Query psy17736
Match_columns 99
No_of_seqs 117 out of 295
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 21:38:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17736.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17736hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1434|consensus 99.4 4.9E-14 1.1E-18 115.2 3.9 46 2-47 211-256 (335)
2 PF08423 Rad51: Rad51; InterP 99.2 8.2E-12 1.8E-16 95.8 4.7 46 2-47 133-178 (256)
3 PLN03187 meiotic recombination 99.1 8.4E-11 1.8E-15 95.2 4.5 46 2-47 221-266 (344)
4 PLN03186 DNA repair protein RA 99.1 1.4E-10 3E-15 93.6 4.8 46 2-47 218-263 (342)
5 PTZ00035 Rad51 protein; Provis 99.1 1.4E-10 3E-15 92.7 4.7 46 2-47 213-258 (337)
6 TIGR02238 recomb_DMC1 meiotic 99.1 1.6E-10 3.4E-15 91.7 4.7 46 2-47 191-236 (313)
7 TIGR02239 recomb_RAD51 DNA rep 99.0 2.7E-10 5.8E-15 90.3 5.1 46 2-47 191-236 (316)
8 COG0468 RecA RecA/RadA recombi 99.0 2.7E-10 5.9E-15 90.5 4.1 47 2-48 141-187 (279)
9 TIGR02236 recomb_radA DNA repa 98.9 2.3E-09 5E-14 82.3 4.8 45 3-47 193-237 (310)
10 PRK04301 radA DNA repair and r 98.9 2.6E-09 5.7E-14 83.0 5.0 46 2-47 198-243 (317)
11 cd01123 Rad51_DMC1_radA Rad51_ 98.5 2E-07 4.4E-12 67.5 5.0 46 2-47 115-160 (235)
12 PRK09361 radB DNA repair and r 98.4 4.2E-07 9.1E-12 66.2 5.0 46 2-47 107-152 (225)
13 cd01393 recA_like RecA is a b 98.4 5E-07 1.1E-11 65.1 4.5 46 2-47 114-159 (226)
14 KOG1564|consensus 98.2 1.2E-06 2.6E-11 72.7 4.2 46 2-47 207-253 (351)
15 cd01394 radB RadB. The archaea 98.2 2.4E-06 5.2E-11 61.8 4.9 46 2-47 103-148 (218)
16 TIGR02237 recomb_radB DNA repa 98.2 2.3E-06 5.1E-11 61.3 4.5 44 2-47 97-140 (209)
17 PRK09519 recA DNA recombinatio 98.0 6.1E-06 1.3E-10 74.0 4.2 46 2-47 138-187 (790)
18 KOG1433|consensus 98.0 7.3E-06 1.6E-10 67.0 3.8 46 2-47 200-245 (326)
19 cd00983 recA RecA is a bacter 97.8 2.1E-05 4.6E-10 63.8 4.1 47 2-48 133-183 (325)
20 PRK09354 recA recombinase A; P 97.7 3.7E-05 7.9E-10 63.2 4.3 46 2-47 138-187 (349)
21 TIGR02012 tigrfam_recA protein 97.5 9.6E-05 2.1E-09 59.9 4.1 46 2-47 133-182 (321)
22 PF13481 AAA_25: AAA domain; P 96.3 0.0092 2E-07 41.8 4.6 39 2-47 141-179 (193)
23 cd01122 GP4d_helicase GP4d_hel 95.7 0.019 4E-07 42.8 4.3 42 2-47 140-181 (271)
24 PRK11823 DNA repair protein Ra 95.6 0.015 3.3E-07 48.4 4.1 42 2-47 156-198 (446)
25 TIGR03878 thermo_KaiC_2 KaiC d 95.2 0.02 4.4E-07 43.8 3.2 16 2-17 131-146 (259)
26 TIGR00416 sms DNA repair prote 94.7 0.042 9.1E-07 46.1 4.0 42 2-47 170-212 (454)
27 cd01121 Sms Sms (bacterial rad 94.7 0.045 9.8E-07 44.9 4.1 42 2-47 158-200 (372)
28 cd00984 DnaB_C DnaB helicase C 94.6 0.045 9.8E-07 39.8 3.6 41 2-47 123-163 (242)
29 PRK09302 circadian clock prote 93.5 0.088 1.9E-06 43.6 3.6 37 2-47 363-399 (509)
30 cd01120 RecA-like_NTPases RecA 93.2 0.058 1.3E-06 35.2 1.7 41 2-45 85-125 (165)
31 PRK04328 hypothetical protein; 92.7 0.13 2.9E-06 39.0 3.3 16 2-17 128-143 (249)
32 TIGR03877 thermo_KaiC_1 KaiC d 92.4 0.15 3.3E-06 38.1 3.2 15 2-16 126-140 (237)
33 TIGR00665 DnaB replicative DNA 91.6 0.26 5.7E-06 39.8 3.9 41 2-47 305-345 (434)
34 PRK05973 replicative DNA helic 90.5 0.23 5E-06 38.8 2.6 37 2-47 147-183 (237)
35 TIGR03600 phage_DnaB phage rep 90.2 0.37 8E-06 39.0 3.6 40 2-47 305-344 (421)
36 cd01125 repA Hexameric Replica 89.9 0.49 1.1E-05 35.2 3.8 39 2-47 111-149 (239)
37 PRK05595 replicative DNA helic 89.9 0.49 1.1E-05 39.0 4.2 41 2-47 311-351 (444)
38 PRK08760 replicative DNA helic 89.7 0.44 9.5E-06 40.2 3.8 41 2-47 339-379 (476)
39 PRK05748 replicative DNA helic 89.6 0.47 1E-05 39.0 3.8 42 2-47 314-355 (448)
40 PRK07773 replicative DNA helic 89.3 0.45 9.8E-06 42.8 3.8 41 2-47 327-367 (886)
41 PF00154 RecA: recA bacterial 89.1 0.48 1E-05 38.8 3.5 45 3-47 132-180 (322)
42 TIGR03880 KaiC_arch_3 KaiC dom 88.5 0.77 1.7E-05 33.5 3.9 34 2-39 107-140 (224)
43 PRK05636 replicative DNA helic 87.7 0.73 1.6E-05 39.4 3.9 41 2-47 375-415 (505)
44 PRK08506 replicative DNA helic 87.3 0.77 1.7E-05 38.6 3.8 41 2-47 302-342 (472)
45 cd01124 KaiC KaiC is a circadi 86.6 1.3 2.7E-05 30.6 3.9 16 2-17 95-110 (187)
46 PF03796 DnaB_C: DnaB-like hel 85.4 2 4.2E-05 32.2 4.7 41 2-47 130-170 (259)
47 PRK09165 replicative DNA helic 85.3 1.2 2.5E-05 37.8 3.8 43 2-47 341-383 (497)
48 PRK08840 replicative DNA helic 85.2 1.2 2.6E-05 37.6 3.9 40 3-47 330-369 (464)
49 PHA02542 41 41 helicase; Provi 85.1 1.1 2.3E-05 38.1 3.6 42 3-47 302-344 (473)
50 PF06745 KaiC: KaiC; InterPro 84.6 1.6 3.4E-05 31.8 3.8 13 2-14 115-127 (226)
51 PRK06321 replicative DNA helic 83.6 1.8 3.8E-05 36.8 4.2 43 2-47 336-379 (472)
52 PRK06067 flagellar accessory p 83.3 2.3 4.9E-05 31.3 4.2 14 2-15 120-133 (234)
53 PRK07004 replicative DNA helic 82.9 1.7 3.7E-05 36.5 3.8 40 3-47 325-364 (460)
54 PRK08006 replicative DNA helic 81.4 1.8 4E-05 36.6 3.5 41 2-47 336-376 (471)
55 PRK06904 replicative DNA helic 79.6 2.7 5.8E-05 35.6 3.9 42 2-48 334-375 (472)
56 TIGR03881 KaiC_arch_4 KaiC dom 77.9 2.6 5.5E-05 30.7 2.9 14 3-16 122-135 (229)
57 TIGR02655 circ_KaiC circadian 76.4 2.9 6.3E-05 35.0 3.2 16 2-17 353-368 (484)
58 COG1066 Sms Predicted ATP-depe 75.8 3.1 6.8E-05 36.3 3.3 42 2-47 168-210 (456)
59 KOG4115|consensus 72.5 6.1 0.00013 28.1 3.6 41 3-48 19-59 (97)
60 COG2874 FlaH Predicted ATPases 69.1 5.7 0.00012 32.1 3.2 34 3-45 124-157 (235)
61 PRK06749 replicative DNA helic 68.4 7.6 0.00017 32.4 3.9 40 4-47 301-340 (428)
62 PRK08533 flagellar accessory p 68.2 8.3 0.00018 29.1 3.7 16 2-17 117-132 (230)
63 PF13479 AAA_24: AAA domain 67.4 3.5 7.5E-05 30.5 1.6 17 2-18 68-84 (213)
64 PRK14976 5'-3' exonuclease; Pr 58.0 18 0.0004 28.7 4.1 43 1-46 1-53 (281)
65 PRK09302 circadian clock prote 56.5 16 0.00034 30.5 3.7 15 2-16 130-144 (509)
66 COG0305 DnaB Replicative DNA h 56.2 12 0.00027 32.1 3.1 41 2-47 306-346 (435)
67 smart00475 53EXOc 5'-3' exonuc 50.8 24 0.00052 27.7 3.7 40 4-46 2-47 (259)
68 PF02739 5_3_exonuc_N: 5'-3' e 49.7 30 0.00065 25.4 3.9 41 4-47 2-50 (169)
69 cd00008 53EXOc 5'-3' exonuclea 47.3 31 0.00068 26.4 3.8 43 4-46 2-48 (240)
70 COG3598 RepA RecA-family ATPas 47.2 27 0.00059 30.2 3.8 37 2-45 194-230 (402)
71 TIGR01618 phage_P_loop phage n 46.6 12 0.00027 28.9 1.5 17 2-18 81-97 (220)
72 PRK05800 cobU adenosylcobinami 43.7 41 0.0009 24.4 3.8 17 3-19 77-93 (170)
73 PHA00520 packaging NTPase P4 42.4 35 0.00076 28.9 3.6 42 1-47 182-227 (330)
74 PF07098 DUF1360: Protein of u 42.2 5.2 0.00011 28.3 -1.0 16 4-19 11-26 (105)
75 KOG2859|consensus 39.7 41 0.00088 28.0 3.6 18 3-20 155-172 (293)
76 PRK09482 flap endonuclease-lik 38.7 48 0.001 26.4 3.8 43 4-47 4-46 (256)
77 KOG1359|consensus 37.7 24 0.00052 30.5 2.0 33 1-48 192-224 (417)
78 PF10483 Elong_Iki1: Elongator 35.6 34 0.00073 27.0 2.4 27 4-40 90-116 (280)
79 PF08361 TetR_C_2: MAATS-type 30.5 1.6E+02 0.0034 19.9 4.8 39 12-51 29-67 (121)
80 cd00544 CobU Adenosylcobinamid 29.8 1.2E+02 0.0026 22.1 4.4 18 3-20 74-91 (169)
81 cd06874 PX_KIF16B_SNX23 The ph 27.9 65 0.0014 22.9 2.6 21 25-45 74-94 (127)
82 KOG0132|consensus 27.3 43 0.00094 31.7 2.0 17 4-20 62-78 (894)
83 smart00382 AAA ATPases associa 25.9 33 0.00072 20.7 0.8 17 3-19 79-95 (148)
84 cd01132 F1_ATPase_alpha F1 ATP 25.1 35 0.00076 27.6 0.9 12 5-16 164-175 (274)
85 COG0156 BioF 7-keto-8-aminopel 24.6 61 0.0013 27.3 2.3 31 3-48 172-202 (388)
86 PRK12608 transcription termina 22.3 49 0.0011 28.1 1.3 14 5-18 223-236 (380)
87 PRK04296 thymidine kinase; Pro 21.9 76 0.0017 23.0 2.1 10 2-11 78-87 (190)
88 PF00006 ATP-synt_ab: ATP synt 21.3 59 0.0013 24.9 1.5 14 5-18 108-121 (215)
89 cd01133 F1-ATPase_beta F1 ATP 20.6 58 0.0013 26.3 1.4 14 5-18 166-179 (274)
90 PRK10281 hypothetical protein; 20.3 1.1E+02 0.0023 24.3 2.8 19 1-22 1-19 (299)
91 PRK06793 fliI flagellum-specif 20.2 54 0.0012 28.1 1.2 15 4-18 248-262 (432)
No 1
>KOG1434|consensus
Probab=99.45 E-value=4.9e-14 Score=115.18 Aligned_cols=46 Identities=59% Similarity=0.894 Sum_probs=44.8
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
.|+|||||||+++||.+|+|||+|+.|||+|+.++.+|.+||.+||
T Consensus 211 ~~rlvIVDsIma~FRvDy~grgeLseRqqkLn~ml~kl~~laeefn 256 (335)
T KOG1434|consen 211 KYRLVIVDSIMALFRVDYDGRGELSERQQKLNQMLQKLNKLAEEFN 256 (335)
T ss_pred cEEEEEEeceehheeecccccccHHHHHHHHHHHHHHHHHHHHhcc
Confidence 5899999999999999999999999999999999999999999997
No 2
>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51. It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....
Probab=99.24 E-value=8.2e-12 Score=95.78 Aligned_cols=46 Identities=48% Similarity=0.800 Sum_probs=44.3
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||||++|||.+|.|++.++.|++.|+++++.|++||.+|+
T Consensus 133 ~ikLIVIDSIaalfr~e~~~~~~~~~R~~~L~~~~~~L~~lA~~~~ 178 (256)
T PF08423_consen 133 KIKLIVIDSIAALFRSEFSGRGDLAERQRMLARLARILKRLARKYN 178 (256)
T ss_dssp CEEEEEEETSSHHHHHHSGSTTTHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred ceEEEEecchHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHHhCC
Confidence 5899999999999999999999999999999999999999999986
No 3
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=99.10 E-value=8.4e-11 Score=95.18 Aligned_cols=46 Identities=50% Similarity=0.845 Sum_probs=44.1
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||+++|||.+|.|+|.++.||++|+++++.|.++|++|+
T Consensus 221 ~~~LvVIDSital~r~~~~~rg~l~~rq~~L~~~~~~L~~lA~~~~ 266 (344)
T PLN03187 221 PFRLLIVDSVIALFRVDFTGRGELAERQQKLAQMLSRLTKIAEEFN 266 (344)
T ss_pred CCCEEEEeCcHHhhhccccCccchHHHHHHHHHHHHHHHHHHHHcC
Confidence 5899999999999999999999999999999999999999999886
No 4
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=99.07 E-value=1.4e-10 Score=93.63 Aligned_cols=46 Identities=74% Similarity=1.100 Sum_probs=43.9
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||+++|||.+|.|+|.++.||+.|+++++.|.+||++|+
T Consensus 218 ~~~LIVIDSI~alfr~~~~~~g~l~~r~~~L~~~l~~L~~lA~~~~ 263 (342)
T PLN03186 218 RFALMIVDSATALYRTEFSGRGELSARQMHLGKFLRSLQRLADEFG 263 (342)
T ss_pred CCCEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHcC
Confidence 5899999999999999999999999999999999999999999885
No 5
>PTZ00035 Rad51 protein; Provisional
Probab=99.07 E-value=1.4e-10 Score=92.70 Aligned_cols=46 Identities=67% Similarity=1.045 Sum_probs=44.0
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||+++|||.+|.|+|.++.||+.|+++++.|.++|+.|+
T Consensus 213 ~~~lvVIDSital~r~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~ 258 (337)
T PTZ00035 213 RFALLIVDSATALFRVDYSGRGELAERQQHLGKFLRALQKLADEFN 258 (337)
T ss_pred CccEEEEECcHHhhhhhccCcccHHHHHHHHHHHHHHHHHHHHHcC
Confidence 5899999999999999999999999999999999999999999886
No 6
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=99.06 E-value=1.6e-10 Score=91.73 Aligned_cols=46 Identities=54% Similarity=0.842 Sum_probs=44.1
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||++++||.+|.|+|.++.||++|+++++.|.++|++|+
T Consensus 191 ~~~LvVIDSisal~r~~~~~~g~~~~r~~~l~~~~~~L~~la~~~~ 236 (313)
T TIGR02238 191 PFRLLIVDSIMALFRVDFSGRGELSERQQKLAQMLSRLNKISEEFN 236 (313)
T ss_pred CCCEEEEEcchHhhhhhccCccchHHHHHHHHHHHHHHHHHHHHcC
Confidence 5899999999999999999999999999999999999999999986
No 7
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=99.04 E-value=2.7e-10 Score=90.25 Aligned_cols=46 Identities=83% Similarity=1.151 Sum_probs=43.8
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||+++|||.+|.|++.++.||+.|+++++.|.++|++|+
T Consensus 191 ~~~LvVIDSI~al~r~~~~~~~~~~~rq~~l~~~~~~L~~la~~~~ 236 (316)
T TIGR02239 191 RFALLIVDSATALYRTDFSGRGELSARQMHLARFLRSLQRLADEFG 236 (316)
T ss_pred CccEEEEECcHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5899999999999999999999999999999999999999999885
No 8
>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]
Probab=99.01 E-value=2.7e-10 Score=90.46 Aligned_cols=47 Identities=40% Similarity=0.502 Sum_probs=44.9
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQKR 48 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~~ 48 (99)
+++||||||++||||.+|.+++.++.|++.|+++|++|.++|++|+.
T Consensus 141 ~i~LvVVDSvaa~~r~~~~~d~~~~~~~r~ls~~l~~L~~~a~~~~~ 187 (279)
T COG0468 141 KIDLLVVDSVAALVRAEEIEDGHLGLRARLLSKALRKLTRLANKYNT 187 (279)
T ss_pred CCCEEEEecCcccchhhhcCcchHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 38999999999999999999999999999999999999999999974
No 9
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=98.88 E-value=2.3e-09 Score=82.32 Aligned_cols=45 Identities=49% Similarity=0.712 Sum_probs=43.0
Q ss_pred cceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 3 v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++||||||+++|||.+|.|++.++.|++.|++++..|.++|++|+
T Consensus 193 ~~lVVIDSisa~~r~e~~~~~~~~~r~~~l~~~~~~L~~~a~~~~ 237 (310)
T TIGR02236 193 VKLLIVDSLTSHFRAEYVGRGALAERQQKLNKHLHDLLRLADLYN 237 (310)
T ss_pred ceEEEEecchHhhhHhhcCchhHHHHHHHHHHHHHHHHHHHHHhC
Confidence 789999999999999999998899999999999999999999986
No 10
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=98.87 E-value=2.6e-09 Score=82.99 Aligned_cols=46 Identities=48% Similarity=0.705 Sum_probs=43.3
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||+++|||.+|.+++.++.|++.|.++++.|.++|.+|+
T Consensus 198 ~~~lvVIDSisa~~~~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~ 243 (317)
T PRK04301 198 NIKLVIVDSLTAHFRAEYVGRGNLAERQQKLNKHLHDLLRLADLYN 243 (317)
T ss_pred ceeEEEEECchHHhhhhccCCccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5899999999999999999998899999999999999999999886
No 11
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=98.50 E-value=2e-07 Score=67.51 Aligned_cols=46 Identities=57% Similarity=0.898 Sum_probs=41.9
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||++++||..+.+.+..+.|++.|.+++..|.++|+.|+
T Consensus 115 ~~~liVIDSis~~~~~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~ 160 (235)
T cd01123 115 RIKLVIVDSVTALFRAEFDGRGELAERQQHLAKLLRTLKRLADEFN 160 (235)
T ss_pred CeeEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5899999999999999988876678889999999999999999886
No 12
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=98.41 E-value=4.2e-07 Score=66.19 Aligned_cols=46 Identities=33% Similarity=0.486 Sum_probs=40.6
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||++++||..+.+.+....|++.|.+++..|.++|++++
T Consensus 107 ~~~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~ 152 (225)
T PRK09361 107 NVGLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHD 152 (225)
T ss_pred cccEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5789999999999999887766677788899999999999999875
No 13
>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.
Probab=98.38 E-value=5e-07 Score=65.12 Aligned_cols=46 Identities=46% Similarity=0.717 Sum_probs=41.1
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||++++||..+.+.+....|++.|.+++..|.++|++|+
T Consensus 114 ~~~lvVIDsis~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~ 159 (226)
T cd01393 114 RVDLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFN 159 (226)
T ss_pred CeeEEEEcCcchhhhhhhcCCchHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5789999999999999988776667888999999999999999875
No 14
>KOG1564|consensus
Probab=98.23 E-value=1.2e-06 Score=72.73 Aligned_cols=46 Identities=35% Similarity=0.555 Sum_probs=41.5
Q ss_pred ccceeeeechhhhhhhhcC-CCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYS-GRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~Eys-GRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||+.|+||++|. -+..+..|.++|.+...+|+.||.+|+
T Consensus 207 ~i~LVIiDSVAa~fR~E~d~~~Sdl~~r~~~l~rla~~Lr~LA~~~~ 253 (351)
T KOG1564|consen 207 KIKLVIIDSVAALFRSEFDYNPSDLKKRARHLFRLAGKLRQLASKFD 253 (351)
T ss_pred cceEEEEehhhHHHHHHhccChhhhhhHHHHHHHHHHHHHHHHHhcC
Confidence 3899999999999999997 345688899999999999999999996
No 15
>cd01394 radB RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
Probab=98.21 E-value=2.4e-06 Score=61.77 Aligned_cols=46 Identities=37% Similarity=0.468 Sum_probs=38.8
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||++++||..+.+....+.+++.|.++++.|..+|++++
T Consensus 103 ~~~lvvIDsi~~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~ 148 (218)
T cd01394 103 KVDLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLWLARKHD 148 (218)
T ss_pred CCcEEEEechHHhhhHHhcCccchHHHHHHHHHHHHHHHHHHHHhC
Confidence 3789999999999999887654456678889999999999998875
No 16
>TIGR02237 recomb_radB DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
Probab=98.19 E-value=2.3e-06 Score=61.30 Aligned_cols=44 Identities=41% Similarity=0.543 Sum_probs=36.7
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||+++|||.++.+... .|.+.|.+++..|.++|++++
T Consensus 97 ~~~lvVIDSis~l~~~~~~~~~~--~~~~~l~~~~~~L~~~~~~~~ 140 (209)
T TIGR02237 97 SASLVVVDSFTALYRLELSDDRI--SRNRELARQLTLLLSLARKKN 140 (209)
T ss_pred CccEEEEeCcHHHhHHHhCCccH--HHHHHHHHHHHHHHHHHHHcC
Confidence 47899999999999998776532 567789999999999998764
No 17
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=97.99 E-value=6.1e-06 Score=73.98 Aligned_cols=46 Identities=17% Similarity=0.315 Sum_probs=38.7
Q ss_pred ccceeeeechhhhh-hhhcCCCc---chHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALY-RTDYSGRG---ELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALF-R~EysGRG---eLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||++||| |.+|+|+. .+..+++.++++|+.|.+++++|+
T Consensus 138 ~~~LVVIDSI~aL~~r~E~~g~~g~~~~~~q~rl~~q~L~~L~~~l~~~n 187 (790)
T PRK09519 138 ALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSG 187 (790)
T ss_pred CCeEEEEcchhhhcchhhccCCCCcccHHHHHHHHHHHHHHHHHHHHhCC
Confidence 58999999999999 89999983 234556667899999999998876
No 18
>KOG1433|consensus
Probab=97.97 E-value=7.3e-06 Score=67.01 Aligned_cols=46 Identities=70% Similarity=0.947 Sum_probs=43.6
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++.|+||||+|++||..|.|++.+..|++++.++++.|.++|++|.
T Consensus 200 ~~~l~~vds~ta~~~~~~~g~~~~~a~~~~~~~~~~~l~~la~~~g 245 (326)
T KOG1433|consen 200 RVKLLIVDSATALYRTTFKGRGELSARQMLLAKFLRSLKKLADEFG 245 (326)
T ss_pred ceeEEEecccccccccccccccchHHHHHHHHHHHHHHHHHHHhcC
Confidence 4789999999999999999999999999999999999999999885
No 19
>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange.
Probab=97.81 E-value=2.1e-05 Score=63.82 Aligned_cols=47 Identities=21% Similarity=0.334 Sum_probs=36.7
Q ss_pred ccceeeeechhhhh-hhhcCCCc-c--hHHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALY-RTDYSGRG-E--LSARQMHLARFLRMLLRLADEQKR 48 (99)
Q Consensus 2 ~v~LIIVDSiTALF-R~EysGRG-e--LA~RQq~L~kqL~~L~rLAr~f~~ 48 (99)
.++||||||++||| |+++.|+. . ...+.+.|.++|+.|..++++++.
T Consensus 133 ~~~lIVIDSvaal~~~~E~~~~~~~~~~~~qaR~l~~~Lr~L~~~~~k~~~ 183 (325)
T cd00983 133 AVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSINKSNT 183 (325)
T ss_pred CCCEEEEcchHhhcccccccccccccchHHHHHHHHHHHHHHHHHHHhCCC
Confidence 47999999999999 58988763 1 122345689999999999998763
No 20
>PRK09354 recA recombinase A; Provisional
Probab=97.73 E-value=3.7e-05 Score=63.16 Aligned_cols=46 Identities=24% Similarity=0.397 Sum_probs=36.1
Q ss_pred ccceeeeechhhhh-hhhcCCC-cc--hHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALY-RTDYSGR-GE--LSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALF-R~EysGR-Ge--LA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
.++||||||++||| |+++.|+ |. ...+.+.++++|+.|..++++++
T Consensus 138 ~~~lIVIDSvaaL~~~~E~eg~~gd~~~~~qar~ms~~Lr~L~~~l~k~~ 187 (349)
T PRK09354 138 AVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNISKSN 187 (349)
T ss_pred CCCEEEEeChhhhcchhhhcCCccccchhHHHHHHHHHHHHHHHHHHHcC
Confidence 47999999999999 7999887 22 12344567888999999998875
No 21
>TIGR02012 tigrfam_recA protein RecA. This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.
Probab=97.54 E-value=9.6e-05 Score=59.89 Aligned_cols=46 Identities=22% Similarity=0.398 Sum_probs=35.6
Q ss_pred ccceeeeechhhhh-hhhcCCC-cc--hHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALY-RTDYSGR-GE--LSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALF-R~EysGR-Ge--LA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
.++||||||++||| |+++.|+ |. ...+.+.++++|+.|..++++++
T Consensus 133 ~~~lIVIDSv~al~~~~E~e~~~g~~~~~~~aR~m~~~lr~L~~~l~~~~ 182 (321)
T TIGR02012 133 AVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALSKSN 182 (321)
T ss_pred CCcEEEEcchhhhccchhhcccccccchhHHHHHHHHHHHHHHHHHHhCC
Confidence 47899999999999 6788876 22 12234567899999999998875
No 22
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=96.25 E-value=0.0092 Score=41.75 Aligned_cols=39 Identities=28% Similarity=0.330 Sum_probs=24.9
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++++++.. + ...... ...++..|.+||+.|+
T Consensus 141 ~~~lvviD~l~~~~~~---~--~~~~~~--~~~~~~~l~~la~~~~ 179 (193)
T PF13481_consen 141 GPDLVVIDPLQSLHDG---D--ENSNSA--VAQLMQELKRLAKEYG 179 (193)
T ss_dssp --SEEEEE-GGGG--S------TT-HHH--HHHHHHHHHHHHHHH-
T ss_pred CCcEEEEcCHHHHhcC---C--CCCHHH--HHHHHHHHHHHHHHcC
Confidence 4789999999999986 1 222222 3889999999999886
No 23
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=95.68 E-value=0.019 Score=42.75 Aligned_cols=42 Identities=14% Similarity=0.217 Sum_probs=31.2
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++|||||++++......+ ..+.+.+..++..|..+|.+++
T Consensus 140 ~~~~vvID~l~~l~~~~~~~----~~~~~~~~~~~~~L~~la~~~~ 181 (271)
T cd01122 140 GIQHIIIDNLSIMVSDERAS----GDERKALDEIMTKLRGFATEHG 181 (271)
T ss_pred CceEEEECCHHHHhccCCCc----hhHHHHHHHHHHHHHHHHHHhC
Confidence 57899999999987543111 2235567889999999999876
No 24
>PRK11823 DNA repair protein RadA; Provisional
Probab=95.63 E-value=0.015 Score=48.36 Aligned_cols=42 Identities=24% Similarity=0.450 Sum_probs=31.7
Q ss_pred ccceeeeechhhhhhhhcCCC-cchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGR-GELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGR-GeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++||||||++++|+.++.+. |.. ..+..++..|.++|+.++
T Consensus 156 ~~~lVVIDSIq~l~~~~~~~~~g~~----~qvr~~~~~L~~~ak~~~ 198 (446)
T PRK11823 156 KPDLVVIDSIQTMYSPELESAPGSV----SQVRECAAELMRLAKQRG 198 (446)
T ss_pred CCCEEEEechhhhccccccCCCCCH----HHHHHHHHHHHHHHHHcC
Confidence 478999999999999887653 332 335666778888888765
No 25
>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family. This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.
Probab=95.22 E-value=0.02 Score=43.85 Aligned_cols=16 Identities=31% Similarity=0.468 Sum_probs=14.1
Q ss_pred ccceeeeechhhhhhh
Q psy17736 2 KYALLIVDSAMALYRT 17 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~ 17 (99)
++++|||||+++||+.
T Consensus 131 ~~~~vVIDSls~l~~~ 146 (259)
T TIGR03878 131 KVKNTVIDSITGLYEA 146 (259)
T ss_pred CCCEEEEcCchHhccc
Confidence 5789999999999874
No 26
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=94.71 E-value=0.042 Score=46.05 Aligned_cols=42 Identities=29% Similarity=0.414 Sum_probs=31.1
Q ss_pred ccceeeeechhhhhhhhcCCC-cchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGR-GELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGR-GeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++|||||++++|..+..+. |..+ .+..++..|.++|++++
T Consensus 170 ~~~~vVIDSIq~l~~~~~~~~~g~~~----q~r~~~~~L~~~ak~~g 212 (454)
T TIGR00416 170 NPQACVIDSIQTLYSPDISSAPGSVS----QVRECTAELMRLAKTRG 212 (454)
T ss_pred CCcEEEEecchhhcccccccCCCCHH----HHHHHHHHHHHHHHHhC
Confidence 578999999999998876542 4433 24466778888888765
No 27
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=94.68 E-value=0.045 Score=44.92 Aligned_cols=42 Identities=29% Similarity=0.510 Sum_probs=31.7
Q ss_pred ccceeeeechhhhhhhhcCC-CcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSG-RGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysG-RGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++|||||+..+|+.++.+ .|..+ .+..++..|.++|+.++
T Consensus 158 ~~~lVVIDSIq~l~~~~~~~~~g~~~----qvr~~~~~L~~lak~~~ 200 (372)
T cd01121 158 KPDLVIIDSIQTVYSSELTSAPGSVS----QVRECTAELMRFAKERN 200 (372)
T ss_pred CCcEEEEcchHHhhccccccCCCCHH----HHHHHHHHHHHHHHHcC
Confidence 57899999999999987643 24432 36677888899988765
No 28
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=94.62 E-value=0.045 Score=39.83 Aligned_cols=41 Identities=24% Similarity=0.276 Sum_probs=29.5
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++|||||++++- ... . ...+...+..++..|..+|.+++
T Consensus 123 ~~~~vvID~l~~l~-~~~--~--~~~~~~~~~~~~~~L~~la~~~~ 163 (242)
T cd00984 123 GLGLIVIDYLQLMS-GSK--K--KGNRQQEVAEISRSLKLLAKELN 163 (242)
T ss_pred CCCEEEEcCchhcC-CCC--C--CCCHHHHHHHHHHHHHHHHHHhC
Confidence 57999999999753 221 1 12345668899999999998775
No 29
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=93.46 E-value=0.088 Score=43.63 Aligned_cols=37 Identities=19% Similarity=0.208 Sum_probs=27.0
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++|||||+++|++.. . ...+.+++..|.+++++++
T Consensus 363 ~~~~vVIDslt~l~~~~--~-------~~~~~~~l~~l~~~~k~~~ 399 (509)
T PRK09302 363 KPSRVAIDPLSALARGG--S-------LNEFRQFVIRLTDYLKSEE 399 (509)
T ss_pred CCCEEEEcCHHHHHHhC--C-------HHHHHHHHHHHHHHHHhCC
Confidence 57899999999998743 1 1345677777888877654
No 30
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=93.18 E-value=0.058 Score=35.22 Aligned_cols=41 Identities=29% Similarity=0.211 Sum_probs=27.0
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADE 45 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~ 45 (99)
++++||||+++++++....+. ......+..++..|..++++
T Consensus 85 ~~~~lviDe~~~~~~~~~~~~---~~~~~~~~~~l~~l~~~~~~ 125 (165)
T cd01120 85 GDDLIILDELTRLVRALREIR---EGYPGELDEELRELLERARK 125 (165)
T ss_pred CCEEEEEEcHHHHHHHHHHHH---hcCChHHHHHHHHHHHHHhc
Confidence 468999999999998764321 11134566667777666654
No 31
>PRK04328 hypothetical protein; Provisional
Probab=92.68 E-value=0.13 Score=39.02 Aligned_cols=16 Identities=31% Similarity=0.426 Sum_probs=13.7
Q ss_pred ccceeeeechhhhhhh
Q psy17736 2 KYALLIVDSAMALYRT 17 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~ 17 (99)
++++|||||+++||+.
T Consensus 128 ~~~~vVIDSlt~l~~~ 143 (249)
T PRK04328 128 GAKRVVIDSVSTLYLT 143 (249)
T ss_pred CCCEEEEeChhHhhcC
Confidence 4689999999999874
No 32
>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family. Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.
Probab=92.35 E-value=0.15 Score=38.12 Aligned_cols=15 Identities=27% Similarity=0.454 Sum_probs=13.1
Q ss_pred ccceeeeechhhhhh
Q psy17736 2 KYALLIVDSAMALYR 16 (99)
Q Consensus 2 ~v~LIIVDSiTALFR 16 (99)
++++|||||+++||.
T Consensus 126 ~~~~vVIDSls~l~~ 140 (237)
T TIGR03877 126 NAKRVVIDSVTTLYI 140 (237)
T ss_pred CCCEEEEcChhHhhc
Confidence 467899999999986
No 33
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=91.58 E-value=0.26 Score=39.78 Aligned_cols=41 Identities=27% Similarity=0.377 Sum_probs=30.6
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++||||++..+ +.. ++ ...|.+.++.++..|..||.+++
T Consensus 305 ~~~~vvID~l~~i-~~~--~~--~~~r~~~i~~i~~~Lk~lA~e~~ 345 (434)
T TIGR00665 305 GLGLIVIDYLQLM-SGS--GR--SENRQQEVSEISRSLKALAKELN 345 (434)
T ss_pred CCCEEEEcchHhc-CCC--CC--CCCHHHHHHHHHHHHHHHHHHhC
Confidence 4799999999865 322 11 12467789999999999999874
No 34
>PRK05973 replicative DNA helicase; Provisional
Probab=90.51 E-value=0.23 Score=38.79 Aligned_cols=37 Identities=24% Similarity=0.300 Sum_probs=26.5
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+.++|||||++.+.. .. +...+..++..|..+|+.++
T Consensus 147 ~~~lVVIDsLq~l~~----~~-----~~~el~~~~~~Lk~~Ak~~g 183 (237)
T PRK05973 147 RGTLVVIDYLQLLDQ----RR-----EKPDLSVQVRALKSFARERG 183 (237)
T ss_pred CCCEEEEEcHHHHhh----cc-----cchhHHHHHHHHHHHHHhCC
Confidence 468999999998742 11 13347788888999988764
No 35
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=90.17 E-value=0.37 Score=38.97 Aligned_cols=40 Identities=30% Similarity=0.346 Sum_probs=31.1
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++..+. .. .+ ..|.+.++.++..|..||++++
T Consensus 305 ~~~lvvIDyLql~~-~~---~~--~~~~~~~~~i~~~Lk~lAke~~ 344 (421)
T TIGR03600 305 GLDLIVVDYIQLMA-PT---RG--RDRNEELGGISRGLKALAKELD 344 (421)
T ss_pred CCCEEEEecccccC-CC---CC--CCHHHHHHHHHHHHHHHHHHhC
Confidence 47899999998763 21 22 2367889999999999999875
No 36
>cd01125 repA Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
Probab=89.92 E-value=0.49 Score=35.15 Aligned_cols=39 Identities=15% Similarity=0.308 Sum_probs=25.5
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++++++... .+. ......++..|.++|+.++
T Consensus 111 ~~~lvviDpl~~~~~~~-----~~d--~~~~~~~~~~L~~~a~~~g 149 (239)
T cd01125 111 RIDLVVIDPLVSFHGVS-----END--NGAMDAVIKALRRIAAQTG 149 (239)
T ss_pred CCCEEEECChHHhCCCC-----cCC--HHHHHHHHHHHHHHHHHhC
Confidence 57999999999884322 122 1234556778888887654
No 37
>PRK05595 replicative DNA helicase; Provisional
Probab=89.90 E-value=0.49 Score=38.95 Aligned_cols=41 Identities=22% Similarity=0.395 Sum_probs=31.4
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++.-+ .. +++ ...|.+.++.....|..||.+++
T Consensus 311 ~~~~vvIDylql~-~~---~~~-~~~r~~~v~~is~~LK~lAke~~ 351 (444)
T PRK05595 311 GIDMILIDYLQLM-SG---GKG-SESRQQEVSEISRSIKALAKEME 351 (444)
T ss_pred CCCEEEEeHHHhc-cC---CCC-CccHHHHHHHHHHHHHHHHHHhC
Confidence 4789999999765 21 111 23578899999999999999875
No 38
>PRK08760 replicative DNA helicase; Provisional
Probab=89.67 E-value=0.44 Score=40.20 Aligned_cols=41 Identities=22% Similarity=0.338 Sum_probs=31.5
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++..+ +.. +. -..|++.++.....|..||++++
T Consensus 339 ~~~lVvIDyLql~-~~~--~~--~~~r~~ei~~Isr~LK~lAkel~ 379 (476)
T PRK08760 339 DLGLIVIDYLQLM-SVP--GN--SENRATEISEISRSLKGLAKELN 379 (476)
T ss_pred CCCEEEEecHHhc-CCC--CC--CcccHHHHHHHHHHHHHHHHHhC
Confidence 4789999999744 422 22 13478899999999999999886
No 39
>PRK05748 replicative DNA helicase; Provisional
Probab=89.59 E-value=0.47 Score=38.96 Aligned_cols=42 Identities=31% Similarity=0.396 Sum_probs=31.5
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++..+ .. .++. ...|++.++..+..|..||++++
T Consensus 314 ~~~~vvIDyL~li-~~--~~~~-~~~r~~~i~~i~~~LK~lAke~~ 355 (448)
T PRK05748 314 GLGLILIDYLQLI-QG--SGRS-GENRQQEVSEISRSLKALAKELK 355 (448)
T ss_pred CCCEEEEccchhc-CC--CCCC-CcCHHHHHHHHHHHHHHHHHHhC
Confidence 5789999999876 21 2221 12478899999999999999875
No 40
>PRK07773 replicative DNA helicase; Validated
Probab=89.28 E-value=0.45 Score=42.85 Aligned_cols=41 Identities=27% Similarity=0.413 Sum_probs=31.8
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++..+ +. +. ....|++.++.++..|..||++++
T Consensus 327 ~~~lvvIDyLql~-~~---~~-~~~~r~~ei~~isr~LK~lAkel~ 367 (886)
T PRK07773 327 NLGLIVVDYLQLM-TS---GK-KYENRQQEVSEISRHLKLLAKELE 367 (886)
T ss_pred CCCEEEEcchhhc-CC---CC-CCCCHHHHHHHHHHHHHHHHHHHC
Confidence 4789999999754 32 21 224578999999999999999875
No 41
>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []. In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....
Probab=89.05 E-value=0.48 Score=38.82 Aligned_cols=45 Identities=24% Similarity=0.378 Sum_probs=30.7
Q ss_pred cceeeeechhhh-hhhhcCCC---cchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMAL-YRTDYSGR---GELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 3 v~LIIVDSiTAL-FR~EysGR---GeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++||||||+.+| =+.+..|. .....+.+.|.++|+.|..+..+++
T Consensus 132 ~~lVVvDSv~al~p~~E~e~~~~~~~~g~~Ar~ms~~lr~lt~~l~~~~ 180 (322)
T PF00154_consen 132 VDLVVVDSVAALVPKAELEGEIGDQQVGLQARLMSQALRKLTPLLSKSN 180 (322)
T ss_dssp ESEEEEE-CTT-B-HHHHTTSTSSTSSSHHHHHHHHHHHHHHHHHHTTT
T ss_pred ccEEEEecCcccCCHHHHhhccccccCcchHHHHHHHHHHHHHHHHhhc
Confidence 689999999997 67777664 2234466788888888887776654
No 42
>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
Probab=88.50 E-value=0.77 Score=33.50 Aligned_cols=34 Identities=24% Similarity=0.323 Sum_probs=20.1
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRML 39 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L 39 (99)
++++|||||++++ +.-+.+ ...+.+.+..++..|
T Consensus 107 ~~~~vVIDsls~l-~~~~~~---~~~~r~~l~~l~~~l 140 (224)
T TIGR03880 107 GASRVVIDPISLL-ETLFDD---DAERRTELFRFYSSL 140 (224)
T ss_pred CCCEEEEcChHHH-hhhcCC---HHHHHHHHHHHHHHH
Confidence 4689999999987 333322 233344455555544
No 43
>PRK05636 replicative DNA helicase; Provisional
Probab=87.68 E-value=0.73 Score=39.43 Aligned_cols=41 Identities=32% Similarity=0.463 Sum_probs=31.8
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||.+.-+ . .++. ...|++.++.+...|..||+.++
T Consensus 375 ~~~lvvIDYLql~-~---~~~~-~~~r~~ei~~isr~LK~lAkel~ 415 (505)
T PRK05636 375 DLKLIVVDYLQLM-S---SGKR-VESRQQEVSEFSRQLKLLAKELD 415 (505)
T ss_pred CCCEEEEcchHhc-C---CCCC-CCcHHHHHHHHHHHHHHHHHHhC
Confidence 4789999999865 1 1221 24588999999999999999874
No 44
>PRK08506 replicative DNA helicase; Provisional
Probab=87.32 E-value=0.77 Score=38.56 Aligned_cols=41 Identities=24% Similarity=0.367 Sum_probs=30.8
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++.-+ .. .+ ....|++.++.....|..||+.++
T Consensus 302 ~~~lvvIDyLql~-~~--~~--~~~~r~~ev~~isr~LK~lAkel~ 342 (472)
T PRK08506 302 EIGLAVIDYLQLM-SG--SG--NFKDRHLQISEISRGLKLLARELD 342 (472)
T ss_pred CCCEEEEcChhhc-cC--CC--CCCCHHHHHHHHHHHHHHHHHHhC
Confidence 3789999999743 32 12 124578889999999999999876
No 45
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=86.57 E-value=1.3 Score=30.63 Aligned_cols=16 Identities=25% Similarity=0.287 Sum_probs=13.7
Q ss_pred ccceeeeechhhhhhh
Q psy17736 2 KYALLIVDSAMALYRT 17 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~ 17 (99)
++++|||||+++++..
T Consensus 95 ~~~~lviD~~~~~~~~ 110 (187)
T cd01124 95 KAKRVVIDSVSGLLLM 110 (187)
T ss_pred CCCEEEEeCcHHHhhc
Confidence 4789999999999874
No 46
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=85.43 E-value=2 Score=32.23 Aligned_cols=41 Identities=24% Similarity=0.306 Sum_probs=30.6
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++||||++..+--.. +. ..+.+.+...+..|..||.+++
T Consensus 130 ~~~~v~IDyl~ll~~~~--~~---~~~~~~~~~i~~~Lk~lA~~~~ 170 (259)
T PF03796_consen 130 KVDVVFIDYLQLLKSED--SS---DNRRQEIGEISRELKALAKELN 170 (259)
T ss_dssp TEEEEEEEEGGGSBTSC--SS---SCCHHHHHHHHHHHHHHHHHHT
T ss_pred CCCEEEechHHHhcCCC--CC---CCHHHHHHHHHHHHHHHHHHcC
Confidence 57899999998754433 11 1245779999999999999885
No 47
>PRK09165 replicative DNA helicase; Provisional
Probab=85.27 E-value=1.2 Score=37.81 Aligned_cols=43 Identities=26% Similarity=0.284 Sum_probs=31.0
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++.-+ +.... +. ...|.+.++.+...|..||+.++
T Consensus 341 ~~~lvvIDyLqli-~~~~~-~~-~~~r~~ev~~is~~LK~lAkel~ 383 (497)
T PRK09165 341 GLDLLVVDYLQLI-RGSSK-RS-SDNRVQEISEITQGLKALAKELN 383 (497)
T ss_pred CCCEEEEcchHhc-cCCCC-CC-CCchHHHHHHHHHHHHHHHHHhC
Confidence 4789999999854 32211 11 12477889999999999999775
No 48
>PRK08840 replicative DNA helicase; Provisional
Probab=85.23 E-value=1.2 Score=37.64 Aligned_cols=40 Identities=25% Similarity=0.350 Sum_probs=31.0
Q ss_pred cceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 3 v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++|||||.+.-+ +.. +. ...|++.++.+...|..||+.++
T Consensus 330 ~~lvvIDYLql~-~~~--~~--~~~r~~ei~~isr~LK~lAkel~ 369 (464)
T PRK08840 330 LSMIMVDYLQLM-RVP--AL--SDNRTLEIAEISRSLKALAKELN 369 (464)
T ss_pred CCEEEEccHHhc-CCC--CC--CCchHHHHHHHHHHHHHHHHHhC
Confidence 789999998754 321 22 23578899999999999999886
No 49
>PHA02542 41 41 helicase; Provisional
Probab=85.09 E-value=1.1 Score=38.13 Aligned_cols=42 Identities=17% Similarity=0.032 Sum_probs=31.3
Q ss_pred cceeeeechhhhhhhh-cCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMALYRTD-YSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 3 v~LIIVDSiTALFR~E-ysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++|||||++.-+ ... ..++ ...|++.++...+.|..||+.++
T Consensus 302 ~dlVvIDYLqL~-~~~~~~~~--~~nr~~ei~~Isr~LK~lAkel~ 344 (473)
T PHA02542 302 PDVIIVDYLGIC-ASSRLRVS--SENSYTYVKAIAEELRGLAVEHD 344 (473)
T ss_pred CCEEEEechhhc-cCCcccCC--CCChHHHHHHHHHHHHHHHHHhC
Confidence 789999999665 211 1112 23578999999999999999886
No 50
>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....
Probab=84.56 E-value=1.6 Score=31.80 Aligned_cols=13 Identities=38% Similarity=0.419 Sum_probs=11.5
Q ss_pred ccceeeeechhhh
Q psy17736 2 KYALLIVDSAMAL 14 (99)
Q Consensus 2 ~v~LIIVDSiTAL 14 (99)
+++.|||||+++|
T Consensus 115 ~~~~vVIDsls~l 127 (226)
T PF06745_consen 115 KPDRVVIDSLSAL 127 (226)
T ss_dssp TSSEEEEETHHHH
T ss_pred CCCEEEEECHHHH
Confidence 3579999999999
No 51
>PRK06321 replicative DNA helicase; Provisional
Probab=83.55 E-value=1.8 Score=36.78 Aligned_cols=43 Identities=30% Similarity=0.376 Sum_probs=31.2
Q ss_pred ccceeeeechhhhhhhhcCCCc-chHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRG-ELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRG-eLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||++.-+ ... |.. ....|++.++.+.+.|..||++++
T Consensus 336 ~~~lvvIDyLql~-~~~--~~~~~~~~r~~ei~~Isr~LK~lAkel~ 379 (472)
T PRK06321 336 DIQFLIIDYLQLL-SGS--GNLRNSESRQTEISEISRMLKNLARELN 379 (472)
T ss_pred CCCEEEEcchHHc-CCC--CccCCcchHHHHHHHHHHHHHHHHHHhC
Confidence 4789999999653 321 210 123578999999999999999875
No 52
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=83.34 E-value=2.3 Score=31.33 Aligned_cols=14 Identities=21% Similarity=0.370 Sum_probs=12.1
Q ss_pred ccceeeeechhhhh
Q psy17736 2 KYALLIVDSAMALY 15 (99)
Q Consensus 2 ~v~LIIVDSiTALF 15 (99)
++++|||||++++.
T Consensus 120 ~~~~iviDs~t~~~ 133 (234)
T PRK06067 120 REDVIIIDSLTIFA 133 (234)
T ss_pred CCCEEEEecHHHHH
Confidence 57899999999874
No 53
>PRK07004 replicative DNA helicase; Provisional
Probab=82.95 E-value=1.7 Score=36.49 Aligned_cols=40 Identities=23% Similarity=0.294 Sum_probs=30.9
Q ss_pred cceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 3 v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++|||||.+.-+ ... +. ...|++.++.....|..||+.++
T Consensus 325 ~~lviIDYLql~-~~~--~~--~~~r~~ei~~Isr~LK~lAkel~ 364 (460)
T PRK07004 325 LGLIIIDYLQLM-SGS--SQ--GENRATEISEISRSLKSLAKELD 364 (460)
T ss_pred CCEEEEChhhhc-cCC--CC--CCcHHHHHHHHHHHHHHHHHHhC
Confidence 689999999765 211 22 13478999999999999999884
No 54
>PRK08006 replicative DNA helicase; Provisional
Probab=81.44 E-value=1.8 Score=36.62 Aligned_cols=41 Identities=24% Similarity=0.345 Sum_probs=30.9
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|||||.+--+ +.. +. ...|++.++..+..|..||+.++
T Consensus 336 ~~~lvvIDYLqli-~~~--~~--~~~r~~ei~~isr~LK~lAkel~ 376 (471)
T PRK08006 336 GLSLIMIDYLQLM-RVP--SL--SDNRTLEIAEISRSLKALAKELQ 376 (471)
T ss_pred CCCEEEEccHHHc-cCC--CC--CCCcHHHHHHHHHHHHHHHHHhC
Confidence 3789999999753 321 11 13478889999999999999886
No 55
>PRK06904 replicative DNA helicase; Validated
Probab=79.58 E-value=2.7 Score=35.57 Aligned_cols=42 Identities=33% Similarity=0.395 Sum_probs=31.3
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQKR 48 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~~ 48 (99)
+++|||||.+. |.+.. +. ...|++.++.+...|..||+.++-
T Consensus 334 ~~~lvvIDYLq-li~~~--~~--~~~r~~ei~~isr~LK~lAkel~i 375 (472)
T PRK06904 334 GLSLIMVDYLQ-LMRAP--GF--EDNRTLEIAEISRSLKALAKELKV 375 (472)
T ss_pred CCCEEEEecHH-hcCCC--CC--CCcHHHHHHHHHHHHHHHHHHhCC
Confidence 36899999985 44432 21 134788999999999999998863
No 56
>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.
Probab=77.90 E-value=2.6 Score=30.68 Aligned_cols=14 Identities=36% Similarity=0.460 Sum_probs=11.9
Q ss_pred cceeeeechhhhhh
Q psy17736 3 YALLIVDSAMALYR 16 (99)
Q Consensus 3 v~LIIVDSiTALFR 16 (99)
.++|||||+++++.
T Consensus 122 ~~~vvIDsl~~l~~ 135 (229)
T TIGR03881 122 HARLVIDSMSAFWL 135 (229)
T ss_pred ceEEEecCchhhhc
Confidence 46899999999875
No 57
>TIGR02655 circ_KaiC circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.
Probab=76.37 E-value=2.9 Score=35.00 Aligned_cols=16 Identities=44% Similarity=0.366 Sum_probs=14.1
Q ss_pred ccceeeeechhhhhhh
Q psy17736 2 KYALLIVDSAMALYRT 17 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~ 17 (99)
++++|||||+++++..
T Consensus 353 ~~~~vvIDsi~~~~~~ 368 (484)
T TIGR02655 353 KPARIAIDSLSALARG 368 (484)
T ss_pred CCCEEEEcCHHHHHHh
Confidence 4789999999999985
No 58
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=75.75 E-value=3.1 Score=36.35 Aligned_cols=42 Identities=29% Similarity=0.488 Sum_probs=31.9
Q ss_pred ccceeeeechhhhhhhhcCCC-cchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGR-GELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGR-GeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
+++|+|||||--+|-.+.++- |+.+. .-.....|.++|+.++
T Consensus 168 ~p~lvVIDSIQT~~s~~~~SapGsVsQ----VRe~t~~L~~~AK~~~ 210 (456)
T COG1066 168 KPDLVVIDSIQTLYSEEITSAPGSVSQ----VREVAAELMRLAKTKN 210 (456)
T ss_pred CCCEEEEeccceeecccccCCCCcHHH----HHHHHHHHHHHHHHcC
Confidence 578999999999999886555 77653 4456677888887764
No 59
>KOG4115|consensus
Probab=72.49 E-value=6.1 Score=28.13 Aligned_cols=41 Identities=22% Similarity=0.263 Sum_probs=34.7
Q ss_pred cceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQKR 48 (99)
Q Consensus 3 v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~~ 48 (99)
.|.||+|+....-|+.+..+ ..+..+.+|+.|...|+...+
T Consensus 19 ~giiv~d~~GvpikTt~d~~-----~t~~ya~~l~~L~~kars~Vr 59 (97)
T KOG4115|consen 19 TGIIVVDNAGVPIKTTLDNT-----TTQQYAALLHPLVEKARSVVR 59 (97)
T ss_pred eeEEEECCCCcEeEeccCch-----HHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999887653 357789999999999998876
No 60
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=69.12 E-value=5.7 Score=32.10 Aligned_cols=34 Identities=26% Similarity=0.403 Sum_probs=25.6
Q ss_pred cceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADE 45 (99)
Q Consensus 3 v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~ 45 (99)
..+|||||++++-+.+ + -+....||..+.+|++.
T Consensus 124 ~dViIIDSls~~~~~~--------~-~~~vl~fm~~~r~l~d~ 157 (235)
T COG2874 124 KDVIIIDSLSAFATYD--------S-EDAVLNFMTFLRKLSDL 157 (235)
T ss_pred CCEEEEecccHHhhcc--------c-HHHHHHHHHHHHHHHhC
Confidence 5789999999976644 1 24467788889888864
No 61
>PRK06749 replicative DNA helicase; Provisional
Probab=68.42 E-value=7.6 Score=32.42 Aligned_cols=40 Identities=28% Similarity=0.281 Sum_probs=29.2
Q ss_pred ceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 4 ALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 4 ~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
.|||||.+.-+ ... .+. ...|.+.++..+..|..||++++
T Consensus 301 ~lvvIDyLqli-~~~-~~~--~~~r~~ei~~isr~LK~lAkel~ 340 (428)
T PRK06749 301 ILIIVDYLQLI-TGD-PKH--KGNRFQEISEISRKLKLLARELN 340 (428)
T ss_pred cEEEEeChhhc-CCC-CCC--CCCHHHHHHHHHHHHHHHHHHhC
Confidence 49999999754 211 111 13478899999999999999885
No 62
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=68.17 E-value=8.3 Score=29.13 Aligned_cols=16 Identities=25% Similarity=0.407 Sum_probs=13.5
Q ss_pred ccceeeeechhhhhhh
Q psy17736 2 KYALLIVDSAMALYRT 17 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~ 17 (99)
+.++|||||++++++.
T Consensus 117 ~~~~lVIDe~t~~l~~ 132 (230)
T PRK08533 117 EKDVIIIDSLSSLISN 132 (230)
T ss_pred CCCEEEEECccHHhcC
Confidence 4689999999998754
No 63
>PF13479 AAA_24: AAA domain
Probab=67.45 E-value=3.5 Score=30.49 Aligned_cols=17 Identities=24% Similarity=0.276 Sum_probs=14.1
Q ss_pred ccceeeeechhhhhhhh
Q psy17736 2 KYALLIVDSAMALYRTD 18 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~E 18 (99)
+|+.|||||++.+++.-
T Consensus 68 ~y~tiVIDsis~~~~~~ 84 (213)
T PF13479_consen 68 DYDTIVIDSISWLEDMC 84 (213)
T ss_pred CCCEEEEECHHHHHHHH
Confidence 58899999999986643
No 64
>PRK14976 5'-3' exonuclease; Provisional
Probab=57.95 E-value=18 Score=28.71 Aligned_cols=43 Identities=21% Similarity=0.448 Sum_probs=31.7
Q ss_pred CccceeeeechhhhhhhhcCC----------CcchHHHHHHHHHHHHHHHHHHHHH
Q psy17736 1 MKYALLIVDSAMALYRTDYSG----------RGELSARQMHLARFLRMLLRLADEQ 46 (99)
Q Consensus 1 ~~v~LIIVDSiTALFR~EysG----------RGeLA~RQq~L~kqL~~L~rLAr~f 46 (99)
|.-.|++||+-.-+||+-|.- .|.. ...+.-+++.|++|.+.|
T Consensus 1 m~~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~---t~a~~gf~~~l~~ll~~~ 53 (281)
T PRK14976 1 MMKKALLIDGNSLIFRSYYATLKQGPKLKNNKGLP---TNAIHTFLTMIFKILKKL 53 (281)
T ss_pred CCCcEEEEeCcHHHHHHHHccCccCCCccCCCCCC---chHHHHHHHHHHHHHHhc
Confidence 445799999999999988762 1221 245677888888888776
No 65
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=56.48 E-value=16 Score=30.51 Aligned_cols=15 Identities=27% Similarity=0.361 Sum_probs=12.3
Q ss_pred ccceeeeechhhhhh
Q psy17736 2 KYALLIVDSAMALYR 16 (99)
Q Consensus 2 ~v~LIIVDSiTALFR 16 (99)
+++.|||||+++++-
T Consensus 130 ~~~~vVIDSls~l~~ 144 (509)
T PRK09302 130 GAKRVVLDSIEALFS 144 (509)
T ss_pred CCCEEEECCHHHHHh
Confidence 467899999999754
No 66
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=56.22 E-value=12 Score=32.13 Aligned_cols=41 Identities=20% Similarity=0.259 Sum_probs=31.7
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
++++||||.+.-+.= .+ ....|++.++.+...|..||+.++
T Consensus 306 ~l~~i~iDYLqLm~~---~~--~~~~r~qevs~iSr~LK~lAkEl~ 346 (435)
T COG0305 306 NLGLIVIDYLQLMTG---GK--KSENRKQEVSEISRSLKGLAKELG 346 (435)
T ss_pred CccEEEEEEEEeecc---cc--cchhHHHHHHHHHHHHHHHHHhcC
Confidence 478999999865332 12 126699999999999999999864
No 67
>smart00475 53EXOc 5'-3' exonuclease.
Probab=50.77 E-value=24 Score=27.72 Aligned_cols=40 Identities=38% Similarity=0.596 Sum_probs=29.3
Q ss_pred ceeeeechhhhhhhhcCC------CcchHHHHHHHHHHHHHHHHHHHHH
Q psy17736 4 ALLIVDSAMALYRTDYSG------RGELSARQMHLARFLRMLLRLADEQ 46 (99)
Q Consensus 4 ~LIIVDSiTALFR~EysG------RGeLA~RQq~L~kqL~~L~rLAr~f 46 (99)
.|++||+..-+||+-|.- .|.. -..+.-+++.|.+|.+.+
T Consensus 2 ~lllIDg~~~i~R~~~a~~~l~~~~G~~---t~a~~g~~~~l~~l~~~~ 47 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALPPLKNSKGEP---TNAVYGFLRMLLKLIKEE 47 (259)
T ss_pred cEEEEeCcHHHHHHHHCCCcccCCCCCc---ccHHHHHHHHHHHHHHHc
Confidence 589999999999988852 2321 245677888888887765
No 68
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=49.69 E-value=30 Score=25.40 Aligned_cols=41 Identities=39% Similarity=0.604 Sum_probs=29.9
Q ss_pred ceeeeechhhhhhhhcCCC--------cchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 4 ALLIVDSAMALYRTDYSGR--------GELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 4 ~LIIVDSiTALFR~EysGR--------GeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
.|++||...=+||+-|.-. |... ..+.-++++|++|.+.+.
T Consensus 2 ~llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t---~ai~g~~~~l~~l~~~~~ 50 (169)
T PF02739_consen 2 KLLLIDGNSLLFRAYYALPKDPLRNSDGEPT---NAIYGFLRMLLKLLKDFK 50 (169)
T ss_dssp EEEEEEHHHHHHHCCCCCTTST-BETTSEB----HHHHHHHHHHHHHHHHTT
T ss_pred eEEEEechHHHHHHHHhhccCCCcCCCCCCh---HHHHHHHHHHHHHHHHcC
Confidence 5899999999999987554 2221 346668888888887764
No 69
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=47.28 E-value=31 Score=26.43 Aligned_cols=43 Identities=28% Similarity=0.363 Sum_probs=30.0
Q ss_pred ceeeeechhhhhhhhcCCCcchH----HHHHHHHHHHHHHHHHHHHH
Q psy17736 4 ALLIVDSAMALYRTDYSGRGELS----ARQMHLARFLRMLLRLADEQ 46 (99)
Q Consensus 4 ~LIIVDSiTALFR~EysGRGeLA----~RQq~L~kqL~~L~rLAr~f 46 (99)
+|++||+-.-+||+-|.-+.... .-...+..+++.|.++.+.+
T Consensus 2 ~~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~ 48 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEY 48 (240)
T ss_pred cEEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhc
Confidence 58999999999998875531100 01246777888888887766
No 70
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=47.22 E-value=27 Score=30.25 Aligned_cols=37 Identities=22% Similarity=0.575 Sum_probs=25.4
Q ss_pred ccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHH
Q psy17736 2 KYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADE 45 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~ 45 (99)
++++||||++.++|- |.. ++ .-...-|+.++.+||..
T Consensus 194 rp~~vViDp~v~f~~----G~s-~s--~vqv~~fi~~~rkla~~ 230 (402)
T COG3598 194 RPDFVVIDPFVAFYE----GKS-IS--DVQVKEFIKKTRKLARN 230 (402)
T ss_pred CCCeEEEcchhhhcC----Ccc-ch--hHHHHHHHHHHHHHHHh
Confidence 478999999999875 542 22 13456677777777764
No 71
>TIGR01618 phage_P_loop phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.
Probab=46.57 E-value=12 Score=28.87 Aligned_cols=17 Identities=29% Similarity=0.366 Sum_probs=14.5
Q ss_pred ccceeeeechhhhhhhh
Q psy17736 2 KYALLIVDSAMALYRTD 18 (99)
Q Consensus 2 ~v~LIIVDSiTALFR~E 18 (99)
+|+.|||||++.|.+.-
T Consensus 81 ~ydtVVIDsI~~l~~~~ 97 (220)
T TIGR01618 81 KYDNIVIDNISALQNLW 97 (220)
T ss_pred cCCEEEEecHHHHHHHH
Confidence 47899999999999943
No 72
>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated
Probab=43.72 E-value=41 Score=24.43 Aligned_cols=17 Identities=12% Similarity=0.002 Sum_probs=14.0
Q ss_pred cceeeeechhhhhhhhc
Q psy17736 3 YALLIVDSAMALYRTDY 19 (99)
Q Consensus 3 v~LIIVDSiTALFR~Ey 19 (99)
.++|+|||++.+-+..+
T Consensus 77 ~~~VlID~Lt~~~~n~l 93 (170)
T PRK05800 77 GRCVLVDCLTTWVTNLL 93 (170)
T ss_pred CCEEEehhHHHHHHHHh
Confidence 46899999999987664
No 73
>PHA00520 packaging NTPase P4
Probab=42.39 E-value=35 Score=28.95 Aligned_cols=42 Identities=21% Similarity=0.280 Sum_probs=29.4
Q ss_pred Cccceeeeechhhhh-hhhcCCC---cchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 1 MKYALLIVDSAMALY-RTDYSGR---GELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 1 ~~v~LIIVDSiTALF-R~EysGR---GeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
|.+++|+|||+-.+| ++- |- |-.+ +.+=.+|+.|-.||..++
T Consensus 182 l~v~VvvvDSlr~vl~~~~--GnatsGGIS---r~~~~~LTdl~~iaas~g 227 (330)
T PHA00520 182 LDVDVVVVDSLRNVLFELG--GNATSGGIS---RGAYGLLTDLGNIAASRG 227 (330)
T ss_pred hhceEEEEechHHHHhhhc--cCCCCCcch---HHHHHHHHHHHHHHHHcC
Confidence 457899999999954 432 32 2232 457778899999998765
No 74
>PF07098 DUF1360: Protein of unknown function (DUF1360); InterPro: IPR010773 This entry is represented by Mycobacterium phage PG1, Gp7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins of around 115 residues in length. Members of this family are found in Bacillus species and Streptomyces coelicolor, the function of the family is unknown.
Probab=42.17 E-value=5.2 Score=28.27 Aligned_cols=16 Identities=19% Similarity=0.407 Sum_probs=14.8
Q ss_pred ceeeeechhhhhhhhc
Q psy17736 4 ALLIVDSAMALYRTDY 19 (99)
Q Consensus 4 ~LIIVDSiTALFR~Ey 19 (99)
+||+-|+||++.|.-|
T Consensus 11 RLi~~D~It~~lR~pF 26 (105)
T PF07098_consen 11 RLIVKDKITSPLRAPF 26 (105)
T ss_pred HHHHHhhhhHHHHHHH
Confidence 7899999999999877
No 75
>KOG2859|consensus
Probab=39.66 E-value=41 Score=28.03 Aligned_cols=18 Identities=39% Similarity=0.473 Sum_probs=15.1
Q ss_pred cceeeeechhhhhhhhcC
Q psy17736 3 YALLIVDSAMALYRTDYS 20 (99)
Q Consensus 3 v~LIIVDSiTALFR~Eys 20 (99)
+-|+++||+.|||=.+..
T Consensus 155 ~cll~~DslsaFyW~Dr~ 172 (293)
T KOG2859|consen 155 ICLLAMDSLSAFYWLDRP 172 (293)
T ss_pred eeEEeecchhhheeeccc
Confidence 558999999999987753
No 76
>PRK09482 flap endonuclease-like protein; Provisional
Probab=38.71 E-value=48 Score=26.41 Aligned_cols=43 Identities=16% Similarity=0.142 Sum_probs=30.8
Q ss_pred ceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 4 ALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQK 47 (99)
Q Consensus 4 ~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~ 47 (99)
.|++||+..=+||+-|........ -..+--|++.|.+|-+.++
T Consensus 4 ~llLiDg~~l~~R~~~a~~~~~g~-t~av~gf~~~l~~ll~~~~ 46 (256)
T PRK09482 4 HLLIIDALNLIRRIHAVQPSPNDI-NACVETCQHALDKLIRHSQ 46 (256)
T ss_pred eEEEEeCcHHHHHHHhCCCCCCCc-chHHHHHHHHHHHHHHHcC
Confidence 599999999999988765311111 3457778888888887764
No 77
>KOG1359|consensus
Probab=37.69 E-value=24 Score=30.55 Aligned_cols=33 Identities=24% Similarity=0.440 Sum_probs=23.7
Q ss_pred CccceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 1 MKYALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQKR 48 (99)
Q Consensus 1 ~~v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~~ 48 (99)
|+.+||+.||+- |-+|..|. |..|..||++|+.
T Consensus 192 ~r~klv~TDg~F-------SMDGdiaP--------l~ei~~La~kYga 224 (417)
T KOG1359|consen 192 MRLKLVVTDGVF-------SMDGDIAP--------LEEISQLAKKYGA 224 (417)
T ss_pred heEEEEEeccee-------ccCCCccc--------HHHHHHHHHhcCc
Confidence 678999999874 34566765 3567778888863
No 78
>PF10483 Elong_Iki1: Elongator subunit Iki1; InterPro: IPR019519 Histone acetylation protein (Hap) 2 (also known as Elongator complex protein 5) is one of three histone acetyltransferases proteins that, in yeasts, are found associated with elongating forms of RNA polymerase II (Elongator). The Haps can be isolated in two forms, as a six-subunit complex with Elongator, and as a complex of the three proteins on their own. The role of the Hap complex in transcription is still speculative, being possibly to keep the histone acetylation activity of free Elongator in check, allowing histone acetylation only in the presence of a transcribing polymerase, or the interaction with Haps might render Elongator susceptible to modifications thereby altering its activity []. This protein family also contains Dermal papilla-derived protein 6, which also belong to the ELP5 family. ; PDB: 4A8J_B 4EJS_B.
Probab=35.57 E-value=34 Score=26.96 Aligned_cols=27 Identities=33% Similarity=0.453 Sum_probs=15.8
Q ss_pred ceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHH
Q psy17736 4 ALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLL 40 (99)
Q Consensus 4 ~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~ 40 (99)
-||||||+..|.+.- + . .|..|++.|.
T Consensus 90 ~lVvIDSLn~ll~~~--~-------~-~l~~fLssl~ 116 (280)
T PF10483_consen 90 FLVVIDSLNYLLNHH--P-------C-QLSQFLSSLL 116 (280)
T ss_dssp EEEEES-GGGS-GG-------------GHHHHHHHH-
T ss_pred eEEEEEcchHHHHHH--H-------H-HHHHHHHhcc
Confidence 589999999887743 1 0 5666666665
No 79
>PF08361 TetR_C_2: MAATS-type transcriptional repressor, C-terminal region; InterPro: IPR013572 This entry is named after the various transcriptional regulatory proteins that it contains, including MtrR (Q6RV06 from SWISSPROT), AcrR (P34000 from SWISSPROT), ArpR (Q9KJC4 from SWISSPROT), TtgR (Q9AIU0 from SWISSPROT) and SmeT (Q8KLP4 from SWISSPROT). These are members of the TetR (tetracycline resistance) family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins [, , ]. ; GO: 0003677 DNA binding; PDB: 3BCG_B 2QOP_A 2UXP_B 2XDN_C 2UXH_A 2UXI_B 2UXO_A 2UXU_B 2WUI_A 2W53_A ....
Probab=30.53 E-value=1.6e+02 Score=19.90 Aligned_cols=39 Identities=13% Similarity=0.174 Sum_probs=22.7
Q ss_pred hhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy17736 12 MALYRTDYSGRGELSARQMHLARFLRMLLRLADEQKRRKR 51 (99)
Q Consensus 12 TALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~~~~~ 51 (99)
+.+.|++|++.-. +.+.++...+...+.+|+.-+.+-.+
T Consensus 29 I~~~kcE~~~e~~-~~~~r~~~~~~~~~~~i~~~l~~A~~ 67 (121)
T PF08361_consen 29 ILFHKCEYVEEMA-PVRERRREAQREALARIERLLRRAQA 67 (121)
T ss_dssp HHHHS--SSTTTH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcccCCccc-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999998733 33455566666666666666655433
No 80
>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.
Probab=29.84 E-value=1.2e+02 Score=22.15 Aligned_cols=18 Identities=6% Similarity=-0.022 Sum_probs=14.5
Q ss_pred cceeeeechhhhhhhhcC
Q psy17736 3 YALLIVDSAMALYRTDYS 20 (99)
Q Consensus 3 v~LIIVDSiTALFR~Eys 20 (99)
.+.|+|||+|.+-...+.
T Consensus 74 ~~~VLIDclt~~~~n~l~ 91 (169)
T cd00544 74 GDVVLIDCLTLWVTNLLF 91 (169)
T ss_pred CCEEEEEcHhHHHHHhCC
Confidence 468999999998777754
No 81
>cd06874 PX_KIF16B_SNX23 The phosphoinositide binding Phox Homology domain of KIF16B kinesin or Sorting Nexin 23. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. KIF16B, also called sorting nexin 23 (SNX23), is a family-3 kinesin which harbors an N-terminal kinesin motor domain containing ATP and microtubule binding sites, a ForkHead Associated (FHA) domain, and a C-terminal PX domain. The PX domain of KIF16B binds to phosphatidylinositol-3-phosphate (PI3P) in early endosomes and plays a role in the transport of early endosomes to the plus end of microtubules. By regulating early endosome plus end motility, KIF16B modulates the balance between recycling and degradation of receptors. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endoso
Probab=27.93 E-value=65 Score=22.94 Aligned_cols=21 Identities=19% Similarity=0.371 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q psy17736 25 LSARQMHLARFLRMLLRLADE 45 (99)
Q Consensus 25 LA~RQq~L~kqL~~L~rLAr~ 45 (99)
+..|++.|..+|..|+.+|..
T Consensus 74 ie~Rr~~Le~yL~~Ll~~~~~ 94 (127)
T cd06874 74 AKERRRQLETYLRNFFSVCLK 94 (127)
T ss_pred HHHHHHHHHHHHHHHHHhchh
Confidence 667999999999999998764
No 82
>KOG0132|consensus
Probab=27.28 E-value=43 Score=31.72 Aligned_cols=17 Identities=24% Similarity=0.493 Sum_probs=15.4
Q ss_pred ceeeeechhhhhhhhcC
Q psy17736 4 ALLIVDSAMALYRTDYS 20 (99)
Q Consensus 4 ~LIIVDSiTALFR~Eys 20 (99)
+|-|||||+.-||-.|-
T Consensus 62 gLYVIDSIVRqsrhq~~ 78 (894)
T KOG0132|consen 62 GLYVIDSIVRQSRHQFG 78 (894)
T ss_pred eeEEehHHHHHHHHhhc
Confidence 68899999999998885
No 83
>smart00382 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Probab=25.89 E-value=33 Score=20.69 Aligned_cols=17 Identities=24% Similarity=0.356 Sum_probs=14.1
Q ss_pred cceeeeechhhhhhhhc
Q psy17736 3 YALLIVDSAMALYRTDY 19 (99)
Q Consensus 3 v~LIIVDSiTALFR~Ey 19 (99)
+.+||||.+..+.....
T Consensus 79 ~~viiiDei~~~~~~~~ 95 (148)
T smart00382 79 PDVLILDEITSLLDAEQ 95 (148)
T ss_pred CCEEEEECCcccCCHHH
Confidence 48999999999887653
No 84
>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.
Probab=25.06 E-value=35 Score=27.58 Aligned_cols=12 Identities=25% Similarity=0.171 Sum_probs=10.3
Q ss_pred eeeeechhhhhh
Q psy17736 5 LLIVDSAMALYR 16 (99)
Q Consensus 5 LIIVDSiTALFR 16 (99)
|||+||+|.|-+
T Consensus 164 lvl~DslTr~A~ 175 (274)
T cd01132 164 LIIYDDLSKQAV 175 (274)
T ss_pred EEEEcChHHHHH
Confidence 789999999944
No 85
>COG0156 BioF 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]
Probab=24.63 E-value=61 Score=27.30 Aligned_cols=31 Identities=23% Similarity=0.416 Sum_probs=22.3
Q ss_pred cceeeeechhhhhhhhcCCCcchHHHHHHHHHHHHHHHHHHHHHHH
Q psy17736 3 YALLIVDSAMALYRTDYSGRGELSARQMHLARFLRMLLRLADEQKR 48 (99)
Q Consensus 3 v~LIIVDSiTALFR~EysGRGeLA~RQq~L~kqL~~L~rLAr~f~~ 48 (99)
-.|||+||+- |-+|.+|. |..|..||++|+-
T Consensus 172 ~~~IvtegVf-------SMdGdiAp--------L~~l~~L~~ky~a 202 (388)
T COG0156 172 RKLIVTEGVF-------SMDGDIAP--------LPELVELAEKYGA 202 (388)
T ss_pred ceEEEEeccc-------cCCCCcCC--------HHHHHHHHHHhCc
Confidence 3689999874 34566665 4678888888863
No 86
>PRK12608 transcription termination factor Rho; Provisional
Probab=22.32 E-value=49 Score=28.10 Aligned_cols=14 Identities=29% Similarity=0.430 Sum_probs=12.4
Q ss_pred eeeeechhhhhhhh
Q psy17736 5 LLIVDSAMALYRTD 18 (99)
Q Consensus 5 LIIVDSiTALFR~E 18 (99)
|||+||+|.|-|+.
T Consensus 223 VLvlDsltr~A~A~ 236 (380)
T PRK12608 223 VILLDSLTRLARAY 236 (380)
T ss_pred EEEEeCcHHHHHHH
Confidence 78999999998865
No 87
>PRK04296 thymidine kinase; Provisional
Probab=21.94 E-value=76 Score=23.02 Aligned_cols=10 Identities=30% Similarity=0.524 Sum_probs=8.5
Q ss_pred ccceeeeech
Q psy17736 2 KYALLIVDSA 11 (99)
Q Consensus 2 ~v~LIIVDSi 11 (99)
++++||||++
T Consensus 78 ~~dvviIDEa 87 (190)
T PRK04296 78 KIDCVLIDEA 87 (190)
T ss_pred CCCEEEEEcc
Confidence 4689999998
No 88
>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....
Probab=21.27 E-value=59 Score=24.90 Aligned_cols=14 Identities=36% Similarity=0.382 Sum_probs=12.1
Q ss_pred eeeeechhhhhhhh
Q psy17736 5 LLIVDSAMALYRTD 18 (99)
Q Consensus 5 LIIVDSiTALFR~E 18 (99)
|||+||+|.+-++-
T Consensus 108 lli~Dsltr~a~A~ 121 (215)
T PF00006_consen 108 LLIIDSLTRWAQAY 121 (215)
T ss_dssp EEEEETHHHHHHHH
T ss_pred eehhhhhHHHHHHH
Confidence 78999999988765
No 89
>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.
Probab=20.59 E-value=58 Score=26.25 Aligned_cols=14 Identities=21% Similarity=0.482 Sum_probs=12.1
Q ss_pred eeeeechhhhhhhh
Q psy17736 5 LLIVDSAMALYRTD 18 (99)
Q Consensus 5 LIIVDSiTALFR~E 18 (99)
|||+||+|.+-++-
T Consensus 166 l~~~Dsltr~a~A~ 179 (274)
T cd01133 166 LLFIDNIFRFTQAG 179 (274)
T ss_pred EEEEeChhHHHHHH
Confidence 78999999988765
No 90
>PRK10281 hypothetical protein; Provisional
Probab=20.31 E-value=1.1e+02 Score=24.33 Aligned_cols=19 Identities=26% Similarity=0.410 Sum_probs=14.4
Q ss_pred CccceeeeechhhhhhhhcCCC
Q psy17736 1 MKYALLIVDSAMALYRTDYSGR 22 (99)
Q Consensus 1 ~~v~LIIVDSiTALFR~EysGR 22 (99)
|++...+||.+|. .-|.|.
T Consensus 1 ~~~~~~~vDaFt~---~~f~GN 19 (299)
T PRK10281 1 MKPQIYHVDAFTS---QPFRGN 19 (299)
T ss_pred CCceEEEEEeccC---CCCCCC
Confidence 6788999999987 445554
No 91
>PRK06793 fliI flagellum-specific ATP synthase; Validated
Probab=20.19 E-value=54 Score=28.08 Aligned_cols=15 Identities=27% Similarity=0.397 Sum_probs=13.2
Q ss_pred ceeeeechhhhhhhh
Q psy17736 4 ALLIVDSAMALYRTD 18 (99)
Q Consensus 4 ~LIIVDSiTALFR~E 18 (99)
-|||+||+|.+.++.
T Consensus 248 VLlilDslTr~a~A~ 262 (432)
T PRK06793 248 VLLMMDSVTRFADAR 262 (432)
T ss_pred EEEEecchHHHHHHH
Confidence 589999999999874
Done!