Query 040436
Match_columns 91
No_of_seqs 114 out of 1118
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 08:27:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040436.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040436hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01476 LysM: LysM domain; I 99.8 6.5E-19 1.4E-23 93.9 4.0 44 45-88 1-44 (44)
2 PRK14125 cell division suppres 99.6 1.7E-14 3.7E-19 90.3 10.1 48 42-90 36-91 (103)
3 cd00118 LysM Lysin domain, fou 99.5 1.1E-13 2.3E-18 71.7 5.7 45 44-88 2-46 (46)
4 smart00257 LysM Lysin motif. 99.3 4.9E-12 1.1E-16 64.6 5.4 44 44-87 1-44 (44)
5 TIGR02899 spore_safA spore coa 99.3 4.4E-12 9.6E-17 66.5 4.8 43 47-89 1-44 (44)
6 PRK06347 autolysin; Reviewed 99.2 3.4E-11 7.3E-16 93.9 6.3 49 39-88 544-592 (592)
7 PRK10783 mltD membrane-bound l 99.2 5.4E-11 1.2E-15 90.4 6.8 51 38-89 398-448 (456)
8 PRK06347 autolysin; Reviewed 99.1 1.1E-10 2.4E-15 91.1 6.2 51 39-90 476-526 (592)
9 PRK13914 invasion associated s 99.1 1.1E-09 2.4E-14 83.5 9.2 47 43-90 28-74 (481)
10 PRK10871 nlpD lipoprotein NlpD 99.1 1.3E-09 2.8E-14 79.8 9.2 48 42-89 60-107 (319)
11 TIGR02907 spore_VI_D stage VI 98.9 2.9E-09 6.3E-14 78.0 5.7 45 43-88 294-338 (338)
12 PRK10783 mltD membrane-bound l 98.8 9.7E-09 2.1E-13 78.2 6.4 49 41-90 342-390 (456)
13 PRK13914 invasion associated s 98.8 9.4E-09 2E-13 78.6 6.2 47 43-90 200-246 (481)
14 PRK11198 LysM domain/BON super 98.7 3.7E-08 8E-13 64.9 5.9 49 41-89 94-147 (147)
15 COG1388 LytE FOG: LysM repeat 98.7 3.3E-08 7.2E-13 62.6 5.2 46 43-89 67-112 (124)
16 PRK10260 L,D-transpeptidase; P 98.5 1.1E-06 2.4E-11 64.1 8.7 49 42-90 40-90 (306)
17 PRK10190 L,D-transpeptidase; P 98.4 2.5E-06 5.5E-11 62.3 8.3 49 42-90 37-87 (310)
18 TIGR03505 FimV_core FimV N-ter 98.2 1.8E-06 3.8E-11 51.1 3.3 40 51-90 1-52 (74)
19 PF04225 OapA: Opacity-associa 97.5 0.00015 3.3E-09 43.8 3.5 45 43-87 3-51 (85)
20 COG1652 XkdP Uncharacterized p 97.3 8.5E-05 1.9E-09 52.9 0.8 47 44-90 212-264 (269)
21 PF05489 Phage_tail_X: Phage T 97.1 0.00095 2E-08 37.9 3.7 43 47-89 5-53 (60)
22 COG3170 FimV Tfp pilus assembl 97.1 0.00048 1E-08 55.2 3.1 49 41-89 187-247 (755)
23 COG3858 Predicted glycosyl hyd 97.0 0.00079 1.7E-08 51.1 3.9 49 42-90 49-97 (423)
24 PRK11649 putative peptidase; P 96.1 0.011 2.4E-07 45.3 4.8 44 44-87 97-141 (439)
25 COG3858 Predicted glycosyl hyd 94.0 0.031 6.8E-07 42.6 1.6 46 44-90 3-48 (423)
26 COG1388 LytE FOG: LysM repeat 92.9 0.083 1.8E-06 33.1 2.1 33 56-89 1-35 (124)
27 PF13518 HTH_28: Helix-turn-he 90.4 0.31 6.8E-06 25.6 2.4 24 48-71 10-33 (52)
28 COG3061 OapA Cell envelope opa 89.2 0.83 1.8E-05 32.4 4.3 47 41-88 158-209 (242)
29 PF01527 HTH_Tnp_1: Transposas 87.8 0.24 5.3E-06 28.1 0.8 25 47-71 20-44 (76)
30 KOG2850 Predicted peptidoglyca 87.7 0.45 9.7E-06 32.8 2.1 46 44-89 11-56 (186)
31 PF02796 HTH_7: Helix-turn-hel 85.8 1.1 2.3E-05 23.4 2.6 24 47-70 18-41 (45)
32 COG0739 NlpD Membrane proteins 83.6 2.7 6E-05 29.1 4.6 47 43-89 2-48 (277)
33 PRK09413 IS2 repressor TnpA; R 83.0 1.5 3.2E-05 27.6 2.7 27 46-72 25-51 (121)
34 PF13384 HTH_23: Homeodomain-l 82.3 1.6 3.5E-05 22.7 2.4 24 48-71 15-38 (50)
35 PF15145 DUF4577: Domain of un 81.6 4.5 9.8E-05 25.9 4.5 28 45-72 84-114 (128)
36 COG4784 Putative Zn-dependent 80.3 4.2 9.1E-05 31.1 4.7 45 43-88 429-477 (479)
37 cd00569 HTH_Hin_like Helix-tur 80.2 2.8 6E-05 18.9 2.7 23 48-70 19-41 (42)
38 COG5004 P2-like prophage tail 77.7 6.2 0.00013 22.8 3.8 46 44-89 4-55 (70)
39 PF04218 CENP-B_N: CENP-B N-te 77.5 0.99 2.2E-05 24.6 0.5 23 47-69 19-41 (53)
40 COG2963 Transposase and inacti 77.1 2.9 6.4E-05 25.7 2.7 25 47-71 21-46 (116)
41 PF13721 SecD-TM1: SecD export 73.9 2 4.3E-05 26.5 1.2 68 4-71 2-69 (101)
42 PF07172 GRP: Glycine rich pro 72.6 8 0.00017 23.7 3.7 13 9-21 6-18 (95)
43 PF04255 DUF433: Protein of un 72.3 4.8 0.0001 22.0 2.5 22 48-69 29-51 (56)
44 PF05225 HTH_psq: helix-turn-h 71.3 4.1 9E-05 21.4 2.0 24 47-70 12-36 (45)
45 PF04545 Sigma70_r4: Sigma-70, 65.9 9.8 0.00021 19.8 2.8 22 48-69 18-39 (50)
46 PF13936 HTH_38: Helix-turn-he 65.2 9.8 0.00021 19.6 2.6 23 47-69 17-39 (44)
47 PF10668 Phage_terminase: Phag 62.6 10 0.00022 21.4 2.5 24 49-72 20-44 (60)
48 PF13978 DUF4223: Protein of u 61.6 19 0.00042 19.8 3.4 53 6-63 1-53 (56)
49 TIGR00247 conserved hypothetic 61.3 41 0.0009 24.9 6.2 42 42-85 39-88 (342)
50 cd04762 HTH_MerR-trunc Helix-T 58.8 13 0.00029 18.3 2.5 19 52-70 2-20 (49)
51 PF11242 DUF2774: Protein of u 57.9 12 0.00025 21.4 2.2 20 48-67 11-30 (63)
52 smart00351 PAX Paired Box doma 57.5 12 0.00025 23.7 2.5 23 48-70 31-53 (125)
53 COG3415 Transposase and inacti 56.6 11 0.00025 24.6 2.3 26 47-72 18-43 (138)
54 PF06056 Terminase_5: Putative 56.2 17 0.00037 20.1 2.7 23 49-71 12-34 (58)
55 PHA00675 hypothetical protein 56.0 15 0.00032 21.9 2.5 23 48-70 37-59 (78)
56 smart00421 HTH_LUXR helix_turn 55.3 20 0.00043 18.1 2.9 23 48-70 16-38 (58)
57 PF08281 Sigma70_r4_2: Sigma-7 54.6 19 0.0004 18.8 2.7 21 49-69 25-45 (54)
58 cd06171 Sigma70_r4 Sigma70, re 52.7 23 0.0005 17.4 2.8 22 49-70 25-46 (55)
59 PF13551 HTH_29: Winged helix- 52.3 16 0.00035 21.6 2.4 25 47-71 8-33 (112)
60 PRK12845 3-ketosteroid-delta-1 51.5 16 0.00034 28.9 2.8 26 47-72 421-450 (564)
61 PRK12837 3-ketosteroid-delta-1 51.5 16 0.00034 28.3 2.7 26 47-72 372-401 (513)
62 PF08765 Mor: Mor transcriptio 51.4 16 0.00035 22.4 2.3 20 50-69 72-91 (108)
63 PF01710 HTH_Tnp_IS630: Transp 51.3 12 0.00026 23.3 1.8 24 47-70 15-38 (119)
64 TIGR02531 yecD_yerC TrpR-relat 51.1 18 0.00038 21.8 2.4 28 46-73 46-73 (88)
65 cd01104 HTH_MlrA-CarA Helix-Tu 50.7 19 0.00042 19.6 2.4 20 52-71 2-21 (68)
66 PF13542 HTH_Tnp_ISL3: Helix-t 50.6 22 0.00048 18.4 2.5 19 51-69 28-46 (52)
67 COG1559 Aminodeoxychorismate l 49.4 65 0.0014 24.2 5.6 41 43-85 46-94 (342)
68 TIGR01764 excise DNA binding d 48.9 25 0.00054 17.4 2.5 20 52-71 3-22 (49)
69 PF06627 DUF1153: Protein of u 48.8 19 0.0004 22.0 2.2 30 47-76 45-75 (90)
70 PF08984 DUF1858: Domain of un 47.7 20 0.00043 19.6 2.1 29 40-68 30-59 (59)
71 cd04761 HTH_MerR-SF Helix-Turn 47.7 25 0.00054 17.7 2.4 19 52-70 2-20 (49)
72 PRK12839 hypothetical protein; 47.3 20 0.00044 28.3 2.8 28 47-74 424-455 (572)
73 KOG3446 NADH:ubiquinone oxidor 46.5 29 0.00063 21.2 2.8 39 43-81 19-62 (97)
74 cd00131 PAX Paired Box domain 46.3 22 0.00048 22.6 2.4 23 48-70 31-53 (128)
75 PF13022 HTH_Tnp_1_2: Helix-tu 46.2 20 0.00044 23.7 2.2 22 50-71 34-55 (142)
76 COG1102 Cmk Cytidylate kinase 45.5 21 0.00046 24.4 2.3 31 44-74 26-59 (179)
77 COG2442 Uncharacterized conser 45.3 31 0.00067 20.4 2.8 23 47-69 40-63 (79)
78 PRK10270 putative aminodeoxych 44.3 88 0.0019 23.3 5.6 43 42-86 39-89 (340)
79 PF04967 HTH_10: HTH DNA bindi 43.6 32 0.0007 18.7 2.5 25 44-68 17-41 (53)
80 PF13510 Fer2_4: 2Fe-2S iron-s 43.5 24 0.00053 20.6 2.2 26 43-68 11-36 (82)
81 PF00356 LacI: Bacterial regul 42.9 34 0.00073 18.0 2.5 18 52-69 1-18 (46)
82 PF10654 DUF2481: Protein of u 42.3 22 0.00047 22.9 1.9 20 48-67 78-97 (126)
83 PF00165 HTH_AraC: Bacterial r 41.6 38 0.00082 16.8 2.5 21 49-69 7-27 (42)
84 PF07027 DUF1318: Protein of u 41.5 14 0.0003 22.7 0.9 36 53-88 53-88 (95)
85 PF13411 MerR_1: MerR HTH fami 41.5 34 0.00074 18.6 2.5 20 52-71 2-21 (69)
86 PRK07843 3-ketosteroid-delta-1 41.1 30 0.00064 27.2 2.9 26 47-72 413-442 (557)
87 PRK06134 putative FAD-binding 40.6 30 0.00064 27.3 2.8 26 47-72 426-455 (581)
88 PF11020 DUF2610: Domain of un 40.4 30 0.00065 20.7 2.2 19 51-69 55-73 (82)
89 smart00422 HTH_MERR helix_turn 40.1 36 0.00077 18.5 2.4 19 52-70 2-20 (70)
90 PF00376 MerR: MerR family reg 39.6 34 0.00074 17.1 2.1 20 52-71 1-20 (38)
91 PF09012 FeoC: FeoC like trans 39.5 33 0.00072 19.1 2.2 18 52-69 16-33 (69)
92 PF14451 Ub-Mut7C: Mut7-C ubiq 39.3 43 0.00093 19.8 2.8 47 41-87 23-73 (81)
93 TIGR00370 conserved hypothetic 39.3 42 0.0009 23.2 3.1 29 45-73 85-113 (202)
94 TIGR02937 sigma70-ECF RNA poly 39.2 39 0.00085 20.3 2.8 23 48-70 124-146 (158)
95 cd06170 LuxR_C_like C-terminal 38.8 52 0.0011 16.6 2.9 22 49-70 14-35 (57)
96 PRK12843 putative FAD-binding 38.7 33 0.00073 27.0 2.8 26 47-72 428-457 (578)
97 PRK13413 mpi multiple promoter 38.7 37 0.00081 22.8 2.8 24 48-71 170-193 (200)
98 cd07446 CRD_SFRP2 Cysteine-ric 38.6 11 0.00024 24.3 0.2 46 37-90 75-121 (128)
99 PF13011 LZ_Tnp_IS481: leucine 38.5 39 0.00085 20.3 2.5 25 46-70 21-45 (85)
100 PF12116 SpoIIID: Stage III sp 38.5 4.5 9.9E-05 24.3 -1.5 30 45-74 14-51 (82)
101 PRK06481 fumarate reductase fl 38.2 34 0.00073 26.5 2.7 26 47-72 375-404 (506)
102 PRK12842 putative succinate de 38.2 32 0.0007 27.0 2.7 26 47-72 423-452 (574)
103 PF02515 CoA_transf_3: CoA-tra 37.6 31 0.00068 23.1 2.3 19 56-74 32-50 (191)
104 PF04760 IF2_N: Translation in 37.4 22 0.00048 18.9 1.2 18 52-69 5-22 (54)
105 PRK07121 hypothetical protein; 37.0 38 0.00082 25.9 2.8 26 47-72 358-387 (492)
106 COG3784 Uncharacterized protei 36.9 20 0.00042 22.5 1.0 35 52-86 66-100 (109)
107 smart00530 HTH_XRE Helix-turn- 36.6 53 0.0012 15.6 2.7 25 48-72 8-32 (56)
108 PF13443 HTH_26: Cro/C1-type H 36.4 40 0.00086 18.0 2.2 22 49-70 9-30 (63)
109 PF11268 DUF3071: Protein of u 36.4 35 0.00077 23.1 2.3 28 44-71 63-90 (170)
110 PRK12844 3-ketosteroid-delta-1 36.3 39 0.00084 26.5 2.9 26 47-72 406-435 (557)
111 PF14493 HTH_40: Helix-turn-he 36.3 48 0.001 19.5 2.7 22 47-68 10-31 (91)
112 TIGR02485 CobZ_N-term precorri 36.3 37 0.00081 25.4 2.7 25 48-72 313-341 (432)
113 cd04764 HTH_MlrA-like_sg1 Heli 36.3 45 0.00098 18.2 2.5 19 52-70 2-20 (67)
114 PF00196 GerE: Bacterial regul 36.2 35 0.00076 18.1 1.9 22 47-68 15-36 (58)
115 PF00046 Homeobox: Homeobox do 36.1 45 0.00097 17.4 2.3 21 50-70 27-47 (57)
116 PRK12835 3-ketosteroid-delta-1 36.1 37 0.0008 26.9 2.7 28 47-74 427-458 (584)
117 TIGR03826 YvyF flagellar opero 35.7 51 0.0011 21.5 2.9 24 47-70 41-66 (137)
118 COG2739 Uncharacterized protei 35.2 42 0.00092 21.0 2.3 19 51-69 34-52 (105)
119 PF10975 DUF2802: Protein of u 35.1 38 0.00083 19.4 2.0 22 45-66 39-60 (70)
120 PF12728 HTH_17: Helix-turn-he 35.1 53 0.0011 16.8 2.5 19 52-70 3-21 (51)
121 PHA01976 helix-turn-helix prot 34.9 59 0.0013 17.5 2.8 22 49-70 14-35 (67)
122 PF01402 RHH_1: Ribbon-helix-h 34.9 50 0.0011 16.0 2.3 18 52-69 13-30 (39)
123 cd00093 HTH_XRE Helix-turn-hel 34.5 59 0.0013 15.5 2.7 25 48-72 10-34 (58)
124 smart00342 HTH_ARAC helix_turn 34.1 54 0.0012 17.7 2.6 18 52-69 3-20 (84)
125 TIGR01813 flavo_cyto_c flavocy 34.0 40 0.00087 25.1 2.5 26 47-72 317-346 (439)
126 PF01381 HTH_3: Helix-turn-hel 34.0 53 0.0011 16.9 2.4 23 48-70 7-29 (55)
127 smart00760 Bac_DnaA_C Bacteria 33.6 33 0.00072 18.6 1.6 21 52-72 5-25 (60)
128 PRK08274 tricarballylate dehyd 33.6 46 0.00099 25.1 2.8 26 47-72 321-350 (466)
129 PF12844 HTH_19: Helix-turn-he 33.0 51 0.0011 17.6 2.3 20 50-69 12-31 (64)
130 COG2771 CsgD DNA-binding HTH d 32.5 54 0.0012 17.2 2.3 23 46-68 15-37 (65)
131 COG3721 HugX Putative heme iro 31.7 72 0.0016 21.6 3.1 28 46-73 23-50 (176)
132 PRK00118 putative DNA-binding 31.6 65 0.0014 20.0 2.8 23 47-69 30-52 (104)
133 PF08299 Bac_DnaA_C: Bacterial 31.5 52 0.0011 18.6 2.2 18 52-69 5-22 (70)
134 PF13693 HTH_35: Winged helix- 31.1 55 0.0012 19.3 2.3 21 48-68 13-33 (78)
135 PF13613 HTH_Tnp_4: Helix-turn 31.0 52 0.0011 17.4 2.0 21 48-68 17-37 (53)
136 PF08356 EF_assoc_2: EF hand a 30.6 25 0.00053 21.4 0.7 18 46-63 41-60 (89)
137 TIGR03070 couple_hipB transcri 30.4 82 0.0018 15.9 2.8 24 48-71 13-36 (58)
138 PRK09570 rpoH DNA-directed RNA 30.4 63 0.0014 19.2 2.5 43 45-87 15-60 (79)
139 PF04539 Sigma70_r3: Sigma-70 30.2 59 0.0013 18.2 2.3 19 52-70 22-40 (78)
140 cd04763 HTH_MlrA-like Helix-Tu 29.8 66 0.0014 17.6 2.4 20 52-71 2-21 (68)
141 cd00086 homeodomain Homeodomai 29.7 45 0.00097 17.3 1.7 21 50-70 27-47 (59)
142 PF14502 HTH_41: Helix-turn-he 29.4 83 0.0018 16.9 2.6 17 52-68 8-24 (48)
143 KOG1618 Predicted phosphatase 29.4 70 0.0015 24.3 3.1 35 45-79 122-162 (389)
144 PF15508 NAAA-beta: beta subun 29.2 54 0.0012 19.6 2.1 22 50-71 69-90 (95)
145 PF13413 HTH_25: Helix-turn-he 29.2 82 0.0018 17.4 2.7 25 47-71 7-31 (62)
146 PF04921 XAP5: XAP5, circadian 29.1 63 0.0014 23.2 2.7 24 38-61 108-131 (239)
147 PTZ00305 NADH:ubiquinone oxido 29.1 43 0.00092 24.8 1.9 29 43-71 76-105 (297)
148 TIGR02008 fdx_plant ferredoxin 28.9 67 0.0014 19.2 2.5 25 42-66 14-38 (97)
149 PF00440 TetR_N: Bacterial reg 28.6 79 0.0017 16.0 2.5 21 50-70 16-36 (47)
150 PF05484 LRV_FeS: LRV protein 28.6 25 0.00055 19.7 0.5 26 47-74 28-53 (57)
151 PF01371 Trp_repressor: Trp re 28.3 57 0.0012 19.6 2.1 26 49-74 48-73 (87)
152 COG3753 Uncharacterized protei 28.2 58 0.0013 21.5 2.2 19 50-68 90-108 (143)
153 PF09035 Tn916-Xis: Excisionas 27.8 43 0.00094 19.2 1.4 37 52-88 15-53 (67)
154 COG4254 Uncharacterized protei 27.5 61 0.0013 24.2 2.5 47 43-89 6-55 (339)
155 PRK07569 bidirectional hydroge 27.5 41 0.00089 23.4 1.5 25 44-68 12-36 (234)
156 cd07453 CRD_crescent Cysteine- 27.2 19 0.00041 23.5 -0.2 45 37-89 70-115 (135)
157 PF12298 Bot1p: Eukaryotic mit 27.2 81 0.0018 21.3 2.9 20 47-66 30-49 (172)
158 PRK14785 lipoprotein signal pe 26.8 55 0.0012 21.9 2.0 13 1-13 7-19 (171)
159 smart00389 HOX Homeodomain. DN 26.8 53 0.0012 16.9 1.6 21 50-70 27-47 (56)
160 PRK00753 psbL photosystem II r 26.5 1E+02 0.0022 15.8 2.7 19 4-22 15-33 (39)
161 TIGR02985 Sig70_bacteroi1 RNA 26.4 88 0.0019 19.3 2.9 22 48-69 127-148 (161)
162 PF08279 HTH_11: HTH domain; 26.3 80 0.0017 16.3 2.3 16 52-67 17-32 (55)
163 PRK12834 putative FAD-binding 26.2 53 0.0012 25.6 2.1 24 47-70 393-423 (549)
164 PF08671 SinI: Anti-repressor 26.0 68 0.0015 15.5 1.7 14 56-69 11-24 (30)
165 COG1476 Predicted transcriptio 25.5 88 0.0019 18.0 2.4 20 52-71 45-64 (68)
166 PF07638 Sigma70_ECF: ECF sigm 25.3 88 0.0019 20.7 2.8 22 48-69 149-170 (185)
167 COG3019 Predicted metal-bindin 25.3 1.6E+02 0.0034 19.7 3.8 22 44-65 52-73 (149)
168 cd00207 fer2 2Fe-2S iron-sulfu 25.1 87 0.0019 17.4 2.4 24 42-65 9-32 (84)
169 PRK06437 hypothetical protein; 25.0 58 0.0012 18.3 1.6 45 43-87 13-60 (67)
170 PF12840 HTH_20: Helix-turn-he 24.9 84 0.0018 16.8 2.2 21 48-68 22-42 (61)
171 COG1804 CaiB Predicted acyl-Co 24.5 44 0.00095 25.6 1.3 22 56-77 102-124 (396)
172 PHA00542 putative Cro-like pro 24.1 1E+02 0.0022 17.9 2.6 24 47-70 28-51 (82)
173 PF13404 HTH_AsnC-type: AsnC-t 24.1 93 0.002 15.8 2.2 19 50-68 17-35 (42)
174 PRK09652 RNA polymerase sigma 24.0 99 0.0022 19.5 2.8 21 48-68 142-162 (182)
175 PF07423 DUF1510: Protein of u 23.7 1.1E+02 0.0024 21.5 3.1 16 7-22 13-28 (217)
176 TIGR02007 fdx_isc ferredoxin, 23.6 89 0.0019 19.1 2.4 24 42-65 15-38 (110)
177 cd07443 CRD_SFRP1 Cysteine-ric 23.6 30 0.00065 22.2 0.2 44 37-89 74-118 (124)
178 PF02419 PsbL: PsbL protein; 23.6 1.2E+02 0.0025 15.4 2.9 20 3-22 12-31 (37)
179 PTZ00306 NADH-dependent fumara 23.4 74 0.0016 27.5 2.6 26 47-72 765-794 (1167)
180 PF07789 DUF1627: Protein of u 23.4 61 0.0013 21.7 1.7 19 48-66 3-22 (155)
181 TIGR02885 spore_sigF RNA polym 23.2 98 0.0021 21.0 2.8 23 48-70 197-219 (231)
182 KOG3309 Ferredoxin [Energy pro 23.1 57 0.0012 22.0 1.5 23 44-66 57-79 (159)
183 COG4823 AbiF Abortive infectio 23.1 72 0.0016 23.5 2.1 21 52-72 181-201 (299)
184 cd07454 CRD_LIN_17 Cysteine-ri 23.0 27 0.00058 22.4 -0.1 46 37-90 73-119 (124)
185 PHA02591 hypothetical protein; 22.9 1.1E+02 0.0024 18.4 2.5 25 44-68 39-66 (83)
186 PF01969 DUF111: Protein of un 22.9 43 0.00093 25.5 1.0 19 51-69 364-382 (382)
187 cd00592 HTH_MerR-like Helix-Tu 22.8 1E+02 0.0022 18.1 2.5 20 52-71 2-21 (100)
188 PF00879 Defensin_propep: Defe 22.8 1.3E+02 0.0029 16.4 2.7 21 11-31 3-23 (52)
189 smart00063 FRI Frizzled. Droso 22.7 28 0.00061 21.7 -0.0 43 38-88 69-112 (113)
190 cd07442 CRD_SFRP4 Cysteine-ric 22.7 27 0.00058 22.5 -0.1 46 36-89 73-120 (127)
191 cd04766 HTH_HspR Helix-Turn-He 22.6 1E+02 0.0022 18.0 2.4 20 52-71 3-22 (91)
192 PF04405 ScdA_N: Domain of Unk 22.5 1.3E+02 0.0027 16.5 2.6 20 50-69 31-50 (56)
193 cd07452 CRD_sizzled Cysteine-r 22.4 35 0.00076 22.4 0.4 44 38-89 77-121 (141)
194 PF02682 AHS1: Allophanate hyd 22.4 72 0.0016 21.9 2.0 28 45-72 94-121 (202)
195 cd07444 CRD_SFRP5 Cysteine-ric 22.4 28 0.00061 22.4 -0.1 45 37-89 74-119 (127)
196 COG3822 ABC-type sugar transpo 22.4 46 0.001 23.4 1.0 12 79-90 157-168 (225)
197 PRK04217 hypothetical protein; 22.1 1.2E+02 0.0026 19.0 2.8 22 48-69 56-77 (110)
198 smart00345 HTH_GNTR helix_turn 22.0 1.3E+02 0.0028 15.2 2.9 17 52-68 22-38 (60)
199 COG5484 Uncharacterized conser 21.9 87 0.0019 22.9 2.3 23 50-72 19-41 (279)
200 TIGR03643 conserved hypothetic 21.9 1.2E+02 0.0025 17.8 2.5 18 51-68 14-31 (72)
201 PF08220 HTH_DeoR: DeoR-like h 21.9 1E+02 0.0022 16.5 2.2 17 52-68 16-32 (57)
202 PF05263 DUF722: Protein of un 21.8 86 0.0019 20.3 2.1 28 45-72 94-121 (130)
203 PF09607 BrkDBD: Brinker DNA-b 21.8 1E+02 0.0023 17.2 2.2 19 53-71 28-46 (58)
204 cd01279 HTH_HspR-like Helix-Tu 21.7 1.1E+02 0.0023 18.3 2.4 19 52-70 3-21 (98)
205 PF07374 DUF1492: Protein of u 21.4 1.3E+02 0.0028 18.1 2.8 22 49-70 70-91 (100)
206 CHL00038 psbL photosystem II p 21.4 1.3E+02 0.0029 15.3 3.0 19 4-22 14-32 (38)
207 PRK10629 EnvZ/OmpR regulon mod 21.4 47 0.001 21.3 0.8 24 48-71 50-73 (127)
208 PRK06759 RNA polymerase factor 21.4 1.3E+02 0.0028 18.7 2.9 23 47-69 119-141 (154)
209 PF13743 Thioredoxin_5: Thiore 21.3 62 0.0013 21.5 1.4 19 51-69 104-122 (176)
210 TIGR02950 SigM_subfam RNA poly 21.3 1.2E+02 0.0027 18.7 2.8 21 48-68 119-139 (154)
211 PF11076 YbhQ: Putative inner 21.1 43 0.00094 21.6 0.6 17 44-60 6-22 (135)
212 cd01109 HTH_YyaN Helix-Turn-He 21.0 1.1E+02 0.0024 18.6 2.4 19 52-70 2-20 (113)
213 PF08822 DUF1804: Protein of u 21.0 1.2E+02 0.0026 20.6 2.7 28 45-72 14-41 (165)
214 cd01105 HTH_GlnR-like Helix-Tu 21.0 1.1E+02 0.0025 17.8 2.4 20 52-71 3-22 (88)
215 COG1641 Uncharacterized conser 20.8 72 0.0016 24.5 1.8 21 51-71 356-376 (387)
216 PF09312 SurA_N: SurA N-termin 20.8 1.1E+02 0.0024 18.8 2.4 19 52-70 75-93 (118)
217 COG0656 ARA1 Aldo/keto reducta 20.7 1.1E+02 0.0024 22.3 2.7 25 47-71 198-223 (280)
218 PF05920 Homeobox_KN: Homeobox 20.6 1.1E+02 0.0025 15.4 2.1 19 52-70 15-33 (40)
219 PRK11924 RNA polymerase sigma 20.6 1.3E+02 0.0028 18.9 2.8 22 48-69 139-160 (179)
220 PRK05803 sporulation sigma fac 20.4 1.2E+02 0.0027 20.7 2.8 23 48-70 193-215 (233)
221 PF04297 UPF0122: Putative hel 20.3 1.2E+02 0.0027 18.7 2.5 24 45-68 28-51 (101)
222 PF13467 RHH_4: Ribbon-helix-h 20.2 75 0.0016 18.2 1.4 18 52-69 25-42 (67)
No 1
>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=99.76 E-value=6.5e-19 Score=93.94 Aligned_cols=44 Identities=36% Similarity=0.713 Sum_probs=38.7
Q ss_pred EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA 88 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp 88 (91)
|+|++|||||+||++|+++.++|+++||+++|+.|++||.||||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 89999999999999999999999999999988889999999998
No 2
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.60 E-value=1.7e-14 Score=90.30 Aligned_cols=48 Identities=21% Similarity=0.212 Sum_probs=40.7
Q ss_pred CceEEecCCCCHHHHHHHcCCC--------HHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 42 DSVYGAQEGDTCSNVTEEFNLS--------TDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~~i~--------~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
...|+|++|||||+||++|+.+ ++++.+.| +++++.|++||+|+||..
T Consensus 36 ~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N-~l~~~~I~~Gq~L~IP~~ 91 (103)
T PRK14125 36 YVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVN-NLPSGHIKAGDKLVIPVL 91 (103)
T ss_pred cEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhc-CCCCCcCCCCCEEEEecC
Confidence 3469999999999999999765 45677778 688889999999999964
No 3
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=99.49 E-value=1.1e-13 Score=71.65 Aligned_cols=45 Identities=29% Similarity=0.485 Sum_probs=42.9
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA 88 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp 88 (91)
+|+|++|||||+|+++|+++.+++.++|+..+|..+.+|+.||+|
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 699999999999999999999999999987689999999999997
No 4
>smart00257 LysM Lysin motif.
Probab=99.33 E-value=4.9e-12 Score=64.58 Aligned_cols=44 Identities=30% Similarity=0.504 Sum_probs=41.2
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEE
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCV 87 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcv 87 (91)
+|+|++|||||+|+++|+++.+++.++|+..+|..+.+|+.+++
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 48999999999999999999999999999778999999999985
No 5
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=99.31 E-value=4.4e-12 Score=66.50 Aligned_cols=43 Identities=23% Similarity=0.481 Sum_probs=39.3
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHhCCCC-CCCCCCCCCEEEEcC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAINPNI-NCDAIFVGQWLCVAG 89 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~Np~v-~c~~l~~G~~lcvp~ 89 (91)
|++|||+|+||++|+++.+++.++|+.+ +...+.+|+.+.+|.
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 6899999999999999999999999876 567899999999984
No 6
>PRK06347 autolysin; Reviewed
Probab=99.20 E-value=3.4e-11 Score=93.94 Aligned_cols=49 Identities=22% Similarity=0.387 Sum_probs=44.1
Q ss_pred CCCCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436 39 PTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA 88 (91)
Q Consensus 39 ~~c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp 88 (91)
..|..+|+|++|||||+||++||+++++|++||+ +..+.|++||.|+|+
T Consensus 544 ~~~~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~-L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 544 NSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNK-LTSNMIHVGQKLTIK 592 (592)
T ss_pred CccceeeecCCCCcHHHHHHHhCCCHHHHHHhcC-CCcccCCCCCEEecC
Confidence 4567789999999999999999999999999996 555789999999985
No 7
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.19 E-value=5.4e-11 Score=90.43 Aligned_cols=51 Identities=14% Similarity=0.195 Sum_probs=45.2
Q ss_pred CCCCCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 38 PPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 38 ~~~c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
...+...|+|++|||||+||++||+++++|++||+.... .|++||.|+|..
T Consensus 398 ~~~~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~-~L~pGq~L~l~v 448 (456)
T PRK10783 398 NNSDSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAK-NLQPGDKLTLFV 448 (456)
T ss_pred ccccceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCC-cCCCCCEEEEec
Confidence 345677899999999999999999999999999986544 899999999965
No 8
>PRK06347 autolysin; Reviewed
Probab=99.13 E-value=1.1e-10 Score=91.06 Aligned_cols=51 Identities=24% Similarity=0.331 Sum_probs=45.9
Q ss_pred CCCCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 39 PTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 39 ~~c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
..|..+|+|++|||||+||++||+++++|++||+ +..+.|++||.|+||..
T Consensus 476 ~~~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~-l~s~~L~~GQ~L~Ip~~ 526 (592)
T PRK06347 476 NTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNN-LKSDFIYPGQKLKVSAG 526 (592)
T ss_pred cccceeeeecCCCCHHHHHHHHCCCHHHHHHhcC-CCcccccCCcEEEEecC
Confidence 4567789999999999999999999999999997 65568999999999863
No 9
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.07 E-value=1.1e-09 Score=83.54 Aligned_cols=47 Identities=28% Similarity=0.286 Sum_probs=43.5
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
..|+|++|||+|+||++||+++++|+++| +++.+.|++||.|.||..
T Consensus 28 ~tytVq~GDTLw~IA~~ygvtv~~I~~~N-~l~~~~I~~Gq~L~Ip~~ 74 (481)
T PRK13914 28 STVVVEAGDTLWGIAQSKGTTVDAIKKAN-NLTTDKIVPGQKLQVNEV 74 (481)
T ss_pred ceEEECCCCCHHHHHHHHCCCHHHHHHHh-CCCcccccCCCEEEeCCC
Confidence 46999999999999999999999999999 587788999999999864
No 10
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=99.06 E-value=1.3e-09 Score=79.78 Aligned_cols=48 Identities=23% Similarity=0.093 Sum_probs=43.1
Q ss_pred CceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 42 DSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
...|+|++|||+|.||.+||+++.+|.+||..-+...|++||.|.||.
T Consensus 60 ~~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~ 107 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGN 107 (319)
T ss_pred CCceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCC
Confidence 357999999999999999999999999999433788999999999964
No 11
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=98.90 E-value=2.9e-09 Score=78.01 Aligned_cols=45 Identities=24% Similarity=0.357 Sum_probs=41.5
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA 88 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp 88 (91)
..|+|++|||+|+||++||+++++|.++|+ +..+.|.+|+.|.||
T Consensus 294 ~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~-L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 294 RMCIVQEGDTIETIAERYEISVSQLIRHNQ-LEDFEVNEGQILYIP 338 (338)
T ss_pred EEEEECCCCCHHHHHHHHCcCHHHHHHHhC-CCccccCCCCEEEeC
Confidence 469999999999999999999999999995 656789999999997
No 12
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=98.82 E-value=9.7e-09 Score=78.24 Aligned_cols=49 Identities=27% Similarity=0.329 Sum_probs=44.1
Q ss_pred CCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 41 CDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 41 c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
....|+|++|||||+||++||++.++|.+||+..+ +.|.+||.|+||..
T Consensus 342 ~~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~-~~L~~Gq~L~Ip~~ 390 (456)
T PRK10783 342 NSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRG-SKLKVGQTLTIGAG 390 (456)
T ss_pred CceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCc-ccCCCCCEEEecCC
Confidence 45679999999999999999999999999997545 78999999999863
No 13
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.82 E-value=9.4e-09 Score=78.57 Aligned_cols=47 Identities=21% Similarity=0.414 Sum_probs=43.3
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
..|+|++|||+|.||++|++++++|.+||+ +....|++||.|.||.+
T Consensus 200 ~tytVq~GDTL~sIAkrYgVtv~eI~~~N~-l~s~~L~pGQ~L~Ip~s 246 (481)
T PRK13914 200 TTHAVKSGDTIWALSVKYGVSVQDIMSWNN-LSSSSIYVGQKLAIKQT 246 (481)
T ss_pred eEEEECCCCCHHHHHHHHCCCHHHHHHhcC-CCccccCCCCEEEecCC
Confidence 579999999999999999999999999995 65568999999999986
No 14
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.72 E-value=3.7e-08 Score=64.92 Aligned_cols=49 Identities=22% Similarity=0.333 Sum_probs=41.3
Q ss_pred CCceEEecCCCCHHHHHHHcC---CCHHHHHHhCCC-C-CCCCCCCCCEEEEcC
Q 040436 41 CDSVYGAQEGDTCSNVTEEFN---LSTDVFLAINPN-I-NCDAIFVGQWLCVAG 89 (91)
Q Consensus 41 c~~~y~v~~GdTc~~Ia~~~~---i~~~~l~~~Np~-v-~c~~l~~G~~lcvp~ 89 (91)
-...|+|++|||+|+||++|. ...++|.++|+. + +.+.|++||.|.+|+
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP~ 147 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIPE 147 (147)
T ss_pred CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecCC
Confidence 345799999999999999984 457799999973 4 667899999999985
No 15
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.71 E-value=3.3e-08 Score=62.64 Aligned_cols=46 Identities=26% Similarity=0.429 Sum_probs=41.7
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
..|+|+.|||++.||++|++++.+++++|. +..+.+++||.+.++.
T Consensus 67 ~~~~V~~gdtL~~Ia~~~~~tv~~l~~~n~-l~~~~i~~gq~l~~~~ 112 (124)
T COG1388 67 VTYTVKKGDTLSKIARKYGVTVAELKQLNN-LSSDKIKVGQKLKLPV 112 (124)
T ss_pred ceEEEecCCCHHHHHHHhCCCHHHHHHHhc-cCCCceecCcEEEEec
Confidence 469999999999999999999999999996 5445999999999975
No 16
>PRK10260 L,D-transpeptidase; Provisional
Probab=98.49 E-value=1.1e-06 Score=64.07 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=43.8
Q ss_pred CceEEecCCC--CHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 42 DSVYGAQEGD--TCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 42 ~~~y~v~~Gd--Tc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
..+|+|+.|+ ++.+||++|++..++|.+.||++|.-...+|+.+.||..
T Consensus 40 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 40 NQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQ 90 (306)
T ss_pred cEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCCc
Confidence 4689999966 599999999999999999999999777789999999863
No 17
>PRK10190 L,D-transpeptidase; Provisional
Probab=98.38 E-value=2.5e-06 Score=62.34 Aligned_cols=49 Identities=10% Similarity=0.126 Sum_probs=43.9
Q ss_pred CceEEecCCC--CHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 42 DSVYGAQEGD--TCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 42 ~~~y~v~~Gd--Tc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
..+|+|+.+| ++.+||++|++..++|.+.||++|.-...+|+.+.||..
T Consensus 37 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 37 SLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQ 87 (310)
T ss_pred eEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence 4679999966 599999999999999999999999877789999999863
No 18
>TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Probab=98.20 E-value=1.8e-06 Score=51.11 Aligned_cols=40 Identities=28% Similarity=0.388 Sum_probs=34.2
Q ss_pred CCHHHHHHHc---C-CCHH----HHHHhCCCC----CCCCCCCCCEEEEcCC
Q 040436 51 DTCSNVTEEF---N-LSTD----VFLAINPNI----NCDAIFVGQWLCVAGS 90 (91)
Q Consensus 51 dTc~~Ia~~~---~-i~~~----~l~~~Np~v----~c~~l~~G~~lcvp~~ 90 (91)
||+|+||+++ + ++++ .|++.||.. |-+.|++|++|+||..
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 8999999999 3 7776 588999977 4568999999999974
No 19
>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=97.48 E-value=0.00015 Score=43.76 Aligned_cols=45 Identities=24% Similarity=0.267 Sum_probs=25.9
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHHHh---CCCC-CCCCCCCCCEEEE
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFLAI---NPNI-NCDAIFVGQWLCV 87 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~---Np~v-~c~~l~~G~~lcv 87 (91)
..|+|++|||+..|-+++|++..+++++ +..- .-..|.|||.+-+
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f 51 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEF 51 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEE
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEE
Confidence 4599999999999999999999886654 3211 3457999999865
No 20
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.28 E-value=8.5e-05 Score=52.88 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=40.6
Q ss_pred eEEecCCCCHHHHHHHc-C--CCHHHHHHhCCC--C-CCCCCCCCCEEEEcCC
Q 040436 44 VYGAQEGDTCSNVTEEF-N--LSTDVFLAINPN--I-NCDAIFVGQWLCVAGS 90 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~-~--i~~~~l~~~Np~--v-~c~~l~~G~~lcvp~~ 90 (91)
+|+|+.|||+|.|+.++ | .....|+..|.. + +.+.|++||++-||..
T Consensus 212 ~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~ 264 (269)
T COG1652 212 TNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ 264 (269)
T ss_pred EEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence 79999999999999985 3 556679999984 5 7889999999999864
No 21
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=97.10 E-value=0.00095 Score=37.88 Aligned_cols=43 Identities=16% Similarity=0.331 Sum_probs=35.3
Q ss_pred ecCCCCHHHHHHHc-CCC---HHHHHHhCCCC-CC-CCCCCCCEEEEcC
Q 040436 47 AQEGDTCSNVTEEF-NLS---TDVFLAINPNI-NC-DAIFVGQWLCVAG 89 (91)
Q Consensus 47 v~~GdTc~~Ia~~~-~i~---~~~l~~~Np~v-~c-~~l~~G~~lcvp~ 89 (91)
.+.|||+..|+-++ |-. .+.+++.||++ +. .-+..|..+.+|.
T Consensus 5 t~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~ 53 (60)
T PF05489_consen 5 TTQGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPD 53 (60)
T ss_pred EeCcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCC
Confidence 34999999999885 543 37899999999 55 6788999999985
No 22
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=97.08 E-value=0.00048 Score=55.18 Aligned_cols=49 Identities=18% Similarity=0.402 Sum_probs=40.5
Q ss_pred CCceEEecCCCCHHHHHHHc----CCCHHH----HHHhCCCC----CCCCCCCCCEEEEcC
Q 040436 41 CDSVYGAQEGDTCSNVTEEF----NLSTDV----FLAINPNI----NCDAIFVGQWLCVAG 89 (91)
Q Consensus 41 c~~~y~v~~GdTc~~Ia~~~----~i~~~~----l~~~Np~v----~c~~l~~G~~lcvp~ 89 (91)
-...|++++|||+|+||... ++|+++ |++.||+. |-+.|..|.+|-||.
T Consensus 187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~ 247 (755)
T COG3170 187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPS 247 (755)
T ss_pred CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccc
Confidence 34689999999999999987 456554 99999987 445799999999985
No 23
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=97.04 E-value=0.00079 Score=51.07 Aligned_cols=49 Identities=18% Similarity=0.237 Sum_probs=43.2
Q ss_pred CceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 42 DSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
...|.|++|||+++||.+++++.+++..+|..+....+.+|-.+.+|..
T Consensus 49 ~~~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~ 97 (423)
T COG3858 49 GHFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSA 97 (423)
T ss_pred ceEEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEeccCC
Confidence 3679999999999999999999999999997655567889998888864
No 24
>PRK11649 putative peptidase; Provisional
Probab=96.13 E-value=0.011 Score=45.28 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=36.7
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHHHhCCCC-CCCCCCCCCEEEE
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNI-NCDAIFVGQWLCV 87 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v-~c~~l~~G~~lcv 87 (91)
.|+|++|||+.+|-+++|++..++.++-... +-.+|.+||.|-+
T Consensus 97 ~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~ 141 (439)
T PRK11649 97 EYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSW 141 (439)
T ss_pred EEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEE
Confidence 6999999999999999999999887763222 4458999999876
No 25
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=93.96 E-value=0.031 Score=42.62 Aligned_cols=46 Identities=22% Similarity=0.202 Sum_probs=40.1
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
.|.|++||+...|++.|+.+..++..-|.-.+ +.+.+||.+.||..
T Consensus 3 i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~-d~~~~~q~~~v~~~ 48 (423)
T COG3858 3 IHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTN-DDLVDGQTFVVPPS 48 (423)
T ss_pred EEEccCCceeeeehhhcccccccccccccccc-ccccCceeEEECCc
Confidence 58999999999999999999999976663336 88999999999874
No 26
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=92.89 E-value=0.083 Score=33.06 Aligned_cols=33 Identities=27% Similarity=0.459 Sum_probs=29.1
Q ss_pred HHHHcCCCHHHHHHhCCCCC--CCCCCCCCEEEEcC
Q 040436 56 VTEEFNLSTDVFLAINPNIN--CDAIFVGQWLCVAG 89 (91)
Q Consensus 56 Ia~~~~i~~~~l~~~Np~v~--c~~l~~G~~lcvp~ 89 (91)
||.+|++++++++++|. ++ .+.+.+|+.+.+++
T Consensus 1 ia~~~~~~v~~l~~~n~-~~~~s~~i~~gq~l~~~~ 35 (124)
T COG1388 1 IASKYGVSVKALKKANA-LTGKSDAIKPGQVLKIPG 35 (124)
T ss_pred CcccccccHHHHHHHhc-ccCCCCccccCceEEccC
Confidence 57899999999999994 54 78899999999986
No 27
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.39 E-value=0.31 Score=25.56 Aligned_cols=24 Identities=21% Similarity=0.401 Sum_probs=21.2
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
..|.|..++|+++||+...+.+|-
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 368899999999999999988875
No 28
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=89.24 E-value=0.83 Score=32.40 Aligned_cols=47 Identities=17% Similarity=0.193 Sum_probs=39.1
Q ss_pred CCceEEecCCCCHHHHHHHcCCCHHHHHHhCCCC----C-CCCCCCCCEEEEc
Q 040436 41 CDSVYGAQEGDTCSNVTEEFNLSTDVFLAINPNI----N-CDAIFVGQWLCVA 88 (91)
Q Consensus 41 c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v----~-c~~l~~G~~lcvp 88 (91)
-.+.|+|+.|+|+--+=+.+++.+.|...+=. + + -++|+.||.+.|.
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMak-veGagkpLSnlkaGq~Vki~ 209 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAK-VEGAGKPLSNLKAGQKVKIS 209 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHh-hccCCCchhhccCCCEEEEE
Confidence 34569999999999999999999999888763 3 1 3479999999884
No 29
>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=87.82 E-value=0.24 Score=28.12 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=21.2
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
.++|.|..++|++|||+...|..|=
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHH
Confidence 3678999999999999999999884
No 30
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=87.69 E-value=0.45 Score=32.76 Aligned_cols=46 Identities=13% Similarity=0.087 Sum_probs=33.6
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
..++|+|||+..||=+|..+..++.+.|....-.....-..+|+|.
T Consensus 11 ~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv 56 (186)
T KOG2850|consen 11 EVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPV 56 (186)
T ss_pred eeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceeccc
Confidence 4789999999999999999999999999322112344444555544
No 31
>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=85.82 E-value=1.1 Score=23.43 Aligned_cols=24 Identities=17% Similarity=0.339 Sum_probs=18.3
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHh
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.+.|-|..+||+.+|++...+++.
T Consensus 18 ~~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 18 YAEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HHTT--HHHHHHHTTS-HHHHHHH
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHH
Confidence 357899999999999999999875
No 32
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=83.62 E-value=2.7 Score=29.11 Aligned_cols=47 Identities=26% Similarity=0.379 Sum_probs=39.4
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
..+.++.|+++..+++++++...++.+.|....-..+..|+.+-++.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPR 48 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecc
Confidence 35899999999999999999999999999655333788888887765
No 33
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=83.02 E-value=1.5 Score=27.64 Aligned_cols=27 Identities=15% Similarity=0.177 Sum_probs=23.6
Q ss_pred EecCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436 46 GAQEGDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 46 ~v~~GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
..+.|.|..+||++|||+...|++|=.
T Consensus 25 ~~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 25 SFEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356799999999999999999999943
No 34
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=82.29 E-value=1.6 Score=22.73 Aligned_cols=24 Identities=13% Similarity=0.203 Sum_probs=18.1
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
..|.|..+||+.+|++...+.+|=
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w~ 38 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRWI 38 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHH
Confidence 349999999999999999988773
No 35
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=81.58 E-value=4.5 Score=25.85 Aligned_cols=28 Identities=21% Similarity=0.292 Sum_probs=24.1
Q ss_pred EEecCCCCHHHHHHHc---CCCHHHHHHhCC
Q 040436 45 YGAQEGDTCSNVTEEF---NLSTDVFLAINP 72 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~---~i~~~~l~~~Np 72 (91)
-.+|.|.-..+++++. |-+.++|++.|.
T Consensus 84 LiiQTgnkMddvSrRL~aEgKdIdeLKKiN~ 114 (128)
T PF15145_consen 84 LIIQTGNKMDDVSRRLTAEGKDIDELKKINS 114 (128)
T ss_pred heeeccchHHHHHHHHHhccCCHHHHHHHHH
Confidence 5688899999999986 788999999884
No 36
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=80.29 E-value=4.2 Score=31.06 Aligned_cols=45 Identities=16% Similarity=0.267 Sum_probs=35.1
Q ss_pred ceEEecCCCCHHHHHHHc-CC--CHHHHHHhCCCC-CCCCCCCCCEEEEc
Q 040436 43 SVYGAQEGDTCSNVTEEF-NL--STDVFLAINPNI-NCDAIFVGQWLCVA 88 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~-~i--~~~~l~~~Np~v-~c~~l~~G~~lcvp 88 (91)
...+|++|||+.++|.+- |+ +++-|.-+|- + -.....||+++.|-
T Consensus 429 rvvtVk~GqT~~~lAA~m~G~~rkldlfRllNa-m~~~a~~~pGd~vKii 477 (479)
T COG4784 429 RVVTVKPGQTMASLAARMMGTDRKLDLFRLLNA-MSPGATVRPGDKVKII 477 (479)
T ss_pred EEEEecCCccHHHHHhhccCchhHHHHHHHHhc-cCCCCcCCCCCeeeec
Confidence 468999999999999875 43 3566888884 5 45589999999873
No 37
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=80.18 E-value=2.8 Score=18.90 Aligned_cols=23 Identities=9% Similarity=0.356 Sum_probs=19.4
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
+.|.+..+|++.+|++...+.++
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 45789999999999999888764
No 38
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=77.73 E-value=6.2 Score=22.80 Aligned_cols=46 Identities=17% Similarity=0.317 Sum_probs=34.2
Q ss_pred eEEecCCCCHHHHHHHc-CCC---HHHHHHhCCCC-CCC-CCCCCCEEEEcC
Q 040436 44 VYGAQEGDTCSNVTEEF-NLS---TDVFLAINPNI-NCD-AIFVGQWLCVAG 89 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~-~i~---~~~l~~~Np~v-~c~-~l~~G~~lcvp~ 89 (91)
.++...|||..+++-++ |=+ .+..++.||++ +-. -+..|-.+.+|.
T Consensus 4 ~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD 55 (70)
T COG5004 4 IVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPD 55 (70)
T ss_pred EEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCC
Confidence 36778899999998874 433 47799999999 433 566788887775
No 39
>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=77.46 E-value=0.99 Score=24.56 Aligned_cols=23 Identities=22% Similarity=0.466 Sum_probs=16.4
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHH
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
++.|.+..+||++||++..++..
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 57899999999999998766653
No 40
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=77.06 E-value=2.9 Score=25.73 Aligned_cols=25 Identities=32% Similarity=0.481 Sum_probs=21.0
Q ss_pred ecCCCCHHHHHHHcCC-CHHHHHHhC
Q 040436 47 AQEGDTCSNVTEEFNL-STDVFLAIN 71 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i-~~~~l~~~N 71 (91)
.++|.|..+||++||+ ....|++|=
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHHH
Confidence 4678999999999996 988888653
No 41
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=73.89 E-value=2 Score=26.55 Aligned_cols=68 Identities=9% Similarity=0.091 Sum_probs=30.6
Q ss_pred cchhhHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCceEEecCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 4 NKTSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 4 ~~~~~l~~~~~l~~l~l~~~~~~~~~~~~~~~~~~~~c~~~y~v~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
|++..+..+++++.+++.+..+..+.++....-+-........+..++.....-++.||....+..-|
T Consensus 2 N~yp~WKyllil~vl~~~~lyALPnlyge~pAvqIs~~~~~~~~~~~~~v~~~L~~~~I~~k~i~~~~ 69 (101)
T PF13721_consen 2 NRYPLWKYLLILVVLLLGALYALPNLYGEDPAVQISASSAGVQLPDAFQVEQALKAAGIAVKSIEQEG 69 (101)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhhhccCCCCcEEEecCCCCccCChHHHHHHHHHHCCCCcceEEeeC
Confidence 55555555555555555555554444331111111111111233334456666666666665544333
No 42
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=72.58 E-value=8 Score=23.69 Aligned_cols=13 Identities=54% Similarity=0.754 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHHH
Q 040436 9 FRNLALVLAVLLI 21 (91)
Q Consensus 9 l~~~~~l~~l~l~ 21 (91)
++-+.++++++|+
T Consensus 6 ~llL~l~LA~lLl 18 (95)
T PF07172_consen 6 FLLLGLLLAALLL 18 (95)
T ss_pred HHHHHHHHHHHHH
Confidence 3444444433333
No 43
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=72.28 E-value=4.8 Score=21.97 Aligned_cols=22 Identities=18% Similarity=0.425 Sum_probs=15.6
Q ss_pred cCCCCHHHHHHHcC-CCHHHHHH
Q 040436 48 QEGDTCSNVTEEFN-LSTDVFLA 69 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~-i~~~~l~~ 69 (91)
+.|.|..+|++.|. ++.+++.+
T Consensus 29 ~~G~s~eeI~~~yp~Lt~~~i~a 51 (56)
T PF04255_consen 29 AAGESPEEIAEDYPSLTLEDIRA 51 (56)
T ss_dssp HTT--HHHHHHHSTT--HHHHHH
T ss_pred HcCCCHHHHHHHCCCCCHHHHHH
Confidence 78999999999997 89988865
No 44
>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=71.28 E-value=4.1 Score=21.36 Aligned_cols=24 Identities=4% Similarity=0.210 Sum_probs=16.9
Q ss_pred ecCC-CCHHHHHHHcCCCHHHHHHh
Q 040436 47 AQEG-DTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 47 v~~G-dTc~~Ia~~~~i~~~~l~~~ 70 (91)
|+.| -+....|++|||+...|.+.
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 4566 79999999999999988753
No 45
>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=65.94 E-value=9.8 Score=19.77 Aligned_cols=22 Identities=23% Similarity=0.280 Sum_probs=17.8
Q ss_pred cCCCCHHHHHHHcCCCHHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
..|-|+.+||+..|++.....+
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 4688999999999999887654
No 46
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=65.17 E-value=9.8 Score=19.63 Aligned_cols=23 Identities=9% Similarity=0.180 Sum_probs=14.9
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHH
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
.+.|.|..+||+..|.+...+.+
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 46899999999999999887654
No 47
>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=62.57 E-value=10 Score=21.44 Aligned_cols=24 Identities=13% Similarity=0.307 Sum_probs=20.4
Q ss_pred CCC-CHHHHHHHcCCCHHHHHHhCC
Q 040436 49 EGD-TCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 49 ~Gd-Tc~~Ia~~~~i~~~~l~~~Np 72 (91)
.|+ ++-+||+++|++..++..|-.
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHhh
Confidence 344 899999999999999998863
No 48
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=61.64 E-value=19 Score=19.83 Aligned_cols=53 Identities=17% Similarity=0.183 Sum_probs=31.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCceEEecCCCCHHHHHHHcCCC
Q 040436 6 TSLFRNLALVLAVLLIVSMAESRTFAGGLETSPPTCDSVYGAQEGDTCSNVTEEFNLS 63 (91)
Q Consensus 6 ~~~l~~~~~l~~l~l~~~~~~~~~~~~~~~~~~~~c~~~y~v~~GdTc~~Ia~~~~i~ 63 (91)
|+.+++..++.+++-.++--..+... ...+|.--|...|.=+...|-.-+|-+
T Consensus 1 M~~~~K~~~~a~vl~~Lt~CTG~v~N-----k~knCsYDYllHPAiSISKiIGGCGp~ 53 (56)
T PF13978_consen 1 MKKFIKIAVVAAVLATLTACTGHVEN-----KEKNCSYDYLLHPAISISKIIGGCGPA 53 (56)
T ss_pred ChhHHHHHHHHHHHHHHhhccceeec-----cCCCCcceeeecchhhHHHHhcCCCCc
Confidence 34566666666544333222222222 578899889998887777776655543
No 49
>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=61.32 E-value=41 Score=24.89 Aligned_cols=42 Identities=19% Similarity=0.349 Sum_probs=26.8
Q ss_pred CceEEecCCCCHHHHHHHc---CCCH-----HHHHHhCCCCCCCCCCCCCEE
Q 040436 42 DSVYGAQEGDTCSNVTEEF---NLST-----DVFLAINPNINCDAIFVGQWL 85 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~---~i~~-----~~l~~~Np~v~c~~l~~G~~l 85 (91)
.....|.+|+|..+|++.. |+-. ..+.+.++ ...+|++|.+-
T Consensus 39 ~v~v~Ip~G~s~~~Ia~~L~~~GvI~s~~~F~~~ak~~~--~~~~lkaG~Y~ 88 (342)
T TIGR00247 39 VYEFNIEKGTGVSKIAKELKKQKLIKSEKLLQYLLKIKG--SLKQFKAGTYL 88 (342)
T ss_pred cEEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHhcC--CcCcccceEEE
Confidence 3468899999999999886 3322 12333343 23457887664
No 50
>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=58.84 E-value=13 Score=18.30 Aligned_cols=19 Identities=16% Similarity=0.158 Sum_probs=16.9
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
|..++|+.+|++...+.+|
T Consensus 2 s~~e~a~~lgvs~~tl~~~ 20 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRW 20 (49)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5678999999999999988
No 51
>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=57.94 E-value=12 Score=21.43 Aligned_cols=20 Identities=5% Similarity=0.258 Sum_probs=17.3
Q ss_pred cCCCCHHHHHHHcCCCHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVF 67 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l 67 (91)
+.|-++-+||+++|++..+.
T Consensus 11 E~g~~FveIAr~~~i~a~e~ 30 (63)
T PF11242_consen 11 ESGLSFVEIARKIGITAKEV 30 (63)
T ss_pred HcCCcHHHHHHHhCCCHHHH
Confidence 56889999999999998763
No 52
>smart00351 PAX Paired Box domain.
Probab=57.50 E-value=12 Score=23.71 Aligned_cols=23 Identities=17% Similarity=0.271 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
+.|.++-+||+++|++.....+|
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kw 53 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKI 53 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 57899999999999999887766
No 53
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.59 E-value=11 Score=24.60 Aligned_cols=26 Identities=19% Similarity=0.350 Sum_probs=22.1
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
+..|.++-.||+++|++....+.|=.
T Consensus 18 ~~~G~S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 18 VGEGLSCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred HHcCccHHHHHHHhCccHHHHHHHHH
Confidence 45799999999999999998777643
No 54
>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=56.24 E-value=17 Score=20.07 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHcCCCHHHHHHhC
Q 040436 49 EGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
.|-+..+||++.|++...++.|-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHH
Confidence 48899999999999999888775
No 55
>PHA00675 hypothetical protein
Probab=55.97 E-value=15 Score=21.89 Aligned_cols=23 Identities=26% Similarity=0.364 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
..|.+...||++||++...+.+.
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I 59 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKI 59 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHH
Confidence 68999999999999999887754
No 56
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=55.30 E-value=20 Score=18.13 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.5
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
..|.+..+||+..|++...+.+.
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999999887654
No 57
>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=54.59 E-value=19 Score=18.81 Aligned_cols=21 Identities=14% Similarity=0.289 Sum_probs=14.5
Q ss_pred CCCCHHHHHHHcCCCHHHHHH
Q 040436 49 EGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
.|-|..+||+..|++...+..
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~ 45 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKR 45 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHH
Confidence 578999999999999987654
No 58
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=52.68 E-value=23 Score=17.42 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHcCCCHHHHHHh
Q 040436 49 EGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.|-+..+||+..|++.+.+.++
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~ 46 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQR 46 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 6789999999999999888754
No 59
>PF13551 HTH_29: Winged helix-turn helix
Probab=52.28 E-value=16 Score=21.62 Aligned_cols=25 Identities=16% Similarity=0.207 Sum_probs=20.2
Q ss_pred ecCCC-CHHHHHHHcCCCHHHHHHhC
Q 040436 47 AQEGD-TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 47 v~~Gd-Tc~~Ia~~~~i~~~~l~~~N 71 (91)
+..|. |..+||+.+|++...+++|=
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~ 33 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWL 33 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence 35677 59999999999998877663
No 60
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=51.54 E-value=16 Score=28.89 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=21.5
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+..+||+.++|++.|++.+. +.++|.
T Consensus 421 ~~kadTleELA~k~gid~~~L~~TV~~yN~ 450 (564)
T PRK12845 421 AHRADSLADLARKIGVPVDTFVATMRRFNE 450 (564)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 45789999999999999765 567785
No 61
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=51.53 E-value=16 Score=28.35 Aligned_cols=26 Identities=15% Similarity=0.248 Sum_probs=21.2
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+..+||+.++|++.|++.+. +.++|.
T Consensus 372 ~~kaDTleELA~k~gid~~~L~~Tv~~yN~ 401 (513)
T PRK12837 372 WRTADTLEELAAKIGVPADALTATVARFNG 401 (513)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 44689999999999999765 567774
No 62
>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=51.40 E-value=16 Score=22.43 Aligned_cols=20 Identities=15% Similarity=0.318 Sum_probs=15.0
Q ss_pred CCCHHHHHHHcCCCHHHHHH
Q 040436 50 GDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~ 69 (91)
|.+..++|.+||+|...+++
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 99999999999999887664
No 63
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=51.34 E-value=12 Score=23.35 Aligned_cols=24 Identities=13% Similarity=0.331 Sum_probs=21.4
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHh
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
++.|.+.-++|+.|+|+...+++|
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W 38 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRW 38 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHH
Confidence 456899999999999999998888
No 64
>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=51.12 E-value=18 Score=21.84 Aligned_cols=28 Identities=21% Similarity=0.234 Sum_probs=24.3
Q ss_pred EecCCCCHHHHHHHcCCCHHHHHHhCCC
Q 040436 46 GAQEGDTCSNVTEEFNLSTDVFLAINPN 73 (91)
Q Consensus 46 ~v~~GdTc~~Ia~~~~i~~~~l~~~Np~ 73 (91)
.+..|.|-.+||+++|++...++++...
T Consensus 46 ll~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 46 MLKQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 3578999999999999999999987653
No 65
>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=50.70 E-value=19 Score=19.56 Aligned_cols=20 Identities=25% Similarity=0.192 Sum_probs=17.0
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
+..++|+.+|++.+.+..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999988764
No 66
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=50.60 E-value=22 Score=18.36 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=16.4
Q ss_pred CCHHHHHHHcCCCHHHHHH
Q 040436 51 DTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 51 dTc~~Ia~~~~i~~~~l~~ 69 (91)
-|..+||+.+|++.+.+.+
T Consensus 28 ~s~~~vA~~~~vs~~TV~r 46 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRR 46 (52)
T ss_pred CCHHHHHHHHCCCHHHHHH
Confidence 4899999999999988765
No 67
>COG1559 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]
Probab=49.39 E-value=65 Score=24.23 Aligned_cols=41 Identities=17% Similarity=0.404 Sum_probs=26.4
Q ss_pred ceEEecCCCCHHHHHHHcC----CC----HHHHHHhCCCCCCCCCCCCCEE
Q 040436 43 SVYGAQEGDTCSNVTEEFN----LS----TDVFLAINPNINCDAIFVGQWL 85 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~----i~----~~~l~~~Np~v~c~~l~~G~~l 85 (91)
....|.+|++...|+.... |. .....+.|+. -+.|++|.+-
T Consensus 46 ~~v~I~~Gs~~~~i~~~Le~~~vI~~~~~f~~~~~~~~~--~~~lkaG~Y~ 94 (342)
T COG1559 46 KTVTIPPGSSVSEIGSELEKQKVIKNARVFRLYLKYNPA--AGSLKAGEYR 94 (342)
T ss_pred eEEEECCCCCHHHHHHHHHhcCccccHHHHHHHHHhcCc--cCCcCCceee
Confidence 7799999999999998752 22 1234445543 2346777653
No 68
>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=48.93 E-value=25 Score=17.38 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=17.2
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
|..++|+.+|++...+.+|-
T Consensus 3 t~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 56789999999999988775
No 69
>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=48.82 E-value=19 Score=22.03 Aligned_cols=30 Identities=13% Similarity=0.278 Sum_probs=23.6
Q ss_pred ecCCC-CHHHHHHHcCCCHHHHHHhCCCCCC
Q 040436 47 AQEGD-TCSNVTEEFNLSTDVFLAINPNINC 76 (91)
Q Consensus 47 v~~Gd-Tc~~Ia~~~~i~~~~l~~~Np~v~c 76 (91)
|..|- |..+-.++|+++.+||..|-..++.
T Consensus 45 V~~Glis~~EA~~rY~Ls~eEf~~W~~av~r 75 (90)
T PF06627_consen 45 VRGGLISVEEACRRYGLSEEEFESWQRAVDR 75 (90)
T ss_dssp HHCTTS-HHHHHHCTTSSHHHHHHHHHHCCT
T ss_pred HHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 55666 6888899999999999999766543
No 70
>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=47.69 E-value=20 Score=19.58 Aligned_cols=29 Identities=3% Similarity=-0.013 Sum_probs=20.9
Q ss_pred CCCc-eEEecCCCCHHHHHHHcCCCHHHHH
Q 040436 40 TCDS-VYGAQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 40 ~c~~-~y~v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
.|+. ..++-+..|+...|+.+|+++++|.
T Consensus 30 ~~p~~~~~~~~~~Tl~~aa~~~gid~~~li 59 (59)
T PF08984_consen 30 GNPVMRNTMAKFETLEQAAKMHGIDLEKLI 59 (59)
T ss_dssp GSCCHHTTHHHHSBHHHHHHHHT--HHHHH
T ss_pred CCcHHHHhhcccCCHHHHHHHcCCCHHHhC
Confidence 3542 4566778899999999999999874
No 71
>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=47.68 E-value=25 Score=17.67 Aligned_cols=19 Identities=11% Similarity=0.058 Sum_probs=16.7
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
|..++|+..|++...|..|
T Consensus 2 ~~~e~a~~~gv~~~tlr~~ 20 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYY 20 (49)
T ss_pred cHHHHHHHHCcCHHHHHHH
Confidence 4678999999999999887
No 72
>PRK12839 hypothetical protein; Provisional
Probab=47.27 E-value=20 Score=28.30 Aligned_cols=28 Identities=18% Similarity=0.249 Sum_probs=22.0
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCCCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINPNI 74 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np~v 74 (91)
+..+||+.++|++.|++.+. +.++|...
T Consensus 424 ~~kadTleELA~k~gid~~~L~~TV~~yN~~~ 455 (572)
T PRK12839 424 LTRGRTIEELAEKCGIDPAGLEATVAEFNENA 455 (572)
T ss_pred EEECCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 34689999999999999765 56778533
No 73
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=46.51 E-value=29 Score=21.23 Aligned_cols=39 Identities=15% Similarity=0.188 Sum_probs=27.4
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHHHhCCCC-----CCCCCCC
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFLAINPNI-----NCDAIFV 81 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v-----~c~~l~~ 81 (91)
+.|..|.+++=..+-....-...+|++.||.+ +|+.++|
T Consensus 19 RI~lcqkspaSagvR~fvEk~Y~~lKkaNP~lPILIREcSgVqP 62 (97)
T KOG3446|consen 19 RIHLCQKSPASAGVREFVEKFYVNLKKANPDLPILIRECSGVQP 62 (97)
T ss_pred eeeecCCCCcchhHHHHHHHhhhhhhhcCCCCcEeehhhcCCch
Confidence 35677777765555444444567899999987 7998877
No 74
>cd00131 PAX Paired Box domain
Probab=46.26 E-value=22 Score=22.59 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=20.1
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
+.|.++-+||++++++.....+|
T Consensus 31 ~~G~s~~~iA~~~~Vs~~tV~r~ 53 (128)
T cd00131 31 QSGIRPCDISRQLRVSHGCVSKI 53 (128)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 57999999999999998876666
No 75
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=46.25 E-value=20 Score=23.69 Aligned_cols=22 Identities=18% Similarity=0.265 Sum_probs=17.5
Q ss_pred CCCHHHHHHHcCCCHHHHHHhC
Q 040436 50 GDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
--|..+||+..|++...|++|-
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr 55 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWR 55 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHH
T ss_pred cchHHHHHHHhCCCHHHHHHHH
Confidence 3489999999999999999984
No 76
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=45.47 E-value=21 Score=24.44 Aligned_cols=31 Identities=19% Similarity=0.278 Sum_probs=25.5
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHHH---hCCCC
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFLA---INPNI 74 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~---~Np~v 74 (91)
.-.|..|+++-++|++.|+++++|.+ -||.+
T Consensus 26 l~~vsaG~iFR~~A~e~gmsl~ef~~~AE~~p~i 59 (179)
T COG1102 26 LKLVSAGTIFREMARERGMSLEEFSRYAEEDPEI 59 (179)
T ss_pred CceeeccHHHHHHHHHcCCCHHHHHHHHhcCchh
Confidence 35678899999999999999998765 46655
No 77
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=45.35 E-value=31 Score=20.40 Aligned_cols=23 Identities=13% Similarity=0.339 Sum_probs=18.4
Q ss_pred ecCCCCHHHHHHHcC-CCHHHHHH
Q 040436 47 AQEGDTCSNVTEEFN-LSTDVFLA 69 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~-i~~~~l~~ 69 (91)
.+.|.|-.+|+..|. ++.+++++
T Consensus 40 l~~G~s~eeil~dyp~Lt~~dI~a 63 (79)
T COG2442 40 LAAGESIEEILADYPDLTLEDIRA 63 (79)
T ss_pred HHCCCCHHHHHHhCCCCCHHHHHH
Confidence 457888888888887 88888764
No 78
>PRK10270 putative aminodeoxychorismate lyase; Provisional
Probab=44.34 E-value=88 Score=23.33 Aligned_cols=43 Identities=14% Similarity=0.349 Sum_probs=27.7
Q ss_pred CceEEecCCCCHHHHHHHc---C-CCHH----HHHHhCCCCCCCCCCCCCEEE
Q 040436 42 DSVYGAQEGDTCSNVTEEF---N-LSTD----VFLAINPNINCDAIFVGQWLC 86 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~---~-i~~~----~l~~~Np~v~c~~l~~G~~lc 86 (91)
.....|.+|+|..+|++.. | |.-. ...+.++. ..+|++|.+--
T Consensus 39 ~v~v~I~~G~t~~~Ia~~L~~~gvI~s~~~F~~~~~~~~~--~~~ikaG~Y~l 89 (340)
T PRK10270 39 ETIFTLKPGTGRLALGEQLYADKIINRPRVFQWLLRIEPD--LSHFKAGTYRF 89 (340)
T ss_pred CEEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHhCCC--CCCccceEEEe
Confidence 4568899999999999985 3 2222 23334532 34688887653
No 79
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=43.60 E-value=32 Score=18.73 Aligned_cols=25 Identities=16% Similarity=0.232 Sum_probs=20.2
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHH
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
+|-+-.+-|+.+||++.||+...+.
T Consensus 17 Yfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 4556667799999999999987764
No 80
>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=43.51 E-value=24 Score=20.57 Aligned_cols=26 Identities=8% Similarity=0.001 Sum_probs=18.4
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHHH
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
+.+.+.+|+|+.+.+.+.|+.+..+-
T Consensus 11 ~~v~~~~G~til~al~~~gi~ip~~c 36 (82)
T PF13510_consen 11 KPVEVPPGETILEALLAAGIDIPRLC 36 (82)
T ss_dssp EEEEEEET-BHHHHHHHTT--B-EET
T ss_pred EEEEEcCCCHHHHHHHHCCCeEEEee
Confidence 45899999999999999998766443
No 81
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=42.91 E-value=34 Score=17.97 Aligned_cols=18 Identities=17% Similarity=0.215 Sum_probs=14.6
Q ss_pred CHHHHHHHcCCCHHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~ 69 (91)
|+.+||+..|++....-+
T Consensus 1 Ti~dIA~~agvS~~TVSr 18 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSR 18 (46)
T ss_dssp CHHHHHHHHTSSHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHH
Confidence 678999999999876543
No 82
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=42.34 E-value=22 Score=22.87 Aligned_cols=20 Identities=25% Similarity=0.547 Sum_probs=16.9
Q ss_pred cCCCCHHHHHHHcCCCHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVF 67 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l 67 (91)
..|-||.+||+-|+|+.+.+
T Consensus 78 ~AGlt~~aIAd~F~iS~s~~ 97 (126)
T PF10654_consen 78 HAGLTCYAIADYFKISKSTV 97 (126)
T ss_pred hcCCChHHHHHHHhHHHHHH
Confidence 46999999999999987654
No 83
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=41.63 E-value=38 Score=16.78 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=14.1
Q ss_pred CCCCHHHHHHHcCCCHHHHHH
Q 040436 49 EGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
.+-++.+||...|++..-|.+
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r 27 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSR 27 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHH
Confidence 456889999999998876654
No 84
>PF07027 DUF1318: Protein of unknown function (DUF1318); InterPro: IPR008309 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=41.49 E-value=14 Score=22.70 Aligned_cols=36 Identities=11% Similarity=0.114 Sum_probs=23.8
Q ss_pred HHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436 53 CSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA 88 (91)
Q Consensus 53 c~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp 88 (91)
...||++.|++++++.+.-..---+.-.+|++|..+
T Consensus 53 Y~~iA~~ng~t~~~V~~~~a~k~~~~a~~G~~vq~~ 88 (95)
T PF07027_consen 53 YQEIAKKNGITVEQVAATAAQKWIERAPPGQYVQDA 88 (95)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhCCCCcEEECC
Confidence 567899999999887655432112345677777664
No 85
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=41.47 E-value=34 Score=18.58 Aligned_cols=20 Identities=15% Similarity=0.162 Sum_probs=16.6
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
|..++|+..|++.+.|..|=
T Consensus 2 ti~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 45789999999999987763
No 86
>PRK07843 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=41.05 E-value=30 Score=27.17 Aligned_cols=26 Identities=15% Similarity=0.268 Sum_probs=21.4
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+..+||+.++|++.|++.+. +.++|.
T Consensus 413 ~~kadTleELA~~~gid~~~L~aTV~~yN~ 442 (557)
T PRK07843 413 IVKADTLAELAAKIGVPADALTATVQRFNG 442 (557)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 45789999999999999765 567885
No 87
>PRK06134 putative FAD-binding dehydrogenase; Reviewed
Probab=40.58 E-value=30 Score=27.31 Aligned_cols=26 Identities=12% Similarity=0.204 Sum_probs=20.9
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+..+||+.++|++.|++.+. +.++|.
T Consensus 426 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 455 (581)
T PRK06134 426 LKRGASLEELARACGIDPDGLEATVARYNR 455 (581)
T ss_pred EEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 44689999999999999765 456774
No 88
>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=40.42 E-value=30 Score=20.74 Aligned_cols=19 Identities=16% Similarity=0.162 Sum_probs=15.8
Q ss_pred CCHHHHHHHcCCCHHHHHH
Q 040436 51 DTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 51 dTc~~Ia~~~~i~~~~l~~ 69 (91)
..+..+|+++|++.+||..
T Consensus 55 ~kL~~La~~N~v~feeLc~ 73 (82)
T PF11020_consen 55 SKLYKLAKENNVSFEELCV 73 (82)
T ss_pred HHHHHHHHHcCCCHHHHHH
Confidence 3588999999999999753
No 89
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=40.09 E-value=36 Score=18.47 Aligned_cols=19 Identities=16% Similarity=0.069 Sum_probs=16.7
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
|..++|+.+|++.+.|..|
T Consensus 2 s~~eva~~~gvs~~tlr~~ 20 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYY 20 (70)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4678999999999998887
No 90
>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=39.65 E-value=34 Score=17.13 Aligned_cols=20 Identities=15% Similarity=0.154 Sum_probs=15.0
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
|..++|+..|++.+.|..|-
T Consensus 1 ti~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 34688999999999887664
No 91
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=39.47 E-value=33 Score=19.11 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=13.3
Q ss_pred CHHHHHHHcCCCHHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~ 69 (91)
|..+||.+++++.+.+..
T Consensus 16 S~~eLa~~~~~s~~~ve~ 33 (69)
T PF09012_consen 16 SLAELAREFGISPEAVEA 33 (69)
T ss_dssp EHHHHHHHTT--HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHH
Confidence 789999999999887543
No 92
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=39.34 E-value=43 Score=19.79 Aligned_cols=47 Identities=15% Similarity=0.154 Sum_probs=36.1
Q ss_pred CCceEEecCCCCHHHHHHHcCCCHHH--HHHhCCCC-CC-CCCCCCCEEEE
Q 040436 41 CDSVYGAQEGDTCSNVTEEFNLSTDV--FLAINPNI-NC-DAIFVGQWLCV 87 (91)
Q Consensus 41 c~~~y~v~~GdTc~~Ia~~~~i~~~~--l~~~Np~v-~c-~~l~~G~~lcv 87 (91)
-...+....+.|..++.+..|++..| +...|..- +- ..+..|+.+.|
T Consensus 23 ~~~~~~~~~~~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V 73 (81)
T PF14451_consen 23 GPFTHPFDGGATVKDVIESLGVPHTEVGLILVNGRPVDFDYRLKDGDRVAV 73 (81)
T ss_pred CceEEecCCCCcHHHHHHHcCCChHHeEEEEECCEECCCcccCCCCCEEEE
Confidence 34568889999999999999999998 45567422 32 36888999887
No 93
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=39.28 E-value=42 Score=23.19 Aligned_cols=29 Identities=28% Similarity=0.431 Sum_probs=23.6
Q ss_pred EEecCCCCHHHHHHHcCCCHHHHHHhCCC
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDVFLAINPN 73 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~ 73 (91)
|--+.|..+..+|+.+|++.+|+.+.--+
T Consensus 85 Y~~~~g~DL~~vA~~~gLs~eevi~~Hs~ 113 (202)
T TIGR00370 85 YGGEFGPDLEEVAKINQLSPEEVIDIHSN 113 (202)
T ss_pred eCCCCCCCHHHHHHHhCcCHHHHHHHHhC
Confidence 44455779999999999999999977643
No 94
>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=39.20 E-value=39 Score=20.32 Aligned_cols=23 Identities=17% Similarity=0.200 Sum_probs=19.5
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
..|.+..+||+++|++.+.+.+.
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 36999999999999999887643
No 95
>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=38.82 E-value=52 Score=16.57 Aligned_cols=22 Identities=18% Similarity=0.309 Sum_probs=18.4
Q ss_pred CCCCHHHHHHHcCCCHHHHHHh
Q 040436 49 EGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.|.+-.+||+.++++...+...
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~ 35 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHH
Confidence 5779999999999998876654
No 96
>PRK12843 putative FAD-binding dehydrogenase; Reviewed
Probab=38.75 E-value=33 Score=27.01 Aligned_cols=26 Identities=8% Similarity=0.109 Sum_probs=21.0
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+...||+.++|++.|++.+. +.++|.
T Consensus 428 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 457 (578)
T PRK12843 428 LTVASTLDELAPKLGIDPAALAATVQRHNQ 457 (578)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 44689999999999999764 567775
No 97
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=38.74 E-value=37 Score=22.76 Aligned_cols=24 Identities=13% Similarity=0.282 Sum_probs=21.2
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
..|.|+.+||+..|++...+++.-
T Consensus 170 ~~g~s~~~iak~lgis~~Tv~r~~ 193 (200)
T PRK13413 170 DKGTSKSEIARKLGVSRTTLARFL 193 (200)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHH
Confidence 569999999999999999988754
No 98
>cd07446 CRD_SFRP2 Cysteine-rich domain of the secreted frizzled-related protein 2 (SFRP2), a regulator of Wnt activity. The cysteine-rich-domain (CRD) is an essential part of the secreted frizzled related protein 2 (SFRP2), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to CRD domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. As a Wnt antagonist, SFRP2 regulates Nkx2.2 expression in the ventral spinal cord and anteroposterior axis elongation. SFRP2 also has a Wnt-independent function as an enhancer of procollagen cleavage by the TLD proteinases. SFRP2 binds both procollagen and TLD, thus facilitating the enzymatic reaction by bringing togeth
Probab=38.58 E-value=11 Score=24.28 Aligned_cols=46 Identities=20% Similarity=0.438 Sum_probs=32.3
Q ss_pred CCCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 37 SPPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 37 ~~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
.-..|... ..| -+.|+.+.+++|.++. ..++|+.+..+..+|++..
T Consensus 75 ~i~PCRslCe~v--r~~C~~~m~~~g~~WP------~~l~C~~fP~~~~~Ci~~~ 121 (128)
T cd07446 75 AIQPCRSLCEAV--KDGCAPVMSAFGFPWP------DMLDCTRFPLDNDLCIPPA 121 (128)
T ss_pred cCCccHHHHHHH--HHHHHHHHHHcCCCCC------CCCCcccCCCCCCcccCcc
Confidence 45566654 333 3789999999997754 3468998887777898753
No 99
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=38.55 E-value=39 Score=20.35 Aligned_cols=25 Identities=16% Similarity=0.198 Sum_probs=21.2
Q ss_pred EecCCCCHHHHHHHcCCCHHHHHHh
Q 040436 46 GAQEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 46 ~v~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.|+.|-+.-.+|+.|||+.....+|
T Consensus 21 vv~~g~~~a~aA~~~gVS~~Ta~kW 45 (85)
T PF13011_consen 21 VVEQGWPVAHAAAEFGVSRRTAYKW 45 (85)
T ss_pred HHHcCCcHHHHHHHhCCCHHHHHHH
Confidence 3567889999999999999887776
No 100
>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=38.49 E-value=4.5 Score=24.28 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=19.7
Q ss_pred EEecCCCCHHHHHHHcCCCHHH--------HHHhCCCC
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDV--------FLAINPNI 74 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~--------l~~~Np~v 74 (91)
|.++...|.-..|+.||++-+. |..+||.+
T Consensus 14 yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L 51 (82)
T PF12116_consen 14 YIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPEL 51 (82)
T ss_dssp HHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred HHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence 6778889999999999999653 67777654
No 101
>PRK06481 fumarate reductase flavoprotein subunit; Validated
Probab=38.23 E-value=34 Score=26.46 Aligned_cols=26 Identities=19% Similarity=0.391 Sum_probs=20.7
Q ss_pred ecCCCCHHHHHHHcCCCHHHH----HHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVF----LAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l----~~~Np 72 (91)
+..+||+.++|++.|++.+.| .++|.
T Consensus 375 ~~kadTleeLA~~~gid~~~L~~tv~~yN~ 404 (506)
T PRK06481 375 VEEGKTIDELAKKINVPAETLTKTLDTWNK 404 (506)
T ss_pred EEEcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 346899999999999998764 45674
No 102
>PRK12842 putative succinate dehydrogenase; Reviewed
Probab=38.21 E-value=32 Score=27.00 Aligned_cols=26 Identities=15% Similarity=0.175 Sum_probs=21.0
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+..+||+.++|++.+++.+. +.++|.
T Consensus 423 ~~kadTleELA~~~gid~~~L~~Tv~~yN~ 452 (574)
T PRK12842 423 LIKGDTLAELAGKAGIDAAGLEATVRRYNE 452 (574)
T ss_pred EEEcCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 45689999999999999765 567775
No 103
>PF02515 CoA_transf_3: CoA-transferase family III; InterPro: IPR003673 CoA-transferases are found in organisms from all kingdoms of life. They catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids. There are at least three families of CoA-transferases, which differ in sequence and reaction mechanism: Family I consists of CoA-transferases for 3-oxoacids (2.8.3.5 from EC, 2.8.3.6 from EC), short-chain fatty acids (2.8.3.8 from EC, 2.8.3.9 from EC) and glutaconate (2.8.3.12 from EC). Most use succinyl-CoA or acetyl-CoA as CoA donors. Family II consists of the homodimeric alpha-subunits of citrate lyase and citramalate lyase (2.8.3.10 from EC, 2.8.3.11 from EC). These enzymes catalyse the transfer of acyl carrier protein (ACP) with a covalently bound CoA derivative, but can accept free CoA thioesters as well. Family III consists of formyl-CoA:oxalate CoA-transferase [], succinyl-CoA:(R)-benzylsuccinate CoA-transferase [], (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase [], and butyrobetainyl-CoA:(R)-carnitine CoA-transferase []. These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate- and stereo-specific manner []. This entry represents family III CoA-transferases.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1PT7_B 1PT8_A 1PQY_A 1Q7E_A 1Q6Y_A 1PT5_A 1XK6_B 1XK7_C 1XVT_A 1XVU_A ....
Probab=37.63 E-value=31 Score=23.11 Aligned_cols=19 Identities=37% Similarity=0.607 Sum_probs=14.3
Q ss_pred HHHHcCCCHHHHHHhCCCC
Q 040436 56 VTEEFNLSTDVFLAINPNI 74 (91)
Q Consensus 56 Ia~~~~i~~~~l~~~Np~v 74 (91)
..++.|++.+++.+.||.+
T Consensus 32 ~~~~lGl~~~~l~~~nP~L 50 (191)
T PF02515_consen 32 VLERLGLDYEALRAINPRL 50 (191)
T ss_dssp HHHHTT-SHHHHHHH-TT-
T ss_pred hhHhcCCCHHHHHhhCCCC
Confidence 4678999999999999987
No 104
>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=37.44 E-value=22 Score=18.88 Aligned_cols=18 Identities=11% Similarity=0.338 Sum_probs=13.8
Q ss_pred CHHHHHHHcCCCHHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~ 69 (91)
+..++|++.|++..++.+
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 456899999999988543
No 105
>PRK07121 hypothetical protein; Validated
Probab=36.99 E-value=38 Score=25.90 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=21.4
Q ss_pred ecCCCCHHHHHHHcCCCHH----HHHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTD----VFLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~----~l~~~Np 72 (91)
+...||+.++|++.|++.+ .+.++|.
T Consensus 358 ~~kadtleeLA~~~gid~~~l~~tv~~yN~ 387 (492)
T PRK07121 358 AWKAETVEELARKLGIPPGGLQATVDAYNR 387 (492)
T ss_pred ccccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4568999999999999987 4667774
No 106
>COG3784 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.93 E-value=20 Score=22.51 Aligned_cols=35 Identities=11% Similarity=0.100 Sum_probs=23.2
Q ss_pred CHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEE
Q 040436 52 TCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLC 86 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lc 86 (91)
+...||++.|++.++.-++-..---....|||++.
T Consensus 66 ~Yq~lA~~n~~s~~~vak~agqklv~Ra~~GqYvq 100 (109)
T COG3784 66 SYQQLAKKNGASTEEVAKLAGQKLVARAAPGQYVQ 100 (109)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhcCCCCeee
Confidence 46778888999999877665322122356777765
No 107
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=36.55 E-value=53 Score=15.60 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=19.6
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
+.|-|..++|+..|++...+.+|-.
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3466888999999999888877654
No 108
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.39 E-value=40 Score=17.99 Aligned_cols=22 Identities=18% Similarity=0.250 Sum_probs=11.0
Q ss_pred CCCCHHHHHHHcCCCHHHHHHh
Q 040436 49 EGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.|=|..++|++.|++...+.++
T Consensus 9 ~~it~~~La~~~gis~~tl~~~ 30 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRI 30 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHH
T ss_pred cCCCHHHHHHHHCcCHHHHHHH
Confidence 3456666677767666665544
No 109
>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=36.39 E-value=35 Score=23.08 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=23.9
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
.-.+..|.|-.+||..+|++++.+.+.=
T Consensus 63 QarIRaGas~eeVA~~~G~~~~rV~rfa 90 (170)
T PF11268_consen 63 QARIRAGASAEEVAEEAGVPVERVRRFA 90 (170)
T ss_pred HHHHHCCCCHHHHHHHhCCCHHHhhhcc
Confidence 3678899999999999999999876653
No 110
>PRK12844 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=36.34 E-value=39 Score=26.55 Aligned_cols=26 Identities=12% Similarity=0.125 Sum_probs=20.6
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+..+||+.++|++.|++.+. +.++|.
T Consensus 406 ~~kadTleELA~k~gid~~~L~atv~~yN~ 435 (557)
T PRK12844 406 MKRADTIEELAGKTGIDPAGLAATVERFNG 435 (557)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 34689999999999999765 445674
No 111
>PF14493 HTH_40: Helix-turn-helix domain
Probab=36.34 E-value=48 Score=19.47 Aligned_cols=22 Identities=14% Similarity=0.163 Sum_probs=18.2
Q ss_pred ecCCCCHHHHHHHcCCCHHHHH
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
.+.|-|..+||++-|++...+.
T Consensus 10 ~~~G~si~eIA~~R~L~~sTI~ 31 (91)
T PF14493_consen 10 FQKGLSIEEIAKIRGLKESTIY 31 (91)
T ss_pred HHcCCCHHHHHHHcCCCHHHHH
Confidence 3579999999999999877644
No 112
>TIGR02485 CobZ_N-term precorrin 3B synthase CobZ. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the N-terminal portion of the R. capsulatus gene which, in other species exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (TIGR02484).
Probab=36.33 E-value=37 Score=25.40 Aligned_cols=25 Identities=12% Similarity=0.085 Sum_probs=20.6
Q ss_pred cCCCCHHHHHHHcCCCHHHH----HHhCC
Q 040436 48 QEGDTCSNVTEEFNLSTDVF----LAINP 72 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l----~~~Np 72 (91)
..+||+.++|++.|++.+.| .++|.
T Consensus 313 ~~adtleeLA~~~gid~~~l~~tv~~yN~ 341 (432)
T TIGR02485 313 LSADTLEELAGLLGIDPGGLAETLDRPNA 341 (432)
T ss_pred eecCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 47899999999999998765 45774
No 113
>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=36.33 E-value=45 Score=18.16 Aligned_cols=19 Identities=16% Similarity=0.158 Sum_probs=16.8
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
+..++|+..|++...|..|
T Consensus 2 ~i~evA~~~gvs~~tlR~~ 20 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYY 20 (67)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4578999999999999888
No 114
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=36.21 E-value=35 Score=18.15 Aligned_cols=22 Identities=18% Similarity=0.324 Sum_probs=17.3
Q ss_pred ecCCCCHHHHHHHcCCCHHHHH
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
+-.|.+..+||+..+++...+.
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 3468999999999999987654
No 115
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=36.07 E-value=45 Score=17.45 Aligned_cols=21 Identities=10% Similarity=0.153 Sum_probs=17.3
Q ss_pred CCCHHHHHHHcCCCHHHHHHh
Q 040436 50 GDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.+....||.+.|++..++..|
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 346789999999999998765
No 116
>PRK12835 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=36.05 E-value=37 Score=26.90 Aligned_cols=28 Identities=11% Similarity=0.156 Sum_probs=21.9
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCCCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINPNI 74 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np~v 74 (91)
+..+||+.++|++.|++.+. +.++|...
T Consensus 427 ~~kAdTleeLA~~~gida~~L~aTV~~yN~~~ 458 (584)
T PRK12835 427 VKKADTWDELAAKIGVPAENLRATAERFNGLA 458 (584)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 34689999999999999654 56788533
No 117
>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=35.75 E-value=51 Score=21.52 Aligned_cols=24 Identities=29% Similarity=0.423 Sum_probs=20.8
Q ss_pred ecCC--CCHHHHHHHcCCCHHHHHHh
Q 040436 47 AQEG--DTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 47 v~~G--dTc~~Ia~~~~i~~~~l~~~ 70 (91)
-.++ -|..+|++..||+.++|.+|
T Consensus 41 ~~p~~~ati~eV~e~tgVs~~~I~~~ 66 (137)
T TIGR03826 41 KHENRQATVSEIVEETGVSEKLILKF 66 (137)
T ss_pred HCCCCCCCHHHHHHHHCcCHHHHHHH
Confidence 4566 89999999999999998875
No 118
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.25 E-value=42 Score=21.03 Aligned_cols=19 Identities=32% Similarity=0.462 Sum_probs=15.7
Q ss_pred CCHHHHHHHcCCCHHHHHH
Q 040436 51 DTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 51 dTc~~Ia~~~~i~~~~l~~ 69 (91)
-++.+||+.++|+...+..
T Consensus 34 lSl~EIAee~~VSRqAIyD 52 (105)
T COG2739 34 LSLSEIAEEFNVSRQAIYD 52 (105)
T ss_pred ccHHHHHHHhCccHHHHHH
Confidence 4899999999999876553
No 119
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=35.07 E-value=38 Score=19.44 Aligned_cols=22 Identities=23% Similarity=0.267 Sum_probs=19.8
Q ss_pred EEecCCCCHHHHHHHcCCCHHH
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDV 66 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~ 66 (91)
--|+.|-+..+|++.+|++.++
T Consensus 39 klv~~Ga~~~el~~~CgL~~aE 60 (70)
T PF10975_consen 39 KLVRQGASVEELMEECGLSRAE 60 (70)
T ss_pred HHHHcCCCHHHHHHHcCCCHHH
Confidence 5688999999999999999876
No 120
>PF12728 HTH_17: Helix-turn-helix domain
Probab=35.06 E-value=53 Score=16.84 Aligned_cols=19 Identities=16% Similarity=0.184 Sum_probs=16.6
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
|..++|+..|++...+++|
T Consensus 3 t~~e~a~~l~is~~tv~~~ 21 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRW 21 (51)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5678999999999999887
No 121
>PHA01976 helix-turn-helix protein
Probab=34.93 E-value=59 Score=17.50 Aligned_cols=22 Identities=0% Similarity=0.101 Sum_probs=11.8
Q ss_pred CCCCHHHHHHHcCCCHHHHHHh
Q 040436 49 EGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.|-|-.++|++.|++...+.+|
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~ 35 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDF 35 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHH
Confidence 4455555555555555555443
No 122
>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=34.87 E-value=50 Score=15.96 Aligned_cols=18 Identities=11% Similarity=0.222 Sum_probs=15.0
Q ss_pred CHHHHHHHcCCCHHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~ 69 (91)
-+..+|++.|.+..++.+
T Consensus 13 ~l~~~a~~~g~s~s~~ir 30 (39)
T PF01402_consen 13 RLDELAKELGRSRSELIR 30 (39)
T ss_dssp HHHHHHHHHTSSHHHHHH
T ss_pred HHHHHHHHHCcCHHHHHH
Confidence 477899999999988764
No 123
>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=34.48 E-value=59 Score=15.54 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=19.4
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
+.|-|...+|+..|++...+.+|-.
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 3477888999999999888776643
No 124
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=34.06 E-value=54 Score=17.71 Aligned_cols=18 Identities=17% Similarity=0.268 Sum_probs=13.6
Q ss_pred CHHHHHHHcCCCHHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~ 69 (91)
|+.+||+..|++...|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~ 20 (84)
T smart00342 3 TLEDLAEALGMSPRHLQR 20 (84)
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 677888888888776543
No 125
>TIGR01813 flavo_cyto_c flavocytochrome c. This model describes a family of redox proteins related to the succinate dehydrogenases and fumarate reductases of E. coli, mitochondria, and other well-characterized systems. A member of this family from Shewanella frigidimarina NCIMB400 is characterized as a water-soluble periplasmic protein with four heme groups, a non-covalently bound FAD, and essentially unidirectional fumarate reductase activity. At least seven distinct members of this family are found in Shewanella oneidensis, a species able to use a wide variety of pathways for respiraton.
Probab=34.03 E-value=40 Score=25.15 Aligned_cols=26 Identities=19% Similarity=0.422 Sum_probs=20.7
Q ss_pred ecCCCCHHHHHHHcCCCHHHH----HHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVF----LAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l----~~~Np 72 (91)
+...||+.++|++.+++.+.| .++|.
T Consensus 317 ~~~adtleeLa~~~g~~~~~l~~tv~~yN~ 346 (439)
T TIGR01813 317 AYKGDSLEELAKQFGIPAAALKKTVKDYNE 346 (439)
T ss_pred EEEeCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 346899999999999987665 57773
No 126
>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=33.96 E-value=53 Score=16.89 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=16.3
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
+.|-|..++|++.|++...+.++
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 56778888888888888777665
No 127
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=33.63 E-value=33 Score=18.63 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=16.6
Q ss_pred CHHHHHHHcCCCHHHHHHhCC
Q 040436 52 TCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~Np 72 (91)
....+++.||++.++|..-..
T Consensus 5 I~~~Va~~~~i~~~~i~s~~R 25 (60)
T smart00760 5 IIEAVAEYFGVKPEDLKSKSR 25 (60)
T ss_pred HHHHHHHHhCCCHHHHhcCCC
Confidence 456789999999999975543
No 128
>PRK08274 tricarballylate dehydrogenase; Validated
Probab=33.56 E-value=46 Score=25.11 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=20.9
Q ss_pred ecCCCCHHHHHHHcCCCHHHHH----HhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFL----AINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~----~~Np 72 (91)
+...||+.++|++.|++.+.|. ++|.
T Consensus 321 ~~~adtleeLA~~~gi~~~~l~~tv~~yN~ 350 (466)
T PRK08274 321 PIQADTLEELAEKLGLDPAAFLRTVAAFNA 350 (466)
T ss_pred ccccCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4578999999999999987654 5664
No 129
>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=32.95 E-value=51 Score=17.59 Aligned_cols=20 Identities=20% Similarity=0.308 Sum_probs=8.6
Q ss_pred CCCHHHHHHHcCCCHHHHHH
Q 040436 50 GDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~ 69 (91)
|-|..++|++.|++...+.+
T Consensus 12 ~lt~~~~a~~~~i~~~~i~~ 31 (64)
T PF12844_consen 12 GLTQKDLAEKLGISRSTISK 31 (64)
T ss_dssp T--HHHHHHHHTS-HHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHH
Confidence 44555555555555444443
No 130
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=32.48 E-value=54 Score=17.19 Aligned_cols=23 Identities=9% Similarity=0.211 Sum_probs=18.8
Q ss_pred EecCCCCHHHHHHHcCCCHHHHH
Q 040436 46 GAQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 46 ~v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
.+..|.+.++||...+++.....
T Consensus 15 l~~~G~s~~eia~~l~is~~tV~ 37 (65)
T COG2771 15 LVAQGKSNKEIARILGISEETVK 37 (65)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHH
Confidence 35679999999999999987643
No 131
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=31.73 E-value=72 Score=21.63 Aligned_cols=28 Identities=18% Similarity=0.299 Sum_probs=23.4
Q ss_pred EecCCCCHHHHHHHcCCCHHHHHHhCCC
Q 040436 46 GAQEGDTCSNVTEEFNLSTDVFLAINPN 73 (91)
Q Consensus 46 ~v~~GdTc~~Ia~~~~i~~~~l~~~Np~ 73 (91)
.-||.-++..||++|+++.-++.+.=|+
T Consensus 23 ~~qPdg~~eamA~~~~v~~~eIv~aLP~ 50 (176)
T COG3721 23 ATQPDGTLEAMAEQYNVTELEIVRALPE 50 (176)
T ss_pred HhCCCCcHHHHHHHhCCCHHHHHHhCch
Confidence 3467779999999999999999887663
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=31.61 E-value=65 Score=20.00 Aligned_cols=23 Identities=22% Similarity=0.346 Sum_probs=19.3
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHH
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
-..|.|..+||+..|++...+.+
T Consensus 30 y~eg~S~~EIAe~lGIS~~TV~r 52 (104)
T PRK00118 30 YLDDYSLGEIAEEFNVSRQAVYD 52 (104)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHH
Confidence 35589999999999999887654
No 133
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=31.50 E-value=52 Score=18.57 Aligned_cols=18 Identities=22% Similarity=0.265 Sum_probs=13.0
Q ss_pred CHHHHHHHcCCCHHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~ 69 (91)
-...+++.||++.++|..
T Consensus 5 Ii~~Va~~~~v~~~~i~s 22 (70)
T PF08299_consen 5 IIEAVAEYFGVSVEDIRS 22 (70)
T ss_dssp HHHHHHHHTT--HHHHHS
T ss_pred HHHHHHHHHCCCHHHHhC
Confidence 356789999999999874
No 134
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=31.12 E-value=55 Score=19.34 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=14.9
Q ss_pred cCCCCHHHHHHHcCCCHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
+.|-|+..||.++|++...+.
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~ 33 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLR 33 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHH
T ss_pred HcCCCHHHHHHHcCCCHHHHH
Confidence 468899999999999987655
No 135
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=31.03 E-value=52 Score=17.40 Aligned_cols=21 Identities=14% Similarity=0.164 Sum_probs=17.0
Q ss_pred cCCCCHHHHHHHcCCCHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
+.|.+...+|..|||+.....
T Consensus 17 R~~~~~~~La~~FgIs~stvs 37 (53)
T PF13613_consen 17 RLNLTFQDLAYRFGISQSTVS 37 (53)
T ss_pred HcCCcHhHHhhheeecHHHHH
Confidence 557889999999999887644
No 136
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=30.61 E-value=25 Score=21.36 Aligned_cols=18 Identities=22% Similarity=0.301 Sum_probs=14.2
Q ss_pred EecCC--CCHHHHHHHcCCC
Q 040436 46 GAQEG--DTCSNVTEEFNLS 63 (91)
Q Consensus 46 ~v~~G--dTc~~Ia~~~~i~ 63 (91)
.+|.| ||.|.|-++||-+
T Consensus 41 fierGR~ETtW~vLR~FgY~ 60 (89)
T PF08356_consen 41 FIERGRHETTWTVLRKFGYD 60 (89)
T ss_pred HHHhCcchHHHHHHHHcCCC
Confidence 34666 7999999999844
No 137
>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=30.38 E-value=82 Score=15.95 Aligned_cols=24 Identities=8% Similarity=0.094 Sum_probs=19.7
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
+.|-|-.++|++.|++...+.+|=
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 457788899999999988887764
No 138
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=30.37 E-value=63 Score=19.19 Aligned_cols=43 Identities=9% Similarity=0.201 Sum_probs=32.5
Q ss_pred EEecCCCCHHHHHHHcCCCHHHHHHhC---CCCCCCCCCCCCEEEE
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDVFLAIN---PNINCDAIFVGQWLCV 87 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~l~~~N---p~v~c~~l~~G~~lcv 87 (91)
|.+-+.|--..+-++|++..++|=+.- |-+..-.+.+||.+.|
T Consensus 15 H~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI 60 (79)
T PRK09570 15 HEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKI 60 (79)
T ss_pred eEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEE
Confidence 677777778899999999999864333 3224457899999988
No 139
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=30.22 E-value=59 Score=18.15 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=14.7
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
|...||+..|++.+++.+.
T Consensus 22 t~eEiA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVREL 40 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHH
Confidence 6789999999999886543
No 140
>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=29.80 E-value=66 Score=17.56 Aligned_cols=20 Identities=20% Similarity=0.126 Sum_probs=17.3
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
+..++|+..|++...|..|-
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye 21 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999998884
No 141
>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=29.70 E-value=45 Score=17.28 Aligned_cols=21 Identities=10% Similarity=0.147 Sum_probs=17.5
Q ss_pred CCCHHHHHHHcCCCHHHHHHh
Q 040436 50 GDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.+....||.+.|++..++..|
T Consensus 27 ~~~~~~la~~~~l~~~qV~~W 47 (59)
T cd00086 27 REEREELAKELGLTERQVKIW 47 (59)
T ss_pred HHHHHHHHHHHCcCHHHHHHH
Confidence 346889999999999998765
No 142
>PF14502 HTH_41: Helix-turn-helix domain
Probab=29.45 E-value=83 Score=16.95 Aligned_cols=17 Identities=29% Similarity=0.401 Sum_probs=14.0
Q ss_pred CHHHHHHHcCCCHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~ 68 (91)
|..+.+++|+++.-.++
T Consensus 8 tI~e~~~~~~vs~GtiQ 24 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQ 24 (48)
T ss_pred CHHHHHHHhCcchhHHH
Confidence 78899999999876544
No 143
>KOG1618 consensus Predicted phosphatase [General function prediction only]
Probab=29.42 E-value=70 Score=24.34 Aligned_cols=35 Identities=14% Similarity=0.252 Sum_probs=28.5
Q ss_pred EEecCCC-CHHHHHHHcC----CCHHHHHHhCCCCC-CCCC
Q 040436 45 YGAQEGD-TCSNVTEEFN----LSTDVFLAINPNIN-CDAI 79 (91)
Q Consensus 45 y~v~~Gd-Tc~~Ia~~~~----i~~~~l~~~Np~v~-c~~l 79 (91)
.++..|+ +--++|+.|| +++|++.+++|.++ |..+
T Consensus 122 ~vLv~G~~~vr~vAegyGFk~Vvt~D~l~k~f~~ldP~t~~ 162 (389)
T KOG1618|consen 122 RVLVVGQGSVREVAEGYGFKNVVTVDELAKYFPLLDPFTDL 162 (389)
T ss_pred eEEEecCCcHHHHhhccCccceeeHHHHHHhCCCcccccch
Confidence 5556666 7899999998 78999999999997 5543
No 144
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=29.25 E-value=54 Score=19.60 Aligned_cols=22 Identities=5% Similarity=0.191 Sum_probs=19.7
Q ss_pred CCCHHHHHHHcCCCHHHHHHhC
Q 040436 50 GDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
.|=...||+..|++..++..+|
T Consensus 69 ~~EirGIA~~~gi~l~~iv~lN 90 (95)
T PF15508_consen 69 AEEIRGIAKAAGIPLGDIVLLN 90 (95)
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 3568899999999999999998
No 145
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=29.19 E-value=82 Score=17.39 Aligned_cols=25 Identities=28% Similarity=0.357 Sum_probs=17.2
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
.+.|-|+.++|++.+|+.+.|..+-
T Consensus 7 ~~~glsl~~va~~t~I~~~~l~aiE 31 (62)
T PF13413_consen 7 EAKGLSLEDVAEETKISVSYLEAIE 31 (62)
T ss_dssp HCTT--HHHHHHHCS--HHHHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4678899999999999998877653
No 146
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=29.09 E-value=63 Score=23.17 Aligned_cols=24 Identities=17% Similarity=0.138 Sum_probs=19.9
Q ss_pred CCCCCceEEecCCCCHHHHHHHcC
Q 040436 38 PPTCDSVYGAQEGDTCSNVTEEFN 61 (91)
Q Consensus 38 ~~~c~~~y~v~~GdTc~~Ia~~~~ 61 (91)
+..++....|+.|||.|.+-++..
T Consensus 108 Gs~hrr~v~vKKGdtI~~FL~~~r 131 (239)
T PF04921_consen 108 GSGHRRTVRVKKGDTIWQFLEKCR 131 (239)
T ss_pred CCCCcceEEEcCCCCHHHHHHHHH
Confidence 455677899999999999988873
No 147
>PTZ00305 NADH:ubiquinone oxidoreductase; Provisional
Probab=29.06 E-value=43 Score=24.79 Aligned_cols=29 Identities=10% Similarity=-0.003 Sum_probs=24.1
Q ss_pred ceEEe-cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 43 SVYGA-QEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 43 ~~y~v-~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
+.+.| .+|.|+.+.|++.||.+..|-...
T Consensus 76 k~VeV~~~G~TILeAAr~~GI~IPtLCy~~ 105 (297)
T PTZ00305 76 RPVEIIPQEENLLEVLEREGIRVPKFCYHP 105 (297)
T ss_pred EEEEecCCCChHHHHHHHcCCCcCccccCC
Confidence 45777 889999999999999998875543
No 148
>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=28.88 E-value=67 Score=19.16 Aligned_cols=25 Identities=8% Similarity=0.118 Sum_probs=21.2
Q ss_pred CceEEecCCCCHHHHHHHcCCCHHH
Q 040436 42 DSVYGAQEGDTCSNVTEEFNLSTDV 66 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~~i~~~~ 66 (91)
...+.+.+|+|+-+.+.+.|+.++-
T Consensus 14 ~~~~~~~~g~tLLda~~~~Gi~i~~ 38 (97)
T TIGR02008 14 EETIECPDDQYILDAAEEAGIDLPY 38 (97)
T ss_pred EEEEEECCCCcHHHHHHHcCCCCCc
Confidence 4678899999999999999987643
No 149
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=28.61 E-value=79 Score=16.01 Aligned_cols=21 Identities=10% Similarity=0.184 Sum_probs=17.5
Q ss_pred CCCHHHHHHHcCCCHHHHHHh
Q 040436 50 GDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
+=|..+|+++-|++...|++.
T Consensus 16 ~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 16 AVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TSSHHHHHHHHTSCHHHHHHH
T ss_pred hCCHHHHHHHHccchhhHHHH
Confidence 447899999999999888764
No 150
>PF05484 LRV_FeS: LRV protein FeS4 cluster; InterPro: IPR008665 This iron sulphur cluster is found at the N terminus of some proteins containing leucine-repeat variant (LRV) repeats (IPR004830 from INTERPRO). These proteins have a two-domain structure, composed of a small N-terminal domain containing a cluster of four Cys residues that houses the 4Fe:4S cluster, and a larger C-terminal domain containing the LRV repeats []. Biochemical studies revealed that the 4Fe:4S cluster is sensitive to oxygen, but does not appear to have reversible redox activity.; PDB: 1LRV_A.
Probab=28.58 E-value=25 Score=19.66 Aligned_cols=26 Identities=27% Similarity=0.692 Sum_probs=17.8
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHhCCCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAINPNI 74 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~Np~v 74 (91)
-++|+.| +.++|.--+|-|.+|||++
T Consensus 28 C~pg~aC--v~dryaRrIdRFF~~NP~l 53 (57)
T PF05484_consen 28 CDPGHAC--VQDRYARRIDRFFRWNPDL 53 (57)
T ss_dssp SBTTTB---SSSS-HHHHHHHHHH-GGG
T ss_pred cCCcchH--HhhhHHHHHHHHHHhChHh
Confidence 4667777 5566777789999999986
No 151
>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=28.30 E-value=57 Score=19.62 Aligned_cols=26 Identities=19% Similarity=0.358 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHcCCCHHHHHHhCCCC
Q 040436 49 EGDTCSNVTEEFNLSTDVFLAINPNI 74 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~~Np~v 74 (91)
.|.|--+|++++|++...+-+.|..+
T Consensus 48 ~g~syreIa~~tgvS~aTItRvsr~L 73 (87)
T PF01371_consen 48 EGKSYREIAEETGVSIATITRVSRCL 73 (87)
T ss_dssp TTSSHHHHHHHHTSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 79999999999999999998877543
No 152
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.23 E-value=58 Score=21.49 Aligned_cols=19 Identities=26% Similarity=0.359 Sum_probs=16.6
Q ss_pred CCCHHHHHHHcCCCHHHHH
Q 040436 50 GDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~ 68 (91)
-+++.+||++.|++..|+.
T Consensus 90 ~~~l~~la~~~Gld~~El~ 108 (143)
T COG3753 90 TDTLSQLAQKTGLDEQELL 108 (143)
T ss_pred hhHHHHHHHHhCCCHHHHH
Confidence 5789999999999998755
No 153
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=27.79 E-value=43 Score=19.20 Aligned_cols=37 Identities=16% Similarity=0.395 Sum_probs=24.7
Q ss_pred CHHHHHHHcCCCHHHHHHhC-CCCCCC-CCCCCCEEEEc
Q 040436 52 TCSNVTEEFNLSTDVFLAIN-PNINCD-AIFVGQWLCVA 88 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N-p~v~c~-~l~~G~~lcvp 88 (91)
|..+-|+-+||....|.++= ..-+|+ -++.|.++.|-
T Consensus 15 Ti~EAa~Y~gIG~~klr~l~~~~~~~~f~~~~G~r~lIk 53 (67)
T PF09035_consen 15 TIEEAAEYFGIGEKKLRELAEENPDCPFVLWIGNRRLIK 53 (67)
T ss_dssp EHHHHHHHT-S-HHHHHHHHHH-TT-SSEEEETTEEEEE
T ss_pred CHHHHHHHhCccHHHHHHHHHhCCCCCEEEEECCEEEEe
Confidence 67888999999988766654 223676 68999998874
No 154
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.51 E-value=61 Score=24.24 Aligned_cols=47 Identities=15% Similarity=-0.029 Sum_probs=35.5
Q ss_pred ceEEecCCCCHHHHHHHcCCCHH---HHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTD---VFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~---~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
..|+|+.|||+--++..|-...+ ..+..|.--++..+.+|..+-||-
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~ 55 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPL 55 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCC
Confidence 56999999999999999854443 466677433677888888877764
No 155
>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated
Probab=27.46 E-value=41 Score=23.40 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=21.8
Q ss_pred eEEecCCCCHHHHHHHcCCCHHHHH
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
.+.+.+|+|+.+.+.+.|+.+..+-
T Consensus 12 ~~~~~~g~til~a~~~~gi~ip~~C 36 (234)
T PRK07569 12 LVSAREGETLLEAAREAGIPIPTLC 36 (234)
T ss_pred EEEeCCCCHHHHHHHHcCCCCCcCc
Confidence 4999999999999999998876643
No 156
>cd07453 CRD_crescent Cysteine-rich domain of the crescent protein. The cysteine-rich domain (CRD) is an essential part of the crescent protein, a member of the secreted frizzled-related protein (SFRP) family, which regulates convergent extension movements (CEMs) during gastrulation and neurulation. Xenopus laevis crescent efficiently forms inhibitory complexes with Wnt5a and Wnt11, but this effect is cancelled in the presence of another member of the SFRP family, Frzb1. A potential role for Crescent in head formation is to regulate a non-canonical Wnt pathway positively in the adjacent posterior mesoderm, and negatively in the overlying anterior neuroectoderm.
Probab=27.21 E-value=19 Score=23.52 Aligned_cols=45 Identities=18% Similarity=0.403 Sum_probs=31.7
Q ss_pred CCCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 37 SPPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 37 ~~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
+-..|... ..|+ +.|+.+.++||.++. ..++|+.+...+.+|++.
T Consensus 70 ~i~PCRslCe~vr--~~C~~~m~~~g~~WP------~~l~C~~fP~~~~~Ci~p 115 (135)
T cd07453 70 PIYPCRSLCEAVR--SSCAPLMACYGYPWP------EILHCDKFPVDHDLCISP 115 (135)
T ss_pred CCCccHHHHHHHH--HHHHHHHHHhCCCCC------CCCChhhCCCCCCcccCC
Confidence 45557654 4443 789999999997654 346888887777788865
No 157
>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=27.20 E-value=81 Score=21.33 Aligned_cols=20 Identities=15% Similarity=0.476 Sum_probs=17.0
Q ss_pred ecCCCCHHHHHHHcCCCHHH
Q 040436 47 AQEGDTCSNVTEEFNLSTDV 66 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~ 66 (91)
.+.|.+...+|++|||...-
T Consensus 30 ~~~~~sv~~vS~~ygi~~~R 49 (172)
T PF12298_consen 30 MQDGKSVREVSQKYGIKIQR 49 (172)
T ss_pred HhCCCCHHHHHHHhCCCHHH
Confidence 36788999999999999754
No 158
>PRK14785 lipoprotein signal peptidase; Provisional
Probab=26.81 E-value=55 Score=21.94 Aligned_cols=13 Identities=15% Similarity=0.107 Sum_probs=9.3
Q ss_pred CCCcchhhHHHHH
Q 040436 1 MASNKTSLFRNLA 13 (91)
Q Consensus 1 ~~~~~~~~l~~~~ 13 (91)
|+.|+||.+..+.
T Consensus 7 ~~~~~~~~~~~~~ 19 (171)
T PRK14785 7 MVANGRRALNWYL 19 (171)
T ss_pred hhhccccHHHHHH
Confidence 7788988776443
No 159
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=26.78 E-value=53 Score=16.90 Aligned_cols=21 Identities=10% Similarity=0.115 Sum_probs=17.5
Q ss_pred CCCHHHHHHHcCCCHHHHHHh
Q 040436 50 GDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.+....||...|++..++..|
T Consensus 27 ~~~~~~la~~~~l~~~qV~~W 47 (56)
T smart00389 27 REEREELAAKLGLSERQVKVW 47 (56)
T ss_pred HHHHHHHHHHHCcCHHHHHHh
Confidence 456889999999999988765
No 160
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=26.54 E-value=1e+02 Score=15.78 Aligned_cols=19 Identities=37% Similarity=0.595 Sum_probs=8.4
Q ss_pred cchhhHHHHHHHHHHHHHH
Q 040436 4 NKTSLFRNLALVLAVLLIV 22 (91)
Q Consensus 4 ~~~~~l~~~~~l~~l~l~~ 22 (91)
||.+...-+.++..+.+++
T Consensus 15 NRTSLy~GlLlifvl~vLF 33 (39)
T PRK00753 15 NRTSLYLGLLLVFVLGILF 33 (39)
T ss_pred chhhHHHHHHHHHHHHHHH
Confidence 3444444444444444444
No 161
>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=26.41 E-value=88 Score=19.28 Aligned_cols=22 Identities=23% Similarity=0.365 Sum_probs=18.1
Q ss_pred cCCCCHHHHHHHcCCCHHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
-.|-+..+||+.+|++...+..
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~ 148 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEY 148 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 4688999999999999887653
No 162
>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=26.31 E-value=80 Score=16.32 Aligned_cols=16 Identities=25% Similarity=0.428 Sum_probs=12.6
Q ss_pred CHHHHHHHcCCCHHHH
Q 040436 52 TCSNVTEEFNLSTDVF 67 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l 67 (91)
|..+||++++++...+
T Consensus 17 t~~eLa~~l~vS~rTi 32 (55)
T PF08279_consen 17 TAKELAEELGVSRRTI 32 (55)
T ss_dssp EHHHHHHHCTS-HHHH
T ss_pred CHHHHHHHhCCCHHHH
Confidence 7899999999997654
No 163
>PRK12834 putative FAD-binding dehydrogenase; Reviewed
Probab=26.24 E-value=53 Score=25.63 Aligned_cols=24 Identities=13% Similarity=0.045 Sum_probs=19.3
Q ss_pred ecCCCCHHHHHHHcC-------CCHHHHHHh
Q 040436 47 AQEGDTCSNVTEEFN-------LSTDVFLAI 70 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~-------i~~~~l~~~ 70 (91)
+...||+.++|++.+ ++.+.|.+.
T Consensus 393 ~~kAdTleELA~k~g~~~~~~~id~~~L~~t 423 (549)
T PRK12834 393 FVVADDLEELVAGMNALTGEPLLDYAHLRRQ 423 (549)
T ss_pred EEEeCCHHHHHHHhcccccccCCCHHHHHHH
Confidence 446899999999998 888776653
No 164
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=25.97 E-value=68 Score=15.48 Aligned_cols=14 Identities=21% Similarity=0.169 Sum_probs=8.5
Q ss_pred HHHHcCCCHHHHHH
Q 040436 56 VTEEFNLSTDVFLA 69 (91)
Q Consensus 56 Ia~~~~i~~~~l~~ 69 (91)
=|.+-|++.++|.+
T Consensus 11 eA~~~Gls~eeir~ 24 (30)
T PF08671_consen 11 EAKESGLSKEEIRE 24 (30)
T ss_dssp HHHHTT--HHHHHH
T ss_pred HHHHcCCCHHHHHH
Confidence 36677999888764
No 165
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=25.51 E-value=88 Score=18.04 Aligned_cols=20 Identities=5% Similarity=0.212 Sum_probs=17.1
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
.|..||+.++.+++++...+
T Consensus 45 La~kia~~f~~~iedIF~~~ 64 (68)
T COG1476 45 LALKIARVFGKTIEDIFQLE 64 (68)
T ss_pred HHHHHHHHhCCCHHHHHhhh
Confidence 57899999999999988654
No 166
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=25.29 E-value=88 Score=20.70 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=18.1
Q ss_pred cCCCCHHHHHHHcCCCHHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
-.|-|..+||+..|++.....+
T Consensus 149 ~~Gls~~EIA~~lgiS~~tV~r 170 (185)
T PF07638_consen 149 FEGLSVEEIAERLGISERTVRR 170 (185)
T ss_pred HCCCCHHHHHHHHCcCHHHHHH
Confidence 3789999999999999877653
No 167
>COG3019 Predicted metal-binding protein [General function prediction only]
Probab=25.28 E-value=1.6e+02 Score=19.66 Aligned_cols=22 Identities=9% Similarity=0.117 Sum_probs=16.2
Q ss_pred eEEecCCCCHHHHHHHcCCCHH
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTD 65 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~ 65 (91)
...+..-|.+..+-+++||+.+
T Consensus 52 ~Vk~~~~~d~~alK~~~gIp~e 73 (149)
T COG3019 52 EVKVVETDDFLALKRRLGIPYE 73 (149)
T ss_pred EEEEeecCcHHHHHHhcCCChh
Confidence 4566667788889888887654
No 168
>cd00207 fer2 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin.
Probab=25.14 E-value=87 Score=17.39 Aligned_cols=24 Identities=17% Similarity=0.196 Sum_probs=20.2
Q ss_pred CceEEecCCCCHHHHHHHcCCCHH
Q 040436 42 DSVYGAQEGDTCSNVTEEFNLSTD 65 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~~i~~~ 65 (91)
...+.+++|+|+-+.+.+.|+.+.
T Consensus 9 ~~~~~~~~g~~ll~al~~~g~~~~ 32 (84)
T cd00207 9 GVEVEVPEGETLLDAAREAGIDIP 32 (84)
T ss_pred CEEEEECCCCcHHHHHHHcCCCcc
Confidence 356889999999999999998854
No 169
>PRK06437 hypothetical protein; Provisional
Probab=24.95 E-value=58 Score=18.25 Aligned_cols=45 Identities=7% Similarity=0.134 Sum_probs=31.3
Q ss_pred ceEEecCCCCHHHHHHHcCCCHHHH-HHhCCCC--CCCCCCCCCEEEE
Q 040436 43 SVYGAQEGDTCSNVTEEFNLSTDVF-LAINPNI--NCDAIFVGQWLCV 87 (91)
Q Consensus 43 ~~y~v~~GdTc~~Ia~~~~i~~~~l-~~~Np~v--~c~~l~~G~~lcv 87 (91)
+.+.++.+-|..++.++.+++.+.+ ...|..+ .-..|..|+++-+
T Consensus 13 ~~~~i~~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~~~~~L~dgD~Vei 60 (67)
T PRK06437 13 KTIEIDHELTVNDIIKDLGLDEEEYVVIVNGSPVLEDHNVKKEDDVLI 60 (67)
T ss_pred eEEEcCCCCcHHHHHHHcCCCCccEEEEECCEECCCceEcCCCCEEEE
Confidence 4577888889999999999876542 2356544 2335778887755
No 170
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=24.94 E-value=84 Score=16.83 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=15.8
Q ss_pred cCCCCHHHHHHHcCCCHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
..+-|+.+||+..|++...+.
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s 42 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVS 42 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHH
Confidence 346689999999999987654
No 171
>COG1804 CaiB Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]
Probab=24.50 E-value=44 Score=25.57 Aligned_cols=22 Identities=36% Similarity=0.684 Sum_probs=17.7
Q ss_pred HHHHcCCCHHHHHHhCCCC-CCC
Q 040436 56 VTEEFNLSTDVFLAINPNI-NCD 77 (91)
Q Consensus 56 Ia~~~~i~~~~l~~~Np~v-~c~ 77 (91)
..+++|++.+.+.+.||.+ .|.
T Consensus 102 ~l~rlGl~ye~L~~~NP~LIy~s 124 (396)
T COG1804 102 VLERLGLGYEALRAINPRLIYCS 124 (396)
T ss_pred HHHHhCCCHHHHHhhCCCeEEEE
Confidence 3456899999999999988 443
No 172
>PHA00542 putative Cro-like protein
Probab=24.12 E-value=1e+02 Score=17.86 Aligned_cols=24 Identities=13% Similarity=0.206 Sum_probs=20.8
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHHh
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.+.|-|-.++|+..|++...+.+|
T Consensus 28 ~~~glTq~elA~~lgIs~~tIsr~ 51 (82)
T PHA00542 28 IRAGWSQEQIADATDVSQPTICRI 51 (82)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHH
Confidence 356789999999999999998877
No 173
>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=24.07 E-value=93 Score=15.80 Aligned_cols=19 Identities=21% Similarity=0.321 Sum_probs=13.7
Q ss_pred CCCHHHHHHHcCCCHHHHH
Q 040436 50 GDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~ 68 (91)
--+..+||++.|++..+..
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 3478899999999988754
No 174
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=24.03 E-value=99 Score=19.52 Aligned_cols=21 Identities=14% Similarity=0.150 Sum_probs=17.6
Q ss_pred cCCCCHHHHHHHcCCCHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
-.|-+..+||+..|++...+.
T Consensus 142 ~~~~s~~eIA~~lgis~~tV~ 162 (182)
T PRK09652 142 IEGLSYEEIAEIMGCPIGTVR 162 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHH
Confidence 468899999999999988764
No 175
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=23.73 E-value=1.1e+02 Score=21.52 Aligned_cols=16 Identities=31% Similarity=0.482 Sum_probs=9.2
Q ss_pred hhHHHHHHHHHHHHHH
Q 040436 7 SLFRNLALVLAVLLIV 22 (91)
Q Consensus 7 ~~l~~~~~l~~l~l~~ 22 (91)
..+|++++.+.++|++
T Consensus 13 N~iLNiaI~IV~lLIi 28 (217)
T PF07423_consen 13 NKILNIAIGIVSLLII 28 (217)
T ss_pred hhhHHHHHHHHHHHHH
Confidence 3477776665554444
No 176
>TIGR02007 fdx_isc ferredoxin, 2Fe-2S type, ISC system. This family consists of proteobacterial ferredoxins associated with and essential to the ISC system of 2Fe-2S cluster assembly. This family is closely related to (but excludes) eukaryotic (mitochondrial) adrenodoxins, which are ferredoxins involved in electron transfer to P450 cytochromes.
Probab=23.63 E-value=89 Score=19.11 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=20.4
Q ss_pred CceEEecCCCCHHHHHHHcCCCHH
Q 040436 42 DSVYGAQEGDTCSNVTEEFNLSTD 65 (91)
Q Consensus 42 ~~~y~v~~GdTc~~Ia~~~~i~~~ 65 (91)
...+.+.+|+|+-+.+.+.|+.+.
T Consensus 15 ~~~~~~~~g~tLL~a~~~~gi~i~ 38 (110)
T TIGR02007 15 GAVVEAKPGETILDVALDNGIEIE 38 (110)
T ss_pred CeEEEECCCChHHHHHHHcCCCcc
Confidence 346888999999999999998764
No 177
>cd07443 CRD_SFRP1 Cysteine-rich domain of the secreted frizzled-related protein 1 (SFRP1), a regulator of Wnt activity. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related protein 1 (SFRP1), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRDs domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. SFRP1 is expressed in many tissues and is involved in the regulation of Wnt signaling in osteoblasts, leading to enhanced trabecular bone formation in adults; it has also been shown to control the gro
Probab=23.63 E-value=30 Score=22.20 Aligned_cols=44 Identities=23% Similarity=0.444 Sum_probs=28.4
Q ss_pred CCCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 37 SPPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 37 ~~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
+-..|..+ -.| -+.|+.+.++||..+ -..++|+.+..++ .||+.
T Consensus 74 ~i~PCRslCe~v--r~~C~~~m~~~g~~W------P~~L~C~~fP~~~-~ci~~ 118 (124)
T cd07443 74 PVYPCRWLCEAV--RDSCEPVMQFFGFYW------PEMLKCDKFPEGE-VCIAM 118 (124)
T ss_pred CCCCCHHHHHHH--HHHHHHHHHHhCCCC------CCCCCcccCCCCC-CccCC
Confidence 44556654 333 267888888888654 3346899876654 68874
No 178
>PF02419 PsbL: PsbL protein; InterPro: IPR003372 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbL found in PSII. PsbL is located in a gene cluster with PsbE, PsbF and PsbJ (PsbEFJL). Both PsbL and PsbJ (IPR002682 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbL prevent the formation of both PSII core dimers and PSII-light harvesting complex []. In addition, both PsbL and PsbJ are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_L 3A0B_l 3ARC_l 1S5L_l 2AXT_l 3BZ2_L 4FBY_L 3PRQ_L 3PRR_L 3KZI_L ....
Probab=23.61 E-value=1.2e+02 Score=15.45 Aligned_cols=20 Identities=30% Similarity=0.572 Sum_probs=9.1
Q ss_pred CcchhhHHHHHHHHHHHHHH
Q 040436 3 SNKTSLFRNLALVLAVLLIV 22 (91)
Q Consensus 3 ~~~~~~l~~~~~l~~l~l~~ 22 (91)
.|+.+...-+.++..+.+++
T Consensus 12 LNRTSLY~GLllifvl~vLF 31 (37)
T PF02419_consen 12 LNRTSLYWGLLLIFVLAVLF 31 (37)
T ss_dssp --CCHHHHHHHHHHHHHHHH
T ss_pred hhHHhHHHHHHHHHHHHHHh
Confidence 34555544444444454444
No 179
>PTZ00306 NADH-dependent fumarate reductase; Provisional
Probab=23.41 E-value=74 Score=27.53 Aligned_cols=26 Identities=8% Similarity=0.046 Sum_probs=21.2
Q ss_pred ecCCCCHHHHHHHcCCCHHH----HHHhCC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV----FLAINP 72 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~----l~~~Np 72 (91)
+..+||+.++|++.|++.+. +.++|.
T Consensus 765 ~~kADTleELA~~~gid~~~L~aTV~rYN~ 794 (1167)
T PTZ00306 765 FQRVDDVKGLAKLIGCPVENLHRTLETYER 794 (1167)
T ss_pred EEEeCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45689999999999999876 456774
No 180
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=23.39 E-value=61 Score=21.73 Aligned_cols=19 Identities=32% Similarity=0.553 Sum_probs=15.0
Q ss_pred cCC-CCHHHHHHHcCCCHHH
Q 040436 48 QEG-DTCSNVTEEFNLSTDV 66 (91)
Q Consensus 48 ~~G-dTc~~Ia~~~~i~~~~ 66 (91)
|.| .||.+||.+||++...
T Consensus 3 q~Ga~T~eELA~~FGvttRk 22 (155)
T PF07789_consen 3 QEGAKTAEELAGKFGVTTRK 22 (155)
T ss_pred ccCcccHHHHHHHhCcchhh
Confidence 344 3999999999999654
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=23.17 E-value=98 Score=21.01 Aligned_cols=23 Identities=13% Similarity=0.115 Sum_probs=19.0
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
..|.|..+||+++|++...+.+.
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 36889999999999998877654
No 182
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=23.14 E-value=57 Score=21.95 Aligned_cols=23 Identities=26% Similarity=0.248 Sum_probs=20.0
Q ss_pred eEEecCCCCHHHHHHHcCCCHHH
Q 040436 44 VYGAQEGDTCSNVTEEFNLSTDV 66 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~~i~~~~ 66 (91)
.+.++.|||+-++|.++|+..+-
T Consensus 57 ~i~g~vGdtlLd~ah~n~idleG 79 (159)
T KOG3309|consen 57 KIKGKVGDTLLDAAHENNLDLEG 79 (159)
T ss_pred EeeeecchHHHHHHHHcCCCccc
Confidence 47888999999999999988764
No 183
>COG4823 AbiF Abortive infection bacteriophage resistance protein [Defense mechanisms]
Probab=23.11 E-value=72 Score=23.45 Aligned_cols=21 Identities=5% Similarity=0.216 Sum_probs=16.8
Q ss_pred CHHHHHHHcCCCHHHHHHhCC
Q 040436 52 TCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~Np 72 (91)
.=..||++||.+.+.|.+|=.
T Consensus 181 nk~kIakkyg~~~~~f~swl~ 201 (299)
T COG4823 181 NKKKIAKKYGYDAEYFQSWLH 201 (299)
T ss_pred hHHHHHHHhCCCHHHHHHHHH
Confidence 345799999999999888743
No 184
>cd07454 CRD_LIN_17 Cysteine-rich domain (CRD) of LIN_17. A cysteine-rich domain (CRD) is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with the
Probab=23.02 E-value=27 Score=22.38 Aligned_cols=46 Identities=24% Similarity=0.441 Sum_probs=31.3
Q ss_pred CCCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcCC
Q 040436 37 SPPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAGS 90 (91)
Q Consensus 37 ~~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~~ 90 (91)
+-..|... ..|+ +.|+.+.++||.++.+ .++|+.+.....+|+...
T Consensus 73 ~i~PCRslCe~vr--~~C~~~m~~fg~~WP~------~l~C~~fP~~~~~C~~p~ 119 (124)
T cd07454 73 AVTSCKSVCEQVK--ADCFSILEEFGIGWPE------PLNCAQFPDPPELCMKPT 119 (124)
T ss_pred cCCCChhHHHHHH--HHHHHHHHHhCCCCCC------CCChhhCCCCCCCCCCcc
Confidence 44567654 3343 7899999999977543 467887776666888653
No 185
>PHA02591 hypothetical protein; Provisional
Probab=22.94 E-value=1.1e+02 Score=18.36 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=16.4
Q ss_pred eEEecCCCCHHHHHHHc---CCCHHHHH
Q 040436 44 VYGAQEGDTCSNVTEEF---NLSTDVFL 68 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~---~i~~~~l~ 68 (91)
.|.|++.|.+-++|.+. |.+.+++-
T Consensus 39 ryfi~~~dd~~~vA~eL~eqGlSqeqIA 66 (83)
T PHA02591 39 RYFVESEDDLISVTHELARKGFTVEKIA 66 (83)
T ss_pred EEEEeccchHHHHHHHHHHcCCCHHHHH
Confidence 47788777777766653 56655554
No 186
>PF01969 DUF111: Protein of unknown function DUF111; InterPro: IPR002822 The proteins in this family have no known function.; PDB: 3C19_A.
Probab=22.88 E-value=43 Score=25.49 Aligned_cols=19 Identities=16% Similarity=0.440 Sum_probs=14.6
Q ss_pred CCHHHHHHHcCCCHHHHHH
Q 040436 51 DTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 51 dTc~~Ia~~~~i~~~~l~~ 69 (91)
|.|..||+++|+++.++++
T Consensus 364 ed~k~iA~~~g~pl~eV~r 382 (382)
T PF01969_consen 364 EDCKRIAEEHGIPLREVYR 382 (382)
T ss_dssp HHHHHHHHHH-S-HHHHH-
T ss_pred HHHHHHHHHHCcCHHHHhC
Confidence 6899999999999999875
No 187
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.80 E-value=1e+02 Score=18.12 Aligned_cols=20 Identities=15% Similarity=0.152 Sum_probs=16.8
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
+..++|+.+|++.+.+..|-
T Consensus 2 ~~~eva~~~gi~~~tlr~~~ 21 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYE 21 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999988773
No 188
>PF00879 Defensin_propep: Defensin propeptide The pattern for this Prosite entry doesn't match the propeptide.; InterPro: IPR002366 Defensins are 2-6 kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses [], containing three pairs of intramolecular disulphide bonds []. On the basis of their size and pattern of disulphide bonding, mammalian defensins are classified into alpha, beta and theta categories. Alpha-defensins, which have been identified in humans, monkeys and several rodent species, are particularly abundant in neutrophils, certain macrophage populations and Paneth cells of the small intestine. Every mammalian species explored thus far has beta-defensins. In cows, as many as 13 beta-defensins exist in neutrophils. However, in other species, beta-defensins are more often produced by epithelial cells lining various organs (e.g. the epidermis, bronchial tree and genitourinary tract). Theta-defensins are cyclic and have so far only been identified in primate phagocytes. Defensins are produced constitutively and/or in response to microbial products or proinflammatory cytokines. Some defensins are also called corticostatins (CS) because they inhibit corticotropin-stimulated corticosteroid production. The mechanism(s) by which microorganisms are killed and/or inactivated by defensins is not understood completely. However, it is generally believed that killing is a consequence of disruption of the microbial membrane. The polar topology of defensins, with spatially separated charged and hydrophobic regions, allows them to insert themselves into the phospholipid membranes so that their hydrophobic regions are buried within the lipid membrane interior and their charged (mostly cationic) regions interact with anionic phospholipid head groups and water. Subsequently, some defensins can aggregate to form `channel-like' pores; others might bind to and cover the microbial membrane in a `carpet-like' manner. The net outcome is the disruption of membrane integrity and function, which ultimately leads to the lysis of microorganisms. Some defensins are synthesized as propeptides which may be relevant to this process - in neutrophils only the mature peptides have been identified but in Paneth cells, the propeptide is stored in vesicles [] and appears to be cleaved by trypsin on activation. ; GO: 0006952 defense response
Probab=22.76 E-value=1.3e+02 Score=16.42 Aligned_cols=21 Identities=33% Similarity=0.493 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHhhhccC
Q 040436 11 NLALVLAVLLIVSMAESRTFA 31 (91)
Q Consensus 11 ~~~~l~~l~l~~~~~~~~~~~ 31 (91)
.+.+|.+++|+..-+.+...+
T Consensus 3 TL~LLaAlLLlAlqaQAepl~ 23 (52)
T PF00879_consen 3 TLALLAALLLLALQAQAEPLQ 23 (52)
T ss_pred HHHHHHHHHHHHHHHhccccc
Confidence 345566666666777665544
No 189
>smart00063 FRI Frizzled. Drosophila melanogaster frizzled mediates signalling that polarises a precursor cell along the anteroposterior axis. Homologues of the N-terminal region of frizzled exist either as transmembrane or secreted molecules. Frizzled homologues are reported to be receptors for the Wnt growth factors. (Not yet in MEDLINE: the FRI domain occurs in several receptor tyrosine kinases [Xu, Y.K. and Nusse, Curr. Biol. 8 R405-R406 (1998); Masiakowski, P. and Yanopoulos, G.D., Curr. Biol. 8, R407 (1998)].
Probab=22.73 E-value=28 Score=21.72 Aligned_cols=43 Identities=26% Similarity=0.475 Sum_probs=27.3
Q ss_pred CCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEc
Q 040436 38 PPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVA 88 (91)
Q Consensus 38 ~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp 88 (91)
-..|..+ ..| -+.|+.+.+++|..+.+ .++|+.+.....+|+.
T Consensus 69 ~~PCRs~Ce~v--r~~C~~~~~~~g~~WP~------~l~C~~fP~~~~~C~~ 112 (113)
T smart00063 69 ILPCRSLCEAA--REGCEPLMEKFGFPWPE------FLRCDRFPVQEELCMD 112 (113)
T ss_pred CCcCHHHHHHH--HHHHHHHHHHhCCCCCC------cCCcccCCCCCCCCCC
Confidence 4556654 333 36788888888876543 3578876655456664
No 190
>cd07442 CRD_SFRP4 Cysteine-rich domain of the secreted frizzled-related protein 4 (SFRP4), a Wnt antagonist. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related Protein 4 (SFRP4), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRDs domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs.
Probab=22.68 E-value=27 Score=22.54 Aligned_cols=46 Identities=26% Similarity=0.509 Sum_probs=30.4
Q ss_pred CCCCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCC-CCEEEEcC
Q 040436 36 TSPPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFV-GQWLCVAG 89 (91)
Q Consensus 36 ~~~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~-G~~lcvp~ 89 (91)
.+-..|... -.| -+.|+.+-++||.++. ..++|+.+.. ++.+|++.
T Consensus 73 ~~i~PCRslCe~v--r~~C~~~m~~fg~~WP------~~L~C~~fP~~~~~~Ci~p 120 (127)
T cd07442 73 DPIKPCRSVCQRA--RDGCEPIMRRYNHSWP------ESLACDDLPVYDRGVCISP 120 (127)
T ss_pred CcCCccHHHHHHH--HHHHHHHHHHhCCCCC------CcCCcccCCCCCCCcccCH
Confidence 345567643 333 3679999999997654 3468988766 56678754
No 191
>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=22.62 E-value=1e+02 Score=18.01 Aligned_cols=20 Identities=10% Similarity=0.009 Sum_probs=17.2
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
|..++|+..|++...+..|-
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye 22 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYE 22 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999988775
No 192
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=22.49 E-value=1.3e+02 Score=16.48 Aligned_cols=20 Identities=20% Similarity=0.245 Sum_probs=17.3
Q ss_pred CCCHHHHHHHcCCCHHHHHH
Q 040436 50 GDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~ 69 (91)
+.|+.+.+++.|++++++.+
T Consensus 31 ~~~L~eA~~~~~ld~~~vl~ 50 (56)
T PF04405_consen 31 NRSLEEACEEKGLDPEEVLE 50 (56)
T ss_pred CchHHHHHHHcCCCHHHHHH
Confidence 57999999999999998653
No 193
>cd07452 CRD_sizzled Cysteine-rich domain of the sizzled protein. The cysteine-rich domain (CRD) is an essential part of the sizzled protein, which regulates bone morphogenetic protein (Bmp) signaling by stabilizing chordin, and plays a critical role in the patterning of vertebrate and invertebrate embryos. Sizzled also functions in the ventral region as a Wnt inhibitor and modulates canonical Wnt signaling. Sizzled proteins belong to the secreted frizzled-related protein family (SFRP), and have be identified in the genomes of birds, fishes and frogs, but not mammals.
Probab=22.44 E-value=35 Score=22.43 Aligned_cols=44 Identities=25% Similarity=0.479 Sum_probs=29.3
Q ss_pred CCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 38 PPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 38 ~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
-..|..+ -.| -+.|+.+.+++|..+.+ .++|+.+...+.+|+..
T Consensus 77 i~PCRslCe~v--r~~C~~~m~~fg~~WP~------~L~C~~fP~~~~~C~~~ 121 (141)
T cd07452 77 IQPCRSMCVAV--RDSCAPVLACHGHSWPE------SLDCDRFPAGEDMCLAS 121 (141)
T ss_pred CcCCHHHHHHH--HHHHHHHHHHcCCCCCC------CCCcccCCCCCCccCCC
Confidence 4556654 333 26788888888876543 36899887766688864
No 194
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=22.43 E-value=72 Score=21.91 Aligned_cols=28 Identities=21% Similarity=0.367 Sum_probs=22.0
Q ss_pred EEecCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
|--+.|..+..+|+..|++.+++.+.=-
T Consensus 94 Y~~~~g~DL~~vA~~~gls~~evi~~H~ 121 (202)
T PF02682_consen 94 YDGEFGPDLEEVAEHNGLSVEEVIRLHS 121 (202)
T ss_dssp ESTTTHTTHHHHHHHHTS-HHHHHHHHH
T ss_pred ECCCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 4445588999999999999999987653
No 195
>cd07444 CRD_SFRP5 Cysteine-rich domain of the secreted frizzled-related protein 5 (SFRP5), a regulator of Wnt activity. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related Protein 5 (SFRP5), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRD domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs.
Probab=22.42 E-value=28 Score=22.42 Aligned_cols=45 Identities=22% Similarity=0.447 Sum_probs=31.0
Q ss_pred CCCCCCce-EEecCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCEEEEcC
Q 040436 37 SPPTCDSV-YGAQEGDTCSNVTEEFNLSTDVFLAINPNINCDAIFVGQWLCVAG 89 (91)
Q Consensus 37 ~~~~c~~~-y~v~~GdTc~~Ia~~~~i~~~~l~~~Np~v~c~~l~~G~~lcvp~ 89 (91)
+-..|..+ -.| -+.|+.+-++||..+. ..++|+.+.....+|++.
T Consensus 74 ~i~PCRslCe~v--r~~C~~~m~~~g~~WP------~~l~C~~fP~~~~~C~~~ 119 (127)
T cd07444 74 PIYPCRSLCEAV--RDSCAPVMESYGFPWP------EMLHCHKFPLDNDLCIAV 119 (127)
T ss_pred CCCCcHHHHHHH--HHHHHHHHHHcCCCCC------CCCChhhCCCCCCccccc
Confidence 45667654 333 3789999999997654 346888877666688864
No 196
>COG3822 ABC-type sugar transport system, auxiliary component [General function prediction only]
Probab=22.42 E-value=46 Score=23.36 Aligned_cols=12 Identities=8% Similarity=0.180 Sum_probs=10.2
Q ss_pred CCCCCEEEEcCC
Q 040436 79 IFVGQWLCVAGS 90 (91)
Q Consensus 79 l~~G~~lcvp~~ 90 (91)
|.||+.||+|+.
T Consensus 157 L~PGesitL~Pg 168 (225)
T COG3822 157 LSPGESITLPPG 168 (225)
T ss_pred ECCCCcEecCCC
Confidence 889999999763
No 197
>PRK04217 hypothetical protein; Provisional
Probab=22.09 E-value=1.2e+02 Score=18.97 Aligned_cols=22 Identities=18% Similarity=0.169 Sum_probs=18.4
Q ss_pred cCCCCHHHHHHHcCCCHHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
..|-|..+||+.+|++...++.
T Consensus 56 ~eGlS~~EIAk~LGIS~sTV~r 77 (110)
T PRK04217 56 YEGLTQEEAGKRMGVSRGTVWR 77 (110)
T ss_pred HcCCCHHHHHHHHCcCHHHHHH
Confidence 3677999999999999887654
No 198
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=22.02 E-value=1.3e+02 Score=15.25 Aligned_cols=17 Identities=6% Similarity=0.147 Sum_probs=14.0
Q ss_pred CHHHHHHHcCCCHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~ 68 (91)
|-.++|+.++++...+.
T Consensus 22 s~~~la~~~~vs~~tv~ 38 (60)
T smart00345 22 SERELAAQLGVSRTTVR 38 (60)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 78899999999976544
No 199
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=21.95 E-value=87 Score=22.90 Aligned_cols=23 Identities=13% Similarity=0.289 Sum_probs=19.9
Q ss_pred CCCHHHHHHHcCCCHHHHHHhCC
Q 040436 50 GDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 50 GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
|--+-+||.+||+++.++..|-.
T Consensus 19 gmk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHH
Confidence 45678999999999999999875
No 200
>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=21.93 E-value=1.2e+02 Score=17.80 Aligned_cols=18 Identities=17% Similarity=0.383 Sum_probs=14.9
Q ss_pred CCHHHHHHHcCCCHHHHH
Q 040436 51 DTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 51 dTc~~Ia~~~~i~~~~l~ 68 (91)
-++..|..+||++..+..
T Consensus 14 tpFeaI~~~fGL~E~eVi 31 (72)
T TIGR03643 14 TPFEAIEQQFGLSEKEVI 31 (72)
T ss_pred CCHHHHHHHHCCCHHHHH
Confidence 368999999999988744
No 201
>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=21.91 E-value=1e+02 Score=16.49 Aligned_cols=17 Identities=24% Similarity=0.378 Sum_probs=13.8
Q ss_pred CHHHHHHHcCCCHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~ 68 (91)
+..++|+.+|++...+.
T Consensus 16 s~~ela~~~~VS~~TiR 32 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIR 32 (57)
T ss_pred EHHHHHHHHCcCHHHHH
Confidence 67899999999987543
No 202
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.83 E-value=86 Score=20.30 Aligned_cols=28 Identities=11% Similarity=0.182 Sum_probs=23.7
Q ss_pred EEecCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
|.=.+|-|+..||.+.+++..+.++|+-
T Consensus 94 y~~r~~~TW~~IA~~l~i~erta~r~~~ 121 (130)
T PF05263_consen 94 YDRRSRRTWYQIAQKLHISERTARRWRD 121 (130)
T ss_pred HcccccchHHHHHHHhCccHHHHHHHHH
Confidence 5555789999999999999998888764
No 203
>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=21.77 E-value=1e+02 Score=17.22 Aligned_cols=19 Identities=16% Similarity=0.146 Sum_probs=14.5
Q ss_pred HHHHHHHcCCCHHHHHHhC
Q 040436 53 CSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 53 c~~Ia~~~~i~~~~l~~~N 71 (91)
.-+-|++|||+...+.+|=
T Consensus 28 ~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 28 QRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHhCccHHHHHHHH
Confidence 3467999999999888874
No 204
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=21.66 E-value=1.1e+02 Score=18.35 Aligned_cols=19 Identities=11% Similarity=0.102 Sum_probs=16.5
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
+..++|+..|++.+.|..|
T Consensus 3 ~i~eva~~~gVs~~tLR~y 21 (98)
T cd01279 3 PISVAAELLGIHPQTLRVY 21 (98)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5678999999999998776
No 205
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=21.43 E-value=1.3e+02 Score=18.10 Aligned_cols=22 Identities=27% Similarity=0.424 Sum_probs=19.0
Q ss_pred CCCCHHHHHHHcCCCHHHHHHh
Q 040436 49 EGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 49 ~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
.+.+.+.|+++.+++...++++
T Consensus 70 ~~~~~~~I~~~l~~S~~t~yr~ 91 (100)
T PF07374_consen 70 NKLTWEQIAEELNISRRTYYRI 91 (100)
T ss_pred cCCCHHHHHHHHCCCHHHHHHH
Confidence 4789999999999999887765
No 206
>CHL00038 psbL photosystem II protein L
Probab=21.41 E-value=1.3e+02 Score=15.29 Aligned_cols=19 Identities=32% Similarity=0.639 Sum_probs=8.6
Q ss_pred cchhhHHHHHHHHHHHHHH
Q 040436 4 NKTSLFRNLALVLAVLLIV 22 (91)
Q Consensus 4 ~~~~~l~~~~~l~~l~l~~ 22 (91)
||.+...-+.++..+.+++
T Consensus 14 NRTSLy~GLLlifvl~vlf 32 (38)
T CHL00038 14 NRTSLYWGLLLIFVLAVLF 32 (38)
T ss_pred hhhhHHHHHHHHHHHHHHH
Confidence 4555444444444444444
No 207
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=21.40 E-value=47 Score=21.34 Aligned_cols=24 Identities=8% Similarity=0.014 Sum_probs=14.7
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHhC
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~N 71 (91)
..++....+-++.||....+..-|
T Consensus 50 ~~~~~v~~~L~~~gI~~ksi~~~~ 73 (127)
T PRK10629 50 PDGFYVYQHLDANGIHIKSITPEN 73 (127)
T ss_pred chHHHHHHHHHHCCCCcceEEeeC
Confidence 555666777777777765544333
No 208
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=21.36 E-value=1.3e+02 Score=18.70 Aligned_cols=23 Identities=13% Similarity=-0.015 Sum_probs=18.5
Q ss_pred ecCCCCHHHHHHHcCCCHHHHHH
Q 040436 47 AQEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
.-.|-|..+||+..|++...+..
T Consensus 119 ~~~~~s~~EIA~~l~is~~tV~~ 141 (154)
T PRK06759 119 FFVGKTMGEIALETEMTYYQVRW 141 (154)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHH
Confidence 34688999999999999887654
No 209
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=21.30 E-value=62 Score=21.47 Aligned_cols=19 Identities=21% Similarity=0.452 Sum_probs=14.8
Q ss_pred CCHHHHHHHcCCCHHHHHH
Q 040436 51 DTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 51 dTc~~Ia~~~~i~~~~l~~ 69 (91)
+++-+||++.|++.+.|.+
T Consensus 104 ~~l~~iA~~~gLD~~~F~~ 122 (176)
T PF13743_consen 104 ELLLEIAEELGLDVEMFKE 122 (176)
T ss_dssp HHHHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHH
Confidence 6799999999999998764
No 210
>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=21.25 E-value=1.2e+02 Score=18.72 Aligned_cols=21 Identities=19% Similarity=0.105 Sum_probs=18.3
Q ss_pred cCCCCHHHHHHHcCCCHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
-.|-+..+||+..|++...+.
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~ 139 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVK 139 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHH
Confidence 378899999999999988765
No 211
>PF11076 YbhQ: Putative inner membrane protein YbhQ; InterPro: IPR021303 This family is conserved in Proteobacteria. The function is not known but most members are annotated as being inner membrane protein YbhQ.
Probab=21.13 E-value=43 Score=21.58 Aligned_cols=17 Identities=12% Similarity=0.196 Sum_probs=13.4
Q ss_pred eEEecCCCCHHHHHHHc
Q 040436 44 VYGAQEGDTCSNVTEEF 60 (91)
Q Consensus 44 ~y~v~~GdTc~~Ia~~~ 60 (91)
..+|-.|.+||.|+-..
T Consensus 6 rirv~TG~sc~~I~lHL 22 (135)
T PF11076_consen 6 RIRVVTGLSCWQIMLHL 22 (135)
T ss_pred hhhhhhcccHHHHHHHH
Confidence 46778899999998653
No 212
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.01 E-value=1.1e+02 Score=18.61 Aligned_cols=19 Identities=32% Similarity=0.314 Sum_probs=16.0
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
|..++|+.+|++.+.|..|
T Consensus 2 ~i~e~a~~~gvs~~tlr~y 20 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYY 20 (113)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 4678999999999998655
No 213
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.98 E-value=1.2e+02 Score=20.55 Aligned_cols=28 Identities=4% Similarity=-0.161 Sum_probs=24.2
Q ss_pred EEecCCCCHHHHHHHcCCCHHHHHHhCC
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDVFLAINP 72 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~l~~~Np 72 (91)
+.|-.+-++..+|.++||+.....+|-.
T Consensus 14 ~YV~~~~sLe~aA~~~gVs~~TarrWK~ 41 (165)
T PF08822_consen 14 AYVFDRLSLEQAAAKCGVSYATARRWKR 41 (165)
T ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4566788999999999999999998875
No 214
>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=20.97 E-value=1.1e+02 Score=17.78 Aligned_cols=20 Identities=10% Similarity=-0.004 Sum_probs=17.7
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 040436 52 TCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~N 71 (91)
|..++|+..|++...|..|.
T Consensus 3 ti~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999884
No 215
>COG1641 Uncharacterized conserved protein [Function unknown]
Probab=20.80 E-value=72 Score=24.46 Aligned_cols=21 Identities=10% Similarity=0.332 Sum_probs=18.3
Q ss_pred CCHHHHHHHcCCCHHHHHHhC
Q 040436 51 DTCSNVTEEFNLSTDVFLAIN 71 (91)
Q Consensus 51 dTc~~Ia~~~~i~~~~l~~~N 71 (91)
|.|-.||+++|+++.++++.=
T Consensus 356 ED~~~ia~~~giP~r~V~~~~ 376 (387)
T COG1641 356 EDCREIAKETGIPLREVYRLI 376 (387)
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 579999999999999988753
No 216
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=20.75 E-value=1.1e+02 Score=18.82 Aligned_cols=19 Identities=21% Similarity=0.296 Sum_probs=13.5
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
....||+++|++.++|.+.
T Consensus 75 ~i~~ia~~n~ls~~ql~~~ 93 (118)
T PF09312_consen 75 AIANIAKQNNLSVEQLRQQ 93 (118)
T ss_dssp HHHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 5778899999998888754
No 217
>COG0656 ARA1 Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]
Probab=20.67 E-value=1.1e+02 Score=22.31 Aligned_cols=25 Identities=4% Similarity=0.134 Sum_probs=19.2
Q ss_pred ecCCCCHHHHHHHcCCCHHH-HHHhC
Q 040436 47 AQEGDTCSNVTEEFNLSTDV-FLAIN 71 (91)
Q Consensus 47 v~~GdTc~~Ia~~~~i~~~~-l~~~N 71 (91)
+-.-..+.+||++||-|+.| +++|.
T Consensus 198 l~~~~~l~~Ia~k~g~t~AQv~L~W~ 223 (280)
T COG0656 198 LLDNPVLAEIAKKYGKTPAQVALRWH 223 (280)
T ss_pred cccChHHHHHHHHhCCCHHHHHHHHH
Confidence 44445899999999888877 56666
No 218
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=20.64 E-value=1.1e+02 Score=15.39 Aligned_cols=19 Identities=11% Similarity=0.064 Sum_probs=14.0
Q ss_pred CHHHHHHHcCCCHHHHHHh
Q 040436 52 TCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~~ 70 (91)
--..||++.|++..++..|
T Consensus 15 ek~~L~~~tgls~~Qi~~W 33 (40)
T PF05920_consen 15 EKEELAKQTGLSRKQISNW 33 (40)
T ss_dssp HHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 3467899999999987654
No 219
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.56 E-value=1.3e+02 Score=18.94 Aligned_cols=22 Identities=14% Similarity=0.226 Sum_probs=18.1
Q ss_pred cCCCCHHHHHHHcCCCHHHHHH
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~ 69 (91)
..|-+..+||+..|++...+..
T Consensus 139 ~~~~~~~eIA~~lgis~~tv~~ 160 (179)
T PRK11924 139 VEGLSYREIAEILGVPVGTVKS 160 (179)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 3688999999999999887654
No 220
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=20.42 E-value=1.2e+02 Score=20.67 Aligned_cols=23 Identities=13% Similarity=0.199 Sum_probs=19.6
Q ss_pred cCCCCHHHHHHHcCCCHHHHHHh
Q 040436 48 QEGDTCSNVTEEFNLSTDVFLAI 70 (91)
Q Consensus 48 ~~GdTc~~Ia~~~~i~~~~l~~~ 70 (91)
..|.|..+||+..|++...+.+.
T Consensus 193 ~e~~S~~EIA~~lgis~~tV~~~ 215 (233)
T PRK05803 193 GKEKTQREIAKALGISRSYVSRI 215 (233)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHH
Confidence 47889999999999999887654
No 221
>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=20.30 E-value=1.2e+02 Score=18.71 Aligned_cols=24 Identities=21% Similarity=0.245 Sum_probs=15.0
Q ss_pred EEecCCCCHHHHHHHcCCCHHHHH
Q 040436 45 YGAQEGDTCSNVTEEFNLSTDVFL 68 (91)
Q Consensus 45 y~v~~GdTc~~Ia~~~~i~~~~l~ 68 (91)
+....+-|+.+||+.+|++.....
T Consensus 28 lyy~eDlSlsEIAe~~~iSRqaV~ 51 (101)
T PF04297_consen 28 LYYEEDLSLSEIAEELGISRQAVY 51 (101)
T ss_dssp HHCTS---HHHHHHHCTS-HHHHH
T ss_pred HHHccCCCHHHHHHHHCCCHHHHH
Confidence 334556699999999999976543
No 222
>PF13467 RHH_4: Ribbon-helix-helix domain; PDB: 3KK4_C.
Probab=20.21 E-value=75 Score=18.20 Aligned_cols=18 Identities=17% Similarity=0.283 Sum_probs=12.6
Q ss_pred CHHHHHHHcCCCHHHHHH
Q 040436 52 TCSNVTEEFNLSTDVFLA 69 (91)
Q Consensus 52 Tc~~Ia~~~~i~~~~l~~ 69 (91)
.+.+||++-|.++.+|..
T Consensus 25 ~L~eiA~~~g~s~~~li~ 42 (67)
T PF13467_consen 25 ALEEIAAREGLSLNALIA 42 (67)
T ss_dssp HHHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHcCCCHHHHHH
Confidence 467889999999988764
Done!