Query 040730
Match_columns 144
No_of_seqs 163 out of 1208
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 11:12:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040730.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040730hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06347 autolysin; Reviewed 99.9 4.7E-25 1E-29 184.8 13.3 135 1-144 430-586 (592)
2 PRK06347 autolysin; Reviewed 99.9 7.7E-23 1.7E-27 171.5 13.1 135 1-144 355-518 (592)
3 PRK10783 mltD membrane-bound l 99.9 1E-21 2.2E-26 161.2 12.5 131 9-144 290-441 (456)
4 PRK13914 invasion associated s 99.7 1.2E-16 2.7E-21 130.6 11.5 46 43-90 28-74 (481)
5 PRK10783 mltD membrane-bound l 99.5 1.1E-13 2.4E-18 113.9 8.5 81 1-90 368-449 (456)
6 PF01476 LysM: LysM domain; I 99.4 5.3E-13 1.1E-17 75.7 3.5 42 45-88 1-44 (44)
7 COG1388 LytE FOG: LysM repeat 99.3 3.2E-12 6.9E-17 87.9 7.0 87 56-144 1-105 (124)
8 PF01476 LysM: LysM domain; I 99.3 3.3E-12 7.2E-17 72.4 3.2 37 108-144 1-38 (44)
9 PRK14125 cell division suppres 99.1 1.7E-10 3.7E-15 77.2 6.5 49 41-91 35-92 (103)
10 COG1388 LytE FOG: LysM repeat 99.0 1E-09 2.2E-14 75.4 6.7 82 2-90 13-113 (124)
11 TIGR02899 spore_safA spore coa 99.0 1.1E-09 2.4E-14 61.4 4.5 40 47-88 1-43 (44)
12 cd00118 LysM Lysin domain, fou 99.0 2.1E-09 4.6E-14 59.6 5.4 43 44-88 2-46 (46)
13 PRK14125 cell division suppres 98.9 1.5E-09 3.3E-14 72.6 5.1 41 104-144 35-83 (103)
14 COG3858 Predicted glycosyl hyd 98.9 1.7E-09 3.8E-14 87.0 4.9 80 43-138 2-82 (423)
15 PRK10871 nlpD lipoprotein NlpD 98.9 2.6E-09 5.7E-14 84.2 5.2 47 42-90 60-108 (319)
16 TIGR02907 spore_VI_D stage VI 98.8 5.7E-09 1.2E-13 82.0 5.7 44 43-88 294-338 (338)
17 cd00118 LysM Lysin domain, fou 98.8 1.6E-08 3.4E-13 55.9 4.7 38 107-144 2-40 (46)
18 TIGR02899 spore_safA spore coa 98.7 1.8E-08 3.9E-13 56.3 3.7 35 110-144 1-37 (44)
19 TIGR02907 spore_VI_D stage VI 98.7 2.9E-08 6.2E-13 78.2 5.1 41 104-144 292-332 (338)
20 smart00257 LysM Lysin motif. 98.6 9.4E-08 2E-12 52.1 5.2 42 44-87 1-44 (44)
21 smart00257 LysM Lysin motif. 98.6 7.3E-08 1.6E-12 52.6 4.3 38 107-144 1-39 (44)
22 PRK13914 invasion associated s 98.6 8.9E-08 1.9E-12 79.0 5.9 46 43-90 200-246 (481)
23 PRK10871 nlpD lipoprotein NlpD 98.6 6.5E-08 1.4E-12 76.4 4.3 39 106-144 61-100 (319)
24 PRK11198 LysM domain/BON super 98.5 1.3E-07 2.8E-12 67.1 5.1 46 43-88 96-146 (147)
25 COG3858 Predicted glycosyl hyd 98.0 9.7E-06 2.1E-10 65.7 5.4 62 16-90 34-97 (423)
26 PRK11198 LysM domain/BON super 98.0 7.8E-06 1.7E-10 58.0 4.2 40 105-144 95-140 (147)
27 COG1652 XkdP Uncharacterized p 97.6 2.7E-05 5.9E-10 60.2 1.2 48 43-90 211-264 (269)
28 PRK10190 L,D-transpeptidase; P 97.5 0.00022 4.8E-09 56.2 6.0 46 43-90 38-87 (310)
29 PRK10260 L,D-transpeptidase; P 97.5 0.00024 5.1E-09 55.9 5.9 46 43-90 41-90 (306)
30 PF04225 OapA: Opacity-associa 97.4 0.00014 3E-09 46.9 2.4 46 43-90 3-54 (85)
31 TIGR03505 FimV_core FimV N-ter 97.0 0.00072 1.6E-08 42.5 3.1 40 51-90 1-52 (74)
32 PF04225 OapA: Opacity-associa 97.0 0.00092 2E-08 43.1 3.4 28 106-133 3-30 (85)
33 PF05489 Phage_tail_X: Phage T 96.7 0.0026 5.7E-08 38.3 3.7 45 45-90 4-54 (60)
34 COG3061 OapA Cell envelope opa 95.9 0.038 8.2E-07 41.6 6.8 75 15-91 131-212 (242)
35 PRK11649 putative peptidase; P 95.8 0.061 1.3E-06 44.7 8.2 91 43-135 96-214 (439)
36 PRK10260 L,D-transpeptidase; P 95.1 0.044 9.6E-07 43.3 4.8 36 104-139 39-76 (306)
37 PRK10190 L,D-transpeptidase; P 95.0 0.048 1E-06 43.2 4.8 36 104-139 36-73 (310)
38 COG3170 FimV Tfp pilus assembl 94.3 0.034 7.3E-07 48.3 2.7 49 42-90 188-248 (755)
39 COG1652 XkdP Uncharacterized p 94.2 0.016 3.4E-07 44.9 0.4 39 106-144 211-256 (269)
40 TIGR03505 FimV_core FimV N-ter 93.8 0.065 1.4E-06 33.6 2.6 22 114-135 1-30 (74)
41 PRK11649 putative peptidase; P 92.8 0.15 3.2E-06 42.4 4.0 28 106-133 96-123 (439)
42 PF05489 Phage_tail_X: Phage T 90.6 0.39 8.4E-06 28.8 3.1 26 111-136 6-35 (60)
43 PF13518 HTH_28: Helix-turn-he 89.6 0.39 8.4E-06 27.1 2.5 24 111-134 10-33 (52)
44 PF02796 HTH_7: Helix-turn-hel 88.4 0.61 1.3E-05 26.0 2.7 23 111-133 19-41 (45)
45 COG4784 Putative Zn-dependent 87.0 1 2.2E-05 36.5 4.1 45 43-87 429-476 (479)
46 PF01527 HTH_Tnp_1: Transposas 85.9 0.51 1.1E-05 28.9 1.6 24 110-133 20-43 (76)
47 COG5004 P2-like prophage tail 85.2 1.6 3.6E-05 26.5 3.4 47 44-90 4-56 (70)
48 COG4254 Uncharacterized protei 84.7 0.91 2E-05 35.9 2.7 49 43-91 6-57 (339)
49 KOG2850 Predicted peptidoglyca 82.5 0.76 1.6E-05 33.9 1.4 47 43-91 10-58 (186)
50 PF13384 HTH_23: Homeodomain-l 80.6 2.1 4.6E-05 23.9 2.6 23 111-133 15-37 (50)
51 COG3170 FimV Tfp pilus assembl 80.0 1.1 2.3E-05 39.4 1.7 33 104-136 187-227 (755)
52 COG2963 Transposase and inacti 79.5 2.1 4.6E-05 28.5 2.8 24 110-133 21-45 (116)
53 PRK09413 IS2 repressor TnpA; R 78.6 2.4 5.1E-05 28.8 2.8 25 109-133 25-49 (121)
54 PF04218 CENP-B_N: CENP-B N-te 77.8 1.1 2.3E-05 26.0 0.8 23 110-132 19-41 (53)
55 PHA00675 hypothetical protein 77.6 2.8 6.1E-05 26.4 2.6 23 111-133 37-59 (78)
56 COG0739 NlpD Membrane proteins 75.4 5.2 0.00011 30.3 4.2 45 44-90 3-49 (277)
57 KOG2850 Predicted peptidoglyca 75.2 2 4.4E-05 31.6 1.8 32 105-136 9-40 (186)
58 COG3061 OapA Cell envelope opa 73.0 7.8 0.00017 29.4 4.4 32 104-135 158-189 (242)
59 cd00569 HTH_Hin_like Helix-tur 72.6 5.8 0.00013 19.2 2.8 23 111-133 19-41 (42)
60 PF05225 HTH_psq: helix-turn-h 72.2 4 8.6E-05 22.8 2.1 24 110-133 12-36 (45)
61 PF13936 HTH_38: Helix-turn-he 70.2 5.9 0.00013 21.8 2.6 23 110-132 17-39 (44)
62 PF00376 MerR: MerR family reg 67.8 7.1 0.00015 21.0 2.5 22 115-136 1-22 (38)
63 PF04545 Sigma70_r4: Sigma-70, 67.3 8.8 0.00019 21.4 3.0 22 111-132 18-39 (50)
64 PF12471 GTP_CH_N: GTP cyclohy 67.0 4.3 9.2E-05 29.9 1.9 24 110-133 167-190 (194)
65 PF10668 Phage_terminase: Phag 65.2 8.2 0.00018 23.1 2.6 23 113-135 22-44 (60)
66 PF13542 HTH_Tnp_ISL3: Helix-t 64.9 8.7 0.00019 21.5 2.6 21 113-133 27-47 (52)
67 COG4784 Putative Zn-dependent 63.9 13 0.00029 30.3 4.3 40 105-144 428-471 (479)
68 PF13693 HTH_35: Winged helix- 63.1 8.4 0.00018 24.4 2.5 22 111-132 13-34 (78)
69 PF04255 DUF433: Protein of un 63.0 9.2 0.0002 22.3 2.5 23 111-133 29-52 (56)
70 cd04762 HTH_MerR-trunc Helix-T 61.2 11 0.00024 20.1 2.6 20 115-134 2-21 (49)
71 PF08765 Mor: Mor transcriptio 61.1 9.3 0.0002 25.3 2.6 20 113-132 72-91 (108)
72 PF09012 FeoC: FeoC like trans 60.9 9.5 0.0002 23.0 2.4 20 114-133 15-34 (69)
73 cd04761 HTH_MerR-SF Helix-Turn 60.4 12 0.00025 20.4 2.6 20 115-134 2-21 (49)
74 cd01104 HTH_MlrA-CarA Helix-Tu 58.6 12 0.00026 22.1 2.6 20 115-134 2-21 (68)
75 PF13613 HTH_Tnp_4: Helix-turn 57.7 10 0.00023 21.6 2.1 23 110-132 16-38 (53)
76 PF01710 HTH_Tnp_IS630: Transp 57.7 8.1 0.00018 26.0 1.9 24 110-133 15-38 (119)
77 PRK10270 putative aminodeoxych 57.2 40 0.00087 27.2 6.0 81 43-123 40-127 (340)
78 PF13411 MerR_1: MerR HTH fami 56.0 15 0.00032 21.7 2.7 21 115-135 2-22 (69)
79 smart00421 HTH_LUXR helix_turn 54.8 19 0.00042 19.7 3.0 24 110-133 15-38 (58)
80 PF00356 LacI: Bacterial regul 54.3 18 0.00039 20.3 2.7 21 115-135 1-22 (46)
81 PF08281 Sigma70_r4_2: Sigma-7 53.9 16 0.00034 20.5 2.5 22 111-132 24-45 (54)
82 smart00351 PAX Paired Box doma 52.9 15 0.00032 25.0 2.6 23 111-133 31-53 (125)
83 PF04967 HTH_10: HTH DNA bindi 52.9 15 0.00033 21.3 2.2 26 106-131 16-41 (53)
84 PF13011 LZ_Tnp_IS481: leucine 52.6 17 0.00036 23.4 2.6 24 110-133 22-45 (85)
85 TIGR02531 yecD_yerC TrpR-relat 51.3 17 0.00037 23.4 2.5 26 110-135 47-72 (88)
86 PF01371 Trp_repressor: Trp re 51.1 16 0.00034 23.6 2.3 25 111-135 47-71 (87)
87 smart00422 HTH_MERR helix_turn 51.1 19 0.00041 21.2 2.6 19 115-133 2-20 (70)
88 PF04760 IF2_N: Translation in 50.8 15 0.00033 20.9 2.0 18 115-132 5-22 (54)
89 PF08220 HTH_DeoR: DeoR-like h 50.4 18 0.0004 20.9 2.4 18 114-131 15-32 (57)
90 cd04764 HTH_MlrA-like_sg1 Heli 50.2 20 0.00044 21.1 2.6 19 115-133 2-20 (67)
91 TIGR01764 excise DNA binding d 50.1 22 0.00049 18.9 2.7 21 115-135 3-23 (49)
92 PRK10344 DNA-binding transcrip 47.2 26 0.00056 22.8 2.8 21 111-131 19-39 (92)
93 PF06056 Terminase_5: Putative 46.6 30 0.00065 20.4 2.9 23 112-134 12-34 (58)
94 TIGR00247 conserved hypothetic 45.6 75 0.0016 25.5 5.9 81 43-123 40-128 (342)
95 COG3415 Transposase and inacti 45.4 21 0.00045 25.1 2.4 25 109-133 17-41 (138)
96 cd06170 LuxR_C_like C-terminal 44.6 35 0.00076 18.7 3.0 23 111-133 13-35 (57)
97 PF12244 DUF3606: Protein of u 44.3 21 0.00045 21.0 1.9 18 116-133 23-40 (57)
98 PRK09413 IS2 repressor TnpA; R 44.2 27 0.00059 23.5 2.8 26 45-72 24-49 (121)
99 cd04763 HTH_MlrA-like Helix-Tu 43.9 28 0.00062 20.6 2.6 20 115-134 2-21 (68)
100 PF13551 HTH_29: Winged helix- 42.5 27 0.00059 22.4 2.5 24 110-133 8-32 (112)
101 smart00760 Bac_DnaA_C Bacteria 42.4 18 0.0004 21.1 1.5 22 114-135 4-25 (60)
102 PHA02591 hypothetical protein; 42.1 32 0.0007 21.8 2.6 21 111-131 57-77 (83)
103 PF11268 DUF3071: Protein of u 41.1 24 0.00053 25.6 2.3 25 109-133 65-89 (170)
104 TIGR02937 sigma70-ECF RNA poly 40.2 34 0.00075 22.5 2.9 23 111-133 124-146 (158)
105 cd00131 PAX Paired Box domain 39.6 31 0.00068 23.6 2.5 23 111-133 31-53 (128)
106 cd06171 Sigma70_r4 Sigma70, re 39.0 49 0.0011 17.5 2.9 22 112-133 25-46 (55)
107 COG3753 Uncharacterized protei 38.0 32 0.00069 24.1 2.3 20 113-132 90-109 (143)
108 cd04766 HTH_HspR Helix-Turn-He 37.7 38 0.00083 21.4 2.6 22 115-136 3-24 (91)
109 PF08299 Bac_DnaA_C: Bacterial 36.9 34 0.00074 20.8 2.2 18 115-132 5-22 (70)
110 PF12728 HTH_17: Helix-turn-he 36.1 48 0.001 18.3 2.6 19 115-133 3-21 (51)
111 TIGR03879 near_KaiC_dom probab 36.0 53 0.0011 20.4 2.9 23 111-133 30-52 (73)
112 smart00345 HTH_GNTR helix_turn 35.8 49 0.0011 18.3 2.7 18 115-132 22-39 (60)
113 PF11242 DUF2774: Protein of u 35.3 59 0.0013 19.6 2.9 21 111-131 11-31 (63)
114 smart00342 HTH_ARAC helix_turn 35.1 47 0.001 19.5 2.7 17 115-131 3-19 (84)
115 PF08984 DUF1858: Domain of un 34.8 43 0.00094 19.5 2.3 22 110-131 38-59 (59)
116 PF00392 GntR: Bacterial regul 34.7 47 0.001 19.4 2.5 22 111-132 19-43 (64)
117 COG0193 Pth Peptidyl-tRNA hydr 34.6 36 0.00078 25.2 2.3 62 53-131 27-89 (190)
118 TIGR02844 spore_III_D sporulat 34.4 46 0.001 21.0 2.5 20 113-132 19-38 (80)
119 PF08279 HTH_11: HTH domain; 34.4 44 0.00096 18.7 2.3 17 114-130 16-32 (55)
120 COG2739 Uncharacterized protei 33.5 44 0.00096 22.3 2.4 17 115-131 35-51 (105)
121 PF02618 YceG: YceG-like famil 33.3 9.4 0.0002 30.0 -1.0 81 44-124 2-89 (297)
122 TIGR01259 comE comEA protein. 33.2 64 0.0014 21.8 3.2 32 59-91 10-41 (120)
123 COG5484 Uncharacterized conser 33.2 42 0.0009 26.2 2.5 24 113-136 19-42 (279)
124 PF15508 NAAA-beta: beta subun 33.2 47 0.001 21.3 2.5 23 113-135 69-91 (95)
125 cd01105 HTH_GlnR-like Helix-Tu 32.9 51 0.0011 20.8 2.6 22 115-136 3-24 (88)
126 PF12844 HTH_19: Helix-turn-he 32.7 28 0.00062 20.1 1.3 19 114-132 42-60 (64)
127 PF00165 HTH_AraC: Bacterial r 32.3 60 0.0013 17.1 2.5 21 112-132 7-27 (42)
128 PRK00118 putative DNA-binding 32.1 59 0.0013 21.6 2.8 22 111-132 31-52 (104)
129 PF06627 DUF1153: Protein of u 31.5 49 0.0011 21.5 2.2 25 110-134 45-70 (90)
130 PF09607 BrkDBD: Brinker DNA-b 31.5 44 0.00096 19.9 1.9 20 115-134 27-46 (58)
131 PF00196 GerE: Bacterial regul 31.4 47 0.001 18.9 2.1 22 110-131 15-36 (58)
132 PF13510 Fer2_4: 2Fe-2S iron-s 31.3 55 0.0012 20.4 2.5 22 106-127 11-32 (82)
133 PF14453 ThiS-like: ThiS-like 30.8 63 0.0014 19.1 2.5 41 43-86 8-52 (57)
134 PF14502 HTH_41: Helix-turn-he 30.2 67 0.0014 18.4 2.4 19 114-132 7-25 (48)
135 COG3721 HugX Putative heme iro 29.8 65 0.0014 23.2 2.8 26 110-135 24-49 (176)
136 PF12116 SpoIIID: Stage III sp 29.8 19 0.00041 23.0 0.1 23 107-129 13-35 (82)
137 cd00093 HTH_XRE Helix-turn-hel 29.7 84 0.0018 16.3 2.9 26 111-136 10-35 (58)
138 PRK12845 3-ketosteroid-delta-1 29.4 52 0.0011 28.3 2.8 27 110-136 421-451 (564)
139 PF01381 HTH_3: Helix-turn-hel 29.1 78 0.0017 17.4 2.7 23 111-133 7-29 (55)
140 PHA01976 helix-turn-helix prot 28.8 84 0.0018 18.2 3.0 23 111-133 13-35 (67)
141 PF12298 Bot1p: Eukaryotic mit 28.8 69 0.0015 23.3 3.0 23 111-133 31-56 (172)
142 COG2442 Uncharacterized conser 28.7 79 0.0017 19.9 2.9 24 110-133 40-64 (79)
143 PF11268 DUF3071: Protein of u 28.5 50 0.0011 24.0 2.2 25 46-72 65-89 (170)
144 PRK07198 hypothetical protein; 28.0 39 0.00084 28.0 1.7 24 110-133 171-194 (418)
145 TIGR02950 SigM_subfam RNA poly 27.6 73 0.0016 21.5 2.9 21 112-132 120-140 (154)
146 PF13443 HTH_26: Cro/C1-type H 27.5 76 0.0016 18.1 2.6 23 112-134 9-31 (63)
147 TIGR00370 conserved hypothetic 27.5 1.4E+02 0.003 22.2 4.4 24 111-134 88-111 (202)
148 TIGR03070 couple_hipB transcri 27.4 94 0.002 17.0 2.9 25 111-135 13-37 (58)
149 PF13404 HTH_AsnC-type: AsnC-t 27.3 78 0.0017 17.2 2.4 19 113-131 17-35 (42)
150 PRK12837 3-ketosteroid-delta-1 26.9 63 0.0014 27.3 2.8 26 111-136 373-402 (513)
151 cd00086 homeodomain Homeodomai 26.5 60 0.0013 18.1 2.0 22 112-133 26-47 (59)
152 smart00530 HTH_XRE Helix-turn- 26.3 1E+02 0.0022 15.7 2.9 26 111-136 8-33 (56)
153 PF08769 Spo0A_C: Sporulation 25.8 79 0.0017 21.0 2.6 20 112-131 39-58 (106)
154 PF04297 UPF0122: Putative hel 25.3 77 0.0017 21.0 2.5 21 111-131 31-51 (101)
155 PRK12839 hypothetical protein; 24.9 71 0.0015 27.5 2.8 25 112-136 426-454 (572)
156 PF01402 RHH_1: Ribbon-helix-h 24.6 99 0.0021 15.9 2.5 19 114-132 12-30 (39)
157 cd07377 WHTH_GntR Winged helix 24.6 96 0.0021 17.4 2.7 18 115-132 27-44 (66)
158 PF14493 HTH_40: Helix-turn-he 24.6 91 0.002 19.7 2.7 21 111-131 11-31 (91)
159 PRK04217 hypothetical protein; 24.5 96 0.0021 20.8 2.8 21 112-132 57-77 (110)
160 PF14549 P22_Cro: DNA-binding 24.4 97 0.0021 18.4 2.6 19 115-133 11-29 (60)
161 PF13994 PgaD: PgaD-like prote 24.4 68 0.0015 22.2 2.2 25 114-138 101-125 (138)
162 PRK09652 RNA polymerase sigma 23.7 94 0.002 21.4 2.9 22 111-132 142-163 (182)
163 PRK12514 RNA polymerase sigma 22.4 96 0.0021 21.7 2.7 22 111-132 143-164 (179)
164 COG2771 CsgD DNA-binding HTH d 22.4 1E+02 0.0022 17.3 2.5 21 110-130 16-36 (65)
165 COG1102 Cmk Cytidylate kinase 22.3 65 0.0014 23.6 1.8 24 110-133 29-52 (179)
166 PF00046 Homeobox: Homeobox do 22.2 78 0.0017 17.7 1.9 21 113-133 27-47 (57)
167 PRK13413 mpi multiple promoter 22.0 1.1E+02 0.0023 22.3 3.0 24 111-134 170-193 (200)
168 PF13412 HTH_24: Winged helix- 21.9 1.4E+02 0.003 16.0 2.8 21 111-131 15-35 (48)
169 PRK12537 RNA polymerase sigma 21.7 1E+02 0.0022 21.8 2.7 23 110-132 146-168 (182)
170 PF01418 HTH_6: Helix-turn-hel 21.7 1E+02 0.0022 18.8 2.5 22 112-133 33-54 (77)
171 PRK11426 hypothetical protein; 21.6 77 0.0017 22.1 2.0 21 112-132 71-91 (132)
172 PF11020 DUF2610: Domain of un 21.5 1.1E+02 0.0025 19.4 2.5 19 114-132 55-73 (82)
173 TIGR03643 conserved hypothetic 21.5 1.2E+02 0.0027 18.8 2.6 20 114-133 14-33 (72)
174 COG3423 Nlp Predicted transcri 21.5 1.2E+02 0.0027 19.1 2.7 22 111-132 19-40 (82)
175 PRK06759 RNA polymerase factor 21.1 1.2E+02 0.0025 20.5 2.9 23 111-133 120-142 (154)
176 TIGR03826 YvyF flagellar opero 21.0 1.2E+02 0.0027 21.1 3.0 23 112-134 43-67 (137)
177 PHA00542 putative Cro-like pro 21.0 1.3E+02 0.0029 18.7 2.9 23 111-133 29-51 (82)
178 PRK11924 RNA polymerase sigma 20.9 1.1E+02 0.0025 20.9 2.8 22 112-133 140-161 (179)
179 TIGR02985 Sig70_bacteroi1 RNA 20.8 1.2E+02 0.0026 20.3 2.9 22 111-132 127-148 (161)
180 PF06413 Neugrin: Neugrin; In 20.8 93 0.002 23.7 2.4 19 115-133 31-49 (225)
181 TIGR02885 spore_sigF RNA polym 20.6 1.1E+02 0.0024 22.6 2.9 23 111-133 197-219 (231)
182 TIGR02008 fdx_plant ferredoxin 20.5 1.1E+02 0.0025 19.5 2.6 22 106-127 15-36 (97)
183 KOG3309 Ferredoxin [Energy pro 20.4 86 0.0019 22.5 2.0 24 105-128 55-78 (159)
184 PRK06134 putative FAD-binding 20.4 99 0.0022 26.6 2.8 26 111-136 427-456 (581)
185 PF10985 DUF2805: Protein of u 20.1 1.3E+02 0.0029 18.7 2.6 20 114-133 13-32 (73)
186 PF10543 ORF6N: ORF6N domain; 20.1 1.2E+02 0.0025 19.2 2.5 26 107-132 6-31 (88)
187 PRK10072 putative transcriptio 20.0 1.4E+02 0.0031 19.4 2.9 26 110-135 43-68 (96)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.93 E-value=4.7e-25 Score=184.80 Aligned_cols=135 Identities=19% Similarity=0.207 Sum_probs=104.1
Q ss_pred CcccCCCCCCCCCCCcceecCCCEEEEccCCCCCCC---------------CcccCceeeEeCCCCCHHHHHHHhCCCCC
Q 040730 1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDG---------------IRHSKSTTNNVRPADTIDSILNGFGGLVS 65 (144)
Q Consensus 1 l~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~~---------------~~~~~~~~y~V~~GdTl~~IA~~y~~~~~ 65 (144)
|+++|+|. .+.|.+||.|+||....-... ........|+|++|||||.||++|+ ++
T Consensus 430 L~~~N~l~-------s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sIAkkyg--VS 500 (592)
T PRK06347 430 LKSWNNLK-------SDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNK--VT 500 (592)
T ss_pred HHHHhCCC-------cceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHHHHHHC--CC
Confidence 46788886 457999999999974321000 0011235799999999999999999 99
Q ss_pred HHHHHhhcCCCCC-CCCCcEEEEecccccCCCC------CCCcccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCC
Q 040730 66 AEQINSTSELSHP-VNDWTKLMIMLPCTCFNNG------NNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQ 138 (144)
Q Consensus 66 ~~~l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~~------~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~ 138 (144)
+++|+++|++... |++||.|.||......... ..........|+|++|||||+||++||+++++|++||+|.+
T Consensus 501 v~~L~~~N~l~s~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~L~~ 580 (592)
T PRK06347 501 IANLKSWNNLKSDFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTS 580 (592)
T ss_pred HHHHHHhcCCCcccccCCcEEEEecCcccccccccCCccCCccCccceeeecCCCCcHHHHHHHhCCCHHHHHHhcCCCc
Confidence 9999999998876 9999999999754321100 00011235689999999999999999999999999999998
Q ss_pred CCcccC
Q 040730 139 SVVETF 144 (144)
Q Consensus 139 ~~i~~~ 144 (144)
..|+||
T Consensus 581 ~~L~~G 586 (592)
T PRK06347 581 NMIHVG 586 (592)
T ss_pred ccCCCC
Confidence 889987
No 2
>PRK06347 autolysin; Reviewed
Probab=99.89 E-value=7.7e-23 Score=171.51 Aligned_cols=135 Identities=19% Similarity=0.170 Sum_probs=103.0
Q ss_pred CcccCCCCCCCCCCCcceecCCCEEEEccCCCCCC-----C-----------CcccCceeeEeCCCCCHHHHHHHhCCCC
Q 040730 1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCID-----G-----------IRHSKSTTNNVRPADTIDSILNGFGGLV 64 (144)
Q Consensus 1 l~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~-----~-----------~~~~~~~~y~V~~GdTl~~IA~~y~~~~ 64 (144)
|++||+|. .+.|.+||.|+||....... . ........|+|++||||+.||++|+ +
T Consensus 355 L~~~N~l~-------~d~L~~Gq~L~VP~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~ytVk~GDTL~sIA~kyg--V 425 (592)
T PRK06347 355 LKAWNNLK-------SDFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGTSTNAKVYTVVKGDSLWRIANNNK--V 425 (592)
T ss_pred HHHHhCCC-------ccccccCcEEEEeccccccccccccccccccccccccccccCceeEEecCCCCHHHHHHHhC--C
Confidence 57889986 46799999999997421100 0 0011225899999999999999999 9
Q ss_pred CHHHHHhhcCCCCC-CCCCcEEEEecccccCCC----C--------CCCcccceEEEEeccCCcHHHHHHHhCCCHHHHH
Q 040730 65 SAEQINSTSELSHP-VNDWTKLMIMLPCTCFNN----G--------NNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 65 ~~~~l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~----~--------~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~ 131 (144)
++++|+++|++... |.+||.|.||........ . ..........|+|++|||||+||++||+++++|+
T Consensus 426 Sv~~L~~~N~l~s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sIAkkygVSv~~L~ 505 (592)
T PRK06347 426 TIANLKSWNNLKSDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLK 505 (592)
T ss_pred CHHHHHHHhCCCcceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHHHHHHCCCHHHHH
Confidence 99999999998766 999999999964211000 0 0001123457999999999999999999999999
Q ss_pred HHcCCCCCCcccC
Q 040730 132 ATNGLSQSVVETF 144 (144)
Q Consensus 132 ~~N~l~~~~i~~~ 144 (144)
+||++.+..|++|
T Consensus 506 ~~N~l~s~~L~~G 518 (592)
T PRK06347 506 SWNNLKSDFIYPG 518 (592)
T ss_pred HhcCCCcccccCC
Confidence 9999988888886
No 3
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.87 E-value=1e-21 Score=161.23 Aligned_cols=131 Identities=18% Similarity=0.182 Sum_probs=99.9
Q ss_pred CCCCCCCcceecC-C-CEEEEccCCCCC------C-C------C----c-ccCceeeEeCCCCCHHHHHHHhCCCCCHHH
Q 040730 9 PMSPSLGNQILGT-K-SLVKVPISCPCI------D-G------I----R-HSKSTTNNVRPADTIDSILNGFGGLVSAEQ 68 (144)
Q Consensus 9 ~~~p~~~~~~l~~-G-q~l~IP~~~~~~------~-~------~----~-~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~ 68 (144)
.+||++....+.+ | +.|+||...... . . . . ......|+|++|||+++||++|+ ++.++
T Consensus 290 ~LNP~~kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p~~~~~~~~~~~~~y~Vk~GDTL~sIA~r~g--vs~~~ 367 (456)
T PRK10783 290 TFNAGYKRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQSTLVADNTPLNSRSYKVRSGDTLSGIASRLN--VSTKD 367 (456)
T ss_pred HhCccccCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhcccccccccCcCCceEEEECCCCcHHHHHHHHC--cCHHH
Confidence 4677776554433 3 788899854310 0 0 0 0 01235799999999999999999 99999
Q ss_pred HHhhcCCCCC-CCCCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730 69 INSTSELSHP-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF 144 (144)
Q Consensus 69 l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~~ 144 (144)
|.++|++... |.+||.|.||..+.+.... ......+|+|++||||++||++||+++++|++||++..+.|+||
T Consensus 368 L~~~N~l~~~~L~~Gq~L~Ip~~~~~~~~~---~~~~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~~L~pG 441 (456)
T PRK10783 368 LQQWNNLRGSKLKVGQTLTIGAGSSAQRLA---NNSDSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAKNLQPG 441 (456)
T ss_pred HHHHcCCCcccCCCCCEEEecCCccccccc---ccccceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCCcCCCC
Confidence 9999998766 9999999999876543211 12235689999999999999999999999999999866688887
No 4
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.70 E-value=1.2e-16 Score=130.58 Aligned_cols=46 Identities=22% Similarity=0.228 Sum_probs=42.5
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEecc
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIMLP 90 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~~ 90 (144)
..|+|++|||||.||++|+ +++++|+++|++... |.+||.|.||..
T Consensus 28 ~tytVq~GDTLw~IA~~yg--vtv~~I~~~N~l~~~~I~~Gq~L~Ip~~ 74 (481)
T PRK13914 28 STVVVEAGDTLWGIAQSKG--TTVDAIKKANNLTTDKIVPGQKLQVNEV 74 (481)
T ss_pred ceEEECCCCCHHHHHHHHC--CCHHHHHHHhCCCcccccCCCEEEeCCC
Confidence 6799999999999999999 999999999998766 999999999843
No 5
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.48 E-value=1.1e-13 Score=113.94 Aligned_cols=81 Identities=19% Similarity=0.215 Sum_probs=67.2
Q ss_pred CcccCCCCCCCCCCCcceecCCCEEEEccCCCCCCCCcccCceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-C
Q 040730 1 ILVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-V 79 (144)
Q Consensus 1 l~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l 79 (144)
|+++|++. . ..|.+||.|.||..+.|...........|+|++||||++||++|+ +++++|+++|++... |
T Consensus 368 L~~~N~l~------~-~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vr~GDTL~sIA~kyg--Vtv~~L~~~N~l~~~~L 438 (456)
T PRK10783 368 LQQWNNLR------G-SKLKVGQTLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAKRHG--VNIKDVMRWNSDTAKNL 438 (456)
T ss_pred HHHHcCCC------c-ccCCCCCEEEecCCcccccccccccceeEEeCCCCCHHHHHHHhC--CCHHHHHHhcCCCCCcC
Confidence 45788886 3 679999999999877664322223347899999999999999999 999999999998765 9
Q ss_pred CCCcEEEEecc
Q 040730 80 NDWTKLMIMLP 90 (144)
Q Consensus 80 ~~Gq~l~IP~~ 90 (144)
++||+|.|+..
T Consensus 439 ~pGq~L~l~v~ 449 (456)
T PRK10783 439 QPGDKLTLFVK 449 (456)
T ss_pred CCCCEEEEecC
Confidence 99999999875
No 6
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=99.37 E-value=5.3e-13 Score=75.74 Aligned_cols=42 Identities=26% Similarity=0.419 Sum_probs=34.5
Q ss_pred eEeCCCCCHHHHHHHhCCCCCHHHHHhhc-CCCCC-CCCCcEEEEe
Q 040730 45 NNVRPADTIDSILNGFGGLVSAEQINSTS-ELSHP-VNDWTKLMIM 88 (144)
Q Consensus 45 y~V~~GdTl~~IA~~y~~~~~~~~l~~~N-~~~~~-l~~Gq~l~IP 88 (144)
|+|++|||++.||++|+ ++.++|+++| .+... |.+||.|+||
T Consensus 1 y~V~~gDtl~~IA~~~~--~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYG--ISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTT--S-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhh--hhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 89999999999999998 9999999999 44444 9999999998
No 7
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.34 E-value=3.2e-12 Score=87.91 Aligned_cols=87 Identities=24% Similarity=0.318 Sum_probs=66.9
Q ss_pred HHHHhCCCCCHHHHHhhcCCC--CC-CCCCcEEEEecccccCC--CC-CCCccc------------ceEEEEeccCCcHH
Q 040730 56 ILNGFGGLVSAEQINSTSELS--HP-VNDWTKLMIMLPCTCFN--NG-NNGVTS------------IYKSYVVQWGESPS 117 (144)
Q Consensus 56 IA~~y~~~~~~~~l~~~N~~~--~~-l~~Gq~l~IP~~~~~~~--~~-~~~~~~------------~~~~y~V~~GdTl~ 117 (144)
||.+|+ +++++|+++|.+. .. +.+||+|.++....... .. ...... ...+|+|+.||||+
T Consensus 1 ia~~~~--~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~ 78 (124)
T COG1388 1 IASKYG--VSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLS 78 (124)
T ss_pred Cccccc--ccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHH
Confidence 466788 8999999999988 55 99999999996311110 00 000111 13589999999999
Q ss_pred HHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730 118 SVGSKFGVTMAELVATNGLSQSVVETF 144 (144)
Q Consensus 118 ~IA~~~~~s~~~l~~~N~l~~~~i~~~ 144 (144)
.||++|++++.+|+++|.+.++.+++|
T Consensus 79 ~Ia~~~~~tv~~l~~~n~l~~~~i~~g 105 (124)
T COG1388 79 KIARKYGVTVAELKQLNNLSSDKIKVG 105 (124)
T ss_pred HHHHHhCCCHHHHHHHhccCCCceecC
Confidence 999999999999999999998888775
No 8
>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=99.28 E-value=3.3e-12 Score=72.42 Aligned_cols=37 Identities=24% Similarity=0.475 Sum_probs=30.4
Q ss_pred EEeccCCcHHHHHHHhCCCHHHHHHHc-CCCCCCcccC
Q 040730 108 YVVQWGESPSSVGSKFGVTMAELVATN-GLSQSVVETF 144 (144)
Q Consensus 108 y~V~~GdTl~~IA~~~~~s~~~l~~~N-~l~~~~i~~~ 144 (144)
|+|++|||+++||++|++++++|+++| ++.++.|++|
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G 38 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPG 38 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTT
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCC
Confidence 899999999999999999999999999 8877668876
No 9
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.13 E-value=1.7e-10 Score=77.17 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=42.2
Q ss_pred CceeeEeCCCCCHHHHHHHhCCCCC--------HHHHHhhcCCCCC-CCCCcEEEEeccc
Q 040730 41 KSTTNNVRPADTIDSILNGFGGLVS--------AEQINSTSELSHP-VNDWTKLMIMLPC 91 (144)
Q Consensus 41 ~~~~y~V~~GdTl~~IA~~y~~~~~--------~~~l~~~N~~~~~-l~~Gq~l~IP~~~ 91 (144)
....|+|++|||||+||++|+ ++ +++|++.|.+.++ |++||.|.||...
T Consensus 35 ~~~~~tV~~GDTLW~IA~~y~--~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~ 92 (103)
T PRK14125 35 QYVEITVQEGDTLWALADQYA--GKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLK 92 (103)
T ss_pred CcEEEEECCCCCHHHHHHHhC--CCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCC
Confidence 347899999999999999997 43 5788889999877 9999999999753
No 10
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.02 E-value=1e-09 Score=75.44 Aligned_cols=82 Identities=18% Similarity=0.265 Sum_probs=63.3
Q ss_pred cccCCCCCCCCCCCcceecCCCEEEEccCCCCCCC-Cc----cc-------------CceeeEeCCCCCHHHHHHHhCCC
Q 040730 2 LVSNSISPMSPSLGNQILGTKSLVKVPISCPCIDG-IR----HS-------------KSTTNNVRPADTIDSILNGFGGL 63 (144)
Q Consensus 2 ~~~N~l~~~~p~~~~~~l~~Gq~l~IP~~~~~~~~-~~----~~-------------~~~~y~V~~GdTl~~IA~~y~~~ 63 (144)
.++|.+.. ..+.+.+||.|.+|....-... .. .. ....|+|++||||+.||++|+
T Consensus 13 ~~~n~~~~-----~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~~Ia~~~~-- 85 (124)
T COG1388 13 KKANALTG-----KSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLSKIARKYG-- 85 (124)
T ss_pred HHHhcccC-----CCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHHHHHHHhC--
Confidence 45677762 2678999999999974221110 00 00 125799999999999999999
Q ss_pred CCHHHHHhhcCCCCC-CCCCcEEEEecc
Q 040730 64 VSAEQINSTSELSHP-VNDWTKLMIMLP 90 (144)
Q Consensus 64 ~~~~~l~~~N~~~~~-l~~Gq~l~IP~~ 90 (144)
+++.+|+++|.+.++ +++||.|.++..
T Consensus 86 ~tv~~l~~~n~l~~~~i~~gq~l~~~~~ 113 (124)
T COG1388 86 VTVAELKQLNNLSSDKIKVGQKLKLPVS 113 (124)
T ss_pred CCHHHHHHHhccCCCceecCcEEEEecc
Confidence 999999999999988 999999999863
No 11
>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=98.97 E-value=1.1e-09 Score=61.38 Aligned_cols=40 Identities=25% Similarity=0.360 Sum_probs=35.7
Q ss_pred eCCCCCHHHHHHHhCCCCCHHHHHhhcCC-CCC--CCCCcEEEEe
Q 040730 47 VRPADTIDSILNGFGGLVSAEQINSTSEL-SHP--VNDWTKLMIM 88 (144)
Q Consensus 47 V~~GdTl~~IA~~y~~~~~~~~l~~~N~~-~~~--l~~Gq~l~IP 88 (144)
|++|||||+||++|+ ++.++|.++|+. .++ +.+||.|.||
T Consensus 1 v~~gdtl~~IA~~~~--~~~~~l~~~N~~~~~~~~~~~g~~l~ip 43 (44)
T TIGR02899 1 VQKGDTLWKIAKKYG--VDFDELIQANPQLSNPNLIYPGMKIKIP 43 (44)
T ss_pred CCCCCCHHHHHHHHC--cCHHHHHHHhhcCCCCCCcCCCCEEecC
Confidence 589999999999999 899999999984 343 9999999998
No 12
>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=98.96 E-value=2.1e-09 Score=59.56 Aligned_cols=43 Identities=35% Similarity=0.474 Sum_probs=39.2
Q ss_pred eeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEe
Q 040730 44 TNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIM 88 (144)
Q Consensus 44 ~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP 88 (144)
.|+|++|||++.||++|+ ++.++|.++|+.... +.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~--~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYG--ISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHC--cCHHHHHHHcCCCCccccCCCCEEecC
Confidence 689999999999999998 999999999998543 9999999987
No 13
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.94 E-value=1.5e-09 Score=72.58 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=36.3
Q ss_pred ceEEEEeccCCcHHHHHHHhCCC--------HHHHHHHcCCCCCCcccC
Q 040730 104 IYKSYVVQWGESPSSVGSKFGVT--------MAELVATNGLSQSVVETF 144 (144)
Q Consensus 104 ~~~~y~V~~GdTl~~IA~~~~~s--------~~~l~~~N~l~~~~i~~~ 144 (144)
...+|+|++|||||+||++|+++ ++.|++.|+++++.|+||
T Consensus 35 ~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~G 83 (103)
T PRK14125 35 QYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAG 83 (103)
T ss_pred CcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCC
Confidence 45789999999999999999875 577888999998899987
No 14
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.90 E-value=1.7e-09 Score=87.03 Aligned_cols=80 Identities=19% Similarity=0.165 Sum_probs=70.6
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHHHHH
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGS 121 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~ 121 (144)
..|.|++||++..|+++|. .+..+|...|.+..+ +.+||.+.||.. ...|.|++|||+++||+
T Consensus 2 ~i~~~~pg~~~~~i~~~~~--~~~~~i~~~~~~~~d~~~~~q~~~v~~~--------------~~~y~~~~~d~~~Sia~ 65 (423)
T COG3858 2 SIHLVGPGDSRLIIAVYFP--YTNNRIVNGNDYTNDDLVDGQTFVVPPS--------------GHFYDVGPGDTLTSIAR 65 (423)
T ss_pred EEEEccCCceeeeehhhcc--ccccccccccccccccccCceeEEECCc--------------ceEEEecCCcchhhhhh
Confidence 3689999999999999999 899999777777766 999999999853 25799999999999999
Q ss_pred HhCCCHHHHHHHcCCCC
Q 040730 122 KFGVTMAELVATNGLSQ 138 (144)
Q Consensus 122 ~~~~s~~~l~~~N~l~~ 138 (144)
+|+++++.+..+|....
T Consensus 66 ~~~vt~~~~~~m~~~~~ 82 (423)
T COG3858 66 TVGVTQDSAAIMNFVIC 82 (423)
T ss_pred hhcCCHHHHHhhccccc
Confidence 99999999999997643
No 15
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.88 E-value=2.6e-09 Score=84.20 Aligned_cols=47 Identities=19% Similarity=0.160 Sum_probs=43.3
Q ss_pred ceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730 42 STTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP 90 (144)
Q Consensus 42 ~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~ 90 (144)
...|+|++|||||.||++|+ +++.+|.++|.+.++ |++||.|.||..
T Consensus 60 ~~~y~Vk~GDTL~~IA~~~g--~~~~~La~~N~l~~p~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAWITG--NDFRDLAQRNNIQAPYSLNVGQTLQVGNA 108 (319)
T ss_pred CCceEECCCCHHHHHHHHHC--cCHHHHHHhcCCCCCccccCCCEEEeCCC
Confidence 36899999999999999999 999999999999876 999999999754
No 16
>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=98.84 E-value=5.7e-09 Score=82.04 Aligned_cols=44 Identities=27% Similarity=0.322 Sum_probs=41.6
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEe
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIM 88 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP 88 (144)
..|+|++|||||.||++|+ ++++.|+++|++... |++||.|.||
T Consensus 294 ~~YiVq~GDTL~sIAkRYG--VSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 294 RMCIVQEGDTIETIAERYE--ISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred EEEEECCCCCHHHHHHHHC--cCHHHHHHHhCCCccccCCCCEEEeC
Confidence 7899999999999999999 999999999998855 9999999997
No 17
>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=98.77 E-value=1.6e-08 Score=55.93 Aligned_cols=38 Identities=29% Similarity=0.588 Sum_probs=33.5
Q ss_pred EEEeccCCcHHHHHHHhCCCHHHHHHHcCC-CCCCcccC
Q 040730 107 SYVVQWGESPSSVGSKFGVTMAELVATNGL-SQSVVETF 144 (144)
Q Consensus 107 ~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l-~~~~i~~~ 144 (144)
+|+|++|||+++||++|+++..+|.++|+. ....+.+|
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g 40 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVG 40 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCC
Confidence 589999999999999999999999999998 44556654
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=1.8e-08 Score=56.32 Aligned_cols=35 Identities=31% Similarity=0.471 Sum_probs=29.6
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHHcC-CCC-CCcccC
Q 040730 110 VQWGESPSSVGSKFGVTMAELVATNG-LSQ-SVVETF 144 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~N~-l~~-~~i~~~ 144 (144)
|++|||||+||++|++++++|.++|+ +.+ ..+++|
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g 37 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPG 37 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCC
Confidence 68899999999999999999999997 433 456665
No 19
>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=98.67 E-value=2.9e-08 Score=78.16 Aligned_cols=41 Identities=17% Similarity=0.341 Sum_probs=37.3
Q ss_pred ceEEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCCCCcccC
Q 040730 104 IYKSYVVQWGESPSSVGSKFGVTMAELVATNGLSQSVVETF 144 (144)
Q Consensus 104 ~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~~~i~~~ 144 (144)
....|+|++|||||+||+|||++++.|+++|++.+..|++|
T Consensus 292 ~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~G 332 (338)
T TIGR02907 292 KLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEG 332 (338)
T ss_pred ccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCC
Confidence 34689999999999999999999999999999987778876
No 20
>smart00257 LysM Lysin motif.
Probab=98.64 E-value=9.4e-08 Score=52.11 Aligned_cols=42 Identities=26% Similarity=0.373 Sum_probs=36.4
Q ss_pred eeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCC-C-CCCCcEEEE
Q 040730 44 TNNVRPADTIDSILNGFGGLVSAEQINSTSELSH-P-VNDWTKLMI 87 (144)
Q Consensus 44 ~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~-~-l~~Gq~l~I 87 (144)
.|+|++|||++.||++|+ ++.++|.++|+... . +.+|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~--~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYG--ISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhC--CCHHHHHHHcCCCCccccCCCCEEeC
Confidence 488999999999999999 89999999999543 3 889998864
No 21
>smart00257 LysM Lysin motif.
Probab=98.62 E-value=7.3e-08 Score=52.57 Aligned_cols=38 Identities=21% Similarity=0.525 Sum_probs=32.5
Q ss_pred EEEeccCCcHHHHHHHhCCCHHHHHHHcCC-CCCCcccC
Q 040730 107 SYVVQWGESPSSVGSKFGVTMAELVATNGL-SQSVVETF 144 (144)
Q Consensus 107 ~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l-~~~~i~~~ 144 (144)
+|+|++|||+++||++|+++.++|.++|+. ....+++|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g 39 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVG 39 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCC
Confidence 388999999999999999999999999994 44556654
No 22
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.59 E-value=8.9e-08 Score=79.02 Aligned_cols=46 Identities=35% Similarity=0.353 Sum_probs=43.4
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEecc
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIMLP 90 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~~ 90 (144)
..|+|++|||||.||++|+ +++++|+++|++... |++||.|.||..
T Consensus 200 ~tytVq~GDTL~sIAkrYg--Vtv~eI~~~N~l~s~~L~pGQ~L~Ip~s 246 (481)
T PRK13914 200 TTHAVKSGDTIWALSVKYG--VSVQDIMSWNNLSSSSIYVGQKLAIKQT 246 (481)
T ss_pred eEEEECCCCCHHHHHHHHC--CCHHHHHHhcCCCccccCCCCEEEecCC
Confidence 5899999999999999999 999999999999877 999999999965
No 23
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.56 E-value=6.5e-08 Score=76.36 Aligned_cols=39 Identities=15% Similarity=0.207 Sum_probs=35.3
Q ss_pred EEEEeccCCcHHHHHHHhCCCHHHHHHHcCCCC-CCcccC
Q 040730 106 KSYVVQWGESPSSVGSKFGVTMAELVATNGLSQ-SVVETF 144 (144)
Q Consensus 106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l~~-~~i~~~ 144 (144)
.+|+|++|||||+||.+||+++.+|.+||+|.+ ..|++|
T Consensus 61 ~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~G 100 (319)
T PRK10871 61 STYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVG 100 (319)
T ss_pred CceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCC
Confidence 479999999999999999999999999999965 468876
No 24
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.55 E-value=1.3e-07 Score=67.12 Aligned_cols=46 Identities=22% Similarity=0.234 Sum_probs=38.8
Q ss_pred eeeEeCCCCCHHHHHHHhCC-CCCHHHHHhhcC--CCCC--CCCCcEEEEe
Q 040730 43 TTNNVRPADTIDSILNGFGG-LVSAEQINSTSE--LSHP--VNDWTKLMIM 88 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~-~~~~~~l~~~N~--~~~~--l~~Gq~l~IP 88 (144)
..|+|++|||||.||++|.+ ...+..|.++|+ +.++ |.+||.|.||
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 67999999999999998743 245789999998 5554 9999999998
No 25
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.02 E-value=9.7e-06 Score=65.70 Aligned_cols=62 Identities=26% Similarity=0.242 Sum_probs=54.9
Q ss_pred cceecCCCEEEEccCCCCCCCCcccCceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730 16 NQILGTKSLVKVPISCPCIDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP 90 (144)
Q Consensus 16 ~~~l~~Gq~l~IP~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~ 90 (144)
++.|..||.+.||.. ...|.|++|||+++||++|+ ++.+.++.+|....+ ++.|-.+.+|..
T Consensus 34 ~d~~~~~q~~~v~~~-----------~~~y~~~~~d~~~Sia~~~~--vt~~~~~~m~~~~~~~~l~~~~~l~~P~~ 97 (423)
T COG3858 34 NDDLVDGQTFVVPPS-----------GHFYDVGPGDTLTSIARTVG--VTQDSAAIMNFVICPGYLQYGLNLYIPSA 97 (423)
T ss_pred cccccCceeEEECCc-----------ceEEEecCCcchhhhhhhhc--CCHHHHHhhcccccccceeeeeEEeccCC
Confidence 377899999999953 35899999999999999999 999999999988875 999999999864
No 26
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.01 E-value=7.8e-06 Score=58.02 Aligned_cols=40 Identities=18% Similarity=0.203 Sum_probs=32.7
Q ss_pred eEEEEeccCCcHHHHHHHhC---CCHHHHHHHcC--CCC-CCcccC
Q 040730 105 YKSYVVQWGESPSSVGSKFG---VTMAELVATNG--LSQ-SVVETF 144 (144)
Q Consensus 105 ~~~y~V~~GdTl~~IA~~~~---~s~~~l~~~N~--l~~-~~i~~~ 144 (144)
..+|+|++|||||+||++|. ..+.+|+++|+ +.+ ..|+||
T Consensus 95 ~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pG 140 (147)
T PRK11198 95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPG 140 (147)
T ss_pred CeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcC
Confidence 35799999999999999985 34789999998 654 458876
No 27
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.56 E-value=2.7e-05 Score=60.23 Aligned_cols=48 Identities=29% Similarity=0.329 Sum_probs=41.2
Q ss_pred eeeEeCCCCCHHHHHH-HhCCCCCHHHHHhhcC---CCCC--CCCCcEEEEecc
Q 040730 43 TTNNVRPADTIDSILN-GFGGLVSAEQINSTSE---LSHP--VNDWTKLMIMLP 90 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~-~y~~~~~~~~l~~~N~---~~~~--l~~Gq~l~IP~~ 90 (144)
.+|+|++|||||.||+ .|+....+..|..+|. +.++ |.+||.|.||..
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~ 264 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ 264 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence 3899999999999999 7887677789999999 3444 999999999964
No 28
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.54 E-value=0.00022 Score=56.22 Aligned_cols=46 Identities=11% Similarity=0.120 Sum_probs=41.5
Q ss_pred eeeEeCCCC--CHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730 43 TTNNVRPAD--TIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP 90 (144)
Q Consensus 43 ~~y~V~~Gd--Tl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~ 90 (144)
..|+|+.+| +|..||++|+ +...+|+++|+..++ .++|++|.||..
T Consensus 38 ~~~~v~~~~~~~le~iA~~f~--~g~~~l~~aNPgvd~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 38 LTVTVPDHNTQPLETFAAQYG--QGLSNMLEANPGADVFLPKSGSQLTIPQQ 87 (310)
T ss_pred EEEEecCCCCccHHHHHHHhC--CCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence 679999866 5999999999 999999999999988 679999999964
No 29
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.52 E-value=0.00024 Score=55.94 Aligned_cols=46 Identities=7% Similarity=0.034 Sum_probs=41.3
Q ss_pred eeeEeCCCC--CHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730 43 TTNNVRPAD--TIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP 90 (144)
Q Consensus 43 ~~y~V~~Gd--Tl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~ 90 (144)
..|+|++|+ +|..||++|+ +...+|+++|+..++ .++|++|.||..
T Consensus 41 ~~~~v~~~~~~~le~iA~~f~--~g~~~l~~aNPgvdp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 41 QVITIPEGNTQPLEYFAAEYQ--MGLSNMMEANPGVDTFLPKGGTVLNIPQQ 90 (306)
T ss_pred EEEEeCCCCCchHHHHHHHhC--CCHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence 689999966 5999999999 999999999999987 579999999964
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=97.36 E-value=0.00014 Score=46.95 Aligned_cols=46 Identities=20% Similarity=0.281 Sum_probs=26.4
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhh---cCCCC---CCCCCcEEEEecc
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINST---SELSH---PVNDWTKLMIMLP 90 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~---N~~~~---~l~~Gq~l~IP~~ 90 (144)
..|+|++||||..|-++++ ++..+|.++ ..... .|+|||.|.+-..
T Consensus 3 ~~~~V~~GDtLs~iF~~~g--ls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAG--LSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp -EEE--TT--HHHHHHHTT----HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred cEEEECCCCcHHHHHHHcC--CCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 3699999999999999998 888776655 32222 2999999998764
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=97.04 E-value=0.00072 Score=42.52 Aligned_cols=40 Identities=18% Similarity=-0.002 Sum_probs=30.5
Q ss_pred CCHHHHHHHhC--CCCCHH----HHHhhcCCC----CC--CCCCcEEEEecc
Q 040730 51 DTIDSILNGFG--GLVSAE----QINSTSELS----HP--VNDWTKLMIMLP 90 (144)
Q Consensus 51 dTl~~IA~~y~--~~~~~~----~l~~~N~~~----~~--l~~Gq~l~IP~~ 90 (144)
||||+||++|. +-+++. .|.+.|+.. +. |++|+.|.||..
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~ 52 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE 52 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence 89999999884 224554 677889854 12 999999999964
No 32
>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=96.98 E-value=0.00092 Score=43.12 Aligned_cols=28 Identities=25% Similarity=0.473 Sum_probs=18.0
Q ss_pred EEEEeccCCcHHHHHHHhCCCHHHHHHH
Q 040730 106 KSYVVQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|+|++||||+.|-+++|++..+|.++
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v 30 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAV 30 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHH
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHH
Confidence 3699999999999999999998777554
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=96.73 E-value=0.0026 Score=38.33 Aligned_cols=45 Identities=20% Similarity=0.158 Sum_probs=34.4
Q ss_pred eEeCCCCCHHHHHH-HhCCCCCH-HHHHhhcCCCC---C-CCCCcEEEEecc
Q 040730 45 NNVRPADTIDSILN-GFGGLVSA-EQINSTSELSH---P-VNDWTKLMIMLP 90 (144)
Q Consensus 45 y~V~~GdTl~~IA~-~y~~~~~~-~~l~~~N~~~~---~-l~~Gq~l~IP~~ 90 (144)
|+. .|||+..|+. .||..-.. +.+.++|+... + |..|..|.+|.-
T Consensus 4 ~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i 54 (60)
T PF05489_consen 4 YTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI 54 (60)
T ss_pred EEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence 444 9999999999 56643223 78999999752 3 999999999953
No 34
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=95.93 E-value=0.038 Score=41.59 Aligned_cols=75 Identities=15% Similarity=0.181 Sum_probs=48.7
Q ss_pred CcceecCCCEEEEccCCCC-CCCCcccCceeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCC---CC---CCCCcEEEE
Q 040730 15 GNQILGTKSLVKVPISCPC-IDGIRHSKSTTNNVRPADTIDSILNGFGGLVSAEQINSTSELS---HP---VNDWTKLMI 87 (144)
Q Consensus 15 ~~~~l~~Gq~l~IP~~~~~-~~~~~~~~~~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~---~~---l~~Gq~l~I 87 (144)
....++.+|...+|..... +.......-.+|+|+.|+||..+-|..+ ....|+-.+-... .+ |+.||.+.|
T Consensus 131 e~~p~q~~q~~~v~~~~~~~P~~~s~g~wqsy~V~~G~TLaQlFRdn~--LpitDVnAMakveGagkpLSnlkaGq~Vki 208 (242)
T COG3061 131 EPEPIQAKQEKKVPRTVDAQPFKPSSGNWQSYTVPQGKTLAQLFRDNN--LPITDVNAMAKVEGAGKPLSNLKAGQKVKI 208 (242)
T ss_pred ccchhhccCccccCCccccCccccCcccceeEEecCCccHHHHHhccC--CChHHhHHHHhhccCCCchhhccCCCEEEE
Confidence 3445667788887743221 1111111347999999999999999776 6666665443322 22 999999999
Q ss_pred eccc
Q 040730 88 MLPC 91 (144)
Q Consensus 88 P~~~ 91 (144)
-...
T Consensus 209 ~~na 212 (242)
T COG3061 209 SLNA 212 (242)
T ss_pred EEcC
Confidence 8764
No 35
>PRK11649 putative peptidase; Provisional
Probab=95.80 E-value=0.061 Score=44.66 Aligned_cols=91 Identities=20% Similarity=0.136 Sum_probs=57.8
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcC-CC--CCCCCCcEEEEecccccCC--------CC-------CCCc---
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSE-LS--HPVNDWTKLMIMLPCTCFN--------NG-------NNGV--- 101 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~-~~--~~l~~Gq~l~IP~~~~~~~--------~~-------~~~~--- 101 (144)
..|+|++||||..|=++++ ++..++.++-. .. ..|++||.|.+-......- .. ..+.
T Consensus 96 ~~~~Vk~GDTl~~iL~r~G--i~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg~F~~ 173 (439)
T PRK11649 96 HEYVVSTGDTLSSILNQYG--IDMSDISQLAAQDKELRNLKIGQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGNGFKE 173 (439)
T ss_pred EEEEeCCCCCHHHHHHHcC--CCHHHHHHHHHcChHhhcCCCCCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCCcEEE
Confidence 4899999999999999999 89888776622 11 2399999999864321100 00 0000
Q ss_pred -------ccceEEEEeccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730 102 -------TSIYKSYVVQWGESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 102 -------~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
..........-..+|+.-|.+-|++...++++..
T Consensus 174 ~~~~~~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~ 214 (439)
T PRK11649 174 TSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIK 214 (439)
T ss_pred EEeecccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHH
Confidence 0000011122256899999999999887776654
No 36
>PRK10260 L,D-transpeptidase; Provisional
Probab=95.06 E-value=0.044 Score=43.32 Aligned_cols=36 Identities=6% Similarity=0.146 Sum_probs=30.7
Q ss_pred ceEEEEeccCC--cHHHHHHHhCCCHHHHHHHcCCCCC
Q 040730 104 IYKSYVVQWGE--SPSSVGSKFGVTMAELVATNGLSQS 139 (144)
Q Consensus 104 ~~~~y~V~~Gd--Tl~~IA~~~~~s~~~l~~~N~l~~~ 139 (144)
....|+|+.|+ +|..||++|++...+|+++|+--++
T Consensus 39 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp 76 (306)
T PRK10260 39 QNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDT 76 (306)
T ss_pred ccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCC
Confidence 34679999966 5999999999999999999997554
No 37
>PRK10190 L,D-transpeptidase; Provisional
Probab=94.96 E-value=0.048 Score=43.20 Aligned_cols=36 Identities=8% Similarity=0.122 Sum_probs=30.7
Q ss_pred ceEEEEeccCC--cHHHHHHHhCCCHHHHHHHcCCCCC
Q 040730 104 IYKSYVVQWGE--SPSSVGSKFGVTMAELVATNGLSQS 139 (144)
Q Consensus 104 ~~~~y~V~~Gd--Tl~~IA~~~~~s~~~l~~~N~l~~~ 139 (144)
....|+|+.+| +|..||++|++...+|+++|+--++
T Consensus 36 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~ 73 (310)
T PRK10190 36 QSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADV 73 (310)
T ss_pred ceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCC
Confidence 34679999866 5999999999999999999997554
No 38
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=94.30 E-value=0.034 Score=48.30 Aligned_cols=49 Identities=18% Similarity=0.121 Sum_probs=37.0
Q ss_pred ceeeEeCCCCCHHHHHHHhCC--CCCH----HHHHhhcCCCC------CCCCCcEEEEecc
Q 040730 42 STTNNVRPADTIDSILNGFGG--LVSA----EQINSTSELSH------PVNDWTKLMIMLP 90 (144)
Q Consensus 42 ~~~y~V~~GdTl~~IA~~y~~--~~~~----~~l~~~N~~~~------~l~~Gq~l~IP~~ 90 (144)
+.+|+|++|||||.||.+-.+ -+|+ ..|.++|+-.. .+++|++|.||..
T Consensus 188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred CcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 478999999999999985432 2344 45677788541 2999999999964
No 39
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=94.15 E-value=0.016 Score=44.86 Aligned_cols=39 Identities=15% Similarity=0.278 Sum_probs=30.2
Q ss_pred EEEEeccCCcHHHHHHH-hCCC--HHHHHHHcC---CC-CCCcccC
Q 040730 106 KSYVVQWGESPSSVGSK-FGVT--MAELVATNG---LS-QSVVETF 144 (144)
Q Consensus 106 ~~y~V~~GdTl~~IA~~-~~~s--~~~l~~~N~---l~-~~~i~~~ 144 (144)
.+|+|++|||||.||++ ||.. ...|..+|+ ++ .+.|+||
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pG 256 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPG 256 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCc
Confidence 38999999999999965 6654 578889998 54 3457775
No 40
>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=93.76 E-value=0.065 Score=33.63 Aligned_cols=22 Identities=14% Similarity=0.253 Sum_probs=17.2
Q ss_pred CcHHHHHHHh---C-CCHH----HHHHHcC
Q 040730 114 ESPSSVGSKF---G-VTMA----ELVATNG 135 (144)
Q Consensus 114 dTl~~IA~~~---~-~s~~----~l~~~N~ 135 (144)
||||+||++| + +++. .|.+.|+
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp 30 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANP 30 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCH
Confidence 8999999999 3 6765 5667775
No 41
>PRK11649 putative peptidase; Provisional
Probab=92.78 E-value=0.15 Score=42.42 Aligned_cols=28 Identities=29% Similarity=0.587 Sum_probs=25.5
Q ss_pred EEEEeccCCcHHHHHHHhCCCHHHHHHH
Q 040730 106 KSYVVQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 106 ~~y~V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|+|++||||++|-+++|++..++.++
T Consensus 96 ~~~~Vk~GDTl~~iL~r~Gi~~~di~~l 123 (439)
T PRK11649 96 HEYVVSTGDTLSSILNQYGIDMSDISQL 123 (439)
T ss_pred EEEEeCCCCCHHHHHHHcCCCHHHHHHH
Confidence 5899999999999999999998887766
No 42
>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=90.56 E-value=0.39 Score=28.81 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=21.0
Q ss_pred ccCCcHHHHH-HHhCCC---HHHHHHHcCC
Q 040730 111 QWGESPSSVG-SKFGVT---MAELVATNGL 136 (144)
Q Consensus 111 ~~GdTl~~IA-~~~~~s---~~~l~~~N~l 136 (144)
+.||||..|+ +.||-. ++.+.++|+-
T Consensus 6 ~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~ 35 (60)
T PF05489_consen 6 TQGDTLDLIAYRHYGREDGAVEALLEANPG 35 (60)
T ss_pred eCcCcHHHHHHHHhCcHHHHHHHHHHHChh
Confidence 4899999999 557765 4788999974
No 43
>PF13518 HTH_28: Helix-turn-helix domain
Probab=89.57 E-value=0.39 Score=27.08 Aligned_cols=24 Identities=21% Similarity=0.288 Sum_probs=20.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHHc
Q 040730 111 QWGESPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~N 134 (144)
..|.|+..+|++||++...+..|=
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 468899999999999998887763
No 44
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=88.45 E-value=0.61 Score=26.02 Aligned_cols=23 Identities=22% Similarity=0.323 Sum_probs=17.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
+.|-++..||+.||++...|.++
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 67899999999999999988764
No 45
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=87.03 E-value=1 Score=36.54 Aligned_cols=45 Identities=20% Similarity=0.214 Sum_probs=34.1
Q ss_pred eeeEeCCCCCHHHHHHHhCCCC-CHHHHHhhcCCCCC--CCCCcEEEE
Q 040730 43 TTNNVRPADTIDSILNGFGGLV-SAEQINSTSELSHP--VNDWTKLMI 87 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~-~~~~l~~~N~~~~~--l~~Gq~l~I 87 (144)
..-+|++|||+.++|.+..|.. +++-++-+|.+... +++|++++|
T Consensus 429 rvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi 476 (479)
T COG4784 429 RVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI 476 (479)
T ss_pred EEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence 3467899999999999665522 34566777888754 999999987
No 46
>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=85.87 E-value=0.51 Score=28.86 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=20.9
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
...|.|+..||++||++...|..|
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 478999999999999999999877
No 47
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=85.16 E-value=1.6 Score=26.53 Aligned_cols=47 Identities=15% Similarity=0.140 Sum_probs=35.5
Q ss_pred eeEeCCCCCHHHHHH-HhCCCCCH-HHHHhhcCCCC---C-CCCCcEEEEecc
Q 040730 44 TNNVRPADTIDSILN-GFGGLVSA-EQINSTSELSH---P-VNDWTKLMIMLP 90 (144)
Q Consensus 44 ~y~V~~GdTl~~IA~-~y~~~~~~-~~l~~~N~~~~---~-l~~Gq~l~IP~~ 90 (144)
+|....|||+..+.. .|+....+ +.+..+|+... + +..|-.|.+|-.
T Consensus 4 ~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~ 56 (70)
T COG5004 4 IVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDI 56 (70)
T ss_pred EEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCC
Confidence 566789999999999 46643222 68889999764 3 888888888854
No 48
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.68 E-value=0.91 Score=35.86 Aligned_cols=49 Identities=24% Similarity=0.267 Sum_probs=39.3
Q ss_pred eeeEeCCCCCHHHHHHHhCCC-CCHHHHHhhcCCCCC--CCCCcEEEEeccc
Q 040730 43 TTNNVRPADTIDSILNGFGGL-VSAEQINSTSELSHP--VNDWTKLMIMLPC 91 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~-~~~~~l~~~N~~~~~--l~~Gq~l~IP~~~ 91 (144)
..|.|+.||||..++..|-.+ ..+..++..|....+ +++|..|.||.+.
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~ 57 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPA 57 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCcc
Confidence 689999999999999977522 123567788888887 9999999999764
No 49
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=82.50 E-value=0.76 Score=33.89 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=38.4
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEeccc
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLPC 91 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~~ 91 (144)
..-+++.||||..||=.|. ..+.+|.+.|.+... +..-..+.+|...
T Consensus 10 l~~~iq~~dt~~a~al~~~--~~va~i~RvN~~~r~q~f~a~~~i~~pv~~ 58 (186)
T KOG2850|consen 10 LEVTIQEGDTLQAIALNYE--SDVADIKRVNNDDREQRFNALRSISIPVTR 58 (186)
T ss_pred eeeeeccCchhhhHHhhcc--cchhhheeeccchhhhhhccccceecccch
Confidence 4567899999999998888 788999999977653 7777788888653
No 50
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=80.57 E-value=2.1 Score=23.88 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=17.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|.|...||+.+|++...+..|
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 34999999999999999888776
No 51
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=80.01 E-value=1.1 Score=39.43 Aligned_cols=33 Identities=24% Similarity=0.287 Sum_probs=24.3
Q ss_pred ceEEEEeccCCcHHHHHHHhC----CCH----HHHHHHcCC
Q 040730 104 IYKSYVVQWGESPSSVGSKFG----VTM----AELVATNGL 136 (144)
Q Consensus 104 ~~~~y~V~~GdTl~~IA~~~~----~s~----~~l~~~N~l 136 (144)
...+|+|++|||||+||.+-- +|+ ..|.++|+-
T Consensus 187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~ 227 (755)
T COG3170 187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQ 227 (755)
T ss_pred CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChh
Confidence 346899999999999997643 454 455666753
No 52
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.48 E-value=2.1 Score=28.52 Aligned_cols=24 Identities=25% Similarity=0.479 Sum_probs=20.2
Q ss_pred eccCCcHHHHHHHhCC-CHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGV-TMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~-s~~~l~~~ 133 (144)
.++|.|+..||++||+ +...|..|
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHH
Confidence 4679999999999995 88888754
No 53
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=78.57 E-value=2.4 Score=28.76 Aligned_cols=25 Identities=24% Similarity=0.234 Sum_probs=22.5
Q ss_pred EeccCCcHHHHHHHhCCCHHHHHHH
Q 040730 109 VVQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 109 ~V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
.+..|.|+..||++||++...|..|
T Consensus 25 ~~~~g~sv~evA~e~gIs~~tl~~W 49 (121)
T PRK09413 25 SFEPGMTVSLVARQHGVAASQLFLW 49 (121)
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHH
Confidence 3567999999999999999999888
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=77.82 E-value=1.1 Score=26.03 Aligned_cols=23 Identities=26% Similarity=0.510 Sum_probs=16.0
Q ss_pred eccCCcHHHHHHHhCCCHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
+..|.+...||++||++..++..
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~ 41 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVST 41 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHH
Confidence 46799999999999997666543
No 55
>PHA00675 hypothetical protein
Probab=77.58 E-value=2.8 Score=26.43 Aligned_cols=23 Identities=17% Similarity=0.160 Sum_probs=20.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
+.|.+.+.||++||++-..+...
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I 59 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKI 59 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHH
Confidence 78999999999999998777654
No 56
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=75.40 E-value=5.2 Score=30.28 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=39.0
Q ss_pred eeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCCC--CCCCcEEEEecc
Q 040730 44 TNNVRPADTIDSILNGFGGLVSAEQINSTSELSHP--VNDWTKLMIMLP 90 (144)
Q Consensus 44 ~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~~--l~~Gq~l~IP~~ 90 (144)
.|.++.++++..|+++++ .....+...|..... +..|+.+.+|..
T Consensus 3 ~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 3 LYVVKKGDTLSAIAARLG--ISAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred eEEecCCCHHHHHHHHcC--CCHHHHHHHHhhccccccCccceeeeccc
Confidence 588999999999999998 888889888887754 888999999865
No 57
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=75.18 E-value=2 Score=31.65 Aligned_cols=32 Identities=13% Similarity=0.196 Sum_probs=28.8
Q ss_pred eEEEEeccCCcHHHHHHHhCCCHHHHHHHcCC
Q 040730 105 YKSYVVQWGESPSSVGSKFGVTMAELVATNGL 136 (144)
Q Consensus 105 ~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~l 136 (144)
...-++|.||||..||-+|..++.++++.|++
T Consensus 9 ~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~ 40 (186)
T KOG2850|consen 9 ELEVTIQEGDTLQAIALNYESDVADIKRVNND 40 (186)
T ss_pred heeeeeccCchhhhHHhhcccchhhheeeccc
Confidence 45678999999999999999999999999965
No 58
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=72.97 E-value=7.8 Score=29.42 Aligned_cols=32 Identities=16% Similarity=0.246 Sum_probs=26.9
Q ss_pred ceEEEEeccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730 104 IYKSYVVQWGESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 104 ~~~~y~V~~GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
.-.+|+|+.|+||..+-+.+++.+.++-++-.
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMak 189 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAK 189 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHh
Confidence 34689999999999999999999888766643
No 59
>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=72.63 E-value=5.8 Score=19.24 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=19.3
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|.+...||+.|+++...+..+
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 46889999999999998887654
No 60
>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=72.16 E-value=4 Score=22.80 Aligned_cols=24 Identities=29% Similarity=0.349 Sum_probs=16.8
Q ss_pred eccC-CcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWG-ESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~G-dTl~~IA~~~~~s~~~l~~~ 133 (144)
|+.| -++...|++|||+...|...
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 4456 89999999999999888643
No 61
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=70.24 E-value=5.9 Score=21.85 Aligned_cols=23 Identities=13% Similarity=0.277 Sum_probs=14.8
Q ss_pred eccCCcHHHHHHHhCCCHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
.+.|.+...||+++|.+...+..
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHH
Confidence 36799999999999999877754
No 62
>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=67.81 E-value=7.1 Score=20.95 Aligned_cols=22 Identities=18% Similarity=0.105 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHHcCC
Q 040730 115 SPSSVGSKFGVTMAELVATNGL 136 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N~l 136 (144)
|...+|+.+|++++.|.-|=..
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
Confidence 4678899999999999877543
No 63
>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=67.27 E-value=8.8 Score=21.40 Aligned_cols=22 Identities=9% Similarity=0.225 Sum_probs=18.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
-.|-|+..||+.+|+|...+..
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~ 39 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRR 39 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHH
Confidence 5688999999999999887754
No 64
>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=67.04 E-value=4.3 Score=29.90 Aligned_cols=24 Identities=25% Similarity=0.255 Sum_probs=18.6
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
|.+==-|.+||+|||++..+|++.
T Consensus 167 vEPVWyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 167 VEPVWYLPGVAERFGISEGELRRA 190 (194)
T ss_pred ecccccchhhHHHcCCCHHHHHHH
Confidence 444445669999999999999863
No 65
>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=65.18 E-value=8.2 Score=23.14 Aligned_cols=23 Identities=13% Similarity=0.179 Sum_probs=19.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHcC
Q 040730 113 GESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
+-++-.||.++|++...|..|=.
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhh
Confidence 45888999999999999988743
No 66
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=64.92 E-value=8.7 Score=21.48 Aligned_cols=21 Identities=19% Similarity=0.268 Sum_probs=17.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 040730 113 GESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~~ 133 (144)
.-|+..||+.+|++...++++
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHH
Confidence 359999999999999888653
No 67
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=63.87 E-value=13 Score=30.30 Aligned_cols=40 Identities=18% Similarity=0.252 Sum_probs=29.9
Q ss_pred eEEEEeccCCcHHHHHHH-hCCC--HHHHHHHcCCC-CCCcccC
Q 040730 105 YKSYVVQWGESPSSVGSK-FGVT--MAELVATNGLS-QSVVETF 144 (144)
Q Consensus 105 ~~~y~V~~GdTl~~IA~~-~~~s--~~~l~~~N~l~-~~~i~~~ 144 (144)
....+||+|||+.++|.+ -|++ ++-++-+|.+. +..++||
T Consensus 428 irvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pG 471 (479)
T COG4784 428 IRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPG 471 (479)
T ss_pred EEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCC
Confidence 345779999999999955 5653 67788899985 4456665
No 68
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=63.14 E-value=8.4 Score=24.37 Aligned_cols=22 Identities=18% Similarity=0.314 Sum_probs=16.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
++|-||..||+.+|++...+..
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~n 34 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRN 34 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHH
T ss_pred HcCCCHHHHHHHcCCCHHHHHH
Confidence 5799999999999999877643
No 69
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=62.97 E-value=9.2 Score=22.26 Aligned_cols=23 Identities=26% Similarity=0.551 Sum_probs=16.7
Q ss_pred ccCCcHHHHHHHhC-CCHHHHHHH
Q 040730 111 QWGESPSSVGSKFG-VTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~-~s~~~l~~~ 133 (144)
..|++...|++.|. ++.+++.++
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 88999999999997 899988764
No 70
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=61.20 E-value=11 Score=20.07 Aligned_cols=20 Identities=15% Similarity=0.142 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 040730 115 SPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N 134 (144)
|+..+|+.+|++...|..|=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998873
No 71
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=61.07 E-value=9.3 Score=25.33 Aligned_cols=20 Identities=15% Similarity=0.405 Sum_probs=14.7
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 040730 113 GESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~ 132 (144)
|.++..||++||+|...+.+
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 99999999999999876654
No 72
>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=60.94 E-value=9.5 Score=23.01 Aligned_cols=20 Identities=20% Similarity=0.336 Sum_probs=14.6
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~~ 133 (144)
=|+..||++|+++.+.+..+
T Consensus 15 ~S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 15 VSLAELAREFGISPEAVEAM 34 (69)
T ss_dssp EEHHHHHHHTT--HHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHH
Confidence 47889999999998887653
No 73
>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=60.36 E-value=12 Score=20.43 Aligned_cols=20 Identities=15% Similarity=0.111 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 040730 115 SPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N 134 (144)
|+..+|+.+|++...|..|=
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998884
No 74
>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=58.56 E-value=12 Score=22.06 Aligned_cols=20 Identities=25% Similarity=0.174 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 040730 115 SPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N 134 (144)
++..+|+++|++...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998764
No 75
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=57.71 E-value=10 Score=21.64 Aligned_cols=23 Identities=9% Similarity=0.293 Sum_probs=19.0
Q ss_pred eccCCcHHHHHHHhCCCHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
.+.|.+...||..||++.....+
T Consensus 16 LR~~~~~~~La~~FgIs~stvsr 38 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSR 38 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHH
Confidence 46789999999999999876644
No 76
>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=57.67 E-value=8.1 Score=26.05 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=21.3
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
+..|.+...+|++|+|+...+..|
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W 38 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRW 38 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHH
Confidence 456889999999999999998887
No 77
>PRK10270 putative aminodeoxychorismate lyase; Provisional
Probab=57.18 E-value=40 Score=27.18 Aligned_cols=81 Identities=6% Similarity=-0.180 Sum_probs=48.1
Q ss_pred eeeEeCCCCCHHHHHH--HhCCCCCHH----HHHhhcCCCCCCCCCcEEEEecccccCC-CCCCCcccceEEEEeccCCc
Q 040730 43 TTNNVRPADTIDSILN--GFGGLVSAE----QINSTSELSHPVNDWTKLMIMLPCTCFN-NGNNGVTSIYKSYVVQWGES 115 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~--~y~~~~~~~----~l~~~N~~~~~l~~Gq~l~IP~~~~~~~-~~~~~~~~~~~~y~V~~GdT 115 (144)
...+|.+|+|...||+ .-.|++.-. ...++++....|++|.-..-+......- ..-..+.......++..|-|
T Consensus 40 v~v~I~~G~t~~~Ia~~L~~~gvI~s~~~F~~~~~~~~~~~~ikaG~Y~l~~~ms~~~il~~L~~g~~~~~~vtIpEG~t 119 (340)
T PRK10270 40 TIFTLKPGTGRLALGEQLYADKIINRPRVFQWLLRIEPDLSHFKAGTYRFTPQMTVREMLKLLESGKEAQFPLRLVEGMR 119 (340)
T ss_pred EEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHhCCCCCCccceEEEeCCCCCHHHHHHHHHcCCceeEEEEEcCCCc
Confidence 5688999999999999 334455532 4444555554599998765442210000 00000111234567889999
Q ss_pred HHHHHHHh
Q 040730 116 PSSVGSKF 123 (144)
Q Consensus 116 l~~IA~~~ 123 (144)
+..|+++.
T Consensus 120 ~~~i~~~l 127 (340)
T PRK10270 120 LSDYLKQL 127 (340)
T ss_pred HHHHHHHH
Confidence 99999765
No 78
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=55.98 E-value=15 Score=21.72 Aligned_cols=21 Identities=19% Similarity=0.177 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHcC
Q 040730 115 SPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N~ 135 (144)
|+..+|+.+|++...|..|=.
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 567899999999999988743
No 79
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=54.76 E-value=19 Score=19.69 Aligned_cols=24 Identities=8% Similarity=0.274 Sum_probs=20.0
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
+..|.+...||+.+|++...+...
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHH
Confidence 357899999999999998877654
No 80
>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=54.34 E-value=18 Score=20.25 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=16.4
Q ss_pred cHHHHHHHhCCCHHHHHH-HcC
Q 040730 115 SPSSVGSKFGVTMAELVA-TNG 135 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~-~N~ 135 (144)
|+.+||++.|++...+.+ +|+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 688999999999877743 444
No 81
>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=53.87 E-value=16 Score=20.54 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=15.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
-.|-+...||+.+|+|...+..
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~ 45 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKR 45 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHH
Confidence 3588999999999999988764
No 82
>smart00351 PAX Paired Box domain.
Probab=52.90 E-value=15 Score=25.03 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=20.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|.+...||++||++...+.+|
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kw 53 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKI 53 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 57999999999999998877665
No 83
>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=52.86 E-value=15 Score=21.33 Aligned_cols=26 Identities=8% Similarity=0.182 Sum_probs=21.8
Q ss_pred EEEEeccCCcHHHHHHHhCCCHHHHH
Q 040730 106 KSYVVQWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 106 ~~y~V~~GdTl~~IA~~~~~s~~~l~ 131 (144)
..|.+.++-|+..||+.+|++...+.
T Consensus 16 GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 16 GYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 35778899999999999999976653
No 84
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=52.65 E-value=17 Score=23.40 Aligned_cols=24 Identities=21% Similarity=0.238 Sum_probs=21.1
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
|..|-++..+|+.||||.....+|
T Consensus 22 v~~g~~~a~aA~~~gVS~~Ta~kW 45 (85)
T PF13011_consen 22 VEQGWPVAHAAAEFGVSRRTAYKW 45 (85)
T ss_pred HHcCCcHHHHHHHhCCCHHHHHHH
Confidence 567889999999999999888776
No 85
>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=51.30 E-value=17 Score=23.39 Aligned_cols=26 Identities=15% Similarity=0.294 Sum_probs=22.5
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730 110 VQWGESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
+..|.|...||+.+|++...+.++.+
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 56799999999999999988887654
No 86
>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=51.11 E-value=16 Score=23.60 Aligned_cols=25 Identities=20% Similarity=0.331 Sum_probs=22.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730 111 QWGESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
+.|-|...||+++|+|...|-+.|+
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4799999999999999999988775
No 87
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=51.10 E-value=19 Score=21.22 Aligned_cols=19 Identities=21% Similarity=0.167 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~ 133 (144)
|+..+|+.+|++...|..|
T Consensus 2 s~~eva~~~gvs~~tlr~~ 20 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYY 20 (70)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5678999999999999988
No 88
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=50.80 E-value=15 Score=20.94 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=14.4
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~ 132 (144)
+++.+|+.+|++..+|.+
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 578899999999887754
No 89
>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=50.39 E-value=18 Score=20.94 Aligned_cols=18 Identities=22% Similarity=0.353 Sum_probs=14.7
Q ss_pred CcHHHHHHHhCCCHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~ 131 (144)
=++..+|+.|++|...+.
T Consensus 15 ~s~~ela~~~~VS~~TiR 32 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIR 32 (57)
T ss_pred EEHHHHHHHHCcCHHHHH
Confidence 367789999999987764
No 90
>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=50.18 E-value=20 Score=21.14 Aligned_cols=19 Identities=21% Similarity=0.121 Sum_probs=17.0
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~ 133 (144)
++..+|+.+|++...|..|
T Consensus 2 ~i~evA~~~gvs~~tlR~~ 20 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYY 20 (67)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4678999999999999988
No 91
>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=50.10 E-value=22 Score=18.94 Aligned_cols=21 Identities=10% Similarity=0.083 Sum_probs=17.1
Q ss_pred cHHHHHHHhCCCHHHHHHHcC
Q 040730 115 SPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N~ 135 (144)
|+..+|+.+|++...|.+|=.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999988877743
No 92
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=47.24 E-value=26 Score=22.83 Aligned_cols=21 Identities=19% Similarity=0.287 Sum_probs=18.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~ 131 (144)
++|-||..||+.+|++...|.
T Consensus 19 KrG~sLa~lsr~~Gls~~TL~ 39 (92)
T PRK10344 19 KKGTSMAAESRRNGLSSSTLA 39 (92)
T ss_pred HcCCcHHHHHHHcCCChHHHH
Confidence 579999999999999887763
No 93
>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=46.60 E-value=30 Score=20.38 Aligned_cols=23 Identities=17% Similarity=0.219 Sum_probs=19.9
Q ss_pred cCCcHHHHHHHhCCCHHHHHHHc
Q 040730 112 WGESPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~~N 134 (144)
.|=++..||+..|++...+..|=
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHH
Confidence 48899999999999988887764
No 94
>TIGR00247 conserved hypothetical protein, YceG family. This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC.
Probab=45.59 E-value=75 Score=25.51 Aligned_cols=81 Identities=11% Similarity=0.019 Sum_probs=48.5
Q ss_pred eeeEeCCCCCHHHHHHHh--CCCCCHH----HHHhhcCCCCCCCCCcEEEEecccccCC-CC-CCCcccceEEEEeccCC
Q 040730 43 TTNNVRPADTIDSILNGF--GGLVSAE----QINSTSELSHPVNDWTKLMIMLPCTCFN-NG-NNGVTSIYKSYVVQWGE 114 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y--~~~~~~~----~l~~~N~~~~~l~~Gq~l~IP~~~~~~~-~~-~~~~~~~~~~y~V~~Gd 114 (144)
...+|.+|+|...|++.. .|++.-. ...+.++....|++|.-..-+......- .. ..+........++..|.
T Consensus 40 v~v~Ip~G~s~~~Ia~~L~~~GvI~s~~~F~~~ak~~~~~~~lkaG~Y~l~~~ms~~~il~~L~~g~~~~~~~vti~eG~ 119 (342)
T TIGR00247 40 YEFNIEKGTGVSKIAKELKKQKLIKSEKLLQYLLKIKGSLKQFKAGTYLLNGDMTVFEILKLLLSGKENVQFDVTIPEGY 119 (342)
T ss_pred EEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHhcCCcCcccceEEEECCCCCHHHHHHHHHcCCcceeEEEEEcCCC
Confidence 567899999999999943 3444432 3344455444589998765543210000 00 01111123467889999
Q ss_pred cHHHHHHHh
Q 040730 115 SPSSVGSKF 123 (144)
Q Consensus 115 Tl~~IA~~~ 123 (144)
|++.||++.
T Consensus 120 t~~~ia~~l 128 (342)
T TIGR00247 120 TLRDIAKKL 128 (342)
T ss_pred cHHHHHHHH
Confidence 999999876
No 95
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.43 E-value=21 Score=25.05 Aligned_cols=25 Identities=28% Similarity=0.353 Sum_probs=21.4
Q ss_pred EeccCCcHHHHHHHhCCCHHHHHHH
Q 040730 109 VVQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 109 ~V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
.+..|.+...||++||++...+..|
T Consensus 17 ~~~~G~S~re~Ak~~gvs~sTvy~w 41 (138)
T COG3415 17 VVGEGLSCREAAKRFGVSISTVYRW 41 (138)
T ss_pred HHHcCccHHHHHHHhCccHHHHHHH
Confidence 3567999999999999999887665
No 96
>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=44.57 E-value=35 Score=18.66 Aligned_cols=23 Identities=9% Similarity=0.253 Sum_probs=19.1
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|-+...||+.++++...+..+
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~ 35 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999998777554
No 97
>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=44.29 E-value=21 Score=21.00 Aligned_cols=18 Identities=28% Similarity=0.346 Sum_probs=14.1
Q ss_pred HHHHHHHhCCCHHHHHHH
Q 040730 116 PSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 116 l~~IA~~~~~s~~~l~~~ 133 (144)
+.--|++||+|.++|.++
T Consensus 23 v~ywa~~~gvt~~~L~~A 40 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREA 40 (57)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 345679999999988765
No 98
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=44.21 E-value=27 Score=23.48 Aligned_cols=26 Identities=23% Similarity=0.294 Sum_probs=22.9
Q ss_pred eEeCCCCCHHHHHHHhCCCCCHHHHHhh
Q 040730 45 NNVRPADTIDSILNGFGGLVSAEQINST 72 (144)
Q Consensus 45 y~V~~GdTl~~IA~~y~~~~~~~~l~~~ 72 (144)
.....|.|+..||+.|+ ++...|..|
T Consensus 24 ~~~~~g~sv~evA~e~g--Is~~tl~~W 49 (121)
T PRK09413 24 QSFEPGMTVSLVARQHG--VAASQLFLW 49 (121)
T ss_pred HHHcCCCCHHHHHHHHC--cCHHHHHHH
Confidence 44578999999999999 999999888
No 99
>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=43.86 E-value=28 Score=20.57 Aligned_cols=20 Identities=20% Similarity=0.061 Sum_probs=17.7
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 040730 115 SPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N 134 (144)
++..+|++.|++...|..|-
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye 21 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999884
No 100
>PF13551 HTH_29: Winged helix-turn helix
Probab=42.54 E-value=27 Score=22.36 Aligned_cols=24 Identities=8% Similarity=0.220 Sum_probs=19.2
Q ss_pred eccCC-cHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGE-SPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~Gd-Tl~~IA~~~~~s~~~l~~~ 133 (144)
+..|. |...||+.+|++...+.+|
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~ 32 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRW 32 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHH
Confidence 35677 6999999999998777654
No 101
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=42.43 E-value=18 Score=21.11 Aligned_cols=22 Identities=27% Similarity=0.354 Sum_probs=17.5
Q ss_pred CcHHHHHHHhCCCHHHHHHHcC
Q 040730 114 ESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~~N~ 135 (144)
+-+..+|+.||+++++|..-.+
T Consensus 4 ~I~~~Va~~~~i~~~~i~s~~R 25 (60)
T smart00760 4 EIIEAVAEYFGVKPEDLKSKSR 25 (60)
T ss_pred HHHHHHHHHhCCCHHHHhcCCC
Confidence 3456789999999999976555
No 102
>PHA02591 hypothetical protein; Provisional
Probab=42.06 E-value=32 Score=21.81 Aligned_cols=21 Identities=19% Similarity=0.317 Sum_probs=10.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~ 131 (144)
+.|-|...||+..|+++..+.
T Consensus 57 eqGlSqeqIA~~LGVsqetVr 77 (83)
T PHA02591 57 RKGFTVEKIASLLGVSVRKVR 77 (83)
T ss_pred HcCCCHHHHHHHhCCCHHHHH
Confidence 345555555555555555443
No 103
>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=41.06 E-value=24 Score=25.61 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=22.0
Q ss_pred EeccCCcHHHHHHHhCCCHHHHHHH
Q 040730 109 VVQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 109 ~V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
.++.|.|...||+.+|++++.+..+
T Consensus 65 rIRaGas~eeVA~~~G~~~~rV~rf 89 (170)
T PF11268_consen 65 RIRAGASAEEVAEEAGVPVERVRRF 89 (170)
T ss_pred HHHCCCCHHHHHHHhCCCHHHhhhc
Confidence 4789999999999999999887654
No 104
>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=40.23 E-value=34 Score=22.53 Aligned_cols=23 Identities=13% Similarity=0.198 Sum_probs=19.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
-.|-++..||+.+|++...+...
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 36999999999999999887653
No 105
>cd00131 PAX Paired Box domain
Probab=39.62 E-value=31 Score=23.58 Aligned_cols=23 Identities=17% Similarity=0.262 Sum_probs=20.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|.+...||++|+++...+.+|
T Consensus 31 ~~G~s~~~iA~~~~Vs~~tV~r~ 53 (128)
T cd00131 31 QSGIRPCDISRQLRVSHGCVSKI 53 (128)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 57999999999999998877665
No 106
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=38.98 E-value=49 Score=17.49 Aligned_cols=22 Identities=14% Similarity=0.193 Sum_probs=19.1
Q ss_pred cCCcHHHHHHHhCCCHHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
.|-+...||..+|++...+..+
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6889999999999999888654
No 107
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.96 E-value=32 Score=24.10 Aligned_cols=20 Identities=25% Similarity=0.366 Sum_probs=17.3
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 040730 113 GESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~ 132 (144)
-+||..||.++|++..++.+
T Consensus 90 ~~~l~~la~~~Gld~~El~~ 109 (143)
T COG3753 90 TDTLSQLAQKTGLDEQELLK 109 (143)
T ss_pred hhHHHHHHHHhCCCHHHHHH
Confidence 58999999999999887743
No 108
>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=37.68 E-value=38 Score=21.43 Aligned_cols=22 Identities=18% Similarity=0.025 Sum_probs=18.5
Q ss_pred cHHHHHHHhCCCHHHHHHHcCC
Q 040730 115 SPSSVGSKFGVTMAELVATNGL 136 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N~l 136 (144)
|+..+|+.+|+++..|..|-..
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5678999999999999888643
No 109
>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=36.86 E-value=34 Score=20.75 Aligned_cols=18 Identities=22% Similarity=0.438 Sum_probs=13.0
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~ 132 (144)
-+..+|+.||++.++|..
T Consensus 5 Ii~~Va~~~~v~~~~i~s 22 (70)
T PF08299_consen 5 IIEAVAEYFGVSVEDIRS 22 (70)
T ss_dssp HHHHHHHHTT--HHHHHS
T ss_pred HHHHHHHHHCCCHHHHhC
Confidence 456789999999999864
No 110
>PF12728 HTH_17: Helix-turn-helix domain
Probab=36.12 E-value=48 Score=18.26 Aligned_cols=19 Identities=5% Similarity=0.139 Sum_probs=15.9
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~ 133 (144)
|...+|+.+|++...+.+|
T Consensus 3 t~~e~a~~l~is~~tv~~~ 21 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRW 21 (51)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5678899999998888776
No 111
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=35.97 E-value=53 Score=20.44 Aligned_cols=23 Identities=17% Similarity=0.307 Sum_probs=19.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|-|...||+..|+|...+..+
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~ 52 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNH 52 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36899999999999998887654
No 112
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=35.79 E-value=49 Score=18.34 Aligned_cols=18 Identities=17% Similarity=0.348 Sum_probs=14.4
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~ 132 (144)
|...||++|+++...+.+
T Consensus 22 s~~~la~~~~vs~~tv~~ 39 (60)
T smart00345 22 SERELAAQLGVSRTTVRE 39 (60)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 677899999999766644
No 113
>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=35.27 E-value=59 Score=19.63 Aligned_cols=21 Identities=29% Similarity=0.382 Sum_probs=17.2
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~ 131 (144)
..|-++-.||+++|++..+..
T Consensus 11 E~g~~FveIAr~~~i~a~e~a 31 (63)
T PF11242_consen 11 ESGLSFVEIARKIGITAKEVA 31 (63)
T ss_pred HcCCcHHHHHHHhCCCHHHHH
Confidence 358899999999999976653
No 114
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=35.09 E-value=47 Score=19.51 Aligned_cols=17 Identities=12% Similarity=0.268 Sum_probs=13.1
Q ss_pred cHHHHHHHhCCCHHHHH
Q 040730 115 SPSSVGSKFGVTMAELV 131 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~ 131 (144)
|+..||+++|++...|.
T Consensus 3 ~~~~la~~~~~s~~~l~ 19 (84)
T smart00342 3 TLEDLAEALGMSPRHLQ 19 (84)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 67788888888876663
No 115
>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=34.78 E-value=43 Score=19.47 Aligned_cols=22 Identities=14% Similarity=0.243 Sum_probs=17.3
Q ss_pred eccCCcHHHHHHHhCCCHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~ 131 (144)
+.+..|+...|+.+|+++++|.
T Consensus 38 ~~~~~Tl~~aa~~~gid~~~li 59 (59)
T PF08984_consen 38 MAKFETLEQAAKMHGIDLEKLI 59 (59)
T ss_dssp HHHHSBHHHHHHHHT--HHHHH
T ss_pred hcccCCHHHHHHHcCCCHHHhC
Confidence 4677999999999999999874
No 116
>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=34.68 E-value=47 Score=19.38 Aligned_cols=22 Identities=14% Similarity=0.335 Sum_probs=14.4
Q ss_pred ccCCcH---HHHHHHhCCCHHHHHH
Q 040730 111 QWGESP---SSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl---~~IA~~~~~s~~~l~~ 132 (144)
++||.| ..||++|+++...+.+
T Consensus 19 ~~g~~lps~~~la~~~~vsr~tvr~ 43 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVSRTTVRE 43 (64)
T ss_dssp -TTSBE--HHHHHHHHTS-HHHHHH
T ss_pred CCCCEeCCHHHHHHHhccCCcHHHH
Confidence 456655 5888999999766653
No 117
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=34.64 E-value=36 Score=25.25 Aligned_cols=62 Identities=13% Similarity=0.278 Sum_probs=38.3
Q ss_pred HHHHHHHhCCCCCHHHHHhhcCCCCC-CCCCcEEEEecccccCCCCCCCcccceEEEEeccCCcHHHHHHHhCCCHHHHH
Q 040730 53 IDSILNGFGGLVSAEQINSTSELSHP-VNDWTKLMIMLPCTCFNNGNNGVTSIYKSYVVQWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 53 l~~IA~~y~~~~~~~~l~~~N~~~~~-l~~Gq~l~IP~~~~~~~~~~~~~~~~~~~y~V~~GdTl~~IA~~~~~s~~~l~ 131 (144)
+..+|++++ ++..+=.+.+..... ...|+.+++-.+ .||-=.+|..+..++..|.+..++|.
T Consensus 27 vD~La~~~~--~~~~~~~kf~~~~~~~~i~g~kv~l~kP---------------~TyMNlSG~~V~~~~~fy~i~~~~il 89 (190)
T COG0193 27 VDLLARRLN--LSFKEEKKFNGLVAKGTIEGEKVILLKP---------------TTYMNLSGKAVGALASFYKIKPEDIL 89 (190)
T ss_pred HHHHHHHhC--CCCccccccCceeEEEEeCCcEEEEecC---------------ccceeCcHHHHHHHHHHhCCCHHHEE
Confidence 456677666 544333444433332 345654444221 35666789999999999999988763
No 118
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=34.40 E-value=46 Score=21.04 Aligned_cols=20 Identities=15% Similarity=0.252 Sum_probs=16.6
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 040730 113 GESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~ 132 (144)
--|+..||+.+|+|...+..
T Consensus 19 ~~ti~dvA~~~gvS~~TVsr 38 (80)
T TIGR02844 19 KATVRETAKVFGVSKSTVHK 38 (80)
T ss_pred CCCHHHHHHHhCCCHHHHHH
Confidence 34889999999999887754
No 119
>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=34.36 E-value=44 Score=18.67 Aligned_cols=17 Identities=12% Similarity=0.335 Sum_probs=12.7
Q ss_pred CcHHHHHHHhCCCHHHH
Q 040730 114 ESPSSVGSKFGVTMAEL 130 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l 130 (144)
=|...||+++++|...+
T Consensus 16 it~~eLa~~l~vS~rTi 32 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTI 32 (55)
T ss_dssp BEHHHHHHHCTS-HHHH
T ss_pred cCHHHHHHHhCCCHHHH
Confidence 37889999999996544
No 120
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.52 E-value=44 Score=22.25 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=14.2
Q ss_pred cHHHHHHHhCCCHHHHH
Q 040730 115 SPSSVGSKFGVTMAELV 131 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~ 131 (144)
++..||..|+||-+++.
T Consensus 35 Sl~EIAee~~VSRqAIy 51 (105)
T COG2739 35 SLSEIAEEFNVSRQAIY 51 (105)
T ss_pred cHHHHHHHhCccHHHHH
Confidence 68899999999976653
No 121
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=33.26 E-value=9.4 Score=30.05 Aligned_cols=81 Identities=7% Similarity=-0.028 Sum_probs=17.1
Q ss_pred eeEeCCCCCHHHHHHHhC--CCCCHH----HHHhhcCCCCCCCCCcEEEEecccccCC-CCCCCcccceEEEEeccCCcH
Q 040730 44 TNNVRPADTIDSILNGFG--GLVSAE----QINSTSELSHPVNDWTKLMIMLPCTCFN-NGNNGVTSIYKSYVVQWGESP 116 (144)
Q Consensus 44 ~y~V~~GdTl~~IA~~y~--~~~~~~----~l~~~N~~~~~l~~Gq~l~IP~~~~~~~-~~~~~~~~~~~~y~V~~GdTl 116 (144)
..+|.+|+|+..|++... |++.-. ...+.++....|++|.-..-+......- ..-..+.......+|..|.|+
T Consensus 2 ~v~I~~G~s~~~Ia~~L~~~gvI~s~~~F~~~~~~~~~~~~lkaG~Y~l~~~mS~~eil~~L~~g~~~~~~vTIpEG~t~ 81 (297)
T PF02618_consen 2 TVTIPPGASASQIADILEEAGVIKSARAFKLYAKLNGYDSKLKAGTYELNPGMSYKEILSILTSGKVAQVRVTIPEGFTL 81 (297)
T ss_dssp --------------------------------------------EEEEE-TT--HHHHHHHHHH-----EEEEE-TT--H
T ss_pred eEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHhCCCCCceeeeEEEeCCCCCHHHHHHHHHhcccceeEEEecCCCcH
Confidence 357889999999998422 222221 2223333333377776654332100000 000001122247889999999
Q ss_pred HHHHHHhC
Q 040730 117 SSVGSKFG 124 (144)
Q Consensus 117 ~~IA~~~~ 124 (144)
..||++..
T Consensus 82 ~~i~~~l~ 89 (297)
T PF02618_consen 82 EQIAQRLA 89 (297)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 99998753
No 122
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=33.23 E-value=64 Score=21.82 Aligned_cols=32 Identities=16% Similarity=0.106 Sum_probs=24.7
Q ss_pred HhCCCCCHHHHHhhcCCCCCCCCCcEEEEeccc
Q 040730 59 GFGGLVSAEQINSTSELSHPVNDWTKLMIMLPC 91 (144)
Q Consensus 59 ~y~~~~~~~~l~~~N~~~~~l~~Gq~l~IP~~~ 91 (144)
.-+|++...++...| +...+..|+.++||...
T Consensus 10 ~agg~~~~ad~~~in-la~~l~d~~~i~vp~~~ 41 (120)
T TIGR01259 10 KAGGFTEQADGLSVN-LAGKLMDEMFVYVPMKG 41 (120)
T ss_pred HccCCCcccchhccc-ccccccCCCEEEECCCC
Confidence 446667778888888 55559999999999753
No 123
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=33.18 E-value=42 Score=26.18 Aligned_cols=24 Identities=17% Similarity=0.238 Sum_probs=20.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHcCC
Q 040730 113 GESPSSVGSKFGVTMAELVATNGL 136 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~~N~l 136 (144)
|--+-.||++||+++.+|.+|-+-
T Consensus 19 gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHHh
Confidence 466789999999999999998653
No 124
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=33.18 E-value=47 Score=21.35 Aligned_cols=23 Identities=17% Similarity=0.317 Sum_probs=20.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHHcC
Q 040730 113 GESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
.|=+.+||+..|++..+|..+|=
T Consensus 69 ~~EirGIA~~~gi~l~~iv~lN~ 91 (95)
T PF15508_consen 69 AEEIRGIAKAAGIPLGDIVLLNL 91 (95)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Confidence 46688999999999999999994
No 125
>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=32.91 E-value=51 Score=20.82 Aligned_cols=22 Identities=18% Similarity=0.040 Sum_probs=18.9
Q ss_pred cHHHHHHHhCCCHHHHHHHcCC
Q 040730 115 SPSSVGSKFGVTMAELVATNGL 136 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N~l 136 (144)
|+..+|+.+|++...|..|-..
T Consensus 3 ti~evA~~~gvs~~tLR~ye~~ 24 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWEEK 24 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 5778999999999999988654
No 126
>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=32.71 E-value=28 Score=20.10 Aligned_cols=19 Identities=21% Similarity=0.464 Sum_probs=15.3
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~ 132 (144)
+++..||..||+++++|..
T Consensus 42 ~~l~~i~~~~~v~~~~l~~ 60 (64)
T PF12844_consen 42 STLKKIAEALGVSLDELFD 60 (64)
T ss_dssp HHHHHHHHHHTS-HHHHCC
T ss_pred HHHHHHHHHhCCCHHHHhc
Confidence 6788999999999998753
No 127
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=32.31 E-value=60 Score=17.13 Aligned_cols=21 Identities=5% Similarity=0.017 Sum_probs=13.6
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~ 132 (144)
..-+|..||...|.+..-+.+
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 456888999999998766543
No 128
>PRK00118 putative DNA-binding protein; Validated
Probab=32.14 E-value=59 Score=21.62 Aligned_cols=22 Identities=14% Similarity=0.107 Sum_probs=18.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
..|-|...||+.+|+|...+..
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r 52 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYD 52 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHH
Confidence 4589999999999999887754
No 129
>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=31.53 E-value=49 Score=21.48 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=17.6
Q ss_pred eccCCcH-HHHHHHhCCCHHHHHHHc
Q 040730 110 VQWGESP-SSVGSKFGVTMAELVATN 134 (144)
Q Consensus 110 V~~GdTl-~~IA~~~~~s~~~l~~~N 134 (144)
|..|-+- ..-.++|++|.+++.+|=
T Consensus 45 V~~Glis~~EA~~rY~Ls~eEf~~W~ 70 (90)
T PF06627_consen 45 VRGGLISVEEACRRYGLSEEEFESWQ 70 (90)
T ss_dssp HHCTTS-HHHHHHCTTSSHHHHHHHH
T ss_pred HHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence 4455544 444489999999999884
No 130
>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=31.49 E-value=44 Score=19.88 Aligned_cols=20 Identities=15% Similarity=0.220 Sum_probs=14.9
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 040730 115 SPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~N 134 (144)
..-.-|++|||+...+.+|=
T Consensus 27 ~~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 27 NQRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp -HHHHHHHTTS-HHHHHHHH
T ss_pred hHHHHHHHhCccHHHHHHHH
Confidence 34567899999999998874
No 131
>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=31.45 E-value=47 Score=18.93 Aligned_cols=22 Identities=14% Similarity=0.318 Sum_probs=17.6
Q ss_pred eccCCcHHHHHHHhCCCHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~ 131 (144)
+-.|-+...||+..+++...+.
T Consensus 15 l~~G~~~~eIA~~l~is~~tV~ 36 (58)
T PF00196_consen 15 LAQGMSNKEIAEELGISEKTVK 36 (58)
T ss_dssp HHTTS-HHHHHHHHTSHHHHHH
T ss_pred HHhcCCcchhHHhcCcchhhHH
Confidence 3579999999999999987764
No 132
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=31.33 E-value=55 Score=20.44 Aligned_cols=22 Identities=23% Similarity=0.140 Sum_probs=16.2
Q ss_pred EEEEeccCCcHHHHHHHhCCCH
Q 040730 106 KSYVVQWGESPSSVGSKFGVTM 127 (144)
Q Consensus 106 ~~y~V~~GdTl~~IA~~~~~s~ 127 (144)
..|.+.+|+||...+.+.|+.+
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 3588999999999999988653
No 133
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=30.75 E-value=63 Score=19.10 Aligned_cols=41 Identities=5% Similarity=0.023 Sum_probs=29.9
Q ss_pred eeeEeCCCCCHHHHHHHhCCCCCHHHHHhhcCCCC--C--CCCCcEEE
Q 040730 43 TTNNVRPADTIDSILNGFGGLVSAEQINSTSELSH--P--VNDWTKLM 86 (144)
Q Consensus 43 ~~y~V~~GdTl~~IA~~y~~~~~~~~l~~~N~~~~--~--l~~Gq~l~ 86 (144)
..+.+..+-||+.+.+.+. +..++.-+|+... + |..|+.|.
T Consensus 8 k~~~~~~~~tl~~lr~~~k---~~~DI~I~NGF~~~~d~~L~e~D~v~ 52 (57)
T PF14453_consen 8 KEIETEENTTLFELRKESK---PDADIVILNGFPTKEDIELKEGDEVF 52 (57)
T ss_pred EEEEcCCCcCHHHHHHhhC---CCCCEEEEcCcccCCccccCCCCEEE
Confidence 4577888889999999776 3456777787663 2 77777764
No 134
>PF14502 HTH_41: Helix-turn-helix domain
Probab=30.25 E-value=67 Score=18.35 Aligned_cols=19 Identities=26% Similarity=0.382 Sum_probs=14.4
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~ 132 (144)
.|+...+++|+++...+..
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~ 25 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQN 25 (48)
T ss_pred CCHHHHHHHhCcchhHHHH
Confidence 4677888999998766543
No 135
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=29.78 E-value=65 Score=23.22 Aligned_cols=26 Identities=19% Similarity=0.190 Sum_probs=21.3
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730 110 VQWGESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
-|+--++..||+.|++++-+|..+=+
T Consensus 24 ~qPdg~~eamA~~~~v~~~eIv~aLP 49 (176)
T COG3721 24 TQPDGTLEAMAEQYNVTELEIVRALP 49 (176)
T ss_pred hCCCCcHHHHHHHhCCCHHHHHHhCc
Confidence 36788999999999999988876533
No 136
>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=29.77 E-value=19 Score=22.95 Aligned_cols=23 Identities=17% Similarity=0.419 Sum_probs=15.7
Q ss_pred EEEeccCCcHHHHHHHhCCCHHH
Q 040730 107 SYVVQWGESPSSVGSKFGVTMAE 129 (144)
Q Consensus 107 ~y~V~~GdTl~~IA~~~~~s~~~ 129 (144)
.|.+..+.|+-..|+.||+|-..
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 47788899999999999998543
No 137
>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=29.73 E-value=84 Score=16.26 Aligned_cols=26 Identities=15% Similarity=0.254 Sum_probs=20.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHHcCC
Q 040730 111 QWGESPSSVGSKFGVTMAELVATNGL 136 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~N~l 136 (144)
+.|-+...+|+..|++...+.+|-.-
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 35778889999999998888776443
No 138
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=29.36 E-value=52 Score=28.27 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=21.4
Q ss_pred eccCCcHHHHHHHhCCCHH----HHHHHcCC
Q 040730 110 VQWGESPSSVGSKFGVTMA----ELVATNGL 136 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~----~l~~~N~l 136 (144)
+..+|||..+|++.|++.+ ++.++|..
T Consensus 421 ~~kadTleELA~k~gid~~~L~~TV~~yN~~ 451 (564)
T PRK12845 421 AHRADSLADLARKIGVPVDTFVATMRRFNEM 451 (564)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3468999999999999864 55678854
No 139
>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=29.10 E-value=78 Score=17.44 Aligned_cols=23 Identities=17% Similarity=0.336 Sum_probs=16.0
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
+.|-|...+|++.|++...+.++
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~ 29 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRI 29 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHH
Confidence 45777888888888888777665
No 140
>PHA01976 helix-turn-helix protein
Probab=28.82 E-value=84 Score=18.18 Aligned_cols=23 Identities=13% Similarity=0.088 Sum_probs=12.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
+.|-|...+|++.|++...+.+|
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~ 35 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDF 35 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH
Confidence 34555555555555555555544
No 141
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=28.82 E-value=69 Score=23.29 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=18.0
Q ss_pred ccCCcHHHHHHHhCCCH---HHHHHH
Q 040730 111 QWGESPSSVGSKFGVTM---AELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~---~~l~~~ 133 (144)
+.|.++-.||++||+.. ++|.++
T Consensus 31 ~~~~sv~~vS~~ygi~~~RV~AIvrL 56 (172)
T PF12298_consen 31 QDGKSVREVSQKYGIKIQRVEAIVRL 56 (172)
T ss_pred hCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 56889999999999975 555444
No 142
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=28.68 E-value=79 Score=19.91 Aligned_cols=24 Identities=21% Similarity=0.357 Sum_probs=20.8
Q ss_pred eccCCcHHHHHHHhC-CCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFG-VTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~-~s~~~l~~~ 133 (144)
.+.|.|...|+.-|. ++.++|.++
T Consensus 40 l~~G~s~eeil~dyp~Lt~~dI~aa 64 (79)
T COG2442 40 LAAGESIEEILADYPDLTLEDIRAA 64 (79)
T ss_pred HHCCCCHHHHHHhCCCCCHHHHHHH
Confidence 478999999999998 999888764
No 143
>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=28.49 E-value=50 Score=24.01 Aligned_cols=25 Identities=16% Similarity=0.381 Sum_probs=21.9
Q ss_pred EeCCCCCHHHHHHHhCCCCCHHHHHhh
Q 040730 46 NVRPADTIDSILNGFGGLVSAEQINST 72 (144)
Q Consensus 46 ~V~~GdTl~~IA~~y~~~~~~~~l~~~ 72 (144)
.++.|.|...||..++ ++++.|.++
T Consensus 65 rIRaGas~eeVA~~~G--~~~~rV~rf 89 (170)
T PF11268_consen 65 RIRAGASAEEVAEEAG--VPVERVRRF 89 (170)
T ss_pred HHHCCCCHHHHHHHhC--CCHHHhhhc
Confidence 4688999999999999 899888765
No 144
>PRK07198 hypothetical protein; Validated
Probab=27.96 E-value=39 Score=28.03 Aligned_cols=24 Identities=25% Similarity=0.270 Sum_probs=18.0
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
|.+==-|..||+|||++..+|++.
T Consensus 171 v~pvwylpgva~rfg~~e~~lrr~ 194 (418)
T PRK07198 171 IEPVWYLPGVAERFGVSETDLRRT 194 (418)
T ss_pred ecccccccchHHHcCCCHHHHHHH
Confidence 434344669999999999988764
No 145
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=27.55 E-value=73 Score=21.54 Aligned_cols=21 Identities=10% Similarity=0.101 Sum_probs=18.7
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~ 132 (144)
.|-++..||+.+|+++..+..
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~ 140 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKS 140 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHH
Confidence 699999999999999988754
No 146
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=27.53 E-value=76 Score=18.13 Aligned_cols=23 Identities=17% Similarity=0.242 Sum_probs=11.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHHc
Q 040730 112 WGESPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~~N 134 (144)
.|=|...+|++-|++...|.++=
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~ 31 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRIL 31 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH
Confidence 45566667777777666665543
No 147
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=27.49 E-value=1.4e+02 Score=22.23 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=20.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHHc
Q 040730 111 QWGESPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~N 134 (144)
.-|..|..+|+..|+|++++++.=
T Consensus 88 ~~g~DL~~vA~~~gLs~eevi~~H 111 (202)
T TIGR00370 88 EFGPDLEEVAKINQLSPEEVIDIH 111 (202)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHH
Confidence 457899999999999999998763
No 148
>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=27.45 E-value=94 Score=16.96 Aligned_cols=25 Identities=12% Similarity=0.178 Sum_probs=20.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730 111 QWGESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
+.|-|...+|++.|++...+.+|=+
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4678888999999999888887743
No 149
>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=27.31 E-value=78 Score=17.17 Aligned_cols=19 Identities=11% Similarity=0.251 Sum_probs=13.5
Q ss_pred CCcHHHHHHHhCCCHHHHH
Q 040730 113 GESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~ 131 (144)
--++..||++.|+|..++.
T Consensus 17 r~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVR 35 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHH
T ss_pred CccHHHHHHHHCcCHHHHH
Confidence 3578899999999987664
No 150
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=26.87 E-value=63 Score=27.26 Aligned_cols=26 Identities=19% Similarity=0.372 Sum_probs=20.8
Q ss_pred ccCCcHHHHHHHhCCCHH----HHHHHcCC
Q 040730 111 QWGESPSSVGSKFGVTMA----ELVATNGL 136 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~----~l~~~N~l 136 (144)
...|||..+|++.|++.+ ++.++|.+
T Consensus 373 ~kaDTleELA~k~gid~~~L~~Tv~~yN~~ 402 (513)
T PRK12837 373 RTADTLEELAAKIGVPADALTATVARFNGF 402 (513)
T ss_pred eecCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 367999999999999864 55678854
No 151
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=26.49 E-value=60 Score=18.06 Aligned_cols=22 Identities=14% Similarity=0.160 Sum_probs=18.3
Q ss_pred cCCcHHHHHHHhCCCHHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..+.+..||...|++...+..|
T Consensus 26 ~~~~~~~la~~~~l~~~qV~~W 47 (59)
T cd00086 26 SREEREELAKELGLTERQVKIW 47 (59)
T ss_pred CHHHHHHHHHHHCcCHHHHHHH
Confidence 3567889999999999998776
No 152
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=26.34 E-value=1e+02 Score=15.73 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=19.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHHcCC
Q 040730 111 QWGESPSSVGSKFGVTMAELVATNGL 136 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~N~l 136 (144)
+.|-+...+|+..|++...+..|-.-
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 34667888999999988888776543
No 153
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=25.84 E-value=79 Score=20.97 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=15.0
Q ss_pred cCCcHHHHHHHhCCCHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~ 131 (144)
..+-...||++|++|...+.
T Consensus 39 tK~LYp~IA~k~~TT~s~VE 58 (106)
T PF08769_consen 39 TKELYPDIAKKYGTTPSRVE 58 (106)
T ss_dssp TTTHHHHHHHHTTS-HHHHH
T ss_pred hhhHHHHHHHHHCCCHHHHH
Confidence 35778899999999986654
No 154
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=25.33 E-value=77 Score=21.00 Aligned_cols=21 Identities=14% Similarity=0.224 Sum_probs=13.4
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~ 131 (144)
-..=|+..||..+|+|-+++.
T Consensus 31 ~eDlSlsEIAe~~~iSRqaV~ 51 (101)
T PF04297_consen 31 EEDLSLSEIAEELGISRQAVY 51 (101)
T ss_dssp TS---HHHHHHHCTS-HHHHH
T ss_pred ccCCCHHHHHHHHCCCHHHHH
Confidence 345688999999999976553
No 155
>PRK12839 hypothetical protein; Provisional
Probab=24.86 E-value=71 Score=27.49 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=20.7
Q ss_pred cCCcHHHHHHHhCCCH----HHHHHHcCC
Q 040730 112 WGESPSSVGSKFGVTM----AELVATNGL 136 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~----~~l~~~N~l 136 (144)
.+|||..+|++.|++. +++.++|.+
T Consensus 426 kadTleELA~k~gid~~~L~~TV~~yN~~ 454 (572)
T PRK12839 426 RGRTIEELAEKCGIDPAGLEATVAEFNEN 454 (572)
T ss_pred ECCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 5799999999999995 455778865
No 156
>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=24.64 E-value=99 Score=15.89 Aligned_cols=19 Identities=21% Similarity=0.405 Sum_probs=15.4
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~ 132 (144)
+-|..+|++.|.|..++++
T Consensus 12 ~~l~~~a~~~g~s~s~~ir 30 (39)
T PF01402_consen 12 ERLDELAKELGRSRSELIR 30 (39)
T ss_dssp HHHHHHHHHHTSSHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHH
Confidence 4577899999999888764
No 157
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=24.64 E-value=96 Score=17.43 Aligned_cols=18 Identities=17% Similarity=0.326 Sum_probs=14.3
Q ss_pred cHHHHHHHhCCCHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~ 132 (144)
+...||+.|+++...+.+
T Consensus 27 ~~~~la~~~~is~~~v~~ 44 (66)
T cd07377 27 SERELAEELGVSRTTVRE 44 (66)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 577999999999766543
No 158
>PF14493 HTH_40: Helix-turn-helix domain
Probab=24.64 E-value=91 Score=19.66 Aligned_cols=21 Identities=19% Similarity=0.170 Sum_probs=17.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~ 131 (144)
+.|-|+..||+.-+++...+.
T Consensus 11 ~~G~si~eIA~~R~L~~sTI~ 31 (91)
T PF14493_consen 11 QKGLSIEEIAKIRGLKESTIY 31 (91)
T ss_pred HcCCCHHHHHHHcCCCHHHHH
Confidence 679999999999999876663
No 159
>PRK04217 hypothetical protein; Provisional
Probab=24.48 E-value=96 Score=20.82 Aligned_cols=21 Identities=19% Similarity=0.337 Sum_probs=18.0
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~ 132 (144)
.|-|...||+.+|++...+..
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r 77 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWR 77 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHH
Confidence 677999999999999877754
No 160
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=24.42 E-value=97 Score=18.37 Aligned_cols=19 Identities=16% Similarity=0.221 Sum_probs=16.0
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~ 133 (144)
+...+|+.+|++...+..|
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 4568999999999999999
No 161
>PF13994 PgaD: PgaD-like protein
Probab=24.40 E-value=68 Score=22.16 Aligned_cols=25 Identities=16% Similarity=0.217 Sum_probs=21.2
Q ss_pred CcHHHHHHHhCCCHHHHHHHcCCCC
Q 040730 114 ESPSSVGSKFGVTMAELVATNGLSQ 138 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~~N~l~~ 138 (144)
-+..++|+.|+++.+++.++.+-+.
T Consensus 101 ~~~~elA~~f~l~~~~l~~lr~~k~ 125 (138)
T PF13994_consen 101 VSDEELARSFGLSPEQLQQLRQAKV 125 (138)
T ss_pred CCHHHHHHHcCCCHHHHHHHHhCCe
Confidence 6778999999999999998876543
No 162
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=23.74 E-value=94 Score=21.43 Aligned_cols=22 Identities=14% Similarity=0.167 Sum_probs=18.8
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
-.|-+...||+.+|++...+..
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~~ 163 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVRS 163 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3689999999999999887753
No 163
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.41 E-value=96 Score=21.71 Aligned_cols=22 Identities=14% Similarity=0.151 Sum_probs=18.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
-.|-+...||+.+|+++..++.
T Consensus 143 ~~g~s~~eIA~~lgis~~tV~~ 164 (179)
T PRK12514 143 LEGLSYKELAERHDVPLNTMRT 164 (179)
T ss_pred HcCCCHHHHHHHHCCChHHHHH
Confidence 3689999999999999887753
No 164
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=22.38 E-value=1e+02 Score=17.32 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=17.8
Q ss_pred eccCCcHHHHHHHhCCCHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAEL 130 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l 130 (144)
+..|.+...||...+++...+
T Consensus 16 ~~~G~s~~eia~~l~is~~tV 36 (65)
T COG2771 16 VAQGKSNKEIARILGISEETV 36 (65)
T ss_pred HHCCCCHHHHHHHHCCCHHHH
Confidence 567899999999999987655
No 165
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=22.30 E-value=65 Score=23.60 Aligned_cols=24 Identities=17% Similarity=0.216 Sum_probs=20.8
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
|-.|+++-.+|++.|++..++-++
T Consensus 29 vsaG~iFR~~A~e~gmsl~ef~~~ 52 (179)
T COG1102 29 VSAGTIFREMARERGMSLEEFSRY 52 (179)
T ss_pred eeccHHHHHHHHHcCCCHHHHHHH
Confidence 678999999999999999877654
No 166
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=22.16 E-value=78 Score=17.71 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=17.1
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 040730 113 GESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 113 GdTl~~IA~~~~~s~~~l~~~ 133 (144)
.+....||...|++...+..|
T Consensus 27 ~~~~~~la~~l~l~~~~V~~W 47 (57)
T PF00046_consen 27 KEEREELAKELGLTERQVKNW 47 (57)
T ss_dssp HHHHHHHHHHHTSSHHHHHHH
T ss_pred ccccccccccccccccccccC
Confidence 356678999999999988766
No 167
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=22.05 E-value=1.1e+02 Score=22.28 Aligned_cols=24 Identities=29% Similarity=0.350 Sum_probs=20.7
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHHc
Q 040730 111 QWGESPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~N 134 (144)
..|.|+..||+.+|++...+.++=
T Consensus 170 ~~g~s~~~iak~lgis~~Tv~r~~ 193 (200)
T PRK13413 170 DKGTSKSEIARKLGVSRTTLARFL 193 (200)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Confidence 568999999999999998887654
No 168
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=21.86 E-value=1.4e+02 Score=16.05 Aligned_cols=21 Identities=10% Similarity=0.183 Sum_probs=14.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELV 131 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~ 131 (144)
.++-|...||++.|++...+.
T Consensus 15 ~~~~t~~ela~~~~is~~tv~ 35 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVN 35 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHH
Confidence 356788899999999876653
No 169
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.73 E-value=1e+02 Score=21.80 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=19.2
Q ss_pred eccCCcHHHHHHHhCCCHHHHHH
Q 040730 110 VQWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
.-.|-+...||+.+|+|+..+..
T Consensus 146 ~~~~~s~~eIA~~lgis~~tV~~ 168 (182)
T PRK12537 146 YVDGCSHAEIAQRLGAPLGTVKA 168 (182)
T ss_pred HHcCCCHHHHHHHHCCChhhHHH
Confidence 35799999999999999877653
No 170
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.69 E-value=1e+02 Score=18.77 Aligned_cols=22 Identities=27% Similarity=0.125 Sum_probs=15.9
Q ss_pred cCCcHHHHHHHhCCCHHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
...|+..||++.+++...+.++
T Consensus 33 ~~~si~elA~~~~vS~sti~Rf 54 (77)
T PF01418_consen 33 AFMSISELAEKAGVSPSTIVRF 54 (77)
T ss_dssp CT--HHHHHHHCTS-HHHHHHH
T ss_pred HHccHHHHHHHcCCCHHHHHHH
Confidence 3678899999999999888765
No 171
>PRK11426 hypothetical protein; Provisional
Probab=21.56 E-value=77 Score=22.11 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=17.6
Q ss_pred cCCcHHHHHHHhCCCHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~ 132 (144)
-.|++..+|+++|++.+++..
T Consensus 71 G~d~i~~lA~q~Gl~~~~~~~ 91 (132)
T PRK11426 71 GTNAVSDLGQKLGVDTSTASS 91 (132)
T ss_pred ChHHHHHHHHHHCcCHHHHHH
Confidence 359999999999999887643
No 172
>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=21.54 E-value=1.1e+02 Score=19.40 Aligned_cols=19 Identities=16% Similarity=0.200 Sum_probs=15.4
Q ss_pred CcHHHHHHHhCCCHHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~ 132 (144)
..|+.+|++.|++.++|-.
T Consensus 55 ~kL~~La~~N~v~feeLc~ 73 (82)
T PF11020_consen 55 SKLYKLAKENNVSFEELCV 73 (82)
T ss_pred HHHHHHHHHcCCCHHHHHH
Confidence 4577899999999888854
No 173
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=21.51 E-value=1.2e+02 Score=18.81 Aligned_cols=20 Identities=15% Similarity=0.386 Sum_probs=16.0
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~~ 133 (144)
-++..|...||++..+++++
T Consensus 14 tpFeaI~~~fGL~E~eVi~l 33 (72)
T TIGR03643 14 TPFEAIEQQFGLSEKEVIKL 33 (72)
T ss_pred CCHHHHHHHHCCCHHHHHHH
Confidence 46778999999998777654
No 174
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=21.50 E-value=1.2e+02 Score=19.14 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=16.9
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
+.|-||.+++++-|++.+.|..
T Consensus 19 k~G~Sl~~LS~~agls~~tL~n 40 (82)
T COG3423 19 KKGTSLAALSREAGLSSSTLAN 40 (82)
T ss_pred HccccHHHHHHHcCCCHHHHHH
Confidence 5688888888888888777653
No 175
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=21.06 E-value=1.2e+02 Score=20.53 Aligned_cols=23 Identities=9% Similarity=0.017 Sum_probs=19.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
-.|-|...||+.+|++...+...
T Consensus 120 ~~~~s~~EIA~~l~is~~tV~~~ 142 (154)
T PRK06759 120 FVGKTMGEIALETEMTYYQVRWI 142 (154)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 35899999999999999887654
No 176
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.03 E-value=1.2e+02 Score=21.14 Aligned_cols=23 Identities=13% Similarity=0.042 Sum_probs=20.2
Q ss_pred cC--CcHHHHHHHhCCCHHHHHHHc
Q 040730 112 WG--ESPSSVGSKFGVTMAELVATN 134 (144)
Q Consensus 112 ~G--dTl~~IA~~~~~s~~~l~~~N 134 (144)
++ -|+..||+..||+++.|.+|=
T Consensus 43 p~~~ati~eV~e~tgVs~~~I~~~I 67 (137)
T TIGR03826 43 ENRQATVSEIVEETGVSEKLILKFI 67 (137)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 55 899999999999999998863
No 177
>PHA00542 putative Cro-like protein
Probab=21.00 E-value=1.3e+02 Score=18.66 Aligned_cols=23 Identities=13% Similarity=0.146 Sum_probs=20.6
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
..|=|...+|+..|++...|.+|
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~ 51 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRI 51 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 56889999999999999999887
No 178
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.87 E-value=1.1e+02 Score=20.94 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=18.8
Q ss_pred cCCcHHHHHHHhCCCHHHHHHH
Q 040730 112 WGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 112 ~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
.|-+...||+.+|++...+...
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~ 161 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSR 161 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHH
Confidence 5899999999999998877643
No 179
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=20.79 E-value=1.2e+02 Score=20.35 Aligned_cols=22 Identities=14% Similarity=0.264 Sum_probs=18.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
-.|-+...||+.+|++...+..
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~ 148 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEY 148 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3688999999999999887653
No 180
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=20.77 E-value=93 Score=23.65 Aligned_cols=19 Identities=11% Similarity=0.183 Sum_probs=16.5
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 040730 115 SPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 115 Tl~~IA~~~~~s~~~l~~~ 133 (144)
|+..+|+.|.|+.+.|.+.
T Consensus 31 t~~~Lae~F~vspe~irrI 49 (225)
T PF06413_consen 31 TVERLAESFKVSPEAIRRI 49 (225)
T ss_pred CHHHHHhhCCCCHHHHHHH
Confidence 7788999999999988764
No 181
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=20.56 E-value=1.1e+02 Score=22.57 Aligned_cols=23 Identities=9% Similarity=0.212 Sum_probs=19.5
Q ss_pred ccCCcHHHHHHHhCCCHHHHHHH
Q 040730 111 QWGESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~~l~~~ 133 (144)
-.|-|+..||+++|+|...+..+
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999998877654
No 182
>TIGR02008 fdx_plant ferredoxin [2Fe-2S]. This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins.
Probab=20.52 E-value=1.1e+02 Score=19.52 Aligned_cols=22 Identities=5% Similarity=0.042 Sum_probs=19.2
Q ss_pred EEEEeccCCcHHHHHHHhCCCH
Q 040730 106 KSYVVQWGESPSSVGSKFGVTM 127 (144)
Q Consensus 106 ~~y~V~~GdTl~~IA~~~~~s~ 127 (144)
.++.+.+|+||-..+.+.|+.+
T Consensus 15 ~~~~~~~g~tLLda~~~~Gi~i 36 (97)
T TIGR02008 15 ETIECPDDQYILDAAEEAGIDL 36 (97)
T ss_pred EEEEECCCCcHHHHHHHcCCCC
Confidence 4688899999999999999865
No 183
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=20.43 E-value=86 Score=22.52 Aligned_cols=24 Identities=4% Similarity=-0.013 Sum_probs=20.6
Q ss_pred eEEEEeccCCcHHHHHHHhCCCHH
Q 040730 105 YKSYVVQWGESPSSVGSKFGVTMA 128 (144)
Q Consensus 105 ~~~y~V~~GdTl~~IA~~~~~s~~ 128 (144)
...+.++.|||+-.+|.++|+..+
T Consensus 55 ~~~i~g~vGdtlLd~ah~n~idle 78 (159)
T KOG3309|consen 55 EIKIKGKVGDTLLDAAHENNLDLE 78 (159)
T ss_pred EEEeeeecchHHHHHHHHcCCCcc
Confidence 456888999999999999998764
No 184
>PRK06134 putative FAD-binding dehydrogenase; Reviewed
Probab=20.36 E-value=99 Score=26.58 Aligned_cols=26 Identities=15% Similarity=0.193 Sum_probs=20.5
Q ss_pred ccCCcHHHHHHHhCCCHH----HHHHHcCC
Q 040730 111 QWGESPSSVGSKFGVTMA----ELVATNGL 136 (144)
Q Consensus 111 ~~GdTl~~IA~~~~~s~~----~l~~~N~l 136 (144)
...|||..+|++.|++.+ ++.++|.+
T Consensus 427 ~kadTleELA~~~gid~~~L~~Tv~~yN~~ 456 (581)
T PRK06134 427 KRGASLEELARACGIDPDGLEATVARYNRH 456 (581)
T ss_pred EecCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 367999999999999854 45677753
No 185
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=20.15 E-value=1.3e+02 Score=18.68 Aligned_cols=20 Identities=15% Similarity=0.380 Sum_probs=16.0
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 040730 114 ESPSSVGSKFGVTMAELVAT 133 (144)
Q Consensus 114 dTl~~IA~~~~~s~~~l~~~ 133 (144)
.++..|...||++..+++++
T Consensus 13 tpFeaI~~qfGl~E~eVi~l 32 (73)
T PF10985_consen 13 TPFEAIERQFGLSEKEVIKL 32 (73)
T ss_pred CCHHHHHHHHCCCHHHHHHH
Confidence 46778999999998777654
No 186
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=20.07 E-value=1.2e+02 Score=19.25 Aligned_cols=26 Identities=15% Similarity=0.185 Sum_probs=19.3
Q ss_pred EEEeccCCcHHHHHHHhCCCHHHHHH
Q 040730 107 SYVVQWGESPSSVGSKFGVTMAELVA 132 (144)
Q Consensus 107 ~y~V~~GdTl~~IA~~~~~s~~~l~~ 132 (144)
.|.=++=-|.+.||+-||++...|.+
T Consensus 6 e~rg~rV~t~~~lA~~yg~~~~~i~~ 31 (88)
T PF10543_consen 6 EYRGQRVMTDEDLAELYGVETKTINR 31 (88)
T ss_pred EEcCEEEEEHHHHHHHhCcCHHHHHH
Confidence 34444556899999999999877743
No 187
>PRK10072 putative transcriptional regulator; Provisional
Probab=20.02 E-value=1.4e+02 Score=19.39 Aligned_cols=26 Identities=15% Similarity=0.108 Sum_probs=22.5
Q ss_pred eccCCcHHHHHHHhCCCHHHHHHHcC
Q 040730 110 VQWGESPSSVGSKFGVTMAELVATNG 135 (144)
Q Consensus 110 V~~GdTl~~IA~~~~~s~~~l~~~N~ 135 (144)
-+.|-|-..+|+++|++...+..|=+
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45689999999999999999999844
Done!