVq~GDTL~sIAk-RYGV--SV~~L~r~N~L~~~~L~~-GQ~L~IP 338 (338)
T TIGR02907 290 FTKLRMCIVQEGDTIETIAE-RYEI--SVSQLIRHNQLEDFEVNE-GQILYIP 338 (338)
T ss_pred ccccEEEEECCCCCHHHHHH-HHCc--CHHHHHHHhCCCccccCC-CCEEEeC
Confidence 34678999999999999997 8985 999999999988788999 9999998
No 18
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=98.71 E-value=2.3e-08 Score=58.90 Aligned_cols=42 Identities=26% Similarity=0.213 Sum_probs=36.0
Q ss_pred ecCCCcHHHHHHHHcCCCCCHHHHHHhCC-C-CCCCccCCCcEEEEcc
Q 047095 56 IISHDTYAKVAETYYANLTTVDWLRANNI-F-PDNNIPDVNTTINVVV 101 (188)
Q Consensus 56 V~~GDTL~~IA~~~y~~l~s~~~L~~~N~-l-~~~~i~~~Gq~L~IP~ 101 (188)
|++|||||+||+ +|+. ++++|.++|+ + ++..+.+ ||.|.||.
T Consensus 1 v~~gdtl~~IA~-~~~~--~~~~l~~~N~~~~~~~~~~~-g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAK-KYGV--DFDELIQANPQLSNPNLIYP-GMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHH-HHCc--CHHHHHHHhhcCCCCCCcCC-CCEEecCC
Confidence 578999999997 8985 8999999997 4 3567889 99999983
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=98.70 E-value=4.6e-08 Score=57.04 Aligned_cols=44 Identities=20% Similarity=0.313 Sum_probs=39.2
Q ss_pred EEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCC-CCCCccCCCcEEEEc
Q 047095 53 SYKIISHDTYAKVAETYYANLTTVDWLRANNIF-PDNNIPDVNTTINVV 100 (188)
Q Consensus 53 ~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l-~~~~i~~~Gq~L~IP 100 (188)
.|+|++|||+++||+ +|+. +..+|.++|+. ....+.+ |+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~-~~~~--~~~~~~~~N~~~~~~~~~~-g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQ-RYGI--SVEELLKLNGLSDPDNLQV-GQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHH-HHCc--CHHHHHHHcCCCCccccCC-CCEEecC
Confidence 699999999999997 8875 89999999998 5677888 9999887
No 20
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.67 E-value=2.6e-08 Score=83.16 Aligned_cols=44 Identities=20% Similarity=0.206 Sum_probs=40.0
Q ss_pred EEEEeecCCcHHHHHHHhCCCHHHHHhhcCCCC---CC-CCEEEEcCC
Q 047095 118 LTYPIELGENLSTIANMSGLSPELLQSYNRGSD---FS-SGLVFIPEK 161 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~~---~~-g~~l~iP~~ 161 (188)
.+|+|++|||||+||.+||+++.+|.+||++.+ +. ||+|.||..
T Consensus 61 ~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 61 STYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNA 108 (319)
T ss_pred CceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCCC
Confidence 479999999999999999999999999999976 44 999999764
No 21
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.63 E-value=4.2e-08 Score=81.88 Aligned_cols=48 Identities=19% Similarity=0.104 Sum_probs=42.9
Q ss_pred ceEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCC-CCCCccCCCcEEEEccc
Q 047095 51 NFSYKIISHDTYAKVAETYYANLTTVDWLRANNIF-PDNNIPDVNTTINVVVN 102 (188)
Q Consensus 51 ~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l-~~~~i~~~Gq~L~IP~~ 102 (188)
..+|+|++|||||.||. .|+. ++.+|.++|++ ++..|++ ||.|.||..
T Consensus 60 ~~~y~Vk~GDTL~~IA~-~~g~--~~~~La~~N~l~~p~~I~~-GQ~L~i~~~ 108 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAW-ITGN--DFRDLAQRNNIQAPYSLNV-GQTLQVGNA 108 (319)
T ss_pred CCceEECCCCHHHHHHH-HHCc--CHHHHHHhcCCCCCccccC-CCEEEeCCC
Confidence 35799999999999996 8985 99999999998 5788999 999999754
No 22
>smart00257 LysM Lysin motif.
Probab=98.48 E-value=2.8e-07 Score=52.95 Aligned_cols=39 Identities=31% Similarity=0.360 Sum_probs=32.8
Q ss_pred EEEeecCCcHHHHHHHhCCCHHHHHhhcCCCC---CC-CCEEE
Q 047095 119 TYPIELGENLSTIANMSGLSPELLQSYNRGSD---FS-SGLVF 157 (188)
Q Consensus 119 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~~---~~-g~~l~ 157 (188)
+|+|++|||+|+||++|+++.++|.++|+..+ +. |+.+.
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ 43 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLK 43 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEe
Confidence 38999999999999999999999999999533 33 66654
No 23
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.42 E-value=4.7e-07 Score=67.95 Aligned_cols=50 Identities=18% Similarity=0.265 Sum_probs=40.1
Q ss_pred CceEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCC--C-CCCCccCCCcEEEEc
Q 047095 50 NNFSYKIISHDTYAKVAETYYANLTTVDWLRANNI--F-PDNNIPDVNTTINVV 100 (188)
Q Consensus 50 ~~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~--l-~~~~i~~~Gq~L~IP 100 (188)
....|+|++|||||+||++.|+....+..|.++|+ + +++.|.+ ||.|.||
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~p-Gq~L~IP 146 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYP-GQVLRIP 146 (147)
T ss_pred CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCc-CCEEecC
Confidence 34689999999999999843443235778999997 5 4678999 9999998
No 24
>smart00257 LysM Lysin motif.
Probab=98.33 E-value=1.4e-06 Score=50.00 Aligned_cols=43 Identities=21% Similarity=0.308 Sum_probs=36.2
Q ss_pred EEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCC-CCCCccCCCcEEEE
Q 047095 53 SYKIISHDTYAKVAETYYANLTTVDWLRANNIF-PDNNIPDVNTTINV 99 (188)
Q Consensus 53 ~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l-~~~~i~~~Gq~L~I 99 (188)
.|+|++|||+++||+ +|+. +..+|.++|+. ....+.+ |+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~-~~~~--~~~~~~~~N~~~~~~~~~~-g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIAR-RYGI--SVSDLLELNNILDPDNLQV-GQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHH-HhCC--CHHHHHHHcCCCCccccCC-CCEEeC
Confidence 389999999999997 8886 88999999994 4567888 988764
No 25
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.27 E-value=1.2e-06 Score=74.80 Aligned_cols=85 Identities=19% Similarity=0.154 Sum_probs=73.2
Q ss_pred hhHHHHcCCCHHHHHhcCCCCCCCCCCCCCCEEEEcCccccCCCccccCceEEEecCCCcHHHHHHHHcCCCCCHHHHHH
Q 047095 2 TFISEMFDTSIDNILSFNPQVPDKDILSVGSRIKVPFKCNCINGQFLANNFSYKIISHDTYAKVAETYYANLTTVDWLRA 81 (188)
Q Consensus 2 ~~IA~~~gvs~~~l~~~Np~l~~~~~l~~Gq~L~IP~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~ 81 (188)
..|+++|+.+..+|...| .+.. +.+..||.+.||.. ...|.|++|||+++||+ ++++ +.+.+..
T Consensus 13 ~~i~~~~~~~~~~i~~~~-~~~~-d~~~~~q~~~v~~~-----------~~~y~~~~~d~~~Sia~-~~~v--t~~~~~~ 76 (423)
T COG3858 13 LIIAVYFPYTNNRIVNGN-DYTN-DDLVDGQTFVVPPS-----------GHFYDVGPGDTLTSIAR-TVGV--TQDSAAI 76 (423)
T ss_pred eeehhhcccccccccccc-cccc-ccccCceeEEECCc-----------ceEEEecCCcchhhhhh-hhcC--CHHHHHh
Confidence 468999999999998888 7877 88999999999974 35899999999999997 8885 9999999
Q ss_pred hCCC-CCCCccCCCcEEEEcccC
Q 047095 82 NNIF-PDNNIPDVNTTINVVVNC 103 (188)
Q Consensus 82 ~N~l-~~~~i~~~Gq~L~IP~~~ 103 (188)
+|.. .+..+.. |-.+.+|...
T Consensus 77 m~~~~~~~~l~~-~~~l~~P~~~ 98 (423)
T COG3858 77 MNFVICPGYLQY-GLNLYIPSAR 98 (423)
T ss_pred hcccccccceee-eeEEeccCCC
Confidence 9986 4667888 9999998643
No 26
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.17 E-value=2.9e-06 Score=63.69 Aligned_cols=42 Identities=21% Similarity=0.223 Sum_probs=35.1
Q ss_pred EEEEeecCCcHHHHHHHhC---CCHHHHHhhcC--CCC---CC-CCEEEEc
Q 047095 118 LTYPIELGENLSTIANMSG---LSPELLQSYNR--GSD---FS-SGLVFIP 159 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~~~~---vs~~~l~~~N~--~~~---~~-g~~l~iP 159 (188)
.+|+|++|||||+||++|. .....|.++|+ +.+ +. |++|.||
T Consensus 96 ~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 96 QFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred eEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 5799999999999999984 35689999997 544 33 9999998
No 27
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.48 E-value=0.00028 Score=58.77 Aligned_cols=47 Identities=26% Similarity=0.288 Sum_probs=41.0
Q ss_pred cceEEEEeecCC--cHHHHHHHhCCCHHHHHhhcCCCCC---C-CCEEEEcCC
Q 047095 115 GLFLTYPIELGE--NLSTIANMSGLSPELLQSYNRGSDF---S-SGLVFIPEK 161 (188)
Q Consensus 115 ~~~~~y~V~~GD--Tl~~IA~~~~vs~~~l~~~N~~~~~---~-g~~l~iP~~ 161 (188)
+....|+|+++| +|..||++|++...+|+++|+..++ . |+.|.||..
T Consensus 35 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 35 GQSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQ 87 (310)
T ss_pred cceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence 445789999966 5999999999999999999999984 3 999999975
No 28
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.47 E-value=4.5e-05 Score=62.66 Aligned_cols=50 Identities=10% Similarity=0.137 Sum_probs=43.4
Q ss_pred eEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCC---C-CCCCccCCCcEEEEccc
Q 047095 52 FSYKIISHDTYAKVAETYYANLTTVDWLRANNI---F-PDNNIPDVNTTINVVVN 102 (188)
Q Consensus 52 ~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~---l-~~~~i~~~Gq~L~IP~~ 102 (188)
.+|+|++|||||.||++.|+..+.+..|..+|. + +++.|.+ ||.|.||..
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~p-Gq~l~iP~~ 264 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKP-GQVLRIPDQ 264 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCC-cceeeCCCc
Confidence 389999999999999988987656677999999 4 5789999 999999964
No 29
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.46 E-value=0.00031 Score=58.42 Aligned_cols=47 Identities=21% Similarity=0.252 Sum_probs=40.7
Q ss_pred cceEEEEeecCC--cHHHHHHHhCCCHHHHHhhcCCCC--C-C-CCEEEEcCC
Q 047095 115 GLFLTYPIELGE--NLSTIANMSGLSPELLQSYNRGSD--F-S-SGLVFIPEK 161 (188)
Q Consensus 115 ~~~~~y~V~~GD--Tl~~IA~~~~vs~~~l~~~N~~~~--~-~-g~~l~iP~~ 161 (188)
+....|+|++|| +|..||++|++...+|+++|+..+ + . |++|.||..
T Consensus 38 G~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 38 GQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQ 90 (306)
T ss_pred cccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence 344689999966 599999999999999999999988 3 3 999999985
No 30
>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=96.87 E-value=0.0015 Score=44.40 Aligned_cols=48 Identities=17% Similarity=0.106 Sum_probs=26.5
Q ss_pred ceEEEecCCCcHHHHHHHHcCCCCCHHHHHHh---CCC--CCCCccCCCcEEEEccc
Q 047095 51 NFSYKIISHDTYAKVAETYYANLTTVDWLRAN---NIF--PDNNIPDVNTTINVVVN 102 (188)
Q Consensus 51 ~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~---N~l--~~~~i~~~Gq~L~IP~~ 102 (188)
|..|+|++||||+.|-+ ++|. +..++.++ ... .-..|++ ||.|.+-..
T Consensus 2 W~~~~V~~GDtLs~iF~-~~gl--s~~dl~~v~~~~~~~k~L~~L~p-Gq~l~f~~d 54 (85)
T PF04225_consen 2 WQEYTVKSGDTLSTIFR-RAGL--SASDLYAVLEADGEAKPLTRLKP-GQTLEFQLD 54 (85)
T ss_dssp --EEE--TT--HHHHHH-HTT----HHHHHHHHHHGGGT--GGG--T-T-EEEEEE-
T ss_pred CcEEEECCCCcHHHHHH-HcCC--CHHHHHHHHhccCccchHhhCCC-CCEEEEEEC
Confidence 56899999999999997 7764 77666554 321 2357999 999998764
No 31
>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=96.84 E-value=0.0018 Score=42.87 Aligned_cols=41 Identities=15% Similarity=0.003 Sum_probs=30.1
Q ss_pred CcHHHHHHHHcCC-C-CCHH----HHHHhCCC-----CCCCccCCCcEEEEccc
Q 047095 60 DTYAKVAETYYAN-L-TTVD----WLRANNIF-----PDNNIPDVNTTINVVVN 102 (188)
Q Consensus 60 DTL~~IA~~~y~~-l-~s~~----~L~~~N~l-----~~~~i~~~Gq~L~IP~~ 102 (188)
||||+||+ +|.. - +++. .|.+.||- +.+.|+. |+.|.||..
T Consensus 1 DTLw~IA~-~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~-G~~L~iP~~ 52 (74)
T TIGR03505 1 DTLWGIAQ-RVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKV-GQILRIPSE 52 (74)
T ss_pred CcHHHHHH-HHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCC-CCEEeCCCH
Confidence 89999998 6631 0 2444 67789982 3578999 999999964
No 32
>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=96.68 E-value=0.0026 Score=42.13 Aligned_cols=37 Identities=22% Similarity=0.274 Sum_probs=28.3
Q ss_pred CcHHHHHHHh---C-CCHH----HHHhhcCCC----C---CC-CCEEEEcCCC
Q 047095 126 ENLSTIANMS---G-LSPE----LLQSYNRGS----D---FS-SGLVFIPEKD 162 (188)
Q Consensus 126 DTl~~IA~~~---~-vs~~----~l~~~N~~~----~---~~-g~~l~iP~~~ 162 (188)
||||+||++| + +++. .|.+.||.. + ++ |++|.||...
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 8999999998 4 6765 666778743 2 55 9999999754
No 33
>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=96.48 E-value=0.0061 Score=38.65 Aligned_cols=47 Identities=23% Similarity=0.149 Sum_probs=35.0
Q ss_pred EEecCCCcHHHHHHHHcCCCCC-HHHHHHhCCC--CC-CCccCCCcEEEEccc
Q 047095 54 YKIISHDTYAKVAETYYANLTT-VDWLRANNIF--PD-NNIPDVNTTINVVVN 102 (188)
Q Consensus 54 Y~V~~GDTL~~IA~~~y~~l~s-~~~L~~~N~l--~~-~~i~~~Gq~L~IP~~ 102 (188)
|+. .||||..|+.+.||...- ++.+.++|+. .- ..+.. |..|.+|.-
T Consensus 4 ~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpa-G~~I~lP~i 54 (60)
T PF05489_consen 4 YTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPA-GTVIILPDI 54 (60)
T ss_pred EEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCC-CCEEECCCC
Confidence 444 999999999988886211 2678999993 22 45666 999999953
No 34
>PRK10260 L,D-transpeptidase; Provisional
Probab=96.42 E-value=0.0086 Score=49.95 Aligned_cols=51 Identities=14% Similarity=-0.016 Sum_probs=40.8
Q ss_pred CceEEEecCCC--cHHHHHHHHcCCCCCHHHHHHhCCC-CCCCccCCCcEEEEcccCC
Q 047095 50 NNFSYKIISHD--TYAKVAETYYANLTTVDWLRANNIF-PDNNIPDVNTTINVVVNCS 104 (188)
Q Consensus 50 ~~~~Y~V~~GD--TL~~IA~~~y~~l~s~~~L~~~N~l-~~~~i~~~Gq~L~IP~~~~ 104 (188)
....|+|++|+ +|..||+ +|+. ...+|+++|+. ++-.... |++|.||..--
T Consensus 39 ~~~~~~v~~~~~~~le~iA~-~f~~--g~~~l~~aNPgvdp~lp~~-G~~i~iP~~~i 92 (306)
T PRK10260 39 QNQVITIPEGNTQPLEYFAA-EYQM--GLSNMMEANPGVDTFLPKG-GTVLNIPQQLI 92 (306)
T ss_pred ccEEEEeCCCCCchHHHHHH-HhCC--CHHHHHHhCcCCCCCcCCC-CCEEEeCCccC
Confidence 44689999966 5999997 8995 99999999995 4445567 99999997533
No 35
>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=96.41 E-value=0.0037 Score=42.50 Aligned_cols=44 Identities=23% Similarity=0.263 Sum_probs=23.7
Q ss_pred EEEEeecCCcHHHHHHHhCCCHHHHHhh---cC----CCCCC-CCEEEEcCC
Q 047095 118 LTYPIELGENLSTIANMSGLSPELLQSY---NR----GSDFS-SGLVFIPEK 161 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~---N~----~~~~~-g~~l~iP~~ 161 (188)
..|+|++||||+.|=+++|++..+|.+. +. +..++ |+.|-+=+.
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 5799999999999999999977655544 42 22255 888766544
No 36
>PRK10190 L,D-transpeptidase; Provisional
Probab=96.36 E-value=0.0097 Score=49.75 Aligned_cols=51 Identities=8% Similarity=0.049 Sum_probs=40.7
Q ss_pred CceEEEecCCC--cHHHHHHHHcCCCCCHHHHHHhCCC-CCCCccCCCcEEEEcccCC
Q 047095 50 NNFSYKIISHD--TYAKVAETYYANLTTVDWLRANNIF-PDNNIPDVNTTINVVVNCS 104 (188)
Q Consensus 50 ~~~~Y~V~~GD--TL~~IA~~~y~~l~s~~~L~~~N~l-~~~~i~~~Gq~L~IP~~~~ 104 (188)
....|+|+++| +|..||+ +|+. ...+|.++|+. ++-...+ |++|.||..-.
T Consensus 36 ~~~~~~v~~~~~~~le~iA~-~f~~--g~~~l~~aNPgvd~~~p~~-G~~i~iP~~~i 89 (310)
T PRK10190 36 QSLTVTVPDHNTQPLETFAA-QYGQ--GLSNMLEANPGADVFLPKS-GSQLTIPQQLI 89 (310)
T ss_pred ceEEEEecCCCCccHHHHHH-HhCC--CHHHHHHhCCCCCCCCCCC-CCEEEecCccc
Confidence 44679999966 5999997 8995 99999999995 4444567 99999997533
No 37
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=96.07 E-value=0.0025 Score=52.32 Aligned_cols=45 Identities=18% Similarity=0.293 Sum_probs=35.4
Q ss_pred EEEEeecCCcHHHHHH-HhCCC--HHHHHhhcCC---CC---CC-CCEEEEcCCC
Q 047095 118 LTYPIELGENLSTIAN-MSGLS--PELLQSYNRG---SD---FS-SGLVFIPEKD 162 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~-~~~vs--~~~l~~~N~~---~~---~~-g~~l~iP~~~ 162 (188)
.+|+|++|||||.||+ .||.. ...|..+|+. .+ +. ||++.||-..
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 4899999999999995 57764 4778899993 33 33 9999999653
No 38
>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=95.34 E-value=0.032 Score=35.33 Aligned_cols=39 Identities=26% Similarity=0.395 Sum_probs=31.0
Q ss_pred ecCCcHHHHH-HHhCCC---HHHHHhhcCCCC-----CC-CCEEEEcCC
Q 047095 123 ELGENLSTIA-NMSGLS---PELLQSYNRGSD-----FS-SGLVFIPEK 161 (188)
Q Consensus 123 ~~GDTl~~IA-~~~~vs---~~~l~~~N~~~~-----~~-g~~l~iP~~ 161 (188)
+.|||+-.|| +.||-. ++.+.++|+... +. |..|.+|--
T Consensus 6 ~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i 54 (60)
T PF05489_consen 6 TQGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI 54 (60)
T ss_pred eCcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence 4999999999 678863 378999999752 34 999999954
No 39
>PRK11649 putative peptidase; Provisional
Probab=94.16 E-value=0.36 Score=42.53 Aligned_cols=95 Identities=11% Similarity=0.144 Sum_probs=58.9
Q ss_pred CceEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCC--CCCCCccCCCcEEEEcccCCCC--------CC-c---ccC-Cc
Q 047095 50 NNFSYKIISHDTYAKVAETYYANLTTVDWLRANNI--FPDNNIPDVNTTINVVVNCSCG--------DK-K---VSK-DY 114 (188)
Q Consensus 50 ~~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~--l~~~~i~~~Gq~L~IP~~~~~~--------~~-~---~~~-~~ 114 (188)
.+..|+|++||||.+|=+ ++|. +..++.++-. .....|++ ||.+.+-....-. +. . ... +.
T Consensus 94 ~~~~~~Vk~GDTl~~iL~-r~Gi--~~~di~~l~~~~~~L~~Lr~-Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg 169 (439)
T PRK11649 94 GVHEYVVSTGDTLSSILN-QYGI--DMSDISQLAAQDKELRNLKI-GQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGN 169 (439)
T ss_pred ceEEEEeCCCCCHHHHHH-HcCC--CHHHHHHHHHcChHhhcCCC-CCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCC
Confidence 456899999999999996 7875 8777776632 12357999 9999986532110 00 0 000 00
Q ss_pred cc------------eEEEEeecCCcHHHHHHHhCCCHHHHHhhcCC
Q 047095 115 GL------------FLTYPIELGENLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 115 ~~------------~~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~ 148 (188)
.+ .......=..+|+.-|.+-|++...++++-.+
T Consensus 170 ~F~~~~~~~~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~~ 215 (439)
T PRK11649 170 GFKETSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKA 215 (439)
T ss_pred cEEEEEeecccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHHH
Confidence 00 00111112468999999999988777766553
No 40
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=94.09 E-value=0.15 Score=40.40 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=38.4
Q ss_pred cceEEEEeecCCcHHHHHHHhCCCHHHHHhh-------cCCCCCC-CCEEEEcCCC
Q 047095 115 GLFLTYPIELGENLSTIANMSGLSPELLQSY-------NRGSDFS-SGLVFIPEKD 162 (188)
Q Consensus 115 ~~~~~y~V~~GDTl~~IA~~~~vs~~~l~~~-------N~~~~~~-g~~l~iP~~~ 162 (188)
+...+|+|+.|+||..+=|..++.+.|+-+. |++++++ ||.+.|-+..
T Consensus 157 g~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 157 GNWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred ccceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 3568999999999999999999877665443 5566688 9999998764
No 41
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=93.79 E-value=0.063 Score=49.30 Aligned_cols=53 Identities=21% Similarity=0.119 Sum_probs=37.8
Q ss_pred cCceEEEecCCCcHHHHHHHHcC-CCCCH----HHHHHhCCC---C--CCCccCCCcEEEEccc
Q 047095 49 ANNFSYKIISHDTYAKVAETYYA-NLTTV----DWLRANNIF---P--DNNIPDVNTTINVVVN 102 (188)
Q Consensus 49 ~~~~~Y~V~~GDTL~~IA~~~y~-~l~s~----~~L~~~N~l---~--~~~i~~~Gq~L~IP~~ 102 (188)
....+|+|++|||||.||.+.-. .-+|+ ..|.++||- + -+.++. |++|.||.-
T Consensus 186 a~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~-GSvLriP~~ 248 (755)
T COG3170 186 APGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRA-GSVLRIPSA 248 (755)
T ss_pred CCCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccc-cceeeccch
Confidence 34678999999999999974322 11233 346678982 2 358899 999999964
No 42
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=91.50 E-value=0.75 Score=36.59 Aligned_cols=73 Identities=16% Similarity=0.104 Sum_probs=44.7
Q ss_pred CCCCCCEEEEcCccccC-CCccccCceEEEecCCCcHHHHHHHHcCCCCCHHHHHHh---CCCC--CCCccCCCcEEEEc
Q 047095 27 ILSVGSRIKVPFKCNCI-NGQFLANNFSYKIISHDTYAKVAETYYANLTTVDWLRAN---NIFP--DNNIPDVNTTINVV 100 (188)
Q Consensus 27 ~l~~Gq~L~IP~~~~~~-~~~~~~~~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~---N~l~--~~~i~~~Gq~L~IP 100 (188)
.+..++...+|...... -......|.+|+|++|+||..+-| ..+ | ...++-++ -+-+ -..++. ||.+.|-
T Consensus 134 p~q~~q~~~v~~~~~~~P~~~s~g~wqsy~V~~G~TLaQlFR-dn~-L-pitDVnAMakveGagkpLSnlka-Gq~Vki~ 209 (242)
T COG3061 134 PIQAKQEKKVPRTVDAQPFKPSSGNWQSYTVPQGKTLAQLFR-DNN-L-PITDVNAMAKVEGAGKPLSNLKA-GQKVKIS 209 (242)
T ss_pred hhhccCccccCCccccCccccCcccceeEEecCCccHHHHHh-ccC-C-ChHHhHHHHhhccCCCchhhccC-CCEEEEE
Confidence 34455666665322111 111233789999999999999996 443 3 54444433 3321 257999 9999998
Q ss_pred ccC
Q 047095 101 VNC 103 (188)
Q Consensus 101 ~~~ 103 (188)
...
T Consensus 210 ~na 212 (242)
T COG3061 210 LNA 212 (242)
T ss_pred EcC
Confidence 754
No 43
>PRK11649 putative peptidase; Provisional
Probab=90.87 E-value=0.46 Score=41.89 Aligned_cols=45 Identities=16% Similarity=0.233 Sum_probs=34.0
Q ss_pred eEEEEeecCCcHHHHHHHhCCCHHHHHhh---cC-CCCCC-CCEEEEcCC
Q 047095 117 FLTYPIELGENLSTIANMSGLSPELLQSY---NR-GSDFS-SGLVFIPEK 161 (188)
Q Consensus 117 ~~~y~V~~GDTl~~IA~~~~vs~~~l~~~---N~-~~~~~-g~~l~iP~~ 161 (188)
...|+|++||||.+|-+++|++..++.++ +. +.+++ |+.+.+=+.
T Consensus 95 ~~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d 144 (439)
T PRK11649 95 VHEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTLT 144 (439)
T ss_pred eEEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEEC
Confidence 46899999999999999999988777765 21 12355 888776443
No 44
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=90.15 E-value=0.2 Score=46.11 Aligned_cols=47 Identities=23% Similarity=0.265 Sum_probs=34.5
Q ss_pred eEEEEeecCCcHHHHHHHh----CCCH----HHHHhhcCCC----C---CC-CCEEEEcCCCC
Q 047095 117 FLTYPIELGENLSTIANMS----GLSP----ELLQSYNRGS----D---FS-SGLVFIPEKDQ 163 (188)
Q Consensus 117 ~~~y~V~~GDTl~~IA~~~----~vs~----~~l~~~N~~~----~---~~-g~~l~iP~~~~ 163 (188)
..+|+|++|||||+||.+- ++|+ ..|.++|+.. + ++ |.+|.||....
T Consensus 188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~~q 250 (755)
T COG3170 188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSAAQ 250 (755)
T ss_pred CcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccchhh
Confidence 3689999999999999653 3555 4556678853 1 34 99999997543
No 45
>PF13518 HTH_28: Helix-turn-helix domain
Probab=87.12 E-value=0.59 Score=27.78 Aligned_cols=24 Identities=25% Similarity=0.275 Sum_probs=20.9
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhhc
Q 047095 123 ELGENLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~N 146 (188)
..|+|+..+|++||++...+..|=
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 368899999999999998888774
No 46
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=82.76 E-value=2.9 Score=26.72 Aligned_cols=50 Identities=14% Similarity=0.045 Sum_probs=36.4
Q ss_pred eEEEecCCCcHHHHHHHHcCCCCC-HHHHHHhCCCC---CCCccCCCcEEEEccc
Q 047095 52 FSYKIISHDTYAKVAETYYANLTT-VDWLRANNIFP---DNNIPDVNTTINVVVN 102 (188)
Q Consensus 52 ~~Y~V~~GDTL~~IA~~~y~~l~s-~~~L~~~N~l~---~~~i~~~Gq~L~IP~~ 102 (188)
..|....|||+..++.+.|+..+. .+.+.++|+.- ...+.. |-.|.+|..
T Consensus 3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~-gl~i~lPD~ 56 (70)
T COG5004 3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPH-GLAITLPDI 56 (70)
T ss_pred eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCcc-ceeEecCCC
Confidence 356778899999999988886322 36688899842 235666 888888854
No 47
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=82.62 E-value=2.5 Score=36.12 Aligned_cols=47 Identities=13% Similarity=0.151 Sum_probs=34.8
Q ss_pred ceEEEecCCCcHHHHHHHHcCCCC-CHHHHHHhCCCC-CCCccCCCcEEEE
Q 047095 51 NFSYKIISHDTYAKVAETYYANLT-TVDWLRANNIFP-DNNIPDVNTTINV 99 (188)
Q Consensus 51 ~~~Y~V~~GDTL~~IA~~~y~~l~-s~~~L~~~N~l~-~~~i~~~Gq~L~I 99 (188)
....+|++|||+.++|. +..+.. +.+-++-+|.+. ...+.+ |+.++|
T Consensus 428 irvvtVk~GqT~~~lAA-~m~G~~rkldlfRllNam~~~a~~~p-Gd~vKi 476 (479)
T COG4784 428 IRVVTVKPGQTMASLAA-RMMGTDRKLDLFRLLNAMSPGATVRP-GDKVKI 476 (479)
T ss_pred EEEEEecCCccHHHHHh-hccCchhHHHHHHHHhccCCCCcCCC-CCeeee
Confidence 45678999999999998 444421 245577788875 457888 999987
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=81.88 E-value=1.5 Score=25.65 Aligned_cols=23 Identities=26% Similarity=0.381 Sum_probs=17.1
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
+.|-|+..||+.||++...|.++
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 56899999999999999887654
No 49
>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=81.38 E-value=0.94 Score=29.25 Aligned_cols=24 Identities=38% Similarity=0.648 Sum_probs=20.9
Q ss_pred eecCCcHHHHHHHhCCCHHHHHhh
Q 047095 122 IELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
...|.|+..+|++|||+...|..|
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 467999999999999999999888
No 50
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=78.95 E-value=1.4 Score=34.22 Aligned_cols=45 Identities=22% Similarity=0.234 Sum_probs=36.5
Q ss_pred EEEEeecCCcHHHHHHHhCCCHHHHHhhcCCCC---CC-CCEEEEcCCC
Q 047095 118 LTYPIELGENLSTIANMSGLSPELLQSYNRGSD---FS-SGLVFIPEKD 162 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~~---~~-g~~l~iP~~~ 162 (188)
..-+++.|||+-.||-+|..++.++.+.|++.. +- -..+.+|+..
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 456899999999999999999999999997654 22 4567777765
No 51
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=75.07 E-value=5.6 Score=32.02 Aligned_cols=44 Identities=27% Similarity=0.386 Sum_probs=37.9
Q ss_pred EEEeecCCcHHHHHHHhCCCHHHHHhhcCCCC---CC-CCEEEEcCCC
Q 047095 119 TYPIELGENLSTIANMSGLSPELLQSYNRGSD---FS-SGLVFIPEKD 162 (188)
Q Consensus 119 ~y~V~~GDTl~~IA~~~~vs~~~l~~~N~~~~---~~-g~~l~iP~~~ 162 (188)
.|.++.|+++..|+++++.+..++...|.... .. |+.+.+|...
T Consensus 3 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (277)
T COG0739 3 LYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRAA 50 (277)
T ss_pred eEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecccc
Confidence 58999999999999999999999999988654 23 8888888874
No 52
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=74.83 E-value=3.6 Score=24.21 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=17.4
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..|.|...||+.+|++...+..|
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 34999999999999999888777
No 53
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=74.14 E-value=3.1 Score=29.30 Aligned_cols=24 Identities=25% Similarity=0.421 Sum_probs=20.5
Q ss_pred eecCCcHHHHHHHhCC-CHHHHHhh
Q 047095 122 IELGENLSTIANMSGL-SPELLQSY 145 (188)
Q Consensus 122 V~~GDTl~~IA~~~~v-s~~~l~~~ 145 (188)
.+.|.|+..||++||+ +...|..|
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHH
Confidence 4679999999999995 88888776
No 54
>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=73.49 E-value=1.5 Score=26.85 Aligned_cols=24 Identities=29% Similarity=0.358 Sum_probs=16.1
Q ss_pred eecCCcHHHHHHHhCCCHHHHHhh
Q 047095 122 IELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
+..|.+...||++||++...+..+
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 467899999999999966555443
No 55
>PHA00675 hypothetical protein
Probab=73.40 E-value=3.6 Score=27.27 Aligned_cols=26 Identities=15% Similarity=0.027 Sum_probs=22.0
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhhcCC
Q 047095 123 ELGENLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~N~~ 148 (188)
+.|.+.+.||++||++...+...=+.
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHcc
Confidence 78999999999999999888776443
No 56
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.86 E-value=4.3 Score=33.89 Aligned_cols=51 Identities=16% Similarity=0.204 Sum_probs=37.3
Q ss_pred eEEEecCCCcHHHHHHHHcCCCC-CHHHHHHhCCC-CCCCccCCCcEEEEcccCC
Q 047095 52 FSYKIISHDTYAKVAETYYANLT-TVDWLRANNIF-PDNNIPDVNTTINVVVNCS 104 (188)
Q Consensus 52 ~~Y~V~~GDTL~~IA~~~y~~l~-s~~~L~~~N~l-~~~~i~~~Gq~L~IP~~~~ 104 (188)
..|.|+.||||-.++. .|-.+. ..-.+...|.. ++-.+++ |..|.||.+.+
T Consensus 6 ~~yrv~~gdtli~l~~-~yl~~~~g~r~~q~an~~~~P~~l~p-gs~l~ip~~~~ 58 (339)
T COG4254 6 LTYRVLFGDTLILLLG-GYLTLLAGSRAAQPANTKRPPFILQP-GSCLPIPLPAS 58 (339)
T ss_pred ceeeeccccHHHHHHH-HhhhccchhhhhcccccCCCCcccCC-CccccCCCccc
Confidence 6899999999999997 554321 23345667776 4667788 99999997643
No 57
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=70.74 E-value=4.4 Score=28.99 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=23.2
Q ss_pred EEeecCCcHHHHHHHhCCCHHHHHhh
Q 047095 120 YPIELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 120 y~V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..+..|.|+..||++|||+...|..|
T Consensus 24 ~~~~~g~sv~evA~e~gIs~~tl~~W 49 (121)
T PRK09413 24 QSFEPGMTVSLVARQHGVAASQLFLW 49 (121)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence 34567999999999999999999999
No 58
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=67.49 E-value=6.3 Score=22.91 Aligned_cols=22 Identities=27% Similarity=0.302 Sum_probs=14.3
Q ss_pred ecCCcHHHHHHHhCCCHHHHHh
Q 047095 123 ELGENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~ 144 (188)
+.|.++..||+++|.+...+..
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHH
Confidence 5799999999999998877654
No 59
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=65.68 E-value=11 Score=30.16 Aligned_cols=46 Identities=15% Similarity=0.062 Sum_probs=38.3
Q ss_pred EEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCCCCC-CccCCCcEEEEccc
Q 047095 53 SYKIISHDTYAKVAETYYANLTTVDWLRANNIFPDN-NIPDVNTTINVVVN 102 (188)
Q Consensus 53 ~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l~~~-~i~~~Gq~L~IP~~ 102 (188)
.|.++.+++|..|++ +++. +...+.+.|..... .+.. |+.+.+|..
T Consensus 3 ~~~~~~~~~l~~~~~-~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 49 (277)
T COG0739 3 LYVVKKGDTLSAIAA-RLGI--SAKDLARLNNLLKKRLLRI-GQLLRVPRA 49 (277)
T ss_pred eEEecCCCHHHHHHH-HcCC--CHHHHHHHHhhccccccCc-cceeeeccc
Confidence 588999999999997 7875 88889998886433 7788 999999875
No 60
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=64.48 E-value=9.2 Score=32.82 Aligned_cols=42 Identities=19% Similarity=0.245 Sum_probs=31.4
Q ss_pred eEEEEeecCCcHHHHHHH-hCC--CHHHHHhhcCCCC---CC-CCEEEE
Q 047095 117 FLTYPIELGENLSTIANM-SGL--SPELLQSYNRGSD---FS-SGLVFI 158 (188)
Q Consensus 117 ~~~y~V~~GDTl~~IA~~-~~v--s~~~l~~~N~~~~---~~-g~~l~i 158 (188)
....+|++|||+.++|.+ -|+ +++.++-+|.+.. .. |+.++|
T Consensus 428 irvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi 476 (479)
T COG4784 428 IRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI 476 (479)
T ss_pred EEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence 456789999999999965 566 5577777787753 44 888776
No 61
>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=63.52 E-value=11 Score=19.24 Aligned_cols=23 Identities=35% Similarity=0.495 Sum_probs=19.0
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..|.+...||+.||++...+..|
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 46889999999999998877653
No 62
>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=63.39 E-value=7.1 Score=22.93 Aligned_cols=24 Identities=17% Similarity=0.264 Sum_probs=16.6
Q ss_pred eecC-CcHHHHHHHhCCCHHHHHhh
Q 047095 122 IELG-ENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 122 V~~G-DTl~~IA~~~~vs~~~l~~~ 145 (188)
|+.| -++...|++|||+...|...
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 78999999999999888754
No 63
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=62.96 E-value=20 Score=22.95 Aligned_cols=44 Identities=14% Similarity=0.254 Sum_probs=31.9
Q ss_pred EEEEeecCCcHHHHHH-HhCCC---HHHHHhhcCCCC-----CC-CCEEEEcCC
Q 047095 118 LTYPIELGENLSTIAN-MSGLS---PELLQSYNRGSD-----FS-SGLVFIPEK 161 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~-~~~vs---~~~l~~~N~~~~-----~~-g~~l~iP~~ 161 (188)
..|....|||+-.|+. -||-+ .+.+.++|++.. +. |-.|-.|--
T Consensus 3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~ 56 (70)
T COG5004 3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDI 56 (70)
T ss_pred eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCC
Confidence 4577788999999994 57743 388899999863 22 666666654
No 64
>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=59.01 E-value=11 Score=23.70 Aligned_cols=21 Identities=24% Similarity=0.426 Sum_probs=18.8
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++-.||.++||+...|..|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 788999999999999999844
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=58.29 E-value=14 Score=21.70 Aligned_cols=23 Identities=26% Similarity=0.251 Sum_probs=18.4
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
-.|-|+..||+.+|+|.+.+...
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 46889999999999999877653
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=57.95 E-value=13 Score=20.98 Aligned_cols=21 Identities=33% Similarity=0.713 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+.+|+++..|..|-.
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 467889999999999999854
No 67
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=55.33 E-value=12 Score=24.84 Aligned_cols=23 Identities=26% Similarity=0.460 Sum_probs=16.4
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
++|-||..||+++|++...|...
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 47999999999999998776544
No 68
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=55.05 E-value=12 Score=22.92 Aligned_cols=23 Identities=26% Similarity=0.212 Sum_probs=16.5
Q ss_pred ecCCcHHHHHHHhC-CCHHHHHhh
Q 047095 123 ELGENLSTIANMSG-LSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~-vs~~~l~~~ 145 (188)
..|++...|++.|. ++.+++.++
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 78999999999998 899888753
No 69
>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=52.14 E-value=15 Score=25.78 Aligned_cols=20 Identities=30% Similarity=0.403 Sum_probs=14.9
Q ss_pred CCcHHHHHHHhCCCHHHHHh
Q 047095 125 GENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 125 GDTl~~IA~~~~vs~~~l~~ 144 (188)
|.++..||++||+|...+.+
T Consensus 72 G~n~~eLA~kyglS~r~I~~ 91 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYR 91 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHH
Confidence 99999999999999877654
No 70
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=51.50 E-value=12 Score=29.19 Aligned_cols=48 Identities=19% Similarity=0.196 Sum_probs=35.2
Q ss_pred ceEEEecCCCcHHHHHHHHcCCCCCHHHHHHhCCCC-CCCccCCCcEEEEccc
Q 047095 51 NFSYKIISHDTYAKVAETYYANLTTVDWLRANNIFP-DNNIPDVNTTINVVVN 102 (188)
Q Consensus 51 ~~~Y~V~~GDTL~~IA~~~y~~l~s~~~L~~~N~l~-~~~i~~~Gq~L~IP~~ 102 (188)
...-+++.||||-.||= .|.. ++.++.+.|++. ...+.. =+.+.+|..
T Consensus 9 ~l~~~iq~~dt~~a~al-~~~~--~va~i~RvN~~~r~q~f~a-~~~i~~pv~ 57 (186)
T KOG2850|consen 9 ELEVTIQEGDTLQAIAL-NYES--DVADIKRVNNDDREQRFNA-LRSISIPVT 57 (186)
T ss_pred heeeeeccCchhhhHHh-hccc--chhhheeeccchhhhhhcc-ccceecccc
Confidence 34568999999999995 7886 888999999764 334444 555666653
No 71
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=50.78 E-value=13 Score=22.43 Aligned_cols=23 Identities=17% Similarity=0.276 Sum_probs=18.7
Q ss_pred eecCCcHHHHHHHhCCCHHHHHh
Q 047095 122 IELGENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~ 144 (188)
.+.|.+...||..||++.+...+
T Consensus 16 LR~~~~~~~La~~FgIs~stvsr 38 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSR 38 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHH
Confidence 46788999999999998866544
No 72
>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=50.75 E-value=19 Score=20.21 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHhhc
Q 047095 127 NLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N 146 (188)
|+..+|+.+|++...|..|=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999884
No 73
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=50.42 E-value=4.9 Score=24.78 Aligned_cols=22 Identities=36% Similarity=0.468 Sum_probs=17.2
Q ss_pred CcHHHHHHHhCCCHHHHHhhcC
Q 047095 126 ENLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 126 DTl~~IA~~~~vs~~~l~~~N~ 147 (188)
|++..||.-||+++++|..+.+
T Consensus 41 ~~l~~ia~~l~~~~~el~~~~~ 62 (63)
T PF13443_consen 41 DTLEKIAKALNCSPEELFEYEP 62 (63)
T ss_dssp HHHHHHHHHHT--HHHCTECCE
T ss_pred HHHHHHHHHcCCCHHHHhhcCC
Confidence 6899999999999999987653
No 74
>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=50.29 E-value=19 Score=20.61 Aligned_cols=21 Identities=33% Similarity=0.762 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+.+|++...|..|-.
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999999943
No 75
>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=49.79 E-value=18 Score=22.45 Aligned_cols=20 Identities=25% Similarity=0.760 Sum_probs=17.7
Q ss_pred cHHHHHHHhCCCHHHHHhhc
Q 047095 127 NLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N 146 (188)
++..+|+++|++...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999984
No 76
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=49.59 E-value=17 Score=24.58 Aligned_cols=25 Identities=20% Similarity=0.187 Sum_probs=21.5
Q ss_pred EeecCCcHHHHHHHhCCCHHHHHhh
Q 047095 121 PIELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 121 ~V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
.|..|-++...|+.||||.....+|
T Consensus 21 vv~~g~~~a~aA~~~gVS~~Ta~kW 45 (85)
T PF13011_consen 21 VVEQGWPVAHAAAEFGVSRRTAYKW 45 (85)
T ss_pred HHHcCCcHHHHHHHhCCCHHHHHHH
Confidence 3567899999999999999877777
No 77
>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=48.46 E-value=12 Score=26.60 Aligned_cols=24 Identities=25% Similarity=0.389 Sum_probs=21.3
Q ss_pred eecCCcHHHHHHHhCCCHHHHHhh
Q 047095 122 IELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
+..|.+...+|++|+|+...+..|
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W 38 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRW 38 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHH
Confidence 456889999999999999888888
No 78
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=48.29 E-value=21 Score=22.24 Aligned_cols=21 Identities=33% Similarity=0.705 Sum_probs=18.2
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+.+|++.+.|..|=.
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 567899999999999999943
No 79
>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=46.36 E-value=20 Score=22.71 Aligned_cols=19 Identities=32% Similarity=0.573 Sum_probs=14.0
Q ss_pred cHHHHHHHhCCCHHHHHhh
Q 047095 127 NLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~ 145 (188)
++..||++|+++.+.+...
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 7889999999999776653
No 80
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=45.88 E-value=25 Score=20.60 Aligned_cols=20 Identities=15% Similarity=0.202 Sum_probs=16.8
Q ss_pred CcHHHHHHHhCCCHHHHHhh
Q 047095 126 ENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 126 DTl~~IA~~~~vs~~~l~~~ 145 (188)
-|+..||+.+|++.+.+.+.
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHH
Confidence 48999999999998877653
No 81
>PHA01976 helix-turn-helix protein
Probab=44.60 E-value=17 Score=22.57 Aligned_cols=19 Identities=21% Similarity=0.261 Sum_probs=16.5
Q ss_pred CCcHHHHHHHhCCCHHHHH
Q 047095 125 GENLSTIANMSGLSPELLQ 143 (188)
Q Consensus 125 GDTl~~IA~~~~vs~~~l~ 143 (188)
-+++..||+.||+++++|.
T Consensus 44 ~~~l~~ia~~l~v~~~~l~ 62 (67)
T PHA01976 44 LKTLLRLADALGVTLDWLC 62 (67)
T ss_pred HHHHHHHHHHHCcCHHHHh
Confidence 3578999999999999884
No 82
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.37 E-value=26 Score=29.40 Aligned_cols=46 Identities=22% Similarity=0.213 Sum_probs=34.5
Q ss_pred EEEEeecCCcHHHHHHHhCC---CHHHHHhhcCCCC-CC---CCEEEEcCCCC
Q 047095 118 LTYPIELGENLSTIANMSGL---SPELLQSYNRGSD-FS---SGLVFIPEKDQ 163 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~~~~v---s~~~l~~~N~~~~-~~---g~~l~iP~~~~ 163 (188)
++|.|+.||||..++..|=. ..-.++..|...+ +. |..|-||....
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 68999999999999998854 3345667788776 22 77777876643
No 83
>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=44.13 E-value=31 Score=21.44 Aligned_cols=23 Identities=22% Similarity=0.315 Sum_probs=20.0
Q ss_pred cCCcHHHHHHHhCCCHHHHHhhc
Q 047095 124 LGENLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 124 ~GDTl~~IA~~~~vs~~~l~~~N 146 (188)
.|-++..||+..|++...+..|=
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHH
Confidence 58899999999999988888773
No 84
>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=44.06 E-value=13 Score=22.05 Aligned_cols=17 Identities=47% Similarity=0.737 Sum_probs=14.4
Q ss_pred CcHHHHHHHhCCCHHHH
Q 047095 126 ENLSTIANMSGLSPELL 142 (188)
Q Consensus 126 DTl~~IA~~~~vs~~~l 142 (188)
|++..||+.||+++++|
T Consensus 39 ~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 39 DTLKKIAKALGVSPEYL 55 (55)
T ss_dssp HHHHHHHHHHTSEHHHH
T ss_pred HHHHHHHHHHCCCHHHC
Confidence 57889999999988765
No 85
>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=43.41 E-value=27 Score=21.76 Aligned_cols=20 Identities=20% Similarity=0.610 Sum_probs=17.7
Q ss_pred cHHHHHHHhCCCHHHHHhhc
Q 047095 127 NLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N 146 (188)
++..+|+.+|++...|..|=
T Consensus 2 ~i~evA~~~gvs~~tlR~~~ 21 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYE 21 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999994
No 86
>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=43.00 E-value=21 Score=27.42 Aligned_cols=28 Identities=18% Similarity=0.327 Sum_probs=25.2
Q ss_pred EEeecCCcHHHHHHHhCCCHHHHHhhcC
Q 047095 120 YPIELGENLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 120 y~V~~GDTl~~IA~~~~vs~~~l~~~N~ 147 (188)
-.++.|.|...||+.+|++++.+..+-.
T Consensus 64 arIRaGas~eeVA~~~G~~~~rV~rfa~ 91 (170)
T PF11268_consen 64 ARIRAGASAEEVAEEAGVPVERVRRFAG 91 (170)
T ss_pred HHHHCCCCHHHHHHHhCCCHHHhhhccc
Confidence 3678999999999999999999998865
No 87
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.66 E-value=34 Score=19.72 Aligned_cols=24 Identities=21% Similarity=0.257 Sum_probs=20.1
Q ss_pred eecCCcHHHHHHHhCCCHHHHHhh
Q 047095 122 IELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
+..|.+...||+.+|++...+..+
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHH
Confidence 357899999999999998877665
No 88
>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=42.50 E-value=33 Score=20.23 Aligned_cols=22 Identities=23% Similarity=0.305 Sum_probs=17.3
Q ss_pred cHHHHHHHhCCCHHHHHhh-cCC
Q 047095 127 NLSTIANMSGLSPELLQSY-NRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~-N~~ 148 (188)
|+.+||++.|++...+-+. |+-
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 6889999999998777654 543
No 89
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=42.36 E-value=28 Score=21.62 Aligned_cols=20 Identities=25% Similarity=0.567 Sum_probs=17.7
Q ss_pred cHHHHHHHhCCCHHHHHhhc
Q 047095 127 NLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N 146 (188)
|+..+|+.+|++.+.|..|-
T Consensus 2 s~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999994
No 90
>smart00351 PAX Paired Box domain.
Probab=42.19 E-value=24 Score=25.37 Aligned_cols=23 Identities=13% Similarity=0.057 Sum_probs=20.0
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..|.+.-.||++||++...+.+|
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kw 53 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKI 53 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 47999999999999999877766
No 91
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=41.54 E-value=30 Score=23.72 Aligned_cols=22 Identities=23% Similarity=0.391 Sum_probs=18.6
Q ss_pred ecCCcHHHHHHHhCCCHHHHHh
Q 047095 123 ELGENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~ 144 (188)
++|-||..||+..|++...|..
T Consensus 19 KrG~sLa~lsr~~Gls~~TL~n 40 (92)
T PRK10344 19 KKGTSMAAESRRNGLSSSTLAN 40 (92)
T ss_pred HcCCcHHHHHHHcCCChHHHHH
Confidence 5799999999999998877643
No 92
>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=40.27 E-value=31 Score=20.37 Aligned_cols=21 Identities=24% Similarity=0.409 Sum_probs=14.6
Q ss_pred cCCcHHHHHHHhCCCHHHHHh
Q 047095 124 LGENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 124 ~GDTl~~IA~~~~vs~~~l~~ 144 (188)
.|-+...||+.+|+|...+..
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~ 45 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKR 45 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHH
Confidence 477899999999999987764
No 93
>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=39.75 E-value=29 Score=23.59 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=22.0
Q ss_pred eecCCcHHHHHHHhCCCHHHHHhhcC
Q 047095 122 IELGENLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~~N~ 147 (188)
+..|.|...||+++|++...+.++.+
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46799999999999999988877654
No 94
>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=39.04 E-value=34 Score=20.86 Aligned_cols=18 Identities=17% Similarity=0.278 Sum_probs=14.5
Q ss_pred cHHHHHHHhCCCHHHHHh
Q 047095 127 NLSTIANMSGLSPELLQS 144 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~ 144 (188)
++..+|+.||+|...+.+
T Consensus 16 s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRR 33 (57)
T ss_pred EHHHHHHHHCcCHHHHHH
Confidence 678999999998866654
No 95
>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=36.55 E-value=24 Score=27.41 Aligned_cols=25 Identities=24% Similarity=0.156 Sum_probs=19.2
Q ss_pred EeecCCcHHHHHHHhCCCHHHHHhh
Q 047095 121 PIELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 121 ~V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
-|.+=.=|-.||+|||++..+|++.
T Consensus 166 AvEPVWyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 166 AVEPVWYLPGVAERFGISEGELRRA 190 (194)
T ss_pred EecccccchhhHHHcCCCHHHHHHH
Confidence 3445555669999999999999863
No 96
>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=36.51 E-value=49 Score=20.97 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=17.6
Q ss_pred ecCCcHHHHHHHhCCCHHHHHh
Q 047095 123 ELGENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~ 144 (188)
..|-++-.||+++|++..+...
T Consensus 11 E~g~~FveIAr~~~i~a~e~a~ 32 (63)
T PF11242_consen 11 ESGLSFVEIARKIGITAKEVAK 32 (63)
T ss_pred HcCCcHHHHHHHhCCCHHHHHH
Confidence 3588999999999998866543
No 97
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=36.35 E-value=40 Score=21.06 Aligned_cols=21 Identities=24% Similarity=0.730 Sum_probs=18.5
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|++.||+...|..|-.
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999999954
No 98
>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=35.97 E-value=30 Score=21.38 Aligned_cols=18 Identities=22% Similarity=0.215 Sum_probs=14.2
Q ss_pred HHHHHHHhCCCHHHHHhh
Q 047095 128 LSTIANMSGLSPELLQSY 145 (188)
Q Consensus 128 l~~IA~~~~vs~~~l~~~ 145 (188)
+.-.|++||+|.++|.++
T Consensus 23 v~ywa~~~gvt~~~L~~A 40 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREA 40 (57)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 345679999999988765
No 99
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=35.85 E-value=25 Score=21.09 Aligned_cols=18 Identities=17% Similarity=0.274 Sum_probs=13.8
Q ss_pred cHHHHHHHhCCCHHHHHh
Q 047095 127 NLSTIANMSGLSPELLQS 144 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~ 144 (188)
++..+|+++|++..+|.+
T Consensus 5 ~V~elAk~l~v~~~~ii~ 22 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIK 22 (54)
T ss_dssp -TTHHHHHHSSSHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHH
Confidence 467899999998866654
No 100
>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=33.54 E-value=27 Score=22.00 Aligned_cols=19 Identities=37% Similarity=0.324 Sum_probs=13.3
Q ss_pred CCcHHHHHHHhCCCHHHHH
Q 047095 125 GENLSTIANMSGLSPELLQ 143 (188)
Q Consensus 125 GDTl~~IA~~~~vs~~~l~ 143 (188)
-|-+..||+++|++++.|.
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 4568899999999999886
No 101
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=32.91 E-value=31 Score=21.25 Aligned_cols=18 Identities=17% Similarity=0.283 Sum_probs=15.6
Q ss_pred hhHHHHcCCCHHHHHhcC
Q 047095 2 TFISEMFDTSIDNILSFN 19 (188)
Q Consensus 2 ~~IA~~~gvs~~~l~~~N 19 (188)
..+|+.||++.++|..-.
T Consensus 7 ~~Va~~~~i~~~~i~s~~ 24 (60)
T smart00760 7 EAVAEYFGVKPEDLKSKS 24 (60)
T ss_pred HHHHHHhCCCHHHHhcCC
Confidence 468999999999998776
No 102
>PF13551 HTH_29: Winged helix-turn helix
Probab=32.69 E-value=42 Score=22.73 Aligned_cols=23 Identities=22% Similarity=0.333 Sum_probs=19.2
Q ss_pred ecCC-cHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGE-NLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GD-Tl~~IA~~~~vs~~~l~~~ 145 (188)
..|. |...||+.+|++...+.+|
T Consensus 9 ~~g~~~~~~ia~~lg~s~~Tv~r~ 32 (112)
T PF13551_consen 9 AEGVSTIAEIARRLGISRRTVYRW 32 (112)
T ss_pred HcCCCcHHHHHHHHCcCHHHHHHH
Confidence 5678 6999999999988777766
No 103
>PHA02591 hypothetical protein; Provisional
Probab=32.41 E-value=49 Score=22.08 Aligned_cols=26 Identities=23% Similarity=0.438 Sum_probs=12.3
Q ss_pred EEEeecCCcHHHHHH---HhCCCHHHHHh
Q 047095 119 TYPIELGENLSTIAN---MSGLSPELLQS 144 (188)
Q Consensus 119 ~y~V~~GDTl~~IA~---~~~vs~~~l~~ 144 (188)
.|-|..-|.+-++|+ +-|.|+++|.+
T Consensus 39 ryfi~~~dd~~~vA~eL~eqGlSqeqIA~ 67 (83)
T PHA02591 39 RYFVESEDDLISVTHELARKGFTVEKIAS 67 (83)
T ss_pred EEEEeccchHHHHHHHHHHcCCCHHHHHH
Confidence 455555555555553 23444444443
No 104
>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=32.34 E-value=95 Score=17.24 Aligned_cols=21 Identities=14% Similarity=0.188 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+.+|++...|.+|=.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999988888843
No 105
>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=31.16 E-value=29 Score=22.24 Aligned_cols=18 Identities=28% Similarity=0.447 Sum_probs=12.8
Q ss_pred hhHHHHcCCCHHHHHhcC
Q 047095 2 TFISEMFDTSIDNILSFN 19 (188)
Q Consensus 2 ~~IA~~~gvs~~~l~~~N 19 (188)
..+|+.||++.++|..-.
T Consensus 7 ~~Va~~~~v~~~~i~s~~ 24 (70)
T PF08299_consen 7 EAVAEYFGVSVEDIRSKS 24 (70)
T ss_dssp HHHHHHTT--HHHHHSS-
T ss_pred HHHHHHHCCCHHHHhCCC
Confidence 468999999999998765
No 106
>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=30.94 E-value=48 Score=20.24 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=20.4
Q ss_pred EEEeecCCcHHHHHHHhCCCHHHHH
Q 047095 119 TYPIELGENLSTIANMSGLSPELLQ 143 (188)
Q Consensus 119 ~y~V~~GDTl~~IA~~~~vs~~~l~ 143 (188)
.|-+-++=|+.+||+.+|++...+.
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 3667778899999999999876554
No 107
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.76 E-value=45 Score=23.39 Aligned_cols=17 Identities=29% Similarity=0.288 Sum_probs=14.3
Q ss_pred cHHHHHHHhCCCHHHHH
Q 047095 127 NLSTIANMSGLSPELLQ 143 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~ 143 (188)
++..||..|+||-+++-
T Consensus 35 Sl~EIAee~~VSRqAIy 51 (105)
T COG2739 35 SLSEIAEEFNVSRQAIY 51 (105)
T ss_pred cHHHHHHHhCccHHHHH
Confidence 78899999999887653
No 108
>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=30.71 E-value=70 Score=18.39 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=19.1
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..|-+...||+.++++...+..+
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~ 35 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999988777655
No 109
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=30.62 E-value=46 Score=25.14 Aligned_cols=26 Identities=23% Similarity=0.253 Sum_probs=22.0
Q ss_pred cceEEEEeecCCcHHHHHHHhCCCHH
Q 047095 115 GLFLTYPIELGENLSTIANMSGLSPE 140 (188)
Q Consensus 115 ~~~~~y~V~~GDTl~~IA~~~~vs~~ 140 (188)
+....+.++.|||+..+|.+.|+..+
T Consensus 53 G~~~~i~g~vGdtlLd~ah~n~idle 78 (159)
T KOG3309|consen 53 GEEIKIKGKVGDTLLDAAHENNLDLE 78 (159)
T ss_pred CCEEEeeeecchHHHHHHHHcCCCcc
Confidence 44577899999999999999998654
No 110
>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=30.53 E-value=34 Score=20.92 Aligned_cols=20 Identities=30% Similarity=0.260 Sum_probs=15.7
Q ss_pred CcHHHHHHHhCCCHHHHHhh
Q 047095 126 ENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 126 DTl~~IA~~~~vs~~~l~~~ 145 (188)
+++..||..||+++++|...
T Consensus 42 ~~l~~i~~~~~v~~~~l~~~ 61 (64)
T PF12844_consen 42 STLKKIAEALGVSLDELFDG 61 (64)
T ss_dssp HHHHHHHHHHTS-HHHHCCC
T ss_pred HHHHHHHHHhCCCHHHHhcc
Confidence 47789999999999988653
No 111
>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=30.28 E-value=53 Score=22.26 Aligned_cols=22 Identities=23% Similarity=0.445 Sum_probs=18.9
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
|+..+|+.+|++...|.-|-..
T Consensus 2 ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999999653
No 112
>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=30.20 E-value=66 Score=21.19 Aligned_cols=22 Identities=14% Similarity=0.164 Sum_probs=16.7
Q ss_pred EEEEeecCCcHHHHHHHhCCCH
Q 047095 118 LTYPIELGENLSTIANMSGLSP 139 (188)
Q Consensus 118 ~~y~V~~GDTl~~IA~~~~vs~ 139 (188)
..|.+.+|+||.+.+.+-|+..
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 4689999999999999988754
No 113
>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=29.41 E-value=59 Score=22.68 Aligned_cols=23 Identities=22% Similarity=0.231 Sum_probs=19.6
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
-.|-++..||+.+|++.+.+..+
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 36999999999999999877654
No 114
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.38 E-value=52 Score=24.26 Aligned_cols=20 Identities=30% Similarity=0.439 Sum_probs=16.6
Q ss_pred CCcHHHHHHHhCCCHHHHHh
Q 047095 125 GENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 125 GDTl~~IA~~~~vs~~~l~~ 144 (188)
-+||.+||.++|++..++.+
T Consensus 90 ~~~l~~la~~~Gld~~El~~ 109 (143)
T COG3753 90 TDTLSQLAQKTGLDEQELLK 109 (143)
T ss_pred hhHHHHHHHHhCCCHHHHHH
Confidence 57999999999998866654
No 115
>cd00131 PAX Paired Box domain
Probab=29.37 E-value=50 Score=23.84 Aligned_cols=23 Identities=13% Similarity=0.073 Sum_probs=20.0
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..|.+.-.||++||++...+.+|
T Consensus 31 ~~G~s~~~iA~~~~Vs~~tV~r~ 53 (128)
T cd00131 31 QSGIRPCDISRQLRVSHGCVSKI 53 (128)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 57999999999999998877666
No 116
>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=28.83 E-value=58 Score=22.34 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=18.8
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
++..+|+++|+|...|.-|-..
T Consensus 3 ~i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999998653
No 117
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=28.37 E-value=76 Score=17.65 Aligned_cols=21 Identities=29% Similarity=0.433 Sum_probs=14.2
Q ss_pred cCCcHHHHHHHhCCCHHHHHh
Q 047095 124 LGENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 124 ~GDTl~~IA~~~~vs~~~l~~ 144 (188)
.+-+|.+||...|++..-+.+
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r 27 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSR 27 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHH
Confidence 456889999999998876654
No 118
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=28.11 E-value=52 Score=27.00 Aligned_cols=24 Identities=38% Similarity=0.642 Sum_probs=19.6
Q ss_pred CCcHHHHHHHhCCCHHHHHhhcCC
Q 047095 125 GENLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 125 GDTl~~IA~~~~vs~~~l~~~N~~ 148 (188)
|=-+.+||.+||+++..|.+|=..
T Consensus 19 gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHHh
Confidence 345679999999999999998543
No 119
>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=27.85 E-value=62 Score=22.08 Aligned_cols=20 Identities=30% Similarity=0.650 Sum_probs=17.9
Q ss_pred cHHHHHHHhCCCHHHHHhhc
Q 047095 127 NLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N 146 (188)
++..+|+.+|++...|..|=
T Consensus 3 ~i~eva~~~gVs~~tLR~ye 22 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYD 22 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57789999999999999993
No 120
>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=27.83 E-value=61 Score=22.61 Aligned_cols=21 Identities=29% Similarity=0.624 Sum_probs=18.4
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+.+|++...|..|-.
T Consensus 2 ~i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999999954
No 121
>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=27.77 E-value=64 Score=21.55 Aligned_cols=21 Identities=38% Similarity=0.703 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+.+|+++..|..|-.
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999999965
No 122
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=27.40 E-value=69 Score=21.27 Aligned_cols=25 Identities=20% Similarity=0.204 Sum_probs=20.8
Q ss_pred EeecCCcHHHHHHHhC-CCHHHHHhh
Q 047095 121 PIELGENLSTIANMSG-LSPELLQSY 145 (188)
Q Consensus 121 ~V~~GDTl~~IA~~~~-vs~~~l~~~ 145 (188)
..+.|.|...|+..|. ++.++|.+.
T Consensus 39 ~l~~G~s~eeil~dyp~Lt~~dI~aa 64 (79)
T COG2442 39 MLAAGESIEEILADYPDLTLEDIRAA 64 (79)
T ss_pred HHHCCCCHHHHHHhCCCCCHHHHHHH
Confidence 3467999999999998 899888764
No 123
>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=27.19 E-value=49 Score=22.44 Aligned_cols=26 Identities=23% Similarity=0.346 Sum_probs=22.5
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhhcCC
Q 047095 123 ELGENLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~N~~ 148 (188)
+.|-|.-.||++.|+|...|.+.|+.
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 46889999999999999999887753
No 124
>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=26.81 E-value=53 Score=20.55 Aligned_cols=18 Identities=11% Similarity=0.154 Sum_probs=13.8
Q ss_pred HHHHHHhCCCHHHHHhhc
Q 047095 129 STIANMSGLSPELLQSYN 146 (188)
Q Consensus 129 ~~IA~~~~vs~~~l~~~N 146 (188)
=.-|++|||+...+.+|=
T Consensus 29 RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 29 RAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp HHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHhCccHHHHHHHH
Confidence 346899999999988883
No 125
>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=26.79 E-value=67 Score=21.95 Aligned_cols=21 Identities=29% Similarity=0.548 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|+.+|++...|..|-.
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye~ 22 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYES 22 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999965
No 126
>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=26.60 E-value=24 Score=23.67 Aligned_cols=23 Identities=26% Similarity=0.336 Sum_probs=15.6
Q ss_pred EEEeecCCcHHHHHHHhCCCHHH
Q 047095 119 TYPIELGENLSTIANMSGLSPEL 141 (188)
Q Consensus 119 ~y~V~~GDTl~~IA~~~~vs~~~ 141 (188)
.|.+..+.|+=..|+.||+|-+.
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 37778889999999999997643
No 127
>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=26.59 E-value=68 Score=21.84 Aligned_cols=21 Identities=24% Similarity=0.458 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|+++|++...|..|-.
T Consensus 2 ~I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 2 KVDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999954
No 128
>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=26.34 E-value=46 Score=18.21 Aligned_cols=17 Identities=6% Similarity=0.208 Sum_probs=13.7
Q ss_pred ChhHHHHcCCCHHHHHh
Q 047095 1 MTFISEMFDTSIDNILS 17 (188)
Q Consensus 1 L~~IA~~~gvs~~~l~~ 17 (188)
|..+|++.|+|.+++.+
T Consensus 14 l~~~a~~~g~s~s~~ir 30 (39)
T PF01402_consen 14 LDELAKELGRSRSELIR 30 (39)
T ss_dssp HHHHHHHHTSSHHHHHH
T ss_pred HHHHHHHHCcCHHHHHH
Confidence 35789999999988764
No 129
>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=26.11 E-value=69 Score=22.21 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=18.2
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|+++|++...|.-|-.
T Consensus 2 ~i~eva~~~gis~~tlR~ye~ 22 (108)
T cd01107 2 TIGEFAKLSNLSIKALRYYDK 22 (108)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999865
No 130
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=25.96 E-value=81 Score=18.39 Aligned_cols=19 Identities=16% Similarity=0.163 Sum_probs=15.0
Q ss_pred cHHHHHHHhCCCHHHHHhh
Q 047095 127 NLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~ 145 (188)
|.-.||++||++...+.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~ 40 (60)
T smart00345 22 SERELAAQLGVSRTTVREA 40 (60)
T ss_pred CHHHHHHHHCCCHHHHHHH
Confidence 6778999999988666553
No 131
>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=25.90 E-value=75 Score=21.24 Aligned_cols=20 Identities=30% Similarity=0.300 Sum_probs=16.7
Q ss_pred CcHHHHHHHhCCCHHHHHhh
Q 047095 126 ENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 126 DTl~~IA~~~~vs~~~l~~~ 145 (188)
..|+.+|++.|++.++|-.+
T Consensus 55 ~kL~~La~~N~v~feeLc~Y 74 (82)
T PF11020_consen 55 SKLYKLAKENNVSFEELCVY 74 (82)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 46889999999999998654
No 132
>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=25.64 E-value=77 Score=21.10 Aligned_cols=19 Identities=16% Similarity=0.223 Sum_probs=16.0
Q ss_pred cHHHHHHHhCCCHHHHHhh
Q 047095 127 NLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~ 145 (188)
|+.+||+.||+|...+...
T Consensus 21 ti~dvA~~~gvS~~TVsr~ 39 (80)
T TIGR02844 21 TVRETAKVFGVSKSTVHKD 39 (80)
T ss_pred CHHHHHHHhCCCHHHHHHH
Confidence 7899999999998777653
No 133
>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=25.62 E-value=73 Score=21.58 Aligned_cols=21 Identities=29% Similarity=0.555 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|+.+|++...|.-|-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 2 KIGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456899999999999999965
No 134
>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=25.31 E-value=74 Score=21.58 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+.+|++...|.-|-.
T Consensus 2 ~i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 2 TTGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999955
No 135
>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=25.24 E-value=96 Score=20.31 Aligned_cols=23 Identities=26% Similarity=0.329 Sum_probs=20.0
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..|-|...||+..|+|...+..+
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~ 52 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNH 52 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999999888766
No 136
>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=25.24 E-value=1e+02 Score=17.12 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.7
Q ss_pred cCCcHHHHHHHhCCCHHHHHhh
Q 047095 124 LGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 124 ~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
.|-+...||..+|++...+..+
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6788999999999998877654
No 137
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=25.23 E-value=69 Score=29.21 Aligned_cols=27 Identities=15% Similarity=0.304 Sum_probs=21.8
Q ss_pred eecCCcHHHHHHHhCCCH----HHHHhhcCC
Q 047095 122 IELGENLSTIANMSGLSP----ELLQSYNRG 148 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~----~~l~~~N~~ 148 (188)
+.++|||..+|++.|++. +.+.+||..
T Consensus 421 ~~kadTleELA~k~gid~~~L~~TV~~yN~~ 451 (564)
T PRK12845 421 AHRADSLADLARKIGVPVDTFVATMRRFNEM 451 (564)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 347899999999999976 456678864
No 138
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.14 E-value=63 Score=23.90 Aligned_cols=25 Identities=16% Similarity=0.127 Sum_probs=21.1
Q ss_pred EeecCCcHHHHHHHhCCCHHHHHhh
Q 047095 121 PIELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 121 ~V~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
.+..|.+.-.||++||++...+..|
T Consensus 17 ~~~~G~S~re~Ak~~gvs~sTvy~w 41 (138)
T COG3415 17 VVGEGLSCREAAKRFGVSISTVYRW 41 (138)
T ss_pred HHHcCccHHHHHHHhCccHHHHHHH
Confidence 3467999999999999998777776
No 139
>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=24.96 E-value=77 Score=21.10 Aligned_cols=22 Identities=18% Similarity=0.572 Sum_probs=19.1
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
|+..+|+.+|++...|..|...
T Consensus 3 ti~evA~~~gvs~~tLR~ye~~ 24 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWEEK 24 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999999653
No 140
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=24.40 E-value=73 Score=28.50 Aligned_cols=26 Identities=15% Similarity=0.264 Sum_probs=21.0
Q ss_pred ecCCcHHHHHHHhCCCH----HHHHhhcCC
Q 047095 123 ELGENLSTIANMSGLSP----ELLQSYNRG 148 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~----~~l~~~N~~ 148 (188)
.+.|||..+|++.|++. +.+.+||..
T Consensus 373 ~kaDTleELA~k~gid~~~L~~Tv~~yN~~ 402 (513)
T PRK12837 373 RTADTLEELAAKIGVPADALTATVARFNGF 402 (513)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 46899999999999976 455678864
No 141
>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=24.27 E-value=77 Score=22.35 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=18.9
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
|+..+|+++|++...|.-|-..
T Consensus 2 ~I~eva~~~gvs~~tLRyYe~~ 23 (123)
T cd04770 2 KIGELAKAAGVSPDTIRYYERI 23 (123)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999988654
No 142
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=23.96 E-value=1.6e+02 Score=22.40 Aligned_cols=44 Identities=20% Similarity=0.096 Sum_probs=28.4
Q ss_pred cHHHHHHHhCC-C----HHHHHhhcCCCCCCCCEEEEcCCCCCCCCCCcccCCCC
Q 047095 127 NLSTIANMSGL-S----PELLQSYNRGSDFSSGLVFIPEKDQSGKYPPLQMSRDG 176 (188)
Q Consensus 127 Tl~~IA~~~~v-s----~~~l~~~N~~~~~~g~~l~iP~~~~~~~~~p~~~~~~~ 176 (188)
|+..||++-|. + +..-...|++ -|+||+...-+.--.+-.++-|
T Consensus 107 TY~eiA~~ig~p~a~rAVG~A~~~NPl------~IiIPCHRVig~~G~L~Gy~~G 155 (168)
T COG0350 107 TYGEIARRLGRPTAVRAVGNANGANPL------PIIIPCHRVIGADGDLGGYAGG 155 (168)
T ss_pred eHHHHHHHhCCCcHHHHHHHHhccCCc------eEEecCeEeEcCCCCccCccch
Confidence 67899999997 3 3333444554 4899998865544444455554
No 143
>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=23.88 E-value=95 Score=17.73 Aligned_cols=18 Identities=22% Similarity=0.350 Sum_probs=13.0
Q ss_pred CcHHHHHHHhCCCHHHHH
Q 047095 126 ENLSTIANMSGLSPELLQ 143 (188)
Q Consensus 126 DTl~~IA~~~~vs~~~l~ 143 (188)
-++..||++.|+|...+.
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 367899999999887654
No 144
>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=23.87 E-value=81 Score=21.53 Aligned_cols=20 Identities=25% Similarity=0.574 Sum_probs=17.5
Q ss_pred cHHHHHHHhCCCHHHHHhhc
Q 047095 127 NLSTIANMSGLSPELLQSYN 146 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N 146 (188)
|...+|+.+|++...|..|=
T Consensus 2 ti~eva~~~gvs~~tlR~ye 21 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYD 21 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999883
No 145
>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=23.52 E-value=82 Score=22.10 Aligned_cols=22 Identities=14% Similarity=0.389 Sum_probs=19.1
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
|+..+|+.+|+|...|.-|-..
T Consensus 2 ~ige~a~~~gvs~~tLryYe~~ 23 (116)
T cd04769 2 YIGELAQQTGVTIKAIRLYEEK 23 (116)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999999764
No 146
>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=23.52 E-value=79 Score=22.60 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=18.7
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
++..+|+++|++...|.-|-..
T Consensus 2 ~I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 2 NIGEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999988553
No 147
>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=23.51 E-value=78 Score=19.02 Aligned_cols=22 Identities=27% Similarity=0.314 Sum_probs=17.2
Q ss_pred ecCCcHHHHHHHhCCCHHHHHh
Q 047095 123 ELGENLSTIANMSGLSPELLQS 144 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~ 144 (188)
..|-+...||+..|++...+..
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~ 37 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKS 37 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHH
T ss_pred HhcCCcchhHHhcCcchhhHHH
Confidence 4688999999999998876654
No 148
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=23.42 E-value=91 Score=19.31 Aligned_cols=18 Identities=39% Similarity=0.597 Sum_probs=14.2
Q ss_pred cHHHHHHHhCCCHHHHHh
Q 047095 127 NLSTIANMSGLSPELLQS 144 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~ 144 (188)
|+..||+++|++...|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~ 20 (84)
T smart00342 3 TLEDLAEALGMSPRHLQR 20 (84)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 678899999998866644
No 149
>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=23.40 E-value=85 Score=21.54 Aligned_cols=22 Identities=27% Similarity=0.430 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
++..+|+++|++...|.-|-..
T Consensus 3 ~i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 3 TISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999988553
No 150
>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=23.20 E-value=65 Score=22.00 Aligned_cols=26 Identities=27% Similarity=0.248 Sum_probs=17.8
Q ss_pred ecCCcHH-HHHHHhCCCHHHHHhhcCC
Q 047095 123 ELGENLS-TIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 123 ~~GDTl~-~IA~~~~vs~~~l~~~N~~ 148 (188)
..|-+-. .-.++|++|.+++..|=..
T Consensus 46 ~~Glis~~EA~~rY~Ls~eEf~~W~~a 72 (90)
T PF06627_consen 46 RGGLISVEEACRRYGLSEEEFESWQRA 72 (90)
T ss_dssp HCTTS-HHHHHHCTTSSHHHHHHHHHH
T ss_pred HcCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3455444 4448999999999999543
No 151
>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=23.16 E-value=91 Score=19.14 Aligned_cols=18 Identities=17% Similarity=0.169 Sum_probs=12.6
Q ss_pred HHHHHHHhCCCHHHHHhh
Q 047095 128 LSTIANMSGLSPELLQSY 145 (188)
Q Consensus 128 l~~IA~~~~vs~~~l~~~ 145 (188)
...||++||++...+.++
T Consensus 27 ~~~la~~~~vsr~tvr~a 44 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREA 44 (64)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHhccCCcHHHHH
Confidence 368899999988666543
No 152
>PF02515 CoA_transf_3: CoA-transferase family III; InterPro: IPR003673 CoA-transferases are found in organisms from all kingdoms of life. They catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids. There are at least three families of CoA-transferases, which differ in sequence and reaction mechanism: Family I consists of CoA-transferases for 3-oxoacids (2.8.3.5 from EC, 2.8.3.6 from EC), short-chain fatty acids (2.8.3.8 from EC, 2.8.3.9 from EC) and glutaconate (2.8.3.12 from EC). Most use succinyl-CoA or acetyl-CoA as CoA donors. Family II consists of the homodimeric alpha-subunits of citrate lyase and citramalate lyase (2.8.3.10 from EC, 2.8.3.11 from EC). These enzymes catalyse the transfer of acyl carrier protein (ACP) with a covalently bound CoA derivative, but can accept free CoA thioesters as well. Family III consists of formyl-CoA:oxalate CoA-transferase [], succinyl-CoA:(R)-benzylsuccinate CoA-transferase [], (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase [], and butyrobetainyl-CoA:(R)-carnitine CoA-transferase []. These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate- and stereo-specific manner []. This entry represents family III CoA-transferases.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1PT7_B 1PT8_A 1PQY_A 1Q7E_A 1Q6Y_A 1PT5_A 1XK6_B 1XK7_C 1XVT_A 1XVU_A ....
Probab=22.97 E-value=60 Score=24.96 Aligned_cols=19 Identities=16% Similarity=0.410 Sum_probs=14.3
Q ss_pred HHHHcCCCHHHHHhcCCCC
Q 047095 4 ISEMFDTSIDNILSFNPQV 22 (188)
Q Consensus 4 IA~~~gvs~~~l~~~Np~l 22 (188)
..+++|++.++|++.||+|
T Consensus 32 ~~~~lGl~~~~l~~~nP~L 50 (191)
T PF02515_consen 32 VLERLGLDYEALRAINPRL 50 (191)
T ss_dssp HHHHTT-SHHHHHHH-TT-
T ss_pred hhHhcCCCHHHHHhhCCCC
Confidence 5678999999999999965
No 153
>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=22.78 E-value=88 Score=21.84 Aligned_cols=22 Identities=23% Similarity=0.409 Sum_probs=18.7
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
++..+|+++|+|...|.-|-..
T Consensus 2 ~i~eva~~~gvs~~tlR~Ye~~ 23 (112)
T cd01282 2 RIGELAARTGVSVRSLRYYEEQ 23 (112)
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
Confidence 4678999999999999999653
No 154
>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=22.51 E-value=85 Score=22.40 Aligned_cols=21 Identities=29% Similarity=0.735 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|+++|+|...|.-|-.
T Consensus 2 ~I~e~a~~~gvs~~tlRyYe~ 22 (127)
T TIGR02044 2 NIGQVAKLTGLSSKMIRYYEE 22 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998854
No 155
>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=22.27 E-value=95 Score=18.23 Aligned_cols=17 Identities=18% Similarity=0.284 Sum_probs=12.8
Q ss_pred cHHHHHHHhCCCHHHHH
Q 047095 127 NLSTIANMSGLSPELLQ 143 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~ 143 (188)
|...||+++|+|...+.
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 77899999999875443
No 156
>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=22.23 E-value=88 Score=22.33 Aligned_cols=22 Identities=18% Similarity=0.388 Sum_probs=18.7
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
++..+|+.+|++...|.-|-..
T Consensus 2 ~I~e~a~~~gvs~~tlR~Ye~~ 23 (126)
T cd04785 2 SIGELARRTGVNVETIRYYESI 23 (126)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999988553
No 157
>PRK12839 hypothetical protein; Provisional
Probab=22.18 E-value=87 Score=28.58 Aligned_cols=26 Identities=19% Similarity=0.521 Sum_probs=21.2
Q ss_pred ecCCcHHHHHHHhCCCH----HHHHhhcCC
Q 047095 123 ELGENLSTIANMSGLSP----ELLQSYNRG 148 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~----~~l~~~N~~ 148 (188)
.++|||..+|++.|++. +.+.+||..
T Consensus 425 ~kadTleELA~k~gid~~~L~~TV~~yN~~ 454 (572)
T PRK12839 425 TRGRTIEELAEKCGIDPAGLEATVAEFNEN 454 (572)
T ss_pred EECCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 36899999999999976 556778864
No 158
>PF14502 HTH_41: Helix-turn-helix domain
Probab=21.86 E-value=1.1e+02 Score=18.41 Aligned_cols=19 Identities=21% Similarity=0.253 Sum_probs=14.6
Q ss_pred cHHHHHHHhCCCHHHHHhh
Q 047095 127 NLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~ 145 (188)
|+.+.+++|+++...++.+
T Consensus 8 tI~e~~~~~~vs~GtiQ~A 26 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNA 26 (48)
T ss_pred CHHHHHHHhCcchhHHHHH
Confidence 6778889999988666554
No 159
>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=21.74 E-value=1e+02 Score=18.84 Aligned_cols=23 Identities=30% Similarity=0.310 Sum_probs=17.2
Q ss_pred EeecCCcHHHHHHHhCCCHHHHH
Q 047095 121 PIELGENLSTIANMSGLSPELLQ 143 (188)
Q Consensus 121 ~V~~GDTl~~IA~~~~vs~~~l~ 143 (188)
++.+-.|+...|+..|++++.|.
T Consensus 37 ~~~~~~Tl~~aa~~~gid~~~li 59 (59)
T PF08984_consen 37 TMAKFETLEQAAKMHGIDLEKLI 59 (59)
T ss_dssp THHHHSBHHHHHHHHT--HHHHH
T ss_pred hhcccCCHHHHHHHcCCCHHHhC
Confidence 44567899999999999998774
No 160
>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=21.67 E-value=79 Score=18.58 Aligned_cols=21 Identities=19% Similarity=0.308 Sum_probs=17.9
Q ss_pred CCcHHHHHHHhCCCHHHHHhh
Q 047095 125 GENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 125 GDTl~~IA~~~~vs~~~l~~~ 145 (188)
.+.+..||...|++...+..|
T Consensus 27 ~~~~~~la~~~~l~~~qV~~W 47 (59)
T cd00086 27 REEREELAKELGLTERQVKIW 47 (59)
T ss_pred HHHHHHHHHHHCcCHHHHHHH
Confidence 346789999999999999887
No 161
>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=21.64 E-value=1.2e+02 Score=16.61 Aligned_cols=26 Identities=23% Similarity=0.327 Sum_probs=20.7
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhhcCC
Q 047095 123 ELGENLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~N~~ 148 (188)
+.|-+...+|+..|++...+.+|-..
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 35778889999999998888887544
No 162
>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=21.53 E-value=95 Score=22.35 Aligned_cols=21 Identities=24% Similarity=0.567 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|+++|++...|..|=.
T Consensus 3 sI~eVA~~~GVs~~TLR~wE~ 23 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWER 23 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998844
No 163
>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=21.30 E-value=98 Score=21.20 Aligned_cols=19 Identities=26% Similarity=0.690 Sum_probs=17.2
Q ss_pred cHHHHHHHhCCCHHHHHhh
Q 047095 127 NLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~ 145 (188)
|+..+|+.+|++...|..|
T Consensus 2 ti~EvA~~~gVs~~tLR~y 20 (99)
T cd04765 2 SIGEVAEILGLPPHVLRYW 20 (99)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4678999999999999999
No 164
>PRK00118 putative DNA-binding protein; Validated
Probab=20.78 E-value=1.2e+02 Score=21.32 Aligned_cols=23 Identities=17% Similarity=0.024 Sum_probs=19.1
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhh
Q 047095 123 ELGENLSTIANMSGLSPELLQSY 145 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~ 145 (188)
..|-|...||+.+|+|...+..+
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r~ 53 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDN 53 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 35889999999999998877654
No 165
>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=20.66 E-value=1.2e+02 Score=17.44 Aligned_cols=26 Identities=19% Similarity=0.507 Sum_probs=21.4
Q ss_pred ecCCcHHHHHHHhCCCHHHHHhhcCC
Q 047095 123 ELGENLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 123 ~~GDTl~~IA~~~~vs~~~l~~~N~~ 148 (188)
+.|-|...+|++.|++...+.+|-+.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 45778899999999999999888544
No 166
>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=20.51 E-value=99 Score=22.02 Aligned_cols=21 Identities=24% Similarity=0.566 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
|+..+|+++|+++..|..|-.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~ 21 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYER 21 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999954
No 167
>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=20.46 E-value=1.1e+02 Score=20.60 Aligned_cols=21 Identities=24% Similarity=0.496 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHhhcC
Q 047095 127 NLSTIANMSGLSPELLQSYNR 147 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~ 147 (188)
++..+|+.+|++...|..|-.
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999999954
No 168
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=20.45 E-value=2.3e+02 Score=21.42 Aligned_cols=34 Identities=26% Similarity=0.347 Sum_probs=26.6
Q ss_pred cHHHHHHHhCCCHHHHHhhcCCCC----CC--CCEEEEcC
Q 047095 127 NLSTIANMSGLSPELLQSYNRGSD----FS--SGLVFIPE 160 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~~~----~~--g~~l~iP~ 160 (188)
+..++|+.|+++.+.+.++..... .+ |+++-|-.
T Consensus 100 ~~dElA~sF~l~~e~i~qLr~~kiltVh~De~G~Ii~V~~ 139 (153)
T PRK14584 100 DDDELASSFALSPELIAQLKSGSCLTLYNDEHGHIIDVKE 139 (153)
T ss_pred ChHHHHHHcCCCHHHHHHHHhCCeEEEEECCCCCEEEeec
Confidence 567899999999999999977654 22 88887743
No 169
>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=20.22 E-value=1e+02 Score=21.91 Aligned_cols=22 Identities=23% Similarity=0.468 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHhhcCC
Q 047095 127 NLSTIANMSGLSPELLQSYNRG 148 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~ 148 (188)
++..+|+++|+|...|.-|-..
T Consensus 2 ~IgevA~~~gvs~~tLRyYe~~ 23 (127)
T cd04784 2 KIGELAKKTGCSVETIRYYEKE 23 (127)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 4678999999999999998653
No 170
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=20.17 E-value=62 Score=24.95 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=22.3
Q ss_pred eecCCcHHHHHHHhCCCHHHHHhh---cCCC
Q 047095 122 IELGENLSTIANMSGLSPELLQSY---NRGS 149 (188)
Q Consensus 122 V~~GDTl~~IA~~~~vs~~~l~~~---N~~~ 149 (188)
|..|+++-.+|++.|++.+++-+. ||-.
T Consensus 29 vsaG~iFR~~A~e~gmsl~ef~~~AE~~p~i 59 (179)
T COG1102 29 VSAGTIFREMARERGMSLEEFSRYAEEDPEI 59 (179)
T ss_pred eeccHHHHHHHHHcCCCHHHHHHHHhcCchh
Confidence 578999999999999998766554 5543
No 171
>PF12728 HTH_17: Helix-turn-helix domain
Probab=20.14 E-value=1.2e+02 Score=17.42 Aligned_cols=34 Identities=21% Similarity=0.318 Sum_probs=22.4
Q ss_pred cHHHHHHHhCCCHHHHHhhcCCCC---CC-CCEEEEcC
Q 047095 127 NLSTIANMSGLSPELLQSYNRGSD---FS-SGLVFIPE 160 (188)
Q Consensus 127 Tl~~IA~~~~vs~~~l~~~N~~~~---~~-g~~l~iP~ 160 (188)
|...+|+.+|++...+.+|=.... +. |...+++.
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g~i~~~~~g~~~~~~~ 40 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQGKIPPFKIGRKWRIPK 40 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCeEEeCCEEEEeH
Confidence 467889999999988888822112 22 55566553
Done!