Query 008449
Match_columns 565
No_of_seqs 205 out of 1403
Neff 7.1
Searched_HMMs 46136
Date Thu Mar 28 12:18:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008449.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008449hhsearch_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 8E-143 2E-147 1142.9 48.0 552 1-565 488-1041(1041)
2 KOG0947 Cytoplasmic exosomal R 100.0 1E-107 2E-112 891.0 42.4 539 1-565 672-1248(1248)
3 COG4581 Superfamily II RNA hel 100.0 4.1E-81 8.9E-86 707.8 40.3 538 1-565 486-1041(1041)
4 PF08148 DSHCT: DSHCT (NUC185) 100.0 1.1E-54 2.5E-59 415.7 14.4 177 387-565 1-180 (180)
5 PF13234 rRNA_proc-arch: rRNA- 100.0 5.9E-44 1.3E-48 363.1 21.2 261 92-364 1-267 (268)
6 PRK02362 ski2-like helicase; P 99.5 3.4E-13 7.4E-18 155.8 13.0 104 1-104 345-457 (737)
7 PRK01172 ski2-like helicase; P 99.4 1.5E-12 3.2E-17 149.1 12.9 105 1-105 327-438 (674)
8 PRK00254 ski2-like helicase; P 99.4 3E-12 6.5E-17 147.6 13.1 104 1-104 337-447 (720)
9 COG1204 Superfamily II helicas 99.3 5.6E-12 1.2E-16 144.4 6.7 106 1-106 356-470 (766)
10 KOG0949 Predicted helicase, DE 99.1 1.5E-10 3.3E-15 129.9 6.0 74 1-84 1004-1077(1330)
11 KOG0952 DNA/RNA helicase MER3/ 98.9 1.1E-09 2.5E-14 124.1 5.8 117 1-119 438-574 (1230)
12 COG1202 Superfamily II helicas 98.9 6.8E-10 1.5E-14 119.1 2.2 66 1-70 506-580 (830)
13 KOG0950 DNA polymerase theta/e 98.7 8E-09 1.7E-13 116.8 5.5 100 1-105 564-672 (1008)
14 KOG0951 RNA helicase BRR2, DEA 98.7 7.1E-09 1.5E-13 119.2 4.3 103 1-105 649-757 (1674)
15 KOG0953 Mitochondrial RNA heli 98.2 1.8E-06 3.9E-11 93.1 5.4 78 2-81 426-505 (700)
16 KOG0951 RNA helicase BRR2, DEA 97.0 0.0013 2.7E-08 77.3 6.9 94 2-102 1447-1547(1674)
17 PF00271 Helicase_C: Helicase 96.1 0.0063 1.4E-07 49.4 3.6 27 3-38 52-78 (78)
18 TIGR00614 recQ_fam ATP-depende 95.7 0.015 3.3E-07 64.1 5.7 41 22-65 305-345 (470)
19 smart00490 HELICc helicase sup 95.6 0.0096 2.1E-07 47.9 2.9 27 3-38 56-82 (82)
20 PRK09751 putative ATP-dependen 95.3 0.045 9.8E-07 67.6 8.5 73 21-94 355-434 (1490)
21 PLN00206 DEAD-box ATP-dependen 95.1 0.027 5.8E-07 63.1 5.2 30 21-52 446-475 (518)
22 PRK13767 ATP-dependent helicas 94.9 0.058 1.3E-06 64.2 7.5 85 21-105 368-461 (876)
23 PTZ00424 helicase 45; Provisio 94.6 0.022 4.8E-07 61.1 2.8 30 21-52 345-374 (401)
24 PRK11057 ATP-dependent DNA hel 94.5 0.044 9.5E-07 62.6 5.1 41 21-64 314-354 (607)
25 PRK01297 ATP-dependent RNA hel 94.5 0.046 9.9E-07 60.4 5.1 30 21-52 413-442 (475)
26 TIGR03817 DECH_helic helicase/ 93.0 0.25 5.4E-06 57.8 7.8 30 21-52 357-386 (742)
27 TIGR01389 recQ ATP-dependent D 92.8 0.14 3.1E-06 58.2 5.4 39 22-63 303-341 (591)
28 TIGR00643 recG ATP-dependent D 92.1 0.23 4.9E-06 57.0 5.9 28 23-52 539-566 (630)
29 PRK11192 ATP-dependent RNA hel 92.0 0.16 3.5E-06 55.3 4.3 29 21-51 323-351 (434)
30 PRK10917 ATP-dependent DNA hel 91.7 0.27 5.8E-06 57.0 5.9 28 23-52 562-589 (681)
31 PRK04837 ATP-dependent RNA hel 91.7 0.099 2.2E-06 56.8 2.2 30 21-52 333-362 (423)
32 PF12029 DUF3516: Domain of un 91.5 0.2 4.2E-06 53.9 4.0 35 54-88 38-72 (461)
33 cd00079 HELICc Helicase superf 91.4 0.098 2.1E-06 46.0 1.5 26 21-48 106-131 (131)
34 PRK11776 ATP-dependent RNA hel 91.2 0.23 4.9E-06 54.6 4.5 29 22-52 321-349 (460)
35 PRK10590 ATP-dependent RNA hel 91.2 0.2 4.2E-06 55.2 3.9 28 22-51 324-351 (456)
36 PLN03137 ATP-dependent DNA hel 91.1 0.25 5.4E-06 59.4 4.9 52 22-77 759-810 (1195)
37 PTZ00110 helicase; Provisional 90.5 0.41 9E-06 54.0 5.8 29 22-52 456-484 (545)
38 PRK04537 ATP-dependent RNA hel 90.0 0.34 7.3E-06 55.0 4.6 30 21-52 335-364 (572)
39 PRK05298 excinuclease ABC subu 89.6 0.78 1.7E-05 52.9 7.1 42 4-52 516-557 (652)
40 PRK11664 ATP-dependent RNA hel 88.6 1.4 3.1E-05 52.0 8.5 45 4-51 285-338 (812)
41 TIGR01967 DEAH_box_HrpA ATP-de 88.6 0.71 1.5E-05 56.6 6.1 57 21-87 376-433 (1283)
42 PRK11634 ATP-dependent RNA hel 88.2 0.61 1.3E-05 53.6 5.0 30 21-52 323-352 (629)
43 TIGR01587 cas3_core CRISPR-ass 87.6 0.5 1.1E-05 49.9 3.6 31 22-52 304-336 (358)
44 TIGR01970 DEAH_box_HrpB ATP-de 87.1 1.7 3.6E-05 51.5 7.8 59 20-88 307-366 (819)
45 TIGR00631 uvrb excinuclease AB 87.0 1.1 2.3E-05 51.8 6.0 42 4-52 512-553 (655)
46 PF04408 HA2: Helicase associa 86.2 0.71 1.5E-05 39.9 3.2 44 378-422 3-46 (102)
47 TIGR00580 mfd transcription-re 85.6 1.3 2.9E-05 53.0 6.0 40 3-52 731-770 (926)
48 PHA02653 RNA helicase NPH-II; 84.5 0.93 2E-05 52.3 4.0 30 20-52 485-514 (675)
49 COG1202 Superfamily II helicas 84.5 22 0.00048 40.1 14.1 163 373-553 618-826 (830)
50 PRK10689 transcription-repair 80.7 2.7 5.8E-05 51.6 6.0 40 3-52 880-919 (1147)
51 PRK11131 ATP-dependent RNA hel 77.5 5.3 0.00011 49.3 7.1 57 21-87 383-440 (1294)
52 COG4098 comFA Superfamily II D 76.8 2.3 5.1E-05 44.6 3.4 37 16-52 380-416 (441)
53 KOG0922 DEAH-box RNA helicase 75.4 3.9 8.5E-05 46.3 4.9 71 11-90 346-422 (674)
54 KOG0924 mRNA splicing factor A 75.2 6.1 0.00013 45.0 6.3 77 19-103 667-753 (1042)
55 PRK04914 ATP-dependent helicas 75.1 35 0.00076 41.2 13.0 44 21-64 574-617 (956)
56 PRK00118 putative DNA-binding 71.7 13 0.00028 32.5 6.3 71 481-551 14-89 (104)
57 PRK13766 Hef nuclease; Provisi 68.7 7 0.00015 46.0 5.3 28 22-52 452-479 (773)
58 smart00421 HTH_LUXR helix_turn 68.2 9 0.00019 28.1 4.1 42 485-526 4-45 (58)
59 COG3079 Uncharacterized protei 68.2 16 0.00036 34.4 6.4 124 422-554 21-163 (186)
60 TIGR00595 priA primosomal prot 68.0 6.1 0.00013 44.2 4.4 27 24-52 355-381 (505)
61 KOG4150 Predicted ATP-dependen 67.6 4.5 9.7E-05 45.1 3.1 29 21-49 611-639 (1034)
62 smart00847 HA2 Helicase associ 66.8 11 0.00024 31.3 4.8 59 378-438 3-61 (92)
63 KOG0923 mRNA splicing factor A 66.4 7.2 0.00016 44.3 4.4 61 21-89 578-638 (902)
64 PRK05580 primosome assembly pr 66.1 6.7 0.00015 45.6 4.4 26 25-52 524-549 (679)
65 PRK11664 ATP-dependent RNA hel 64.1 26 0.00057 41.6 8.8 65 372-438 384-448 (812)
66 cd06170 LuxR_C_like C-terminal 63.5 12 0.00025 27.6 3.9 33 491-523 7-39 (57)
67 KOG4284 DEAD box protein [Tran 62.2 6.1 0.00013 44.8 2.9 31 22-54 351-381 (980)
68 KOG0345 ATP-dependent RNA heli 61.1 14 0.00031 40.5 5.3 50 21-74 335-385 (567)
69 PRK04217 hypothetical protein; 61.0 21 0.00045 31.6 5.5 52 484-535 42-94 (110)
70 cd06171 Sigma70_r4 Sigma70, re 59.5 9.4 0.0002 27.4 2.7 42 486-527 12-54 (55)
71 KOG0332 ATP-dependent RNA heli 59.4 17 0.00037 38.8 5.4 40 11-56 408-447 (477)
72 COG1205 Distinct helicase fami 57.1 8.3 0.00018 45.9 3.1 26 23-50 395-420 (851)
73 PRK02362 ski2-like helicase; P 56.8 95 0.0021 36.5 11.8 66 490-556 581-646 (737)
74 PF12246 MKT1_C: Temperature d 56.5 19 0.00041 36.3 5.2 45 379-423 1-53 (243)
75 PHA02558 uvsW UvsW helicase; P 56.5 11 0.00024 42.1 3.8 19 23-41 425-443 (501)
76 PF13518 HTH_28: Helix-turn-he 55.8 21 0.00046 26.1 4.1 35 491-525 4-38 (52)
77 COG1198 PriA Primosomal protei 54.8 12 0.00026 43.6 3.8 39 23-64 576-614 (730)
78 COG0513 SrmB Superfamily II DN 54.5 8.1 0.00018 43.3 2.3 38 21-60 351-388 (513)
79 KOG0330 ATP-dependent RNA heli 54.0 12 0.00026 40.1 3.3 38 21-61 378-415 (476)
80 PRK09200 preprotein translocas 53.9 12 0.00025 44.2 3.5 31 20-52 511-541 (790)
81 KOG0347 RNA helicase [RNA proc 51.9 21 0.00045 40.0 4.8 90 22-118 542-635 (731)
82 PF04545 Sigma70_r4: Sigma-70, 51.9 25 0.00053 25.8 3.9 38 492-529 13-50 (50)
83 TIGR01970 DEAH_box_HrpB ATP-de 51.5 22 0.00048 42.3 5.3 60 372-433 381-442 (819)
84 PF10985 DUF2805: Protein of u 51.3 13 0.00029 30.1 2.4 29 494-522 7-35 (73)
85 KOG0926 DEAH-box RNA helicase 51.1 6.6 0.00014 45.6 0.9 31 19-52 674-704 (1172)
86 KOG0350 DEAD-box ATP-dependent 50.1 16 0.00035 40.3 3.6 40 21-63 511-550 (620)
87 PRK12906 secA preprotein trans 49.8 63 0.0014 38.2 8.6 32 19-52 522-553 (796)
88 PRK12900 secA preprotein trans 49.0 80 0.0017 38.2 9.2 30 21-52 682-711 (1025)
89 KOG0326 ATP-dependent RNA heli 48.5 29 0.00063 36.4 4.9 51 23-75 402-454 (459)
90 PRK12898 secA preprotein trans 48.3 20 0.00043 41.4 4.1 30 21-52 557-586 (656)
91 TIGR03643 conserved hypothetic 47.7 21 0.00045 28.9 3.0 29 494-522 8-36 (72)
92 PRK12543 RNA polymerase sigma 46.8 28 0.0006 32.8 4.4 43 497-539 131-177 (179)
93 COG1643 HrpA HrpA-like helicas 45.9 36 0.00077 40.5 5.8 29 20-51 358-386 (845)
94 TIGR00963 secA preprotein tran 43.1 51 0.0011 38.6 6.5 31 20-52 487-517 (745)
95 PF13384 HTH_23: Homeodomain-l 42.7 13 0.00028 27.2 1.1 34 491-524 9-42 (50)
96 PRK01172 ski2-like helicase; P 42.6 5.9E+02 0.013 29.4 15.3 159 372-554 444-604 (674)
97 PRK00254 ski2-like helicase; P 40.4 82 0.0018 36.9 7.8 71 487-557 569-640 (720)
98 KOG0201 Serine/threonine prote 40.1 31 0.00068 37.6 3.8 96 450-563 47-143 (467)
99 PF13936 HTH_38: Helix-turn-he 37.0 37 0.00081 24.5 2.7 31 492-522 13-43 (44)
100 PF04420 CHD5: CHD5-like prote 36.7 90 0.0019 29.4 6.0 45 107-153 41-85 (161)
101 TIGR02621 cas3_GSU0051 CRISPR- 35.5 32 0.00069 40.9 3.3 27 22-48 362-388 (844)
102 TIGR00603 rad25 DNA repair hel 35.3 48 0.001 38.8 4.7 30 23-52 573-607 (732)
103 KOG0352 ATP-dependent DNA heli 35.0 24 0.00052 38.3 2.0 45 23-70 335-379 (641)
104 TIGR02337 HpaR homoprotocatech 34.2 1.1E+02 0.0023 26.7 5.8 53 464-525 16-68 (118)
105 KOG0342 ATP-dependent RNA heli 33.4 89 0.0019 34.7 6.0 37 23-63 410-446 (543)
106 TIGR03714 secA2 accessory Sec 33.3 38 0.00082 39.8 3.4 26 25-52 512-537 (762)
107 COG1203 CRISPR-associated heli 33.2 30 0.00064 40.7 2.6 30 23-52 521-550 (733)
108 cd00238 ERp29c ERp29 and ERp38 32.1 3.1E+02 0.0068 23.3 8.1 34 351-384 59-93 (93)
109 PRK03573 transcriptional regul 30.6 1.2E+02 0.0025 27.5 5.6 37 489-525 36-72 (144)
110 KOG0333 U5 snRNP-like RNA heli 30.5 54 0.0012 36.7 3.8 51 23-76 597-653 (673)
111 PRK11512 DNA-binding transcrip 30.3 97 0.0021 28.1 5.1 62 371-435 68-139 (144)
112 smart00351 PAX Paired Box doma 29.2 70 0.0015 28.6 3.8 35 491-525 25-59 (125)
113 PF02796 HTH_7: Helix-turn-hel 29.1 59 0.0013 23.5 2.7 33 488-520 10-42 (45)
114 PF13613 HTH_Tnp_4: Helix-turn 28.3 1.1E+02 0.0024 22.8 4.2 43 488-530 8-50 (53)
115 COG0514 RecQ Superfamily II DN 26.8 77 0.0017 36.2 4.3 40 21-63 308-347 (590)
116 KOG0351 ATP-dependent DNA heli 26.6 55 0.0012 39.5 3.3 38 25-65 567-604 (941)
117 KOG0346 RNA helicase [RNA proc 26.3 1.7E+02 0.0036 32.3 6.5 29 22-52 382-410 (569)
118 COG3845 ABC-type uncharacteriz 26.1 1.2E+02 0.0025 33.8 5.4 126 384-535 51-188 (501)
119 cd00090 HTH_ARSR Arsenical Res 26.0 88 0.0019 23.8 3.5 30 496-525 17-46 (78)
120 cd06571 Bac_DnaA_C C-terminal 25.9 1.9E+02 0.0041 24.1 5.7 45 498-551 43-88 (90)
121 KOG0329 ATP-dependent RNA heli 25.6 43 0.00094 34.0 1.9 28 23-52 328-355 (387)
122 COG5570 Uncharacterized small 23.9 2.6E+02 0.0057 21.3 5.2 20 342-361 36-55 (57)
123 PF07749 ERp29: Endoplasmic re 23.8 1.1E+02 0.0024 26.0 3.9 34 351-384 61-94 (95)
124 PRK11448 hsdR type I restricti 23.6 84 0.0018 38.9 4.2 18 22-39 785-802 (1123)
125 KOG4196 bZIP transcription fac 23.6 4.2E+02 0.0092 24.1 7.5 77 307-386 43-119 (135)
126 PF04420 CHD5: CHD5-like prote 23.4 5.7E+02 0.012 23.9 9.0 51 312-364 41-91 (161)
127 PRK13777 transcriptional regul 23.4 2E+02 0.0042 27.8 5.9 29 497-525 57-85 (185)
128 PF04325 DUF465: Protein of un 23.3 3.1E+02 0.0067 20.2 5.8 43 315-360 3-48 (49)
129 PF13730 HTH_36: Helix-turn-he 23.0 70 0.0015 23.7 2.2 25 501-525 27-51 (55)
130 KOG1247 Methionyl-tRNA synthet 22.9 2.3E+02 0.005 30.9 6.7 68 1-75 307-385 (567)
131 PF12802 MarR_2: MarR family; 22.7 68 0.0015 24.2 2.2 30 496-525 16-47 (62)
132 PF04977 DivIC: Septum formati 22.7 2.4E+02 0.0051 22.4 5.5 42 347-393 32-74 (80)
133 PRK14873 primosome assembly pr 22.7 86 0.0019 36.4 3.9 24 24-49 513-536 (665)
134 PRK11415 hypothetical protein; 22.6 2.6E+02 0.0056 22.7 5.6 56 305-360 11-67 (74)
135 PF00196 GerE: Bacterial regul 22.5 1E+02 0.0022 23.3 3.1 44 484-527 3-46 (58)
136 TIGR01967 DEAH_box_HrpA ATP-de 22.4 1.2E+02 0.0027 37.8 5.3 62 373-438 450-515 (1283)
137 KOG0920 ATP-dependent RNA heli 22.3 80 0.0017 37.9 3.6 30 19-51 514-543 (924)
138 PRK11512 DNA-binding transcrip 22.0 1.5E+02 0.0034 26.7 4.8 37 488-525 44-80 (144)
139 PF12917 HD_2: HD containing h 21.5 5.4E+02 0.012 25.5 8.5 114 417-555 49-171 (215)
140 TIGR02984 Sig-70_plancto1 RNA 21.4 1.3E+02 0.0027 28.2 4.2 46 485-530 141-187 (189)
141 KOG0923 mRNA splicing factor A 21.0 8.4E+02 0.018 28.6 10.8 135 372-538 652-791 (902)
142 PF08281 Sigma70_r4_2: Sigma-7 20.4 1.5E+02 0.0033 21.8 3.6 30 496-525 23-52 (54)
143 PRK13104 secA preprotein trans 20.3 87 0.0019 37.5 3.3 22 27-50 564-585 (896)
144 KOG0328 Predicted ATP-dependen 20.3 1E+02 0.0022 32.0 3.3 28 23-52 346-373 (400)
145 smart00418 HTH_ARSR helix_turn 20.3 1.5E+02 0.0032 21.7 3.7 29 497-525 8-36 (66)
146 PRK00888 ftsB cell division pr 20.2 3.1E+02 0.0068 23.8 6.0 39 350-392 45-83 (105)
No 1
>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=8.4e-143 Score=1142.90 Aligned_cols=552 Identities=56% Similarity=0.865 Sum_probs=526.4
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCChHHH
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYNML 80 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~~~i 80 (565)
||||||||++.+||||+.|||+++|||+||+|||||||+|+.|.||+|.+..++++.++.|+.|.++||+|+||+||||+
T Consensus 488 MPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~~ak~m~kG~aD~LnSaFhLtYnMi 567 (1041)
T KOG0948|consen 488 MPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQVAKDMLKGSADPLNSAFHLTYNMI 567 (1041)
T ss_pred CcceeEEEeeccccCCcceeeecccceEEecccccccCCCCCceEEEEecCcCCHHHHHHHhcCCCcchhhhhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCHHHHHHhhHHHHhhcCCchHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhcCcccc
Q 008449 81 LNQIRCEEGSPENLLRNSFYQFQADHAIPDLEKQAKVLEEERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVFSPKYC 160 (565)
Q Consensus 81 L~l~~~~~~~~~~~l~~sf~~~~~~~~~~~~~~~~~~l~~~l~~i~~~~e~~i~~Y~~l~~~l~~~~~~~~~~~~~~~~~ 160 (565)
|||+|++++++++|+++||+|||+.+.+|.+++++.+++++++.+.+++|..+.+|++++.++.++++++++.+.+|++|
T Consensus 568 LNLlRvEei~pe~~l~~SF~QFQ~~~~~P~i~~kl~~~~~~~~~i~i~~E~~v~~yh~l~~ql~~~~k~i~~~~~~P~~~ 647 (1041)
T KOG0948|consen 568 LNLLRVEEISPEYMLERSFHQFQNYKALPDIEEKLKQLEEELDSINIPNEEEVKEYHDLELQLEKYGKDIREVITHPKYC 647 (1041)
T ss_pred HHHHHHccCCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHHHHHHHHHHcCcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcEEEEecCCCCCCCCCCCCCCccceEEEEEeeeeccCcCCCCCCCCCCCCCceEEEEeeccccCC-CCCCCcc
Q 008449 161 LPFLQPGRFVCIECTRGDDNSPSFSTEDHQVTWGVVIEFEKVKGVYEDDANKKPEDSNYTVNILTRCVVSKD-GAGKKTL 239 (565)
Q Consensus 161 ~~~L~~GRlV~i~~~~~~~~~~~~~~~~~~~~~gvvv~~~~~~~~~~~~~~~~~~~~~~~v~vl~~~~~~~~-~~~~~~~ 239 (565)
++||+|||+|.|..+ +.+|+|||++++.+.++..+++. ...+.+.|+|+++++|..... .......
T Consensus 648 l~fLq~GRlV~v~~g------------~~d~~WGvvv~f~k~~~~~~~~~-~~~p~e~Y~vdvll~~~~~~~~~~~~~~~ 714 (1041)
T KOG0948|consen 648 LPFLQPGRLVKVKVG------------GDDFFWGVVVNFIKRKNSSKNSD-QVGPHESYIVDVLLHCSTESSPVGAKKVN 714 (1041)
T ss_pred cccccCCceEEEecC------------CCCCceeEEEEEEeccCCCCCcc-ccCCCcceEEEEEeeeeccccccccCcCC
Confidence 999999999999998 67899999999988765443321 122334899999999962211 1112223
Q ss_pred cccCCCCCCCeEEEeecccceecccceeeeCCCCCCCHHHHHHHHHHHHHHHHhcCCCCC-CCcccccCCCChHHHHHHH
Q 008449 240 KIVPLKESGEPLVVSVPISQIIKLSSARLPMPKDLLPLQTRENMLKSTSEFLARNASGLP-LDPEANMGIRSSSYQKLVR 318 (565)
Q Consensus 240 ~p~~~~~~~~~~~~~v~~~~i~~is~~~~~~~~~~~~~~~r~~~~~~l~e~~~~~~~~~p-l~~~~~~~i~~~~~~~~~~ 318 (565)
.|+.+++.+.|.++|+.++.|..||++|+++|+++++.++|..+.+.++++.++||+|+| +||++||+|.+.++.++.+
T Consensus 715 ~p~~~~ek~~~~vvpv~l~~i~~is~~r~~iP~dl~~~d~r~~~~k~v~e~~~rfp~gip~LdPv~dM~I~~~~~~~~~~ 794 (1041)
T KOG0948|consen 715 VPPRPNEKGEMEVVPVLLTLIDAISSIRLYIPKDLRSVDARLSVLKAVQEVKSRFPDGIPLLDPVKDMNIKDVEFKKLVK 794 (1041)
T ss_pred CCCCCCCCCceEEEeeeHHHHhhhhHHHhcCcccccCcchHHHHHHHHHHHHHhcCCCCCCcChhhccCccchHHHHHHH
Confidence 455577899999999999999999999999999999999999999999999999999999 9999999999999999999
Q ss_pred HHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhchhcchhHHHHHHHHHHHhHhCCccCCCccchhhh
Q 008449 319 RIEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRSSTELAFKDELKARKRVLRRLGYATSDDVVELKGK 398 (565)
Q Consensus 319 ~~~~l~~~l~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~l~~~~e~~~~~~VL~~Lgyid~~~~vt~KGr 398 (565)
+++.|+.++.+||.|+.|+.++.|+.+.++..|..++++++.++++++...+++|+++|++|||||||++.+++|.+|||
T Consensus 795 k~e~lE~~l~~hp~~k~~~~~~~~~~f~~K~~l~~~ik~lk~~l~~~~~i~~ldELk~RkRVLrrLG~~t~ddvie~KGr 874 (1041)
T KOG0948|consen 795 KIESLEARLESHPLHKSSELEELYKEFQRKETLRAEIKDLKAELKSSQAILQLDELKNRKRVLRRLGYCTSDDVIELKGR 874 (1041)
T ss_pred HHHHHHHhhccCcccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhCCCCCCCeEEEcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceeeccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHcCCCccc
Q 008449 399 VACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQDASKPREELELLFTQLQDTARRVAKVQLECKVQIDV 478 (565)
Q Consensus 399 vAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~qek~~~~~~l~~~L~~~~~~l~~ia~~I~~v~~~~~l~~~~ 478 (565)
|||||+|+|||++|||||+|.|++|+|+|+||||||||||+|+++.+++.++|+.++.+|++.|++|++|+.+|++++++
T Consensus 875 vACEIsSgDELlLTEliFnG~Fndl~~eq~aaLLSCfVf~eks~e~~~l~~el~~~l~~lqe~ArrIAkVs~ecKlEide 954 (1041)
T KOG0948|consen 875 VACEISSGDELLLTELIFNGIFNDLPVEQAAALLSCFVFQEKSSEAPKLKEELAGPLRQLQESARRIAKVSKECKLEIDE 954 (1041)
T ss_pred EEEEecccchHHHHHHHHhccccCCCHHHHHHHHhheeehhcccccccchHHHHHHHHHHHHHHHHHHHHHHhhccccCH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCCcc
Q 008449 479 EGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKIKRDIV 558 (565)
Q Consensus 479 ~~~~~~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn~~L~~k~e~a~~~IkRDIV 558 (565)
++|+++|+|+||+|||+||+|++|++||++||+||||||||+|||+||||||++||++|||++|++||++|+.+||||||
T Consensus 955 ~~Yv~sFkp~LMdvVy~W~~GatF~eIckmTdvfEGSiIR~~RRLeElLrQl~~AAk~iGnteLe~Kf~~~~~~ikRDIV 1034 (1041)
T KOG0948|consen 955 EDYVESFKPELMDVVYAWAKGATFAEICKMTDVFEGSIIRTFRRLEELLRQLIDAAKVIGNTELENKFEEAIKKIKRDIV 1034 (1041)
T ss_pred HHHHHhcChHHHHHHHHHHccccHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHhhcee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCC
Q 008449 559 FAASLYL 565 (565)
Q Consensus 559 fa~SLYl 565 (565)
||+||||
T Consensus 1035 FAaSLYL 1041 (1041)
T KOG0948|consen 1035 FAASLYL 1041 (1041)
T ss_pred ehhhccC
Confidence 9999997
No 2
>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]
Probab=100.00 E-value=1.1e-107 Score=891.00 Aligned_cols=539 Identities=32% Similarity=0.487 Sum_probs=455.6
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCC-CCHHHHHHHhcCCCCcccccCCCChHH
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK-MEPSTAKMMLKGSADSLNSAFHLSYNM 79 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~-~~~~~~~~~~~~~~~~l~S~f~~~~~~ 79 (565)
||||||||.|++||||+++|+|.|+||+||||||||||+|.+|+|||+|... ++...+++++.|.+.+|+|||++||+|
T Consensus 672 MPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~vp~~a~l~~li~G~~~~L~SQFRlTY~M 751 (1248)
T KOG0947|consen 672 MPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDSVPSAATLKRLIMGGPTRLESQFRLTYGM 751 (1248)
T ss_pred CCceeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCCCCCHHHHhhHhcCCCchhhhhhhhHHHH
Confidence 8999999999999999999999999999999999999999999999999887 789999999999999999999999999
Q ss_pred HHHHHhcCCCCHHHHHHhhHHHHhhcCCchHHHHHHHHHHHHhhcccccc----hhhHHHHHHHHHHHHHHHHHHHHHhc
Q 008449 80 LLNQIRCEEGSPENLLRNSFYQFQADHAIPDLEKQAKVLEEERDSMVIEE----EDSLKNYYNLLQQYKSLKKDVRDIVF 155 (565)
Q Consensus 80 iL~l~~~~~~~~~~~l~~sf~~~~~~~~~~~~~~~~~~l~~~l~~i~~~~----e~~i~~Y~~l~~~l~~~~~~~~~~~~ 155 (565)
||||+|++.+.+++||++||++|..++..|..++++.++++++..+.... +.++.+|+....++..+++.++...+
T Consensus 752 ILnLLRve~lrvEdm~krSf~E~~s~~~~~~~eq~l~~~~eel~sie~s~c~~~~~~l~kyl~a~~e~~e~~~~l~~~~~ 831 (1248)
T KOG0947|consen 752 ILNLLRVEALRVEDMMKRSFSEFVSQRLSPEHEQELKELDEELLSIEESDCAIDLKDLRKYLSAYEEITEYNEKLREEKM 831 (1248)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhcCHHHHHHHHHHHHHHhhhcccccccchHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999998887654 47899999999999999999999999
Q ss_pred CcccccCCCCCCcEEEEecCCCCCCCCCCCCCCccceEEEEEeeeeccCcCCCCCCCCCCCCCceEEEEeeccccCCCCC
Q 008449 156 SPKYCLPFLQPGRFVCIECTRGDDNSPSFSTEDHQVTWGVVIEFEKVKGVYEDDANKKPEDSNYTVNILTRCVVSKDGAG 235 (565)
Q Consensus 156 ~~~~~~~~L~~GRlV~i~~~~~~~~~~~~~~~~~~~~~gvvv~~~~~~~~~~~~~~~~~~~~~~~v~vl~~~~~~~~~~~ 235 (565)
+..+.+.+|+.||+|.+++. +.....|+|+.....++ ...+.++..|..+.++.+
T Consensus 832 ~s~~~~~~l~~GR~vv~k~~------------~~~~~lg~vl~~s~~t~-------------~~~~~~~~~~~~p~~~~~ 886 (1248)
T KOG0947|consen 832 KSANILRILKEGRVVVLKNL------------KEENNLGVVLKVSLNTN-------------GRVCVVLVAYLKPLDNKN 886 (1248)
T ss_pred hchhhhhhhhcCcEEEEcCh------------hhhcccceEEEEecCCC-------------cceEEEEEeeccCCcCcC
Confidence 99999999999999999984 34455777765544321 012222222221111100
Q ss_pred C-------Ccccc----------------cCCCCCCCeEEEeec-----ccceecccceeeeCCCCCCCHHHHHHHHHHH
Q 008449 236 K-------KTLKI----------------VPLKESGEPLVVSVP-----ISQIIKLSSARLPMPKDLLPLQTRENMLKST 287 (565)
Q Consensus 236 ~-------~~~~p----------------~~~~~~~~~~~~~v~-----~~~i~~is~~~~~~~~~~~~~~~r~~~~~~l 287 (565)
. ..+.| .+.+....+....++ ++.|+-++...+..+...........+....
T Consensus 887 ~~~~~s~a~~~~p~~l~af~~~~~~~~~~~~~~~~~~~~~~~v~~~~~g~~~ie~l~~~~~~~~~~~~~D~~~aal~~~~ 966 (1248)
T KOG0947|consen 887 GSLDPSFALNLIPDSLLAFEKFFPNVPRNVPLGSLNPLYLSGVTAYVKGVPNIEILCGDALRQIIGKVADGQKAALNEST 966 (1248)
T ss_pred CCcCcccccccCcchhhccccccCCcccccceecccccchhccchhhcCCcchhhhhccccccccccccccHHHHHHHHH
Confidence 0 00001 112222333333333 2233333322222222211111111222222
Q ss_pred HHH---HHhcCCCCC-CCcccccCCCChHHHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 008449 288 SEF---LARNASGLP-LDPEANMGIRSSSYQKLVRRIEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMR 363 (565)
Q Consensus 288 ~e~---~~~~~~~~p-l~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~ 363 (565)
.++ +..-+.++| .+|+++.+.++.++.+...+...+++.+...||+.||+|++||...++..+++.++++|..+++
T Consensus 967 ~~~l~l~~~~~~~~~~~epv~~~k~kd~e~~~~~l~~~n~~~~~~~~~~i~c~~f~~h~s~~~~~~~~~~ei~~L~~~~s 1046 (1248)
T KOG0947|consen 967 AQVLDLLEGSLETPTWKEPVNDSKLKDDEVVEMLLERTNLQNLIQGNPCISCPKFDQHYSLARREYKIEKEIENLEFELS 1046 (1248)
T ss_pred HHhhhhhhcCccCcchhhhhhhhhhccHHHHHHHHHHHHHHHHHhcCCccCCccHHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence 222 222234577 8999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhcchhHHHHHHHHHHHhHhCCccCCCccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceeeccCCC
Q 008449 364 SSTELAFKDELKARKRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQD 443 (565)
Q Consensus 364 ~~~~l~~~~e~~~~~~VL~~Lgyid~~~~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~qek~~~ 443 (565)
+ +++.+.|+|.+|++||+.+||||+..+|++||||||||+|++|||+|||||+|.|.+|+|+|||||||+||||+++..
T Consensus 1047 d-~~L~l~pey~~RlevLk~~g~vD~~~~V~lkGRvAceI~s~~ELllteli~dn~l~~l~peeiaallSslV~e~~~e~ 1125 (1248)
T KOG0947|consen 1047 D-QSLLLSPEYHNRLEVLKPLGFVDEMRTVLLKGRVACEINSGNELLLTELIFDNALVDLSPEEIAALLSSLVCEGKTER 1125 (1248)
T ss_pred h-hhhhhCHHHHHHHHHHhhcCcccccceeeecceeeeeecCCcchhHHHHHHhhhhhhcCHHHHHHHHHHHHhcCcccc
Confidence 9 999999999999999999999999999999999999999999999999999999999999999999999999999977
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHcCCCcccc-cccccCCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHH
Q 008449 444 ASKPREELELLFTQLQDTARRVAKVQLECKVQIDVE-GFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRR 522 (565)
Q Consensus 444 ~~~l~~~L~~~~~~l~~ia~~I~~v~~~~~l~~~~~-~~~~~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irR 522 (565)
.|.+++.+.++-+++.++++++.+++..|++.++++ +|...++||||+|||+||+|+||.+||++|++.||+|||||+|
T Consensus 1126 ~~~~~~~l~k~~e~v~~v~~rl~ev~~~~~~~~~~~e~f~~~lrF~l~evVYeWA~G~sf~eim~~t~~~EG~iVR~I~R 1205 (1248)
T KOG0947|consen 1126 PPTLTPYLKKGKERVRDVAKRLEEVQSSHQLLQTPEEEFPCELRFGLVEVVYEWARGLSFKEIMELTDVLEGLIVRLIQR 1205 (1248)
T ss_pred CCCCChhhhhHHHHHHHHHHHHHHHHHhhccccCchhhccccccccHHHHHHHHHcCCCHHHHHhhhCCcchhHHHHHHH
Confidence 789999999999999999999999999999988775 6778899999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCCcccccCCCC
Q 008449 523 LEEVLQQLILAAKSIGETELEAKFEEAVSKIKRDIVFAASLYL 565 (565)
Q Consensus 523 LdEllrqv~~Aa~~iGn~~L~~k~e~a~~~IkRDIVfa~SLYl 565 (565)
|||+|||+++||++||||.|..||++|+++|||||||++|||+
T Consensus 1206 LdE~cre~~~aa~ivGd~~L~~Km~~as~~ikRdIVFaaSLY~ 1248 (1248)
T KOG0947|consen 1206 LDEVCRELRNAARIVGDPVLHEKMEAASALIKRDIVFAASLYL 1248 (1248)
T ss_pred HHHHHHhhhccceecCcHHHHHHHHHHHHHhccCccchhhccC
Confidence 9999999999999999999999999999999999999999997
No 3
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.1e-81 Score=707.77 Aligned_cols=538 Identities=34% Similarity=0.499 Sum_probs=458.7
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCC-CHHHHHHHhcCCCCcccccCCCChHH
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKM-EPSTAKMMLKGSADSLNSAFHLSYNM 79 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~-~~~~~~~~~~~~~~~l~S~f~~~~~~ 79 (565)
||||||||++++||||+++|+|+++||+||+|||||||+|..|+||++..+.. +++.+..+..|.++||.|+|+++|||
T Consensus 486 mPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~~~~~~e~~~l~~~~~~~L~s~f~~sy~m 565 (1041)
T COG4581 486 MPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPFESEPSEAAGLASGKLDPLRSQFRLSYNM 565 (1041)
T ss_pred CcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCCCCCChHHHHHhhcCCCccchhheecchhH
Confidence 89999999999999999999999999999999999999999999999976654 49999999999999999999999999
Q ss_pred HHHHHhcCCCC-HHHHHHhhHHHHhhcCCchHHHHHHHHHHHHhhccccc----chhhHHHHHHHHHHHHHHHHHHHHHh
Q 008449 80 LLNQIRCEEGS-PENLLRNSFYQFQADHAIPDLEKQAKVLEEERDSMVIE----EEDSLKNYYNLLQQYKSLKKDVRDIV 154 (565)
Q Consensus 80 iL~l~~~~~~~-~~~~l~~sf~~~~~~~~~~~~~~~~~~l~~~l~~i~~~----~e~~i~~Y~~l~~~l~~~~~~~~~~~ 154 (565)
+||++++++++ ++.++++||++||+.+.++...+++..+++++..+... ++.++..| ...+.++++++....
T Consensus 566 ilnll~v~~l~~~e~ll~~Sf~q~~~~~~l~~~~~~l~~~~~~~~~i~~~~~~~d~~~~~~~---~~~~~k~~~~l~~~~ 642 (1041)
T COG4581 566 ILNLLRVEGLQTAEDLLERSFAQFQNSRSLPEIVEKLERLEKELNDIATELFGTDENDAPKL---SLDYEKLRKKLNEEM 642 (1041)
T ss_pred HHhhhhhcccCcHHHHHHhhHHHHhhhhhhHHHHHHHHHHHHHHHhhhhhhccccccchHHH---HHHHHHHHHHHHHHH
Confidence 99999999998 99999999999999999999999999999999998766 46666776 566777788888888
Q ss_pred cCcccccCCCCCCcEEEEecCCCCCCCCCCCCCCccceEEEEEeeeeccCcCCCCCCCCCCCCCceEEEEeeccccCCC-
Q 008449 155 FSPKYCLPFLQPGRFVCIECTRGDDNSPSFSTEDHQVTWGVVIEFEKVKGVYEDDANKKPEDSNYTVNILTRCVVSKDG- 233 (565)
Q Consensus 155 ~~~~~~~~~L~~GRlV~i~~~~~~~~~~~~~~~~~~~~~gvvv~~~~~~~~~~~~~~~~~~~~~~~v~vl~~~~~~~~~- 233 (565)
.++..++.+++.||++.+..+ .....||.++...+... . .+.....+...++.... +.+.
T Consensus 643 ~~~a~~~r~~~~gr~~~~~~~------------~~~~~~g~~~~~~~r~~---~---~~t~~~~~~~~~~~~~~-~~~~~ 703 (1041)
T COG4581 643 RLQAAGLRALRKGRVVQIKDG------------LAALFWGRLLKLTKRYT---T---KLTDHELYLAVLVEPNA-DFSFP 703 (1041)
T ss_pred HHHHhHHHHhhhcceeeeecc------------hhhhhheeeeeeccccc---c---ccccchheehheecccC-Cccch
Confidence 888889999999999999987 23357888887655421 0 00000112222211110 0000
Q ss_pred -C----CCCcccccCCCCCCCeEEEeecccceecccceeeeCCCCCCCHHHHHHHHHHHHHHHHhcCCC-CC-CCccccc
Q 008449 234 -A----GKKTLKIVPLKESGEPLVVSVPISQIIKLSSARLPMPKDLLPLQTRENMLKSTSEFLARNASG-LP-LDPEANM 306 (565)
Q Consensus 234 -~----~~~~~~p~~~~~~~~~~~~~v~~~~i~~is~~~~~~~~~~~~~~~r~~~~~~l~e~~~~~~~~-~p-l~~~~~~ 306 (565)
. .+...++........+++..+++..+..+....+.+|..+.....+..-...+......+.++ .+ +.++..+
T Consensus 704 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~v~~~ 783 (1041)
T COG4581 704 RPLVKAMPHMNRESRWLVKILFRISFVYLLNATEILELILTMPRRLLSRQGKLRRGEPSNEAIAAGLDGNEKILENVVEM 783 (1041)
T ss_pred hHHhhcccccccccccccccceeeeeeeeccccccchhhhcCCHhHhhcccchhccchhHHHHHhccccchhhhhhcccc
Confidence 0 000111112233446678888888888888888888866432222222334455555666666 44 8999999
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhchhcchhHHHHHHHHHHHhHhCC
Q 008449 307 GIRSSSYQKLVRRIEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRSSTELAFKDELKARKRVLRRLGY 386 (565)
Q Consensus 307 ~i~~~~~~~~~~~~~~l~~~l~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~l~~~~e~~~~~~VL~~Lgy 386 (565)
++.++++.............+..+|.+.|+.+++|++.......|..+++++...+ +.+.+.++|..+.+||+.+||
T Consensus 784 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~i~~l~~~~---~~~~~l~~~~~l~~~l~~~g~ 860 (1041)
T COG4581 784 KIQVPELTVSLLKLRFGRYHLSENPLMNFDGAERLIENELLLSDLQAEIEDLSSSI---EALSFLDDYKTLQEVLKKLGF 860 (1041)
T ss_pred cccchhHHHHHHHHhhcccccCCCccccchHHHHHHHhHhHHHHHHHHHHHHHHHH---HHhhhhHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999999999999999999998 556788999999999999999
Q ss_pred ccCCCccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceeeccCC----CCCCCcHHHHHHHHHHHHHH
Q 008449 387 ATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQ----DASKPREELELLFTQLQDTA 462 (565)
Q Consensus 387 id~~~~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~qek~~----~~~~l~~~L~~~~~~l~~ia 462 (565)
++.+..|+.|||+||||+|++||++|||||+|.|++|+|+|+||++|||||+++++ +.+.++|.|..++..+.+++
T Consensus 861 ~~~~~~v~~kGr~a~eI~s~~ellL~e~i~~g~f~~l~p~e~aallSa~v~e~~~~d~~~~~~~~~~~l~~~~~~l~e~~ 940 (1041)
T COG4581 861 IEDNAVVLIKGRVAAEISSEDELLLTELIFSGEFNDLEPEELAALLSAFVFEEKTDDGTAEAPEITPALRDALLRLLELA 940 (1041)
T ss_pred CCcccccccccceeeeecCCCchHHHHHHHcCCccCCCHHHHHHHHHheeeccCCcccccccccCCHHHHhHHHHHHHHH
Confidence 99989999999999999999999999999999999999999999999999999987 45778999999999999999
Q ss_pred HHHHHHHHHcCCCcccccccccCCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHhhcCCHHH
Q 008449 463 RRVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGETEL 542 (565)
Q Consensus 463 ~~I~~v~~~~~l~~~~~~~~~~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn~~L 542 (565)
.+|.+++++|++++..+ ++.|.++||+|||+||+|++|.+||.+|++.|||+||+++|++|+|+|+.+||.+|||++|
T Consensus 941 ~kl~~~~~~~~i~~~~~--l~~~~~~lm~vv~~wa~g~s~~~i~~~~~~~eGs~vR~~~r~~ell~ql~~aa~~ig~~~L 1018 (1041)
T COG4581 941 RKLNKDQNSSQIEIYPE--LNDFSVGLMEVVYEWARGLSFADICGLTSLLEGSFVRIFRRLRELLRQLRKAASVIGNPEL 1018 (1041)
T ss_pred HHHHHHHHhcCCcCCcc--cccccccHHHHHHHHHhhcchhhhhcCCcccccchhhhhhHHHHHHHHhhhcccccCCHHH
Confidence 99999999999999865 7889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCcccccCCCC
Q 008449 543 EAKFEEAVSKIKRDIVFAASLYL 565 (565)
Q Consensus 543 ~~k~e~a~~~IkRDIVfa~SLYl 565 (565)
.+||..|+..|||||||++|||+
T Consensus 1019 ~~k~~~~~~~irr~iv~~~sly~ 1041 (1041)
T COG4581 1019 EEKAYRAIQEIRRDIVFVDSLYL 1041 (1041)
T ss_pred HHHHHHHHHhhhcCeEecccccC
Confidence 99999999999999999999996
No 4
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=100.00 E-value=1.1e-54 Score=415.73 Aligned_cols=177 Identities=51% Similarity=0.834 Sum_probs=147.8
Q ss_pred ccCCCccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceeeccCCCCC---CCcHHHHHHHHHHHHHHH
Q 008449 387 ATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQDAS---KPREELELLFTQLQDTAR 463 (565)
Q Consensus 387 id~~~~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~qek~~~~~---~l~~~L~~~~~~l~~ia~ 463 (565)
||++++||+|||+||+|+++|||++|||||+|+|++|+|+|+||+|||||||+++++.. .+++.+..+++++.++++
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 78999999999999999999999999999999999999999999999999998887651 223489999999999999
Q ss_pred HHHHHHHHcCCCcccccccccCCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHhhcCCHHHH
Q 008449 464 RVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGETELE 543 (565)
Q Consensus 464 ~I~~v~~~~~l~~~~~~~~~~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn~~L~ 543 (565)
+|.+++.+||+ +.++|+++++|+||++||+||+|+||++||++|+++|||||||+||++|+||||++||+++|||+|.
T Consensus 81 ~l~~~~~~~~l--~~~~~~~~~~~~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~aa~~~g~~~L~ 158 (180)
T PF08148_consen 81 RLAKVEREHGL--DEEEYVERFDPGLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANAAKIIGDPELA 158 (180)
T ss_dssp HHHHHHHHTT---HHHHHHHCSTTTTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHHHHCCT-HHHH
T ss_pred HHHHHHHHhCC--CCcccccCCCccHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHHHHhcCCHHHH
Confidence 99999999999 6678998999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCcccccCCCC
Q 008449 544 AKFEEAVSKIKRDIVFAASLYL 565 (565)
Q Consensus 544 ~k~e~a~~~IkRDIVfa~SLYl 565 (565)
+|+++|+++|||||||++||||
T Consensus 159 ~~~~~a~~~i~R~iV~~~SLYl 180 (180)
T PF08148_consen 159 EKAREAIDLIRRDIVFASSLYL 180 (180)
T ss_dssp HHHHHHHHHHSHCCCC---TT-
T ss_pred HHHHHHHHhccCCccccccccC
Confidence 9999999999999999999997
No 5
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=100.00 E-value=5.9e-44 Score=363.10 Aligned_cols=261 Identities=41% Similarity=0.699 Sum_probs=216.4
Q ss_pred HHHHHhhHHHHhhcCCchHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhcCcccccCCCCCCcEEE
Q 008449 92 ENLLRNSFYQFQADHAIPDLEKQAKVLEEERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVFSPKYCLPFLQPGRFVC 171 (565)
Q Consensus 92 ~~~l~~sf~~~~~~~~~~~~~~~~~~l~~~l~~i~~~~e~~i~~Y~~l~~~l~~~~~~~~~~~~~~~~~~~~L~~GRlV~ 171 (565)
|+||++||+|||+++.+|++++++++++++++.+...+++++.+||+++.++..+++++++++.+|+++++||+|||||+
T Consensus 1 E~mikrSF~qfq~~~~lP~~~~~~~~~e~~~~~i~~~~~~~v~~y~~l~~~l~~~~~~~~~~i~~p~~~~~fL~~GRlV~ 80 (268)
T PF13234_consen 1 EYMIKRSFSQFQNQRKLPELEKKLKELEEELDAIKIEDEEDVEEYYDLRQELEELRKELRKIITSPKYCLPFLQPGRLVV 80 (268)
T ss_dssp HHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHCS--TTCTCCHHHHHHHHHHHHHHHHHHHHHCTCCCHHHHS-TTEEEE
T ss_pred ChhHHHhHHHHcccccCHHHHHHHHHHHHHHHhcccccHhHHHHHHHHHHHHHHHHHHHHHHHhCcHHHHHhCCCCCEEE
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCCCCCCCCCCCccceEEEEEeeeeccCcCCCCCCCCCCCCCceEEEEeeccccCCCC-----CCCcccccCCCC
Q 008449 172 IECTRGDDNSPSFSTEDHQVTWGVVIEFEKVKGVYEDDANKKPEDSNYTVNILTRCVVSKDGA-----GKKTLKIVPLKE 246 (565)
Q Consensus 172 i~~~~~~~~~~~~~~~~~~~~~gvvv~~~~~~~~~~~~~~~~~~~~~~~v~vl~~~~~~~~~~-----~~~~~~p~~~~~ 246 (565)
|+++ +.+||||||+++.+.++...+.+........|+|+||++|....... .+..+.|...++
T Consensus 81 v~~~------------~~~~~wgvvv~~~~~~~~~~~~~~~~~~~~~~vVdvL~~~~~~~~~~~~~~~~~~~~~p~~~~~ 148 (268)
T PF13234_consen 81 VRDG------------DRDFGWGVVVNFAKKSNPKGNLGSSSSKEKSYVVDVLLPCSPDSKSAKNSSDLPEPVKPCSPGE 148 (268)
T ss_dssp EEET------------TCEEEEEEEEEEEE---SS--TT-SSSTCCCEEEEEECCCEETTS-CCGTTTGGCTS-BS-TT-
T ss_pred EecC------------CCccceeEEEeccccccccccccccCCCCCcEEEEEEeeccccccccccccCCCCCCCCCCCCC
Confidence 9988 68999999999988753221100112334579999999995221111 134566766678
Q ss_pred CCCeEEEeecccceecccceeeeCCCCCCCHHHHHHHHHHHHHHHHhcCCCCC-CCcccccCCCChHHHHHHHHHHHHHH
Q 008449 247 SGEPLVVSVPISQIIKLSSARLPMPKDLLPLQTRENMLKSTSEFLARNASGLP-LDPEANMGIRSSSYQKLVRRIEALES 325 (565)
Q Consensus 247 ~~~~~~~~v~~~~i~~is~~~~~~~~~~~~~~~r~~~~~~l~e~~~~~~~~~p-l~~~~~~~i~~~~~~~~~~~~~~l~~ 325 (565)
.+++.+++|++++|..||++|+++|.++++.++|+.+.++++++.++||+|+| |||++||+|++.+|.++..+++.|++
T Consensus 149 ~~~~~vv~v~l~~I~~ISs~rl~lp~dl~~~~~r~~~~~~l~el~~r~~~giP~LDPi~DmkI~d~~~~e~~~k~~~Le~ 228 (268)
T PF13234_consen 149 KGEMEVVPVPLSCISSISSVRLKLPKDLRPQEARKQVLKSLQELLKRFPDGIPLLDPIKDMKIKDPEFVELVKKIEALEK 228 (268)
T ss_dssp -EEEEEEEEECCGEEEEEEEE----TTTTSCCCHHHHHHHHHHHHHHSSS--TCHHCHHHH----HHHHHHHHHHHHHHH
T ss_pred CCeEEEEEeeHHHHHHhhceeeeCcccccchHHHHHHHHHHHHHHHhCCCCCCccChHHhCCCCcHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999 99999999999999999999999999
Q ss_pred HHhhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 008449 326 LFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRS 364 (565)
Q Consensus 326 ~l~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~ 364 (565)
+|.+||||+||++++||+.+++|.+|+++++.|+++|++
T Consensus 229 rl~~~~~~~~~~~~~~~~~~~~k~~l~~~i~~Lk~~l~~ 267 (268)
T PF13234_consen 229 RLSSHPLHKCPDFEEHYALYHEKAELQEEIKALKRQLSD 267 (268)
T ss_dssp HHHHSCHCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999986
No 6
>PRK02362 ski2-like helicase; Provisional
Probab=99.45 E-value=3.4e-13 Score=155.78 Aligned_cols=104 Identities=27% Similarity=0.428 Sum_probs=87.8
Q ss_pred CCccEEEEcCCeeecCC-cceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCH-HHHHHHhcCCCCcccccCCCCh-
Q 008449 1 MPAKTVVFTNVRKFDGD-KFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEP-STAKMMLKGSADSLNSAFHLSY- 77 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~-~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~-~~~~~~~~~~~~~l~S~f~~~~- 77 (565)
+||++|||.++.+|||. ++.+++..+|.||+|||||+|+|+.|.+|+++.+..+. +.+.+++.++++|++|+|...+
T Consensus 345 lPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~~~~l~~~~~~i~S~l~~~~~ 424 (737)
T PRK02362 345 LPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSYDELDELFERYIWADPEDVRSKLATEPA 424 (737)
T ss_pred CCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCchhHHHHHHHHHhCCCCceeecCCChhh
Confidence 69999999999999986 56789999999999999999999999999999775223 3456778899999999997654
Q ss_pred --HHHHHHHhcCCCC----HHHHHHhhHHHHhh
Q 008449 78 --NMLLNQIRCEEGS----PENLLRNSFYQFQA 104 (565)
Q Consensus 78 --~~iL~l~~~~~~~----~~~~l~~sf~~~~~ 104 (565)
..+++.++.+.+. +.+|+++||+.+|.
T Consensus 425 l~~~lla~I~~~~~~~~~d~~~~l~~Tf~~~~~ 457 (737)
T PRK02362 425 LRTHVLSTIASGFARTRDGLLEFLEATFYATQT 457 (737)
T ss_pred HHHHHHHHHHhCccCCHHHHHHHHHhChHHhhc
Confidence 4577778777553 68899999998875
No 7
>PRK01172 ski2-like helicase; Provisional
Probab=99.40 E-value=1.5e-12 Score=149.12 Aligned_cols=105 Identities=24% Similarity=0.339 Sum_probs=88.7
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCC---h
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLS---Y 77 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~---~ 77 (565)
+||++|||.++.+|++.+++++++.+|.||+|||||+|+|..|.+++++.+..+.+.+++++.++++|++|++... .
T Consensus 327 ipa~~VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~~~~~~~~~l~~~~~pi~S~l~~~~~~~ 406 (674)
T PRK01172 327 LPARLVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAKKYLSGEPEPVISYMGSQRKVR 406 (674)
T ss_pred CcceEEEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcccHHHHHHHHcCCCCceeecCCCcccHH
Confidence 6999999999999999888999999999999999999999999999998765445678888989999999999744 2
Q ss_pred HHHHHHHhcCCC----CHHHHHHhhHHHHhhc
Q 008449 78 NMLLNQIRCEEG----SPENLLRNSFYQFQAD 105 (565)
Q Consensus 78 ~~iL~l~~~~~~----~~~~~l~~sf~~~~~~ 105 (565)
..+|+.+..+.+ ++.+|+.+||+..++.
T Consensus 407 ~~~l~~i~~g~~~~~~d~~~~l~~tf~~~~~~ 438 (674)
T PRK01172 407 FNTLAAISMGLASSMEDLILFYNETLMAIQNG 438 (674)
T ss_pred HHHHHHHHhcccCCHHHHHHHHHhhhhHhcCc
Confidence 335666776654 3788999999988653
No 8
>PRK00254 ski2-like helicase; Provisional
Probab=99.37 E-value=3e-12 Score=147.58 Aligned_cols=104 Identities=26% Similarity=0.323 Sum_probs=89.6
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCC---h
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLS---Y 77 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~---~ 77 (565)
+||++|||.++.+|++.++.+++..+|.||+|||||+|+|..|.+|+++.+....+.+.+++.|.++++.|.+... +
T Consensus 337 ipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~~~~~~~~~~~~~pe~l~s~l~~es~l~ 416 (720)
T PRK00254 337 LPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMERYIFGKPEKLFSMLSNESAFR 416 (720)
T ss_pred CCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcchHHHHHHHHhCCchhhhccCCchHHHH
Confidence 6999999999999997788889999999999999999999999999999764224557788999999999998654 5
Q ss_pred HHHHHHHhcCCCC----HHHHHHhhHHHHhh
Q 008449 78 NMLLNQIRCEEGS----PENLLRNSFYQFQA 104 (565)
Q Consensus 78 ~~iL~l~~~~~~~----~~~~l~~sf~~~~~ 104 (565)
.++++.+..+.+. +.+|+.+||+.+|+
T Consensus 417 ~~ll~~i~~~~~~~~~~~~~~l~~Tf~~~~~ 447 (720)
T PRK00254 417 SQVLALITNFGVSNFKELVNFLERTFYAHQR 447 (720)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHhCHHHHhh
Confidence 6789999887653 57899999998765
No 9
>COG1204 Superfamily II helicase [General function prediction only]
Probab=99.25 E-value=5.6e-12 Score=144.43 Aligned_cols=106 Identities=25% Similarity=0.450 Sum_probs=84.7
Q ss_pred CCccEEEEcCCeeec-CCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCC-HHHHHHHhcCCCCcccccCCCCh-
Q 008449 1 MPAKTVVFTNVRKFD-GDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKME-PSTAKMMLKGSADSLNSAFHLSY- 77 (565)
Q Consensus 1 mPAr~Vv~~~~~k~d-g~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~-~~~~~~~~~~~~~~l~S~f~~~~- 77 (565)
+|||+|||+++.+|| ..+++++++.||+||+|||||||+|+.|.++|++....+ ......++.+.++|+.|++...-
T Consensus 356 LPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~~~~~~~~~~~~~~~~e~~~s~l~~~~~ 435 (766)
T COG1204 356 LPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHDELEYLAELYIQSEPEPIESKLGDELN 435 (766)
T ss_pred CcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecCccchhHHHHHhhccCcchHHHhhccccc
Confidence 699999999999999 345899999999999999999999999999999955423 34456778999999999886553
Q ss_pred --HHHHHHHhcCCC----CHHHHHHhhHHHHhhcC
Q 008449 78 --NMLLNQIRCEEG----SPENLLRNSFYQFQADH 106 (565)
Q Consensus 78 --~~iL~l~~~~~~----~~~~~l~~sf~~~~~~~ 106 (565)
..++.+++.+.+ ..++|+.++|+..|.+.
T Consensus 436 ~~~~l~~v~~~~~~v~~~~~~~f~~~t~~~~~~~~ 470 (766)
T COG1204 436 LRTFLLGVISVGDAVSWLELTDFYERTFYNPQTYG 470 (766)
T ss_pred chheEEEEEeccchhhHHHHHHHHHHHHhhhhhcc
Confidence 335555555443 26889999999888654
No 10
>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]
Probab=99.06 E-value=1.5e-10 Score=129.89 Aligned_cols=74 Identities=30% Similarity=0.442 Sum_probs=65.6
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCChHHH
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYNML 80 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~~~i 80 (565)
||||||||.+ +.-.|+|-.|.||||||||||+|+.|+|+.|.=+ .+.++++++.....|..++..|-..+
T Consensus 1004 MPCrTVvF~g-------DsLQL~plny~QmaGRAGRRGFD~lGnV~FmgiP---~~kv~rLlts~L~diqG~~p~T~~~~ 1073 (1330)
T KOG0949|consen 1004 MPCRTVVFAG-------DSLQLDPLNYKQMAGRAGRRGFDTLGNVVFMGIP---RQKVQRLLTSLLPDIQGAYPYTNTSF 1073 (1330)
T ss_pred CCceeEEEec-------cccccCchhHHhhhccccccccccccceEEEeCc---HHHHHHHHHHhhhcccCCCcchhhHH
Confidence 9999999986 2245899999999999999999999999999654 68899999999999999999998888
Q ss_pred HHHH
Q 008449 81 LNQI 84 (565)
Q Consensus 81 L~l~ 84 (565)
|.|-
T Consensus 1074 l~l~ 1077 (1330)
T KOG0949|consen 1074 LGLD 1077 (1330)
T ss_pred HHHH
Confidence 7774
No 11
>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]
Probab=98.91 E-value=1.1e-09 Score=124.12 Aligned_cols=117 Identities=21% Similarity=0.318 Sum_probs=89.8
Q ss_pred CCccEEEEcCCeeecCC--cceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCChH
Q 008449 1 MPAKTVVFTNVRKFDGD--KFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYN 78 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~--~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~~ 78 (565)
+||..|||.++.-||.+ ++.+++..+++||.||||||++|+.|.+||+++.. ..+.+..++.| ..|++|+|...--
T Consensus 438 LPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~d-kl~~Y~sLl~~-~~piES~~~~~L~ 515 (1230)
T KOG0952|consen 438 LPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRD-KLDHYESLLTG-QNPIESQLLPCLI 515 (1230)
T ss_pred CcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEeccc-HHHHHHHHHcC-CChhHHHHHHHHH
Confidence 69999999999999987 48899999999999999999999999999999876 36777888776 6999999976543
Q ss_pred HHHHH-HhcCCC---C-HHHHHHhhHHHHhhc-------------CCchHHHHHHHHHH
Q 008449 79 MLLNQ-IRCEEG---S-PENLLRNSFYQFQAD-------------HAIPDLEKQAKVLE 119 (565)
Q Consensus 79 ~iL~l-~~~~~~---~-~~~~l~~sf~~~~~~-------------~~~~~~~~~~~~l~ 119 (565)
--||. +..+.+ + +-+||+.||.+.... ...|.++++.+++-
T Consensus 516 dnLnAEi~LgTVt~VdeAVeWL~yTylYVRm~KNP~~Ygi~~~~l~~dp~l~s~~~~l~ 574 (1230)
T KOG0952|consen 516 DNLNAEISLGTVTNVDEAVEWLKYTYLYVRMRKNPMAYGISYEELEPDPRLESHRRELC 574 (1230)
T ss_pred HhhhhheeeceeecHHHHHHHhhceeEEEEeccChHHhhhhhhcccCCchHHHHHHHHH
Confidence 33333 333433 2 577999998654332 23366666666654
No 12
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=98.87 E-value=6.8e-10 Score=119.11 Aligned_cols=66 Identities=33% Similarity=0.585 Sum_probs=57.1
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCC------C---CHHHHHHHhcCCCCccc
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK------M---EPSTAKMMLKGSADSLN 70 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~------~---~~~~~~~~~~~~~~~l~ 70 (565)
+||..|||.|+. .+..||++.||.||+||||||++++.|.|++++.+. + +.+.+.+++.+.++|+.
T Consensus 506 FPASQVIFEsLa----MG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~~Y~~~m~~TEdevA~kLL~s~~e~V~ 580 (830)
T COG1202 506 FPASQVIFESLA----MGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKKYHASMEETEDEVAFKLLESEPEPVI 580 (830)
T ss_pred CchHHHHHHHHH----cccccCCHHHHHHHhcccCCCCcccCceEEEEecCChhhcccccccHHHHHHHHhcCCCCcce
Confidence 699999999985 677899999999999999999999999999999765 1 24556788888888876
No 13
>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]
Probab=98.74 E-value=8e-09 Score=116.80 Aligned_cols=100 Identities=26% Similarity=0.426 Sum_probs=81.1
Q ss_pred CCccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCCh---
Q 008449 1 MPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSY--- 77 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~--- 77 (565)
+|||+|||... +-|. ..++..+|+||+|||||.|+|+.|.+|+++.+. +.+.+..++.++..|+.|.+.-..
T Consensus 564 LPArRVIiraP--~~g~--~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~-e~~~~~~lv~~~~~~~~S~l~~e~~g~ 638 (1008)
T KOG0950|consen 564 LPARRVIIRAP--YVGR--EFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSS-EKKRVRELVNSPLKPLNSCLSNEVNGP 638 (1008)
T ss_pred CCcceeEEeCC--cccc--chhhhhhHHhhhhhhhhcccccCcceEEEeecc-chhHHHHHHhccccccccccccccccc
Confidence 69999999987 3444 458999999999999999999999999999987 678888999999999999984331
Q ss_pred --HHHHHHHhcCCCC----HHHHHHhhHHHHhhc
Q 008449 78 --NMLLNQIRCEEGS----PENLLRNSFYQFQAD 105 (565)
Q Consensus 78 --~~iL~l~~~~~~~----~~~~l~~sf~~~~~~ 105 (565)
..+|.++..+.+. +..+...||+..|..
T Consensus 639 ~~~~ilsvI~~~ia~t~~di~~~va~tl~s~q~~ 672 (1008)
T KOG0950|consen 639 ILMAILSLISLKIAETAEDILHFVAVTLLSAQEK 672 (1008)
T ss_pred cceeehhhhcchhhhhHHHHHHHHHHhhhhcccc
Confidence 3467777665442 566788888887755
No 14
>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]
Probab=98.72 E-value=7.1e-09 Score=119.22 Aligned_cols=103 Identities=23% Similarity=0.274 Sum_probs=78.3
Q ss_pred CCccEEEEcCCeeecCCc--ceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCChH
Q 008449 1 MPAKTVVFTNVRKFDGDK--FRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYN 78 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~--~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~~ 78 (565)
+||+||||+++.-||... ++.|+|-|..||.|||||+++|+.|..||..+.+ +.+.+..+ ..+..|++|||.....
T Consensus 649 lpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~s-e~qyyls~-mn~qLpiesq~~~rl~ 726 (1674)
T KOG0951|consen 649 LPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHS-ELQYYLSL-MNQQLPIESQFVSRLA 726 (1674)
T ss_pred CCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCch-HhhhhHHh-hhhcCCChHHHHHHhh
Confidence 699999999999999874 5569999999999999999999999999998765 33444444 4577999999976544
Q ss_pred HHHHHHhcCCC----CHHHHHHhhHHHHhhc
Q 008449 79 MLLNQIRCEEG----SPENLLRNSFYQFQAD 105 (565)
Q Consensus 79 ~iL~l~~~~~~----~~~~~l~~sf~~~~~~ 105 (565)
--||.=-+-++ +..+|+..||+.-...
T Consensus 727 d~lnaeiv~Gv~~~~d~~~wl~yTylyvRm~ 757 (1674)
T KOG0951|consen 727 DCLNAEIVLGVRSARDAVDWLGYTYLYVRMV 757 (1674)
T ss_pred hhhhhhhhcchhhHHHHHhhhcceeeEEeec
Confidence 44444222223 3678888888876543
No 15
>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]
Probab=98.18 E-value=1.8e-06 Score=93.09 Aligned_cols=78 Identities=21% Similarity=0.352 Sum_probs=64.5
Q ss_pred CccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCC-CceEEEEEccCCCCHHHHHHHhcCCCCccccc-CCCChHH
Q 008449 2 PAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGID-ERGICILMVDDKMEPSTAKMMLKGSADSLNSA-FHLSYNM 79 (565)
Q Consensus 2 PAr~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D-~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~-f~~~~~~ 79 (565)
-.|||||+++.||+|.+-.+++.++.+|+||||||.|-- ..|.+..+-.. +...+.+.+.-+++||.-. +.+|+..
T Consensus 426 ~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~e--DL~~L~~~l~~p~epi~~agl~pt~eq 503 (700)
T KOG0953|consen 426 NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSE--DLKLLKRILKRPVEPIKNAGLWPTDEQ 503 (700)
T ss_pred ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeHh--hHHHHHHHHhCCchHHHhccCCccHHH
Confidence 468999999999999999999999999999999999875 57888777654 4788889898888888644 4566544
Q ss_pred HH
Q 008449 80 LL 81 (565)
Q Consensus 80 iL 81 (565)
+-
T Consensus 504 ie 505 (700)
T KOG0953|consen 504 IE 505 (700)
T ss_pred HH
Confidence 43
No 16
>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]
Probab=96.99 E-value=0.0013 Score=77.33 Aligned_cols=94 Identities=19% Similarity=0.267 Sum_probs=69.9
Q ss_pred CccEEEEcCCeeecCCc--ceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCC----
Q 008449 2 PAKTVVFTNVRKFDGDK--FRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHL---- 75 (565)
Q Consensus 2 PAr~Vv~~~~~k~dg~~--~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~---- 75 (565)
-|..||+.++.-|||+. |.+++.++.+||.|+|.| .|.|||+|+.+ .+.+++-+..++.|++|.+..
T Consensus 1447 ~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~-----~~k~vi~~~~~--~k~yykkfl~e~lPves~lq~~lhd 1519 (1674)
T KOG0951|consen 1447 KAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG-----AGKCVIMCHTP--KKEYYKKFLYEPLPVESHLQHCLHD 1519 (1674)
T ss_pred cceEEEEecceeecccccccccCchhHHHHHhhhhcC-----CccEEEEecCc--hHHHHHHhccCcCchHHHHHHHHHh
Confidence 47789999999999985 456999999999999999 69999999876 566777778899999999742
Q ss_pred ChHH-HHHHHhcCCCCHHHHHHhhHHHH
Q 008449 76 SYNM-LLNQIRCEEGSPENLLRNSFYQF 102 (565)
Q Consensus 76 ~~~~-iL~l~~~~~~~~~~~l~~sf~~~ 102 (565)
++|- +.+-.-.+-.+.-+++..||..-
T Consensus 1520 ~~n~ei~~~tienkqd~vd~lt~s~~yr 1547 (1674)
T KOG0951|consen 1520 NFNAEIVTKTIENKQDAVDYLTWSFMYR 1547 (1674)
T ss_pred hhhHHHHHHHHHhHHHHHHHHHHHHhhh
Confidence 2221 11111111234678888888754
No 17
>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....
Probab=96.07 E-value=0.0063 Score=49.41 Aligned_cols=27 Identities=52% Similarity=0.655 Sum_probs=21.9
Q ss_pred ccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCC
Q 008449 3 AKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRG 38 (565)
Q Consensus 3 Ar~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg 38 (565)
+..||+.++ +.++.+|.|++|||||.|
T Consensus 52 ~~~vi~~~~---------~~~~~~~~Q~~GR~~R~g 78 (78)
T PF00271_consen 52 ASHVIFYDP---------PWSPEEYIQRIGRAGRIG 78 (78)
T ss_dssp ESEEEESSS---------ESSHHHHHHHHTTSSTTT
T ss_pred ccccccccc---------CCCHHHHHHHhhcCCCCC
Confidence 455666664 578999999999999997
No 18
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.68 E-value=0.015 Score=64.14 Aligned_cols=41 Identities=32% Similarity=0.464 Sum_probs=31.8
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCC
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGS 65 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~ 65 (565)
-+..+|.||+|||||.|.+ |.++++..+. +...+..++...
T Consensus 305 ~s~~~y~Qr~GRaGR~G~~--~~~~~~~~~~-d~~~~~~~~~~~ 345 (470)
T TIGR00614 305 KSMESYYQESGRAGRDGLP--SECHLFYAPA-DINRLRRLLMEE 345 (470)
T ss_pred CCHHHHHhhhcCcCCCCCC--ceEEEEechh-HHHHHHHHHhcC
Confidence 4789999999999999976 8888887765 456666666543
No 19
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=95.63 E-value=0.0096 Score=47.89 Aligned_cols=27 Identities=41% Similarity=0.586 Sum_probs=21.8
Q ss_pred ccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCC
Q 008449 3 AKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRG 38 (565)
Q Consensus 3 Ar~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg 38 (565)
++.||+.+. +.+...|.||.||+||.|
T Consensus 56 ~~~vi~~~~---------~~~~~~~~Q~~gR~~R~g 82 (82)
T smart00490 56 VDLVIIYDL---------PWSPASYIQRIGRAGRAG 82 (82)
T ss_pred CCEEEEeCC---------CCCHHHHHHhhcccccCC
Confidence 556666554 578999999999999986
No 20
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=95.34 E-value=0.045 Score=67.59 Aligned_cols=73 Identities=12% Similarity=0.151 Sum_probs=53.6
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCH----HHHHHHhcCCCCcccccCCCC---hHHHHHHHhcCCCCHHH
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEP----STAKMMLKGSADSLNSAFHLS---YNMLLNQIRCEEGSPEN 93 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~----~~~~~~~~~~~~~l~S~f~~~---~~~iL~l~~~~~~~~~~ 93 (565)
+.+...|+||+|||||+ .+..+.++++..+..+. -.+..++.|..+++...-..- ...++.+...+.+++++
T Consensus 355 P~sVas~LQRiGRAGR~-~gg~s~gli~p~~r~dlle~~~~ve~~l~g~iE~~~~p~nplDVLaqqiva~a~~~~~~~d~ 433 (1490)
T PRK09751 355 PLSVASGLQRIGRAGHQ-VGGVSKGLFFPRTRRDLVDSAVIVECMFAGRLENLTPPHNPLDVLAQQTVAAAAMDALQVDE 433 (1490)
T ss_pred CCCHHHHHHHhCCCCCC-CCCccEEEEEeCcHHHHHhhHHHHHHHhcCCCCccCCCCChHHHHHHHHHHHHhcCCCCHHH
Confidence 57899999999999998 67777788777664221 135577889999877665432 57788888777777665
Q ss_pred H
Q 008449 94 L 94 (565)
Q Consensus 94 ~ 94 (565)
+
T Consensus 434 l 434 (1490)
T PRK09751 434 W 434 (1490)
T ss_pred H
Confidence 5
No 21
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=95.09 E-value=0.027 Score=63.06 Aligned_cols=30 Identities=37% Similarity=0.575 Sum_probs=25.8
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.+..+|.||+|||||.|. .|.+|++..+.
T Consensus 446 P~s~~~yihRiGRaGR~g~--~G~ai~f~~~~ 475 (518)
T PLN00206 446 PNTIKEYIHQIGRASRMGE--KGTAIVFVNEE 475 (518)
T ss_pred CCCHHHHHHhccccccCCC--CeEEEEEEchh
Confidence 4578999999999999985 59999998754
No 22
>PRK13767 ATP-dependent helicase; Provisional
Probab=94.88 E-value=0.058 Score=64.17 Aligned_cols=85 Identities=19% Similarity=0.153 Sum_probs=54.4
Q ss_pred ecCHHHHHHhhccCCCCCC-CCceEEEEEccCCC-CHH-HHHHHhcCCCCcccccCC---CChHHHHHHHhcCCCC---H
Q 008449 21 WISSGEYIQMSGRAGRRGI-DERGICILMVDDKM-EPS-TAKMMLKGSADSLNSAFH---LSYNMLLNQIRCEEGS---P 91 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~-D~~G~~ii~~~~~~-~~~-~~~~~~~~~~~~l~S~f~---~~~~~iL~l~~~~~~~---~ 91 (565)
+.+...|.||+|||||++- ...|.++....... +.. ....+..|..+++.+... +-...++.+...+..+ +
T Consensus 368 P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~~~l~e~~~~~~~~~~~~ie~~~~~~~~~dvl~q~i~~~~~~~~~~~~~~ 447 (876)
T PRK13767 368 PKSVSRLLQRIGRAGHRLGEVSKGRIIVVDRDDLVECAVLLKKAREGKIDRVHIPKNPLDVLAQHIVGMAIERPWDIEEA 447 (876)
T ss_pred CCCHHHHHHhcccCCCCCCCCCcEEEEEcCchhHHHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHHHHcCCCCHHHH
Confidence 3578999999999999854 46788777543321 111 234556788887655432 2356677777666666 4
Q ss_pred HHHHHhhHHHHhhc
Q 008449 92 ENLLRNSFYQFQAD 105 (565)
Q Consensus 92 ~~~l~~sf~~~~~~ 105 (565)
-++++++|...+-.
T Consensus 448 ~~~~~~~~~~~~l~ 461 (876)
T PRK13767 448 YNIVRRAYPYRDLS 461 (876)
T ss_pred HHHHhccCCcccCC
Confidence 55677777655433
No 23
>PTZ00424 helicase 45; Provisional
Probab=94.58 E-value=0.022 Score=61.14 Aligned_cols=30 Identities=37% Similarity=0.530 Sum_probs=25.8
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.+..+|.||+|||||.|.+ |.+|+++.+.
T Consensus 345 p~s~~~y~qr~GRagR~g~~--G~~i~l~~~~ 374 (401)
T PTZ00424 345 PASPENYIHRIGRSGRFGRK--GVAINFVTPD 374 (401)
T ss_pred CCCHHHEeecccccccCCCC--ceEEEEEcHH
Confidence 35889999999999999864 9999998765
No 24
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=94.51 E-value=0.044 Score=62.56 Aligned_cols=41 Identities=27% Similarity=0.358 Sum_probs=30.5
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKG 64 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~ 64 (565)
+.+...|.||+|||||.|.+ |.++++.++. +...+..++..
T Consensus 314 P~s~~~y~Qr~GRaGR~G~~--~~~ill~~~~-d~~~~~~~~~~ 354 (607)
T PRK11057 314 PRNIESYYQETGRAGRDGLP--AEAMLFYDPA-DMAWLRRCLEE 354 (607)
T ss_pred CCCHHHHHHHhhhccCCCCC--ceEEEEeCHH-HHHHHHHHHhc
Confidence 35789999999999999976 8888887764 34445555543
No 25
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=94.50 E-value=0.046 Score=60.42 Aligned_cols=30 Identities=27% Similarity=0.559 Sum_probs=25.3
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.+...|.||+|||||+|.+ |.+|++..+.
T Consensus 413 P~s~~~y~Qr~GRaGR~g~~--g~~i~~~~~~ 442 (475)
T PRK01297 413 PEDPDDYVHRIGRTGRAGAS--GVSISFAGED 442 (475)
T ss_pred CCCHHHHHHhhCccCCCCCC--ceEEEEecHH
Confidence 35789999999999999986 8888887654
No 26
>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.
Probab=93.00 E-value=0.25 Score=57.76 Aligned_cols=30 Identities=33% Similarity=0.501 Sum_probs=25.2
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+-+...|.||+|||||+|.+ |.+|+++.+.
T Consensus 357 P~s~~~y~qRiGRaGR~G~~--g~ai~v~~~~ 386 (742)
T TIGR03817 357 PGTRASLWQQAGRAGRRGQG--ALVVLVARDD 386 (742)
T ss_pred CCCHHHHHHhccccCCCCCC--cEEEEEeCCC
Confidence 35789999999999999976 8888888643
No 27
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=92.83 E-value=0.14 Score=58.19 Aligned_cols=39 Identities=28% Similarity=0.394 Sum_probs=27.7
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhc
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLK 63 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~ 63 (565)
-+...|.||+|||||.|.. |.++++.+.. +...+..++.
T Consensus 303 ~s~~~y~Q~~GRaGR~G~~--~~~il~~~~~-d~~~~~~~i~ 341 (591)
T TIGR01389 303 GNLESYYQEAGRAGRDGLP--AEAILLYSPA-DIALLKRRIE 341 (591)
T ss_pred CCHHHHhhhhccccCCCCC--ceEEEecCHH-HHHHHHHHHh
Confidence 4678999999999999854 7777776654 3444444443
No 28
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=92.11 E-value=0.23 Score=57.05 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=23.6
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
..+.|.||+|||||.|. .|.||++..++
T Consensus 539 gls~lhQ~~GRvGR~g~--~g~~il~~~~~ 566 (630)
T TIGR00643 539 GLSQLHQLRGRVGRGDH--QSYCLLVYKNP 566 (630)
T ss_pred CHHHHHHHhhhcccCCC--CcEEEEEECCC
Confidence 46899999999999975 59999998543
No 29
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=92.03 E-value=0.16 Score=55.35 Aligned_cols=29 Identities=34% Similarity=0.558 Sum_probs=23.8
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDD 51 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~ 51 (565)
+.+...|.||+|||||.|.+ |.++++...
T Consensus 323 p~s~~~yiqr~GR~gR~g~~--g~ai~l~~~ 351 (434)
T PRK11192 323 PRSADTYLHRIGRTGRAGRK--GTAISLVEA 351 (434)
T ss_pred CCCHHHHhhcccccccCCCC--ceEEEEecH
Confidence 35789999999999999876 777777654
No 30
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=91.68 E-value=0.27 Score=56.97 Aligned_cols=28 Identities=29% Similarity=0.609 Sum_probs=23.6
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
..+.|.||.||+||.|. .|.||+++.++
T Consensus 562 gls~lhQ~~GRvGR~g~--~g~~ill~~~~ 589 (681)
T PRK10917 562 GLAQLHQLRGRVGRGAA--QSYCVLLYKDP 589 (681)
T ss_pred CHHHHHHHhhcccCCCC--ceEEEEEECCC
Confidence 45789999999999975 59999998643
No 31
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=91.66 E-value=0.099 Score=56.81 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=25.2
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.++.+|.||+|||||.|.. |.+|.+..+.
T Consensus 333 P~s~~~yiqR~GR~gR~G~~--G~ai~~~~~~ 362 (423)
T PRK04837 333 PDDCEDYVHRIGRTGRAGAS--GHSISLACEE 362 (423)
T ss_pred CCchhheEeccccccCCCCC--eeEEEEeCHH
Confidence 35789999999999999955 9999887654
No 32
>PF12029 DUF3516: Domain of unknown function (DUF3516); InterPro: IPR021904 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with PF00270 from PFAM, PF00271 from PFAM.
Probab=91.45 E-value=0.2 Score=53.86 Aligned_cols=35 Identities=23% Similarity=0.365 Sum_probs=32.2
Q ss_pred CHHHHHHHhcCCCCcccccCCCChHHHHHHHhcCC
Q 008449 54 EPSTAKMMLKGSADSLNSAFHLSYNMLLNQIRCEE 88 (565)
Q Consensus 54 ~~~~~~~~~~~~~~~l~S~f~~~~~~iL~l~~~~~ 88 (565)
+.+.+.+++.+.|+||.|+|++|.+|+||+|...+
T Consensus 38 ~e~TF~rL~~a~PE~L~s~f~vthaMlLnvl~r~g 72 (461)
T PF12029_consen 38 SEKTFERLIEAEPEPLTSRFRVTHAMLLNVLARPG 72 (461)
T ss_pred CHHHHHHHhcCCCCCCccCeeccHHHHHHHHcCCC
Confidence 47899999999999999999999999999997654
No 33
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=91.37 E-value=0.098 Score=46.00 Aligned_cols=26 Identities=46% Similarity=0.709 Sum_probs=21.8
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEE
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILM 48 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~ 48 (565)
+.+..+|.||.|||||.|- .|.++++
T Consensus 106 ~~~~~~~~Q~~GR~~R~~~--~~~~~~~ 131 (131)
T cd00079 106 PWSPSSYLQRIGRAGRAGQ--KGTAILL 131 (131)
T ss_pred CCCHHHheecccccccCCC--CceEEeC
Confidence 3578999999999999995 6887764
No 34
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=91.25 E-value=0.23 Score=54.64 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=24.6
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
-++..|.||+|||||.|.+ |.+|.++.+.
T Consensus 321 ~~~~~yiqR~GRtGR~g~~--G~ai~l~~~~ 349 (460)
T PRK11776 321 RDPEVHVHRIGRTGRAGSK--GLALSLVAPE 349 (460)
T ss_pred CCHhHhhhhcccccCCCCc--ceEEEEEchh
Confidence 4689999999999999865 8888887654
No 35
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=91.19 E-value=0.2 Score=55.19 Aligned_cols=28 Identities=25% Similarity=0.413 Sum_probs=22.8
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccC
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDD 51 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~ 51 (565)
-++.+|.||+|||||.|.. |.+|.++..
T Consensus 324 ~~~~~yvqR~GRaGR~g~~--G~ai~l~~~ 351 (456)
T PRK10590 324 NVPEDYVHRIGRTGRAAAT--GEALSLVCV 351 (456)
T ss_pred CCHHHhhhhccccccCCCC--eeEEEEecH
Confidence 4678999999999999975 777766654
No 36
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=91.11 E-value=0.25 Score=59.35 Aligned_cols=52 Identities=29% Similarity=0.408 Sum_probs=35.3
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCCh
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSY 77 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~ 77 (565)
-+...|.|++|||||.|.. |.||++.... +...+..++.. ...-.|.+...|
T Consensus 759 kSiEsYyQriGRAGRDG~~--g~cILlys~~-D~~~~~~lI~~-~~~~~s~~~~~~ 810 (1195)
T PLN03137 759 KSIEGYHQECGRAGRDGQR--SSCVLYYSYS-DYIRVKHMISQ-GGVEQSPMAMGY 810 (1195)
T ss_pred CCHHHHHhhhcccCCCCCC--ceEEEEecHH-HHHHHHHHHhc-cccccchhhhhh
Confidence 4779999999999999975 8999998653 44555666642 223344444433
No 37
>PTZ00110 helicase; Provisional
Probab=90.53 E-value=0.41 Score=53.95 Aligned_cols=29 Identities=24% Similarity=0.510 Sum_probs=24.7
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
-+...|.||+|||||.|. .|.+|.+..+.
T Consensus 456 ~s~~~yvqRiGRtGR~G~--~G~ai~~~~~~ 484 (545)
T PTZ00110 456 NQIEDYVHRIGRTGRAGA--KGASYTFLTPD 484 (545)
T ss_pred CCHHHHHHHhcccccCCC--CceEEEEECcc
Confidence 467899999999999986 49998888764
No 38
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=90.00 E-value=0.34 Score=55.00 Aligned_cols=30 Identities=23% Similarity=0.431 Sum_probs=25.4
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.+...|.||+|||||.|.+ |.+|+++.+.
T Consensus 335 P~s~~~yvqRiGRaGR~G~~--G~ai~~~~~~ 364 (572)
T PRK04537 335 PFDAEDYVHRIGRTARLGEE--GDAISFACER 364 (572)
T ss_pred CCCHHHHhhhhcccccCCCC--ceEEEEecHH
Confidence 46889999999999999985 8888887653
No 39
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=89.56 E-value=0.78 Score=52.92 Aligned_cols=42 Identities=33% Similarity=0.369 Sum_probs=30.0
Q ss_pred cEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 4 KTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 4 r~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.||+++...|. + +-+...|.|++|||||. ..|.+|++++..
T Consensus 516 ~lVii~d~eifG---~-~~~~~~yiqr~GR~gR~---~~G~~i~~~~~~ 557 (652)
T PRK05298 516 SLVAILDADKEG---F-LRSERSLIQTIGRAARN---VNGKVILYADKI 557 (652)
T ss_pred cEEEEeCCcccc---c-CCCHHHHHHHhccccCC---CCCEEEEEecCC
Confidence 456666654332 1 13667899999999994 479999999853
No 40
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=88.57 E-value=1.4 Score=51.99 Aligned_cols=45 Identities=36% Similarity=0.582 Sum_probs=32.5
Q ss_pred cEEEEcCCee---ecCCc------ceecCHHHHHHhhccCCCCCCCCceEEEEEccC
Q 008449 4 KTVVFTNVRK---FDGDK------FRWISSGEYIQMSGRAGRRGIDERGICILMVDD 51 (565)
Q Consensus 4 r~Vv~~~~~k---~dg~~------~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~ 51 (565)
+.||=.++.| ||... -.++|...|.|++|||||- ..|.||-+...
T Consensus 285 ~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~---~~G~cyrL~t~ 338 (812)
T PRK11664 285 RLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL---EPGICLHLYSK 338 (812)
T ss_pred eEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC---CCcEEEEecCH
Confidence 3455445543 66441 2358899999999999998 47999999864
No 41
>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=88.57 E-value=0.71 Score=56.62 Aligned_cols=57 Identities=23% Similarity=0.324 Sum_probs=38.0
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHh-cCCCCcccccCCCChHHHHHHHhcC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMML-KGSADSLNSAFHLSYNMLLNQIRCE 87 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~-~~~~~~l~S~f~~~~~~iL~l~~~~ 87 (565)
++|.+.|.|++|||||.| .|.||-+... +.+..+. ...|+-+.+.+. +++|.+.+.+
T Consensus 376 ~ISkasa~QRaGRAGR~~---~G~cyRLyte----~~~~~~~~~~~PEIlR~~L~---~viL~l~~lg 433 (1283)
T TIGR01967 376 PISQASANQRKGRCGRVA---PGICIRLYSE----EDFNSRPEFTDPEILRTNLA---SVILQMLALR 433 (1283)
T ss_pred cCCHHHHHHHhhhhCCCC---CceEEEecCH----HHHHhhhhccCcccccccHH---HHHHHHHhcC
Confidence 467899999999999998 7999988764 3333322 234554444332 5677766654
No 42
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=88.18 E-value=0.61 Score=53.55 Aligned_cols=30 Identities=33% Similarity=0.650 Sum_probs=25.7
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.++..|.||+|||||.|. .|.+|+++.+.
T Consensus 323 P~~~e~yvqRiGRtGRaGr--~G~ai~~v~~~ 352 (629)
T PRK11634 323 PMDSESYVHRIGRTGRAGR--AGRALLFVENR 352 (629)
T ss_pred CCCHHHHHHHhccccCCCC--cceEEEEechH
Confidence 4578999999999999996 59999998764
No 43
>TIGR01587 cas3_core CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Probab=87.59 E-value=0.5 Score=49.92 Aligned_cols=31 Identities=23% Similarity=0.144 Sum_probs=25.4
Q ss_pred cCHHHHHHhhccCCCCCCC--CceEEEEEccCC
Q 008449 22 ISSGEYIQMSGRAGRRGID--ERGICILMVDDK 52 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D--~~G~~ii~~~~~ 52 (565)
.++..|.|++||+||.|.. +.|.++++...+
T Consensus 304 ~~~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~ 336 (358)
T TIGR01587 304 APIDSLIQRLGRLHRYGRKNGENFEVYIITIAP 336 (358)
T ss_pred CCHHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence 5778999999999999875 347999887654
No 44
>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=87.07 E-value=1.7 Score=51.46 Aligned_cols=59 Identities=22% Similarity=0.349 Sum_probs=37.9
Q ss_pred eecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhc-CCCCcccccCCCChHHHHHHHhcCC
Q 008449 20 RWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLK-GSADSLNSAFHLSYNMLLNQIRCEE 88 (565)
Q Consensus 20 r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~-~~~~~l~S~f~~~~~~iL~l~~~~~ 88 (565)
.++|.+.|.|++|||||- ..|.||-+.... .+..+.. ..|+-+.+.+ .+.+|.+.+.+.
T Consensus 307 ~~iSkasa~QR~GRAGR~---~~G~cyrL~t~~----~~~~l~~~~~PEI~r~~L---~~~~L~l~~~g~ 366 (819)
T TIGR01970 307 VRISQASATQRAGRAGRL---EPGVCYRLWSEE----QHQRLPAQDEPEILQADL---SGLALELAQWGA 366 (819)
T ss_pred EEECHHHHHhhhhhcCCC---CCCEEEEeCCHH----HHHhhhcCCCcceeccCc---HHHHHHHHHcCC
Confidence 468999999999999998 579999998643 3333322 2333333332 256666665543
No 45
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=87.00 E-value=1.1 Score=51.80 Aligned_cols=42 Identities=29% Similarity=0.279 Sum_probs=30.0
Q ss_pred cEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 4 KTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 4 r~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.||+.+..+|. .+-+...|+|++|||||. ..|.||++++..
T Consensus 512 ~lVvi~DadifG----~p~~~~~~iqriGRagR~---~~G~vi~~~~~~ 553 (655)
T TIGR00631 512 SLVAILDADKEG----FLRSERSLIQTIGRAARN---VNGKVIMYADKI 553 (655)
T ss_pred cEEEEeCccccc----CCCCHHHHHHHhcCCCCC---CCCEEEEEEcCC
Confidence 446666544332 233677899999999997 369999998864
No 46
>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=86.17 E-value=0.71 Score=39.89 Aligned_cols=44 Identities=11% Similarity=0.160 Sum_probs=28.8
Q ss_pred HHHHhHhCCccCCCccchhhhhhhhhccCchhHHHHHHHhCCCCC
Q 008449 378 KRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKD 422 (565)
Q Consensus 378 ~~VL~~Lgyid~~~~vt~KGrvAceI~s~dELllTEllf~g~f~~ 422 (565)
.+.|+.||.||+++.+|.-|+..+.+-- +.-+---+++...|+-
T Consensus 3 ~~~L~~Lgald~~~~lT~lG~~~~~lPl-~p~~a~~Ll~~~~~~~ 46 (102)
T PF04408_consen 3 LELLKSLGALDENGNLTPLGRKMSQLPL-DPRLAKMLLYGIQFGC 46 (102)
T ss_dssp HHHHHHTTSB-TTS-B-HHHHHHTTSSS--HHHHHHHHHHHHCT-
T ss_pred HHHHHHCCCCCCCCCcCHHHHHHHHCCC-chHhHhHhhhcccccc
Confidence 4679999999999999999999999973 4444444444445544
No 47
>TIGR00580 mfd transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.
Probab=85.64 E-value=1.3 Score=52.96 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=29.8
Q ss_pred ccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 3 AKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 3 Ar~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.+||+....+ ...++|.|+.||+||.|. .|.||++..+.
T Consensus 731 v~~VIi~~a~~--------~gls~l~Qr~GRvGR~g~--~g~aill~~~~ 770 (926)
T TIGR00580 731 ANTIIIERADK--------FGLAQLYQLRGRVGRSKK--KAYAYLLYPHQ 770 (926)
T ss_pred CCEEEEecCCC--------CCHHHHHHHhcCCCCCCC--CeEEEEEECCc
Confidence 56777665432 234689999999999875 69999998653
No 48
>PHA02653 RNA helicase NPH-II; Provisional
Probab=84.55 E-value=0.93 Score=52.33 Aligned_cols=30 Identities=30% Similarity=0.397 Sum_probs=26.1
Q ss_pred eecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 20 RWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 20 r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
.+++...|.|++|||||. ..|.|+-+....
T Consensus 485 ~~iSkasa~QRaGRAGR~---~~G~c~rLyt~~ 514 (675)
T PHA02653 485 MFISKSMRTQRKGRVGRV---SPGTYVYFYDLD 514 (675)
T ss_pred cccCHHHHHHhccCcCCC---CCCeEEEEECHH
Confidence 468999999999999998 469999998754
No 49
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=84.54 E-value=22 Score=40.07 Aligned_cols=163 Identities=17% Similarity=0.181 Sum_probs=103.1
Q ss_pred HHHHHHHHHhHhCCccCCC---ccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceeeccCCCCCCCcH
Q 008449 373 ELKARKRVLRRLGYATSDD---VVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQDASKPRE 449 (565)
Q Consensus 373 e~~~~~~VL~~Lgyid~~~---~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~qek~~~~~~l~~ 449 (565)
+.+..+.-|+.+|||+.+| .+|-.||+++-=. -.---+|.|.+|+....+|=.||+-|.-|--. .+++
T Consensus 618 ~~~k~l~~Lee~g~i~~~G~~v~~T~yGrava~~F--l~p~~a~~Ir~~v~~~~~pl~i~~~l~pfE~a-------yls~ 688 (830)
T COG1202 618 DPKKALSKLEEYGMIKKKGNIVRPTPYGRAVAMSF--LGPSEAEFIREGVLASMDPLRIAAELEPFENA-------YLSG 688 (830)
T ss_pred CHHHHHHHHHhcCCeeccCCEeeeccccceeEEee--cCchHHHHHHHhhhccCChHhHhhcccccccc-------ccCh
Confidence 5678899999999999765 5999999876322 22345899999999999999999988766432 2222
Q ss_pred HHHHHH-----------------HHHHHH-----------HHHHHHHHHHcCCCcccccccccCCccHHHH---------
Q 008449 450 ELELLF-----------------TQLQDT-----------ARRVAKVQLECKVQIDVEGFVNSFRPDIMEA--------- 492 (565)
Q Consensus 450 ~L~~~~-----------------~~l~~i-----------a~~I~~v~~~~~l~~~~~~~~~~~~~~Lm~v--------- 492 (565)
.|+.++ ..+.+- .+++..++.+ |....+-+.++.
T Consensus 689 ~l~r~i~~~~~~~vpsr~f~~a~~~I~~e~d~ii~ld~k~~e~l~~i~~d---------f~~c~c~d~ce~~~~~lse~i 759 (830)
T COG1202 689 FLKRAIESALRGRVPSRLFDSALLDILEEGDKIIELDPKLKEKLLLIYMD---------FLNCTCRDCCECAEQRLSEKI 759 (830)
T ss_pred HHHHHHHHHhcCCCchhhhhHHHHHHHhchhhhhcCCHHHHHHHHHHHHH---------HhcCchhhhHHHHHHHHHHHH
Confidence 222222 221111 1111112111 111111111222
Q ss_pred HHHHhCCCCHHHHHhh------CCCCCChHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhh
Q 008449 493 VYAWAKGSKFYEIMEI------TPVFEGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKI 553 (565)
Q Consensus 493 Vy~WA~G~~F~eI~~~------Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn~~L~~k~e~a~~~I 553 (565)
+..--.|.+-.+|-.. -..+.|||--|+-.+-.+|.-+...|++.+-++..+.+......|
T Consensus 760 i~lR~~gk~p~~Isr~l~~~Ygi~aYpgDif~wLd~~vr~Lea~~rIArvf~kr~~~~ea~~lk~~i 826 (830)
T COG1202 760 IELRIEGKDPSQISRILEKRYGIQAYPGDIFTWLDTLVRLLEAIGRIARVFKKREVEAEAKALKKKI 826 (830)
T ss_pred HHHHhcCCCHHHHHHHHHHhhCeeecChhHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence 2333478888777766 357899999998888888888888888888887776665544443
No 50
>PRK10689 transcription-repair coupling factor; Provisional
Probab=80.70 E-value=2.7 Score=51.61 Aligned_cols=40 Identities=20% Similarity=0.359 Sum_probs=29.1
Q ss_pred ccEEEEcCCeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 3 AKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 3 Ar~Vv~~~~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+.+||+..... +....|.|+.||+||.|. .|.|+++..++
T Consensus 880 v~~VIi~~ad~--------fglaq~~Qr~GRvGR~g~--~g~a~ll~~~~ 919 (1147)
T PRK10689 880 ANTIIIERADH--------FGLAQLHQLRGRVGRSHH--QAYAWLLTPHP 919 (1147)
T ss_pred CCEEEEecCCC--------CCHHHHHHHhhccCCCCC--ceEEEEEeCCC
Confidence 56677654322 234679999999999976 59999998543
No 51
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=77.51 E-value=5.3 Score=49.27 Aligned_cols=57 Identities=23% Similarity=0.281 Sum_probs=37.0
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHh-cCCCCcccccCCCChHHHHHHHhcC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMML-KGSADSLNSAFHLSYNMLLNQIRCE 87 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~-~~~~~~l~S~f~~~~~~iL~l~~~~ 87 (565)
++|...|.|++|||||.+ .|.||-+... +.+..+- ...|+-+.+.+ -+++|.+.+.+
T Consensus 383 ~iSkasa~QRaGRAGR~~---~G~c~rLyte----~d~~~~~~~~~PEIlR~~L---~~viL~lk~lg 440 (1294)
T PRK11131 383 PISQASANQRKGRCGRVS---EGICIRLYSE----DDFLSRPEFTDPEILRTNL---ASVILQMTALG 440 (1294)
T ss_pred ecCHhhHhhhccccCCCC---CcEEEEeCCH----HHHHhhhcccCCccccCCH---HHHHHHHHHcC
Confidence 467789999999999994 6999998764 3333331 22333333322 35677776654
No 52
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=76.82 E-value=2.3 Score=44.60 Aligned_cols=37 Identities=24% Similarity=0.399 Sum_probs=32.3
Q ss_pred CCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 16 GDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 16 g~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
|..++-+|.+-..|||||+||----+.|.++.+..+.
T Consensus 380 gaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~G~ 416 (441)
T COG4098 380 GAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGK 416 (441)
T ss_pred cCCcccccHHHHHHHhhhccCCCcCCCCcEEEEeccc
Confidence 4567889999999999999998877899999998664
No 53
>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]
Probab=75.37 E-value=3.9 Score=46.32 Aligned_cols=71 Identities=23% Similarity=0.217 Sum_probs=46.4
Q ss_pred CeeecCCc------ceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCChHHHHHHH
Q 008449 11 VRKFDGDK------FRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYNMLLNQI 84 (565)
Q Consensus 11 ~~k~dg~~------~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~~~iL~l~ 84 (565)
.++|+++. ..++|...-.|++|||||.|- |.|+-+.. +..+.+ |.....|-.-.-.++ .++|.|.
T Consensus 346 ~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~p---GkcyRLYt----e~~~~~-~~~~~~PEI~R~~Ls-~~vL~Lk 416 (674)
T KOG0922|consen 346 QKKYNPRTGLDSLIVVPISKASANQRAGRAGRTGP---GKCYRLYT----ESAYDK-MPLQTVPEIQRVNLS-SAVLQLK 416 (674)
T ss_pred EEeeccccCccceeEEechHHHHhhhcccCCCCCC---ceEEEeee----HHHHhh-cccCCCCceeeechH-HHHHHHH
Confidence 45577652 345899999999999999964 99988865 455544 444555544444444 5677776
Q ss_pred hcCCCC
Q 008449 85 RCEEGS 90 (565)
Q Consensus 85 ~~~~~~ 90 (565)
+.+.-+
T Consensus 417 algi~d 422 (674)
T KOG0922|consen 417 ALGIND 422 (674)
T ss_pred hcCCCC
Confidence 654433
No 54
>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=75.21 E-value=6.1 Score=45.02 Aligned_cols=77 Identities=29% Similarity=0.255 Sum_probs=47.7
Q ss_pred ceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCChHHHHHHHhcCC--------CC
Q 008449 19 FRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYNMLLNQIRCEE--------GS 90 (565)
Q Consensus 19 ~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~~~iL~l~~~~~--------~~ 90 (565)
..+++...=-|.+|||||.|- |+|+-+... ..+..=|.-.+-| +-|-..-.|++|-|.+.+. ++
T Consensus 667 ~~pIS~AnA~QRaGRAGRt~p---G~cYRlYTe----~ay~~eml~stvP-EIqRTNl~nvVLlLkslgV~dll~FdFmD 738 (1042)
T KOG0924|consen 667 IVPISQANADQRAGRAGRTGP---GTCYRLYTE----DAYKNEMLPSTVP-EIQRTNLSNVVLLLKSLGVDDLLKFDFMD 738 (1042)
T ss_pred EEechhccchhhccccCCCCC---cceeeehhh----hHHHhhcccCCCc-hhhhcchhhHHHHHHhcChhhhhCCCcCC
Confidence 456888889999999999865 999888653 3333333333444 2233333588887776542 12
Q ss_pred --HHHHHHhhHHHHh
Q 008449 91 --PENLLRNSFYQFQ 103 (565)
Q Consensus 91 --~~~~l~~sf~~~~ 103 (565)
+++-|.+|+++.-
T Consensus 739 ~Pped~~~~sly~Lw 753 (1042)
T KOG0924|consen 739 PPPEDNLLNSLYQLW 753 (1042)
T ss_pred CCHHHHHHHHHHHHH
Confidence 4666666666543
No 55
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=75.08 E-value=35 Score=41.24 Aligned_cols=44 Identities=11% Similarity=-0.096 Sum_probs=28.6
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKG 64 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~ 64 (565)
+.+|..|.|+.||+||-|-...-.+++++...-..+.+..++..
T Consensus 574 P~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~ 617 (956)
T PRK04914 574 PFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHE 617 (956)
T ss_pred CCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhh
Confidence 46899999999999999986433333433333224555555544
No 56
>PRK00118 putative DNA-binding protein; Validated
Probab=71.72 E-value=13 Score=32.49 Aligned_cols=71 Identities=15% Similarity=0.084 Sum_probs=51.7
Q ss_pred ccccCCccHHHHHHHH-hCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHhhc----CCHHHHHHHHHHHH
Q 008449 481 FVNSFRPDIMEAVYAW-AKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSI----GETELEAKFEEAVS 551 (565)
Q Consensus 481 ~~~~~~~~Lm~vVy~W-A~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~~i----Gn~~L~~k~e~a~~ 551 (565)
|.+.+++.--.++..+ ..|.|+.+|.+.+++.+++|=+.+.|.-.-||+.-..-..+ -..++..+.+.+.+
T Consensus 14 ~~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (104)
T PRK00118 14 YGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNELFDKIAYLKE 89 (104)
T ss_pred HhccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHH
Confidence 4455666666666665 78999999999999999999999999999988876654332 23455555554443
No 57
>PRK13766 Hef nuclease; Provisional
Probab=68.70 E-value=7 Score=45.96 Aligned_cols=28 Identities=29% Similarity=0.408 Sum_probs=23.0
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
.++..|.|++||+||.|- |.++++....
T Consensus 452 ~s~~r~iQR~GR~gR~~~---~~v~~l~~~~ 479 (773)
T PRK13766 452 PSEIRSIQRKGRTGRQEE---GRVVVLIAKG 479 (773)
T ss_pred CCHHHHHHHhcccCcCCC---CEEEEEEeCC
Confidence 577899999999999864 8888887654
No 58
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=68.25 E-value=9 Score=28.11 Aligned_cols=42 Identities=19% Similarity=0.162 Sum_probs=34.0
Q ss_pred CCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHH
Q 008449 485 FRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEV 526 (565)
Q Consensus 485 ~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEl 526 (565)
+++.-..++..|+.|.+..+|.+..++.++++=+.++|+-+-
T Consensus 4 l~~~e~~i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 334445567778999999999999999999999999887443
No 59
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.20 E-value=16 Score=34.40 Aligned_cols=124 Identities=19% Similarity=0.199 Sum_probs=69.2
Q ss_pred CCChHHHHHhhhcceeeccCCCC-------------CCCcHHHHHHHHHHHHHHH-HHHHHHHHcCCCcccccccccCCc
Q 008449 422 DVKVEEMVSLLSCFVWQEKLQDA-------------SKPREELELLFTQLQDTAR-RVAKVQLECKVQIDVEGFVNSFRP 487 (565)
Q Consensus 422 ~L~p~eiaAlLS~fV~qek~~~~-------------~~l~~~L~~~~~~l~~ia~-~I~~v~~~~~l~~~~~~~~~~~~~ 487 (565)
.++|+|+=++||.++|-. .++. -..+..|..++++|.+... .+..---.+.+-+++++ .-=|
T Consensus 21 ~~t~aElHG~LsG~lcgG-~~d~sWq~l~~~~tneg~A~p~~l~~~l~~l~~a~s~~L~d~~F~f~LlLpe~e---~~vf 96 (186)
T COG3079 21 GLTPAELHGLLSGLLCGG-LNDSSWQPLLHDLTNEGMAPPHGLLQALEQLLQATSQQLEDDGFAFQLLLPEGE---DVVF 96 (186)
T ss_pred CCCHHHHHHHHHhhhhcC-CCchhHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHhcCCCeEEEEecCCCC---cHHH
Confidence 689999999999999943 2222 2245566677666654322 22221111122223222 1136
Q ss_pred cHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHhhcCCH-----HHHHHHHHHHHhhc
Q 008449 488 DIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGET-----ELEAKFEEAVSKIK 554 (565)
Q Consensus 488 ~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn~-----~L~~k~e~a~~~Ik 554 (565)
...+++.+||++- --=..+| -.+++.+. --..|.++++++.|++=+|. ++..-.++.++-+|
T Consensus 97 ~rADAL~eW~nhF--L~GlGL~-~~~l~~~~--gE~~EaldDL~~iaQlg~Deded~EE~~~~leEiiEyvR 163 (186)
T COG3079 97 DRADALAEWCNHF--LLGLGLT-QPKLSKLT--GEAGEALDDLANIAQLGYDEDEDQEELEESLEEIIEYVR 163 (186)
T ss_pred HHHHHHHHHHHHH--HHhhccc-ccchhhhc--ccHHHHHHHHHHHHHhcCCccccHHHHHHHHHHHHHHHH
Confidence 7799999999842 1111111 11111111 12478899999999885553 67777777777665
No 60
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.02 E-value=6.1 Score=44.19 Aligned_cols=27 Identities=30% Similarity=0.327 Sum_probs=21.8
Q ss_pred HHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 24 SGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 24 ~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
..-|+|++|||||.+. .|.|+|.+.++
T Consensus 355 ~~ll~q~~GRagR~~~--~g~viiqt~~p 381 (505)
T TIGR00595 355 FQLLTQVAGRAGRAED--PGQVIIQTYNP 381 (505)
T ss_pred HHHHHHHHhccCCCCC--CCEEEEEeCCC
Confidence 4679999999999765 59999876553
No 61
>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]
Probab=67.65 E-value=4.5 Score=45.08 Aligned_cols=29 Identities=28% Similarity=0.312 Sum_probs=23.5
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEc
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMV 49 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~ 49 (565)
+++.+.+.|-+||||||..|....+|...
T Consensus 611 P~S~aNl~QQ~GRAGRRNk~SLavyva~~ 639 (1034)
T KOG4150|consen 611 PGSIANLWQQAGRAGRRNKPSLAVYVAFL 639 (1034)
T ss_pred chhHHHHHHHhccccccCCCceEEEEEec
Confidence 57889999999999999998665555443
No 62
>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=66.84 E-value=11 Score=31.30 Aligned_cols=59 Identities=14% Similarity=0.195 Sum_probs=42.7
Q ss_pred HHHHhHhCCccCCCccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceee
Q 008449 378 KRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQ 438 (565)
Q Consensus 378 ~~VL~~Lgyid~~~~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~q 438 (565)
.+.|..||-||+++.+|..|+..+++-- + --++-+|..+...+=-..++++++|++-.+
T Consensus 3 ~~~L~~LgAld~~~~lT~lG~~m~~lPl-~-Prla~~Ll~a~~~~~c~~~~~~i~a~ls~~ 61 (92)
T smart00847 3 LELLYELGALDDDGRLTPLGRKMAELPL-D-PRLAKMLLAAAELFGCLDEILTIAAMLSVG 61 (92)
T ss_pred HHHHHHCCCcCCCCCcCHHHHHHHHCCC-C-hHHHHHHHHHHhhcCcHHHHHHHHHHhcCC
Confidence 4679999999999999999999999963 3 444555555543211356888888877654
No 63
>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=66.38 E-value=7.2 Score=44.35 Aligned_cols=61 Identities=23% Similarity=0.103 Sum_probs=37.1
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCcccccCCCChHHHHHHHhcCCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYNMLLNQIRCEEG 89 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~S~f~~~~~~iL~l~~~~~~ 89 (565)
++|-+--.|++|||||-|- |.|+-+.... .+.+-+..-+-|- -|=..--|.+|+|.+.+.-
T Consensus 578 piSKAsA~QRaGRAGRtgP---GKCfRLYt~~----aY~~eLE~~t~PE-IqRtnL~nvVL~LkSLGI~ 638 (902)
T KOG0923|consen 578 PISKASANQRAGRAGRTGP---GKCFRLYTAW----AYEHELEEMTVPE-IQRTNLGNVVLLLKSLGIH 638 (902)
T ss_pred eechhhhhhhccccCCCCC---CceEEeechh----hhhhhhccCCCcc-eeeccchhHHHHHHhcCcc
Confidence 4777899999999999976 8998876533 2222222112121 1112223888888876643
No 64
>PRK05580 primosome assembly protein PriA; Validated
Probab=66.08 E-value=6.7 Score=45.56 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=21.6
Q ss_pred HHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 25 GEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 25 ~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
..|+|++|||||.+. .|.+||.+.++
T Consensus 524 ~~l~q~~GRagR~~~--~g~viiqT~~p 549 (679)
T PRK05580 524 QLLTQVAGRAGRAEK--PGEVLIQTYHP 549 (679)
T ss_pred HHHHHHHhhccCCCC--CCEEEEEeCCC
Confidence 679999999999754 59999987654
No 65
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=64.10 E-value=26 Score=41.59 Aligned_cols=65 Identities=15% Similarity=0.189 Sum_probs=45.8
Q ss_pred HHHHHHHHHHhHhCCccCCCccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceee
Q 008449 372 DELKARKRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQ 438 (565)
Q Consensus 372 ~e~~~~~~VL~~Lgyid~~~~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~q 438 (565)
..+.+=+..|+.||.+|+++.+|..||..+++-. +.-+-.-+|....|. -..-.+||.++++..+
T Consensus 384 ~~~~~A~~~L~~lgald~~g~lT~~G~~m~~lp~-~Prla~~ll~a~~~~-~~~l~~a~~laall~e 448 (812)
T PRK11664 384 AALAAAKRLLQQLGALDGQGRLTARGRKMAALGN-DPRLAAMLVAAKEDD-EAALATAAKLAAILEE 448 (812)
T ss_pred HHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC-chHHHHHHHHHHhcC-chhhHHHHHHHHhhcc
Confidence 3577778899999999999999999999999973 544444444443443 1111368888887664
No 66
>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=63.54 E-value=12 Score=27.62 Aligned_cols=33 Identities=24% Similarity=0.318 Sum_probs=29.2
Q ss_pred HHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHH
Q 008449 491 EAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRL 523 (565)
Q Consensus 491 ~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRL 523 (565)
.+++.|+.|.+..+|++..++.+++|-+.+.|+
T Consensus 7 ~i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 7 EVLRLLAEGKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456678999999999999999999999888876
No 67
>KOG4284 consensus DEAD box protein [Transcription]
Probab=62.23 E-value=6.1 Score=44.82 Aligned_cols=31 Identities=32% Similarity=0.610 Sum_probs=24.9
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCCCC
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDKME 54 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~ 54 (565)
..--.|.++.|||||.|-. |.+|.+|....+
T Consensus 351 ~d~eTY~HRIGRAgRFG~~--G~aVT~~~~~~e 381 (980)
T KOG4284|consen 351 ADEETYFHRIGRAGRFGAH--GAAVTLLEDERE 381 (980)
T ss_pred cchHHHHHHhhhccccccc--ceeEEEeccchh
Confidence 3446799999999999965 999999876533
No 68
>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=61.13 E-value=14 Score=40.46 Aligned_cols=50 Identities=16% Similarity=0.243 Sum_probs=36.5
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCC-CcccccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSA-DSLNSAFH 74 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~-~~l~S~f~ 74 (565)
+..++-|.+++||+||.|- .|.+|++..+. +..+..+|.-.. .++++.-.
T Consensus 335 P~~~~~FvHR~GRTaR~gr--~G~Aivfl~p~--E~aYveFl~i~~~v~le~~~~ 385 (567)
T KOG0345|consen 335 PKDPSSFVHRCGRTARAGR--EGNAIVFLNPR--EEAYVEFLRIKGKVELERIDT 385 (567)
T ss_pred CCChhHHHhhcchhhhccC--ccceEEEeccc--HHHHHHHHHhcCccchhhhcc
Confidence 3578999999999999996 59999998874 666667665442 44554443
No 69
>PRK04217 hypothetical protein; Provisional
Probab=61.04 E-value=21 Score=31.58 Aligned_cols=52 Identities=17% Similarity=0.179 Sum_probs=43.6
Q ss_pred cCCccHHHHHHHHh-CCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHh
Q 008449 484 SFRPDIMEAVYAWA-KGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAK 535 (565)
Q Consensus 484 ~~~~~Lm~vVy~WA-~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~ 535 (565)
.+...--+++..|. .|.|+.+|.+..++.+++|=+.+.|..+.|++.-....
T Consensus 42 ~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~ 94 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGR 94 (110)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34444457888886 99999999999999999999999999999988766543
No 70
>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=59.48 E-value=9.4 Score=27.39 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=32.1
Q ss_pred CccHHHHHHHH-hCCCCHHHHHhhCCCCCChHHHHHHHHHHHH
Q 008449 486 RPDIMEAVYAW-AKGSKFYEIMEITPVFEGSLIRAIRRLEEVL 527 (565)
Q Consensus 486 ~~~Lm~vVy~W-A~G~~F~eI~~~Tdv~EGsIVR~irRLdEll 527 (565)
++.--.++..+ ..|.+..+|.+..++.++.|-+.+.|..+-|
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 12 PEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 33334444444 3999999999999999999999998876544
No 71
>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=59.35 E-value=17 Score=38.81 Aligned_cols=40 Identities=35% Similarity=0.582 Sum_probs=30.8
Q ss_pred CeeecCCcceecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHH
Q 008449 11 VRKFDGDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPS 56 (565)
Q Consensus 11 ~~k~dg~~~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~ 56 (565)
..||+|. =.+-.|+++.||+||.|. .|.+|=+.+..-+..
T Consensus 408 P~~~~~~----pD~etYlHRiGRtGRFGk--kG~a~n~v~~~~s~~ 447 (477)
T KOG0332|consen 408 PVKYTGE----PDYETYLHRIGRTGRFGK--KGLAINLVDDKDSMN 447 (477)
T ss_pred ccccCCC----CCHHHHHHHhcccccccc--cceEEEeecccCcHH
Confidence 5577776 255789999999999997 599998887763433
No 72
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=57.11 E-value=8.3 Score=45.92 Aligned_cols=26 Identities=35% Similarity=0.656 Sum_probs=20.5
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEcc
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVD 50 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~ 50 (565)
+..++.|++|||||++ ..+.++++..
T Consensus 395 s~~~~~Q~~GRaGR~~--~~~l~~~v~~ 420 (851)
T COG1205 395 SVLSFRQRAGRAGRRG--QESLVLVVLR 420 (851)
T ss_pred hHHHHHHhhhhccCCC--CCceEEEEeC
Confidence 5689999999999999 4455555554
No 73
>PRK02362 ski2-like helicase; Provisional
Probab=56.85 E-value=95 Score=36.47 Aligned_cols=66 Identities=15% Similarity=0.105 Sum_probs=49.3
Q ss_pred HHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhhcCC
Q 008449 490 MEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKIKRD 556 (565)
Q Consensus 490 m~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn~~L~~k~e~a~~~IkRD 556 (565)
.-+.++|-++.++.+|.+.-++..||+-.......-++..+...|...| ..+...+.+-+..|+-+
T Consensus 581 ~~ll~~~i~~~~~~~i~~~~~~~~gdl~~~~~~~~~l~~a~~~i~~~~~-~~~~~~~~~l~~~l~~g 646 (737)
T PRK02362 581 ALLLEDWIDEVDEERITERYGVGPGDIRGKVETAEWLLHAAERLASELD-LDLARAARELEKRVEYG 646 (737)
T ss_pred HHHHHHHHhCCCHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHhC
Confidence 4578999999999999999999999997788888888777777777655 44444444444444433
No 74
>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=56.53 E-value=19 Score=36.26 Aligned_cols=45 Identities=31% Similarity=0.333 Sum_probs=38.0
Q ss_pred HHHhHhCCccCCCccchhhhhhhhhccC------ch--hHHHHHHHhCCCCCC
Q 008449 379 RVLRRLGYATSDDVVELKGKVACEISSA------EE--LTLTELIFNGVLKDV 423 (565)
Q Consensus 379 ~VL~~Lgyid~~~~vt~KGrvAceI~s~------dE--LllTEllf~g~f~~L 423 (565)
+.|.-+||+|+...+|.-|++.....+. +| +++.|||.-|+++.=
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 3578899999999999999999887643 22 889999999999866
No 75
>PHA02558 uvsW UvsW helicase; Provisional
Probab=56.47 E-value=11 Score=42.07 Aligned_cols=19 Identities=26% Similarity=0.116 Sum_probs=15.9
Q ss_pred CHHHHHHhhccCCCCCCCC
Q 008449 23 SSGEYIQMSGRAGRRGIDE 41 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~ 41 (565)
+...|.||+||+||.+-+.
T Consensus 425 s~~~~~QriGR~~R~~~~K 443 (501)
T PHA02558 425 SKIIVLQSIGRVLRKHGSK 443 (501)
T ss_pred chhhhhhhhhccccCCCCC
Confidence 4578999999999998753
No 76
>PF13518 HTH_28: Helix-turn-helix domain
Probab=55.83 E-value=21 Score=26.06 Aligned_cols=35 Identities=23% Similarity=0.294 Sum_probs=31.6
Q ss_pred HHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 491 EAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 491 ~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
.+|-.+.+|.|..+++...+|..++|-||+++..+
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 56777889999999999999999999999998876
No 77
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=54.81 E-value=12 Score=43.56 Aligned_cols=39 Identities=23% Similarity=0.439 Sum_probs=27.7
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKG 64 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~ 64 (565)
+-.-++|-+|||||.+.. |.|+|-+.++ +-..+..++.+
T Consensus 576 ~fqll~QvaGRAgR~~~~--G~VvIQT~~P-~hp~i~~~~~~ 614 (730)
T COG1198 576 TFQLLMQVAGRAGRAGKP--GEVVIQTYNP-DHPAIQALKRG 614 (730)
T ss_pred HHHHHHHHHhhhccCCCC--CeEEEEeCCC-CcHHHHHHHhc
Confidence 345689999999999776 9999887664 44444444444
No 78
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=54.54 E-value=8.1 Score=43.31 Aligned_cols=38 Identities=29% Similarity=0.552 Sum_probs=29.0
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHH
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKM 60 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~ 60 (565)
+.++-.|.+.+||+||-| ..|.+|.++.+..+...+..
T Consensus 351 p~~~e~yvHRiGRTgRaG--~~G~ai~fv~~~~e~~~l~~ 388 (513)
T COG0513 351 PLDPEDYVHRIGRTGRAG--RKGVAISFVTEEEEVKKLKR 388 (513)
T ss_pred CCCHHHheeccCccccCC--CCCeEEEEeCcHHHHHHHHH
Confidence 367899999999999999 56999999986323333333
No 79
>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=54.03 E-value=12 Score=40.10 Aligned_cols=38 Identities=26% Similarity=0.426 Sum_probs=31.0
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHH
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMM 61 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~ 61 (565)
+.++..|++++||.||.| ..|.+|-++.. .|-+.+.++
T Consensus 378 P~~skDYIHRvGRtaRaG--rsG~~ItlVtq-yDve~~qrI 415 (476)
T KOG0330|consen 378 PTHSKDYIHRVGRTARAG--RSGKAITLVTQ-YDVELVQRI 415 (476)
T ss_pred CCcHHHHHHHcccccccC--CCcceEEEEeh-hhhHHHHHH
Confidence 467899999999999999 78999999887 466655544
No 80
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=53.94 E-value=12 Score=44.16 Aligned_cols=31 Identities=29% Similarity=0.432 Sum_probs=25.2
Q ss_pred eecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 20 RWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 20 r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
++-++..|.|.+||+||.|-- |.++.+++..
T Consensus 511 ~p~s~r~y~qr~GRtGR~G~~--G~s~~~is~e 541 (790)
T PRK09200 511 RMESRRVDLQLRGRSGRQGDP--GSSQFFISLE 541 (790)
T ss_pred CCCCHHHHHHhhccccCCCCC--eeEEEEEcch
Confidence 345778999999999999864 8888887653
No 81
>KOG0347 consensus RNA helicase [RNA processing and modification]
Probab=51.95 E-value=21 Score=39.97 Aligned_cols=90 Identities=17% Similarity=0.241 Sum_probs=54.6
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHh----cCCCCcccccCCCChHHHHHHHhcCCCCHHHHHHh
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMML----KGSADSLNSAFHLSYNMLLNQIRCEEGSPENLLRN 97 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~----~~~~~~l~S~f~~~~~~iL~l~~~~~~~~~~~l~~ 97 (565)
=++--|.+++||.-|.+.+ |..+++|.+. +...+.++. .-...|| |.+ ..-+++.++....=+.++-+.
T Consensus 542 rtseiYVHRSGRTARA~~~--Gvsvml~~P~-e~~~~~KL~ktL~k~~dlpi---fPv-~~~~m~~lkeRvrLA~ei~~~ 614 (731)
T KOG0347|consen 542 RTSEIYVHRSGRTARANSE--GVSVMLCGPQ-EVGPLKKLCKTLKKKEDLPI---FPV-ETDIMDALKERVRLAREIDKL 614 (731)
T ss_pred CccceeEecccccccccCC--CeEEEEeChH-HhHHHHHHHHHHhhccCCCc---eec-cHHHHHHHHHHHHHHHHHHHh
Confidence 3567799999999999876 9999999986 333333332 2333444 444 455777776543334555566
Q ss_pred hHHHHhhcCCchHHHHHHHHH
Q 008449 98 SFYQFQADHAIPDLEKQAKVL 118 (565)
Q Consensus 98 sf~~~~~~~~~~~~~~~~~~l 118 (565)
.|..++....-.=+++-.+++
T Consensus 615 e~k~~~v~~~~sWlkkaA~el 635 (731)
T KOG0347|consen 615 EIKSKRVRKEESWLKKAADEL 635 (731)
T ss_pred hhhhhhhhhhHHHHHHHHHHh
Confidence 666666555433333333433
No 82
>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=51.89 E-value=25 Score=25.84 Aligned_cols=38 Identities=18% Similarity=0.241 Sum_probs=31.2
Q ss_pred HHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHH
Q 008449 492 AVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQ 529 (565)
Q Consensus 492 vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrq 529 (565)
+...|-.|.|+.+|-+..++.+|.+=+..+|..+-||+
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 34556899999999999999999999888888777664
No 83
>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=51.54 E-value=22 Score=42.27 Aligned_cols=60 Identities=18% Similarity=0.312 Sum_probs=41.1
Q ss_pred HHHHHHHHHHhHhCCccCCCccchhhhhhhhhccCchhHHHHHHHhC-CCCCCC-hHHHHHhhh
Q 008449 372 DELKARKRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNG-VLKDVK-VEEMVSLLS 433 (565)
Q Consensus 372 ~e~~~~~~VL~~Lgyid~~~~vt~KGrvAceI~s~dELllTEllf~g-~f~~L~-p~eiaAlLS 433 (565)
..+.+=+..|+.||.||+++.+|.-|+..+++-- | --++-||..+ .|.-++ ...|||+||
T Consensus 381 ~~i~~a~~~L~~lgald~~~~lT~~G~~~~~lp~-~-p~l~~~ll~~~~~~~~~~~~~iaa~ls 442 (819)
T TIGR01970 381 VALAAARQLLQRLGALDAQGRLTAHGKAMAALGC-H-PRLAAMLLSAHSTGLAALACDLAALLE 442 (819)
T ss_pred HHHHHHHHHHHHCCCCCCCCCcCHHHHHHHhcCC-C-HHHHHHHHHhhhcCCHHHHHHHHHHHc
Confidence 3566778899999999999999999999999973 4 4445555544 444322 224444454
No 84
>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=51.27 E-value=13 Score=30.08 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=27.3
Q ss_pred HHHhCCCCHHHHHhhCCCCCChHHHHHHH
Q 008449 494 YAWAKGSKFYEIMEITPVFEGSLIRAIRR 522 (565)
Q Consensus 494 y~WA~G~~F~eI~~~Tdv~EGsIVR~irR 522 (565)
-+|..-.||..|-...++.|.++|..||+
T Consensus 7 MAweDRtpFeaI~~qfGl~E~eVi~lMR~ 35 (73)
T PF10985_consen 7 MAWEDRTPFEAIERQFGLSEKEVIKLMRK 35 (73)
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 58999999999999999999999999886
No 85
>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=51.08 E-value=6.6 Score=45.56 Aligned_cols=31 Identities=39% Similarity=0.658 Sum_probs=26.0
Q ss_pred ceecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 19 FRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 19 ~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
..|++..-=-|+||||||-|- |+|+-+.++.
T Consensus 674 V~wiSkASadQRAGRAGRtgp---GHcYRLYSSA 704 (1172)
T KOG0926|consen 674 VDWISKASADQRAGRAGRTGP---GHCYRLYSSA 704 (1172)
T ss_pred EEeeeccccchhccccCCCCC---CceeehhhhH
Confidence 457888888999999999976 9999887654
No 86
>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]
Probab=50.10 E-value=16 Score=40.33 Aligned_cols=40 Identities=33% Similarity=0.505 Sum_probs=32.5
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhc
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLK 63 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~ 63 (565)
+.+...|.+++||.||.|-| |.+|.+.++. +...+.+++.
T Consensus 511 P~~~ktyVHR~GRTARAgq~--G~a~tll~~~-~~r~F~klL~ 550 (620)
T KOG0350|consen 511 PASDKTYVHRAGRTARAGQD--GYAITLLDKH-EKRLFSKLLK 550 (620)
T ss_pred CchhhHHHHhhcccccccCC--ceEEEeeccc-cchHHHHHHH
Confidence 46778999999999999987 9999998775 5666666654
No 87
>PRK12906 secA preprotein translocase subunit SecA; Reviewed
Probab=49.82 E-value=63 Score=38.19 Aligned_cols=32 Identities=28% Similarity=0.277 Sum_probs=25.8
Q ss_pred ceecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 19 FRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 19 ~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
.++-+.-.|.|..|||||.|-. |.++.+++-.
T Consensus 522 e~pes~ri~~Ql~GRtGRqG~~--G~s~~~~sle 553 (796)
T PRK12906 522 ERHESRRIDNQLRGRSGRQGDP--GSSRFYLSLE 553 (796)
T ss_pred ecCCcHHHHHHHhhhhccCCCC--cceEEEEecc
Confidence 3556788899999999999975 8888877643
No 88
>PRK12900 secA preprotein translocase subunit SecA; Reviewed
Probab=49.02 E-value=80 Score=38.17 Aligned_cols=30 Identities=33% Similarity=0.371 Sum_probs=23.8
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+-+.--|.|..|||||.|- .|.++.+++..
T Consensus 682 hes~Rid~Ql~GRtGRqGd--pGsS~ffvSle 711 (1025)
T PRK12900 682 HESRRIDRQLRGRAGRQGD--PGESVFYVSLE 711 (1025)
T ss_pred CchHHHHHHHhhhhhcCCC--CcceEEEechh
Confidence 3445559999999999996 49998888753
No 89
>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=48.52 E-value=29 Score=36.37 Aligned_cols=51 Identities=22% Similarity=0.380 Sum_probs=34.6
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEc--cCCCCHHHHHHHhcCCCCcccccCCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMV--DDKMEPSTAKMMLKGSADSLNSAFHL 75 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~--~~~~~~~~~~~~~~~~~~~l~S~f~~ 75 (565)
++-.|+...||+||.|.= |.+|=+. .+.+....+.+-+-.+..|+-|....
T Consensus 402 ~aEtYLHRIGRsGRFGhl--GlAInLityedrf~L~~IE~eLGtEI~pip~~iDk 454 (459)
T KOG0326|consen 402 NAETYLHRIGRSGRFGHL--GLAINLITYEDRFNLYRIEQELGTEIKPIPSNIDK 454 (459)
T ss_pred CHHHHHHHccCCccCCCc--ceEEEEEehhhhhhHHHHHHHhccccccCCCcCCc
Confidence 678899999999999975 6665544 33333444555566667777766543
No 90
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=48.29 E-value=20 Score=41.42 Aligned_cols=30 Identities=27% Similarity=0.283 Sum_probs=24.4
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+-+...|.|.+||+||.|- .|.++.+.+..
T Consensus 557 P~s~r~y~hr~GRTGRqG~--~G~s~~~is~e 586 (656)
T PRK12898 557 HDSARIDRQLAGRCGRQGD--PGSYEAILSLE 586 (656)
T ss_pred CCCHHHHHHhcccccCCCC--CeEEEEEechh
Confidence 3456689999999999995 49999988753
No 91
>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=47.72 E-value=21 Score=28.94 Aligned_cols=29 Identities=24% Similarity=0.424 Sum_probs=27.3
Q ss_pred HHHhCCCCHHHHHhhCCCCCChHHHHHHH
Q 008449 494 YAWAKGSKFYEIMEITPVFEGSLIRAIRR 522 (565)
Q Consensus 494 y~WA~G~~F~eI~~~Tdv~EGsIVR~irR 522 (565)
-+|..-.||..|-...++.|+.+|..||+
T Consensus 8 MAweDRtpFeaI~~~fGL~E~eVi~lMR~ 36 (72)
T TIGR03643 8 MAWEDRTPFEAIEQQFGLSEKEVIKLMRQ 36 (72)
T ss_pred HHHccCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 58999999999999999999999998886
No 92
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=46.79 E-value=28 Score=32.78 Aligned_cols=43 Identities=16% Similarity=0.184 Sum_probs=37.0
Q ss_pred hCCCCHHHHHhhCCCCCCh----HHHHHHHHHHHHHHHHHHHhhcCC
Q 008449 497 AKGSKFYEIMEITPVFEGS----LIRAIRRLEEVLQQLILAAKSIGE 539 (565)
Q Consensus 497 A~G~~F~eI~~~Tdv~EGs----IVR~irRLdEllrqv~~Aa~~iGn 539 (565)
-.|.|..||.+..++++|+ +-|+.++|-+.|.+....=+-+||
T Consensus 131 ~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~~~~~~~ 177 (179)
T PRK12543 131 LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIFLGEVGN 177 (179)
T ss_pred HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence 4899999999999999999 778888888888888777776676
No 93
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=45.90 E-value=36 Score=40.51 Aligned_cols=29 Identities=41% Similarity=0.611 Sum_probs=24.9
Q ss_pred eecCHHHHHHhhccCCCCCCCCceEEEEEccC
Q 008449 20 RWISSGEYIQMSGRAGRRGIDERGICILMVDD 51 (565)
Q Consensus 20 r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~ 51 (565)
.++|...-.|++|||||-+ .|.||=+...
T Consensus 358 ~~ISqAsA~QRaGRAGR~~---pGicyRLyse 386 (845)
T COG1643 358 EPISKASADQRAGRAGRTG---PGICYRLYSE 386 (845)
T ss_pred EEechhhhhhhccccccCC---CceEEEecCH
Confidence 4589999999999999985 5999988764
No 94
>TIGR00963 secA preprotein translocase, SecA subunit. The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.
Probab=43.14 E-value=51 Score=38.59 Aligned_cols=31 Identities=29% Similarity=0.347 Sum_probs=25.3
Q ss_pred eecCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 20 RWISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 20 r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
++-+.-.|.|..||+||.|-. |.++.+.+..
T Consensus 487 ~p~s~ri~~q~~GRtGRqG~~--G~s~~~ls~e 517 (745)
T TIGR00963 487 RHESRRIDNQLRGRSGRQGDP--GSSRFFLSLE 517 (745)
T ss_pred CCCcHHHHHHHhccccCCCCC--cceEEEEecc
Confidence 456788999999999999975 8888777653
No 95
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=42.69 E-value=13 Score=27.24 Aligned_cols=34 Identities=21% Similarity=0.229 Sum_probs=24.2
Q ss_pred HHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHH
Q 008449 491 EAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLE 524 (565)
Q Consensus 491 ~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLd 524 (565)
.++..+..|.|-.+|++..++...+|-|+++|-.
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 3566666799999999999999999999999864
No 96
>PRK01172 ski2-like helicase; Provisional
Probab=42.57 E-value=5.9e+02 Score=29.45 Aligned_cols=159 Identities=11% Similarity=0.139 Sum_probs=89.6
Q ss_pred HHHHHHHHHHhHhCCccCCC--ccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceeeccCCCCCCCcH
Q 008449 372 DELKARKRVLRRLGYATSDD--VVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQDASKPRE 449 (565)
Q Consensus 372 ~e~~~~~~VL~~Lgyid~~~--~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~qek~~~~~~l~~ 449 (565)
.-...-++-|.+.|+|++++ .+|.-|++++..+-.- -..+.+.+.+=...+...+-.++|.. .+...+..
T Consensus 444 ~~v~~~l~~L~~~~~i~~~~~~~~t~lG~~~s~~~l~~--~t~~~~~~~l~~~~~~~~~l~~~~~~------~e~~~~~~ 515 (674)
T PRK01172 444 YYIESSLKFLKENGFIKGDVTLRATRLGKLTSDLYIDP--ESALILKSAFDHDYDEDLALYYISLC------REIIPANT 515 (674)
T ss_pred HHHHHHHHHHHHCCCcccCCcEeECHHHHHHHHhCCCH--HHHHHHHHHhhccCCHHHHHHHhhcC------cccccccc
Confidence 34567788999999998654 5899999999887422 22333333332233444444444321 11111111
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCcccccccccCCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHH
Q 008449 450 ELELLFTQLQDTARRVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQ 529 (565)
Q Consensus 450 ~L~~~~~~l~~ia~~I~~v~~~~~l~~~~~~~~~~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrq 529 (565)
.-. ..+.+.+..+ +. .+.+. .++.-.-+.++|-++.+..+|.+.-.+..|++=+++....=+..-
T Consensus 516 ~~~---~~~~~~~~~~-------~~---~~~~~--~~~k~~~ll~~~~~~~~~~~i~~~~~~~~g~l~~~~~~~~~~~~a 580 (674)
T PRK01172 516 RDD---YYAMEFLEDI-------GV---IDGDI--SAAKTAMVLRGWISEASMQKITDTYGIAPGDVQARASSADWISYS 580 (674)
T ss_pred chH---HHHHHHHHHh-------cc---ccchh--HHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHH
Confidence 000 1122222222 21 11111 234456789999999999999999999999988886555555444
Q ss_pred HHHHHhhcCCHHHHHHHHHHHHhhc
Q 008449 530 LILAAKSIGETELEAKFEEAVSKIK 554 (565)
Q Consensus 530 v~~Aa~~iGn~~L~~k~e~a~~~Ik 554 (565)
+...++.+ .++|.+.+..-..-|.
T Consensus 581 ~~~~~~~~-~~~~~~~l~~~~~rl~ 604 (674)
T PRK01172 581 LARLSSIY-KPEMRRKLEILNIRIK 604 (674)
T ss_pred HHHHHHHh-hHHHHHHHHHHHHHHH
Confidence 44545553 4777666555444443
No 97
>PRK00254 ski2-like helicase; Provisional
Probab=40.41 E-value=82 Score=36.88 Aligned_cols=71 Identities=18% Similarity=0.194 Sum_probs=57.9
Q ss_pred ccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHHHHHhhcCC-HHHHHHHHHHHHhhcCCc
Q 008449 487 PDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGE-TELEAKFEEAVSKIKRDI 557 (565)
Q Consensus 487 ~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn-~~L~~k~e~a~~~IkRDI 557 (565)
+.-.-+.++|.+|.+...|++--++..||+-+.+.+..-++.-+...+..+|. .++...+.+.+..|+=++
T Consensus 569 ~k~~~ll~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~ 640 (720)
T PRK00254 569 FKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADWLMYSLIELYKLFEPKQEVLDYLETLHLRVKHGV 640 (720)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCC
Confidence 44567899999999999999998999999999999999999999999988884 566666665555555444
No 98
>KOG0201 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=40.06 E-value=31 Score=37.56 Aligned_cols=96 Identities=16% Similarity=0.222 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCcccccccccCCccHHHHHHHHhCCCCHHHHHhhCCC-CCChHHHHHHHHHHHHH
Q 008449 450 ELELLFTQLQDTARRVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPV-FEGSLIRAIRRLEEVLQ 528 (565)
Q Consensus 450 ~L~~~~~~l~~ia~~I~~v~~~~~l~~~~~~~~~~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv-~EGsIVR~irRLdEllr 528 (565)
.|..+-..+.+++++|.-+ .+|.-+.-.+-|...+.-..+.++-+|+.|-+..+.++...+ .|=.|+=. +|
T Consensus 47 ~Le~~~deIediqqei~~L-s~~~~~~it~yygsyl~g~~LwiiMey~~gGsv~~lL~~~~~~~E~~i~~i-------lr 118 (467)
T KOG0201|consen 47 DLEEAEDEIEDIQQEISVL-SQCDSPNITEYYGSYLKGTKLWIIMEYCGGGSVLDLLKSGNILDEFEIAVI-------LR 118 (467)
T ss_pred chhhcchhhHHHHHHHHHH-HhcCcchHHhhhhheeecccHHHHHHHhcCcchhhhhccCCCCccceeeee-------hH
Confidence 4677777788888887644 345553333556677888999999999999999999999876 44222211 22
Q ss_pred HHHHHHhhcCCHHHHHHHHHHHHhhcCCcccccCC
Q 008449 529 QLILAAKSIGETELEAKFEEAVSKIKRDIVFAASL 563 (565)
Q Consensus 529 qv~~Aa~~iGn~~L~~k~e~a~~~IkRDIVfa~SL 563 (565)
++ -...++......|.|||-.|.-|
T Consensus 119 e~----------l~~l~ylH~~~kiHrDIKaanil 143 (467)
T KOG0201|consen 119 EV----------LKGLDYLHSEKKIHRDIKAANIL 143 (467)
T ss_pred HH----------HHHhhhhhhcceeccccccccee
Confidence 22 23345777788999999876543
No 99
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=37.02 E-value=37 Score=24.52 Aligned_cols=31 Identities=16% Similarity=0.157 Sum_probs=22.8
Q ss_pred HHHHHhCCCCHHHHHhhCCCCCChHHHHHHH
Q 008449 492 AVYAWAKGSKFYEIMEITPVFEGSLIRAIRR 522 (565)
Q Consensus 492 vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irR 522 (565)
+..-|..|.|..+|-+.-++...+|-|.|+|
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 4445789999999999999999999999987
No 100
>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=36.71 E-value=90 Score=29.36 Aligned_cols=45 Identities=13% Similarity=0.319 Sum_probs=35.5
Q ss_pred CchHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHHHH
Q 008449 107 AIPDLEKQAKVLEEERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDI 153 (565)
Q Consensus 107 ~~~~~~~~~~~l~~~l~~i~~~~e~~i~~Y~~l~~~l~~~~~~~~~~ 153 (565)
....+++++.++++++.+++..+ +...|.++++++.++.+++.+.
T Consensus 41 ~~~~l~~Ei~~l~~E~~~iS~qD--eFAkwaKl~Rk~~kl~~el~~~ 85 (161)
T PF04420_consen 41 EQRQLRKEILQLKRELNAISAQD--EFAKWAKLNRKLDKLEEELEKL 85 (161)
T ss_dssp HHHHHHHHHHHHHHHHTTS-TTT--SHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCcHH--HHHHHHHHHHHHHHHHHHHHHH
Confidence 34567889999999999886554 7889999999999888888753
No 101
>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.
Probab=35.51 E-value=32 Score=40.86 Aligned_cols=27 Identities=19% Similarity=0.054 Sum_probs=21.5
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEE
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILM 48 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~ 48 (565)
.+...|+|.+||.||.|....+.++++
T Consensus 362 aP~esyIQRiGRtgR~G~~~~~~i~vv 388 (844)
T TIGR02621 362 APFESMQQRFGRVNRFGELQACQIAVV 388 (844)
T ss_pred CCHHHHHHHhcccCCCCCCCCceEEEE
Confidence 356889999999999999766655555
No 102
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.26 E-value=48 Score=38.83 Aligned_cols=30 Identities=20% Similarity=0.121 Sum_probs=22.1
Q ss_pred CHHHHHHhhccCCCCCCCCce-----EEEEEccCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERG-----ICILMVDDK 52 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G-----~~ii~~~~~ 52 (565)
++.+|.|+.||.+|++-+..+ ..|.++...
T Consensus 573 S~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~d 607 (732)
T TIGR00603 573 SRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKD 607 (732)
T ss_pred CHHHHHHHhcccccCCCCCccccccceEEEEecCC
Confidence 679999999999999977543 335555544
No 103
>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]
Probab=34.96 E-value=24 Score=38.34 Aligned_cols=45 Identities=29% Similarity=0.518 Sum_probs=31.9
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCCCCccc
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLN 70 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~~~~l~ 70 (565)
+..-|-|=+|||||-|+- ..|-++.... |...+.-++.++.-.+.
T Consensus 335 n~AgYYQESGRAGRDGk~--SyCRLYYsR~-D~~~i~FLi~~e~aklr 379 (641)
T KOG0352|consen 335 NLAGYYQESGRAGRDGKR--SYCRLYYSRQ-DKNALNFLVSGELAKLR 379 (641)
T ss_pred hhHHHHHhccccccCCCc--cceeeeeccc-chHHHHHHHhhHHHHHH
Confidence 457899999999999986 4555555443 56677777777655544
No 104
>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=34.17 E-value=1.1e+02 Score=26.72 Aligned_cols=53 Identities=13% Similarity=0.155 Sum_probs=37.6
Q ss_pred HHHHHHHHcCCCcccccccccCCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 464 RVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 464 ~I~~v~~~~~l~~~~~~~~~~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
.+......+|+... .+.++..++. ..|.+.++|++...+.-.++.|.+.+|++
T Consensus 16 ~~~~~l~~~~lt~~--------q~~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 16 FFRPILAQHGLTEQ--------QWRILRILAE-QGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred HHHHHHHHcCCCHH--------HHHHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 34444455666432 2345555543 56779999999999999999999999986
No 105
>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]
Probab=33.37 E-value=89 Score=34.67 Aligned_cols=37 Identities=27% Similarity=0.394 Sum_probs=27.6
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhc
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLK 63 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~ 63 (565)
.+.+|+++.||.||-|. .|.++++..+. +.-+-+++.
T Consensus 410 d~~~YIHRvGRTaR~gk--~G~alL~l~p~--El~Flr~LK 446 (543)
T KOG0342|consen 410 DPEQYIHRVGRTAREGK--EGKALLLLAPW--ELGFLRYLK 446 (543)
T ss_pred CHHHHHHHhccccccCC--CceEEEEeChh--HHHHHHHHh
Confidence 57899999999999665 58888888765 333444444
No 106
>TIGR03714 secA2 accessory Sec system translocase SecA2. Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.
Probab=33.27 E-value=38 Score=39.82 Aligned_cols=26 Identities=31% Similarity=0.480 Sum_probs=21.4
Q ss_pred HHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 25 GEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 25 ~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
.+..|..|||||.|-- |.++.+++..
T Consensus 512 rid~qr~GRtGRqG~~--G~s~~~is~e 537 (762)
T TIGR03714 512 RVDLQLRGRSGRQGDP--GSSQFFVSLE 537 (762)
T ss_pred HHHHHhhhcccCCCCc--eeEEEEEccc
Confidence 4669999999999864 9888888753
No 107
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=33.21 E-value=30 Score=40.66 Aligned_cols=30 Identities=30% Similarity=0.464 Sum_probs=26.6
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
+..-..|++||.+|+|.+..|.+++.....
T Consensus 521 PidSLIQR~GRv~R~g~~~~~~~~v~~~~~ 550 (733)
T COG1203 521 PIDSLIQRAGRVNRHGKKENGKIYVYNDEE 550 (733)
T ss_pred CHHHHHHHHHHHhhcccccCCceeEeeccc
Confidence 558899999999999999999999988665
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=32.14 E-value=3.1e+02 Score=23.27 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHhchh-cchhHHHHHHHHHHHhHh
Q 008449 351 LTAKIKSIKRQMRSST-ELAFKDELKARKRVLRRL 384 (565)
Q Consensus 351 l~~~~~~l~~~l~~~~-~l~~~~e~~~~~~VL~~L 384 (565)
+..|+++|.+-+.... +..-.+||..|++||+.+
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 5677888888777633 445779999999999864
No 109
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=30.58 E-value=1.2e+02 Score=27.47 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=30.2
Q ss_pred HHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 489 IMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 489 Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
++..++..-.|.+.++|.+.+.+..+++-|++.||++
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 4555544335689999999999999999999999986
No 110
>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]
Probab=30.46 E-value=54 Score=36.68 Aligned_cols=51 Identities=27% Similarity=0.354 Sum_probs=34.6
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCCCCHH---HHHHHhc---CCCCcccccCCCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDKMEPS---TAKMMLK---GSADSLNSAFHLS 76 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~---~~~~~~~---~~~~~l~S~f~~~ 76 (565)
+.-.|++..||.||.|.- |++|-+.... +.. +++.++. -...|.+++++..
T Consensus 597 sieDYtHRIGRTgRAGk~--GtaiSflt~~-dt~v~ydLkq~l~es~~s~~P~Ela~h~~ 653 (673)
T KOG0333|consen 597 SIEDYTHRIGRTGRAGKS--GTAISFLTPA-DTAVFYDLKQALRESVKSHCPPELANHPD 653 (673)
T ss_pred hHHHHHHHhccccccccC--ceeEEEeccc-hhHHHHHHHHHHHHhhhccCChhhccChh
Confidence 457899999999999975 9998888765 222 3333333 2346777776654
No 111
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=30.34 E-value=97 Score=28.09 Aligned_cols=62 Identities=16% Similarity=0.237 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHhHhCCccC-----CC-----ccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcc
Q 008449 371 KDELKARKRVLRRLGYATS-----DD-----VVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCF 435 (565)
Q Consensus 371 ~~e~~~~~~VL~~Lgyid~-----~~-----~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~f 435 (565)
.+..-+.++-|.+.|||.- |. .+|.||+-+.+-- . -.+.+-+.+.+|.+++++|++++...+
T Consensus 68 ~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~--~-~~~~~~~~~~l~~~ls~ee~~~l~~~L 139 (144)
T PRK11512 68 LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQC--H-QLVGQDLHQELTKNLTADEVATLEHLL 139 (144)
T ss_pred HHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHH--H-HHHHHHHHHHHHccCCHHHHHHHHHHH
Confidence 4567788999999999963 22 4899999765331 0 122345667789999999999886543
No 112
>smart00351 PAX Paired Box domain.
Probab=29.18 E-value=70 Score=28.63 Aligned_cols=35 Identities=20% Similarity=0.159 Sum_probs=30.4
Q ss_pred HHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 491 EAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 491 ~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
.+|..+..|.+..+|++..++...++.||++|-.+
T Consensus 25 riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 25 RIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44556679999999999999999999999999755
No 113
>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=29.14 E-value=59 Score=23.46 Aligned_cols=33 Identities=24% Similarity=0.240 Sum_probs=25.7
Q ss_pred cHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHH
Q 008449 488 DIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAI 520 (565)
Q Consensus 488 ~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~i 520 (565)
..-+++..++.|+|-.+|++.++|.-.+|=|.+
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 466788889999999999999999988887765
No 114
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=28.31 E-value=1.1e+02 Score=22.85 Aligned_cols=43 Identities=9% Similarity=0.114 Sum_probs=39.4
Q ss_pred cHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHH
Q 008449 488 DIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQL 530 (565)
Q Consensus 488 ~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv 530 (565)
.++-+...|..|-++.++-..-+|.+.++-|++....++|.+.
T Consensus 8 ~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 8 QLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 5777888899999999999999999999999999999998764
No 115
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=26.76 E-value=77 Score=36.18 Aligned_cols=40 Identities=28% Similarity=0.397 Sum_probs=28.1
Q ss_pred ecCHHHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhc
Q 008449 21 WISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLK 63 (565)
Q Consensus 21 ~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~ 63 (565)
+-+.-.|-|=+|||||-|.- -.+|++..+. |......++.
T Consensus 308 P~s~EsYyQE~GRAGRDG~~--a~aill~~~~-D~~~~~~~i~ 347 (590)
T COG0514 308 PGSIESYYQETGRAGRDGLP--AEAILLYSPE-DIRWQRYLIE 347 (590)
T ss_pred CCCHHHHHHHHhhccCCCCc--ceEEEeeccc-cHHHHHHHHH
Confidence 34778999999999999985 6677777654 3343444443
No 116
>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]
Probab=26.64 E-value=55 Score=39.47 Aligned_cols=38 Identities=32% Similarity=0.581 Sum_probs=31.3
Q ss_pred HHHHHhhccCCCCCCCCceEEEEEccCCCCHHHHHHHhcCC
Q 008449 25 GEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGS 65 (565)
Q Consensus 25 ~E~~QM~GRAGRrg~D~~G~~ii~~~~~~~~~~~~~~~~~~ 65 (565)
-.|-|=+|||||-|.. -.|+++.+.. +-..+..++...
T Consensus 567 E~YYQE~GRAGRDG~~--s~C~l~y~~~-D~~~l~~ll~s~ 604 (941)
T KOG0351|consen 567 EGYYQEAGRAGRDGLP--SSCVLLYGYA-DISELRRLLTSG 604 (941)
T ss_pred HHHHHhccccCcCCCc--ceeEEecchh-HHHHHHHHHHcc
Confidence 5799999999999997 6788888776 677777877755
No 117
>KOG0346 consensus RNA helicase [RNA processing and modification]
Probab=26.29 E-value=1.7e+02 Score=32.28 Aligned_cols=29 Identities=28% Similarity=0.447 Sum_probs=23.7
Q ss_pred cCHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 22 ISSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
=++.-|++++||.+|.|. .|+++-++.+.
T Consensus 382 ~t~~sYIHRvGRTaRg~n--~GtalSfv~P~ 410 (569)
T KOG0346|consen 382 ETVTSYIHRVGRTARGNN--KGTALSFVSPK 410 (569)
T ss_pred CchHHHHHhccccccCCC--CCceEEEecch
Confidence 367899999999999886 48888877664
No 118
>COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]
Probab=26.06 E-value=1.2e+02 Score=33.83 Aligned_cols=126 Identities=16% Similarity=0.193 Sum_probs=82.3
Q ss_pred hCCccCC-CccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHHHHHhhhcceeeccCCC-CCCCcHHHHH-------H
Q 008449 384 LGYATSD-DVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQEKLQD-ASKPREELEL-------L 454 (565)
Q Consensus 384 Lgyid~~-~~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~eiaAlLS~fV~qek~~~-~~~l~~~L~~-------~ 454 (565)
+|++..+ |.+..+|+-. .|+ +|.+..++==+.|||.-.=. ..+..+.+.- .
T Consensus 51 ~G~~~P~~GeI~v~G~~v-~~~-------------------sP~dA~~~GIGMVhQHF~Lv~~lTV~ENiiLg~e~~~~~ 110 (501)
T COG3845 51 FGLYQPDSGEIRVDGKEV-RIK-------------------SPRDAIRLGIGMVHQHFMLVPTLTVAENIILGLEPSKGG 110 (501)
T ss_pred hCcccCCcceEEECCEEe-ccC-------------------CHHHHHHcCCcEEeeccccccccchhhhhhhcCcccccc
Confidence 3555443 5666677654 344 48888888888999865421 1222233322 2
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcccccccccCCccH---HHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHHH
Q 008449 455 FTQLQDTARRVAKVQLECKVQIDVEGFVNSFRPDI---MEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLI 531 (565)
Q Consensus 455 ~~~l~~ia~~I~~v~~~~~l~~~~~~~~~~~~~~L---m~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv~ 531 (565)
+-...+..++|.++++++|++++++.++..+..|. +|++-.-.+|..+-= +.|=+=|-+=+-.++|+.=++
T Consensus 111 ~~~~~~~~~~i~~l~~~yGl~vdp~~~V~dLsVG~qQRVEIlKaLyr~a~iLI------LDEPTaVLTP~E~~~lf~~l~ 184 (501)
T COG3845 111 LIDRRQARARIKELSERYGLPVDPDAKVADLSVGEQQRVEILKALYRGARLLI------LDEPTAVLTPQEADELFEILR 184 (501)
T ss_pred ccCHHHHHHHHHHHHHHhCCCCCccceeecCCcchhHHHHHHHHHhcCCCEEE------EcCCcccCCHHHHHHHHHHHH
Confidence 33667888999999999999999999999988876 788888888875532 344455555555555555555
Q ss_pred HHHh
Q 008449 532 LAAK 535 (565)
Q Consensus 532 ~Aa~ 535 (565)
+.++
T Consensus 185 ~l~~ 188 (501)
T COG3845 185 RLAA 188 (501)
T ss_pred HHHH
Confidence 4443
No 119
>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=25.95 E-value=88 Score=23.77 Aligned_cols=30 Identities=20% Similarity=0.254 Sum_probs=25.5
Q ss_pred HhCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 496 WAKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 496 WA~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
|..+.++.+|++..++..+++-|.+.+|.+
T Consensus 17 ~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 17 LEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred HHCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 445599999999999999999888888754
No 120
>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=25.91 E-value=1.9e+02 Score=24.15 Aligned_cols=45 Identities=27% Similarity=0.394 Sum_probs=36.3
Q ss_pred CCCCHHHHHhhCC-CCCChHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 008449 498 KGSKFYEIMEITP-VFEGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAVS 551 (565)
Q Consensus 498 ~G~~F~eI~~~Td-v~EGsIVR~irRLdEllrqv~~Aa~~iGn~~L~~k~e~a~~ 551 (565)
-|.|+++|-+.-+ ..--+++..++|+++.+.+ |+.+...++....
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 3999999999988 9999999999999998764 5666666655443
No 121
>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=25.58 E-value=43 Score=34.03 Aligned_cols=28 Identities=39% Similarity=0.717 Sum_probs=23.8
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
.+..|+...|||||.|. .|.+|.+....
T Consensus 328 ~~DtYlHrv~rAgrfGt--kglaitfvs~e 355 (387)
T KOG0329|consen 328 DSDTYLHRVARAGRFGT--KGLAITFVSDE 355 (387)
T ss_pred CchHHHHHhhhhhcccc--ccceeehhcch
Confidence 56789999999999995 59999888754
No 122
>COG5570 Uncharacterized small protein [Function unknown]
Probab=23.92 E-value=2.6e+02 Score=21.28 Aligned_cols=20 Identities=25% Similarity=0.307 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 008449 342 LKVLHMKQELTAKIKSIKRQ 361 (565)
Q Consensus 342 ~~~~~~~~~l~~~~~~l~~~ 361 (565)
..+-+++..|+++|+.|+.+
T Consensus 36 ~eLKRrKL~lKeeIEkLka~ 55 (57)
T COG5570 36 RELKRRKLRLKEEIEKLKAQ 55 (57)
T ss_pred HHHHHHHHHHHHHHHHHhcc
Confidence 44556777888888888765
No 123
>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=23.79 E-value=1.1e+02 Score=26.02 Aligned_cols=34 Identities=24% Similarity=0.383 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhchhcchhHHHHHHHHHHHhHh
Q 008449 351 LTAKIKSIKRQMRSSTELAFKDELKARKRVLRRL 384 (565)
Q Consensus 351 l~~~~~~l~~~l~~~~~l~~~~e~~~~~~VL~~L 384 (565)
++.|+++|.+-+...-+..-.++|..|++||+.+
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 5677888888877655555779999999999875
No 124
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=23.59 E-value=84 Score=38.86 Aligned_cols=18 Identities=44% Similarity=0.239 Sum_probs=15.6
Q ss_pred cCHHHHHHhhccCCCCCC
Q 008449 22 ISSGEYIQMSGRAGRRGI 39 (565)
Q Consensus 22 l~~~E~~QM~GRAGRrg~ 39 (565)
-+...|.||.||+.|.--
T Consensus 785 kS~~lf~QmIGRgtR~~~ 802 (1123)
T PRK11448 785 RSRILYEQMLGRATRLCP 802 (1123)
T ss_pred CCHHHHHHHHhhhccCCc
Confidence 378999999999999755
No 125
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=23.57 E-value=4.2e+02 Score=24.12 Aligned_cols=77 Identities=17% Similarity=0.181 Sum_probs=46.6
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhchhcchhHHHHHHHHHHHhHhCC
Q 008449 307 GIRSSSYQKLVRRIEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRSSTELAFKDELKARKRVLRRLGY 386 (565)
Q Consensus 307 ~i~~~~~~~~~~~~~~l~~~l~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~l~~~~e~~~~~~VL~~Lgy 386 (565)
+...+++..+-++...|.++=++..|.- -...+.-.+-.++..|.++++.|+.+++... .-.+-|+.+..-|..+++
T Consensus 43 G~~reEVvrlKQrRRTLKNRGYA~sCR~-KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~--~E~da~k~k~e~l~~~~~ 119 (135)
T KOG4196|consen 43 GLSREEVVRLKQRRRTLKNRGYAQSCRV-KRVQQKHELEKEKAELQQQVEKLKEENSRLR--RELDAYKSKYEALQNSAV 119 (135)
T ss_pred CCCHHHHHHHHHHHHHHhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHhhhh
Confidence 3345677777788888887766665531 1122223333456666677777776665521 134667888888888777
No 126
>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=23.38 E-value=5.7e+02 Score=23.92 Aligned_cols=51 Identities=14% Similarity=0.194 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 008449 312 SYQKLVRRIEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRS 364 (565)
Q Consensus 312 ~~~~~~~~~~~l~~~l~~~p~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~ 364 (565)
+..++..++.++.+++.+- ..-.+|.+..++-++-.++++|+++++.+++.
T Consensus 41 ~~~~l~~Ei~~l~~E~~~i--S~qDeFAkwaKl~Rk~~kl~~el~~~~~~~~~ 91 (161)
T PF04420_consen 41 EQRQLRKEILQLKRELNAI--SAQDEFAKWAKLNRKLDKLEEELEKLNKSLSS 91 (161)
T ss_dssp HHHHHHHHHHHHHHHHTTS---TTTSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcC--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666777777777543 22346776677667777777777777777665
No 127
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=23.36 E-value=2e+02 Score=27.82 Aligned_cols=29 Identities=24% Similarity=0.337 Sum_probs=26.6
Q ss_pred hCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 497 AKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 497 A~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
..|.+-++|++.+.+.-+++.|.+.||++
T Consensus 57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~ 85 (185)
T PRK13777 57 LKGASISEIAKFGVMHVSTAFNFSKKLEE 85 (185)
T ss_pred CCCcCHHHHHHHHCCCHhhHHHHHHHHHH
Confidence 46889999999999999999999999986
No 128
>PF04325 DUF465: Protein of unknown function (DUF465); InterPro: IPR007420 Family members are found in small bacterial proteins, and also in the heavy chains of eukaryotic myosin and kinesin, C-terminal of the motor domain. Members of this family may form coiled coil structures.; PDB: 1ZHC_A.
Probab=23.27 E-value=3.1e+02 Score=20.19 Aligned_cols=43 Identities=21% Similarity=0.212 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHh---hCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Q 008449 315 KLVRRIEALESLFD---KHEISKSPLIEQKLKVLHMKQELTAKIKSIKR 360 (565)
Q Consensus 315 ~~~~~~~~l~~~l~---~~p~~~~~~~~~~~~~~~~~~~l~~~~~~l~~ 360 (565)
.+..+.+.|...+. .+|- +.-.+.-.+-.+|-.|+.+|..+..
T Consensus 3 ~L~~~h~~Ld~~I~~~e~~~~---~~d~~l~~LKk~kL~LKDei~~ll~ 48 (49)
T PF04325_consen 3 RLFEEHHELDKEIHRLEKRPE---PDDEELERLKKEKLRLKDEIYRLLR 48 (49)
T ss_dssp HHHHHHHHHHHHHHHHHTT-----S-HHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHhCCC---CCHHHHHHHHHHHHHHHHHHHHHHc
Confidence 34444455554443 3432 3333333344456666666665543
No 129
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.97 E-value=70 Score=23.72 Aligned_cols=25 Identities=28% Similarity=0.243 Sum_probs=23.0
Q ss_pred CHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 501 KFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 501 ~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
|-.+|++.+++.+-+|.|.+++|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6789999999999999999999987
No 130
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=22.91 E-value=2.3e+02 Score=30.94 Aligned_cols=68 Identities=24% Similarity=0.313 Sum_probs=43.1
Q ss_pred CCccEEEEcCCeeecCCc---ceecCHHHHHHhhc-------cCCCCCCCCceEEEEEccCCCCHHHHHHH-hcCCCCcc
Q 008449 1 MPAKTVVFTNVRKFDGDK---FRWISSGEYIQMSG-------RAGRRGIDERGICILMVDDKMEPSTAKMM-LKGSADSL 69 (565)
Q Consensus 1 mPAr~Vv~~~~~k~dg~~---~r~l~~~E~~QM~G-------RAGRrg~D~~G~~ii~~~~~~~~~~~~~~-~~~~~~~l 69 (565)
.|.+||||-+..-=.|.. .+.|+.+||+|--- +.|-.|.|..| ..++++..+-+ +.-+|+.-
T Consensus 307 VpFHtviFP~s~lgt~en~t~v~~l~aTeYLnyE~gKFSKSrgvGvFG~~aqd-------~gi~~~vWRyYLl~~RPEss 379 (567)
T KOG1247|consen 307 VPFHTVIFPCSQLGTEENYTVVHHLSATEYLNYEDGKFSKSRGVGVFGNDAQD-------TGIPASVWRYYLLYIRPESS 379 (567)
T ss_pred CcceeeecchhhhcCCCCchhheeechhhhhccccCccccccccccccccccc-------CCCCHHHHHHHHhhccCccc
Confidence 488999999865333433 24589999999643 55555555333 23456655444 45677777
Q ss_pred cccCCC
Q 008449 70 NSAFHL 75 (565)
Q Consensus 70 ~S~f~~ 75 (565)
.|.|.-
T Consensus 380 Ds~Fsw 385 (567)
T KOG1247|consen 380 DSAFSW 385 (567)
T ss_pred CCcCcH
Confidence 888853
No 131
>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=22.72 E-value=68 Score=24.20 Aligned_cols=30 Identities=23% Similarity=0.309 Sum_probs=25.7
Q ss_pred HhCC--CCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 496 WAKG--SKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 496 WA~G--~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
+..| .+..+|++.+.+...++-|.+++|++
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 3455 79999999999999999999999986
No 132
>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=22.69 E-value=2.4e+02 Score=22.42 Aligned_cols=42 Identities=19% Similarity=0.387 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHhchhcchhHHHHHHHHHHHh-HhCCccCCCcc
Q 008449 347 MKQELTAKIKSIKRQMRSSTELAFKDELKARKRVLR-RLGYATSDDVV 393 (565)
Q Consensus 347 ~~~~l~~~~~~l~~~l~~~~~l~~~~e~~~~~~VL~-~Lgyid~~~~v 393 (565)
+..+++.+.++|+.+++...+ .|+|- -++-| +|||+-++++|
T Consensus 32 ~i~~l~~e~~~L~~ei~~l~~---~~~~i--e~~AR~~lgm~~~~E~v 74 (80)
T PF04977_consen 32 EIEELKKENEELKEEIERLKN---DPDYI--EKVAREKLGMVKPGEIV 74 (80)
T ss_pred HHHHHHHHHHHHHHHHHHhcC---CHHHH--HHHHHHHcCCcCCCCEE
Confidence 344556666666666655311 23333 34444 89999877654
No 133
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.68 E-value=86 Score=36.44 Aligned_cols=24 Identities=8% Similarity=0.173 Sum_probs=19.2
Q ss_pred HHHHHHhhccCCCCCCCCceEEEEEc
Q 008449 24 SGEYIQMSGRAGRRGIDERGICILMV 49 (565)
Q Consensus 24 ~~E~~QM~GRAGRrg~D~~G~~ii~~ 49 (565)
-.-++|-+|||||.+. .|.|+|..
T Consensus 513 ~qll~qvagragr~~~--~G~V~iq~ 536 (665)
T PRK14873 513 LRRWMAAAALVRPRAD--GGQVVVVA 536 (665)
T ss_pred HHHHHHHHHhhcCCCC--CCEEEEEe
Confidence 3556899999999764 49999975
No 134
>PRK11415 hypothetical protein; Provisional
Probab=22.63 E-value=2.6e+02 Score=22.72 Aligned_cols=56 Identities=13% Similarity=0.188 Sum_probs=33.1
Q ss_pred ccCCCChHHHHHHHHHHHHHHHHhhCCCCCCCcHHHH-HHHHHHHHHHHHHHHHHHH
Q 008449 305 NMGIRSSSYQKLVRRIEALESLFDKHEISKSPLIEQK-LKVLHMKQELTAKIKSIKR 360 (565)
Q Consensus 305 ~~~i~~~~~~~~~~~~~~l~~~l~~~p~~~~~~~~~~-~~~~~~~~~l~~~~~~l~~ 360 (565)
.++-.|..|..+..+.+.|..++...-....|--+.+ -.+-.+|..|+.+|.++-.
T Consensus 11 ~Lk~~D~~F~~L~~~h~~Ld~~I~~lE~~~~~~~d~~i~~LKk~KL~LKDeI~~~L~ 67 (74)
T PRK11415 11 RLKNENPRFMSLFDKHNKLDHEIARKEGSDGRGYNAEVVRMKKQKLQLKDEMLKILQ 67 (74)
T ss_pred HHHhcCHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHHHHHHHH
Confidence 3445788999999999999888854333222211223 2333455566666655543
No 135
>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=22.48 E-value=1e+02 Score=23.29 Aligned_cols=44 Identities=25% Similarity=0.216 Sum_probs=35.0
Q ss_pred cCCccHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHHHH
Q 008449 484 SFRPDIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVL 527 (565)
Q Consensus 484 ~~~~~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEll 527 (565)
.|.+.=.+|+..|+.|.+-.+|.+.-++.+.+|-..++++-.-+
T Consensus 3 ~LT~~E~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 35556678999999999999999999999999988877765443
No 136
>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=22.42 E-value=1.2e+02 Score=37.81 Aligned_cols=62 Identities=18% Similarity=0.329 Sum_probs=44.1
Q ss_pred HHHHHHHHHhHhCCccCCC---ccchhhhhhhhhccCchhHHHHHHHhCC-CCCCChHHHHHhhhcceee
Q 008449 373 ELKARKRVLRRLGYATSDD---VVELKGKVACEISSAEELTLTELIFNGV-LKDVKVEEMVSLLSCFVWQ 438 (565)
Q Consensus 373 e~~~~~~VL~~Lgyid~~~---~vt~KGrvAceI~s~dELllTEllf~g~-f~~L~p~eiaAlLS~fV~q 438 (565)
.+.+=+..|..||.||+++ .+|.-||..+++-- | --++-||..+. |.-+ .+++.+.|++-.+
T Consensus 450 ~i~~A~~~L~~LGAld~~~~~~~LT~lGr~ma~LPl-d-PrlarmLl~a~~~gcl--~e~l~IaA~Ls~~ 515 (1283)
T TIGR01967 450 AIRDGFRLLEELGALDDDEAEPQLTPIGRQLAQLPV-D-PRLARMLLEAHRLGCL--QEVLIIASALSIQ 515 (1283)
T ss_pred HHHHHHHHHHHCCCCCCCCCCccccHHHHHHhhcCC-C-hHHHHHHHHhhhcCCH--HHHHHHHHHHcCC
Confidence 4677788999999999987 79999999999974 4 45566666554 4433 3455555555443
No 137
>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]
Probab=22.35 E-value=80 Score=37.87 Aligned_cols=30 Identities=37% Similarity=0.697 Sum_probs=25.0
Q ss_pred ceecCHHHHHHhhccCCCCCCCCceEEEEEccC
Q 008449 19 FRWISSGEYIQMSGRAGRRGIDERGICILMVDD 51 (565)
Q Consensus 19 ~r~l~~~E~~QM~GRAGRrg~D~~G~~ii~~~~ 51 (565)
-.|++...-.|+.|||||- ..|.|+=+...
T Consensus 514 ~~wvSkAna~QR~GRAGRv---~~G~cy~L~~~ 543 (924)
T KOG0920|consen 514 LSWVSKANAKQRRGRAGRV---RPGICYHLYTR 543 (924)
T ss_pred eeeccccchHHhcccccCc---cCCeeEEeech
Confidence 3568999999999999998 56999877654
No 138
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=21.98 E-value=1.5e+02 Score=26.73 Aligned_cols=37 Identities=22% Similarity=0.219 Sum_probs=30.4
Q ss_pred cHHHHHHHHhCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 488 DIMEAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 488 ~Lm~vVy~WA~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
.++..++ ...|.+.++|.+...+..+++.|.+.||++
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 3454443 256689999999999999999999999986
No 139
>PF12917 HD_2: HD containing hydrolase-like enzyme ; PDB: 3MZO_B.
Probab=21.51 E-value=5.4e+02 Score=25.52 Aligned_cols=114 Identities=19% Similarity=0.313 Sum_probs=63.7
Q ss_pred hCCCCCCChHHHHHhhhcceeecc-CCCCCCC----cHHHHHHHHHHHHHHHHHHHHHHHcCCCcccccccc-cCCccHH
Q 008449 417 NGVLKDVKVEEMVSLLSCFVWQEK-LQDASKP----REELELLFTQLQDTARRVAKVQLECKVQIDVEGFVN-SFRPDIM 490 (565)
Q Consensus 417 ~g~f~~L~p~eiaAlLS~fV~qek-~~~~~~l----~~~L~~~~~~l~~ia~~I~~v~~~~~l~~~~~~~~~-~~~~~Lm 490 (565)
+...++.++..++...-+=-+-|. ++|.+++ +|+|.+.+.++.+.... +|+. .+...+-
T Consensus 49 e~~G~~vd~~~lyekAL~HD~~E~FtGDI~TPVKy~tPelr~~~~~VE~~m~~---------------~~i~~~iP~e~q 113 (215)
T PF12917_consen 49 EQFGNEVDWKELYEKALNHDYPEIFTGDIKTPVKYATPELREMLAQVEEEMTE---------------NFIKKEIPEEFQ 113 (215)
T ss_dssp HHTT----HHHHHHHHHHTTGGGGTS----S-SSSS-HHHHHHHHHHHHHHHH---------------HHHHHHS-GGGH
T ss_pred HHhCCccCHHHHHHHHhccccHHHHcCCCCCcccccCHHHHHHHHHHHHHHHH---------------HHHHhhCCHHHH
Confidence 345667888888776555544444 3455543 79999998887765331 1111 1222344
Q ss_pred HHHHHHhCCCCHHHHHhh-CCCCCChHHHHHHHHHHHHHHHHHHHhhcCCHH--HHHHHHHHHHhhcC
Q 008449 491 EAVYAWAKGSKFYEIMEI-TPVFEGSLIRAIRRLEEVLQQLILAAKSIGETE--LEAKFEEAVSKIKR 555 (565)
Q Consensus 491 ~vVy~WA~G~~F~eI~~~-Tdv~EGsIVR~irRLdEllrqv~~Aa~~iGn~~--L~~k~e~a~~~IkR 555 (565)
++-..|. .+. .+--||-||+..-.++=++.-....-+ ||++ ..+.+.++.+.|+.
T Consensus 114 ~~Y~~~l--------~E~KDdt~EG~Iv~~ADkidal~e~~~Ei~~--GN~E~~F~e~y~e~l~~i~~ 171 (215)
T PF12917_consen 114 EAYRRRL--------KEGKDDTLEGQIVKAADKIDALYECFGEIQK--GNPEKVFKEIYRESLEKIKK 171 (215)
T ss_dssp HHHHHHH--------S---SSSHHHHHHHHHHHHHHHHHHHHHHHT--T-S-THHHHHHHHHHHHHHT
T ss_pred HHHHHHh--------hcCCcccHHHHHHHHHHHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHHHh
Confidence 4444432 233 357899999998888877776666654 8999 78888888888765
No 140
>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=21.36 E-value=1.3e+02 Score=28.15 Aligned_cols=46 Identities=24% Similarity=0.214 Sum_probs=35.8
Q ss_pred CCccHHHHHHH-HhCCCCHHHHHhhCCCCCChHHHHHHHHHHHHHHH
Q 008449 485 FRPDIMEAVYA-WAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQL 530 (565)
Q Consensus 485 ~~~~Lm~vVy~-WA~G~~F~eI~~~Tdv~EGsIVR~irRLdEllrqv 530 (565)
+++.--+++.. +-.|.|..+|.+..++.+|+|-..+.|.-.-||.+
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 33444444443 55999999999999999999999999988877764
No 141
>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=21.03 E-value=8.4e+02 Score=28.61 Aligned_cols=135 Identities=13% Similarity=0.094 Sum_probs=86.7
Q ss_pred HHHHHHHHHHhHhCCccCCCccchhhhhhhhhccCchhHHHHHHHhCCCCCCChHH---HHHhhhcceee-ccCCCCCCC
Q 008449 372 DELKARKRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEE---MVSLLSCFVWQ-EKLQDASKP 447 (565)
Q Consensus 372 ~e~~~~~~VL~~Lgyid~~~~vt~KGrvAceI~s~dELllTEllf~g~f~~L~p~e---iaAlLS~fV~q-ek~~~~~~l 447 (565)
+.+..-+..|--||-+|..|.+|--||--||.- +|..+--.++-++... -+ +| |||+||+.-.- .+..
T Consensus 652 etL~~aLE~LyaLGALn~~GeLTk~GrrMaEfP-~dPmlsKmi~as~ky~-cs-~EiitiaamlS~~~svfyrpk----- 723 (902)
T KOG0923|consen 652 ETLLKALEQLYALGALNHLGELTKLGRRMAEFP-VDPMLSKMIVASEKYK-CS-EEIITIAAMLSVGASVFYRPK----- 723 (902)
T ss_pred HHHHHHHHHHHHhhccccccchhhhhhhhhhcC-CCHHHHhHHhhhcccc-ch-HHHHHHHHHHhcCchheecch-----
Confidence 456667888899999999999999999999998 4777777777777766 33 45 46667665321 1111
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHcCCCcccccccccCCccHHHHHHHHhCC-CCHHHHHhhCCCCCChHHHHHHHHHHH
Q 008449 448 REELELLFTQLQDTARRVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKG-SKFYEIMEITPVFEGSLIRAIRRLEEV 526 (565)
Q Consensus 448 ~~~L~~~~~~l~~ia~~I~~v~~~~~l~~~~~~~~~~~~~~Lm~vVy~WA~G-~~F~eI~~~Tdv~EGsIVR~irRLdEl 526 (565)
. +. ++.. -..-....... =+-.++.|--.|..- .+++-++++ +.-.|++.|.-++
T Consensus 724 -~-------~~--v~ad----~a~~~f~~~~g-----Dhi~~L~vyn~w~es~~s~~wC~e~-----~iq~~sm~rardi 779 (902)
T KOG0923|consen 724 -D-------KQ--VHAD----NARKNFEEPVG-----DHIVLLNVYNQWKESKYSTQWCYEN-----FIQYRSMKRARDI 779 (902)
T ss_pred -h-------hh--hhhh----hhhhccCCCCc-----chhhhhHHHHHHhhcchhhHHHHHh-----hhhHHHHHHHHHH
Confidence 1 00 0100 00111222222 234578888889654 466666665 5668999999999
Q ss_pred HHHHHHHHhhcC
Q 008449 527 LQQLILAAKSIG 538 (565)
Q Consensus 527 lrqv~~Aa~~iG 538 (565)
+.|+-....-++
T Consensus 780 r~qL~gll~~v~ 791 (902)
T KOG0923|consen 780 RDQLEGLLERVE 791 (902)
T ss_pred HHHHHHHhhhcc
Confidence 999988765443
No 142
>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=20.43 E-value=1.5e+02 Score=21.75 Aligned_cols=30 Identities=30% Similarity=0.504 Sum_probs=22.0
Q ss_pred HhCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 496 WAKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 496 WA~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
--.|.|+.||.+..++.++.+=+.+.|--.
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 469999999999999999999888877543
No 143
>PRK13104 secA preprotein translocase subunit SecA; Reviewed
Probab=20.33 E-value=87 Score=37.50 Aligned_cols=22 Identities=36% Similarity=0.530 Sum_probs=16.4
Q ss_pred HHHhhccCCCCCCCCceEEEEEcc
Q 008449 27 YIQMSGRAGRRGIDERGICILMVD 50 (565)
Q Consensus 27 ~~QM~GRAGRrg~D~~G~~ii~~~ 50 (565)
=.|..|||||.|-- |.+-++.+
T Consensus 564 D~QLrGRaGRQGDP--Gss~f~lS 585 (896)
T PRK13104 564 DNQLRGRAGRQGDP--GSSRFYLS 585 (896)
T ss_pred HHHhccccccCCCC--CceEEEEE
Confidence 46999999999965 66655554
No 144
>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]
Probab=20.29 E-value=1e+02 Score=31.99 Aligned_cols=28 Identities=36% Similarity=0.616 Sum_probs=23.7
Q ss_pred CHHHHHHhhccCCCCCCCCceEEEEEccCC
Q 008449 23 SSGEYIQMSGRAGRRGIDERGICILMVDDK 52 (565)
Q Consensus 23 ~~~E~~QM~GRAGRrg~D~~G~~ii~~~~~ 52 (565)
..--|+++.||+||.|- .|.+|=+..+.
T Consensus 346 nre~YIHRIGRSGRFGR--kGvainFVk~~ 373 (400)
T KOG0328|consen 346 NRELYIHRIGRSGRFGR--KGVAINFVKSD 373 (400)
T ss_pred cHHHHhhhhccccccCC--cceEEEEecHH
Confidence 45789999999999996 59999888764
No 145
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.29 E-value=1.5e+02 Score=21.71 Aligned_cols=29 Identities=17% Similarity=0.252 Sum_probs=25.9
Q ss_pred hCCCCHHHHHhhCCCCCChHHHHHHHHHH
Q 008449 497 AKGSKFYEIMEITPVFEGSLIRAIRRLEE 525 (565)
Q Consensus 497 A~G~~F~eI~~~Tdv~EGsIVR~irRLdE 525 (565)
....++.+|.+..++..+++-+.+++|.+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56789999999999999999999988876
No 146
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=20.18 E-value=3.1e+02 Score=23.83 Aligned_cols=39 Identities=13% Similarity=0.182 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHhchhcchhHHHHHHHHHHHhHhCCccCCCc
Q 008449 350 ELTAKIKSIKRQMRSSTELAFKDELKARKRVLRRLGYATSDDV 392 (565)
Q Consensus 350 ~l~~~~~~l~~~l~~~~~l~~~~e~~~~~~VL~~Lgyid~~~~ 392 (565)
+++.+.+.|+.++...++- ++|-..+ .=++|||+.++.+
T Consensus 45 ~l~~~n~~L~~eI~~L~~~---~dyiEe~-AR~~Lg~vk~gEi 83 (105)
T PRK00888 45 KLKARNDQLFAEIDDLKGG---QEAIEER-ARNELGMVKPGET 83 (105)
T ss_pred HHHHHHHHHHHHHHHhhCc---HHHHHHH-HHHHcCCCCCCCE
Confidence 4455555555555442221 1222211 2246999988765
Done!