Query 024969
Match_columns 260
No_of_seqs 115 out of 654
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 08:55:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024969.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024969hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0948 Nuclear exosomal RNA h 100.0 3.6E-70 7.8E-75 527.9 25.4 259 1-260 782-1041(1041)
2 KOG0947 Cytoplasmic exosomal R 100.0 4.6E-58 1E-62 452.2 22.4 258 2-260 990-1248(1248)
3 PF08148 DSHCT: DSHCT (NUC185) 100.0 1.8E-57 4E-62 386.6 16.9 177 81-260 1-180 (180)
4 COG4581 Superfamily II RNA hel 100.0 5.5E-44 1.2E-48 361.8 22.6 254 1-260 783-1041(1041)
5 PF13234 rRNA_proc-arch: rRNA- 95.7 0.029 6.2E-07 50.5 6.6 30 1-30 209-238 (268)
6 PRK02362 ski2-like helicase; P 94.1 0.9 2E-05 46.7 13.0 176 65-252 464-647 (737)
7 PF04408 HA2: Helicase associa 94.0 0.06 1.3E-06 41.3 3.3 44 72-116 3-46 (102)
8 COG1202 Superfamily II helicas 93.7 0.6 1.3E-05 46.6 10.3 178 67-248 618-826 (830)
9 PRK00254 ski2-like helicase; P 93.6 0.94 2E-05 46.4 12.1 176 65-252 454-640 (720)
10 PRK01172 ski2-like helicase; P 91.3 4.5 9.7E-05 41.1 13.5 162 65-251 443-606 (674)
11 smart00847 HA2 Helicase associ 89.7 1.2 2.5E-05 32.9 5.9 60 72-133 3-62 (92)
12 PRK11664 ATP-dependent RNA hel 84.4 7 0.00015 40.9 9.9 66 66-133 384-449 (812)
13 TIGR03643 conserved hypothetic 84.0 1.4 3.1E-05 31.8 3.3 31 188-218 7-37 (72)
14 PF10985 DUF2805: Protein of u 82.9 1.7 3.6E-05 31.6 3.3 31 188-218 6-36 (73)
15 PRK00118 putative DNA-binding 81.8 8.3 0.00018 30.0 7.1 66 180-245 18-88 (104)
16 TIGR01970 DEAH_box_HrpB ATP-de 79.7 3.7 8E-05 42.9 5.9 49 66-115 381-429 (819)
17 cd06171 Sigma70_r4 Sigma70, re 79.6 4.1 8.9E-05 25.7 4.2 43 180-222 11-54 (55)
18 smart00421 HTH_LUXR helix_turn 78.8 4.8 0.00011 26.0 4.4 43 180-222 4-46 (58)
19 cd06170 LuxR_C_like C-terminal 77.5 5.5 0.00012 25.8 4.4 34 186-219 7-40 (57)
20 PF04545 Sigma70_r4: Sigma-70, 76.7 6.4 0.00014 25.7 4.5 38 187-224 13-50 (50)
21 PRK11512 DNA-binding transcrip 75.8 7.3 0.00016 31.3 5.5 62 65-129 68-139 (144)
22 PRK04217 hypothetical protein; 73.7 12 0.00026 29.4 5.9 51 180-230 43-94 (110)
23 PF12246 MKT1_C: Temperature d 73.2 2.6 5.7E-05 37.5 2.4 45 73-117 1-53 (243)
24 PF13518 HTH_28: Helix-turn-he 72.3 9.1 0.0002 24.7 4.4 35 186-220 4-38 (52)
25 PRK03573 transcriptional regul 70.5 10 0.00022 30.3 5.1 61 65-129 60-130 (144)
26 KOG0923 mRNA splicing factor A 69.5 66 0.0014 33.2 11.3 135 66-232 652-790 (902)
27 TIGR01967 DEAH_box_HrpA ATP-de 69.5 76 0.0017 35.1 12.7 63 66-132 449-515 (1283)
28 PRK11131 ATP-dependent RNA hel 67.0 1.4E+02 0.0031 33.1 14.0 63 66-132 456-524 (1294)
29 PF13384 HTH_23: Homeodomain-l 65.4 4.4 9.6E-05 26.3 1.6 34 186-219 9-42 (50)
30 COG3079 Uncharacterized protei 62.4 48 0.001 28.1 7.5 121 116-249 21-163 (186)
31 PF13936 HTH_38: Helix-turn-he 55.7 16 0.00035 23.4 3.0 31 187-217 13-43 (44)
32 PRK12543 RNA polymerase sigma 55.0 44 0.00096 27.5 6.4 44 191-234 130-177 (179)
33 PF10482 CtIP_N: Tumour-suppre 54.0 53 0.0012 26.0 6.1 27 11-37 54-81 (120)
34 COG1846 MarR Transcriptional r 52.8 39 0.00085 25.1 5.3 54 65-122 50-113 (126)
35 PF00196 GerE: Bacterial regul 50.4 27 0.00059 23.3 3.6 43 180-222 4-46 (58)
36 TIGR02337 HpaR homoprotocatech 50.3 69 0.0015 24.5 6.4 37 183-220 32-68 (118)
37 PRK03573 transcriptional regul 50.2 60 0.0013 25.7 6.2 38 183-220 35-72 (144)
38 PF14947 HTH_45: Winged helix- 48.4 18 0.00039 26.1 2.6 41 56-97 25-68 (77)
39 PF08461 HTH_12: Ribonuclease 47.7 46 0.00099 23.4 4.5 28 65-92 32-63 (66)
40 KOG4196 bZIP transcription fac 46.7 97 0.0021 25.1 6.6 77 2-80 43-119 (135)
41 smart00529 HTH_DTXR Helix-turn 45.6 41 0.0009 24.6 4.3 65 65-131 13-81 (96)
42 smart00351 PAX Paired Box doma 45.6 37 0.0008 26.8 4.2 35 186-220 25-59 (125)
43 PF02796 HTH_7: Helix-turn-hel 44.8 31 0.00067 22.1 3.1 33 183-215 10-42 (45)
44 PF13613 HTH_Tnp_4: Helix-turn 44.4 44 0.00095 22.2 3.9 44 182-225 7-50 (53)
45 PF04420 CHD5: CHD5-like prote 44.4 1.8E+02 0.0039 24.0 9.1 51 6-58 40-91 (161)
46 TIGR02985 Sig70_bacteroi1 RNA 44.2 58 0.0012 25.6 5.3 45 180-224 114-159 (161)
47 PF14193 DUF4315: Domain of un 44.2 98 0.0021 23.0 6.0 58 42-129 3-60 (83)
48 PF03333 PapB: Adhesin biosynt 44.1 80 0.0017 23.9 5.6 48 183-230 41-89 (91)
49 COG1204 Superfamily II helicas 44.0 2.2E+02 0.0048 29.8 10.6 54 182-235 591-651 (766)
50 PF03444 HrcA_DNA-bdg: Winged 43.7 27 0.0006 25.7 2.9 31 66-96 38-74 (78)
51 KOG0922 DEAH-box RNA helicase 43.4 2.5E+02 0.0054 28.9 10.4 139 66-233 435-575 (674)
52 PF08281 Sigma70_r4_2: Sigma-7 43.4 48 0.001 21.6 3.9 30 191-220 23-52 (54)
53 PF06969 HemN_C: HemN C-termin 43.2 23 0.00049 24.3 2.4 29 64-92 34-65 (66)
54 TIGR02989 Sig-70_gvs1 RNA poly 41.7 63 0.0014 25.6 5.2 45 180-224 112-157 (159)
55 PRK11512 DNA-binding transcrip 41.6 73 0.0016 25.3 5.5 37 183-220 44-80 (144)
56 COG5570 Uncharacterized small 41.5 1E+02 0.0022 21.0 5.1 46 8-55 7-55 (57)
57 COG1643 HrpA HrpA-like helicas 41.4 60 0.0013 34.3 6.0 65 66-133 433-497 (845)
58 COG1393 ArsC Arsenate reductas 41.4 41 0.00089 26.5 3.8 80 161-257 19-100 (117)
59 TIGR02984 Sig-70_plancto1 RNA 40.0 76 0.0016 25.9 5.5 44 182-225 143-187 (189)
60 PF12690 BsuPI: Intracellular 39.7 2.8 6.1E-05 31.0 -2.9 25 186-210 36-60 (82)
61 COG4910 PduE Propanediol dehyd 39.5 41 0.00088 27.4 3.5 78 166-248 31-109 (170)
62 cd06571 Bac_DnaA_C C-terminal 38.2 1.2E+02 0.0026 22.3 5.8 45 193-246 43-88 (90)
63 TIGR02937 sigma70-ECF RNA poly 38.1 83 0.0018 23.9 5.2 36 189-224 121-156 (158)
64 PRK10870 transcriptional repre 37.7 82 0.0018 26.3 5.4 72 53-129 74-155 (176)
65 PF00440 TetR_N: Bacterial reg 37.1 26 0.00056 22.5 1.7 34 192-225 14-47 (47)
66 PRK06759 RNA polymerase factor 36.8 62 0.0013 25.5 4.4 45 180-224 107-152 (154)
67 PRK09639 RNA polymerase sigma 36.6 69 0.0015 25.6 4.7 37 189-226 123-159 (166)
68 KOG0920 ATP-dependent RNA heli 36.5 43 0.00093 35.6 4.1 61 66-127 592-653 (924)
69 PF06330 TRI5: Trichodiene syn 36.2 2.9E+02 0.0063 26.4 9.2 57 154-223 222-278 (376)
70 PRK09642 RNA polymerase sigma 36.1 73 0.0016 25.4 4.7 46 180-225 107-153 (160)
71 PF13601 HTH_34: Winged helix 35.5 29 0.00063 25.3 2.0 37 183-220 4-40 (80)
72 PF04977 DivIC: Septum formati 35.1 1.5E+02 0.0032 20.7 5.7 15 72-86 58-73 (80)
73 cd00090 HTH_ARSR Arsenical Res 34.9 77 0.0017 21.0 4.1 30 191-220 17-46 (78)
74 PRK12514 RNA polymerase sigma 34.8 1.1E+02 0.0024 24.9 5.7 45 180-224 130-175 (179)
75 PF12917 HD_2: HD containing h 34.4 3.2E+02 0.007 24.0 10.3 113 113-250 51-171 (215)
76 TIGR02948 SigW_bacill RNA poly 33.8 96 0.0021 25.3 5.2 35 191-225 149-183 (187)
77 PRK13777 transcriptional regul 33.6 1.6E+02 0.0035 25.0 6.6 32 189-220 53-85 (185)
78 TIGR02999 Sig-70_X6 RNA polyme 33.5 79 0.0017 25.8 4.6 46 180-225 135-181 (183)
79 KOG4253 Tryptophan-rich basic 32.9 3E+02 0.0065 23.1 8.2 23 36-58 66-88 (175)
80 KOG0925 mRNA splicing factor A 32.9 75 0.0016 31.7 4.8 61 66-127 433-494 (699)
81 PF13412 HTH_24: Winged helix- 32.5 55 0.0012 20.8 2.8 29 192-220 15-43 (48)
82 PRK12525 RNA polymerase sigma 32.4 1.1E+02 0.0023 24.8 5.2 34 191-224 131-164 (168)
83 PRK09047 RNA polymerase factor 32.0 1.1E+02 0.0025 24.1 5.2 36 191-226 119-154 (161)
84 KOG0286 G-protein beta subunit 31.6 30 0.00064 32.0 1.8 52 43-94 5-56 (343)
85 cd00180 PKc Catalytic domain o 31.6 30 0.00065 27.4 1.7 52 183-234 64-117 (215)
86 PRK09648 RNA polymerase sigma 31.4 84 0.0018 25.9 4.5 36 191-226 152-187 (189)
87 PRK12522 RNA polymerase sigma 30.9 99 0.0022 25.1 4.8 37 189-225 130-166 (173)
88 PRK13919 putative RNA polymera 30.1 99 0.0022 25.3 4.7 45 180-224 136-181 (186)
89 PF13730 HTH_36: Helix-turn-he 30.0 59 0.0013 21.2 2.7 25 196-220 27-51 (55)
90 PRK06930 positive control sigm 29.8 1.3E+02 0.0028 25.1 5.3 46 180-225 115-161 (170)
91 PF01022 HTH_5: Bacterial regu 29.5 83 0.0018 20.1 3.2 37 184-220 4-41 (47)
92 PF02885 Glycos_trans_3N: Glyc 29.3 1.1E+02 0.0025 21.1 4.1 24 106-132 24-47 (66)
93 KOG0660 Mitogen-activated prot 29.2 28 0.00061 32.8 1.2 41 187-236 208-248 (359)
94 PF04363 DUF496: Protein of un 29.2 2.2E+02 0.0048 21.5 5.7 32 32-63 4-35 (95)
95 PF13551 HTH_29: Winged helix- 29.0 92 0.002 23.0 4.0 34 186-219 3-37 (112)
96 TIGR02479 FliA_WhiG RNA polyme 28.9 1.4E+02 0.003 25.5 5.5 35 191-225 188-222 (224)
97 PF07900 DUF1670: Protein of u 28.9 1.4E+02 0.003 26.4 5.4 61 155-216 122-185 (220)
98 TIGR02941 Sigma_B RNA polymera 28.8 98 0.0021 27.1 4.6 37 189-225 216-252 (255)
99 PF12802 MarR_2: MarR family; 28.6 64 0.0014 21.3 2.7 30 191-220 16-47 (62)
100 KOG0662 Cyclin-dependent kinas 28.5 49 0.0011 28.9 2.5 39 188-235 183-222 (292)
101 PRK12542 RNA polymerase sigma 28.4 1.4E+02 0.003 24.6 5.2 49 180-228 123-172 (185)
102 PF01047 MarR: MarR family; I 28.4 78 0.0017 20.8 3.1 37 183-220 7-43 (59)
103 smart00418 HTH_ARSR helix_turn 28.4 1.1E+02 0.0025 19.5 3.9 29 192-220 8-36 (66)
104 PRK15443 pduE propanediol dehy 28.3 1E+02 0.0023 25.0 4.2 54 192-249 21-78 (138)
105 PF07749 ERp29: Endoplasmic re 28.2 1E+02 0.0022 23.2 4.0 34 45-78 61-94 (95)
106 PF04255 DUF433: Protein of un 27.9 56 0.0012 22.0 2.3 30 183-212 20-50 (56)
107 CHL00073 chlN photochlorophyll 27.8 76 0.0017 31.0 4.0 68 188-256 49-135 (457)
108 PRK12511 RNA polymerase sigma 27.6 1.6E+02 0.0035 24.4 5.5 48 180-227 112-160 (182)
109 KOG0661 MAPK related serine/th 26.9 35 0.00076 33.6 1.5 41 188-237 191-231 (538)
110 PRK09645 RNA polymerase sigma 26.7 1.7E+02 0.0037 23.5 5.5 45 182-226 121-166 (173)
111 PRK09644 RNA polymerase sigma 26.7 1.5E+02 0.0033 23.7 5.1 49 180-228 109-158 (165)
112 PF14493 HTH_40: Helix-turn-he 26.6 1.5E+02 0.0032 21.8 4.6 35 187-221 6-40 (91)
113 PRK12531 RNA polymerase sigma 26.6 1.9E+02 0.0042 23.9 5.9 48 180-227 142-190 (194)
114 PRK10573 type IV pilin biogene 26.1 2.9E+02 0.0062 26.0 7.5 59 183-245 301-365 (399)
115 cd00131 PAX Paired Box domain 26.0 1.2E+02 0.0027 24.0 4.3 33 188-220 27-59 (128)
116 PRK12541 RNA polymerase sigma 26.0 1.1E+02 0.0024 24.4 4.2 47 180-226 113-160 (161)
117 PRK13344 spxA transcriptional 25.8 71 0.0015 25.5 2.9 22 235-256 77-98 (132)
118 PF00165 HTH_AraC: Bacterial r 25.6 65 0.0014 19.9 2.1 29 190-218 4-32 (42)
119 PF13404 HTH_AsnC-type: AsnC-t 25.4 74 0.0016 20.2 2.4 35 183-219 7-42 (42)
120 PRK00888 ftsB cell division pr 25.2 3E+02 0.0066 21.1 6.2 10 77-86 74-83 (105)
121 PRK08583 RNA polymerase sigma 25.1 1.3E+02 0.0029 26.3 4.8 35 191-225 218-252 (257)
122 PRK09643 RNA polymerase sigma 25.0 1.8E+02 0.0039 24.2 5.4 45 190-234 146-190 (192)
123 TIGR02950 SigM_subfam RNA poly 24.8 82 0.0018 24.8 3.1 35 191-225 118-152 (154)
124 COG1420 HrcA Transcriptional r 24.8 60 0.0013 30.6 2.6 27 66-92 42-73 (346)
125 PF10153 DUF2361: Uncharacteri 24.8 1.9E+02 0.0042 22.8 5.1 73 9-81 24-101 (114)
126 KOG0594 Protein kinase PCTAIRE 24.7 40 0.00087 31.5 1.4 38 190-236 204-241 (323)
127 PF01527 HTH_Tnp_1: Transposas 24.6 52 0.0011 22.9 1.7 29 191-219 20-48 (76)
128 PRK12528 RNA polymerase sigma 24.5 1.4E+02 0.0029 23.9 4.4 44 180-223 114-158 (161)
129 KOG4456 Inner centromere prote 24.4 1E+02 0.0023 24.8 3.5 51 188-251 66-117 (134)
130 COG2442 Uncharacterized conser 24.1 1.2E+02 0.0026 22.3 3.5 34 183-216 32-66 (79)
131 PRK02166 hypothetical protein; 23.8 2.8E+02 0.0061 23.6 6.3 60 182-249 96-161 (184)
132 PRK12547 RNA polymerase sigma 23.6 2.2E+02 0.0047 22.8 5.5 46 180-225 113-159 (164)
133 PF11917 DUF3435: Protein of u 23.1 2E+02 0.0044 27.5 5.9 21 4-24 286-306 (418)
134 PF11985 DUF3486: Protein of u 23.1 4.4E+02 0.0096 21.9 10.5 115 104-230 17-136 (180)
135 COG4985 ABC-type phosphate tra 23.1 2.5E+02 0.0054 25.2 5.9 45 14-58 194-239 (289)
136 TIGR02511 type_III_tyeA type I 23.0 1.8E+02 0.0038 21.2 4.3 56 189-246 16-72 (79)
137 TIGR02952 Sig70_famx2 RNA poly 23.0 2.2E+02 0.0048 22.6 5.4 34 191-224 135-168 (170)
138 cd03033 ArsC_15kD Arsenate Red 22.8 1.6E+02 0.0034 22.9 4.3 78 162-256 19-96 (113)
139 PRK06986 fliA flagellar biosyn 22.6 1.5E+02 0.0033 25.6 4.6 35 191-225 197-231 (236)
140 TIGR02983 SigE-fam_strep RNA p 22.4 1.6E+02 0.0035 23.3 4.5 36 191-226 123-158 (162)
141 PRK06811 RNA polymerase factor 22.3 2.1E+02 0.0045 23.6 5.3 45 180-224 132-177 (189)
142 PRK05803 sporulation sigma fac 22.3 1.9E+02 0.0042 24.9 5.2 36 192-227 193-228 (233)
143 PRK12539 RNA polymerase sigma 22.3 2.4E+02 0.0051 23.1 5.6 46 180-225 132-178 (184)
144 TIGR02835 spore_sigmaE RNA pol 22.1 1.5E+02 0.0033 25.6 4.5 33 193-225 197-229 (234)
145 TIGR02531 yecD_yerC TrpR-relat 22.0 1.2E+02 0.0027 22.6 3.3 36 180-217 37-72 (88)
146 COG2771 CsgD DNA-binding HTH d 21.7 2E+02 0.0044 18.8 4.2 43 180-222 5-47 (65)
147 cd00569 HTH_Hin_like Helix-tur 21.6 1E+02 0.0022 16.7 2.4 29 186-214 13-41 (42)
148 PF15002 ERK-JNK_inhib: ERK an 21.6 3E+02 0.0065 24.0 6.1 103 104-224 51-153 (207)
149 TIGR02846 spore_sigmaK RNA pol 21.6 2.2E+02 0.0047 24.5 5.4 45 180-224 175-224 (227)
150 KOG0201 Serine/threonine prote 21.1 1.2E+02 0.0026 29.7 3.8 96 144-258 47-143 (467)
151 PF13463 HTH_27: Winged helix 21.1 1.4E+02 0.0031 20.0 3.4 28 193-220 17-44 (68)
152 PRK10026 arsenate reductase; P 20.7 68 0.0015 26.2 1.9 38 163-203 22-61 (141)
153 COG2926 Uncharacterized protei 20.7 2E+02 0.0043 22.1 4.2 33 31-63 10-42 (109)
154 PF01638 HxlR: HxlR-like helix 20.1 1.2E+02 0.0025 22.3 2.9 46 49-98 21-76 (90)
155 COG1510 Predicted transcriptio 20.1 2.9E+02 0.0064 23.5 5.5 56 156-220 12-67 (177)
No 1
>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=3.6e-70 Score=527.92 Aligned_cols=259 Identities=55% Similarity=0.863 Sum_probs=255.9
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHcCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhHhC
Q 024969 1 MKIEDPEVVDLVNQIEELEHKLFAHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLG 79 (260)
Q Consensus 1 ~~i~~~~~~~~~~~~~~l~~~l~~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~~lg 79 (260)
|+|++.+|.++.++++.++.++..||.|.. ...+.++.+.++..+..++++++.++++.+...+.+|++++++||++||
T Consensus 782 M~I~~~~~~~~~~k~e~lE~~l~~hp~~k~~~~~~~~~~f~~K~~l~~~ik~lk~~l~~~~~i~~ldELk~RkRVLrrLG 861 (1041)
T KOG0948|consen 782 MNIKDVEFKKLVKKIESLEARLESHPLHKSSELEELYKEFQRKETLRAEIKDLKAELKSSQAILQLDELKNRKRVLRRLG 861 (1041)
T ss_pred cCccchHHHHHHHHHHHHHHhhccCcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhC
Confidence 899999999999999999999999999999 9999999999999999999999999999888889999999999999999
Q ss_pred CCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhccccCCCccccccHHHHHHHHHHHHHHHHH
Q 024969 80 HINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQINLRMELAKPLQQLQESARKI 159 (260)
Q Consensus 80 yid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~~~~~~~~~~~~l~~~~~~l~~~~~~i 159 (260)
|++.++++.+||||||||+|+|||++||+||+|.|++|+|+|+||+||||||++++++.+.+.+++..++..|++.+++|
T Consensus 862 ~~t~ddvie~KGrvACEIsSgDELlLTEliFnG~Fndl~~eq~aaLLSCfVf~eks~e~~~l~~el~~~l~~lqe~ArrI 941 (1041)
T KOG0948|consen 862 YCTSDDVIELKGRVACEISSGDELLLTELIFNGIFNDLPVEQAAALLSCFVFQEKSSEAPKLKEELAGPLRQLQESARRI 941 (1041)
T ss_pred CCCCCCeEEEcceEEEEecccchHHHHHHHHhccccCCCHHHHHHHHhheeehhcccccccchHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999988899999999999999999999
Q ss_pred HHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHH
Q 024969 160 AEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEK 239 (260)
Q Consensus 160 ~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~~ 239 (260)
++++.+|++++++++||.+ |+|++|+|||+|++|+||.+||++|+++||+|||++|||+||||||.+||+.|||.+|.+
T Consensus 942 AkVs~ecKlEide~~Yv~s-Fkp~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeElLrQl~~AAk~iGnteLe~ 1020 (1041)
T KOG0948|consen 942 AKVSKECKLEIDEEDYVES-FKPELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEELLRQLIDAAKVIGNTELEN 1020 (1041)
T ss_pred HHHHHhhccccCHHHHHHh-cChHHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcchHHHH
Confidence 9999999999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCccccCCCCC
Q 024969 240 KFAAASESLRRGIMFSNSLYL 260 (260)
Q Consensus 240 k~~~a~~~i~RdIVf~~SLYl 260 (260)
||+.++.+|+|||||++||||
T Consensus 1021 Kf~~~~~~ikRDIVFAaSLYL 1041 (1041)
T KOG0948|consen 1021 KFEEAIKKIKRDIVFAASLYL 1041 (1041)
T ss_pred HHHHHHHHHhhceeehhhccC
Confidence 999999999999999999997
No 2
>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=4.6e-58 Score=452.22 Aligned_cols=258 Identities=34% Similarity=0.556 Sum_probs=246.5
Q ss_pred CCCChHHHHHHHHHHHHHHHHHcCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhHhCC
Q 024969 2 KIEDPEVVDLVNQIEELEHKLFAHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGH 80 (260)
Q Consensus 2 ~i~~~~~~~~~~~~~~l~~~l~~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~~lgy 80 (260)
+.++.+|.+...+...+++.+..+||+.| .+.+|+....+..+++.++++|+.++++ +++.+.++|.++++||+.+||
T Consensus 990 k~kd~e~~~~~l~~~n~~~~~~~~~~i~c~~f~~h~s~~~~~~~~~~ei~~L~~~~sd-~~L~l~pey~~RlevLk~~g~ 1068 (1248)
T KOG0947|consen 990 KLKDDEVVEMLLERTNLQNLIQGNPCISCPKFDQHYSLARREYKIEKEIENLEFELSD-QSLLLSPEYHNRLEVLKPLGF 1068 (1248)
T ss_pred hhccHHHHHHHHHHHHHHHHHhcCCccCCccHHHHHHHHHHHHHHHHHhhhhhhhhhh-hhhhhCHHHHHHHHHHhhcCc
Confidence 45788999999999999999999999999 9999999999999999999999999999 777788999999999999999
Q ss_pred CCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhccccCCCccccccHHHHHHHHHHHHHHHHHH
Q 024969 81 INADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQINLRMELAKPLQQLQESARKIA 160 (260)
Q Consensus 81 id~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~~~~~~~~~~~~l~~~~~~l~~~~~~i~ 160 (260)
+|...++++|||+||+|++++|||+|||||+|.|.+++|+|+||+||+||||.++...+.+++.+.++-+++.++++++.
T Consensus 1069 vD~~~~V~lkGRvAceI~s~~ELllteli~dn~l~~l~peeiaallSslV~e~~~e~~~~~~~~l~k~~e~v~~v~~rl~ 1148 (1248)
T KOG0947|consen 1069 VDEMRTVLLKGRVACEINSGNELLLTELIFDNALVDLSPEEIAALLSSLVCEGKTERPPTLTPYLKKGKERVRDVAKRLE 1148 (1248)
T ss_pred ccccceeeecceeeeeecCCcchhHHHHHHhhhhhhcCHHHHHHHHHHHHhcCccccCCCCChhhhhHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999886557889999999999999999999
Q ss_pred HHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHH
Q 024969 161 EIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKK 240 (260)
Q Consensus 161 ~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~~k 240 (260)
.++..|++.++++++...+++|+||+|||+||+|.||.+||++|++.||+|||+|+||+|+|||+++|+.++|||.|.+|
T Consensus 1149 ev~~~~~~~~~~~e~f~~~lrF~l~evVYeWA~G~sf~eim~~t~~~EG~iVR~I~RLdE~cre~~~aa~ivGd~~L~~K 1228 (1248)
T KOG0947|consen 1149 EVQSSHQLLQTPEEEFPCELRFGLVEVVYEWARGLSFKEIMELTDVLEGLIVRLIQRLDEVCRELRNAARIVGDPVLHEK 1228 (1248)
T ss_pred HHHHhhccccCchhhccccccccHHHHHHHHHcCCCHHHHHhhhCCcchhHHHHHHHHHHHHHhhhccceecCcHHHHHH
Confidence 99999999988764434449999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCccccCCCCC
Q 024969 241 FAAASESLRRGIMFSNSLYL 260 (260)
Q Consensus 241 ~~~a~~~i~RdIVf~~SLYl 260 (260)
+++|+++|||||||++|||+
T Consensus 1229 m~~as~~ikRdIVFaaSLY~ 1248 (1248)
T KOG0947|consen 1229 MEAASALIKRDIVFAASLYL 1248 (1248)
T ss_pred HHHHHHHhccCccchhhccC
Confidence 99999999999999999997
No 3
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=100.00 E-value=1.8e-57 Score=386.64 Aligned_cols=177 Identities=47% Similarity=0.788 Sum_probs=147.4
Q ss_pred CCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhccccCCCcc---ccccHHHHHHHHHHHHHHH
Q 024969 81 INADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQ---INLRMELAKPLQQLQESAR 157 (260)
Q Consensus 81 id~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~~~~~~---~~~~~~l~~~~~~l~~~~~ 157 (260)
||++++||+|||+||+|+++|||++||+||+|+|++|+|+||||++|||||++++++. ..+++.+.++++++.++++
T Consensus 1 id~~~~vt~kGr~a~~I~~~~eLl~te~l~~g~f~~L~p~elAa~lS~~v~e~~~~~~~~~~~~~~~l~~~~~~l~~~~~ 80 (180)
T PF08148_consen 1 IDEDNVVTLKGRVACEIYSEDELLLTELLFSGVFDDLDPAELAALLSCFVYEPRREDEEERYPPSPRLREALEQLQEIAE 80 (180)
T ss_dssp B-TTS-BSHHHHHHCC--SSTHHHHHHHHHCTCCCCS-HHHHHHHHHHHC-----SS---------HHHHHHHHHHHHHH
T ss_pred CCCCCccCHHHHHHHHHcCcccHHHHHHHHcCCCCCCCHHHHHHHHHHhhcccccCcccccccccHHHHHHHHHHHHHHH
Confidence 6889999999999999999999999999999999999999999999999999888765 1233489999999999999
Q ss_pred HHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHH
Q 024969 158 KIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNL 237 (260)
Q Consensus 158 ~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L 237 (260)
+|..++.+||+ +.++|+.+ ++|++|++||+||+|+||++||+.|+++||||||++||++|+||||++|++++|||+|
T Consensus 81 ~l~~~~~~~~l--~~~~~~~~-~~~~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~~~L 157 (180)
T PF08148_consen 81 RLAKVEREHGL--DEEEYVER-FDPGLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGDPEL 157 (180)
T ss_dssp HHHHHHHHTT---HHHHHHHC-STTTTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-HHH
T ss_pred HHHHHHHHhCC--CCcccccC-CCccHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHHH
Confidence 99999999999 66779888 7999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCccccCCCCC
Q 024969 238 EKKFAAASESLRRGIMFSNSLYL 260 (260)
Q Consensus 238 ~~k~~~a~~~i~RdIVf~~SLYl 260 (260)
++|+++|+++|+|||||++||||
T Consensus 158 ~~~~~~a~~~i~R~iV~~~SLYl 180 (180)
T PF08148_consen 158 AEKAREAIDLIRRDIVFASSLYL 180 (180)
T ss_dssp HHHHHHHHHHHSHCCCC---TT-
T ss_pred HHHHHHHHHhccCCccccccccC
Confidence 99999999999999999999997
No 4
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.5e-44 Score=361.80 Aligned_cols=254 Identities=38% Similarity=0.569 Sum_probs=240.6
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHcCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhHhC
Q 024969 1 MKIEDPEVVDLVNQIEELEHKLFAHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLG 79 (260)
Q Consensus 1 ~~i~~~~~~~~~~~~~~l~~~l~~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~~lg 79 (260)
|+|.++++.+...+....+..+..+|.+.| ....|++.......|..+++.+...+ ....+.+++..+.++|+.+|
T Consensus 783 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~i~~l~~~~---~~~~~l~~~~~l~~~l~~~g 859 (1041)
T COG4581 783 MKIQVPELTVSLLKLRFGRYHLSENPLMNFDGAERLIENELLLSDLQAEIEDLSSSI---EALSFLDDYKTLQEVLKKLG 859 (1041)
T ss_pred ccccchhHHHHHHHHhhcccccCCCccccchHHHHHHHhHhHHHHHHHHHHHHHHHH---HHhhhhHHHHHHHHHHHhhc
Confidence 678899999999999999999999999999 99999999999999999999999998 33446689999999999999
Q ss_pred CCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhccccCCCc----cccccHHHHHHHHHHHHH
Q 024969 80 HINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSE----QINLRMELAKPLQQLQES 155 (260)
Q Consensus 80 yid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~~~~~----~~~~~~~l~~~~~~l~~~ 155 (260)
|++.+..++.|||+||+|++++|+|+|||+++|.|++++|+++||++|||||++++++ .+.++|.+..+...+.++
T Consensus 860 ~~~~~~~v~~kGr~a~eI~s~~ellL~e~i~~g~f~~l~p~e~aallSa~v~e~~~~d~~~~~~~~~~~l~~~~~~l~e~ 939 (1041)
T COG4581 860 FIEDNAVVLIKGRVAAEISSEDELLLTELIFSGEFNDLEPEELAALLSAFVFEEKTDDGTAEAPEITPALRDALLRLLEL 939 (1041)
T ss_pred CCCcccccccccceeeeecCCCchHHHHHHHcCCccCCCHHHHHHHHHheeeccCCcccccccccCCHHHHhHHHHHHHH
Confidence 9998899999999999999999999999999999999999999999999999999873 356789999999999999
Q ss_pred HHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCH
Q 024969 156 ARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEV 235 (260)
Q Consensus 156 ~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~ 235 (260)
+.+|..++..+++++++. ++. +.+++|++||.||+|++|.+||.+|++.|||+||+++|++|+|+|+.+++.++||+
T Consensus 940 ~~kl~~~~~~~~i~~~~~--l~~-~~~~lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r~~ell~ql~~aa~~ig~~ 1016 (1041)
T COG4581 940 ARKLNKDQNSSQIEIYPE--LND-FSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRRLRELLRQLRKAASVIGNP 1016 (1041)
T ss_pred HHHHHHHHHhcCCcCCcc--ccc-ccccHHHHHHHHHhhcchhhhhcCCcccccchhhhhhHHHHHHHHhhhcccccCCH
Confidence 999999999999998865 556 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCccccCCCCC
Q 024969 236 NLEKKFAAASESLRRGIMFSNSLYL 260 (260)
Q Consensus 236 ~L~~k~~~a~~~i~RdIVf~~SLYl 260 (260)
+|.++++.|+..|||||||.+|||+
T Consensus 1017 ~L~~k~~~~~~~irr~iv~~~sly~ 1041 (1041)
T COG4581 1017 ELEEKAYRAIQEIRRDIVFVDSLYL 1041 (1041)
T ss_pred HHHHHHHHHHHhhhcCeEecccccC
Confidence 9999999999999999999999996
No 5
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=95.72 E-value=0.029 Score=50.47 Aligned_cols=30 Identities=60% Similarity=0.970 Sum_probs=25.7
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHcCCCCCC
Q 024969 1 MKIEDPEVVDLVNQIEELEHKLFAHPLNKS 30 (260)
Q Consensus 1 ~~i~~~~~~~~~~~~~~l~~~l~~~p~~~c 30 (260)
|||+|++|.++..+++.|++++.+||||.|
T Consensus 209 mkI~d~~~~e~~~k~~~Le~rl~~~~~~~~ 238 (268)
T PF13234_consen 209 MKIKDPEFVELVKKIEALEKRLSSHPLHKC 238 (268)
T ss_dssp H----HHHHHHHHHHHHHHHHHHHSCHCCS
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 799999999999999999999999999999
No 6
>PRK02362 ski2-like helicase; Provisional
Probab=94.06 E-value=0.9 Score=46.66 Aligned_cols=176 Identities=13% Similarity=0.119 Sum_probs=95.8
Q ss_pred HHHHHHHHHHHhHhCCCCCCC---ccchhhHHHhhhccCChHHHHHHHhhCCCCC---CCHHHHHHHhhhhccccCCCcc
Q 024969 65 RDELKNRSRVLKKLGHINADG---VVQLKGRAACLIDTGDELLVTELMFNGTFND---LDHHQVAALASCFIPVDKSSEQ 138 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~~~---~~t~kGrva~eI~~~~eLlltEll~~g~f~~---L~p~elaallS~~v~e~~~~~~ 138 (260)
.+-.+..++.|++.|+|+.++ .+|..|++++..+- +.. .++.+.++. .. .+...+--++| .-+..++.
T Consensus 464 ~~~v~~~l~~L~~~~~i~~~~~~~~~t~lG~~~s~~~l-~~~-t~~~~~~~l-~~~~~~~~~~~l~~i~---~~~e~~~~ 537 (737)
T PRK02362 464 ERVVDDVLDFLERNGMIEEDGETLEATELGHLVSRLYI-DPL-SAAEIIDGL-EAAKKPTDLGLLHLVC---STPDMYEL 537 (737)
T ss_pred HHHHHHHHHHHHHCCCeeecCCeEeEChHHHHHHHhcC-CHH-HHHHHHHHh-hhcccCchHHHHHHhh---cCcccccc
Confidence 345678899999999998653 59999999998874 332 222232221 21 23333333333 11111111
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCC--hhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHH
Q 024969 139 INLRMELAKPLQQLQESARKIAEIQNECKLEVN--VDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSAR 216 (260)
Q Consensus 139 ~~~~~~l~~~~~~l~~~~~~i~~~~~~~~l~~~--~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~r 216 (260)
+.-..+. ..+..+... ....+. -+++.. ..+|-.--......-+.+.|.++.++.+|.+..++..||+-....
T Consensus 538 ~~r~~e~-~~l~~~~~~--~~~~~~--~~~p~~~~~~~~~~~~~~~k~~~ll~~~i~~~~~~~i~~~~~~~~gdl~~~~~ 612 (737)
T PRK02362 538 YLRSGDY-EWLNEYLYE--HEDELL--GDVPSEFEDDEFEDFLSAVKTALLLEDWIDEVDEERITERYGVGPGDIRGKVE 612 (737)
T ss_pred ccChhHH-HHHHHHHHh--cccchh--ccCCchhhhhhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCchHHHHHHH
Confidence 1101111 111111100 000000 112211 111110001124466799999999999999999999999988888
Q ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCCc
Q 024969 217 RLDEFLNQLRAAAQAVGEVNLEKKFAAASESLRRGI 252 (260)
Q Consensus 217 Rl~elLrql~~a~~~ig~~~L~~k~~~a~~~i~RdI 252 (260)
...-++..+...+...| ..++..+..-...|+-++
T Consensus 613 ~~~~l~~a~~~i~~~~~-~~~~~~~~~l~~~l~~gv 647 (737)
T PRK02362 613 TAEWLLHAAERLASELD-LDLARAARELEKRVEYGV 647 (737)
T ss_pred HHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHhCC
Confidence 88888888888887755 445555555444444443
No 7
>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length. It is found as a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.; GO: 0004386 helicase activity; PDB: 3I4U_A 2XAU_B 3KX2_B.
Probab=93.97 E-value=0.06 Score=41.28 Aligned_cols=44 Identities=25% Similarity=0.394 Sum_probs=28.8
Q ss_pred HHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCC
Q 024969 72 SRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFND 116 (260)
Q Consensus 72 ~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~ 116 (260)
++.|..+|.||+++.+|..|+..+.+-- ++-+---++....|.-
T Consensus 3 ~~~L~~Lgald~~~~lT~lG~~~~~lPl-~p~~a~~Ll~~~~~~~ 46 (102)
T PF04408_consen 3 LELLKSLGALDENGNLTPLGRKMSQLPL-DPRLAKMLLYGIQFGC 46 (102)
T ss_dssp HHHHHHTTSB-TTS-B-HHHHHHTTSSS--HHHHHHHHHHHHCT-
T ss_pred HHHHHHCCCCCCCCCcCHHHHHHHHCCC-chHhHhHhhhcccccc
Confidence 4679999999999999999999999973 5544444444444433
No 8
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=93.68 E-value=0.6 Score=46.62 Aligned_cols=178 Identities=18% Similarity=0.173 Sum_probs=107.9
Q ss_pred HHHHHHHHHhHhCCCCCCC---ccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhccccCCCcc-----
Q 024969 67 ELKNRSRVLKKLGHINADG---VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQ----- 138 (260)
Q Consensus 67 e~~~~~~vL~~lgyid~~~---~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~~~~~~----- 138 (260)
+.++.+.-|+.+|||+.+| .+|..||+++.= --..-.+|.|..|+....+|-.|++-+.-|-...=+...
T Consensus 618 ~~~k~l~~Lee~g~i~~~G~~v~~T~yGrava~~--Fl~p~~a~~Ir~~v~~~~~pl~i~~~l~pfE~ayls~~l~r~i~ 695 (830)
T COG1202 618 DPKKALSKLEEYGMIKKKGNIVRPTPYGRAVAMS--FLGPSEAEFIREGVLASMDPLRIAAELEPFENAYLSGFLKRAIE 695 (830)
T ss_pred CHHHHHHHHHhcCCeeccCCEeeeccccceeEEe--ecCchHHHHHHHhhhccCChHhHhhccccccccccChHHHHHHH
Confidence 5678889999999999654 699999988632 234557899999999999999999887766433222110
Q ss_pred ----ccccHHHHH-HHHHHHHHHHHH-----------HHHHHHcCCCCChhhhhhccCcccHH-HHHHHhhCCCCHHHHH
Q 024969 139 ----INLRMELAK-PLQQLQESARKI-----------AEIQNECKLEVNVDEYVESTVRPFLM-DVIYCWSKGATFAEVI 201 (260)
Q Consensus 139 ----~~~~~~l~~-~~~~l~~~~~~i-----------~~~~~~~~l~~~~~~~~~~~~~~~l~-~vv~~Wa~G~~f~~i~ 201 (260)
...|..+.. ++..+.+-..+| -.++.++- .-+..++..- -.--+. .++..--.|.+-.+|-
T Consensus 696 ~~~~~~vpsr~f~~a~~~I~~e~d~ii~ld~k~~e~l~~i~~df~-~c~c~d~ce~-~~~~lse~ii~lR~~gk~p~~Is 773 (830)
T COG1202 696 SALRGRVPSRLFDSALLDILEEGDKIIELDPKLKEKLLLIYMDFL-NCTCRDCCEC-AEQRLSEKIIELRIEGKDPSQIS 773 (830)
T ss_pred HHhcCCCchhhhhHHHHHHHhchhhhhcCCHHHHHHHHHHHHHHh-cCchhhhHHH-HHHHHHHHHHHHHhcCCCHHHHH
Confidence 012222222 332222222221 11111110 0001110000 000111 2334446888888877
Q ss_pred hh------cCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 024969 202 QM------TDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESL 248 (260)
Q Consensus 202 ~~------t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~i 248 (260)
.. -..++|||.-|+-.+..+|.-+..+|++.+-++..+.+......|
T Consensus 774 r~l~~~Ygi~aYpgDif~wLd~~vr~Lea~~rIArvf~kr~~~~ea~~lk~~i 826 (830)
T COG1202 774 RILEKRYGIQAYPGDIFTWLDTLVRLLEAIGRIARVFKKREVEAEAKALKKKI 826 (830)
T ss_pred HHHHHhhCeeecChhHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence 66 377899999999999999988888898888888877666554444
No 9
>PRK00254 ski2-like helicase; Provisional
Probab=93.60 E-value=0.94 Score=46.40 Aligned_cols=176 Identities=12% Similarity=0.094 Sum_probs=101.6
Q ss_pred HHHHHHHHHHHhHhCCCCCC----CccchhhHHHhhhccCChHHHH---HHHhhCCCCCCCHHHHHHHhhhhccccCCCc
Q 024969 65 RDELKNRSRVLKKLGHINAD----GVVQLKGRAACLIDTGDELLVT---ELMFNGTFNDLDHHQVAALASCFIPVDKSSE 137 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~~----~~~t~kGrva~eI~~~~eLllt---Ell~~g~f~~L~p~elaallS~~v~e~~~~~ 137 (260)
.+.....+..|.+.|+|+.+ ..+|..|++++..+- +...+- ..|.. .-.+.+-..+.-++|.. +....
T Consensus 454 ~~~v~~~l~~L~~~~~i~~~~~~~~~~t~lG~~~s~~~i-~~~t~~~~~~~l~~-~~~~~~~~~~l~~~~~~---~e~~~ 528 (720)
T PRK00254 454 EEKAKEIVYFLLENEFIDIDLEDRFIPLPLGIRTSQLYI-DPLTAKKFKDAFPK-IEKNPNPLGIFQLIAST---PDMTP 528 (720)
T ss_pred HHHHHHHHHHHHHCCCeEEcCCCCEeeChHHHHHHHHhC-CHHHHHHHHHHHHh-hccCCCHHHHHHHhhCC---ccccc
Confidence 35567788899999999642 368999999998774 543322 22221 11123333344333322 11111
Q ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHH--cCCCCCh-hhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHH
Q 024969 138 QINLRMELAKPLQQLQESARKIAEIQNE--CKLEVNV-DEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRS 214 (260)
Q Consensus 138 ~~~~~~~l~~~~~~l~~~~~~i~~~~~~--~~l~~~~-~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~ 214 (260)
.+.-..+... +.+....+ ..+ ..++... .+|..-.......-+.++|.+|.+...+++..++..||+-+.
T Consensus 529 ~~~r~~e~~~----l~~~~~~~---~~~l~~~~~~~~~~~~~~~~~~~k~~~ll~~~~~~~~~~~~~~~~~~~~gd~~~~ 601 (720)
T PRK00254 529 LNYSRKEMED----LLDEAYEM---EDRLYFNIPYWEDYKFQKFLRAFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRI 601 (720)
T ss_pred cCcchhhHHH----HHHHHHhh---cccccccCCcchhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHH
Confidence 1100111111 11111111 111 1122211 122110023456788999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhcCC-HHHHHHHHHHHHhhcCCc
Q 024969 215 ARRLDEFLNQLRAAAQAVGE-VNLEKKFAAASESLRRGI 252 (260)
Q Consensus 215 ~rRl~elLrql~~a~~~ig~-~~L~~k~~~a~~~i~RdI 252 (260)
+.+..-++.-+...++.+|. +.+...+.+....|.-++
T Consensus 602 ~~~~~~l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~ 640 (720)
T PRK00254 602 LELADWLMYSLIELYKLFEPKQEVLDYLETLHLRVKHGV 640 (720)
T ss_pred HHHHHHHHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCC
Confidence 99999999999999988884 565566665555555444
No 10
>PRK01172 ski2-like helicase; Provisional
Probab=91.27 E-value=4.5 Score=41.08 Aligned_cols=162 Identities=15% Similarity=0.115 Sum_probs=93.2
Q ss_pred HHHHHHHHHHHhHhCCCCCC--CccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhccccCCCcccccc
Q 024969 65 RDELKNRSRVLKKLGHINAD--GVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQINLR 142 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~~--~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~~~~~~~~~~ 142 (260)
.+.....++-|.+.|+|+.+ ..+|..|++++..+- +.-. ++.+.+..=...+...+-.++|.. .| -.+- ...
T Consensus 443 ~~~v~~~l~~L~~~~~i~~~~~~~~t~lG~~~s~~~l-~~~t-~~~~~~~l~~~~~~~~~l~~~~~~-~e-~~~~--~~~ 516 (674)
T PRK01172 443 DYYIESSLKFLKENGFIKGDVTLRATRLGKLTSDLYI-DPES-ALILKSAFDHDYDEDLALYYISLC-RE-IIPA--NTR 516 (674)
T ss_pred HHHHHHHHHHHHHCCCcccCCcEeECHHHHHHHHhCC-CHHH-HHHHHHHhhccCCHHHHHHHhhcC-cc-cccc--ccc
Confidence 34567788999999999854 368999999999885 4322 233333222233444554444321 11 1000 011
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 024969 143 MELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFL 222 (260)
Q Consensus 143 ~~l~~~~~~l~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elL 222 (260)
++ ..+.+++.+ .+. .+.+. ......-+.++|-++.+..+|.+..++..|++=+++....-+.
T Consensus 517 ~~-----~~~~~~~~~-------~~~---~~~~~---~~~k~~~ll~~~~~~~~~~~i~~~~~~~~g~l~~~~~~~~~~~ 578 (674)
T PRK01172 517 DD-----YYAMEFLED-------IGV---IDGDI---SAAKTAMVLRGWISEASMQKITDTYGIAPGDVQARASSADWIS 578 (674)
T ss_pred hH-----HHHHHHHHH-------hcc---ccchh---HHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence 11 111122221 222 11111 2345667899999999999999999999999988865555555
Q ss_pred HHHHHHHhhcCCHHHHHHHHHHHHhhcCC
Q 024969 223 NQLRAAAQAVGEVNLEKKFAAASESLRRG 251 (260)
Q Consensus 223 rql~~a~~~ig~~~L~~k~~~a~~~i~Rd 251 (260)
.-+...++. +.+++.+.++....-|.=|
T Consensus 579 ~a~~~~~~~-~~~~~~~~l~~~~~rl~~g 606 (674)
T PRK01172 579 YSLARLSSI-YKPEMRRKLEILNIRIKEG 606 (674)
T ss_pred HHHHHHHHH-hhHHHHHHHHHHHHHHHcC
Confidence 455555555 3477776655544444433
No 11
>smart00847 HA2 Helicase associated domain (HA2) Add an annotation. This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.
Probab=89.70 E-value=1.2 Score=32.90 Aligned_cols=60 Identities=18% Similarity=0.214 Sum_probs=42.5
Q ss_pred HHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhcccc
Q 024969 72 SRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVD 133 (260)
Q Consensus 72 ~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~ 133 (260)
.+.|..+|.||.++.+|..|+..+++-- ++-+ +-+|..+...+=-..++++++|.....+
T Consensus 3 ~~~L~~LgAld~~~~lT~lG~~m~~lPl-~Prl-a~~Ll~a~~~~~c~~~~~~i~a~ls~~~ 62 (92)
T smart00847 3 LELLYELGALDDDGRLTPLGRKMAELPL-DPRL-AKMLLAAAELFGCLDEILTIAAMLSVGD 62 (92)
T ss_pred HHHHHHCCCcCCCCCcCHHHHHHHHCCC-ChHH-HHHHHHHHhhcCcHHHHHHHHHHhcCCC
Confidence 4679999999998999999999999964 4444 4444444422114567888888776543
No 12
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=84.38 E-value=7 Score=40.86 Aligned_cols=66 Identities=20% Similarity=0.279 Sum_probs=48.9
Q ss_pred HHHHHHHHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhcccc
Q 024969 66 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVD 133 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~ 133 (260)
..+.+-+..|..+|.+|+++.+|..|+..+++- .++-+-.-+|....|. -..-.+|+.++++..+.
T Consensus 384 ~~~~~A~~~L~~lgald~~g~lT~~G~~m~~lp-~~Prla~~ll~a~~~~-~~~l~~a~~laall~e~ 449 (812)
T PRK11664 384 AALAAAKRLLQQLGALDGQGRLTARGRKMAALG-NDPRLAAMLVAAKEDD-EAALATAAKLAAILEEP 449 (812)
T ss_pred HHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcC-CchHHHHHHHHHHhcC-chhhHHHHHHHHhhccC
Confidence 578888999999999999999999999999996 3655555555544443 11113688888877764
No 13
>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=84.02 E-value=1.4 Score=31.79 Aligned_cols=31 Identities=19% Similarity=0.347 Sum_probs=28.3
Q ss_pred HHHhhCCCCHHHHHhhcCCCcchHHHHHHHH
Q 024969 188 IYCWSKGATFAEVIQMTDIFEGSIIRSARRL 218 (260)
Q Consensus 188 v~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl 218 (260)
--+|.+-.||..|-...++.|+++|..||+-
T Consensus 7 eMAweDRtpFeaI~~~fGL~E~eVi~lMR~~ 37 (72)
T TIGR03643 7 EMAWEDRTPFEAIEQQFGLSEKEVIKLMRQN 37 (72)
T ss_pred HHHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3589999999999999999999999999874
No 14
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=82.91 E-value=1.7 Score=31.56 Aligned_cols=31 Identities=16% Similarity=0.349 Sum_probs=28.3
Q ss_pred HHHhhCCCCHHHHHhhcCCCcchHHHHHHHH
Q 024969 188 IYCWSKGATFAEVIQMTDIFEGSIIRSARRL 218 (260)
Q Consensus 188 v~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl 218 (260)
--+|.+-.||..|-...++.|+++|..||+-
T Consensus 6 eMAweDRtpFeaI~~qfGl~E~eVi~lMR~~ 36 (73)
T PF10985_consen 6 EMAWEDRTPFEAIERQFGLSEKEVIKLMRKE 36 (73)
T ss_pred HHHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3589999999999999999999999999874
No 15
>PRK00118 putative DNA-binding protein; Validated
Probab=81.76 E-value=8.3 Score=29.96 Aligned_cols=66 Identities=9% Similarity=0.126 Sum_probs=48.8
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcC----CHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVG----EVNLEKKFAAAS 245 (260)
Q Consensus 180 ~~~~l~~vv~~W-a~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig----~~~L~~k~~~a~ 245 (260)
+++.--.++..+ ..|.|..+|.+..+++++++=+.+.|...-|++.-..-..+. ..++-.+++.+.
T Consensus 18 L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (104)
T PRK00118 18 LTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNELFDKIAYLK 88 (104)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHH
Confidence 556666666665 789999999999999999999999999999998766654322 344444444443
No 16
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=79.71 E-value=3.7 Score=42.95 Aligned_cols=49 Identities=20% Similarity=0.342 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCC
Q 024969 66 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFN 115 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~ 115 (260)
..+..-+..|..+|.||+++.+|..|+..+++-. ++-+---++..-.|.
T Consensus 381 ~~i~~a~~~L~~lgald~~~~lT~~G~~~~~lp~-~p~l~~~ll~~~~~~ 429 (819)
T TIGR01970 381 VALAAARQLLQRLGALDAQGRLTAHGKAMAALGC-HPRLAAMLLSAHSTG 429 (819)
T ss_pred HHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC-CHHHHHHHHHhhhcC
Confidence 4677888999999999999999999999999974 554444444443343
No 17
>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=79.57 E-value=4.1 Score=25.74 Aligned_cols=43 Identities=16% Similarity=0.223 Sum_probs=32.9
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFL 222 (260)
Q Consensus 180 ~~~~l~~vv~~W-a~G~~f~~i~~~t~l~EGdiVR~~rRl~elL 222 (260)
+++.--.++... ..|.+..+|.+..++.+|.+-+.+.|...-|
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 444444455554 4999999999999999999999998876543
No 18
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=78.78 E-value=4.8 Score=25.98 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=34.6
Q ss_pred CcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFL 222 (260)
Q Consensus 180 ~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elL 222 (260)
+++.-..++..|..|.|..+|.+..+++++.+=+.+.|+..-|
T Consensus 4 l~~~e~~i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444455677789999999999999999999999998874433
No 19
>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=77.51 E-value=5.5 Score=25.84 Aligned_cols=34 Identities=21% Similarity=0.295 Sum_probs=29.2
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHH
Q 024969 186 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLD 219 (260)
Q Consensus 186 ~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~ 219 (260)
.+++.+..|.|..+|.+..+++++.+-+.+.|+.
T Consensus 7 ~i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3556678999999999999999999988888763
No 20
>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=76.73 E-value=6.4 Score=25.67 Aligned_cols=38 Identities=18% Similarity=0.242 Sum_probs=31.8
Q ss_pred HHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 187 VIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 187 vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+...|-.|.|+.+|-+..++++|.+=+..+|..+-||+
T Consensus 13 i~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 13 IRLRYFEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 34556899999999999999999999999988887764
No 21
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=75.80 E-value=7.3 Score=31.28 Aligned_cols=62 Identities=19% Similarity=0.174 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHhHhCCCCC----C------CccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhh
Q 024969 65 RDELKNRSRVLKKLGHINA----D------GVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCF 129 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~----~------~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~ 129 (260)
....-++++-|++.|||.. + -.+|.+|+-+.+--. -.+.+-+...+|++++|+|++.+...+
T Consensus 68 ~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~---~~~~~~~~~~l~~~ls~ee~~~l~~~L 139 (144)
T PRK11512 68 LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCH---QLVGQDLHQELTKNLTADEVATLEHLL 139 (144)
T ss_pred HHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHHH---HHHHHHHHHHHHccCCHHHHHHHHHHH
Confidence 3577789999999999964 1 269999997653211 112234556688999999999876543
No 22
>PRK04217 hypothetical protein; Provisional
Probab=73.68 E-value=12 Score=29.39 Aligned_cols=51 Identities=12% Similarity=0.107 Sum_probs=43.8
Q ss_pred CcccHHHHHHHhh-CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHh
Q 024969 180 VRPFLMDVIYCWS-KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQ 230 (260)
Q Consensus 180 ~~~~l~~vv~~Wa-~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~ 230 (260)
+...--+++..|. .|.|+.+|.+..+++++++=+.+.|....|++.-....
T Consensus 43 Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~ 94 (110)
T PRK04217 43 MTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGR 94 (110)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 5556668888886 99999999999999999999999999999998665543
No 23
>PF12246 MKT1_C: Temperature dependent protein affecting M2 dsRNA replication; InterPro: IPR022039 This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the C-terminal region of MKT1.
Probab=73.17 E-value=2.6 Score=37.48 Aligned_cols=45 Identities=24% Similarity=0.189 Sum_probs=37.8
Q ss_pred HHHhHhCCCCCCCccchhhHHHhhhccC--------ChHHHHHHHhhCCCCCC
Q 024969 73 RVLKKLGHINADGVVQLKGRAACLIDTG--------DELLVTELMFNGTFNDL 117 (260)
Q Consensus 73 ~vL~~lgyid~~~~~t~kGrva~eI~~~--------~eLlltEll~~g~f~~L 117 (260)
+.|.-+||+++...+|.-|++....... .=+++-|+|..|+++.=
T Consensus 1 R~L~l~Gyi~~~~~lT~wGk~L~~~~~~~~~~~~~E~~ll~lELlR~g~L~~~ 53 (243)
T PF12246_consen 1 RFLELRGYIDKSHELTPWGKALAKALKSLKPNDLQEALLLLLELLRFGVLTLN 53 (243)
T ss_pred CchhHHhHhcCCCCcCHHHHHHHHHHhccCchhhhhHHHHHHHHHHcCCcCCC
Confidence 3578899999999999999999887743 23889999999998866
No 24
>PF13518 HTH_28: Helix-turn-helix domain
Probab=72.30 E-value=9.1 Score=24.72 Aligned_cols=35 Identities=17% Similarity=0.327 Sum_probs=30.9
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 186 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 186 ~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.+|..+.+|.|..++....+++.+.+-+|+++-.+
T Consensus 4 ~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 4 QIVELYLEGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 46777789999999999999999999999998765
No 25
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=70.49 E-value=10 Score=30.34 Aligned_cols=61 Identities=11% Similarity=0.061 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHhHhCCCCCC----------CccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhh
Q 024969 65 RDELKNRSRVLKKLGHINAD----------GVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCF 129 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~~----------~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~ 129 (260)
.+..-+.++-|++.|||... -.+|.+|+-..+--. -..+-+...+|.+++|+|+..+...+
T Consensus 60 ~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~----~~~~~~~~~~~~~l~~ee~~~l~~~l 130 (144)
T PRK03573 60 QPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVE----AVINKTRAEILHGISAEEIEQLITLI 130 (144)
T ss_pred hhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHH----HHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 45777899999999999651 159999998765321 12234555578889999988876654
No 26
>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=69.54 E-value=66 Score=33.25 Aligned_cols=135 Identities=19% Similarity=0.187 Sum_probs=84.1
Q ss_pred HHHHHHHHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHH---HHHhhhhccccCCCcccccc
Q 024969 66 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQV---AALASCFIPVDKSSEQINLR 142 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~el---aallS~~v~e~~~~~~~~~~ 142 (260)
+.+.+-+..|--||.+|..|.+|-.||.-||.-. |+.+---++-++..+ -+ +|| ||++|+...--. .+.
T Consensus 652 etL~~aLE~LyaLGALn~~GeLTk~GrrMaEfP~-dPmlsKmi~as~ky~-cs-~EiitiaamlS~~~svfy-----rpk 723 (902)
T KOG0923|consen 652 ETLLKALEQLYALGALNHLGELTKLGRRMAEFPV-DPMLSKMIVASEKYK-CS-EEIITIAAMLSVGASVFY-----RPK 723 (902)
T ss_pred HHHHHHHHHHHHhhccccccchhhhhhhhhhcCC-CHHHHhHHhhhcccc-ch-HHHHHHHHHHhcCchhee-----cch
Confidence 5666777888889999999999999999999874 776666666677765 33 454 455554432111 111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCC-CCHHHHHhhcCCCcchHHHHHHHHHHH
Q 024969 143 MELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKG-ATFAEVIQMTDIFEGSIIRSARRLDEF 221 (260)
Q Consensus 143 ~~l~~~~~~l~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G-~~f~~i~~~t~l~EGdiVR~~rRl~el 221 (260)
... ++.. -..-++..+..|+ -.++.+--.|..- .|++-+.++ +--.|+++|..|+
T Consensus 724 ~~~---------v~ad----~a~~~f~~~~gDh------i~~L~vyn~w~es~~s~~wC~e~-----~iq~~sm~rardi 779 (902)
T KOG0923|consen 724 DKQ---------VHAD----NARKNFEEPVGDH------IVLLNVYNQWKESKYSTQWCYEN-----FIQYRSMKRARDI 779 (902)
T ss_pred hhh---------hhhh----hhhhccCCCCcch------hhhhHHHHHHhhcchhhHHHHHh-----hhhHHHHHHHHHH
Confidence 100 0000 0111233333332 3567777788665 455555544 4558999999999
Q ss_pred HHHHHHHHhhc
Q 024969 222 LNQLRAAAQAV 232 (260)
Q Consensus 222 Lrql~~a~~~i 232 (260)
..|+-....-+
T Consensus 780 r~qL~gll~~v 790 (902)
T KOG0923|consen 780 RDQLEGLLERV 790 (902)
T ss_pred HHHHHHHhhhc
Confidence 99999887543
No 27
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=69.53 E-value=76 Score=35.11 Aligned_cols=63 Identities=19% Similarity=0.354 Sum_probs=44.7
Q ss_pred HHHHHHHHHHhHhCCCCCCC---ccchhhHHHhhhccCChHHHHHHHhhCC-CCCCCHHHHHHHhhhhccc
Q 024969 66 DELKNRSRVLKKLGHINADG---VVQLKGRAACLIDTGDELLVTELMFNGT-FNDLDHHQVAALASCFIPV 132 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~---~~t~kGrva~eI~~~~eLlltEll~~g~-f~~L~p~elaallS~~v~e 132 (260)
..+..-+..|..+|.||+++ .+|..|+..+.+-- ++- ++.+|..|. |.-+ .+++.++|++-.+
T Consensus 449 ~~i~~A~~~L~~LGAld~~~~~~~LT~lGr~ma~LPl-dPr-larmLl~a~~~gcl--~e~l~IaA~Ls~~ 515 (1283)
T TIGR01967 449 RAIRDGFRLLEELGALDDDEAEPQLTPIGRQLAQLPV-DPR-LARMLLEAHRLGCL--QEVLIIASALSIQ 515 (1283)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCccccHHHHHHhhcCC-ChH-HHHHHHHhhhcCCH--HHHHHHHHHHcCC
Confidence 45778889999999999877 79999999999974 554 455555444 4433 3455566666444
No 28
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=67.01 E-value=1.4e+02 Score=33.13 Aligned_cols=63 Identities=17% Similarity=0.290 Sum_probs=42.9
Q ss_pred HHHHHHHHHHhHhCCCCCC-----CccchhhHHHhhhccCChHHHHHHHh-hCCCCCCCHHHHHHHhhhhccc
Q 024969 66 DELKNRSRVLKKLGHINAD-----GVVQLKGRAACLIDTGDELLVTELMF-NGTFNDLDHHQVAALASCFIPV 132 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~-----~~~t~kGrva~eI~~~~eLlltEll~-~g~f~~L~p~elaallS~~v~e 132 (260)
+...+-+..|..+|.||.+ +.+|..|+..+++-- |+- ++-+|. ...|.-++ ++..++|++-.+
T Consensus 456 ~~i~~al~~L~~LgAld~~~~~~~~~LT~lG~~la~LPl-dPr-lakmLl~a~~~~c~~--evl~IaA~Lsv~ 524 (1294)
T PRK11131 456 RNIQDGVRLLEELGAITTDEQASAYKLTPLGRQLAQLPV-DPR-LARMVLEAQKHGCVR--EVMIITSALSIQ 524 (1294)
T ss_pred HHHHHHHHHHHHCCCCCccccCCCccCcHHHHHHHhCCC-ChH-HHHHHHHhhhcCCHH--HHHHHHHHHcCC
Confidence 4566778999999999853 479999999999974 544 445554 44455443 455556666554
No 29
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=65.36 E-value=4.4 Score=26.28 Aligned_cols=34 Identities=15% Similarity=0.267 Sum_probs=24.1
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHH
Q 024969 186 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLD 219 (260)
Q Consensus 186 ~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~ 219 (260)
.++..+..|.|..+|.+..+++..++-|+++|-.
T Consensus 9 ~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 9 QIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3566666799999999999999999999998854
No 30
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.44 E-value=48 Score=28.10 Aligned_cols=121 Identities=17% Similarity=0.141 Sum_probs=67.9
Q ss_pred CCCHHHHHHHhhhhccccCCCcc-------------ccccHHHHHHHHHHHHHHHHHHHHHHHcCCCC----Chhhhhhc
Q 024969 116 DLDHHQVAALASCFIPVDKSSEQ-------------INLRMELAKPLQQLQESARKIAEIQNECKLEV----NVDEYVES 178 (260)
Q Consensus 116 ~L~p~elaallS~~v~e~~~~~~-------------~~~~~~l~~~~~~l~~~~~~i~~~~~~~~l~~----~~~~~~~~ 178 (260)
.++|+|+-+.+|+.+|-- .++. -.+|..+..+++++.+.. .+.-..-++.+ |.++-
T Consensus 21 ~~t~aElHG~LsG~lcgG-~~d~sWq~l~~~~tneg~A~p~~l~~~l~~l~~a~---s~~L~d~~F~f~LlLpe~e~--- 93 (186)
T COG3079 21 GLTPAELHGLLSGLLCGG-LNDSSWQPLLHDLTNEGMAPPHGLLQALEQLLQAT---SQQLEDDGFAFQLLLPEGED--- 93 (186)
T ss_pred CCCHHHHHHHHHhhhhcC-CCchhHHHHHHHHhhccCCCcHHHHHHHHHHHHHH---HHHhcCCCeEEEEecCCCCc---
Confidence 689999999999999953 3322 123445666666554432 22222223322 22211
Q ss_pred cCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCC-----HHHHHHHHHHHHhhc
Q 024969 179 TVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGE-----VNLEKKFAAASESLR 249 (260)
Q Consensus 179 ~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~-----~~L~~k~~~a~~~i~ 249 (260)
.=+.-.+.+..|+++- +-.-++..-..-..---..|.++.++++|++=+| .++.+..++.++-+|
T Consensus 94 -~vf~rADAL~eW~nhF-----L~GlGL~~~~l~~~~gE~~EaldDL~~iaQlg~Deded~EE~~~~leEiiEyvR 163 (186)
T COG3079 94 -VVFDRADALAEWCNHF-----LLGLGLTQPKLSKLTGEAGEALDDLANIAQLGYDEDEDQEELEESLEEIIEYVR 163 (186)
T ss_pred -HHHHHHHHHHHHHHHH-----HHhhcccccchhhhcccHHHHHHHHHHHHHhcCCccccHHHHHHHHHHHHHHHH
Confidence 2367889999999852 2221121111111111346778888888887454 467777777777665
No 31
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=55.74 E-value=16 Score=23.41 Aligned_cols=31 Identities=13% Similarity=0.212 Sum_probs=22.8
Q ss_pred HHHHhhCCCCHHHHHhhcCCCcchHHHHHHH
Q 024969 187 VIYCWSKGATFAEVIQMTDIFEGSIIRSARR 217 (260)
Q Consensus 187 vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rR 217 (260)
+..-|..|.|..+|-+.-+.+..+|-|.++|
T Consensus 13 I~~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 13 IEALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp HHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4455789999999999999999999999987
No 32
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=54.98 E-value=44 Score=27.47 Aligned_cols=44 Identities=18% Similarity=0.182 Sum_probs=34.2
Q ss_pred hhCCCCHHHHHhhcCCCcch----HHHHHHHHHHHHHHHHHHHhhcCC
Q 024969 191 WSKGATFAEVIQMTDIFEGS----IIRSARRLDEFLNQLRAAAQAVGE 234 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGd----iVR~~rRl~elLrql~~a~~~ig~ 234 (260)
--.|.|..+|-+..++++|. +-|+..+|-+.|.+....-+-+||
T Consensus 130 ~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~~~~~~~ 177 (179)
T PRK12543 130 YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIFLGEVGN 177 (179)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence 45899999999999999999 666777777777766666555555
No 33
>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].
Probab=54.00 E-value=53 Score=25.99 Aligned_cols=27 Identities=22% Similarity=0.283 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHcCCCCCC-ChHHHHH
Q 024969 11 LVNQIEELEHKLFAHPLNKS-QDENQIR 37 (260)
Q Consensus 11 ~~~~~~~l~~~l~~~p~~~c-~~~~~~~ 37 (260)
+...+..|++.|++-+|..| --+++.+
T Consensus 54 L~e~i~~LE~RLRaGlCDRC~VtqE~ak 81 (120)
T PF10482_consen 54 LHENIKVLENRLRAGLCDRCTVTQELAK 81 (120)
T ss_pred HHHHHHHHHHHHhcccchHHHHHHHHHH
Confidence 34578889999999999999 8888876
No 34
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=52.79 E-value=39 Score=25.13 Aligned_cols=54 Identities=15% Similarity=0.185 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhHhCCCCC----CC------ccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHH
Q 024969 65 RDELKNRSRVLKKLGHINA----DG------VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQV 122 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~----~~------~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~el 122 (260)
.....+.++-|++-|||.. ++ .+|.+|+-+.+-... ..+-+....|.++++.|+
T Consensus 50 ~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~----~~~~~~~~~~~~l~~~e~ 113 (126)
T COG1846 50 RSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP----AAQELLAEILAGLSEEEL 113 (126)
T ss_pred HHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc----HHHHHHHHhccCCCHHHH
Confidence 4577789999999999965 22 699999988877654 667777889999999995
No 35
>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=50.45 E-value=27 Score=23.35 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=35.8
Q ss_pred CcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFL 222 (260)
Q Consensus 180 ~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elL 222 (260)
|.+.=.+++..|+.|.+-.+|-+.-++.++++-..++++..-+
T Consensus 4 LT~~E~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 4 LTERELEVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp S-HHHHHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 6667788999999999999999999999999988888776544
No 36
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=50.33 E-value=69 Score=24.49 Aligned_cols=37 Identities=14% Similarity=0.230 Sum_probs=29.2
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.++..++. ..|.+..+|.+..+++.+++.|.+.+|++
T Consensus 32 ~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 32 RILRILAE-QGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred HHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 34444432 45679999999999999999999999876
No 37
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=50.16 E-value=60 Score=25.75 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=29.5
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.++..++..-.|.+..+|.+...++.+++-|.+.||++
T Consensus 35 ~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 35 VTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 34444443334689999999999999999999999875
No 38
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=48.36 E-value=18 Score=26.05 Aligned_cols=41 Identities=17% Similarity=0.067 Sum_probs=29.1
Q ss_pred hhhhhhhHHHHHHHHHHHHHhHhCCCCCC---CccchhhHHHhhh
Q 024969 56 MRDSQIQKFRDELKNRSRVLKKLGHINAD---GVVQLKGRAACLI 97 (260)
Q Consensus 56 i~~~~~~~~~~e~~~~~~vL~~lgyid~~---~~~t~kGrva~eI 97 (260)
+....++. +..+.+.++.|.+.|+|..+ ..+|.||+-+.+.
T Consensus 25 i~~~~~L~-~~~~~~yL~~L~~~gLI~~~~~~Y~lTekG~~~l~~ 68 (77)
T PF14947_consen 25 IMYKANLN-YSTLKKYLKELEEKGLIKKKDGKYRLTEKGKEFLEE 68 (77)
T ss_dssp HHTTST---HHHHHHHHHHHHHTTSEEEETTEEEE-HHHHHHHHH
T ss_pred HHHHhCcC-HHHHHHHHHHHHHCcCeeCCCCEEEECccHHHHHHH
Confidence 33334554 47999999999999999763 3799999877654
No 39
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=47.70 E-value=46 Score=23.37 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhHhCCCCCCC----ccchhhH
Q 024969 65 RDELKNRSRVLKKLGHINADG----VVQLKGR 92 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~~~----~~t~kGr 92 (260)
-+.+.++++.|++-||+...+ .+|.||.
T Consensus 32 e~avRrrLr~me~~Glt~~~g~~G~~iT~~G~ 63 (66)
T PF08461_consen 32 EEAVRRRLRAMERDGLTRKVGRQGRIITEKGL 63 (66)
T ss_pred HHHHHHHHHHHHHCCCccccCCcccccCHHHH
Confidence 368889999999999998632 5888886
No 40
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=46.67 E-value=97 Score=25.10 Aligned_cols=77 Identities=18% Similarity=0.267 Sum_probs=44.2
Q ss_pred CCCChHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhHhCC
Q 024969 2 KIEDPEVVDLVNQIEELEHKLFAHPLNKSQDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGH 80 (260)
Q Consensus 2 ~i~~~~~~~~~~~~~~l~~~l~~~p~~~c~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~~lgy 80 (260)
|.+..|+..+.++-+.|.+.=.+-.|-.-...+.-.+-.++..|..+++.|+.+.+... .. .+-|+.++.-|..+|+
T Consensus 43 G~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~-~E-~da~k~k~e~l~~~~~ 119 (135)
T KOG4196|consen 43 GLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQVEKLKEENSRLR-RE-LDAYKSKYEALQNSAV 119 (135)
T ss_pred CCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HH-HHHHHHHHHHHHhhhh
Confidence 44445555555666666554444333211223333444567777778888877777622 21 3567777777777777
No 41
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=45.63 E-value=41 Score=24.55 Aligned_cols=65 Identities=15% Similarity=0.130 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHhHhCCCCCC----CccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhcc
Q 024969 65 RDELKNRSRVLKKLGHINAD----GVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIP 131 (260)
Q Consensus 65 ~~e~~~~~~vL~~lgyid~~----~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~ 131 (260)
.+...+.++-|++.|||... ..+|++|+-...--...--.+.+.+.. ..+++++++..++..|-.
T Consensus 13 ~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~~~~~~~~~l~~--~~~~~~~e~~~l~~~l~~ 81 (96)
T smart00529 13 PPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLRKHRLLERFLVD--VLGVDEEEVHEEAERLEH 81 (96)
T ss_pred hHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHHHHHHHHHHHHH--HhCCCHHHHHHHHHHHHc
Confidence 35677889999999999763 258999987542221111122333332 226888888887776643
No 42
>smart00351 PAX Paired Box domain.
Probab=45.57 E-value=37 Score=26.84 Aligned_cols=35 Identities=11% Similarity=0.147 Sum_probs=29.9
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 186 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 186 ~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.+|..+..|.|..+|.+..+++.+.+.||++|-.+
T Consensus 25 riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 25 RIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44555679999999999999999999999998654
No 43
>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=44.83 E-value=31 Score=22.09 Aligned_cols=33 Identities=12% Similarity=0.262 Sum_probs=25.8
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSA 215 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~ 215 (260)
..-.++...++|.|-.+|.+.++++-.+|=|.+
T Consensus 10 ~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 10 QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 466778888999999999999999998887765
No 44
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=44.44 E-value=44 Score=22.15 Aligned_cols=44 Identities=16% Similarity=0.132 Sum_probs=40.0
Q ss_pred ccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 182 PFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 182 ~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
..+.-+...|..|-++.++-..-++++..+-|.+....++|.+.
T Consensus 7 d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 7 DQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 46777888899999999999999999999999999999998764
No 45
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=44.38 E-value=1.8e+02 Score=24.02 Aligned_cols=51 Identities=16% Similarity=0.218 Sum_probs=29.7
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024969 6 PEVVDLVNQIEELEHKLFAHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRD 58 (260)
Q Consensus 6 ~~~~~~~~~~~~l~~~l~~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~ 58 (260)
.+..++..++.++++++++- ..- .+.+..+.-++..++.+|++.++++...
T Consensus 40 ~~~~~l~~Ei~~l~~E~~~i--S~qDeFAkwaKl~Rk~~kl~~el~~~~~~~~~ 91 (161)
T PF04420_consen 40 KEQRQLRKEILQLKRELNAI--SAQDEFAKWAKLNRKLDKLEEELEKLNKSLSS 91 (161)
T ss_dssp HHHHHHHHHHHHHHHHHTTS---TTTSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcC--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777888887766643 222 5555555555555555555555555554
No 46
>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=44.24 E-value=58 Score=25.57 Aligned_cols=45 Identities=9% Similarity=0.064 Sum_probs=36.5
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+.+.-..+++. ...|.|+.+|-+..+++++.+=..+.|...-|++
T Consensus 114 L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 44555666655 5799999999999999999998888888777765
No 47
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=44.16 E-value=98 Score=23.01 Aligned_cols=58 Identities=17% Similarity=0.308 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHH
Q 024969 42 KAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQ 121 (260)
Q Consensus 42 ~~~l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~e 121 (260)
..++..+++..+.++...+.- + .++...+.=++.+..++ ++++ -.|||++
T Consensus 3 leKi~~eieK~k~Kiae~Q~r-l-K~Le~qk~E~EN~EIv~-------------------------~VR~---~~mtp~e 52 (83)
T PF14193_consen 3 LEKIRAEIEKTKEKIAELQAR-L-KELEAQKTEAENLEIVQ-------------------------MVRS---MKMTPEE 52 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHHHHHH-------------------------HHHH---cCCCHHH
Confidence 345666666666666663332 2 34444444444444333 2222 3499999
Q ss_pred HHHHhhhh
Q 024969 122 VAALASCF 129 (260)
Q Consensus 122 laallS~~ 129 (260)
|+++|+..
T Consensus 53 L~~~L~~~ 60 (83)
T PF14193_consen 53 LAAFLRAM 60 (83)
T ss_pred HHHHHHHH
Confidence 99999877
No 48
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=44.12 E-value=80 Score=23.94 Aligned_cols=48 Identities=10% Similarity=0.162 Sum_probs=35.2
Q ss_pred cHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHh
Q 024969 183 FLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQ 230 (260)
Q Consensus 183 ~l~~vv~~W-a~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~ 230 (260)
....+.+.- ..|.|=.++|+..++..|-|-++++|+..+=+-+..++.
T Consensus 41 kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~~v~~~V~~l~~ 89 (91)
T PF03333_consen 41 KIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLNRVSQIVEQLSP 89 (91)
T ss_dssp HHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHGG
T ss_pred HHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 444455554 899999999999999999999999999998888777653
No 49
>COG1204 Superfamily II helicase [General function prediction only]
Probab=44.04 E-value=2.2e+02 Score=29.76 Aligned_cols=54 Identities=15% Similarity=0.155 Sum_probs=43.5
Q ss_pred ccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHH-------HHHHHHHHhhcCCH
Q 024969 182 PFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEF-------LNQLRAAAQAVGEV 235 (260)
Q Consensus 182 ~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~el-------Lrql~~a~~~ig~~ 235 (260)
+.-+..+..|++..+-..|+..+++..||+.+..-...-+ ..-+..-+.++|.+
T Consensus 591 ~~~~~~l~~wi~~~~~~~i~~~~~~~~~dl~~~~~~a~w~~~~~~~l~~~~~r~~~~~~~~ 651 (766)
T COG1204 591 LKTAARLLDWINEADEDEILNAYGVAPGDLLRIAETAEWLSADLLALGKAAERLAKILGLG 651 (766)
T ss_pred HHHHHHHHHHHHhCcHHHHHHHhCcchhhHHhhcchhhhhhhhhhhhhhhhhhhHhhhCCC
Confidence 4678899999999999999999999999999887777766 55555555555543
No 50
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=43.71 E-value=27 Score=25.70 Aligned_cols=31 Identities=19% Similarity=0.219 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhHhCCCCC------CCccchhhHHHhh
Q 024969 66 DELKNRSRVLKKLGHINA------DGVVQLKGRAACL 96 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~------~~~~t~kGrva~e 96 (260)
...++.+..|+++|||+. +.+||.||=-+-.
T Consensus 38 aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~ 74 (78)
T PF03444_consen 38 ATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALN 74 (78)
T ss_pred HHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHc
Confidence 467888999999999973 2379999865543
No 51
>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]
Probab=43.36 E-value=2.5e+02 Score=28.89 Aligned_cols=139 Identities=19% Similarity=0.215 Sum_probs=81.6
Q ss_pred HHHHHHHHHHhHhCCCCCCCccch-hhHHHhhhccCChHHHHHHHhhCCCCCCCH-HHHHHHhhhhccccCCCccccccH
Q 024969 66 DELKNRSRVLKKLGHINADGVVQL-KGRAACLIDTGDELLVTELMFNGTFNDLDH-HQVAALASCFIPVDKSSEQINLRM 143 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~~~t~-kGrva~eI~~~~eLlltEll~~g~f~~L~p-~elaallS~~v~e~~~~~~~~~~~ 143 (260)
+....=+..|..+|-||+++.+|. -|+..+++-- +.-+---++.++.|.-.+. --|||.|| .+...- .+++
T Consensus 435 ~~l~~AL~~L~~lgald~~g~lt~p~G~~ma~~Pl-~p~lsk~ll~s~~~gc~~e~l~i~a~Ls---v~~~f~---~p~~ 507 (674)
T KOG0922|consen 435 EALEEALEELYSLGALDDRGKLTSPLGRQMAELPL-EPHLSKMLLKSSELGCSEEILTIAAMLS---VQSVFS---RPKD 507 (674)
T ss_pred HHHHHHHHHHHhcCcccCcCCcCchHHhhhhhcCC-CcchhhhhhhccccCCcchhhhheeeee---ccceec---Cccc
Confidence 345556677888999999898888 9999999974 4444444555666665443 34555555 332211 1111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 024969 144 ELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLN 223 (260)
Q Consensus 144 ~l~~~~~~l~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLr 223 (260)
.-.+ . ..+...++..+..|+ ..+..+...|..-..=..-|..-.+. +|.++|..++=+
T Consensus 508 ~~~~---~---------a~~~~~kf~~~eGDh------~tlL~vy~~~~~~~~~~~wC~en~i~----~r~l~~a~~ir~ 565 (674)
T KOG0922|consen 508 KKAE---D---------ADRKRAKFANPEGDH------LTLLNVYESWKENGTSKKWCKENFIN----ARSLKRAKDIRK 565 (674)
T ss_pred hhhh---h---------hhHHHHhhcCcccCH------HHHHHHHHHHHhcCChhhHHHHhccc----HHHHHHHHHHHH
Confidence 1101 0 011222333333222 46677777886544444445444444 899999999999
Q ss_pred HHHHHHhhcC
Q 024969 224 QLRAAAQAVG 233 (260)
Q Consensus 224 ql~~a~~~ig 233 (260)
|+....+-+|
T Consensus 566 QL~~i~~~~~ 575 (674)
T KOG0922|consen 566 QLRRILDKFG 575 (674)
T ss_pred HHHHHHHHcC
Confidence 9998885443
No 52
>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=43.36 E-value=48 Score=21.56 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=22.6
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
--.|.|+.+|.+..+++++.+=+.+.|-..
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 469999999999999999999888888654
No 53
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=43.21 E-value=23 Score=24.29 Aligned_cols=29 Identities=31% Similarity=0.540 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHhHhCCCCCCC---ccchhhH
Q 024969 64 FRDELKNRSRVLKKLGHINADG---VVQLKGR 92 (260)
Q Consensus 64 ~~~e~~~~~~vL~~lgyid~~~---~~t~kGr 92 (260)
+.+.|...++-|.+.|++.-++ .+|.+|+
T Consensus 34 ~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 34 FAEEFQKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp THHH-HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HHHHHHHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 5678888899999999996533 6899997
No 54
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=41.73 E-value=63 Score=25.59 Aligned_cols=45 Identities=9% Similarity=0.184 Sum_probs=36.2
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+.+.--.++.. +..|.|..+|.+..++++|.+=..+.|.-.-|++
T Consensus 112 L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 112 LPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 44444444444 7899999999999999999999999888877765
No 55
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=41.65 E-value=73 Score=25.35 Aligned_cols=37 Identities=19% Similarity=0.100 Sum_probs=29.5
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.++..++ ...|.+..+|.+..++..+++-|.+.||++
T Consensus 44 ~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 44 KVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred HHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3444442 245689999999999999999999999975
No 56
>COG5570 Uncharacterized small protein [Function unknown]
Probab=41.54 E-value=1e+02 Score=21.02 Aligned_cols=46 Identities=26% Similarity=0.361 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHH---cCCCCCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 024969 8 VVDLVNQIEELEHKLF---AHPLNKSQDENQIRCFQRKAEVNHEIQQLKSK 55 (260)
Q Consensus 8 ~~~~~~~~~~l~~~l~---~~p~~~c~~~~~~~~~~~~~~l~~~~~~l~~~ 55 (260)
+.++.++=..|+..+. ++|- |+-..-..+-+++-+++.+|+.|+.+
T Consensus 7 l~eL~kkHg~le~ei~ea~n~Ps--~dd~~i~eLKRrKL~lKeeIEkLka~ 55 (57)
T COG5570 7 LAELEKKHGNLEREIQEAMNSPS--SDDLAIRELKRRKLRLKEEIEKLKAQ 55 (57)
T ss_pred HHHHHHhhchHHHHHHHHhcCCC--cchHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4455555555655553 4443 33333444556777888888888765
No 57
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=41.45 E-value=60 Score=34.30 Aligned_cols=65 Identities=22% Similarity=0.285 Sum_probs=46.6
Q ss_pred HHHHHHHHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHHHHHhhhhcccc
Q 024969 66 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVD 133 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~elaallS~~v~e~ 133 (260)
..+..=...|..+|.+|.++.+|.-|+-++.+-- ++=+-..++..+.+..+ .|.+.+.|++-.++
T Consensus 433 ~~i~~A~~~L~~LGAld~~g~LT~lG~~ms~lpl-dprLA~mLl~a~~~g~~--~e~~~Ias~Ls~~~ 497 (845)
T COG1643 433 AAIQAALTLLQELGALDDSGKLTPLGKQMSLLPL-DPRLARMLLTAPEGGCL--GEAATIASMLSEQD 497 (845)
T ss_pred HHHHHHHHHHHHcCCcCCCCCCCHHHHHHHhCCC-ChHHHHHHHhccccCcH--HHHHHHHHhhccCC
Confidence 4667778899999999999999999999999974 55444455555443322 35666666666665
No 58
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=41.40 E-value=41 Score=26.50 Aligned_cols=80 Identities=15% Similarity=0.200 Sum_probs=44.4
Q ss_pred HHHHHcCCCCChhhhhhccCcccHHHHHHHhh--CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHH
Q 024969 161 EIQNECKLEVNVDEYVESTVRPFLMDVIYCWS--KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLE 238 (260)
Q Consensus 161 ~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa--~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~ 238 (260)
..-+++|++....+|....++.+ -...|. .|.+|.+++... | ..-+++...-.-+.+.++.
T Consensus 19 ~~L~~~gi~~~~~~y~~~~~s~~---eL~~~l~~~g~~~~~li~t~----~----------~~~r~L~~~~~~~~~~~~~ 81 (117)
T COG1393 19 AWLEEHGIEYTFIDYLKTPPSRE---ELKKILSKLGDGVEELINTR----G----------TTYRELNLDKEDLSDEELI 81 (117)
T ss_pred HHHHHcCCCcEEEEeecCCCCHH---HHHHHHHHcCccHHHHHHhc----c----------chHHHcCCcccccChHHHH
Confidence 33467899888777765533322 233442 233355555432 2 2222333111123567777
Q ss_pred HHHHHHHHhhcCCccccCC
Q 024969 239 KKFAAASESLRRGIMFSNS 257 (260)
Q Consensus 239 ~k~~~a~~~i~RdIVf~~S 257 (260)
+.+-+.-.+|||+||...-
T Consensus 82 ~~i~~~~~LikRPivv~~~ 100 (117)
T COG1393 82 EALLENPSLIKRPIVVDNK 100 (117)
T ss_pred HHHHhChhhccCCeEEeCC
Confidence 7777777999999998553
No 59
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=39.97 E-value=76 Score=25.89 Aligned_cols=44 Identities=30% Similarity=0.212 Sum_probs=35.0
Q ss_pred ccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 182 PFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 182 ~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
|.--.++.. +..|.|..+|.+..++++|.+-+.+.|...-|+.+
T Consensus 143 ~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 143 EDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 333333333 56999999999999999999999999988888764
No 60
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=39.71 E-value=2.8 Score=30.98 Aligned_cols=25 Identities=24% Similarity=0.589 Sum_probs=13.7
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcch
Q 024969 186 DVIYCWSKGATFAEVIQMTDIFEGS 210 (260)
Q Consensus 186 ~vv~~Wa~G~~f~~i~~~t~l~EGd 210 (260)
..||+|++|+.|.+++..+.+.+|.
T Consensus 36 ~~vwrwS~~~~FtQal~~~~l~pGe 60 (82)
T PF12690_consen 36 KEVWRWSDGKMFTQALQEETLEPGE 60 (82)
T ss_dssp -EEEETTTT-------EEEEE-TT-
T ss_pred CEEEEecCCchhhheeeEEEECCCC
Confidence 5689999999999999999998885
No 61
>COG4910 PduE Propanediol dehydratase, small subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=39.49 E-value=41 Score=27.43 Aligned_cols=78 Identities=18% Similarity=0.267 Sum_probs=51.4
Q ss_pred cCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHH-HHHHHHHHHHHHHHHHhhcCCHHHHHHHHHH
Q 024969 166 CKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIR-SARRLDEFLNQLRAAAQAVGEVNLEKKFAAA 244 (260)
Q Consensus 166 ~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR-~~rRl~elLrql~~a~~~ig~~~L~~k~~~a 244 (260)
.|...++.||.-.+-.|+.+ .=+.|+|+.+|.-.+ +-.||+-- -+|=+-+.|+-=++.++=.|-|.|+..|+.|
T Consensus 31 ag~s~tv~DYPLa~k~Pe~V----Kta~~KsLddiTL~s-VL~g~vt~eD~RiTpetL~~QA~vArDaGR~tLA~NFERa 105 (170)
T COG4910 31 AGMSHTVADYPLAEKQPEAV----KTARGKSLDDITLDS-VLAGDVTMEDLRITPETLQAQADVARDAGRPTLALNFERA 105 (170)
T ss_pred ccccceeccCccccCChhhh----hccccCcHHHhhHHH-HhcCCCcHHHhhcCHHHHHHHHHHHHhcCchHHHhhHHhh
Confidence 34444555564332345532 346788999987553 44455533 3445667788777788877999999999999
Q ss_pred HHhh
Q 024969 245 SESL 248 (260)
Q Consensus 245 ~~~i 248 (260)
.++.
T Consensus 106 AELt 109 (170)
T COG4910 106 AELT 109 (170)
T ss_pred hhhh
Confidence 8864
No 62
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=38.21 E-value=1.2e+02 Score=22.27 Aligned_cols=45 Identities=13% Similarity=0.352 Sum_probs=36.4
Q ss_pred CCCCHHHHHhhcC-CCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 024969 193 KGATFAEVIQMTD-IFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASE 246 (260)
Q Consensus 193 ~G~~f~~i~~~t~-l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~ 246 (260)
-|.|+.+|=+.-+ .+--+++..++|+.+.+.+ |+.+...++....
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~---------d~~~~~~v~~i~~ 88 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE---------DPELKEDVEELEK 88 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh---------CHHHHHHHHHHHH
Confidence 4999999999988 9999999999999997753 5666666665544
No 63
>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=38.13 E-value=83 Score=23.93 Aligned_cols=36 Identities=19% Similarity=0.399 Sum_probs=31.4
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 189 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 189 ~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+.+..|.|+.+|.+..+++++++=+...|...-|+.
T Consensus 121 ~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 345689999999999999999999999998877764
No 64
>PRK10870 transcriptional repressor MprA; Provisional
Probab=37.74 E-value=82 Score=26.31 Aligned_cols=72 Identities=15% Similarity=0.093 Sum_probs=0.0
Q ss_pred HHHhhhhhhhHHHHHHHHHHHHHhHhCCCCCCC----------ccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHHH
Q 024969 53 KSKMRDSQIQKFRDELKNRSRVLKKLGHINADG----------VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQV 122 (260)
Q Consensus 53 ~~~i~~~~~~~~~~e~~~~~~vL~~lgyid~~~----------~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~el 122 (260)
..++.. .-..-.+..-++++-|++.|||.... .+|.+|+-+.+-- .=...-....+|.+++++|+
T Consensus 74 ~~eLa~-~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i----~~~~~~~~~~~~~~ls~~e~ 148 (176)
T PRK10870 74 PSELSC-ALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREV----LPPQHNCLHQLWSALSTTEK 148 (176)
T ss_pred HHHHHH-HHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH----HHHHHHHHHHHHhcCCHHHH
Q ss_pred HHHhhhh
Q 024969 123 AALASCF 129 (260)
Q Consensus 123 aallS~~ 129 (260)
..+...+
T Consensus 149 ~~l~~~L 155 (176)
T PRK10870 149 DQLEQIT 155 (176)
T ss_pred HHHHHHH
No 65
>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=37.09 E-value=26 Score=22.49 Aligned_cols=34 Identities=15% Similarity=0.301 Sum_probs=29.1
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 192 SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 192 a~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
-.+.|..+|++.+++..|.|-+.+.=-++|+..+
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~~a~ 47 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRYFPSKDDLLRAV 47 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHHCSSHHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHHcCCHHHHHhhC
Confidence 3578999999999999999999988888887654
No 66
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.82 E-value=62 Score=25.54 Aligned_cols=45 Identities=16% Similarity=0.034 Sum_probs=36.4
Q ss_pred CcccHHHHH-HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVI-YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 180 ~~~~l~~vv-~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+.+.-=.++ ..+-.|.|..||-+..++++|++-..+.|...-||+
T Consensus 107 L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 444444443 567899999999999999999999999998887775
No 67
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=36.63 E-value=69 Score=25.63 Aligned_cols=37 Identities=16% Similarity=0.267 Sum_probs=33.1
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 024969 189 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 226 (260)
Q Consensus 189 ~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~ 226 (260)
... .|.|..+|-+..++++|.+-..+.|...-|++.-
T Consensus 123 l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 123 LRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred HHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 455 9999999999999999999999999998888753
No 68
>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]
Probab=36.48 E-value=43 Score=35.61 Aligned_cols=61 Identities=23% Similarity=0.251 Sum_probs=50.9
Q ss_pred HHHHHHHHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCHHH-HHHHhh
Q 024969 66 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQ-VAALAS 127 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p~e-laallS 127 (260)
+...+=+..|++.|-++.+..+|+-|+.++.+- .|.-+==.+++.+.|.-|+|.= |||.+|
T Consensus 592 ~~v~~a~~~L~~igaL~~~e~LT~LG~~la~lP-vd~~igK~ll~g~if~cLdp~l~iaa~Ls 653 (924)
T KOG0920|consen 592 DAVDLAIERLKQIGALDESEELTPLGLHLASLP-VDVRIGKLLLFGAIFGCLDPALTIAAALS 653 (924)
T ss_pred HHHHHHHHHHHHhccccCcccchHHHHHHHhCC-CccccchhheehhhccccchhhhHHHHhc
Confidence 466777899999999999999999999999997 4666666777899999999964 555666
No 69
>PF06330 TRI5: Trichodiene synthase (TRI5); InterPro: IPR024652 This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species [, ].; GO: 0045482 trichodiene synthase activity, 0016106 sesquiterpenoid biosynthetic process; PDB: 1YYT_A 2PS5_A 2AEL_A 1YYS_A 1YJ4_A 2Q9Y_A 2PS4_A 2AEK_B 1KIY_B 2PS7_A ....
Probab=36.25 E-value=2.9e+02 Score=26.42 Aligned_cols=57 Identities=14% Similarity=0.218 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 024969 154 ESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLN 223 (260)
Q Consensus 154 ~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLr 223 (260)
...++|-..-++....-....|+. -++++.|.|..+.++.. -++.|++.+|+...|.
T Consensus 222 ~~~NDILSFYKE~l~a~E~~NyI~----------n~A~~~g~S~~eaL~~l---~~eti~a~~rv~~vL~ 278 (376)
T PF06330_consen 222 NYVNDILSFYKEELVAGETGNYIH----------NRARVHGVSILEALREL---TDETIEAVERVRRVLS 278 (376)
T ss_dssp HHHHHHHHHHHHHTTSSSSSSHHH----------HHHHHHT--HHHHHHHH---HHHHHHHHHHHHHHHT
T ss_pred HhhhhHHHHHHhhcccccccchhh----------hhhhccCCCHHHHHHHH---HHHHHHHHHHHHHHhc
Confidence 344445555555544444333432 35667999999888763 4677788777766653
No 70
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=36.11 E-value=73 Score=25.42 Aligned_cols=46 Identities=11% Similarity=0.154 Sum_probs=34.7
Q ss_pred CcccHHHHH-HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVI-YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 180 ~~~~l~~vv-~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
+.+.--.++ ..+-.|.|..||-+..++++|++=..+.|....|++.
T Consensus 107 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 333333344 4467999999999999999999977777777776664
No 71
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=35.53 E-value=29 Score=25.27 Aligned_cols=37 Identities=22% Similarity=0.548 Sum_probs=27.7
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.++...+. ..+++|.+|.+..++..|++=+.++.|+|
T Consensus 4 ~Il~~L~~-~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~ 40 (80)
T PF13601_consen 4 AILALLYA-NEEATFSELKEELGLTDGNLSKHLKKLEE 40 (80)
T ss_dssp HHHHHHHH-HSEEEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHhh-cCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 34445555 57789999999999999999888887765
No 72
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=35.07 E-value=1.5e+02 Score=20.71 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=9.4
Q ss_pred HHHHh-HhCCCCCCCc
Q 024969 72 SRVLK-KLGHINADGV 86 (260)
Q Consensus 72 ~~vL~-~lgyid~~~~ 86 (260)
-++=+ ++||+-++.+
T Consensus 58 e~~AR~~lgm~~~~E~ 73 (80)
T PF04977_consen 58 EKVAREKLGMVKPGEI 73 (80)
T ss_pred HHHHHHHcCCcCCCCE
Confidence 34444 7888876654
No 73
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=34.88 E-value=77 Score=21.01 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=24.7
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
|..+.+..+|.+..++..+++-|.+.++.+
T Consensus 17 ~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 17 LEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred HHCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 445599999999999999999888877754
No 74
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=34.77 E-value=1.1e+02 Score=24.93 Aligned_cols=45 Identities=13% Similarity=0.048 Sum_probs=35.7
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 180 ~~~~l~~vv~~W-a~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+.+..-.++... -.|.|..+|.+..++++|++=..+.|...-|++
T Consensus 130 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 444555555544 589999999999999999998888888777776
No 75
>PF12917 HD_2: HD containing hydrolase-like enzyme ; PDB: 3MZO_B.
Probab=34.37 E-value=3.2e+02 Score=24.01 Aligned_cols=113 Identities=15% Similarity=0.252 Sum_probs=60.7
Q ss_pred CCCCCCHHHHHHHhhhhccccCC-Ccccc----ccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHH
Q 024969 113 TFNDLDHHQVAALASCFIPVDKS-SEQIN----LRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDV 187 (260)
Q Consensus 113 ~f~~L~p~elaallS~~v~e~~~-~~~~~----~~~~l~~~~~~l~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~v 187 (260)
...+.++..++....+=-+.+.. .|.++ -+|+++..+.++.+...+ +++.+.+...+-++
T Consensus 51 ~G~~vd~~~lyekAL~HD~~E~FtGDI~TPVKy~tPelr~~~~~VE~~m~~---------------~~i~~~iP~e~q~~ 115 (215)
T PF12917_consen 51 FGNEVDWKELYEKALNHDYPEIFTGDIKTPVKYATPELREMLAQVEEEMTE---------------NFIKKEIPEEFQEA 115 (215)
T ss_dssp TT----HHHHHHHHHHTTGGGGTS----S-SSSS-HHHHHHHHHHHHHHHH---------------HHHHHHS-GGGHHH
T ss_pred hCCccCHHHHHHHHhccccHHHHcCCCCCcccccCHHHHHHHHHHHHHHHH---------------HHHHhhCCHHHHHH
Confidence 45578888887755444443343 23332 378888888877765421 12211122234443
Q ss_pred HHHhh-CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHH--HHHHHHHHHHhhcC
Q 024969 188 IYCWS-KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVN--LEKKFAAASESLRR 250 (260)
Q Consensus 188 v~~Wa-~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~--L~~k~~~a~~~i~R 250 (260)
-..+. .|+ .+--||-||+..-.++=++.-....-+ |||+ ..+.+.++...|+.
T Consensus 116 Y~~~l~E~K--------Ddt~EG~Iv~~ADkidal~e~~~Ei~~--GN~E~~F~e~y~e~l~~i~~ 171 (215)
T PF12917_consen 116 YRRRLKEGK--------DDTLEGQIVKAADKIDALYECFGEIQK--GNPEKVFKEIYRESLEKIKK 171 (215)
T ss_dssp HHHHHS-----------SSSHHHHHHHHHHHHHHHHHHHHHHHT--T-S-THHHHHHHHHHHHHHT
T ss_pred HHHHhhcCC--------cccHHHHHHHHHHHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHHHh
Confidence 33332 222 245689999888887777777766665 9988 88888888888755
No 76
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=33.85 E-value=96 Score=25.26 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=31.4
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
+..|.|..+|.+..++++|.+=..+.|...-|++.
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56899999999999999999999999988877764
No 77
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=33.62 E-value=1.6e+02 Score=25.04 Aligned_cols=32 Identities=19% Similarity=0.413 Sum_probs=27.3
Q ss_pred HHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 189 YCW-SKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 189 ~~W-a~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.-| ..|.+-.+|.+...+..+++.|.+.||++
T Consensus 53 ~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~ 85 (185)
T PRK13777 53 IAYHLKGASISEIAKFGVMHVSTAFNFSKKLEE 85 (185)
T ss_pred HHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHH
Confidence 334 46789999999999999999999999875
No 78
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=33.47 E-value=79 Score=25.77 Aligned_cols=46 Identities=20% Similarity=0.249 Sum_probs=37.1
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
+.+.--.|+.. .-.|.|..||-+.+++++|++=..+.|....|++.
T Consensus 135 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 33444455544 46999999999999999999999999998888864
No 79
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=32.92 E-value=3e+02 Score=23.14 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q 024969 36 IRCFQRKAEVNHEIQQLKSKMRD 58 (260)
Q Consensus 36 ~~~~~~~~~l~~~~~~l~~~i~~ 58 (260)
.+.+.+|.+++++++.+-++++.
T Consensus 66 qD~fAkwaRlnRKi~kl~~ele~ 88 (175)
T KOG4253|consen 66 QDNFAKWARLNRKINKLDKELET 88 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667788888888888777765
No 80
>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=32.87 E-value=75 Score=31.70 Aligned_cols=61 Identities=23% Similarity=0.263 Sum_probs=41.1
Q ss_pred HHHHHHHHHHhHhCCCCCCCccchhhHHHhhhccCChHHHHHHHhhCCCCCCCH-HHHHHHhh
Q 024969 66 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDH-HQVAALAS 127 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~~~~t~kGrva~eI~~~~eLlltEll~~g~f~~L~p-~elaallS 127 (260)
+.+.+-+++|--|+.+|++|.+|.-|++++|.-- |+-+.--+|-+-.|+=-+. --|+|.+|
T Consensus 433 EtLMrALE~LnYLaaLdDdGnLT~lG~imSEFPL-dPqLAkmLi~S~efnCsnEiLsisAMLs 494 (699)
T KOG0925|consen 433 ETLMRALEVLNYLAALDDDGNLTSLGEIMSEFPL-DPQLAKMLIGSCEFNCSNEILSISAMLS 494 (699)
T ss_pred HHHHHHHHHhhhhhhhCCCcccchhhhhhhcCCC-ChHHHHHHhhcCCCCchHHHHHHHhccc
Confidence 3444444555555556888999999999999986 7777777887877764332 23445554
No 81
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=32.54 E-value=55 Score=20.81 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=23.6
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 192 SKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 192 a~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
-.|.|..+|.+.++++.|.+=+.++++.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34589999999999999999999998875
No 82
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=32.42 E-value=1.1e+02 Score=24.84 Aligned_cols=34 Identities=15% Similarity=0.020 Sum_probs=30.7
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
...|.|..||.+..++++|.+=..++|...-|++
T Consensus 131 ~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 131 QLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999998888888877776
No 83
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=31.96 E-value=1.1e+02 Score=24.13 Aligned_cols=36 Identities=19% Similarity=0.170 Sum_probs=32.3
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 226 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~ 226 (260)
.-.|.|..+|-+..++++|.+=..+.|...-|++.-
T Consensus 119 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 119 YWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 569999999999999999999999999888888743
No 84
>KOG0286 consensus G-protein beta subunit [General function prediction only]
Probab=31.63 E-value=30 Score=32.02 Aligned_cols=52 Identities=25% Similarity=0.350 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhHhCCCCCCCccchhhHHH
Q 024969 43 AEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGHINADGVVQLKGRAA 94 (260)
Q Consensus 43 ~~l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~~lgyid~~~~~t~kGrva 94 (260)
..|.+|.++|++++++......--++.++..=|...|.+.=...-|+||..+
T Consensus 5 ~~l~~Eae~L~~qi~~~r~~~~D~~l~q~a~~~~~~~~i~~~~rr~LkGH~~ 56 (343)
T KOG0286|consen 5 EQLRQEAEQLKNQIRDARKKLNDVTLAQIAERLESVGRIQMRTRRTLKGHLN 56 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccHHHHhhccccceeeeeeeEEEeccccc
Confidence 4455555555555555332222234556667777788887667788899876
No 85
>cd00180 PKc Catalytic domain of Protein Kinases. Protein Kinases (PKs), catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The PK family is part of a larger superfamily that includes the catalytic domains of RIO kinases, aminoglycoside phosphotransferase, choline kinase, phosphoinositide 3-kinase (PI3K), and actin-fragmin kinase. PKs make up a large family of serine/threonine kinases, protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins. Majority of protein phosphorylation, about 95%, occurs on serine residues while only 1% occurs on tyrosine residues. Protein phosphorylation is a mechanism by which a wide variety of cellular proteins, such as enzymes and membrane channels, are reversibly regulated in response to certain stimuli. PKs often function as components of signal transduction pathways in which
Probab=31.61 E-value=30 Score=27.38 Aligned_cols=52 Identities=13% Similarity=0.227 Sum_probs=42.3
Q ss_pred cHHHHHHHhhCCCCHHHHHhhc--CCCcchHHHHHHHHHHHHHHHHHHHhhcCC
Q 024969 183 FLMDVIYCWSKGATFAEVIQMT--DIFEGSIIRSARRLDEFLNQLRAAAQAVGE 234 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t--~l~EGdiVR~~rRl~elLrql~~a~~~ig~ 234 (260)
+-..+++.|..|.++.+.+... .+.+..+.++++++...+..+....-+-||
T Consensus 64 ~~~~~~~e~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~~~~H~d 117 (215)
T cd00180 64 NHLYLVMEYCEGGSLKDLLKENEGKLSEDEILRILLQILEGLEYLHSNGIIHRD 117 (215)
T ss_pred CeEEEEEecCCCCcHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhCCeeccC
Confidence 3445688899999999999886 789999999999999999888876544444
No 86
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=31.38 E-value=84 Score=25.92 Aligned_cols=36 Identities=14% Similarity=0.019 Sum_probs=32.3
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 226 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~ 226 (260)
.-.|.|+.||-+..++++|++-..+.|...-||+.-
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 152 VVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 457999999999999999999999999998888753
No 87
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=30.92 E-value=99 Score=25.07 Aligned_cols=37 Identities=8% Similarity=0.156 Sum_probs=32.4
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 189 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 189 ~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
..+-.|.|..+|.+..++++|.+-..+.|...-|++.
T Consensus 130 l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 130 LYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999999998888888877763
No 88
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.14 E-value=99 Score=25.31 Aligned_cols=45 Identities=27% Similarity=0.265 Sum_probs=36.0
Q ss_pred CcccHHHHHH-HhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIY-CWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 180 ~~~~l~~vv~-~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+.+.--.++. .+-.|.|..+|-+..++++|.+-..+.|...-|+.
T Consensus 136 L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 136 LSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444445554 46899999999999999999999888888777765
No 89
>PF13730 HTH_36: Helix-turn-helix domain
Probab=30.04 E-value=59 Score=21.22 Aligned_cols=25 Identities=12% Similarity=0.240 Sum_probs=22.6
Q ss_pred CHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 196 TFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 196 ~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
|...|.+.+++..-++.|.+++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6789999999999999999999876
No 90
>PRK06930 positive control sigma-like factor; Validated
Probab=29.76 E-value=1.3e+02 Score=25.12 Aligned_cols=46 Identities=11% Similarity=0.183 Sum_probs=37.3
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
+.+.--.|+.. ...|.|+.+|-+..++++|.+=..+.|...-|+..
T Consensus 115 L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 115 LTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 55555566665 68999999999999999999988888887777653
No 91
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=29.53 E-value=83 Score=20.10 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=29.2
Q ss_pred HHHHHHHhhCC-CCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 184 LMDVIYCWSKG-ATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 184 l~~vv~~Wa~G-~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
=..++..-++| .++.+|.+.++++.+.+-+-++.|.+
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 34556666666 59999999999999999999988865
No 92
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=29.33 E-value=1.1e+02 Score=21.09 Aligned_cols=24 Identities=17% Similarity=0.324 Sum_probs=15.8
Q ss_pred HHHHhhCCCCCCCHHHHHHHhhhhccc
Q 024969 106 TELMFNGTFNDLDHHQVAALASCFIPV 132 (260)
Q Consensus 106 tEll~~g~f~~L~p~elaallS~~v~e 132 (260)
...+++| +++|.+++|+|.++-..
T Consensus 24 ~~~i~~g---~~s~~qiaAfL~al~~k 47 (66)
T PF02885_consen 24 FDAILDG---EVSDAQIAAFLMALRMK 47 (66)
T ss_dssp HHHHHTT---SS-HHHHHHHHHHHHHH
T ss_pred HHHHHcC---CCCHHHHHHHHHHHHHh
Confidence 3445554 46788888888888774
No 93
>KOG0660 consensus Mitogen-activated protein kinase [Signal transduction mechanisms]
Probab=29.19 E-value=28 Score=32.84 Aligned_cols=41 Identities=27% Similarity=0.565 Sum_probs=33.0
Q ss_pred HHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHH
Q 024969 187 VIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVN 236 (260)
Q Consensus 187 vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~ 236 (260)
.|--|+-|+-|+|++....+|+|. |-+.||.-.-.++|.|+
T Consensus 208 aiDiWSvGCI~AEmL~gkplFpG~---------d~v~Ql~lI~~~lGtP~ 248 (359)
T KOG0660|consen 208 AIDIWSVGCILAEMLTGKPLFPGK---------DYVHQLQLILELLGTPS 248 (359)
T ss_pred hhhhhhhhHHHHHHHcCCCCCCCC---------chHHHHHHHHHhcCCCC
Confidence 366799999999999999999994 66677777767777653
No 94
>PF04363 DUF496: Protein of unknown function (DUF496); InterPro: IPR007458 Members of this family are uncharacterised proteins.
Probab=29.17 E-value=2.2e+02 Score=21.54 Aligned_cols=32 Identities=28% Similarity=0.449 Sum_probs=25.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhH
Q 024969 32 DENQIRCFQRKAEVNHEIQQLKSKMRDSQIQK 63 (260)
Q Consensus 32 ~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~ 63 (260)
.-+..+.+.++.+|++++..-.++|.+.+..+
T Consensus 4 VlE~Vr~~RrKNKl~REi~Dn~kKIRDNqKRV 35 (95)
T PF04363_consen 4 VLEFVRMYRRKNKLKREIEDNEKKIRDNQKRV 35 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence 34567888999999999999999888755443
No 95
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.05 E-value=92 Score=23.02 Aligned_cols=34 Identities=18% Similarity=0.343 Sum_probs=29.5
Q ss_pred HHHHHhhCCCC-HHHHHhhcCCCcchHHHHHHHHH
Q 024969 186 DVIYCWSKGAT-FAEVIQMTDIFEGSIIRSARRLD 219 (260)
Q Consensus 186 ~vv~~Wa~G~~-f~~i~~~t~l~EGdiVR~~rRl~ 219 (260)
.++...+.|.+ -.+|++..++...++=|+++|..
T Consensus 3 ~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 3 QILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46777889996 99999999999999999999955
No 96
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=28.88 E-value=1.4e+02 Score=25.53 Aligned_cols=35 Identities=9% Similarity=0.082 Sum_probs=30.3
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
...|.|+.+|.+..++++|.+=+.+.|...-|++.
T Consensus 188 y~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 188 YYEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999988888887777653
No 97
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=28.86 E-value=1.4e+02 Score=26.36 Aligned_cols=61 Identities=20% Similarity=0.225 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHcCCCCChhhhhhccCcccH---HHHHHHhhCCCCHHHHHhhcCCCcchHHHHHH
Q 024969 155 SARKIAEIQNECKLEVNVDEYVESTVRPFL---MDVIYCWSKGATFAEVIQMTDIFEGSIIRSAR 216 (260)
Q Consensus 155 ~~~~i~~~~~~~~l~~~~~~~~~~~~~~~l---~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~r 216 (260)
+.+.|...++++|+-+|.--++.. .-|++ ..++..|-.|.+..+|-..|.-+++.+=|-|+
T Consensus 122 I~~~i~~yq~e~g~vvPtrG~i~D-iGp~~tHK~~ii~~~l~g~~~~eiar~t~HS~~av~rYi~ 185 (220)
T PF07900_consen 122 ISKDIKEYQKEHGVVVPTRGTIHD-IGPGVTHKKIIIRLYLKGKPTPEIARRTNHSPEAVDRYIK 185 (220)
T ss_pred HHHHHHHHHHHcCceeccCCcccc-cCCcchHHHHHHHHHHcCCCHHHHHHHhccCHHHHHHHHH
Confidence 566788889999987774333334 55665 36788999999999999999999988866654
No 98
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=28.85 E-value=98 Score=27.13 Aligned_cols=37 Identities=14% Similarity=0.056 Sum_probs=32.6
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 189 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 189 ~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
..+..|.|..+|-+..++++|.+-+.+.|...-||+.
T Consensus 216 l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 216 CTFEENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4467999999999999999999988888888888764
No 99
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=28.64 E-value=64 Score=21.33 Aligned_cols=30 Identities=23% Similarity=0.349 Sum_probs=25.2
Q ss_pred hhCC--CCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 191 WSKG--ATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 191 Wa~G--~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
...| .+..+|.+.+++..+.+-|.+++|++
T Consensus 16 ~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 16 RHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3445 79999999999999999999999875
No 100
>KOG0662 consensus Cyclin-dependent kinase CDK5 [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=28.48 E-value=49 Score=28.85 Aligned_cols=39 Identities=31% Similarity=0.566 Sum_probs=31.6
Q ss_pred HHHhhCCCCHHHHHhh-cCCCcchHHHHHHHHHHHHHHHHHHHhhcCCH
Q 024969 188 IYCWSKGATFAEVIQM-TDIFEGSIIRSARRLDEFLNQLRAAAQAVGEV 235 (260)
Q Consensus 188 v~~Wa~G~~f~~i~~~-t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~ 235 (260)
+--|..|+-|+|+-.. -.+++|. |+..|+..+.+.+|.|
T Consensus 183 idmwsagcifaelanagrplfpg~---------dvddqlkrif~~lg~p 222 (292)
T KOG0662|consen 183 IDMWSAGCIFAELANAGRPLFPGN---------DVDDQLKRIFRLLGTP 222 (292)
T ss_pred hHhhhcchHHHHHhhcCCCCCCCC---------cHHHHHHHHHHHhCCC
Confidence 5679999999999887 4899995 6677888887777754
No 101
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.42 E-value=1.4e+02 Score=24.58 Aligned_cols=49 Identities=12% Similarity=0.114 Sum_probs=40.0
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAA 228 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a 228 (260)
+.+.--.++.. +-.|.|..+|.+..++++|.+=..+.|...-|++.-..
T Consensus 123 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 172 (185)
T PRK12542 123 LNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGG 172 (185)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 55555556654 78999999999999999999999999988888886533
No 102
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=28.41 E-value=78 Score=20.80 Aligned_cols=37 Identities=22% Similarity=0.420 Sum_probs=28.2
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.++..++. ..|.+..+|-+..++..+.+-|.+++|.+
T Consensus 7 ~iL~~l~~-~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 7 RILRILYE-NGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHHHH-HSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 34444444 34579999999999999999999999875
No 103
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=28.38 E-value=1.1e+02 Score=19.50 Aligned_cols=29 Identities=10% Similarity=0.250 Sum_probs=24.9
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 192 SKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 192 a~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
..+.++.+|.+..++..+++-+.++++.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45679999999999999998888888775
No 104
>PRK15443 pduE propanediol dehydratase small subunit; Provisional
Probab=28.31 E-value=1e+02 Score=25.03 Aligned_cols=54 Identities=19% Similarity=0.262 Sum_probs=35.9
Q ss_pred hCCCCHHHHHhhc----CCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhc
Q 024969 192 SKGATFAEVIQMT----DIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESLR 249 (260)
Q Consensus 192 a~G~~f~~i~~~t----~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~~i~ 249 (260)
..|+++.+|.-.. ++...|+ |.-. |.|.-=+.+|+-.|.+.|+..|+.|.++..
T Consensus 21 ~tGk~l~diTle~V~~G~v~~~Dl-RItp---etL~~QaqiAe~~Gr~~la~NfrRAAELt~ 78 (138)
T PRK15443 21 PTGKSLDDITLENVLSGKVTAEDL-RITP---ETLRMQAQIAEDAGRPQLAMNFRRAAELTA 78 (138)
T ss_pred CCCCChhHhhHHHHHcCCCCHHHh-ccCH---HHHHHHHHHHHHcCCHHHHHHHHHHHhccC
Confidence 5788999886542 4444443 4433 444444444444599999999999999864
No 105
>PF07749 ERp29: Endoplasmic reticulum protein ERp29, C-terminal domain; InterPro: IPR011679 ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals []. This protein is found associated with an N-terminal thioredoxin-like domain (IPR006662 from INTERPRO), which is homologous to the domain of human protein disulphide isomerase (PDI). ERp29 may help mediate the chaperone function of PDI. The C-terminal Erp29 domain has a 5-helical bundle fold. ERp29 is thought to form part of the thyroglobulin folding complex []. ; GO: 0005783 endoplasmic reticulum; PDB: 2QC7_B 1G7D_A 2C0G_B 1OVN_A 2C0F_A 2C0E_A 2C1Y_A.
Probab=28.18 E-value=1e+02 Score=23.17 Aligned_cols=34 Identities=26% Similarity=0.420 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHhHh
Q 024969 45 VNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKL 78 (260)
Q Consensus 45 l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~~l 78 (260)
+..|+++|.+-+...-+..-.++|..+.+||+.|
T Consensus 61 v~~E~~RL~~lL~~~l~~~K~del~~R~NIL~~F 94 (95)
T PF07749_consen 61 VAKEIARLERLLEGKLSPEKKDELQKRLNILSSF 94 (95)
T ss_dssp HHHHHHHHHHHHHSSS-HHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHc
Confidence 4567777877777544445668999999999865
No 106
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=27.94 E-value=56 Score=22.04 Aligned_cols=30 Identities=13% Similarity=0.091 Sum_probs=20.7
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcC-CCcchHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTD-IFEGSII 212 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~-l~EGdiV 212 (260)
..-.++..|+.|.|..+|.+..+ +...++-
T Consensus 20 ~v~~i~~~~~~G~s~eeI~~~yp~Lt~~~i~ 50 (56)
T PF04255_consen 20 PVRDILDLLAAGESPEEIAEDYPSLTLEDIR 50 (56)
T ss_dssp BHHHHHHHHHTT--HHHHHHHSTT--HHHHH
T ss_pred cHHHHHHHHHcCCCHHHHHHHCCCCCHHHHH
Confidence 45677888899999999999976 7766653
No 107
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=27.82 E-value=76 Score=31.05 Aligned_cols=68 Identities=19% Similarity=0.266 Sum_probs=45.7
Q ss_pred HHHh-hCC-CCHHHH-HhhcCCCcchHH---HHHHHHHHHHHHHHHH-------------HhhcCCHHHHHHHHHHHHhh
Q 024969 188 IYCW-SKG-ATFAEV-IQMTDIFEGSII---RSARRLDEFLNQLRAA-------------AQAVGEVNLEKKFAAASESL 248 (260)
Q Consensus 188 v~~W-a~G-~~f~~i-~~~t~l~EGdiV---R~~rRl~elLrql~~a-------------~~~ig~~~L~~k~~~a~~~i 248 (260)
-|.| +.| ++|++- ..+|++.|+||| -.-++|..++.|+..- +.+||| +|...+.++.+.+
T Consensus 49 ~~~~~~~g~~~~~~~r~~~tdl~E~Di~~~~g~~~~L~~~i~ei~~~~~p~~ifv~~TC~t~iIGd-Dle~va~~~~~~~ 127 (457)
T CHL00073 49 YFLQNALGVMIFAEPRYAMAELEEGDISAQLNDYEELKRLCLQIKKDRNPSVIVWIGTCTTEIIKM-DLEGMAPKLEAEI 127 (457)
T ss_pred cchhccccCcccCCccceecccCchhhhhhcCCHHHHHHHHHHHHHhCCCCEEEEEccCcHHhhcc-CHHHHHHHHHHhh
Confidence 3556 555 466651 112899999999 6667788888887653 344555 6777777777777
Q ss_pred cCCccccC
Q 024969 249 RRGIMFSN 256 (260)
Q Consensus 249 ~RdIVf~~ 256 (260)
.=+||.+.
T Consensus 128 gipVV~v~ 135 (457)
T CHL00073 128 GIPIVVAR 135 (457)
T ss_pred CCCEEEEe
Confidence 77777654
No 108
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.56 E-value=1.6e+02 Score=24.42 Aligned_cols=48 Identities=13% Similarity=0.133 Sum_probs=36.5
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRA 227 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~ 227 (260)
+.+.--.++.. ...|.|+.+|.+..++++|++=..+.|...-|+.+-.
T Consensus 112 Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 112 LPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444 4689999999999999999998888888777776544
No 109
>KOG0661 consensus MAPK related serine/threonine protein kinase [Signal transduction mechanisms]
Probab=26.88 E-value=35 Score=33.63 Aligned_cols=41 Identities=20% Similarity=0.477 Sum_probs=35.4
Q ss_pred HHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHH
Q 024969 188 IYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNL 237 (260)
Q Consensus 188 v~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L 237 (260)
|--||-|+=+.||.....+|+| .+=+.||-.++.++|.|.-
T Consensus 191 vD~wA~GcI~aEl~sLrPLFPG---------~sE~Dqi~KIc~VLGtP~~ 231 (538)
T KOG0661|consen 191 VDMWAVGCIMAELYSLRPLFPG---------ASEIDQIYKICEVLGTPDK 231 (538)
T ss_pred hHHHHHHHHHHHHHHhcccCCC---------CcHHHHHHHHHHHhCCCcc
Confidence 6679999999999999999999 3557888889999998653
No 110
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=26.71 E-value=1.7e+02 Score=23.53 Aligned_cols=45 Identities=18% Similarity=0.107 Sum_probs=34.4
Q ss_pred ccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 024969 182 PFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 226 (260)
Q Consensus 182 ~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~ 226 (260)
+.--.|+.. ...|.|..||.+..++++|.+=..+.|-..-|++.-
T Consensus 121 ~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 121 PEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 333334333 568999999999999999999888888777777643
No 111
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=26.66 E-value=1.5e+02 Score=23.71 Aligned_cols=49 Identities=14% Similarity=0.053 Sum_probs=40.5
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAA 228 (260)
Q Consensus 180 ~~~~l~~vv~~W-a~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a 228 (260)
+.+.--.++..+ ..|.|..+|.+..++++|.+=-.+.|...-|++.-.-
T Consensus 109 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 109 LPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 556666677765 6999999999999999999998888888888876543
No 112
>PF14493 HTH_40: Helix-turn-helix domain
Probab=26.60 E-value=1.5e+02 Score=21.78 Aligned_cols=35 Identities=20% Similarity=0.254 Sum_probs=29.0
Q ss_pred HHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHH
Q 024969 187 VIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEF 221 (260)
Q Consensus 187 vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~el 221 (260)
-...|.+|.|..+|-+.-++.+|+|..-+-+....
T Consensus 6 T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 6 TYELFQKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 34568899999999999999999998877766543
No 113
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=26.60 E-value=1.9e+02 Score=23.94 Aligned_cols=48 Identities=21% Similarity=0.160 Sum_probs=36.6
Q ss_pred CcccHHHHHH-HhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIY-CWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRA 227 (260)
Q Consensus 180 ~~~~l~~vv~-~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~ 227 (260)
+.+.--.|+. ..-.|.|+.+|.+..++++|.+=..+.|....|++.-.
T Consensus 142 Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 142 LPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4444444444 35599999999999999999998888888888876443
No 114
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=26.08 E-value=2.9e+02 Score=25.98 Aligned_cols=59 Identities=15% Similarity=0.124 Sum_probs=42.2
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHH------HHHHHHHHHHHHHhhcCCHHHHHHHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSAR------RLDEFLNQLRAAAQAVGEVNLEKKFAAAS 245 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~r------Rl~elLrql~~a~~~ig~~~L~~k~~~a~ 245 (260)
.+-.+...=.+|.|+++.++.+++++..+++.++ ++++.|.++++--+ .++..+.+...
T Consensus 301 ~~~~i~~~v~~G~sls~al~~~~~fp~~~~~~i~~GE~sG~L~~~L~~la~~~~----~~~~~~~~~~~ 365 (399)
T PRK10573 301 ALTQIQQQIAQGIPLWLALKNHPLFPPLCLQLVRVGEESGSLDLMLENLAHWHQ----EQTQALADNLA 365 (399)
T ss_pred HHHHHHHHHHCcccHHHHHhhCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHH----HHHHHHHHHHH
Confidence 4455555567899999999999999999998887 47777777766653 44554444433
No 115
>cd00131 PAX Paired Box domain
Probab=26.01 E-value=1.2e+02 Score=24.02 Aligned_cols=33 Identities=12% Similarity=0.154 Sum_probs=27.8
Q ss_pred HHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 188 IYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 188 v~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
+.....|.|-.+|.+..++..+.+.||++|-.+
T Consensus 27 v~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 27 VELAQSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 333468999999999999999999999998665
No 116
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=26.00 E-value=1.1e+02 Score=24.40 Aligned_cols=47 Identities=13% Similarity=0.087 Sum_probs=36.4
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 226 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~ 226 (260)
+.+.--.++.. +..|.|..+|.+..++++|.+=..+.|...-|+.+.
T Consensus 113 L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 113 LPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred CCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 44444444444 679999999999999999998888888888777653
No 117
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=25.82 E-value=71 Score=25.53 Aligned_cols=22 Identities=9% Similarity=0.170 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHhhcCCccccC
Q 024969 235 VNLEKKFAAASESLRRGIMFSN 256 (260)
Q Consensus 235 ~~L~~k~~~a~~~i~RdIVf~~ 256 (260)
.++.+.+-+=-.+|||+||...
T Consensus 77 ~e~i~ll~~~P~LikRPIv~~~ 98 (132)
T PRK13344 77 NEVIDLIQENPRILKSPILIDD 98 (132)
T ss_pred HHHHHHHHhCccceeCcEEEeC
Confidence 3344444444457999998753
No 118
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=25.60 E-value=65 Score=19.94 Aligned_cols=29 Identities=7% Similarity=0.072 Sum_probs=21.2
Q ss_pred HhhCCCCHHHHHhhcCCCcchHHHHHHHH
Q 024969 190 CWSKGATFAEVIQMTDIFEGSIIRSARRL 218 (260)
Q Consensus 190 ~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl 218 (260)
.+.++.++.+|.+..++++.-+.|.+++.
T Consensus 4 ~~~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 4 NLQQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp TT-SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 35677889999999999999999998875
No 119
>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=25.44 E-value=74 Score=20.22 Aligned_cols=35 Identities=23% Similarity=0.444 Sum_probs=24.9
Q ss_pred cHHHHHHHhhCC-CCHHHHHhhcCCCcchHHHHHHHHH
Q 024969 183 FLMDVIYCWSKG-ATFAEVIQMTDIFEGSIIRSARRLD 219 (260)
Q Consensus 183 ~l~~vv~~Wa~G-~~f~~i~~~t~l~EGdiVR~~rRl~ 219 (260)
.+..+... +| .||.+|-+..++++..+.+-++|+.
T Consensus 7 ~Il~~Lq~--d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 7 KILRLLQE--DGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHH---TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHH--cCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 44444443 34 6999999999999999999999874
No 120
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=25.25 E-value=3e+02 Score=21.09 Aligned_cols=10 Identities=20% Similarity=0.468 Sum_probs=7.1
Q ss_pred HhCCCCCCCc
Q 024969 77 KLGHINADGV 86 (260)
Q Consensus 77 ~lgyid~~~~ 86 (260)
+|||+.++.+
T Consensus 74 ~Lg~vk~gEi 83 (105)
T PRK00888 74 ELGMVKPGET 83 (105)
T ss_pred HcCCCCCCCE
Confidence 5888886653
No 121
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.07 E-value=1.3e+02 Score=26.33 Aligned_cols=35 Identities=14% Similarity=0.054 Sum_probs=31.3
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
+..|.|+.+|-+..++++|.+=+...|...-||+.
T Consensus 218 ~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 218 FIENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred HhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999999888888877754
No 122
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=24.96 E-value=1.8e+02 Score=24.19 Aligned_cols=45 Identities=22% Similarity=0.240 Sum_probs=36.5
Q ss_pred HhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCC
Q 024969 190 CWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGE 234 (260)
Q Consensus 190 ~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~ 234 (260)
....|.|..||.+..++++|.+-..+.|...-|+..-.....-||
T Consensus 146 ~~~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~~~~~~ 190 (192)
T PRK09643 146 VDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYLRAGGN 190 (192)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 356999999999999999999999988888888776655544444
No 123
>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=24.83 E-value=82 Score=24.77 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=30.9
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
.-.|.|+.+|.+..++++|++-..+.|...-|++.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999998888777764
No 124
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=24.80 E-value=60 Score=30.57 Aligned_cols=27 Identities=33% Similarity=0.370 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhHhCCCCCC-----CccchhhH
Q 024969 66 DELKNRSRVLKKLGHINAD-----GVVQLKGR 92 (260)
Q Consensus 66 ~e~~~~~~vL~~lgyid~~-----~~~t~kGr 92 (260)
-..++.+..|+++|||... -+||.+|=
T Consensus 42 ATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gy 73 (346)
T COG1420 42 ATIRNEMADLEKLGLIEKPHTSSGRVPTDKGY 73 (346)
T ss_pred hhHHHHHHHHHHCCCccCccccCCcCCcHhHH
Confidence 4778999999999999873 37999995
No 125
>PF10153 DUF2361: Uncharacterised conserved protein (DUF2361); InterPro: IPR019310 This entry represents the rRNA-processing protein EFG1 family. EFG1 is involved in rRNA processing.
Probab=24.76 E-value=1.9e+02 Score=22.76 Aligned_cols=73 Identities=18% Similarity=0.292 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCC----ChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHh-HhCCC
Q 024969 9 VDLVNQIEELEHKLFAHPLNKS----QDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLK-KLGHI 81 (260)
Q Consensus 9 ~~~~~~~~~l~~~l~~~p~~~c----~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~e~~~~~~vL~-~lgyi 81 (260)
.+....+..|+..+..+.-..- -..-|.--|.++.++.+.+.++++++....+..-..++..-+..++ ++.|+
T Consensus 24 ~~~Er~L~~L~~~l~~~~~~~~~kk~~~kYh~VRFfERkKa~R~lkql~k~l~~~~~~~~~~~l~~~l~~~~~DL~Yv 101 (114)
T PF10153_consen 24 VEKERELEALKRELEEAERKEKEKKMAKKYHMVRFFERKKATRKLKQLEKKLEEAEDKKEIKELEKELHKLEVDLNYV 101 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHH
Confidence 3444556666666554332211 1122555566778888888888888877442222344444444333 45554
No 126
>KOG0594 consensus Protein kinase PCTAIRE and related kinases [General function prediction only]
Probab=24.69 E-value=40 Score=31.45 Aligned_cols=38 Identities=32% Similarity=0.527 Sum_probs=33.6
Q ss_pred HhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHH
Q 024969 190 CWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVN 236 (260)
Q Consensus 190 ~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~ 236 (260)
-|.-|+-|+|+...-.++.||-- .+|+..+.+++|.|.
T Consensus 204 iWs~GcIfaEm~~~~~LFpG~se---------~~ql~~If~~lGtP~ 241 (323)
T KOG0594|consen 204 IWSLGCIFAEMFTRRPLFPGDSE---------IDQLFRIFRLLGTPN 241 (323)
T ss_pred hHhHHHHHHHHHhCCCCCCCCcH---------HHHHHHHHHHcCCCC
Confidence 39999999999999999999987 788888888888764
No 127
>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=24.58 E-value=52 Score=22.88 Aligned_cols=29 Identities=14% Similarity=0.206 Sum_probs=25.3
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLD 219 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~ 219 (260)
...|.|..+++...++.+..|-+|++...
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHHHHHh
Confidence 47899999999999999999999999876
No 128
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=24.48 E-value=1.4e+02 Score=23.86 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=33.9
Q ss_pred CcccHHHHH-HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVI-YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLN 223 (260)
Q Consensus 180 ~~~~l~~vv-~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLr 223 (260)
+.+.-=.++ .....|.|..||-+.+++++|++=..+.|-...|+
T Consensus 114 L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 114 LPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 333333344 34579999999999999999999998888877665
No 129
>KOG4456 consensus Inner centromere protein (INCENP), C-terminal domain [Cell cycle control, cell division, chromosome partitioning]
Probab=24.42 E-value=1e+02 Score=24.80 Aligned_cols=51 Identities=14% Similarity=0.222 Sum_probs=38.6
Q ss_pred HHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH-hhcCC
Q 024969 188 IYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASE-SLRRG 251 (260)
Q Consensus 188 v~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~-~i~Rd 251 (260)
+=.||+|+...+-..+.....-++|-.| .-+|+-++|.+.|.++.. ..||+
T Consensus 66 ~PtWar~~v~~eai~~qa~~pp~~v~~F-------------f~~~pkpdLkeIF~~~~p~~~KR~ 117 (134)
T KOG4456|consen 66 FPTWARDMVIVEAIEEQAKNPPFNVNTF-------------FGSMPKPDLKEIFGEMVPSKKKRG 117 (134)
T ss_pred CchhhhhchHHHHHHHHhhCCchHHHHH-------------hcccCCcCHHHHHHhhhhhhhhcc
Confidence 5579999999997777666666555443 344577999999999888 78886
No 130
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=24.08 E-value=1.2e+02 Score=22.30 Aligned_cols=34 Identities=15% Similarity=0.197 Sum_probs=26.4
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcC-CCcchHHHHHH
Q 024969 183 FLMDVIYCWSKGATFAEVIQMTD-IFEGSIIRSAR 216 (260)
Q Consensus 183 ~l~~vv~~Wa~G~~f~~i~~~t~-l~EGdiVR~~r 216 (260)
..-.++..|+.|.|..||++..+ +..=||--+++
T Consensus 32 ~V~~Il~~l~~G~s~eeil~dyp~Lt~~dI~aal~ 66 (79)
T COG2442 32 PVWDILEMLAAGESIEEILADYPDLTLEDIRAALR 66 (79)
T ss_pred cHHHHHHHHHCCCCHHHHHHhCCCCCHHHHHHHHH
Confidence 34567889999999999999986 77666655544
No 131
>PRK02166 hypothetical protein; Reviewed
Probab=23.81 E-value=2.8e+02 Score=23.62 Aligned_cols=60 Identities=22% Similarity=0.223 Sum_probs=34.6
Q ss_pred ccHHHHHHHhhCCC--CHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcC----CHHHHHHHHHHHHhhc
Q 024969 182 PFLMDVIYCWSKGA--TFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVG----EVNLEKKFAAASESLR 249 (260)
Q Consensus 182 ~~l~~vv~~Wa~G~--~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig----~~~L~~k~~~a~~~i~ 249 (260)
+.-++.+-.|++|- -|.-.-+...++ --+-|.|+.++.++++=- +.+...-+.+.++=+|
T Consensus 96 ~~Ra~AL~~W~~gFL~G~Gl~~~~~~~s--------~e~~E~l~Dl~~Iaql~~d~dd~ee~E~al~Ei~EyvR 161 (184)
T PRK02166 96 TERAAALGQWCQGFLAGFGLNAGGKDLS--------GEAKEVLQDLAAISQVQDALEESEDGETDYMEVMEYLR 161 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCccCCC--------HHHHHHHHHHHHHHccCCCCCCCchHHHHHHHHHHHHH
Confidence 46788899999984 333331112221 246788888888887621 2444445555555443
No 132
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.56 E-value=2.2e+02 Score=22.84 Aligned_cols=46 Identities=15% Similarity=0.192 Sum_probs=35.6
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
+.+.--.++.. ...|.|..||.+..++++|++=..+.|...-|+..
T Consensus 113 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 113 LSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 44444444444 35999999999999999999999888888877764
No 133
>PF11917 DUF3435: Protein of unknown function (DUF3435); InterPro: IPR021842 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to PF00589 from PFAM suggesting it may be an integrase enzyme.
Probab=23.09 E-value=2e+02 Score=27.46 Aligned_cols=21 Identities=29% Similarity=0.574 Sum_probs=17.1
Q ss_pred CChHHHHHHHHHHHHHHHHHc
Q 024969 4 EDPEVVDLVNQIEELEHKLFA 24 (260)
Q Consensus 4 ~~~~~~~~~~~~~~l~~~l~~ 24 (260)
+++++.++..+...|...+..
T Consensus 286 ~dpei~~l~~~~~~L~~~i~~ 306 (418)
T PF11917_consen 286 QDPEIQELQRRRDELKKEIRR 306 (418)
T ss_pred cCcHHHHHHHHHHHHHhhhhh
Confidence 578888888999998887765
No 134
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.08 E-value=4.4e+02 Score=21.91 Aligned_cols=115 Identities=12% Similarity=0.093 Sum_probs=62.4
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHhhhh---ccccCCCccccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccC
Q 024969 104 LVTELMFNGTFNDLDHHQVAALASCF---IPVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTV 180 (260)
Q Consensus 104 lltEll~~g~f~~L~p~elaallS~~---v~e~~~~~~~~~~~~l~~~~~~l~~~~~~i~~~~~~~~l~~~~~~~~~~~~ 180 (260)
++-++|.+|-|... ..++.++.-+ .++..++...+-...+......+++....-..+..+.|- . +
T Consensus 17 ~l~~~L~~~~~t~~--ei~~~~~~~~~~~g~~iSrSav~RY~~~~~~~~~~lr~are~a~al~~~~~~---------~-~ 84 (180)
T PF11985_consen 17 WLDQMLRDGGFTQY--EILAEWLEELAEEGYDISRSAVHRYAQRFEEVLERLREAREIAEALAEELGD---------E-P 84 (180)
T ss_pred HHHHHHHhCCCChH--HHHHHHHHhhhccCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---------C-C
Confidence 67788888776544 3455566655 332222111111223333333433333322233333332 1 4
Q ss_pred cccHHHHHHHhhCCCCHHHHHhhcCCCcchH--HHHHHHHHHHHHHHHHHHh
Q 024969 181 RPFLMDVIYCWSKGATFAEVIQMTDIFEGSI--IRSARRLDEFLNQLRAAAQ 230 (260)
Q Consensus 181 ~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdi--VR~~rRl~elLrql~~a~~ 230 (260)
+.....++-++....-|.-++...+-..++. +..+..+...+..+..|+.
T Consensus 85 ~~~~~~al~~~~~~~~f~~l~~~~~~~~~~~~~~k~l~~la~~~~~l~~A~~ 136 (180)
T PF11985_consen 85 EDDVTEALIEMLQTLLFEALMSAQEEDEEDDDPPKDLMKLAKALARLSRASV 136 (180)
T ss_pred cchHHHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHH
Confidence 4567777788888888888888776666665 5666666666666666654
No 135
>COG4985 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]
Probab=23.07 E-value=2.5e+02 Score=25.23 Aligned_cols=45 Identities=27% Similarity=0.346 Sum_probs=25.9
Q ss_pred HHHHHHHHHHcCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024969 14 QIEELEHKLFAHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRD 58 (260)
Q Consensus 14 ~~~~l~~~l~~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~ 58 (260)
++++|+-+-+.....+- +-+...+...++.+|+++...+..+++.
T Consensus 194 qlErLRL~krrlQl~g~Ld~~~q~~~~ae~seLq~r~~~l~~~L~~ 239 (289)
T COG4985 194 QLERLRLEKRRLQLNGQLDDEFQQHYVAEKSELQKRLAQLQTELDA 239 (289)
T ss_pred HHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444455554 4444444556677777777777777666
No 136
>TIGR02511 type_III_tyeA type III secretion effector delivery regulator, TyeA family. Members of this family include both small proteins, about 90 amino acids, in which this model covers the whole, and longer proteins of about 360 residues which match in the C-terminal region. The longer proteins (HrpJ) have N-terminal regions that match Pfam model pfam07201. Members of this family belong to bacterial type III secretion systems, and include TyeA from the well-studied Yersinia systems. TyeA appears involved in calcium-responsive regulation of the delivery of type III effectors.
Probab=23.05 E-value=1.8e+02 Score=21.23 Aligned_cols=56 Identities=13% Similarity=0.090 Sum_probs=44.5
Q ss_pred HHhhCCCCHHHHHhhcCCCcchH-HHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 024969 189 YCWSKGATFAEVIQMTDIFEGSI-IRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASE 246 (260)
Q Consensus 189 ~~Wa~G~~f~~i~~~t~l~EGdi-VR~~rRl~elLrql~~a~~~ig~~~L~~k~~~a~~ 246 (260)
..|.....+..+.+.....+.-- |+.++++.++++.++..+- .|++=++++-++..
T Consensus 16 q~Wl~~~~l~~l~~~l~~~~~~~qv~fl~~l~~l~~~lP~~lf--~D~eqR~~~L~~~~ 72 (79)
T TIGR02511 16 ERWLGPDWIEQLANALGLPELEHRVAFLQGLKRLLRLLPIALF--SDEEQRQNLLQALQ 72 (79)
T ss_pred cccCCHHHHHHHHHHccCccHHHHHHHHHHHHHHHHHCCHHHh--CCHHHHHHHHHHHH
Confidence 46877777778888877777666 9999999999999999875 68877777666554
No 137
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=23.02 E-value=2.2e+02 Score=22.60 Aligned_cols=34 Identities=21% Similarity=0.199 Sum_probs=31.0
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
.-.|.|..+|-+..++++|++=..+.|...-||+
T Consensus 135 ~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 135 FGQNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999998888875
No 138
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=22.83 E-value=1.6e+02 Score=22.85 Aligned_cols=78 Identities=15% Similarity=0.166 Sum_probs=40.6
Q ss_pred HHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHH
Q 024969 162 IQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKF 241 (260)
Q Consensus 162 ~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~a~~~ig~~~L~~k~ 241 (260)
...++|+++..-+|...+++. +-+..|.....+.+++... |...|.. .....-+.+.++.+.+
T Consensus 19 ~L~~~gi~~~~~d~~~~p~s~---~eL~~~l~~~g~~~l~n~~----~~~~r~~----------~~~~~~ls~~e~~~ll 81 (113)
T cd03033 19 LLEAAGHEVEVRDLLTEPWTA---ETLRPFFGDLPVAEWFNPA----APRVKSG----------EVVPEALDEEEALALM 81 (113)
T ss_pred HHHHcCCCcEEeehhcCCCCH---HHHHHHHHHcCHHHHHhcc----cHHHHhc----------CCCccCCCHHHHHHHH
Confidence 346678888877776542332 3355665555555555422 4444421 0000111234444444
Q ss_pred HHHHHhhcCCccccC
Q 024969 242 AAASESLRRGIMFSN 256 (260)
Q Consensus 242 ~~a~~~i~RdIVf~~ 256 (260)
-+==.+|+|+||...
T Consensus 82 ~~~P~LikRPIv~~~ 96 (113)
T cd03033 82 IADPLLIRRPLMQVG 96 (113)
T ss_pred HhCcceeeCCeEEEC
Confidence 444558999999753
No 139
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.64 E-value=1.5e+02 Score=25.59 Aligned_cols=35 Identities=9% Similarity=0.083 Sum_probs=31.4
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
...|.|+.+|-+..++++|.+=..+.|...-||+.
T Consensus 197 ~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 197 YQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999998888888888764
No 140
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=22.36 E-value=1.6e+02 Score=23.33 Aligned_cols=36 Identities=19% Similarity=0.160 Sum_probs=32.1
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 024969 191 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 226 (260)
Q Consensus 191 Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~ 226 (260)
...|.|..+|-+..++++|++=..+.|...-|+..-
T Consensus 123 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 123 YYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred HHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999999999988887643
No 141
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=22.33 E-value=2.1e+02 Score=23.63 Aligned_cols=45 Identities=11% Similarity=0.148 Sum_probs=35.9
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+.+.--.++.. +-.|.|..||.+..++++|.+=..+.|.-.-|+.
T Consensus 132 L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 132 LEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55565666653 5799999999999999999998888888766653
No 142
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=22.26 E-value=1.9e+02 Score=24.91 Aligned_cols=36 Identities=19% Similarity=0.065 Sum_probs=30.7
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHH
Q 024969 192 SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRA 227 (260)
Q Consensus 192 a~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql~~ 227 (260)
-.|.|..+|.+..++++|.+-+.+.|...-|++.-.
T Consensus 193 ~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 193 GKEKTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999988888777776543
No 143
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.25 E-value=2.4e+02 Score=23.11 Aligned_cols=46 Identities=20% Similarity=0.106 Sum_probs=34.9
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 180 ~~~~l~~vv~~-Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
+.+.--.++.. .-.|.|..+|.+..++++|++=..+.|...-|++.
T Consensus 132 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 132 LPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 33333334432 34899999999999999999999888888888764
No 144
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=22.07 E-value=1.5e+02 Score=25.59 Aligned_cols=33 Identities=27% Similarity=0.229 Sum_probs=29.1
Q ss_pred CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 024969 193 KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 225 (260)
Q Consensus 193 ~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrql 225 (260)
.|.|+.||-+..++++|++-+.+.|...-||+.
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 789999999999999999988888877777763
No 145
>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=22.00 E-value=1.2e+02 Score=22.64 Aligned_cols=36 Identities=19% Similarity=0.308 Sum_probs=29.5
Q ss_pred CcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHH
Q 024969 180 VRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARR 217 (260)
Q Consensus 180 ~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rR 217 (260)
+.+. ..+...+++|.|-.+|.+..+++..+|-| ++|
T Consensus 37 Ls~R-~~I~~ll~~G~S~~eIA~~LgISrsTIyR-i~R 72 (88)
T TIGR02531 37 LAQR-LQVAKMLKQGKTYSDIEAETGASTATISR-VKR 72 (88)
T ss_pred hhHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHH-HHH
Confidence 5566 55556669999999999999999999988 555
No 146
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=21.74 E-value=2e+02 Score=18.76 Aligned_cols=43 Identities=16% Similarity=0.240 Sum_probs=34.7
Q ss_pred CcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFL 222 (260)
Q Consensus 180 ~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elL 222 (260)
+.+.=.++...|+.|.|-.+|...-++.+.++---.+++..-+
T Consensus 5 Lt~rE~~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 5 LTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4455567788889999999999999999999887777765443
No 147
>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=21.65 E-value=1e+02 Score=16.69 Aligned_cols=29 Identities=14% Similarity=0.228 Sum_probs=19.6
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHH
Q 024969 186 DVIYCWSKGATFAEVIQMTDIFEGSIIRS 214 (260)
Q Consensus 186 ~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~ 214 (260)
.++..|-+|.+..++.+..++....+-++
T Consensus 13 ~i~~~~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 13 EARRLLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHh
Confidence 34445567888888888887776665543
No 148
>PF15002 ERK-JNK_inhib: ERK and JNK pathways, inhibitor
Probab=21.63 E-value=3e+02 Score=24.01 Aligned_cols=103 Identities=13% Similarity=0.228 Sum_probs=62.4
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHhhhhccccCCCccccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCccc
Q 024969 104 LVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPF 183 (260)
Q Consensus 104 lltEll~~g~f~~L~p~elaallS~~v~e~~~~~~~~~~~~l~~~~~~l~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~ 183 (260)
-+.+.+++|+|.-|..+...=--|.+..+... | .++.+.+|+..+.|.---++++.- ++|--+..|++.+.+
T Consensus 51 k~i~~ll~~i~~vL~~Sr~~L~~a~~~p~~~f---P-~d~~~kdAls~vlENtAffgDl~L--rfPdi~h~~~~~~~~-- 122 (207)
T PF15002_consen 51 KLIEILLEKIFKVLEESRAVLESADYIPDSPF---P-KDDKLKDALSSVLENTAFFGDLVL--RFPDIVHHILDRNSD-- 122 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCC---C-CChHHHHHHHHHHHHHHHHHHHHH--HccHHHHHHHHhcch--
Confidence 34566677777777666544334444433211 2 356788888888777766666654 444334555544222
Q ss_pred HHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 184 LMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 184 l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
.. .+..||= ..|..|+++.|+- ..+..|+.|
T Consensus 123 w~-~ll~Wa~-----~f~~~s~l~d~~~----~~lL~L~~Q 153 (207)
T PF15002_consen 123 WN-DLLRWAL-----NFCNQSGLYDESH----EKLLHLMAQ 153 (207)
T ss_pred HH-HHHHHHH-----HHHHhcCCcCccH----HHHHHHHHH
Confidence 22 3667886 7888999999853 555666665
No 149
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=21.62 E-value=2.2e+02 Score=24.50 Aligned_cols=45 Identities=18% Similarity=0.075 Sum_probs=33.9
Q ss_pred CcccHHHHHHHhh-----CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 024969 180 VRPFLMDVIYCWS-----KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 224 (260)
Q Consensus 180 ~~~~l~~vv~~Wa-----~G~~f~~i~~~t~l~EGdiVR~~rRl~elLrq 224 (260)
+++.--.++...- .|.|..+|.+.+++.+|++-+.+.|..--|++
T Consensus 175 L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 175 LDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred CCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444445555543 89999999999999999998888886666554
No 150
>KOG0201 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=21.10 E-value=1.2e+02 Score=29.67 Aligned_cols=96 Identities=15% Similarity=0.252 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCC-CcchHHHHHHHHHHHH
Q 024969 144 ELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDI-FEGSIIRSARRLDEFL 222 (260)
Q Consensus 144 ~l~~~~~~l~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l-~EGdiVR~~rRl~elL 222 (260)
.|..+-..+.++.++|.-+ ..|+.+--.+-|... +....+.++-.|+.|-|..+.++...+ .|=-|+ ++ +
T Consensus 47 ~Le~~~deIediqqei~~L-s~~~~~~it~yygsy-l~g~~LwiiMey~~gGsv~~lL~~~~~~~E~~i~-~i------l 117 (467)
T KOG0201|consen 47 DLEEAEDEIEDIQQEISVL-SQCDSPNITEYYGSY-LKGTKLWIIMEYCGGGSVLDLLKSGNILDEFEIA-VI------L 117 (467)
T ss_pred chhhcchhhHHHHHHHHHH-HhcCcchHHhhhhhe-eecccHHHHHHHhcCcchhhhhccCCCCccceee-ee------h
Confidence 4555556666677776544 334432112334445 778899999999999999999999776 332211 11 1
Q ss_pred HHHHHHHhhcCCHHHHHHHHHHHHhhcCCccccCCC
Q 024969 223 NQLRAAAQAVGEVNLEKKFAAASESLRRGIMFSNSL 258 (260)
Q Consensus 223 rql~~a~~~ig~~~L~~k~~~a~~~i~RdIVf~~SL 258 (260)
|++ -...++.-...+|+|||-.+.-|
T Consensus 118 re~----------l~~l~ylH~~~kiHrDIKaanil 143 (467)
T KOG0201|consen 118 REV----------LKGLDYLHSEKKIHRDIKAANIL 143 (467)
T ss_pred HHH----------HHHhhhhhhcceeccccccccee
Confidence 222 22334555667788888766543
No 151
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=21.10 E-value=1.4e+02 Score=19.97 Aligned_cols=28 Identities=18% Similarity=0.281 Sum_probs=22.7
Q ss_pred CCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 193 KGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 193 ~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
.+.+..+|.+.++++.+.+-|.+++|.+
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4478999999999999999999999876
No 152
>PRK10026 arsenate reductase; Provisional
Probab=20.72 E-value=68 Score=26.19 Aligned_cols=38 Identities=11% Similarity=0.099 Sum_probs=21.2
Q ss_pred HHHcCCCCChhhhhhccCcccHHHHHHHhh--CCCCHHHHHhh
Q 024969 163 QNECKLEVNVDEYVESTVRPFLMDVIYCWS--KGATFAEVIQM 203 (260)
Q Consensus 163 ~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa--~G~~f~~i~~~ 203 (260)
-.++|+++..-+|....++.. -+..|. .|.++.+++..
T Consensus 22 L~~~gi~~~~~d~~~~ppt~~---eL~~~l~~~g~~~~~lint 61 (141)
T PRK10026 22 IRNSGTEPTIIHYLETPPTRD---ELVKLIADMGISVRALLRK 61 (141)
T ss_pred HHHCCCCcEEEeeeCCCcCHH---HHHHHHHhCCCCHHHHHHc
Confidence 356799888777766534432 234442 34445555544
No 153
>COG2926 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.71 E-value=2e+02 Score=22.11 Aligned_cols=33 Identities=30% Similarity=0.457 Sum_probs=25.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhH
Q 024969 31 QDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQK 63 (260)
Q Consensus 31 ~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~ 63 (260)
+.-+..+.++++.+++++++...+++.+.+..+
T Consensus 10 ~VlE~Vr~~RrKNkl~Rei~DnekKIRDNqKRv 42 (109)
T COG2926 10 DVLEFVRLFRRKNKLQREIEDNEKKIRDNQKRV 42 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHH
Confidence 345667788899999999999999988755443
No 154
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=20.05 E-value=1.2e+02 Score=22.26 Aligned_cols=46 Identities=15% Similarity=0.225 Sum_probs=30.7
Q ss_pred HHHHHHHhhhhhhhHHHHHHHHHHHHHhHhCCCCCC----------CccchhhHHHhhhc
Q 024969 49 IQQLKSKMRDSQIQKFRDELKNRSRVLKKLGHINAD----------GVVQLKGRAACLID 98 (260)
Q Consensus 49 ~~~l~~~i~~~~~~~~~~e~~~~~~vL~~lgyid~~----------~~~t~kGrva~eI~ 98 (260)
..++++.+.+.+ ...+...++-|++.|.|... +.+|.+|+-...+-
T Consensus 21 f~el~~~l~~is----~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~~l 76 (90)
T PF01638_consen 21 FSELQRRLPGIS----PKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLPVL 76 (90)
T ss_dssp HHHHHHHSTTS-----HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHHHH
T ss_pred HHHHHHhcchhH----HHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHHHH
Confidence 345566665422 24667889999999999652 57899998776553
No 155
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=20.05 E-value=2.9e+02 Score=23.52 Aligned_cols=56 Identities=14% Similarity=0.261 Sum_probs=43.0
Q ss_pred HHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 024969 156 ARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 220 (260)
Q Consensus 156 ~~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~~i~~~t~l~EGdiVR~~rRl~e 220 (260)
...++..+..+|++-++. .+.+++|.=-.-.+++||.+.|+++-+.+=-.++-|.+
T Consensus 12 Ie~fae~m~r~G~nrtVG---------~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 12 IEHFAETMSRWGINRTVG---------QIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HHHHHHHHHHhCCcchHH---------HHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHh
Confidence 345677888999988863 45666666455579999999999999988877777765
Done!