Query 021133
Match_columns 317
No_of_seqs 147 out of 662
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 07:51:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021133.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021133hhsearch_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 2.7E-84 5.8E-89 645.2 28.8 316 1-317 725-1041(1041)
2 KOG0947 Cytoplasmic exosomal R 100.0 4E-61 8.7E-66 488.6 25.2 284 32-317 960-1248(1248)
3 PF08148 DSHCT: DSHCT (NUC185) 100.0 3.4E-57 7.4E-62 398.1 16.6 177 138-317 1-180 (180)
4 COG4581 Superfamily II RNA hel 100.0 6.9E-48 1.5E-52 403.3 24.1 310 2-317 726-1041(1041)
5 PF13234 rRNA_proc-arch: rRNA- 99.8 3.5E-21 7.6E-26 179.3 9.4 115 1-115 152-267 (268)
6 COG1202 Superfamily II helicas 93.2 2.7 5.7E-05 43.6 14.1 176 124-305 618-826 (830)
7 PF04408 HA2: Helicase associa 92.8 0.12 2.5E-06 41.1 3.3 44 129-173 3-46 (102)
8 PRK02362 ski2-like helicase; P 89.9 5.7 0.00012 42.4 13.4 175 122-309 464-647 (737)
9 PRK00254 ski2-like helicase; P 89.7 4.3 9.3E-05 43.2 12.2 176 123-309 455-640 (720)
10 smart00847 HA2 Helicase associ 85.8 2.4 5.2E-05 32.3 5.7 59 129-189 3-61 (92)
11 PRK01172 ski2-like helicase; P 82.4 56 0.0012 34.4 15.9 161 122-307 443-605 (674)
12 PRK11664 ATP-dependent RNA hel 81.9 8.6 0.00019 41.7 9.8 66 123-190 384-449 (812)
13 cd06171 Sigma70_r4 Sigma70, re 79.1 4 8.7E-05 26.8 4.1 43 237-279 11-54 (55)
14 PRK00118 putative DNA-binding 77.7 12 0.00026 30.0 7.1 52 237-288 18-70 (104)
15 smart00421 HTH_LUXR helix_turn 77.6 5.3 0.00012 26.7 4.5 43 237-279 4-46 (58)
16 PF10985 DUF2805: Protein of u 76.5 2.8 6.1E-05 31.4 2.8 30 246-275 7-36 (73)
17 TIGR03643 conserved hypothetic 75.5 3.9 8.5E-05 30.5 3.4 30 246-275 8-37 (72)
18 PF04545 Sigma70_r4: Sigma-70, 75.3 7.1 0.00015 26.3 4.5 38 244-281 13-50 (50)
19 TIGR01970 DEAH_box_HrpB ATP-de 74.8 5.8 0.00013 43.0 5.9 49 123-172 381-429 (819)
20 cd06170 LuxR_C_like C-terminal 74.7 7 0.00015 26.3 4.4 34 243-276 7-40 (57)
21 PRK04217 hypothetical protein; 71.5 13 0.00028 30.1 5.9 51 237-287 43-94 (110)
22 PF13518 HTH_28: Helix-turn-he 70.4 10 0.00022 25.4 4.4 35 243-277 4-38 (52)
23 PRK11512 DNA-binding transcrip 68.4 12 0.00026 31.1 5.3 62 122-186 68-139 (144)
24 PF12246 MKT1_C: Temperature d 67.4 3.9 8.4E-05 37.7 2.3 45 130-174 1-53 (243)
25 PRK03573 transcriptional regul 63.4 19 0.00041 29.8 5.5 61 122-186 60-130 (144)
26 PF13384 HTH_23: Homeodomain-l 62.7 5.4 0.00012 26.8 1.7 34 243-276 9-42 (50)
27 COG3079 Uncharacterized protei 53.8 75 0.0016 27.8 7.5 124 173-306 21-163 (186)
28 PF12917 HD_2: HD containing h 53.7 1.5E+02 0.0032 27.0 9.7 114 169-307 50-171 (215)
29 KOG0923 mRNA splicing factor A 52.3 1.9E+02 0.0042 31.0 11.4 136 123-290 652-791 (902)
30 PF13936 HTH_38: Helix-turn-he 52.2 20 0.00043 23.8 3.1 31 244-274 13-43 (44)
31 TIGR01967 DEAH_box_HrpA ATP-de 51.7 28 0.0006 39.7 5.8 62 123-188 449-514 (1283)
32 PRK11131 ATP-dependent RNA hel 47.7 3.6E+02 0.0078 31.2 13.6 61 124-188 457-523 (1294)
33 COG1846 MarR Transcriptional r 46.7 65 0.0014 24.8 5.9 55 121-179 49-113 (126)
34 PRK12543 RNA polymerase sigma 46.5 66 0.0014 27.4 6.3 44 248-291 130-177 (179)
35 COG4910 PduE Propanediol dehyd 45.9 34 0.00073 28.8 4.1 78 223-305 31-109 (170)
36 TIGR02337 HpaR homoprotocatech 45.1 83 0.0018 24.9 6.3 54 214-277 15-68 (118)
37 PF04420 CHD5: CHD5-like prote 45.1 2E+02 0.0043 24.7 9.2 53 62-115 39-91 (161)
38 smart00351 PAX Paired Box doma 44.6 38 0.00083 27.7 4.3 35 243-277 25-59 (125)
39 PF13613 HTH_Tnp_4: Helix-turn 41.9 65 0.0014 22.1 4.5 44 239-282 7-50 (53)
40 PRK03573 transcriptional regul 41.5 86 0.0019 25.7 6.1 38 240-277 35-72 (144)
41 KOG0925 mRNA splicing factor A 40.7 85 0.0018 32.3 6.7 61 124-185 434-495 (699)
42 PF02796 HTH_7: Helix-turn-hel 40.3 40 0.00088 22.3 3.2 33 240-272 10-42 (45)
43 TIGR02985 Sig70_bacteroi1 RNA 40.2 67 0.0014 26.2 5.2 45 237-281 114-159 (161)
44 PRK15443 pduE propanediol dehy 40.2 49 0.0011 27.8 4.2 54 249-306 21-78 (138)
45 cd05495 Bromo_cbp_like Bromodo 39.0 2E+02 0.0043 22.9 7.9 66 29-94 3-72 (108)
46 PF00196 GerE: Bacterial regul 38.6 54 0.0012 22.6 3.8 43 237-279 4-46 (58)
47 PF04977 DivIC: Septum formati 38.0 1.1E+02 0.0025 22.1 5.7 41 98-143 32-73 (80)
48 TIGR02984 Sig-70_plancto1 RNA 37.5 81 0.0018 26.7 5.5 46 237-282 141-187 (189)
49 PF11985 DUF3486: Protein of u 37.2 2.8E+02 0.006 24.0 10.2 115 161-287 17-136 (180)
50 PF08281 Sigma70_r4_2: Sigma-7 37.2 67 0.0015 21.6 4.0 30 248-277 23-52 (54)
51 PF12690 BsuPI: Intracellular 36.7 3.4 7.3E-05 31.6 -2.9 25 243-267 36-60 (82)
52 PF08461 HTH_12: Ribonuclease 36.5 84 0.0018 22.8 4.6 28 122-149 32-63 (66)
53 PRK11512 DNA-binding transcrip 35.8 93 0.002 25.6 5.4 37 240-277 44-80 (144)
54 TIGR02989 Sig-70_gvs1 RNA poly 35.4 84 0.0018 25.8 5.1 45 237-281 112-157 (159)
55 KOG4253 Tryptophan-rich basic 35.2 3E+02 0.0065 23.9 8.2 42 66-115 47-88 (175)
56 PF00440 TetR_N: Bacterial reg 35.2 32 0.00069 22.8 2.0 34 249-282 14-47 (47)
57 TIGR02937 sigma70-ECF RNA poly 34.9 92 0.002 24.6 5.2 36 246-281 121-156 (158)
58 PRK01736 hypothetical protein; 33.9 2.5E+02 0.0054 24.8 8.1 59 240-306 98-164 (190)
59 PF03333 PapB: Adhesin biosynt 33.6 88 0.0019 24.5 4.5 48 240-287 41-89 (91)
60 PF07749 ERp29: Endoplasmic re 33.3 69 0.0015 25.0 4.0 34 102-135 61-94 (95)
61 cd06571 Bac_DnaA_C C-terminal 32.6 1.6E+02 0.0035 22.4 5.9 45 250-303 43-88 (90)
62 PF06330 TRI5: Trichodiene syn 32.3 3.2E+02 0.007 27.0 9.1 87 179-279 187-277 (376)
63 smart00529 HTH_DTXR Helix-turn 32.2 85 0.0018 23.7 4.3 64 122-187 13-80 (96)
64 KOG0286 G-protein beta subunit 32.1 29 0.00062 33.2 1.8 53 99-151 4-56 (343)
65 PF06969 HemN_C: HemN C-termin 31.8 45 0.00098 23.5 2.5 29 121-149 34-65 (66)
66 PRK04758 hypothetical protein; 31.6 1.8E+02 0.004 25.6 6.7 60 239-306 93-160 (181)
67 cd00090 HTH_ARSR Arsenical Res 31.3 91 0.002 21.4 4.1 30 248-277 17-46 (78)
68 TIGR02999 Sig-70_X6 RNA polyme 31.2 1.1E+02 0.0024 25.8 5.4 46 237-282 135-181 (183)
69 PF14947 HTH_45: Winged helix- 30.8 48 0.001 24.6 2.6 42 113-155 25-69 (77)
70 PRK09639 RNA polymerase sigma 30.6 96 0.0021 25.7 4.7 37 246-283 123-159 (166)
71 PRK06759 RNA polymerase factor 30.4 1.1E+02 0.0025 24.9 5.1 45 237-281 107-152 (154)
72 PF13412 HTH_24: Winged helix- 30.4 59 0.0013 21.4 2.7 29 249-277 15-43 (48)
73 PRK13777 transcriptional regul 30.2 1.8E+02 0.0039 25.7 6.5 29 249-277 57-85 (185)
74 COG1643 HrpA HrpA-like helicas 30.2 1.1E+02 0.0024 33.5 6.0 65 123-190 433-497 (845)
75 PRK12525 RNA polymerase sigma 30.0 1.2E+02 0.0025 25.5 5.2 34 248-281 131-164 (168)
76 PRK09642 RNA polymerase sigma 30.0 1E+02 0.0022 25.5 4.8 46 237-282 107-153 (160)
77 PF11917 DUF3435: Protein of u 30.0 1.7E+02 0.0036 29.0 7.0 52 30-81 253-306 (418)
78 PF07900 DUF1670: Protein of u 29.9 1.3E+02 0.0028 27.4 5.6 95 147-274 89-186 (220)
79 PRK09047 RNA polymerase factor 29.8 1.3E+02 0.0028 24.7 5.4 36 248-283 119-154 (161)
80 PRK11415 hypothetical protein; 29.8 1.9E+02 0.004 21.6 5.6 55 56-111 10-67 (74)
81 KOG4196 bZIP transcription fac 29.7 2.4E+02 0.0053 23.6 6.6 74 62-137 46-119 (135)
82 KOG2163 Centromere/kinetochore 29.5 7.1E+02 0.015 26.4 11.6 119 152-272 563-704 (719)
83 PF10482 CtIP_N: Tumour-suppre 29.4 2.7E+02 0.0058 22.8 6.7 28 67-94 53-81 (120)
84 TIGR02948 SigW_bacill RNA poly 29.4 1.2E+02 0.0025 25.7 5.1 35 248-282 149-183 (187)
85 PRK12514 RNA polymerase sigma 29.1 1.4E+02 0.003 25.2 5.6 45 237-281 130-175 (179)
86 PF13730 HTH_36: Helix-turn-he 28.7 63 0.0014 21.9 2.7 25 253-277 27-51 (55)
87 COG1393 ArsC Arsenate reductas 28.6 82 0.0018 25.6 3.8 79 219-314 20-100 (117)
88 KOG0201 Serine/threonine prote 28.1 86 0.0019 31.6 4.4 96 201-315 47-143 (467)
89 KOG0920 ATP-dependent RNA heli 28.1 71 0.0015 35.2 4.2 61 123-184 592-653 (924)
90 PRK00888 ftsB cell division pr 27.9 2.4E+02 0.0053 22.4 6.3 40 99-143 43-83 (105)
91 TIGR02479 FliA_WhiG RNA polyme 27.7 1.4E+02 0.003 26.5 5.5 43 239-281 178-221 (224)
92 PF13404 HTH_AsnC-type: AsnC-t 27.6 64 0.0014 21.2 2.4 25 252-276 18-42 (42)
93 PF12802 MarR_2: MarR family; 26.6 72 0.0016 21.9 2.8 30 248-277 16-47 (62)
94 KOG4456 Inner centromere prote 26.6 86 0.0019 26.1 3.5 50 246-308 67-117 (134)
95 PRK06930 positive control sigm 26.5 1.5E+02 0.0033 25.6 5.3 45 237-281 115-160 (170)
96 PF13601 HTH_34: Winged helix 26.4 51 0.0011 24.8 2.0 37 240-277 4-40 (80)
97 cd00180 PKc Catalytic domain o 26.2 41 0.0009 27.6 1.7 52 240-291 64-117 (215)
98 PRK09648 RNA polymerase sigma 25.9 1.5E+02 0.0032 25.3 5.2 35 248-282 152-186 (189)
99 PRK12522 RNA polymerase sigma 25.7 1.3E+02 0.0027 25.4 4.6 37 246-282 130-166 (173)
100 smart00418 HTH_ARSR helix_turn 25.5 1.3E+02 0.0029 19.9 4.0 29 249-277 8-36 (66)
101 PRK13919 putative RNA polymera 25.4 1.7E+02 0.0036 24.8 5.4 45 237-281 136-181 (186)
102 PRK12511 RNA polymerase sigma 25.2 1.7E+02 0.0037 25.1 5.5 48 237-284 112-160 (182)
103 PRK12542 RNA polymerase sigma 25.2 1.7E+02 0.0036 24.9 5.4 49 237-285 123-172 (185)
104 CHL00073 chlN photochlorophyll 25.1 67 0.0014 32.6 3.2 68 246-314 50-136 (457)
105 cd00131 PAX Paired Box domain 25.0 1.1E+02 0.0024 25.1 4.0 34 244-277 26-59 (128)
106 PF13551 HTH_29: Winged helix- 25.0 1.2E+02 0.0025 23.3 4.0 34 243-276 3-37 (112)
107 PRK12531 RNA polymerase sigma 24.6 1.7E+02 0.0037 25.2 5.4 47 237-283 142-189 (194)
108 cd00238 ERp29c ERp29 and ERp38 24.6 3.4E+02 0.0073 21.1 8.0 34 102-135 59-93 (93)
109 TIGR02941 Sigma_B RNA polymera 24.4 1.3E+02 0.0028 27.4 4.7 37 246-282 216-252 (255)
110 COG2926 Uncharacterized protei 24.3 2E+02 0.0044 22.8 4.9 30 90-119 12-41 (109)
111 PF01047 MarR: MarR family; I 24.2 1E+02 0.0022 21.0 3.2 38 239-277 6-43 (59)
112 PF01527 HTH_Tnp_1: Transposas 24.1 54 0.0012 23.6 1.8 29 248-276 20-48 (76)
113 COG1204 Superfamily II helicas 24.1 6.5E+02 0.014 27.3 10.5 165 121-291 474-650 (766)
114 PRK09644 RNA polymerase sigma 23.8 1.7E+02 0.0038 24.3 5.1 48 237-284 109-157 (165)
115 PRK09645 RNA polymerase sigma 23.2 2E+02 0.0044 24.0 5.5 45 238-282 120-165 (173)
116 PF04363 DUF496: Protein of un 22.8 2.8E+02 0.0061 21.7 5.4 30 90-119 5-34 (95)
117 PF03444 HrcA_DNA-bdg: Winged 22.5 88 0.0019 23.8 2.6 28 124-151 39-72 (78)
118 PF13463 HTH_27: Winged helix 22.2 76 0.0017 22.2 2.2 29 250-278 17-45 (68)
119 TIGR02950 SigM_subfam RNA poly 21.7 98 0.0021 25.2 3.1 35 248-282 118-152 (154)
120 PF08232 Striatin: Striatin fa 21.6 3.3E+02 0.0071 22.7 6.2 40 92-133 20-59 (134)
121 COG4985 ABC-type phosphate tra 21.5 2.6E+02 0.0057 25.9 5.9 22 94-115 218-239 (289)
122 KOG0660 Mitogen-activated prot 21.4 48 0.001 32.4 1.2 39 245-292 209-247 (359)
123 PF09340 NuA4: Histone acetylt 21.3 2.2E+02 0.0048 21.6 4.7 31 91-121 3-33 (80)
124 PRK08583 RNA polymerase sigma 21.3 1.7E+02 0.0036 26.6 4.8 35 248-282 218-252 (257)
125 PRK10573 type IV pilin biogene 21.2 3.8E+02 0.0082 26.1 7.6 59 240-302 301-365 (399)
126 PRK02166 hypothetical protein; 21.1 3.2E+02 0.0069 24.1 6.3 60 239-306 96-161 (184)
127 PF14493 HTH_40: Helix-turn-he 21.0 2.1E+02 0.0046 21.7 4.6 34 245-278 7-40 (91)
128 KOG0594 Protein kinase PCTAIRE 20.8 50 0.0011 31.9 1.2 37 248-293 205-241 (323)
129 PF04255 DUF433: Protein of un 20.8 94 0.002 21.6 2.4 32 238-269 18-50 (56)
130 PRK12528 RNA polymerase sigma 20.5 1.8E+02 0.0038 24.1 4.5 35 246-280 124-158 (161)
131 PRK12547 RNA polymerase sigma 20.3 2.6E+02 0.0055 23.3 5.5 46 237-282 113-159 (164)
132 TIGR02846 spore_sigmaK RNA pol 20.1 2.2E+02 0.0049 25.3 5.3 45 237-281 175-224 (227)
133 PF11887 DUF3407: Protein of u 20.1 2.4E+02 0.0052 26.3 5.6 19 170-188 6-24 (267)
134 KOG0922 DEAH-box RNA helicase 20.0 9.8E+02 0.021 25.6 10.4 137 124-289 436-574 (674)
No 1
>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=2.7e-84 Score=645.19 Aligned_cols=316 Identities=57% Similarity=0.887 Sum_probs=312.6
Q ss_pred CEEEEeecCccccccceeEEcCCCCCChhHHHHHHHHHHHHHHhCCCCCCCCCccccCCCCChHHHHHHHHHHHHHHHHH
Q 021133 1 MHVVPVQLPLISTLSKIRLSVPPDLRPLDARQSILLAVQELESRFPQGLPKLNPVKDMKIEDPEVVDLVNQIEELEHKLF 80 (317)
Q Consensus 1 ~~~~~v~~~~i~~is~~~~~lp~~~~~~~~r~~~~~~l~~~~~~~~~~~p~l~p~~~~~i~~~~~~~~~~~~~~l~~~l~ 80 (317)
|.++||+++.|..||++|+++|+++++.++|..+..++.++.++||.|+|.+||++||+|.+.++.++.++++.|+.++.
T Consensus 725 ~~vvpv~l~~i~~is~~r~~iP~dl~~~d~r~~~~k~v~e~~~rfp~gip~LdPv~dM~I~~~~~~~~~~k~e~lE~~l~ 804 (1041)
T KOG0948|consen 725 MEVVPVLLTLIDAISSIRLYIPKDLRSVDARLSVLKAVQEVKSRFPDGIPLLDPVKDMNIKDVEFKKLVKKIESLEARLE 804 (1041)
T ss_pred eEEEeeeHHHHhhhhHHHhcCcccccCcchHHHHHHHHHHHHHhcCCCCCCcChhhccCccchHHHHHHHHHHHHHHhhc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCCh
Q 021133 81 AHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDE 159 (317)
Q Consensus 81 ~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~e 159 (317)
.||.|.. ..++.++.+.++..|..++.++++++++.+...+++|+++|++||++|||++.++++.+||||||||+|+||
T Consensus 805 ~hp~~k~~~~~~~~~~f~~K~~l~~~ik~lk~~l~~~~~i~~ldELk~RkRVLrrLG~~t~ddvie~KGrvACEIsSgDE 884 (1041)
T KOG0948|consen 805 SHPLHKSSELEELYKEFQRKETLRAEIKDLKAELKSSQAILQLDELKNRKRVLRRLGYCTSDDVIELKGRVACEISSGDE 884 (1041)
T ss_pred cCcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhCCCCCCCeEEEcceEEEEecccch
Confidence 9999999 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHhhhcccccCCCccccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcc
Q 021133 160 LLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRP 239 (317)
Q Consensus 160 LlltEll~~g~f~~L~p~elaAllS~~v~e~~~~~~~~~~~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~ 239 (317)
|++|||||+|.|++|+|+|+||+|||||||++.++.+.+.++|..++.++++.|++|++++.+|++++++++|+++ |+|
T Consensus 885 LlLTEliFnG~Fndl~~eq~aaLLSCfVf~eks~e~~~l~~el~~~l~~lqe~ArrIAkVs~ecKlEide~~Yv~s-Fkp 963 (1041)
T KOG0948|consen 885 LLLTELIFNGIFNDLPVEQAAALLSCFVFQEKSSEAPKLKEELAGPLRQLQESARRIAKVSKECKLEIDEEDYVES-FKP 963 (1041)
T ss_pred HHHHHHHHhccccCCCHHHHHHHHhheeehhcccccccchHHHHHHHHHHHHHHHHHHHHHHhhccccCHHHHHHh-cCh
Confidence 9999999999999999999999999999999999889999999999999999999999999999999999999999 999
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCCccccCCCCC
Q 021133 240 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESLRRGIMFSNSLYL 317 (317)
Q Consensus 240 ~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L~~k~~~a~~~I~RdIVf~~SLYl 317 (317)
+||+|||+||+|+||++||++||+|||+|||++|||+||||||.+||++|||.+|.+||+.|+.+||||||||+||||
T Consensus 964 ~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeElLrQl~~AAk~iGnteLe~Kf~~~~~~ikRDIVFAaSLYL 1041 (1041)
T KOG0948|consen 964 ELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEELLRQLIDAAKVIGNTELENKFEEAIKKIKRDIVFAASLYL 1041 (1041)
T ss_pred HHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHhhceeehhhccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=4e-61 Score=488.65 Aligned_cols=284 Identities=32% Similarity=0.511 Sum_probs=266.5
Q ss_pred HHHHHHHHHHHHh---CCCCCCCCCccccCCCCChHHHHHHHHHHHHHHHHHcCCCCCC-ChHHHHHHHHHHHHHHHHHH
Q 021133 32 QSILLAVQELESR---FPQGLPKLNPVKDMKIEDPEVVDLVNQIEELEHKLFAHPLNKS-QDENQIRCFQRKAEVNHEIQ 107 (317)
Q Consensus 32 ~~~~~~l~~~~~~---~~~~~p~l~p~~~~~i~~~~~~~~~~~~~~l~~~l~~~p~~~c-~~~~~~~~~~~~~~l~~~~~ 107 (317)
..+.....++... -+.++|..+|+++.+.++.++.+...+...+.+.+...||+.| .+++|+....+..+.+.+++
T Consensus 960 aal~~~~~~~l~l~~~~~~~~~~~epv~~~k~kd~e~~~~~l~~~n~~~~~~~~~~i~c~~f~~h~s~~~~~~~~~~ei~ 1039 (1248)
T KOG0947|consen 960 AALNESTAQVLDLLEGSLETPTWKEPVNDSKLKDDEVVEMLLERTNLQNLIQGNPCISCPKFDQHYSLARREYKIEKEIE 1039 (1248)
T ss_pred HHHHHHHHHhhhhhhcCccCcchhhhhhhhhhccHHHHHHHHHHHHHHHHHhcCCccCCccHHHHHHHHHHHHHHHHHhh
Confidence 3344444444333 2566999999999999999999999999999999999999999 99999999999999999999
Q ss_pred HHHHHHhhhhhhHHHHHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhcc
Q 021133 108 QLKSKMRDSQIQKFRDELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFI 187 (317)
Q Consensus 108 ~l~~~i~~~~~~~~~~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v 187 (317)
+|+.++++ +++.+.++|.+++.||+.+||+|...+|++|||+||||++++|||+|||||+|.|.+|+|+|+||+||+||
T Consensus 1040 ~L~~~~sd-~~L~l~pey~~RlevLk~~g~vD~~~~V~lkGRvAceI~s~~ELllteli~dn~l~~l~peeiaallSslV 1118 (1248)
T KOG0947|consen 1040 NLEFELSD-QSLLLSPEYHNRLEVLKPLGFVDEMRTVLLKGRVACEINSGNELLLTELIFDNALVDLSPEEIAALLSSLV 1118 (1248)
T ss_pred hhhhhhhh-hhhhhCHHHHHHHHHHhhcCcccccceeeecceeeeeecCCcchhHHHHHHhhhhhhcCHHHHHHHHHHHH
Confidence 99999999 88889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCccccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChh-hhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcc
Q 021133 188 PVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVD-EYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEG 266 (317)
Q Consensus 188 ~e~~~~~~~~~~~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~-~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EG 266 (317)
||++.+..|.+++.+.++.+.+.++++++..++..|++.++++ +|... ++|+||+|||+||+|.||.+||.+|++.||
T Consensus 1119 ~e~~~e~~~~~~~~l~k~~e~v~~v~~rl~ev~~~~~~~~~~~e~f~~~-lrF~l~evVYeWA~G~sf~eim~~t~~~EG 1197 (1248)
T KOG0947|consen 1119 CEGKTERPPTLTPYLKKGKERVRDVAKRLEEVQSSHQLLQTPEEEFPCE-LRFGLVEVVYEWARGLSFKEIMELTDVLEG 1197 (1248)
T ss_pred hcCccccCCCCChhhhhHHHHHHHHHHHHHHHHHhhccccCchhhcccc-ccccHHHHHHHHHcCCCHHHHHhhhCCcch
Confidence 9999866688999999999999999999999999999999877 45555 999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCCccccCCCCC
Q 021133 267 SIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESLRRGIMFSNSLYL 317 (317)
Q Consensus 267 diVR~irRl~ellrQl~~aa~~ig~~~L~~k~~~a~~~I~RdIVf~~SLYl 317 (317)
+|||+|+||+|+|||+++|+.++|||.|.+||++|+++|||||||++|||+
T Consensus 1198 ~iVR~I~RLdE~cre~~~aa~ivGd~~L~~Km~~as~~ikRdIVFaaSLY~ 1248 (1248)
T KOG0947|consen 1198 LIVRLIQRLDEVCRELRNAARIVGDPVLHEKMEAASALIKRDIVFAASLYL 1248 (1248)
T ss_pred hHHHHHHHHHHHHHhhhccceecCcHHHHHHHHHHHHHhccCccchhhccC
Confidence 999999999999999999999999999999999999999999999999996
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=3.4e-57 Score=398.10 Aligned_cols=177 Identities=47% Similarity=0.786 Sum_probs=147.7
Q ss_pred CCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhcccccCCCcc-cc--ccHHHHHHHHHHHHHHH
Q 021133 138 INADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQ-IN--LRMELAKPLQQLQESAR 214 (317)
Q Consensus 138 id~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v~e~~~~~~-~~--~~~~l~~~~~~l~~~a~ 214 (317)
||++++||+|||+||+|+++|||++|||||+|+|++|+|+|+||++||||||+++++. .. +++.+.++++++.++++
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 6889999999999999999999999999999999999999999999999999987654 12 23389999999999999
Q ss_pred HHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHH
Q 021133 215 KIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNL 294 (317)
Q Consensus 215 ~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L 294 (317)
+|.+++.+||+ +.++|+++ ++|++|++||+||+|+||++||++|+++||||||++||++|+||||++|++++||++|
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 66789999 8999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCccccCCCCC
Q 021133 295 EKKFAAASESLRRGIMFSNSLYL 317 (317)
Q Consensus 295 ~~k~~~a~~~I~RdIVf~~SLYl 317 (317)
++|+++|+++|||||||++||||
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=6.9e-48 Score=403.32 Aligned_cols=310 Identities=34% Similarity=0.480 Sum_probs=283.9
Q ss_pred EEEEeecCccccccceeEEcCCCCCChhHHHHHHHHHHHHHHhCCCC-CCCCCccccCCCCChHHHHHHHHHHHHHHHHH
Q 021133 2 HVVPVQLPLISTLSKIRLSVPPDLRPLDARQSILLAVQELESRFPQG-LPKLNPVKDMKIEDPEVVDLVNQIEELEHKLF 80 (317)
Q Consensus 2 ~~~~v~~~~i~~is~~~~~lp~~~~~~~~r~~~~~~l~~~~~~~~~~-~p~l~p~~~~~i~~~~~~~~~~~~~~l~~~l~ 80 (317)
.+.++++..+..+....+.+|+.......+..-...+......+++| .+.++++.+|++.+.++..........+..+.
T Consensus 726 ~~~~~~~~~~~~~~~~~l~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~v~~~~~~~~~~~~~~~~~~~~~~~~~ 805 (1041)
T COG4581 726 RISFVYLLNATEILELILTMPRRLLSRQGKLRRGEPSNEAIAAGLDGNEKILENVVEMKIQVPELTVSLLKLRFGRYHLS 805 (1041)
T ss_pred eeeeeeeccccccchhhhcCCHhHhhcccchhccchhHHHHHhccccchhhhhhcccccccchhHHHHHHHHhhcccccC
Confidence 46778888888888888999977554444555555666666666555 56899999999999999999999999999999
Q ss_pred cCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCCh
Q 021133 81 AHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDE 159 (317)
Q Consensus 81 ~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~e 159 (317)
.+|.+.| ..++|++.......|..+++++...+ ....+.+++..+.++|+.+||++.+..++.|||+||+|++++|
T Consensus 806 ~~~~~~~~~~~~~~~~~~~~~~L~~~i~~l~~~~---~~~~~l~~~~~l~~~l~~~g~~~~~~~v~~kGr~a~eI~s~~e 882 (1041)
T COG4581 806 ENPLMNFDGAERLIENELLLSDLQAEIEDLSSSI---EALSFLDDYKTLQEVLKKLGFIEDNAVVLIKGRVAAEISSEDE 882 (1041)
T ss_pred CCccccchHHHHHHHhHhHHHHHHHHHHHHHHHH---HHhhhhHHHHHHHHHHHhhcCCCcccccccccceeeeecCCCc
Confidence 9999999 99999999999999999999999998 4445678999999999999999988999999999999999999
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHhhhcccccCCC----ccccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhc
Q 021133 160 LLVTELMFNGTFNDLDHHQVAALASCFIPVDKSS----EQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVES 235 (317)
Q Consensus 160 LlltEll~~g~f~~L~p~elaAllS~~v~e~~~~----~~~~~~~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~ 235 (317)
||+||||++|.|++|+|+++||++|||||+++++ +.+.++|.+.+++..+.+++.+|.+++.+++++++++ +++
T Consensus 883 llL~e~i~~g~f~~l~p~e~aallSa~v~e~~~~d~~~~~~~~~~~l~~~~~~l~e~~~kl~~~~~~~~i~~~~~--l~~ 960 (1041)
T COG4581 883 LLLTELIFSGEFNDLEPEELAALLSAFVFEEKTDDGTAEAPEITPALRDALLRLLELARKLNKDQNSSQIEIYPE--LND 960 (1041)
T ss_pred hHHHHHHHcCCccCCCHHHHHHHHHheeeccCCcccccccccCCHHHHhHHHHHHHHHHHHHHHHHhcCCcCCcc--ccc
Confidence 9999999999999999999999999999999986 3466789999999999999999999999999998865 667
Q ss_pred cCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCCccccCCC
Q 021133 236 TVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESLRRGIMFSNSL 315 (317)
Q Consensus 236 ~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L~~k~~~a~~~I~RdIVf~~SL 315 (317)
|.+++|++||.||+|++|.+||.+|++.|||+||+++|++|+|+|+..++.++||++|.+||..|+..|||||||++||
T Consensus 961 -~~~~lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r~~ell~ql~~aa~~ig~~~L~~k~~~~~~~irr~iv~~~sl 1039 (1041)
T COG4581 961 -FSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRRLRELLRQLRKAASVIGNPELEEKAYRAIQEIRRDIVFVDSL 1039 (1041)
T ss_pred -ccccHHHHHHHHHhhcchhhhhcCCcccccchhhhhhHHHHHHHHhhhcccccCCHHHHHHHHHHHHhhhcCeEecccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CC
Q 021133 316 YL 317 (317)
Q Consensus 316 Yl 317 (317)
|+
T Consensus 1040 y~ 1041 (1041)
T COG4581 1040 YL 1041 (1041)
T ss_pred cC
Confidence 96
No 5
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=99.84 E-value=3.5e-21 Score=179.26 Aligned_cols=115 Identities=50% Similarity=0.855 Sum_probs=102.5
Q ss_pred CEEEEeecCccccccceeEEcCCCCCChhHHHHHHHHHHHHHHhCCCCCCCCCccccCCCCChHHHHHHHHHHHHHHHHH
Q 021133 1 MHVVPVQLPLISTLSKIRLSVPPDLRPLDARQSILLAVQELESRFPQGLPKLNPVKDMKIEDPEVVDLVNQIEELEHKLF 80 (317)
Q Consensus 1 ~~~~~v~~~~i~~is~~~~~lp~~~~~~~~r~~~~~~l~~~~~~~~~~~p~l~p~~~~~i~~~~~~~~~~~~~~l~~~l~ 80 (317)
++++||+++||..||++|+++|+++++.++|+++.+++.++.++||+|+|.+||++||+|++.+|.++..+++.|+++|.
T Consensus 152 ~~vv~v~l~~I~~ISs~rl~lp~dl~~~~~r~~~~~~l~el~~r~~~giP~LDPi~DmkI~d~~~~e~~~k~~~Le~rl~ 231 (268)
T PF13234_consen 152 MEVVPVPLSCISSISSVRLKLPKDLRPQEARKQVLKSLQELLKRFPDGIPLLDPIKDMKIKDPEFVELVKKIEALEKRLS 231 (268)
T ss_dssp EEEEEEECCGEEEEEEEE----TTTTSCCCHHHHHHHHHHHHHHSSS--TCHHCHHHH----HHHHHHHHHHHHHHHHHH
T ss_pred EEEEEeeHHHHHHhhceeeeCcccccchHHHHHHHHHHHHHHHhCCCCCCccChHHhCCCCcHHHHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 021133 81 AHPLNKS-QDENQIRCFQRKAEVNHEIQQLKSKMRD 115 (317)
Q Consensus 81 ~~p~~~c-~~~~~~~~~~~~~~l~~~~~~l~~~i~~ 115 (317)
+||||.| ++++||..++++..|+++++.|++++++
T Consensus 232 ~~~~~~~~~~~~~~~~~~~k~~l~~~i~~Lk~~l~~ 267 (268)
T PF13234_consen 232 SHPLHKCPDFEEHYALYHEKAELQEEIKALKRQLSD 267 (268)
T ss_dssp HSCHCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999 9999999999999999999999999986
No 6
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=93.17 E-value=2.7 Score=43.57 Aligned_cols=176 Identities=18% Similarity=0.157 Sum_probs=107.1
Q ss_pred HHHHHHHHHHHhCCCCCCC---ccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhcccccCCCc------
Q 021133 124 ELKNRSRVLKKLGHINADG---VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSE------ 194 (317)
Q Consensus 124 ef~~~~~vL~~lgyid~~~---~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v~e~~~~~------ 194 (317)
+.++.+.-|+.+|||+.+| .+|..||+++.=. -.--.+|.|..|+..+.+|-.+|+-+.-|-...=+..
T Consensus 618 ~~~k~l~~Lee~g~i~~~G~~v~~T~yGrava~~F--l~p~~a~~Ir~~v~~~~~pl~i~~~l~pfE~ayls~~l~r~i~ 695 (830)
T COG1202 618 DPKKALSKLEEYGMIKKKGNIVRPTPYGRAVAMSF--LGPSEAEFIREGVLASMDPLRIAAELEPFENAYLSGFLKRAIE 695 (830)
T ss_pred CHHHHHHHHHhcCCeeccCCEeeeccccceeEEee--cCchHHHHHHHhhhccCChHhHhhccccccccccChHHHHHHH
Confidence 5678889999999999765 4999999886433 2335689999999999999999988776632111100
Q ss_pred ---cccccHHHHH-HHHHHHH-----------HHHHHHHHHHHcCC--CCChhhhhhccCcccHH-HHHHHhhCCCCHHH
Q 021133 195 ---QINLRMELAK-PLQQLQE-----------SARKIAEIQNECKL--EVNVDEYVESTVRPFLM-DVIYCWSKGATFAE 256 (317)
Q Consensus 195 ---~~~~~~~l~~-~~~~l~~-----------~a~~i~~~~~~~~l--~~~~~~~~~~~~~~~l~-~vv~~Wa~G~~f~e 256 (317)
.-.+|.++-. ++..+.+ +.+++-.++.++-- ..+..++..+ -+. .++..--.|.+-.+
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~~ 771 (830)
T COG1202 696 SALRGRVPSRLFDSALLDILEEGDKIIELDPKLKEKLLLIYMDFLNCTCRDCCECAEQ----RLSEKIIELRIEGKDPSQ 771 (830)
T ss_pred HHhcCCCchhhhhHHHHHHHhchhhhhcCCHHHHHHHHHHHHHHhcCchhhhHHHHHH----HHHHHHHHHHhcCCCHHH
Confidence 0011211111 2222111 12222222222111 1111111111 111 13334468888888
Q ss_pred HHhhc------CCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 021133 257 VIQMT------DIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESL 305 (317)
Q Consensus 257 i~~~t------~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L~~k~~~a~~~I 305 (317)
|-+.- ..+.|||.-|+-.+..+|.-+...|++.+-++..+.+..-.+.|
T Consensus 772 Isr~l~~~Ygi~aYpgDif~wLd~~vr~Lea~~rIArvf~kr~~~~ea~~lk~~i 826 (830)
T COG1202 772 ISRILEKRYGIQAYPGDIFTWLDTLVRLLEAIGRIARVFKKREVEAEAKALKKKI 826 (830)
T ss_pred HHHHHHHhhCeeecChhHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence 77652 57899999999999999999999999888888877666554443
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=92.79 E-value=0.12 Score=41.06 Aligned_cols=44 Identities=25% Similarity=0.394 Sum_probs=28.8
Q ss_pred HHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCC
Q 021133 129 SRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFND 173 (317)
Q Consensus 129 ~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~ 173 (317)
.+.|..+|.||+++.+|..|+.++.+-- +.-+---+++...|.-
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 4679999999999999999999999974 5444444444444444
No 8
>PRK02362 ski2-like helicase; Provisional
Probab=89.93 E-value=5.7 Score=42.38 Aligned_cols=175 Identities=13% Similarity=0.119 Sum_probs=94.8
Q ss_pred HHHHHHHHHHHHHhCCCCCCC---ccchhhHHhhhhcCCChHHHHHHHhhCCCCC---CCHHHHHHHhhhcccccCCCcc
Q 021133 122 RDELKNRSRVLKKLGHINADG---VVQLKGRAACLIDTGDELLVTELMFNGTFND---LDHHQVAALASCFIPVDKSSEQ 195 (317)
Q Consensus 122 ~~ef~~~~~vL~~lgyid~~~---~vt~kGrvA~eI~s~~eLlltEll~~g~f~~---L~p~elaAllS~~v~e~~~~~~ 195 (317)
.+-....++-|.+.|+|+.++ .+|..|++++.-+- +. ..++.+.+++ .. .+...+--++| .-+..++.
T Consensus 464 ~~~v~~~l~~L~~~~~i~~~~~~~~~t~lG~~~s~~~l-~~-~t~~~~~~~l-~~~~~~~~~~~l~~i~---~~~e~~~~ 537 (737)
T PRK02362 464 ERVVDDVLDFLERNGMIEEDGETLEATELGHLVSRLYI-DP-LSAAEIIDGL-EAAKKPTDLGLLHLVC---STPDMYEL 537 (737)
T ss_pred HHHHHHHHHHHHHCCCeeecCCeEeEChHHHHHHHhcC-CH-HHHHHHHHHh-hhcccCchHHHHHHhh---cCcccccc
Confidence 344577889999999998654 49999999998774 32 2333333332 21 22233332222 11111111
Q ss_pred ccccHHHHHHHHHHHHHHHH-HHHHHHHcCCCCC--hhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHH
Q 021133 196 INLRMELAKPLQQLQESARK-IAEIQNECKLEVN--VDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSA 272 (317)
Q Consensus 196 ~~~~~~l~~~~~~l~~~a~~-i~~~~~~~~l~~~--~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~i 272 (317)
+.-..+. +.+.. +... ...+. -+++.. ..+|-.......-.-+.++|.++.++.+|.+..++..||+-...
T Consensus 538 ~~r~~e~-~~l~~---~~~~~~~~~~--~~~p~~~~~~~~~~~~~~~k~~~ll~~~i~~~~~~~i~~~~~~~~gdl~~~~ 611 (737)
T PRK02362 538 YLRSGDY-EWLNE---YLYEHEDELL--GDVPSEFEDDEFEDFLSAVKTALLLEDWIDEVDEERITERYGVGPGDIRGKV 611 (737)
T ss_pred ccChhHH-HHHHH---HHHhcccchh--ccCCchhhhhhHHHHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCchHHHHHH
Confidence 1101111 11111 1100 00000 112211 11111100112345678999999999999999999999998888
Q ss_pred HHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCCc
Q 021133 273 RRLDEFLNQLRAAAQAVGEVNLEKKFAAASESLRRGI 309 (317)
Q Consensus 273 rRl~ellrQl~~aa~~ig~~~L~~k~~~a~~~I~RdI 309 (317)
....-++..+...+...| ..++..+.+-...|+-++
T Consensus 612 ~~~~~l~~a~~~i~~~~~-~~~~~~~~~l~~~l~~gv 647 (737)
T PRK02362 612 ETAEWLLHAAERLASELD-LDLARAARELEKRVEYGV 647 (737)
T ss_pred HHHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHhCC
Confidence 888888888888877655 445555555555554443
No 9
>PRK00254 ski2-like helicase; Provisional
Probab=89.65 E-value=4.3 Score=43.17 Aligned_cols=176 Identities=12% Similarity=0.086 Sum_probs=100.1
Q ss_pred HHHHHHHHHHHHhCCCCCC----CccchhhHHhhhhcCCChHHHHHHHhhCCC---CCCCHHHHHHHhhhcccccCCCcc
Q 021133 123 DELKNRSRVLKKLGHINAD----GVVQLKGRAACLIDTGDELLVTELMFNGTF---NDLDHHQVAALASCFIPVDKSSEQ 195 (317)
Q Consensus 123 ~ef~~~~~vL~~lgyid~~----~~vt~kGrvA~eI~s~~eLlltEll~~g~f---~~L~p~elaAllS~~v~e~~~~~~ 195 (317)
+.+...+..|.+.|+|+.+ -.+|.-|++++..|- +... ++.+.+++= .+.+-..+.-++|.. +.....
T Consensus 455 ~~v~~~l~~L~~~~~i~~~~~~~~~~t~lG~~~s~~~i-~~~t-~~~~~~~l~~~~~~~~~~~~l~~~~~~---~e~~~~ 529 (720)
T PRK00254 455 EKAKEIVYFLLENEFIDIDLEDRFIPLPLGIRTSQLYI-DPLT-AKKFKDAFPKIEKNPNPLGIFQLIAST---PDMTPL 529 (720)
T ss_pred HHHHHHHHHHHHCCCeEEcCCCCEeeChHHHHHHHHhC-CHHH-HHHHHHHHHhhccCCCHHHHHHHhhCC---cccccc
Confidence 4567778889999999643 248999999998775 4322 222222211 123333333333222 111111
Q ss_pred ccccHHHHHHHHHHHHHHHHHH-HHHHHcCCCCCh-hhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHH
Q 021133 196 INLRMELAKPLQQLQESARKIA-EIQNECKLEVNV-DEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSAR 273 (317)
Q Consensus 196 ~~~~~~l~~~~~~l~~~a~~i~-~~~~~~~l~~~~-~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~ir 273 (317)
+.-..+... +.+.+..+. ++. ..++... .+|......+...-+.++|.+|.+...|++..++..||+-+.+.
T Consensus 530 ~~r~~e~~~----l~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~k~~~ll~~~~~~~~~~~~~~~~~~~~gd~~~~~~ 603 (720)
T PRK00254 530 NYSRKEMED----LLDEAYEMEDRLY--FNIPYWEDYKFQKFLRAFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILE 603 (720)
T ss_pred CcchhhHHH----HHHHHHhhccccc--ccCCcchhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHH
Confidence 111112111 111111111 111 1222211 12211002345577899999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCC-HHHHHHHHHHHHhhcCCc
Q 021133 274 RLDEFLNQLRAAAQAVGE-VNLEKKFAAASESLRRGI 309 (317)
Q Consensus 274 Rl~ellrQl~~aa~~ig~-~~L~~k~~~a~~~I~RdI 309 (317)
+..-++.-+...+..+|. +.+...+.+-...|.=|+
T Consensus 604 ~~~~l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~ 640 (720)
T PRK00254 604 LADWLMYSLIELYKLFEPKQEVLDYLETLHLRVKHGV 640 (720)
T ss_pred HHHHHHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCC
Confidence 999999999999988884 566666665555555544
No 10
>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=85.83 E-value=2.4 Score=32.30 Aligned_cols=59 Identities=15% Similarity=0.179 Sum_probs=41.8
Q ss_pred HHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhcccc
Q 021133 129 SRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPV 189 (317)
Q Consensus 129 ~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v~e 189 (317)
...|..+|-||.++.+|..|+..+++-- +.- ++-+|..+...+=-..++++++|..-.+
T Consensus 3 ~~~L~~LgAld~~~~lT~lG~~m~~lPl-~Pr-la~~Ll~a~~~~~c~~~~~~i~a~ls~~ 61 (92)
T smart00847 3 LELLYELGALDDDGRLTPLGRKMAELPL-DPR-LAKMLLAAAELFGCLDEILTIAAMLSVG 61 (92)
T ss_pred HHHHHHCCCcCCCCCcCHHHHHHHHCCC-ChH-HHHHHHHHHhhcCcHHHHHHHHHHhcCC
Confidence 4679999999999999999999999974 443 4444444442201456788888777543
No 11
>PRK01172 ski2-like helicase; Provisional
Probab=82.36 E-value=56 Score=34.42 Aligned_cols=161 Identities=15% Similarity=0.110 Sum_probs=91.8
Q ss_pred HHHHHHHHHHHHHhCCCCCCC--ccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhcccccCCCcccccc
Q 021133 122 RDELKNRSRVLKKLGHINADG--VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQINLR 199 (317)
Q Consensus 122 ~~ef~~~~~vL~~lgyid~~~--~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v~e~~~~~~~~~~ 199 (317)
.+.....++-|.+.|+|+.++ .+|.-|++++..+- +. -.++.+.+.+=...+...+-.++|... +...+.
T Consensus 443 ~~~v~~~l~~L~~~~~i~~~~~~~~t~lG~~~s~~~l-~~-~t~~~~~~~l~~~~~~~~~l~~~~~~~------e~~~~~ 514 (674)
T PRK01172 443 DYYIESSLKFLKENGFIKGDVTLRATRLGKLTSDLYI-DP-ESALILKSAFDHDYDEDLALYYISLCR------EIIPAN 514 (674)
T ss_pred HHHHHHHHHHHHHCCCcccCCcEeECHHHHHHHHhCC-CH-HHHHHHHHHhhccCCHHHHHHHhhcCc------cccccc
Confidence 344677889999999998653 58999999999885 33 223334333323344444444443211 111111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 021133 200 MELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFL 279 (317)
Q Consensus 200 ~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ell 279 (317)
..-. ..+.+++.++ +. .+.+. ......-+.++|-++.+..+|.+.-.+..|++=+++....-+.
T Consensus 515 ~~~~---~~~~~~~~~~-------~~---~~~~~---~~~k~~~ll~~~~~~~~~~~i~~~~~~~~g~l~~~~~~~~~~~ 578 (674)
T PRK01172 515 TRDD---YYAMEFLEDI-------GV---IDGDI---SAAKTAMVLRGWISEASMQKITDTYGIAPGDVQARASSADWIS 578 (674)
T ss_pred cchH---HHHHHHHHHh-------cc---ccchh---HHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence 1000 1112222222 21 11111 2345567899999999999999999999999888865555554
Q ss_pred HHHHHHHhhcCCHHHHHHHHHHHHhhcC
Q 021133 280 NQLRAAAQAVGEVNLEKKFAAASESLRR 307 (317)
Q Consensus 280 rQl~~aa~~ig~~~L~~k~~~a~~~I~R 307 (317)
.-+...++. +.+++.+.+..-..-|.=
T Consensus 579 ~a~~~~~~~-~~~~~~~~l~~~~~rl~~ 605 (674)
T PRK01172 579 YSLARLSSI-YKPEMRRKLEILNIRIKE 605 (674)
T ss_pred HHHHHHHHH-hhHHHHHHHHHHHHHHHc
Confidence 444554554 346776665544444433
No 12
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=81.95 E-value=8.6 Score=41.68 Aligned_cols=66 Identities=20% Similarity=0.279 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhccccc
Q 021133 123 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVD 190 (317)
Q Consensus 123 ~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v~e~ 190 (317)
..+.+-+..|..+|.||+++.+|..|+..+++-. +.-+-.-+|....|. -..-.+||.++++..+.
T Consensus 384 ~~~~~A~~~L~~lgald~~g~lT~~G~~m~~lp~-~Prla~~ll~a~~~~-~~~l~~a~~laall~e~ 449 (812)
T PRK11664 384 AALAAAKRLLQQLGALDGQGRLTARGRKMAALGN-DPRLAAMLVAAKEDD-EAALATAAKLAAILEEP 449 (812)
T ss_pred HHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC-chHHHHHHHHHHhcC-chhhHHHHHHHHhhccC
Confidence 4688889999999999999999999999999963 555544444444443 11113688888877653
No 13
>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=79.06 E-value=4 Score=26.75 Aligned_cols=43 Identities=16% Similarity=0.223 Sum_probs=33.2
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFL 279 (317)
Q Consensus 237 ~~~~l~~vv~~W-a~G~~f~ei~~~t~l~EGdiVR~irRl~ell 279 (317)
+++.--.++..+ ..|.+..+|.+..++.+|.+-+++.|..+-|
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 444444555555 4999999999999999999999998876543
No 14
>PRK00118 putative DNA-binding protein; Validated
Probab=77.72 E-value=12 Score=30.01 Aligned_cols=52 Identities=6% Similarity=0.153 Sum_probs=43.1
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhh
Q 021133 237 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQA 288 (317)
Q Consensus 237 ~~~~l~~vv~~W-a~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ 288 (317)
+++.--.++..+ ..|.|..+|.+..+++++++=+.+.|...-|++.-..-..
T Consensus 18 L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 18 LTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 666666666665 7899999999999999999999999999888887666443
No 15
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=77.61 E-value=5.3 Score=26.73 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=34.5
Q ss_pred CcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFL 279 (317)
Q Consensus 237 ~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ell 279 (317)
+++.-..++..|..|.|..+|.+..+++.+++=+.+.|+..-|
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 3444455677789999999999999999999999988874433
No 16
>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=76.53 E-value=2.8 Score=31.38 Aligned_cols=30 Identities=17% Similarity=0.390 Sum_probs=27.8
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHH
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRL 275 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl 275 (317)
-+|..-.||..|-...++.|+++|..||+-
T Consensus 7 MAweDRtpFeaI~~qfGl~E~eVi~lMR~~ 36 (73)
T PF10985_consen 7 MAWEDRTPFEAIERQFGLSEKEVIKLMRKE 36 (73)
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 589999999999999999999999999863
No 17
>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=75.50 E-value=3.9 Score=30.51 Aligned_cols=30 Identities=20% Similarity=0.388 Sum_probs=27.8
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHH
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRL 275 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl 275 (317)
-+|..-.||..|-...++.|+++|..||+-
T Consensus 8 MAweDRtpFeaI~~~fGL~E~eVi~lMR~~ 37 (72)
T TIGR03643 8 MAWEDRTPFEAIEQQFGLSEKEVIKLMRQN 37 (72)
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 589999999999999999999999999863
No 18
>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=75.27 E-value=7.1 Score=26.33 Aligned_cols=38 Identities=18% Similarity=0.242 Sum_probs=31.8
Q ss_pred HHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 244 VIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 244 vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+...|-.|.|+.||-+..++++|.+=+..+|..+-||+
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 44567899999999999999999999998888877764
No 19
>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=74.76 E-value=5.8 Score=42.97 Aligned_cols=49 Identities=20% Similarity=0.342 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCC
Q 021133 123 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFN 172 (317)
Q Consensus 123 ~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~ 172 (317)
..+..-+..|..+|.||.++.+|..|+..+++-- +.-+---++..-.|.
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 4577888999999999999999999999999974 554444444443344
No 20
>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=74.66 E-value=7 Score=26.27 Aligned_cols=34 Identities=21% Similarity=0.295 Sum_probs=29.2
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHH
Q 021133 243 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLD 276 (317)
Q Consensus 243 ~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ 276 (317)
.+++.|..|.|..+|.+..++.++++-+.+.|+.
T Consensus 7 ~i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3556688999999999999999999998888763
No 21
>PRK04217 hypothetical protein; Provisional
Probab=71.50 E-value=13 Score=30.14 Aligned_cols=51 Identities=12% Similarity=0.107 Sum_probs=43.7
Q ss_pred CcccHHHHHHHhh-CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHh
Q 021133 237 VRPFLMDVIYCWS-KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQ 287 (317)
Q Consensus 237 ~~~~l~~vv~~Wa-~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~ 287 (317)
+...--+++..|. .|.|+.+|.+..+++++++=+.+.|....|++.-....
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 5555568888886 99999999999999999999999999999988766543
No 22
>PF13518 HTH_28: Helix-turn-helix domain
Probab=70.36 E-value=10 Score=25.35 Aligned_cols=35 Identities=17% Similarity=0.327 Sum_probs=31.2
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 243 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 243 ~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
.+|..+.+|.|..++++..+++.+++-+|+++..+
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 46777889999999999999999999999988765
No 23
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=68.43 E-value=12 Score=31.13 Aligned_cols=62 Identities=21% Similarity=0.221 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHhCCCCC-----CC-----ccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhc
Q 021133 122 RDELKNRSRVLKKLGHINA-----DG-----VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCF 186 (317)
Q Consensus 122 ~~ef~~~~~vL~~lgyid~-----~~-----~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~ 186 (317)
.+..-++++-|++.|||.. |. .+|.+|+-+.+-- .+ .+.+-+.+.+|++++++|++++...+
T Consensus 68 ~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~--~~-~~~~~~~~~l~~~ls~ee~~~l~~~L 139 (144)
T PRK11512 68 LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQC--HQ-LVGQDLHQELTKNLTADEVATLEHLL 139 (144)
T ss_pred HHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHH--HH-HHHHHHHHHHHccCCHHHHHHHHHHH
Confidence 4578889999999999954 21 5999999765321 11 22234566788999999999876543
No 24
>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=67.45 E-value=3.9 Score=37.67 Aligned_cols=45 Identities=24% Similarity=0.189 Sum_probs=37.8
Q ss_pred HHHHHhCCCCCCCccchhhHHhhhhcCC--------ChHHHHHHHhhCCCCCC
Q 021133 130 RVLKKLGHINADGVVQLKGRAACLIDTG--------DELLVTELMFNGTFNDL 174 (317)
Q Consensus 130 ~vL~~lgyid~~~~vt~kGrvA~eI~s~--------~eLlltEll~~g~f~~L 174 (317)
|.|.-+||+|+...+|.-|+++....+. .=+++-|+|+.|+++.=
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 4678899999999999999999887743 23889999999998865
No 25
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=63.36 E-value=19 Score=29.79 Aligned_cols=61 Identities=13% Similarity=0.122 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHhCCCCC-----CC-----ccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhc
Q 021133 122 RDELKNRSRVLKKLGHINA-----DG-----VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCF 186 (317)
Q Consensus 122 ~~ef~~~~~vL~~lgyid~-----~~-----~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~ 186 (317)
.+...+.++-|++.|||.. |. .+|.+|+-..+-- .+ ..+-+.+.+|.+++++|+..+...+
T Consensus 60 ~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~--~~--~~~~~~~~~~~~l~~ee~~~l~~~l 130 (144)
T PRK03573 60 QPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV--EA--VINKTRAEILHGISAEEIEQLITLI 130 (144)
T ss_pred hhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHH--HH--HHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 4578899999999999964 11 4999999876532 22 2234556678899999998877665
No 26
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=62.71 E-value=5.4 Score=26.76 Aligned_cols=34 Identities=15% Similarity=0.267 Sum_probs=24.2
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHH
Q 021133 243 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLD 276 (317)
Q Consensus 243 ~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ 276 (317)
.++..+..|.|-.+|++..+++..++-||++|-.
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 3566677799999999999999999999998854
No 27
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.84 E-value=75 Score=27.84 Aligned_cols=124 Identities=17% Similarity=0.147 Sum_probs=65.2
Q ss_pred CCCHHHHHHHhhhcccccCCCcc-------------ccccHHHHHHHHHHHHHH-HHHHHHHHHcCCCCChhhhhhccCc
Q 021133 173 DLDHHQVAALASCFIPVDKSSEQ-------------INLRMELAKPLQQLQESA-RKIAEIQNECKLEVNVDEYVESTVR 238 (317)
Q Consensus 173 ~L~p~elaAllS~~v~e~~~~~~-------------~~~~~~l~~~~~~l~~~a-~~i~~~~~~~~l~~~~~~~~~~~~~ 238 (317)
.++|+|+=+.+|..++-. .++. -..+..+..+++++.... +.+.+-.-.+.+-.|.++- .=
T Consensus 21 ~~t~aElHG~LsG~lcgG-~~d~sWq~l~~~~tneg~A~p~~l~~~l~~l~~a~s~~L~d~~F~f~LlLpe~e~----~v 95 (186)
T COG3079 21 GLTPAELHGLLSGLLCGG-LNDSSWQPLLHDLTNEGMAPPHGLLQALEQLLQATSQQLEDDGFAFQLLLPEGED----VV 95 (186)
T ss_pred CCCHHHHHHHHHhhhhcC-CCchhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHhcCCCeEEEEecCCCCc----HH
Confidence 689999999999999843 2221 112345555555544322 2222211111111222211 23
Q ss_pred ccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCC-----HHHHHHHHHHHHhhc
Q 021133 239 PFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGE-----VNLEKKFAAASESLR 306 (317)
Q Consensus 239 ~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~-----~~L~~k~~~a~~~I~ 306 (317)
+.-.+++..|+++- +.--++..-..-..---..|.++.+++.|++=+| .++.+..++.++-+|
T Consensus 96 f~rADAL~eW~nhF-----L~GlGL~~~~l~~~~gE~~EaldDL~~iaQlg~Deded~EE~~~~leEiiEyvR 163 (186)
T COG3079 96 FDRADALAEWCNHF-----LLGLGLTQPKLSKLTGEAGEALDDLANIAQLGYDEDEDQEELEESLEEIIEYVR 163 (186)
T ss_pred HHHHHHHHHHHHHH-----HHhhcccccchhhhcccHHHHHHHHHHHHHhcCCccccHHHHHHHHHHHHHHHH
Confidence 67889999999851 1111111100001111346778888888876444 467777777777665
No 28
>PF12917 HD_2: HD containing hydrolase-like enzyme ; PDB: 3MZO_B.
Probab=53.66 E-value=1.5e+02 Score=27.00 Aligned_cols=114 Identities=15% Similarity=0.229 Sum_probs=62.8
Q ss_pred CCCCCCCHHHHHHHhhhcccccCC-Ccccc----ccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHH
Q 021133 169 GTFNDLDHHQVAALASCFIPVDKS-SEQIN----LRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMD 243 (317)
Q Consensus 169 g~f~~L~p~elaAllS~~v~e~~~-~~~~~----~~~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~ 243 (317)
...++.++..++....+=-+-+.. .|.+. -+|+|++.+.++.+.+.. .|+.+.+...+-+
T Consensus 50 ~~G~~vd~~~lyekAL~HD~~E~FtGDI~TPVKy~tPelr~~~~~VE~~m~~---------------~~i~~~iP~e~q~ 114 (215)
T PF12917_consen 50 QFGNEVDWKELYEKALNHDYPEIFTGDIKTPVKYATPELREMLAQVEEEMTE---------------NFIKKEIPEEFQE 114 (215)
T ss_dssp HTT----HHHHHHHHHHTTGGGGTS----S-SSSS-HHHHHHHHHHHHHHHH---------------HHHHHHS-GGGHH
T ss_pred HhCCccCHHHHHHHHhccccHHHHcCCCCCcccccCHHHHHHHHHHHHHHHH---------------HHHHhhCCHHHHH
Confidence 345678888887765554444442 34333 378999888887765431 1222113333444
Q ss_pred HHHHhhCCCCHHHHHhh-cCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHH--HHHHHHHHHHhhcC
Q 021133 244 VIYCWSKGATFAEVIQM-TDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVN--LEKKFAAASESLRR 307 (317)
Q Consensus 244 vv~~Wa~G~~f~ei~~~-t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~--L~~k~~~a~~~I~R 307 (317)
+-..+.. +. .+--||-||+..-.++=++.-....-. ||++ ..+.+.++.+.|+.
T Consensus 115 ~Y~~~l~--------E~KDdt~EG~Iv~~ADkidal~e~~~Ei~~--GN~E~~F~e~y~e~l~~i~~ 171 (215)
T PF12917_consen 115 AYRRRLK--------EGKDDTLEGQIVKAADKIDALYECFGEIQK--GNPEKVFKEIYRESLEKIKK 171 (215)
T ss_dssp HHHHHHS-----------SSSHHHHHHHHHHHHHHHHHHHHHHHT--T-S-THHHHHHHHHHHHHHT
T ss_pred HHHHHhh--------cCCcccHHHHHHHHHHHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHHHh
Confidence 4444421 12 245689999988777777776666654 8998 88899999888765
No 29
>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=52.30 E-value=1.9e+02 Score=30.97 Aligned_cols=136 Identities=18% Similarity=0.189 Sum_probs=82.4
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHH---HHHHhhhcccccCCCcccccc
Q 021133 123 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQ---VAALASCFIPVDKSSEQINLR 199 (317)
Q Consensus 123 ~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~e---laAllS~~v~e~~~~~~~~~~ 199 (317)
+.+.+-+..|--||-+|..|.+|--||.-||.-. |+.+--.++-++... -+ +| |||++|+...--.+ +.
T Consensus 652 etL~~aLE~LyaLGALn~~GeLTk~GrrMaEfP~-dPmlsKmi~as~ky~-cs-~EiitiaamlS~~~svfyr-----pk 723 (902)
T KOG0923|consen 652 ETLLKALEQLYALGALNHLGELTKLGRRMAEFPV-DPMLSKMIVASEKYK-CS-EEIITIAAMLSVGASVFYR-----PK 723 (902)
T ss_pred HHHHHHHHHHHHhhccccccchhhhhhhhhhcCC-CHHHHhHHhhhcccc-ch-HHHHHHHHHHhcCchheec-----ch
Confidence 4566777888899999999999999999999874 776665566666655 33 44 45666665321011 11
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCC-CCHHHHHhhcCCCcchHHHHHHHHHHH
Q 021133 200 MELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKG-ATFAEVIQMTDIFEGSIIRSARRLDEF 278 (317)
Q Consensus 200 ~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G-~~f~ei~~~t~l~EGdiVR~irRl~el 278 (317)
... ++.. -..-.+..+..+ .-.++.+-..|..- .|++-..++ +--.|+++|.-++
T Consensus 724 ~~~---------v~ad----~a~~~f~~~~gD------hi~~L~vyn~w~es~~s~~wC~e~-----~iq~~sm~rardi 779 (902)
T KOG0923|consen 724 DKQ---------VHAD----NARKNFEEPVGD------HIVLLNVYNQWKESKYSTQWCYEN-----FIQYRSMKRARDI 779 (902)
T ss_pred hhh---------hhhh----hhhhccCCCCcc------hhhhhHHHHHHhhcchhhHHHHHh-----hhhHHHHHHHHHH
Confidence 000 0000 011122222222 24667777888655 444444332 4458999999999
Q ss_pred HHHHHHHHhhcC
Q 021133 279 LNQLRAAAQAVG 290 (317)
Q Consensus 279 lrQl~~aa~~ig 290 (317)
..|+-....-++
T Consensus 780 r~qL~gll~~v~ 791 (902)
T KOG0923|consen 780 RDQLEGLLERVE 791 (902)
T ss_pred HHHHHHHhhhcc
Confidence 999998865443
No 30
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=52.19 E-value=20 Score=23.81 Aligned_cols=31 Identities=13% Similarity=0.212 Sum_probs=22.7
Q ss_pred HHHHhhCCCCHHHHHhhcCCCcchHHHHHHH
Q 021133 244 VIYCWSKGATFAEVIQMTDIFEGSIIRSARR 274 (317)
Q Consensus 244 vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irR 274 (317)
+..-|..|.|..+|.+.-+.+..+|-|.++|
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 4445799999999999999999999999987
No 31
>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=51.67 E-value=28 Score=39.72 Aligned_cols=62 Identities=19% Similarity=0.368 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHhCCCCCCC---ccchhhHHhhhhcCCChHHHHHHHhhCC-CCCCCHHHHHHHhhhccc
Q 021133 123 DELKNRSRVLKKLGHINADG---VVQLKGRAACLIDTGDELLVTELMFNGT-FNDLDHHQVAALASCFIP 188 (317)
Q Consensus 123 ~ef~~~~~vL~~lgyid~~~---~vt~kGrvA~eI~s~~eLlltEll~~g~-f~~L~p~elaAllS~~v~ 188 (317)
..+..-+..|..+|.||+++ .+|..|+..+++-- +. -++-+|..|. |.-+ .+++.++|++-.
T Consensus 449 ~~i~~A~~~L~~LGAld~~~~~~~LT~lGr~ma~LPl-dP-rlarmLl~a~~~gcl--~e~l~IaA~Ls~ 514 (1283)
T TIGR01967 449 RAIRDGFRLLEELGALDDDEAEPQLTPIGRQLAQLPV-DP-RLARMLLEAHRLGCL--QEVLIIASALSI 514 (1283)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCccccHHHHHHhhcCC-Ch-HHHHHHHHhhhcCCH--HHHHHHHHHHcC
Confidence 35778889999999999887 79999999999984 54 4566665554 4433 345555555543
No 32
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=47.69 E-value=3.6e+02 Score=31.16 Aligned_cols=61 Identities=18% Similarity=0.324 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhCCCCCC-----CccchhhHHhhhhcCCChHHHHHHHhhC-CCCCCCHHHHHHHhhhccc
Q 021133 124 ELKNRSRVLKKLGHINAD-----GVVQLKGRAACLIDTGDELLVTELMFNG-TFNDLDHHQVAALASCFIP 188 (317)
Q Consensus 124 ef~~~~~vL~~lgyid~~-----~~vt~kGrvA~eI~s~~eLlltEll~~g-~f~~L~p~elaAllS~~v~ 188 (317)
...+-+..|..+|.||.+ +.+|.-|+..+++.- |. -++-+|..| .|.-++ ++..++|++-.
T Consensus 457 ~i~~al~~L~~LgAld~~~~~~~~~LT~lG~~la~LPl-dP-rlakmLl~a~~~~c~~--evl~IaA~Lsv 523 (1294)
T PRK11131 457 NIQDGVRLLEELGAITTDEQASAYKLTPLGRQLAQLPV-DP-RLARMVLEAQKHGCVR--EVMIITSALSI 523 (1294)
T ss_pred HHHHHHHHHHHCCCCCccccCCCccCcHHHHHHHhCCC-Ch-HHHHHHHHhhhcCCHH--HHHHHHHHHcC
Confidence 466668899999999853 469999999999984 44 455555544 455443 44445555543
No 33
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=46.66 E-value=65 Score=24.79 Aligned_cols=55 Identities=16% Similarity=0.160 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHhCCCCC-----CC-----ccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHH
Q 021133 121 FRDELKNRSRVLKKLGHINA-----DG-----VVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQV 179 (317)
Q Consensus 121 ~~~ef~~~~~vL~~lgyid~-----~~-----~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~el 179 (317)
-.....+.++-|.+-|||.. |. .+|.+|+-+.+-... ..+-+...+|.+++++++
T Consensus 49 ~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~----~~~~~~~~~~~~l~~~e~ 113 (126)
T COG1846 49 DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP----AAQELLAEILAGLSEEEL 113 (126)
T ss_pred CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc----HHHHHHHHhccCCCHHHH
Confidence 34678899999999999954 22 599999988776643 666777889999999995
No 34
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=46.51 E-value=66 Score=27.39 Aligned_cols=44 Identities=18% Similarity=0.182 Sum_probs=34.3
Q ss_pred hhCCCCHHHHHhhcCCCcch----HHHHHHHHHHHHHHHHHHHhhcCC
Q 021133 248 WSKGATFAEVIQMTDIFEGS----IIRSARRLDEFLNQLRAAAQAVGE 291 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGd----iVR~irRl~ellrQl~~aa~~ig~ 291 (317)
--.|.|..||.+..++++|+ +-|+.++|-+.|.+....=+-+||
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 667777777777776666554454
No 35
>COG4910 PduE Propanediol dehydratase, small subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=45.92 E-value=34 Score=28.78 Aligned_cols=78 Identities=18% Similarity=0.276 Sum_probs=52.7
Q ss_pred cCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHH-HHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHH
Q 021133 223 CKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSII-RSARRLDEFLNQLRAAAQAVGEVNLEKKFAAA 301 (317)
Q Consensus 223 ~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiV-R~irRl~ellrQl~~aa~~ig~~~L~~k~~~a 301 (317)
.|...+..+|--.+-.|+.+ .=++|+|+.+|.-.+ +-.|++- --+|=+-|.|+-=+.+|+-.|-+.|+..|+.|
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 34444455553322345443 247889999997544 4455553 33555678888888888888999999999999
Q ss_pred HHhh
Q 021133 302 SESL 305 (317)
Q Consensus 302 ~~~I 305 (317)
.++.
T Consensus 106 AELt 109 (170)
T COG4910 106 AELT 109 (170)
T ss_pred hhhh
Confidence 8864
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=45.10 E-value=83 Score=24.94 Aligned_cols=54 Identities=13% Similarity=0.140 Sum_probs=37.8
Q ss_pred HHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 214 RKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 214 ~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
..+......+|+... .+.++..++. ..|.+..+|++...+..+++.|.+.+|++
T Consensus 15 ~~~~~~l~~~~lt~~---------q~~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 15 SFFRPILAQHGLTEQ---------QWRILRILAE-QGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred HHHHHHHHHcCCCHH---------HHHHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 334444455676422 2345555543 46689999999999999999999999876
No 37
>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=45.05 E-value=2e+02 Score=24.65 Aligned_cols=53 Identities=15% Similarity=0.216 Sum_probs=31.8
Q ss_pred ChHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 021133 62 DPEVVDLVNQIEELEHKLFAHPLNKSQDENQIRCFQRKAEVNHEIQQLKSKMRD 115 (317)
Q Consensus 62 ~~~~~~~~~~~~~l~~~l~~~p~~~c~~~~~~~~~~~~~~l~~~~~~l~~~i~~ 115 (317)
..+..++..++.++++++.+-.- +.++.+..+.-++..++.+|++.++++.+.
T Consensus 39 ~~~~~~l~~Ei~~l~~E~~~iS~-qDeFAkwaKl~Rk~~kl~~el~~~~~~~~~ 91 (161)
T PF04420_consen 39 SKEQRQLRKEILQLKRELNAISA-QDEFAKWAKLNRKLDKLEEELEKLNKSLSS 91 (161)
T ss_dssp HHHHHHHHHHHHHHHHHHTTS-T-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHcCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667778888888888875422 115555555555555555555555555554
No 38
>smart00351 PAX Paired Box domain.
Probab=44.60 E-value=38 Score=27.73 Aligned_cols=35 Identities=11% Similarity=0.147 Sum_probs=30.1
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 243 DVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 243 ~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
.+|..+..|.|..+|++..+++.+++.||++|-.+
T Consensus 25 riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 25 RIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45666679999999999999999999999998654
No 39
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=41.88 E-value=65 Score=22.07 Aligned_cols=44 Identities=16% Similarity=0.132 Sum_probs=39.6
Q ss_pred ccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 239 PFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 239 ~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
..+.-+...|..|-++.++-..-++++.++-|.+....++|.+.
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 46677778899999999999999999999999999999998764
No 40
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=41.52 E-value=86 Score=25.72 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=29.7
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 240 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 240 ~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
.++..++..-.|.+..+|.+...+..+++-|.+.||++
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 41
>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=40.71 E-value=85 Score=32.34 Aligned_cols=61 Identities=23% Similarity=0.235 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCC-HHHHHHHhhh
Q 021133 124 ELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLD-HHQVAALASC 185 (317)
Q Consensus 124 ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~-p~elaAllS~ 185 (317)
.+-+-..+|--|+.+|+||.+|.-|++++|.-- |.-+.-.+|-+--|+=-+ .--|+|+||.
T Consensus 434 tLMrALE~LnYLaaLdDdGnLT~lG~imSEFPL-dPqLAkmLi~S~efnCsnEiLsisAMLsv 495 (699)
T KOG0925|consen 434 TLMRALEVLNYLAALDDDGNLTSLGEIMSEFPL-DPQLAKMLIGSCEFNCSNEILSISAMLSV 495 (699)
T ss_pred HHHHHHHHhhhhhhhCCCcccchhhhhhhcCCC-ChHHHHHHhhcCCCCchHHHHHHHhcccC
Confidence 344444455555556889999999999999876 666777777777776322 2345666663
No 42
>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=40.33 E-value=40 Score=22.30 Aligned_cols=33 Identities=12% Similarity=0.262 Sum_probs=26.0
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHH
Q 021133 240 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSA 272 (317)
Q Consensus 240 ~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~i 272 (317)
..-.++...+.|.|-.+|++.++++-.+|=|.+
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 566788889999999999999999999888765
No 43
>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=40.20 E-value=67 Score=26.16 Aligned_cols=45 Identities=9% Similarity=0.064 Sum_probs=36.2
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+++.-..+++. ...|.|+.||.+..+++++++=..+.|.-.-|++
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 44555566655 5799999999999999999998888887776665
No 44
>PRK15443 pduE propanediol dehydratase small subunit; Provisional
Probab=40.15 E-value=49 Score=27.79 Aligned_cols=54 Identities=19% Similarity=0.251 Sum_probs=37.3
Q ss_pred hCCCCHHHHHhhc----CCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhc
Q 021133 249 SKGATFAEVIQMT----DIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASESLR 306 (317)
Q Consensus 249 a~G~~f~ei~~~t----~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L~~k~~~a~~~I~ 306 (317)
..|+++.+|.-.. ++...|+ |. .-|.|.-=+.+|+-.|++.|+..|++|.++..
T Consensus 21 ~tGk~l~diTle~V~~G~v~~~Dl-RI---tpetL~~QaqiAe~~Gr~~la~NfrRAAELt~ 78 (138)
T PRK15443 21 PTGKSLDDITLENVLSGKVTAEDL-RI---TPETLRMQAQIAEDAGRPQLAMNFRRAAELTA 78 (138)
T ss_pred CCCCChhHhhHHHHHcCCCCHHHh-cc---CHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC
Confidence 6899999986432 3444443 33 33555555555566699999999999999864
No 45
>cd05495 Bromo_cbp_like Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=39.02 E-value=2e+02 Score=22.88 Aligned_cols=66 Identities=21% Similarity=0.373 Sum_probs=44.3
Q ss_pred hHHHHHHHHHHHHHHhCCCCCCCCCccccCCCCChHHHHHHH---HHHHHHHHHHcCCCCCC-ChHHHHH
Q 021133 29 DARQSILLAVQELESRFPQGLPKLNPVKDMKIEDPEVVDLVN---QIEELEHKLFAHPLNKS-QDENQIR 94 (317)
Q Consensus 29 ~~r~~~~~~l~~~~~~~~~~~p~l~p~~~~~i~~~~~~~~~~---~~~~l~~~l~~~p~~~c-~~~~~~~ 94 (317)
+-|+.+...+.++.+..+.+.|++.|+..-+..-+++.+.+. .+..++..|.++...+. .+...++
T Consensus 3 ~l~~~~~~il~~l~~~~~~s~~F~~PV~~~~~~~pdY~~iIk~PmDL~tI~~kL~~~~Y~s~~ef~~D~~ 72 (108)
T cd05495 3 ELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVW 72 (108)
T ss_pred HHHHHHHHHHHHHHHcCcccchhcCCCCccccCCCcHHHHhCCCCCHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 346667777777777667889999997653333456666666 47778888888777665 5544444
No 46
>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=38.62 E-value=54 Score=22.65 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=34.8
Q ss_pred CcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFL 279 (317)
Q Consensus 237 ~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ell 279 (317)
|.+.=.+++..|+.|.+-.+|.+.-++.++++-..++++-.-|
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 5666678999999999999999999999999988877765543
No 47
>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=37.99 E-value=1.1e+02 Score=22.10 Aligned_cols=41 Identities=20% Similarity=0.376 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHH-HhCCCCCCCc
Q 021133 98 RKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLK-KLGHINADGV 143 (317)
Q Consensus 98 ~~~~l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL~-~lgyid~~~~ 143 (317)
+..+++.+.++++.+++... .+-+.+-++-+ ++||+-++..
T Consensus 32 ~i~~l~~e~~~L~~ei~~l~-----~~~~~ie~~AR~~lgm~~~~E~ 73 (80)
T PF04977_consen 32 EIEELKKENEELKEEIERLK-----NDPDYIEKVAREKLGMVKPGEI 73 (80)
T ss_pred HHHHHHHHHHHHHHHHHHhc-----CCHHHHHHHHHHHcCCcCCCCE
Confidence 34455555555666555531 12233344445 8999977654
No 48
>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=37.50 E-value=81 Score=26.71 Aligned_cols=46 Identities=28% Similarity=0.209 Sum_probs=35.5
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
+++.--.++.. +..|.|..+|.+..++++|.+-..+.|.-.-|+.+
T Consensus 141 L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 141 LPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 33333334333 56999999999999999999999999888877764
No 49
>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=37.20 E-value=2.8e+02 Score=24.04 Aligned_cols=115 Identities=13% Similarity=0.103 Sum_probs=63.7
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHhhhc---ccccCCCccccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccC
Q 021133 161 LVTELMFNGTFNDLDHHQVAALASCF---IPVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTV 237 (317)
Q Consensus 161 lltEll~~g~f~~L~p~elaAllS~~---v~e~~~~~~~~~~~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~ 237 (317)
++-++|.+|-|... +.++.++.-+ .++-.++..-+-...+.+....+.+....-..+..+.|-. .
T Consensus 17 ~l~~~L~~~~~t~~--ei~~~~~~~~~~~g~~iSrSav~RY~~~~~~~~~~lr~are~a~al~~~~~~~----------~ 84 (180)
T PF11985_consen 17 WLDQMLRDGGFTQY--EILAEWLEELAEEGYDISRSAVHRYAQRFEEVLERLREAREIAEALAEELGDE----------P 84 (180)
T ss_pred HHHHHHHhCCCChH--HHHHHHHHhhhccCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC----------C
Confidence 77788888776644 3556666665 3322221111112234444444443333333333444421 3
Q ss_pred cccHHHHHHHhhCCCCHHHHHhhcCCCcchH--HHHHHHHHHHHHHHHHHHh
Q 021133 238 RPFLMDVIYCWSKGATFAEVIQMTDIFEGSI--IRSARRLDEFLNQLRAAAQ 287 (317)
Q Consensus 238 ~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdi--VR~irRl~ellrQl~~aa~ 287 (317)
......++-++....-|.-++...+-..++. +..+..+-..+..+..|+.
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 4566777778888888888887776666665 5566666666666666654
No 50
>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=37.15 E-value=67 Score=21.61 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=22.5
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
--.|.|+.||.+..+++++++=+.+.|--.
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 579999999999999999999888887644
No 51
>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=36.75 E-value=3.4 Score=31.60 Aligned_cols=25 Identities=24% Similarity=0.589 Sum_probs=13.5
Q ss_pred HHHHHhhCCCCHHHHHhhcCCCcch
Q 021133 243 DVIYCWSKGATFAEVIQMTDIFEGS 267 (317)
Q Consensus 243 ~vv~~Wa~G~~f~ei~~~t~l~EGd 267 (317)
..||+|.+|+.|.+++....+.+|.
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 5689999999999999998888885
No 52
>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=36.48 E-value=84 Score=22.79 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHhCCCCCCC----ccchhhH
Q 021133 122 RDELKNRSRVLKKLGHINADG----VVQLKGR 149 (317)
Q Consensus 122 ~~ef~~~~~vL~~lgyid~~~----~vt~kGr 149 (317)
...+.++++.|.+-||+...+ .+|.||.
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 368999999999999997642 4888885
No 53
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=35.83 E-value=93 Score=25.64 Aligned_cols=37 Identities=19% Similarity=0.100 Sum_probs=29.9
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 240 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 240 ~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
.++..++ ...|.+..+|.+..++..+++-|.+.||++
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 4444443 245689999999999999999999999986
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=35.41 E-value=84 Score=25.80 Aligned_cols=45 Identities=9% Similarity=0.184 Sum_probs=35.6
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+++.--.++.. +..|.|..||.+..++++|++=..+.|.-.-|++
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 7899999999999999999999888888776664
No 55
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=35.20 E-value=3e+02 Score=23.88 Aligned_cols=42 Identities=21% Similarity=0.363 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 021133 66 VDLVNQIEELEHKLFAHPLNKSQDENQIRCFQRKAEVNHEIQQLKSKMRD 115 (317)
Q Consensus 66 ~~~~~~~~~l~~~l~~~p~~~c~~~~~~~~~~~~~~l~~~~~~l~~~i~~ 115 (317)
.+..++++++++.+.+-. ..+.+.+|.++.++++.+.++++.
T Consensus 47 ~q~~~ei~dmKqelnavs--------~qD~fAkwaRlnRKi~kl~~ele~ 88 (175)
T KOG4253|consen 47 SQKVAEIQDMKQELNAVS--------MQDNFAKWARLNRKINKLDKELET 88 (175)
T ss_pred HHHHHHHHHHHHHHhhhh--------hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566777777666432 356788888999999888888866
No 56
>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=35.20 E-value=32 Score=22.81 Aligned_cols=34 Identities=15% Similarity=0.301 Sum_probs=29.6
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 249 SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 249 a~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
..+.|..+|++.+++..|+|-+-+.=-++|+.++
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 4678999999999999999999988888887754
No 57
>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=34.88 E-value=92 Score=24.60 Aligned_cols=36 Identities=19% Similarity=0.399 Sum_probs=31.2
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+.+..|.|+.+|.+..+++++++=+...|..+-|+.
T Consensus 121 ~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 335689999999999999999999999998777764
No 58
>PRK01736 hypothetical protein; Reviewed
Probab=33.91 E-value=2.5e+02 Score=24.82 Aligned_cols=59 Identities=19% Similarity=0.258 Sum_probs=31.3
Q ss_pred cHHHHHHHhhCC--CCHHHHH-hhcCCCcchHHHHHHHHHHHHHHHHHHHhhc-----CCHHHHHHHHHHHHhhc
Q 021133 240 FLMDVIYCWSKG--ATFAEVI-QMTDIFEGSIIRSARRLDEFLNQLRAAAQAV-----GEVNLEKKFAAASESLR 306 (317)
Q Consensus 240 ~l~~vv~~Wa~G--~~f~ei~-~~t~l~EGdiVR~irRl~ellrQl~~aa~~i-----g~~~L~~k~~~a~~~I~ 306 (317)
.-++.+..||+| ..|.-.- +.+.+. + -+.|.|+.++..+++= .+.+.++-+.+.++=+|
T Consensus 98 ~Ra~AL~~W~~GFl~G~gl~~~~~~~~~-~-------e~~E~l~Dl~~Ia~~~~d~~ed~ee~e~~~~Ei~EyvR 164 (190)
T PRK01736 98 DRADALAGWVNHFLLGLGLAQPKLDKVS-G-------ETGEAIDDLRNIAQLGYDEDEDQEELAQSLEEVIEYVR 164 (190)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccccCC-H-------HHHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHHHH
Confidence 455677999998 2222110 111112 1 4567888888887752 12444555555555443
No 59
>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=33.57 E-value=88 Score=24.53 Aligned_cols=48 Identities=10% Similarity=0.162 Sum_probs=34.4
Q ss_pred cHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHh
Q 021133 240 FLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQ 287 (317)
Q Consensus 240 ~l~~vv~~W-a~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~ 287 (317)
....+.+.- ..|.|=.++|+..++..|-|-++++||..+=+-+..+..
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 334444444 899999999999999999999999999998887777653
No 60
>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=33.34 E-value=69 Score=24.99 Aligned_cols=34 Identities=26% Similarity=0.420 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHh
Q 021133 102 VNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKL 135 (317)
Q Consensus 102 l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL~~l 135 (317)
+..|+.+|.+-+...-+..-.++|..+.+||+.+
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 4566777777777655555678999999999865
No 61
>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=32.59 E-value=1.6e+02 Score=22.42 Aligned_cols=45 Identities=13% Similarity=0.352 Sum_probs=36.0
Q ss_pred CCCCHHHHHhhcC-CCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 021133 250 KGATFAEVIQMTD-IFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASE 303 (317)
Q Consensus 250 ~G~~f~ei~~~t~-l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L~~k~~~a~~ 303 (317)
.|.|+.+|-+.-+ ..--++...++|+++.+.+ |+++...++....
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 9999999999999987653 5666666655443
No 62
>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=32.33 E-value=3.2e+02 Score=27.00 Aligned_cols=87 Identities=13% Similarity=0.198 Sum_probs=46.7
Q ss_pred HHHHhhhcccccCC-CccccccHHHHHHH---HHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCH
Q 021133 179 VAALASCFIPVDKS-SEQINLRMELAKPL---QQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATF 254 (317)
Q Consensus 179 laAllS~~v~e~~~-~~~~~~~~~l~~~~---~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f 254 (317)
++..-++|+|.... ++.... .....+. .......+.|-.-.+|.........|+.. ++++.|.|.
T Consensus 187 lsEaYA~FiFPk~~fpe~~~~-~~y~~AIpdl~~fi~~~NDILSFYKE~l~a~E~~NyI~n----------~A~~~g~S~ 255 (376)
T PF06330_consen 187 LSEAYAFFIFPKALFPEVEYF-IQYTPAIPDLMRFINYVNDILSFYKEELVAGETGNYIHN----------RARVHGVSI 255 (376)
T ss_dssp -HHHHHHHT--TTTS-TTTTH-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSSSSHHHH----------HHHHHT--H
T ss_pred cchhheeeecccccCChHHHH-HHHHHHHHHHHHHHHhhhhHHHHHHhhcccccccchhhh----------hhhccCCCH
Confidence 45567788884432 111100 1111122 22234555666667777655555556655 777899999
Q ss_pred HHHHhhcCCCcchHHHHHHHHHHHH
Q 021133 255 AEVIQMTDIFEGSIIRSARRLDEFL 279 (317)
Q Consensus 255 ~ei~~~t~l~EGdiVR~irRl~ell 279 (317)
.+.++.. -++.|++.+|+...|
T Consensus 256 ~eaL~~l---~~eti~a~~rv~~vL 277 (376)
T PF06330_consen 256 LEALREL---TDETIEAVERVRRVL 277 (376)
T ss_dssp HHHHHHH---HHHHHHHHHHHHHHH
T ss_pred HHHHHHH---HHHHHHHHHHHHHHh
Confidence 9988754 467777777766655
No 63
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=32.17 E-value=85 Score=23.68 Aligned_cols=64 Identities=16% Similarity=0.138 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHhCCCCCC----CccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhcc
Q 021133 122 RDELKNRSRVLKKLGHINAD----GVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFI 187 (317)
Q Consensus 122 ~~ef~~~~~vL~~lgyid~~----~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v 187 (317)
.+...+.++-|++.|||... -.+|.+|+-...--...--.+.+.+.. ..+++++++..++..|-
T Consensus 13 ~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~~~~~~~~~l~~--~~~~~~~e~~~l~~~l~ 80 (96)
T smart00529 13 PPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLRKHRLLERFLVD--VLGVDEEEVHEEAERLE 80 (96)
T ss_pred hHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHHHHHHHHHHHHH--HhCCCHHHHHHHHHHHH
Confidence 45778889999999999753 248899987543221111123333332 12688888888777664
No 64
>KOG0286 consensus G-protein beta subunit [General function prediction only]
Probab=32.12 E-value=29 Score=33.16 Aligned_cols=53 Identities=25% Similarity=0.330 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhCCCCCCCccchhhHHh
Q 021133 99 KAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGHINADGVVQLKGRAA 151 (317)
Q Consensus 99 ~~~l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL~~lgyid~~~~vt~kGrvA 151 (317)
...|.+|.++|+.+|++......--++.++..=|...|.+.-...-|+||..+
T Consensus 4 ~~~l~~Eae~L~~qi~~~r~~~~D~~l~q~a~~~~~~~~i~~~~rr~LkGH~~ 56 (343)
T KOG0286|consen 4 LEQLRQEAEQLKNQIRDARKKLNDVTLAQIAERLESVGRIQMRTRRTLKGHLN 56 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccHHHHhhccccceeeeeeeEEEeccccc
Confidence 34555666666666655333222235666777777888887666778898776
No 65
>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=31.75 E-value=45 Score=23.55 Aligned_cols=29 Identities=31% Similarity=0.540 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHhCCCCCCC---ccchhhH
Q 021133 121 FRDELKNRSRVLKKLGHINADG---VVQLKGR 149 (317)
Q Consensus 121 ~~~ef~~~~~vL~~lgyid~~~---~vt~kGr 149 (317)
+.+.|...+.-|.+.|++.-++ .+|.+|+
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 5677888899999999996543 4899997
No 66
>PRK04758 hypothetical protein; Validated
Probab=31.60 E-value=1.8e+02 Score=25.59 Aligned_cols=60 Identities=23% Similarity=0.294 Sum_probs=35.6
Q ss_pred ccHHHHHHHhhCC--CCHHHHH-hhcCCCcchHHHHHHHHHHHHHHHHHHHhhc-----CCHHHHHHHHHHHHhhc
Q 021133 239 PFLMDVIYCWSKG--ATFAEVI-QMTDIFEGSIIRSARRLDEFLNQLRAAAQAV-----GEVNLEKKFAAASESLR 306 (317)
Q Consensus 239 ~~l~~vv~~Wa~G--~~f~ei~-~~t~l~EGdiVR~irRl~ellrQl~~aa~~i-----g~~~L~~k~~~a~~~I~ 306 (317)
+.-++.+..||+| .-|.-.- +.+.+++ -+-|.|+.++++|++= .+.+.++-+.+.++=+|
T Consensus 93 ~~Ra~AL~~W~~gFL~G~Gl~~~~~~~~s~--------e~~E~L~Dl~~Iaql~~d~~ed~ee~E~al~El~EyvR 160 (181)
T PRK04758 93 AARADALFDWCRAFLGGFGLAAQQRPALSE--------EGEEALQDLARLAQASSDDFDAAEEDDTALAEIEEFVR 160 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccccCCH--------HHHHHHHHHHHHHccCCCcccCchHHHHHHHHHHHHHH
Confidence 5678889999998 3333321 2223333 4568888888888762 12455555666555444
No 67
>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=31.35 E-value=91 Score=21.41 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=25.0
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
|..+.++.+|.+..++..+++-|.+.+|.+
T Consensus 17 ~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 17 LEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred HHCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 445599999999999999999888877754
No 68
>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=31.22 E-value=1.1e+02 Score=25.79 Aligned_cols=46 Identities=20% Similarity=0.249 Sum_probs=37.0
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
+.+.--.|+.. .-.|.|..||-+..++++|++=..+.|.-..|++.
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 44444455554 46999999999999999999999999988888764
No 69
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=30.79 E-value=48 Score=24.63 Aligned_cols=42 Identities=17% Similarity=0.033 Sum_probs=29.3
Q ss_pred HhhhhhhHHHHHHHHHHHHHHHhCCCCCC---CccchhhHHhhhhc
Q 021133 113 MRDSQIQKFRDELKNRSRVLKKLGHINAD---GVVQLKGRAACLID 155 (317)
Q Consensus 113 i~~~~~~~~~~ef~~~~~vL~~lgyid~~---~~vt~kGrvA~eI~ 155 (317)
+....++. ...|.+.++-|.+.|+|..+ ..+|.||+-+.+..
T Consensus 25 i~~~~~L~-~~~~~~yL~~L~~~gLI~~~~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 25 IMYKANLN-YSTLKKYLKELEEKGLIKKKDGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp HHTTST---HHHHHHHHHHHHHTTSEEEETTEEEE-HHHHHHHHHH
T ss_pred HHHHhCcC-HHHHHHHHHHHHHCcCeeCCCCEEEECccHHHHHHHH
Confidence 33334553 46999999999999999663 25999998776543
No 70
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.55 E-value=96 Score=25.72 Aligned_cols=37 Identities=16% Similarity=0.267 Sum_probs=32.8
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 283 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~ 283 (317)
... .|.|..+|-+..++++|++-..+.|.-.-|++.-
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 9999999999999999999999999888888753
No 71
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=30.45 E-value=1.1e+02 Score=24.88 Aligned_cols=45 Identities=16% Similarity=0.034 Sum_probs=35.9
Q ss_pred CcccHHHHH-HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVI-YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 237 ~~~~l~~vv-~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+++.-=.++ ..+-.|.|..||.+..++++|++-..+.|...-||+
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 444434443 567899999999999999999999999998777765
No 72
>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=30.43 E-value=59 Score=21.43 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=23.8
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 249 SKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 249 a~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
-.|.|..+|.+.++++.|.+=+.+++|.+
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 45599999999999999999999988875
No 73
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=30.23 E-value=1.8e+02 Score=25.66 Aligned_cols=29 Identities=21% Similarity=0.410 Sum_probs=26.4
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 249 SKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 249 a~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
..|.+-.+|++...+..+++.|.+.||++
T Consensus 57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~ 85 (185)
T PRK13777 57 LKGASISEIAKFGVMHVSTAFNFSKKLEE 85 (185)
T ss_pred CCCcCHHHHHHHHCCCHhhHHHHHHHHHH
Confidence 46899999999999999999999999875
No 74
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=30.15 E-value=1.1e+02 Score=33.51 Aligned_cols=65 Identities=22% Similarity=0.285 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhccccc
Q 021133 123 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVD 190 (317)
Q Consensus 123 ~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v~e~ 190 (317)
..+..=...|..||-+|.+|.+|.-|+-++.+-- +.=+-..++..+.+..+ .|.+.+.|++-.++
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 4567778899999999999999999999999974 44455555555553322 35556666666655
No 75
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=29.98 E-value=1.2e+02 Score=25.53 Aligned_cols=34 Identities=15% Similarity=0.020 Sum_probs=30.4
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
...|.|+.||.+..++++|.+=..++|-..-|++
T Consensus 131 ~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 131 QLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999998888887777765
No 76
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.96 E-value=1e+02 Score=25.47 Aligned_cols=46 Identities=11% Similarity=0.154 Sum_probs=34.0
Q ss_pred CcccHHHHH-HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVI-YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 237 ~~~~l~~vv-~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
+++.-=.++ ..+-.|.|..||.+..++++|++=..+.|.-..|++.
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 333333343 4578999999999999999999977777766666653
No 77
>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=29.96 E-value=1.7e+02 Score=29.03 Aligned_cols=52 Identities=21% Similarity=0.417 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHhC-CCCCCCCCccccCCC-CChHHHHHHHHHHHHHHHHHc
Q 021133 30 ARQSILLAVQELESRF-PQGLPKLNPVKDMKI-EDPEVVDLVNQIEELEHKLFA 81 (317)
Q Consensus 30 ~r~~~~~~l~~~~~~~-~~~~p~l~p~~~~~i-~~~~~~~~~~~~~~l~~~l~~ 81 (317)
.+..+.+....+.... |..+..+++-..-.+ .++++.++.+++..|...+..
T Consensus 253 ~~~~l~~~~~~ms~~rDp~~P~~Lt~~q~~~i~~dpei~~l~~~~~~L~~~i~~ 306 (418)
T PF11917_consen 253 PREELIRAARSMSRSRDPRAPRELTDEQKASIEQDPEIQELQRRRDELKKEIRR 306 (418)
T ss_pred chHHHHHHhhhhhhhhCCCCCccCCHHHHhhhhcCcHHHHHHHHHHHHHhhhhh
Confidence 4566666776665543 433334443222222 378888889999999887765
No 78
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=29.93 E-value=1.3e+02 Score=27.44 Aligned_cols=95 Identities=21% Similarity=0.213 Sum_probs=67.4
Q ss_pred hhHHhhhhcCCChHHHHHHHhhCCCCCCCHHHHHHHhhhcccccCCCccccccHHHHHHHHHHHHHHHHHHHHHHHcCCC
Q 021133 147 KGRAACLIDTGDELLVTELMFNGTFNDLDHHQVAALASCFIPVDKSSEQINLRMELAKPLQQLQESARKIAEIQNECKLE 226 (317)
Q Consensus 147 kGrvA~eI~s~~eLlltEll~~g~f~~L~p~elaAllS~~v~e~~~~~~~~~~~~l~~~~~~l~~~a~~i~~~~~~~~l~ 226 (317)
++|+++ +.-|.-..|.+ |+..++|-+|.|-.. -+.+.|...++++|+-
T Consensus 89 ~~rIvR--------l~~EAy~Qggl--LT~~Dla~LL~~S~~----------------------TI~~~i~~yq~e~g~v 136 (220)
T PF07900_consen 89 KHRIVR--------LTNEAYDQGGL--LTQEDLAMLLGISPR----------------------TISKDIKEYQKEHGVV 136 (220)
T ss_pred HHHHHH--------HHHHHHHcCCc--ccHHHHHHHHCCCHH----------------------HHHHHHHHHHHHcCce
Confidence 566665 33455555543 677888877766432 2667788899999987
Q ss_pred CChhhhhhccCcccH---HHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHH
Q 021133 227 VNVDEYVESTVRPFL---MDVIYCWSKGATFAEVIQMTDIFEGSIIRSARR 274 (317)
Q Consensus 227 ~~~~~~~~~~~~~~l---~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irR 274 (317)
+|.--++.. .-|++ ..++..|-.|.+..||-..|.-+++.+=|-|+-
T Consensus 137 vPtrG~i~D-iGp~~tHK~~ii~~~l~g~~~~eiar~t~HS~~av~rYi~~ 186 (220)
T PF07900_consen 137 VPTRGTIHD-IGPGVTHKKIIIRLYLKGKPTPEIARRTNHSPEAVDRYIKD 186 (220)
T ss_pred eccCCcccc-cCCcchHHHHHHHHHHcCCCHHHHHHHhccCHHHHHHHHHh
Confidence 764333333 55665 478899999999999999999999988776653
No 79
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=29.83 E-value=1.3e+02 Score=24.74 Aligned_cols=36 Identities=19% Similarity=0.170 Sum_probs=32.1
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 283 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~ 283 (317)
.-.|.|..||.+..++++|++=..+.|....|++.-
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 579999999999999999999999998888887644
No 80
>PRK11415 hypothetical protein; Provisional
Probab=29.78 E-value=1.9e+02 Score=21.57 Aligned_cols=55 Identities=16% Similarity=0.327 Sum_probs=32.9
Q ss_pred ccCCCCChHHHHHHHHHHHHHHHH---HcCCCCCCChHHHHHHHHHHHHHHHHHHHHHH
Q 021133 56 KDMKIEDPEVVDLVNQIEELEHKL---FAHPLNKSQDENQIRCFQRKAEVNHEIQQLKS 111 (317)
Q Consensus 56 ~~~~i~~~~~~~~~~~~~~l~~~l---~~~p~~~c~~~~~~~~~~~~~~l~~~~~~l~~ 111 (317)
..++-.|+.|..+..+...|..++ ..+|-... -.+--++-.++..|..+|.++-+
T Consensus 10 ~~Lk~~D~~F~~L~~~h~~Ld~~I~~lE~~~~~~~-d~~i~~LKk~KL~LKDeI~~~L~ 67 (74)
T PRK11415 10 SRLKNENPRFMSLFDKHNKLDHEIARKEGSDGRGY-NAEVVRMKKQKLQLKDEMLKILQ 67 (74)
T ss_pred HHHHhcCHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHHHHhHHHHHHHHH
Confidence 345556889999999999988888 44443333 12223334455556655555443
No 81
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=29.69 E-value=2.4e+02 Score=23.59 Aligned_cols=74 Identities=19% Similarity=0.246 Sum_probs=41.7
Q ss_pred ChHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhCC
Q 021133 62 DPEVVDLVNQIEELEHKLFAHPLNKSQDENQIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLKKLGH 137 (317)
Q Consensus 62 ~~~~~~~~~~~~~l~~~l~~~p~~~c~~~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL~~lgy 137 (317)
.++...+.++...|++.=.+-.|..-...+.-.+-.++..|.++++.|+.+.+... . -.+-|+.++.-|..+|+
T Consensus 46 reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~-~-E~da~k~k~e~l~~~~~ 119 (135)
T KOG4196|consen 46 REEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQVEKLKEENSRLR-R-ELDAYKSKYEALQNSAV 119 (135)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHHhhhh
Confidence 34555555555555554443333211223333444567777777888877777622 1 23567777777777776
No 82
>KOG2163 consensus Centromere/kinetochore protein zw10 involved in mitotic chromosome segregation [Cell cycle control, cell division, chromosome partitioning]
Probab=29.52 E-value=7.1e+02 Score=26.45 Aligned_cols=119 Identities=15% Similarity=0.246 Sum_probs=63.0
Q ss_pred hhhcCCChHHHHHHHh-----hCCCCCCCHH-----HHHHHhhhcccccCCC-----cc-ccccHHHHHHHHHHHHHHHH
Q 021133 152 CLIDTGDELLVTELMF-----NGTFNDLDHH-----QVAALASCFIPVDKSS-----EQ-INLRMELAKPLQQLQESARK 215 (317)
Q Consensus 152 ~eI~s~~eLlltEll~-----~g~f~~L~p~-----elaAllS~~v~e~~~~-----~~-~~~~~~l~~~~~~l~~~a~~ 215 (317)
-+.+++-+.++-+|++ .++|.+.=|+ -++++++.++.+-=+. |. .....+|.+.+..+.+.+-.
T Consensus 563 ee~~ssa~klVrQcL~qLkll~~vw~~vLpe~vYck~mc~Llnt~~~elir~V~tl~Disa~da~eL~dLik~vL~~~p~ 642 (719)
T KOG2163|consen 563 EEMSSSADKLVRQCLLQLKLLAKVWREVLPEVVYCKVMCSLLNTLLDELIRHVVTLSDISANDANELADLIKRVLEVVPN 642 (719)
T ss_pred HhhcccHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHhhHHhhhhhhhHHHHHHHHHHHHhhhh
Confidence 4566667777777766 4566654443 3455666665432121 11 11123555555555444444
Q ss_pred HHHHHHHc-CCCCChhhhhhc-----cCcccHHHHHHHhhCCC-CHHHHHhhcCCCcchHHHHH
Q 021133 216 IAEIQNEC-KLEVNVDEYVES-----TVRPFLMDVIYCWSKGA-TFAEVIQMTDIFEGSIIRSA 272 (317)
Q Consensus 216 i~~~~~~~-~l~~~~~~~~~~-----~~~~~l~~vv~~Wa~G~-~f~ei~~~t~l~EGdiVR~i 272 (317)
+-.--.+. -.++...+|... -++-.||++.++|.+|. ||+.-.+.+++. ++||.+
T Consensus 643 vfa~~~e~~et~v~v~~w~pl~el~~mL~asLmeIt~rW~dgkGplaa~fsrsEVk--~lIkAL 704 (719)
T KOG2163|consen 643 VFAYKEETKETDVCVREWFPLNELVFMLGASLMEITHRWFDGKGPLAAHFSRSEVK--GLIKAL 704 (719)
T ss_pred hhcChhhccCccccHHHhccHHHHHHHhCchHhHHHHHHhcCCccHHhhccHHHHH--HHHHHH
Confidence 32222221 122223333221 26778999999999998 888777666542 445543
No 83
>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=29.43 E-value=2.7e+02 Score=22.84 Aligned_cols=28 Identities=21% Similarity=0.273 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHcCCCCCC-ChHHHHH
Q 021133 67 DLVNQIEELEHKLFAHPLNKS-QDENQIR 94 (317)
Q Consensus 67 ~~~~~~~~l~~~l~~~p~~~c-~~~~~~~ 94 (317)
-+...+..|+..|++-.|..| -.+++++
T Consensus 53 ~L~e~i~~LE~RLRaGlCDRC~VtqE~ak 81 (120)
T PF10482_consen 53 TLHENIKVLENRLRAGLCDRCTVTQELAK 81 (120)
T ss_pred HHHHHHHHHHHHHhcccchHHHHHHHHHH
Confidence 344578899999999999999 8888876
No 84
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=29.42 E-value=1.2e+02 Score=25.70 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=31.0
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
+..|.|..||.+..++.+|.+=..+.|.-.-|++.
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 66899999999999999999999888887777764
No 85
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=29.12 E-value=1.4e+02 Score=25.19 Aligned_cols=45 Identities=13% Similarity=0.048 Sum_probs=35.4
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 237 ~~~~l~~vv~~W-a~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+.+..-+++..+ -.|.|..||.+..++.+|++=..+.|.-.-|++
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 445555555555 589999999999999999998888887777665
No 86
>PF13730 HTH_36: Helix-turn-helix domain
Probab=28.71 E-value=63 Score=21.85 Aligned_cols=25 Identities=12% Similarity=0.240 Sum_probs=22.6
Q ss_pred CHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 253 TFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 253 ~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
|-..|++.+++..-++.|.+++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6788999999999999999999886
No 87
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=28.56 E-value=82 Score=25.64 Aligned_cols=79 Identities=15% Similarity=0.237 Sum_probs=43.3
Q ss_pred HHHHcCCCCChhhhhhccCcccHHHHHHHhh--CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHH
Q 021133 219 IQNECKLEVNVDEYVESTVRPFLMDVIYCWS--KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEK 296 (317)
Q Consensus 219 ~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa--~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L~~ 296 (317)
.-.++|++...-+|....++. +-...|. .|.+|.+++... |+ .-+++...-.-+.+.++.+
T Consensus 20 ~L~~~gi~~~~~~y~~~~~s~---~eL~~~l~~~g~~~~~li~t~----~~----------~~r~L~~~~~~~~~~~~~~ 82 (117)
T COG1393 20 WLEEHGIEYTFIDYLKTPPSR---EELKKILSKLGDGVEELINTR----GT----------TYRELNLDKEDLSDEELIE 82 (117)
T ss_pred HHHHcCCCcEEEEeecCCCCH---HHHHHHHHHcCccHHHHHHhc----cc----------hHHHcCCcccccChHHHHH
Confidence 346789888776676542221 2233442 233355555322 22 2223331111235677788
Q ss_pred HHHHHHHhhcCCccccCC
Q 021133 297 KFAAASESLRRGIMFSNS 314 (317)
Q Consensus 297 k~~~a~~~I~RdIVf~~S 314 (317)
.+-+.-.+|||.||...-
T Consensus 83 ~i~~~~~LikRPivv~~~ 100 (117)
T COG1393 83 ALLENPSLIKRPIVVDNK 100 (117)
T ss_pred HHHhChhhccCCeEEeCC
Confidence 888888999999998653
No 88
>KOG0201 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=28.15 E-value=86 Score=31.62 Aligned_cols=96 Identities=15% Similarity=0.245 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCC-CcchHHHHHHHHHHHH
Q 021133 201 ELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDI-FEGSIIRSARRLDEFL 279 (317)
Q Consensus 201 ~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l-~EGdiVR~irRl~ell 279 (317)
.|..+-..+.+++++|.-+ .+|.-+--.+-|... +.-..++++-+|+.|-+..+.++...+ .|=-|+=. +
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-LKGTKLWIIMEYCGGGSVLDLLKSGNILDEFEIAVI-------L 117 (467)
T ss_pred chhhcchhhHHHHHHHHHH-HhcCcchHHhhhhhe-eecccHHHHHHHhcCcchhhhhccCCCCccceeeee-------h
Confidence 5777777788888887655 334442222335545 888999999999999999999999876 33222211 2
Q ss_pred HHHHHHHhhcCCHHHHHHHHHHHHhhcCCccccCCC
Q 021133 280 NQLRAAAQAVGEVNLEKKFAAASESLRRGIMFSNSL 315 (317)
Q Consensus 280 rQl~~aa~~ig~~~L~~k~~~a~~~I~RdIVf~~SL 315 (317)
|++ -...++.....+|+|||-.++-|
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 22334566677899999776543
No 89
>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]
Probab=28.10 E-value=71 Score=35.19 Aligned_cols=61 Identities=23% Similarity=0.251 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCHHH-HHHHhh
Q 021133 123 DELKNRSRVLKKLGHINADGVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDHHQ-VAALAS 184 (317)
Q Consensus 123 ~ef~~~~~vL~~lgyid~~~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p~e-laAllS 184 (317)
+...+=+..|++.|-++.+..+|.-|+.++.+- .|.-+==.+++.++|.-|+|.- +||.||
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 467777899999999999999999999999998 4666777788899999999974 566777
No 90
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=27.93 E-value=2.4e+02 Score=22.40 Aligned_cols=40 Identities=15% Similarity=0.171 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH-HHhCCCCCCCc
Q 021133 99 KAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVL-KKLGHINADGV 143 (317)
Q Consensus 99 ~~~l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL-~~lgyid~~~~ 143 (317)
-.+++++.+.|+.+++..++. .+-.-..- ++|||+-++.+
T Consensus 43 ~~~l~~~n~~L~~eI~~L~~~-----~dyiEe~AR~~Lg~vk~gEi 83 (105)
T PRK00888 43 NAKLKARNDQLFAEIDDLKGG-----QEAIEERARNELGMVKPGET 83 (105)
T ss_pred HHHHHHHHHHHHHHHHHhhCc-----HHHHHHHHHHHcCCCCCCCE
Confidence 345566666666666664331 11111122 36999987654
No 91
>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=27.71 E-value=1.4e+02 Score=26.50 Aligned_cols=43 Identities=9% Similarity=0.016 Sum_probs=32.9
Q ss_pred ccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 239 PFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 239 ~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+.--.++.. ...|.|+.||.+..++.+|.+=+.+.|...-|++
T Consensus 178 ~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 178 EREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 333333333 4799999999999999999988888887776665
No 92
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=27.56 E-value=64 Score=21.25 Aligned_cols=25 Identities=28% Similarity=0.501 Sum_probs=21.3
Q ss_pred CCHHHHHhhcCCCcchHHHHHHHHH
Q 021133 252 ATFAEVIQMTDIFEGSIIRSARRLD 276 (317)
Q Consensus 252 ~~f~ei~~~t~l~EGdiVR~irRl~ 276 (317)
.||.+|-+..++++..+.+-++||.
T Consensus 18 ~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 8999999999999999999999874
No 93
>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=26.65 E-value=72 Score=21.86 Aligned_cols=30 Identities=23% Similarity=0.349 Sum_probs=25.5
Q ss_pred hhCC--CCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 248 WSKG--ATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 248 Wa~G--~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
+..| .+..+|.+.+++..+++-|.+++|++
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 3555 79999999999999999999999875
No 94
>KOG4456 consensus Inner centromere protein (INCENP), C-terminal domain [Cell cycle control, cell division, chromosome partitioning]
Probab=26.63 E-value=86 Score=26.10 Aligned_cols=50 Identities=14% Similarity=0.220 Sum_probs=37.7
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH-hhcCC
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVNLEKKFAAASE-SLRRG 308 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~L~~k~~~a~~-~I~Rd 308 (317)
=.||+|+...+...+-....-++|-.+ ..+||-+.|.+.|.++.- ..||+
T Consensus 67 PtWar~~v~~eai~~qa~~pp~~v~~F-------------f~~~pkpdLkeIF~~~~p~~~KR~ 117 (134)
T KOG4456|consen 67 PTWARDMVIVEAIEEQAKNPPFNVNTF-------------FGSMPKPDLKEIFGEMVPSKKKRG 117 (134)
T ss_pred chhhhhchHHHHHHHHhhCCchHHHHH-------------hcccCCcCHHHHHHhhhhhhhhcc
Confidence 469999999997766655555555443 456678999999999888 77886
No 95
>PRK06930 positive control sigma-like factor; Validated
Probab=26.46 E-value=1.5e+02 Score=25.64 Aligned_cols=45 Identities=11% Similarity=0.199 Sum_probs=36.3
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+++.--.++.. ...|.|+.+|.+..++++|++=..+.|...-|+.
T Consensus 115 L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 55555566665 6899999999999999999998888887776664
No 96
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=26.38 E-value=51 Score=24.83 Aligned_cols=37 Identities=22% Similarity=0.548 Sum_probs=27.9
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 240 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 240 ~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
++|...+. ..+++|.+|.+..++..|++=+.++.|+|
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 44555555 67799999999999999999888887765
No 97
>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=26.24 E-value=41 Score=27.58 Aligned_cols=52 Identities=13% Similarity=0.227 Sum_probs=42.0
Q ss_pred cHHHHHHHhhCCCCHHHHHhhc--CCCcchHHHHHHHHHHHHHHHHHHHhhcCC
Q 021133 240 FLMDVIYCWSKGATFAEVIQMT--DIFEGSIIRSARRLDEFLNQLRAAAQAVGE 291 (317)
Q Consensus 240 ~l~~vv~~Wa~G~~f~ei~~~t--~l~EGdiVR~irRl~ellrQl~~aa~~ig~ 291 (317)
+...+++.|..|.++.+.+... .+.+..+.++++++...+..+....-+-||
T Consensus 64 ~~~~~~~e~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~lh~~~~~H~d 117 (215)
T cd00180 64 NHLYLVMEYCEGGSLKDLLKENEGKLSEDEILRILLQILEGLEYLHSNGIIHRD 117 (215)
T ss_pred CeEEEEEecCCCCcHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhCCeeccC
Confidence 3445678899999999999886 789999999999999999888877544344
No 98
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.91 E-value=1.5e+02 Score=25.29 Aligned_cols=35 Identities=14% Similarity=0.042 Sum_probs=31.7
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
.-.|.|+.||.+..++++|++-..+.|.-.-||+.
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 152 VVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45799999999999999999999999988888865
No 99
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=25.74 E-value=1.3e+02 Score=25.38 Aligned_cols=37 Identities=8% Similarity=0.156 Sum_probs=31.9
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
..+..|.|..||.+..++++|++-..+.|.-.-|++.
T Consensus 130 l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 130 LYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999999988888887777753
No 100
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=25.49 E-value=1.3e+02 Score=19.91 Aligned_cols=29 Identities=10% Similarity=0.250 Sum_probs=25.2
Q ss_pred hCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 249 SKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 249 a~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
-.+.++.+|.+..++..+++-+.+++|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55689999999999999999888888776
No 101
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.38 E-value=1.7e+02 Score=24.84 Aligned_cols=45 Identities=27% Similarity=0.265 Sum_probs=35.5
Q ss_pred CcccHHHHHH-HhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIY-CWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 237 ~~~~l~~vv~-~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+.+.--.++. .+..|.|..||.+..++++|.+-..+.|.-.-|+.
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 4444444544 46899999999999999999999888887777665
No 102
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=25.22 E-value=1.7e+02 Score=25.14 Aligned_cols=48 Identities=13% Similarity=0.133 Sum_probs=35.6
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRA 284 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~ 284 (317)
+++.--+++.. ...|.|+.||.+..++++|++=..+.|.-.-|+..-.
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 44444444444 5699999999999999999998777777776665544
No 103
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=25.20 E-value=1.7e+02 Score=24.94 Aligned_cols=49 Identities=12% Similarity=0.114 Sum_probs=39.8
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAA 285 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~a 285 (317)
+++.--+++.. +-.|.|+.||.+..++++|++=..+.|.-..|++.-..
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 55555566655 78999999999999999999999888888888876533
No 104
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=25.15 E-value=67 Score=32.56 Aligned_cols=68 Identities=19% Similarity=0.280 Sum_probs=46.4
Q ss_pred HHh-hCC-CCHHHH-HhhcCCCcchHH---HHHHHHHHHHHHHHH-------------HHhhcCCHHHHHHHHHHHHhhc
Q 021133 246 YCW-SKG-ATFAEV-IQMTDIFEGSII---RSARRLDEFLNQLRA-------------AAQAVGEVNLEKKFAAASESLR 306 (317)
Q Consensus 246 ~~W-a~G-~~f~ei-~~~t~l~EGdiV---R~irRl~ellrQl~~-------------aa~~ig~~~L~~k~~~a~~~I~ 306 (317)
|.| ++| ++|++- ..+|++.|+||| =.-++|..+|+|+.. +..+||| ++...+.++.+.+.
T Consensus 50 ~~~~~~g~~~~~~~r~~~tdl~E~Di~~~~g~~~~L~~~i~ei~~~~~p~~ifv~~TC~t~iIGd-Dle~va~~~~~~~g 128 (457)
T CHL00073 50 FLQNALGVMIFAEPRYAMAELEEGDISAQLNDYEELKRLCLQIKKDRNPSVIVWIGTCTTEIIKM-DLEGMAPKLEAEIG 128 (457)
T ss_pred chhccccCcccCCccceecccCchhhhhhcCCHHHHHHHHHHHHHhCCCCEEEEEccCcHHhhcc-CHHHHHHHHHHhhC
Confidence 446 555 566541 123899999999 666778888888764 3456665 67777788877777
Q ss_pred CCccccCC
Q 021133 307 RGIMFSNS 314 (317)
Q Consensus 307 RdIVf~~S 314 (317)
=.||.+.+
T Consensus 129 ipVV~v~~ 136 (457)
T CHL00073 129 IPIVVARA 136 (457)
T ss_pred CCEEEEeC
Confidence 77776543
No 105
>cd00131 PAX Paired Box domain
Probab=25.05 E-value=1.1e+02 Score=25.12 Aligned_cols=34 Identities=12% Similarity=0.179 Sum_probs=28.4
Q ss_pred HHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 244 VIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 244 vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
++...+.|.|-.+|.+..++..+.+.||++|-.+
T Consensus 26 Iv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 26 IVELAQSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444468999999999999999999999998665
No 106
>PF13551 HTH_29: Winged helix-turn helix
Probab=25.03 E-value=1.2e+02 Score=23.28 Aligned_cols=34 Identities=18% Similarity=0.343 Sum_probs=29.7
Q ss_pred HHHHHhhCCCC-HHHHHhhcCCCcchHHHHHHHHH
Q 021133 243 DVIYCWSKGAT-FAEVIQMTDIFEGSIIRSARRLD 276 (317)
Q Consensus 243 ~vv~~Wa~G~~-f~ei~~~t~l~EGdiVR~irRl~ 276 (317)
.++...+.|.+ -.+|++..++...++=||+++..
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 46677899996 99999999999999999999955
No 107
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=24.65 E-value=1.7e+02 Score=25.17 Aligned_cols=47 Identities=21% Similarity=0.165 Sum_probs=35.8
Q ss_pred CcccHHHHHH-HhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIY-CWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLR 283 (317)
Q Consensus 237 ~~~~l~~vv~-~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~ 283 (317)
+.+.--.++. ..-.|.|+.||.+..++++|.+=..+.|....|++.-
T Consensus 142 Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 142 LPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 4444444444 3569999999999999999999888888777777643
No 108
>cd00238 ERp29c ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5.
Probab=24.61 E-value=3.4e+02 Score=21.09 Aligned_cols=34 Identities=24% Similarity=0.414 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHhhhh-hhHHHHHHHHHHHHHHHh
Q 021133 102 VNHEIQQLKSKMRDSQ-IQKFRDELKNRSRVLKKL 135 (317)
Q Consensus 102 l~~~~~~l~~~i~~~~-~~~~~~ef~~~~~vL~~l 135 (317)
+..|+++|.+-+.... +..-.++|..+.+||+.+
T Consensus 59 v~~E~~RL~~iL~~~~ls~~K~del~~R~NIL~~F 93 (93)
T cd00238 59 VEKELARLERLLEKKGLAPEKADELTRRLNILRSF 93 (93)
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhcC
Confidence 4566778877777633 445678999999999864
No 109
>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=24.37 E-value=1.3e+02 Score=27.39 Aligned_cols=37 Identities=14% Similarity=0.056 Sum_probs=32.1
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
..+..|.|+.||.+..++++|.+-+.+.|...-||+.
T Consensus 216 l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 216 CTFEENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4468999999999999999999988888888777764
No 110
>COG2926 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.28 E-value=2e+02 Score=22.80 Aligned_cols=30 Identities=33% Similarity=0.543 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 021133 90 ENQIRCFQRKAEVNHEIQQLKSKMRDSQIQ 119 (317)
Q Consensus 90 ~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~ 119 (317)
-+..+.++++.+++.+++...++|.+.+..
T Consensus 12 lE~Vr~~RrKNkl~Rei~DnekKIRDNqKR 41 (109)
T COG2926 12 LEFVRLFRRKNKLQREIEDNEKKIRDNQKR 41 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcchHH
Confidence 345677889999999999999998884443
No 111
>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=24.15 E-value=1e+02 Score=20.97 Aligned_cols=38 Identities=21% Similarity=0.376 Sum_probs=29.7
Q ss_pred ccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHH
Q 021133 239 PFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDE 277 (317)
Q Consensus 239 ~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~e 277 (317)
+.++..+++ ..|.+..+|-+..++.-+.+-|.+++|++
T Consensus 6 ~~iL~~l~~-~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 6 FRILRILYE-NGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHHHHH-HSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHH-cCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 345555555 45689999999999999999999999875
No 112
>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=24.11 E-value=54 Score=23.62 Aligned_cols=29 Identities=14% Similarity=0.206 Sum_probs=25.7
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLD 276 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ 276 (317)
...|.|..++|...++.+..|-+|+++..
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 58899999999999999999999998876
No 113
>COG1204 Superfamily II helicase [General function prediction only]
Probab=24.06 E-value=6.5e+02 Score=27.32 Aligned_cols=165 Identities=14% Similarity=0.152 Sum_probs=86.4
Q ss_pred HHHHHHHHHHHHHHhC-CCCCC---CccchhhHHhhhhcCCChHHHHHHHhhCCCCCCCH-HHHHHHhhhcccccCCCcc
Q 021133 121 FRDELKNRSRVLKKLG-HINAD---GVVQLKGRAACLIDTGDELLVTELMFNGTFNDLDH-HQVAALASCFIPVDKSSEQ 195 (317)
Q Consensus 121 ~~~ef~~~~~vL~~lg-yid~~---~~vt~kGrvA~eI~s~~eLlltEll~~g~f~~L~p-~elaAllS~~v~e~~~~~~ 195 (317)
...+..+-++.|.+.+ .++.. -..|.-|++++..|-..+ +...+...+.++.. +....++.-+... +|.
T Consensus 474 ~~~~i~~~~~~L~~~~~~~~~~~~~~~ate~g~~~s~~yi~~~---sa~~~~~~l~~~~~~~~~~~~l~~is~~---pd~ 547 (766)
T COG1204 474 LREEILASLRYLEENGLILDADWEALHATELGKLVSRLYIDPE---SAKIFRDLLAELALEPTEIGLLYLISLT---PDL 547 (766)
T ss_pred hHHHHHHHHHHHHhccceeeccccccchhHHHHHhhhccCCHH---HHHHHHHHHHHhccccchHHHhhhhhcC---ccc
Confidence 3456777788888886 55543 358899999999886333 22334444444443 2333333333321 121
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHH
Q 021133 196 INLRMELAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRL 275 (317)
Q Consensus 196 ~~~~~~l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl 275 (317)
..++-........+.+...........+.......+|-...-.+..+..+..|++..+-..|+..+++..||+.+..-..
T Consensus 548 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~~~~~~l~~wi~~~~~~~i~~~~~~~~~dl~~~~~~a 627 (766)
T COG1204 548 MPIKLRERESSELVLDELEEQSDYLLGERLDELAVEYNLLLQALKTAARLLDWINEADEDEILNAYGVAPGDLLRIAETA 627 (766)
T ss_pred hhhhhhhhhhhhhhHHHHHhcchHHhhccccccchhhHHHHHHHHHHHHHHHHHHhCcHHHHHHHhCcchhhHHhhcchh
Confidence 11100000000000111111111111122211111110000124678899999999999999999999999999887777
Q ss_pred HHH-------HHHHHHHHhhcCC
Q 021133 276 DEF-------LNQLRAAAQAVGE 291 (317)
Q Consensus 276 ~el-------lrQl~~aa~~ig~ 291 (317)
.-+ +.-+..-+.++|.
T Consensus 628 ~w~~~~~~~l~~~~~r~~~~~~~ 650 (766)
T COG1204 628 EWLSADLLALGKAAERLAKILGL 650 (766)
T ss_pred hhhhhhhhhhhhhhhhhHhhhCC
Confidence 666 5555555555544
No 114
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.80 E-value=1.7e+02 Score=24.27 Aligned_cols=48 Identities=15% Similarity=0.054 Sum_probs=39.4
Q ss_pred CcccHHHHHHHh-hCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYCW-SKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRA 284 (317)
Q Consensus 237 ~~~~l~~vv~~W-a~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~ 284 (317)
+++.--.++..+ ..|.|..||.+..++++|.+=-.+.|.-.-|++.-.
T Consensus 109 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 109 LPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 556666677766 699999999999999999998888888887777654
No 115
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.18 E-value=2e+02 Score=23.96 Aligned_cols=45 Identities=18% Similarity=0.122 Sum_probs=33.8
Q ss_pred cccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 238 RPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 238 ~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
++.--+|+.. ...|.|..||.+..++++|++=..+.|--..|++.
T Consensus 120 ~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 120 SPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3333334333 57899999999999999999977777777777664
No 116
>PF04363 DUF496: Protein of unknown function (DUF496); InterPro: IPR007458 Members of this family are uncharacterised proteins.
Probab=22.78 E-value=2.8e+02 Score=21.69 Aligned_cols=30 Identities=30% Similarity=0.530 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 021133 90 ENQIRCFQRKAEVNHEIQQLKSKMRDSQIQ 119 (317)
Q Consensus 90 ~~~~~~~~~~~~l~~~~~~l~~~i~~~~~~ 119 (317)
-+..+.++++.+|+.++..-.++|.+.+..
T Consensus 5 lE~Vr~~RrKNKl~REi~Dn~kKIRDNqKR 34 (95)
T PF04363_consen 5 LEFVRMYRRKNKLKREIEDNEKKIRDNQKR 34 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 355678899999999999999998884443
No 117
>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=22.51 E-value=88 Score=23.82 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhCCCCC-----C-CccchhhHHh
Q 021133 124 ELKNRSRVLKKLGHINA-----D-GVVQLKGRAA 151 (317)
Q Consensus 124 ef~~~~~vL~~lgyid~-----~-~~vt~kGrvA 151 (317)
.-++.+..|+++|||+. . .++|.||=-+
T Consensus 39 TIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~ 72 (78)
T PF03444_consen 39 TIRNEMADLEELGLVESQPHPSGGRIPTDKAYRA 72 (78)
T ss_pred HHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHH
Confidence 67788899999999974 1 3688888544
No 118
>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=22.23 E-value=76 Score=22.16 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=23.2
Q ss_pred CCCCHHHHHhhcCCCcchHHHHHHHHHHH
Q 021133 250 KGATFAEVIQMTDIFEGSIIRSARRLDEF 278 (317)
Q Consensus 250 ~G~~f~ei~~~t~l~EGdiVR~irRl~el 278 (317)
.+++..+|.+.+++..+.+-|.+++|.+.
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45889999999999999999999998763
No 119
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=21.72 E-value=98 Score=25.25 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=30.7
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
+-.|.|+.+|.+..++.+|++-..+.|.-.-|++.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999888887777763
No 120
>PF08232 Striatin: Striatin family; InterPro: IPR013258 This domain is associated with the N terminus of striatin. Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (IPR001680 from INTERPRO) repeat domain []. It acts as a scaffold protein [] and is involved in signalling pathways [, ].
Probab=21.60 E-value=3.3e+02 Score=22.67 Aligned_cols=40 Identities=23% Similarity=0.326 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHH
Q 021133 92 QIRCFQRKAEVNHEIQQLKSKMRDSQIQKFRDELKNRSRVLK 133 (317)
Q Consensus 92 ~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~~~ef~~~~~vL~ 133 (317)
...|--++.+++.+|..|+-+.....++ ..++.+++..|+
T Consensus 20 R~~WeiERaEmkarIa~LEGE~r~~e~l--~~dL~rrIkMLE 59 (134)
T PF08232_consen 20 RNQWEIERAEMKARIAFLEGERRGQENL--KKDLKRRIKMLE 59 (134)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Confidence 3456778899999999999998886554 468999998886
No 121
>COG4985 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]
Probab=21.55 E-value=2.6e+02 Score=25.89 Aligned_cols=22 Identities=18% Similarity=0.418 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 021133 94 RCFQRKAEVNHEIQQLKSKMRD 115 (317)
Q Consensus 94 ~~~~~~~~l~~~~~~l~~~i~~ 115 (317)
+...++.+|+++...+..+++.
T Consensus 218 ~~~ae~seLq~r~~~l~~~L~~ 239 (289)
T COG4985 218 HYVAEKSELQKRLAQLQTELDA 239 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555555555555555555
No 122
>KOG0660 consensus Mitogen-activated protein kinase [Signal transduction mechanisms]
Probab=21.42 E-value=48 Score=32.39 Aligned_cols=39 Identities=28% Similarity=0.585 Sum_probs=30.6
Q ss_pred HHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCH
Q 021133 245 IYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEV 292 (317)
Q Consensus 245 v~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~ 292 (317)
|--|+-|+-|+|++....+|+|. |-+.|+.-.-.++|.|
T Consensus 209 iDiWSvGCI~AEmL~gkplFpG~---------d~v~Ql~lI~~~lGtP 247 (359)
T KOG0660|consen 209 IDIWSVGCILAEMLTGKPLFPGK---------DYVHQLQLILELLGTP 247 (359)
T ss_pred hhhhhhhHHHHHHHcCCCCCCCC---------chHHHHHHHHHhcCCC
Confidence 45599999999999999999994 5556666666666654
No 123
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=21.35 E-value=2.2e+02 Score=21.56 Aligned_cols=31 Identities=13% Similarity=0.318 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhHH
Q 021133 91 NQIRCFQRKAEVNHEIQQLKSKMRDSQIQKF 121 (317)
Q Consensus 91 ~~~~~~~~~~~l~~~~~~l~~~i~~~~~~~~ 121 (317)
+...+..++.+|..++..++++|-+.+..++
T Consensus 3 ~L~~l~~~k~~Le~~L~~lE~qIy~~Et~YL 33 (80)
T PF09340_consen 3 ELKELLQKKKKLEKDLAALEKQIYDKETSYL 33 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345678899999999999999999666543
No 124
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.34 E-value=1.7e+02 Score=26.64 Aligned_cols=35 Identities=14% Similarity=0.054 Sum_probs=31.0
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
+..|.|+.||-+..++.+|.+=+...|...-||+.
T Consensus 218 ~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 218 FIENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred HhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999988888888777753
No 125
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=21.24 E-value=3.8e+02 Score=26.10 Aligned_cols=59 Identities=14% Similarity=0.119 Sum_probs=41.1
Q ss_pred cHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHH------HHHHHHHHHHHHHhhcCCHHHHHHHHHHH
Q 021133 240 FLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSAR------RLDEFLNQLRAAAQAVGEVNLEKKFAAAS 302 (317)
Q Consensus 240 ~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~ir------Rl~ellrQl~~aa~~ig~~~L~~k~~~a~ 302 (317)
.+-.+...=.+|.+|++.++.+++++..+++.++ ++++.|.++++-- ..++..+.+.-.
T Consensus 301 ~~~~i~~~v~~G~sls~al~~~~~fp~~~~~~i~~GE~sG~L~~~L~~la~~~----~~~~~~~~~~~~ 365 (399)
T PRK10573 301 ALTQIQQQIAQGIPLWLALKNHPLFPPLCLQLVRVGEESGSLDLMLENLAHWH----QEQTQALADNLA 365 (399)
T ss_pred HHHHHHHHHHCcccHHHHHhhCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHH----HHHHHHHHHHHH
Confidence 4444555557899999999999999999988887 4667777766554 334444444433
No 126
>PRK02166 hypothetical protein; Reviewed
Probab=21.11 E-value=3.2e+02 Score=24.14 Aligned_cols=60 Identities=23% Similarity=0.249 Sum_probs=34.1
Q ss_pred ccHHHHHHHhhCC--CCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcC----CHHHHHHHHHHHHhhc
Q 021133 239 PFLMDVIYCWSKG--ATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVG----EVNLEKKFAAASESLR 306 (317)
Q Consensus 239 ~~l~~vv~~Wa~G--~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig----~~~L~~k~~~a~~~I~ 306 (317)
+.-++.+..||+| .-|.-.-+...++ --+-|.|+.++++|++=- +.+.++-+.+.++=+|
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 5667888999998 3333331122221 145678888888877521 2445555555555444
No 127
>PF14493 HTH_40: Helix-turn-helix domain
Probab=20.97 E-value=2.1e+02 Score=21.70 Aligned_cols=34 Identities=21% Similarity=0.261 Sum_probs=28.2
Q ss_pred HHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHH
Q 021133 245 IYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEF 278 (317)
Q Consensus 245 v~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~el 278 (317)
...|.+|.|..+|.+.-++.+|+|..-+-+....
T Consensus 7 ~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 7 YELFQKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 4568899999999999999999998876665443
No 128
>KOG0594 consensus Protein kinase PCTAIRE and related kinases [General function prediction only]
Probab=20.85 E-value=50 Score=31.89 Aligned_cols=37 Identities=32% Similarity=0.551 Sum_probs=32.8
Q ss_pred hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHhhcCCHH
Q 021133 248 WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQLRAAAQAVGEVN 293 (317)
Q Consensus 248 Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl~~aa~~ig~~~ 293 (317)
|.-|+-|+|+...-.+|.|+-- .+|+....+++|.|.
T Consensus 205 Ws~GcIfaEm~~~~~LFpG~se---------~~ql~~If~~lGtP~ 241 (323)
T KOG0594|consen 205 WSLGCIFAEMFTRRPLFPGDSE---------IDQLFRIFRLLGTPN 241 (323)
T ss_pred HhHHHHHHHHHhCCCCCCCCcH---------HHHHHHHHHHcCCCC
Confidence 9999999999999999999987 788888888888764
No 129
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=20.77 E-value=94 Score=21.64 Aligned_cols=32 Identities=16% Similarity=0.107 Sum_probs=21.0
Q ss_pred cccHHHHHHHhhCCCCHHHHHhhcC-CCcchHH
Q 021133 238 RPFLMDVIYCWSKGATFAEVIQMTD-IFEGSII 269 (317)
Q Consensus 238 ~~~l~~vv~~Wa~G~~f~ei~~~t~-l~EGdiV 269 (317)
+-..-.++..|+.|.|..+|.+..+ +...++-
T Consensus 18 RI~v~~i~~~~~~G~s~eeI~~~yp~Lt~~~i~ 50 (56)
T PF04255_consen 18 RIPVRDILDLLAAGESPEEIAEDYPSLTLEDIR 50 (56)
T ss_dssp S-BHHHHHHHHHTT--HHHHHHHSTT--HHHHH
T ss_pred eecHHHHHHHHHcCCCHHHHHHHCCCCCHHHHH
Confidence 3456677888899999999999876 7766553
No 130
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.52 E-value=1.8e+02 Score=24.06 Aligned_cols=35 Identities=11% Similarity=0.062 Sum_probs=30.0
Q ss_pred HHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 021133 246 YCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLN 280 (317)
Q Consensus 246 ~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellr 280 (317)
.....|.|..||.+..++++|++=..+.|-...|+
T Consensus 124 L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 124 LAQVDGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34579999999999999999999888888766665
No 131
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.33 E-value=2.6e+02 Score=23.27 Aligned_cols=46 Identities=15% Similarity=0.192 Sum_probs=35.3
Q ss_pred CcccHHHHHHH-hhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYC-WSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQL 282 (317)
Q Consensus 237 ~~~~l~~vv~~-Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQl 282 (317)
+++.--.++.. ...|.|..||.+..++++|++=..+.|.-.-|+..
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 35999999999999999999988888887777754
No 132
>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=20.14 E-value=2.2e+02 Score=25.31 Aligned_cols=45 Identities=18% Similarity=0.075 Sum_probs=33.4
Q ss_pred CcccHHHHHHHhh-----CCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 237 VRPFLMDVIYCWS-----KGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 237 ~~~~l~~vv~~Wa-----~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
+++.-=.++.... .|.|..||.+..++.+|++-+.+.|.---|++
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 89999999999999999998887776555553
No 133
>PF11887 DUF3407: Protein of unknown function (DUF3407); InterPro: IPR024516 This entry represents a domain of unknown function found at the C terminus of many proteins in the mammalian cell entry family.
Probab=20.08 E-value=2.4e+02 Score=26.27 Aligned_cols=19 Identities=16% Similarity=0.249 Sum_probs=16.0
Q ss_pred CCCCCCHHHHHHHhhhccc
Q 021133 170 TFNDLDHHQVAALASCFIP 188 (317)
Q Consensus 170 ~f~~L~p~elaAllS~~v~ 188 (317)
+++.++|+++.++|+++..
T Consensus 6 ll~~vdP~kLn~tL~ala~ 24 (267)
T PF11887_consen 6 LLDAVDPAKLNATLSALAT 24 (267)
T ss_pred HHHhCCHHHHHHHHHHHHH
Confidence 4567999999999999864
No 134
>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]
Probab=20.01 E-value=9.8e+02 Score=25.55 Aligned_cols=137 Identities=19% Similarity=0.199 Sum_probs=80.1
Q ss_pred HHHHHHHHHHHhCCCCCCCccch-hhHHhhhhcCCChHHHHHHHhhCCCCCCCH-HHHHHHhhhcccccCCCccccccHH
Q 021133 124 ELKNRSRVLKKLGHINADGVVQL-KGRAACLIDTGDELLVTELMFNGTFNDLDH-HQVAALASCFIPVDKSSEQINLRME 201 (317)
Q Consensus 124 ef~~~~~vL~~lgyid~~~~vt~-kGrvA~eI~s~~eLlltEll~~g~f~~L~p-~elaAllS~~v~e~~~~~~~~~~~~ 201 (317)
....=+..|..+|-||++|.+|. -|+-.+++-- +.-+---+|.++-|.-.+. --+||.|| .|..-- .+.+.
T Consensus 436 ~l~~AL~~L~~lgald~~g~lt~p~G~~ma~~Pl-~p~lsk~ll~s~~~gc~~e~l~i~a~Ls---v~~~f~---~p~~~ 508 (674)
T KOG0922|consen 436 ALEEALEELYSLGALDDRGKLTSPLGRQMAELPL-EPHLSKMLLKSSELGCSEEILTIAAMLS---VQSVFS---RPKDK 508 (674)
T ss_pred HHHHHHHHHHhcCcccCcCCcCchHHhhhhhcCC-CcchhhhhhhccccCCcchhhhheeeee---ccceec---Cccch
Confidence 44555677888999999998888 9999999875 3333444444656654443 34566666 322210 11111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCChhhhhhccCcccHHHHHHHhhCCCCHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 021133 202 LAKPLQQLQESARKIAEIQNECKLEVNVDEYVESTVRPFLMDVIYCWSKGATFAEVIQMTDIFEGSIIRSARRLDEFLNQ 281 (317)
Q Consensus 202 l~~~~~~l~~~a~~i~~~~~~~~l~~~~~~~~~~~~~~~l~~vv~~Wa~G~~f~ei~~~t~l~EGdiVR~irRl~ellrQ 281 (317)
-.+ ...+...++..+..| ...|..+...|..-..=..-|..-.+. +|.++|..++=+|
T Consensus 509 ~~~------------~a~~~~~kf~~~eGD------h~tlL~vy~~~~~~~~~~~wC~en~i~----~r~l~~a~~ir~Q 566 (674)
T KOG0922|consen 509 KAE------------DADRKRAKFANPEGD------HLTLLNVYESWKENGTSKKWCKENFIN----ARSLKRAKDIRKQ 566 (674)
T ss_pred hhh------------hhhHHHHhhcCcccC------HHHHHHHHHHHHhcCChhhHHHHhccc----HHHHHHHHHHHHH
Confidence 111 011122233333221 246777777886654444555544444 8999999999999
Q ss_pred HHHHHhhc
Q 021133 282 LRAAAQAV 289 (317)
Q Consensus 282 l~~aa~~i 289 (317)
+....+-+
T Consensus 567 L~~i~~~~ 574 (674)
T KOG0922|consen 567 LRRILDKF 574 (674)
T ss_pred HHHHHHHc
Confidence 99887544
Done!