Query psy12659
Match_columns 1051
No_of_seqs 785 out of 3373
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 16:13:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12659.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12659hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1806|consensus 100.0 2.5E-88 5.4E-93 797.7 23.8 475 451-1048 373-889 (1320)
2 KOG1806|consensus 100.0 2.5E-63 5.4E-68 586.5 13.7 404 13-455 604-1007(1320)
3 KOG1802|consensus 99.9 1.7E-23 3.8E-28 241.8 15.1 169 89-262 321-491 (935)
4 TIGR00376 DNA helicase, putati 99.9 2.3E-21 5.1E-26 236.0 21.1 284 116-442 102-405 (637)
5 KOG1803|consensus 99.9 6E-22 1.3E-26 229.7 9.9 285 121-459 128-418 (649)
6 PF13086 AAA_11: AAA domain; P 99.9 8.1E-22 1.8E-26 207.7 9.0 94 177-270 1-107 (236)
7 KOG1805|consensus 99.8 9.2E-20 2E-24 219.2 9.9 184 176-456 668-853 (1100)
8 TIGR00376 DNA helicase, putati 99.7 2.3E-17 5.1E-22 201.2 3.6 221 659-895 1-233 (637)
9 KOG1803|consensus 99.6 5.2E-16 1.1E-20 180.9 8.4 86 810-903 180-266 (649)
10 KOG1802|consensus 99.6 8.6E-15 1.9E-19 170.6 11.9 137 720-896 351-487 (935)
11 PF13086 AAA_11: AAA domain; P 99.5 9.7E-15 2.1E-19 154.0 9.4 82 815-896 1-94 (236)
12 KOG1807|consensus 99.4 3.3E-13 7.1E-18 159.6 12.3 87 172-260 373-463 (1025)
13 KOG1805|consensus 99.3 3.3E-12 7E-17 155.1 9.9 116 815-935 669-793 (1100)
14 PF13245 AAA_19: Part of AAA d 99.3 8.2E-12 1.8E-16 112.7 7.5 59 184-242 1-62 (76)
15 PF13245 AAA_19: Part of AAA d 99.2 1.1E-11 2.4E-16 111.8 7.0 59 822-880 1-62 (76)
16 KOG1807|consensus 99.0 6.5E-10 1.4E-14 132.3 7.3 84 814-899 377-464 (1025)
17 PF13604 AAA_30: AAA domain; P 98.9 1.7E-09 3.6E-14 114.5 8.5 64 177-242 1-66 (196)
18 PF13604 AAA_30: AAA domain; P 98.9 3.5E-09 7.6E-14 112.0 8.3 64 815-880 1-66 (196)
19 PF00580 UvrD-helicase: UvrD/R 98.8 1.4E-08 3.1E-13 112.4 8.5 66 178-245 1-68 (315)
20 PF00580 UvrD-helicase: UvrD/R 98.7 2.5E-08 5.3E-13 110.5 8.3 66 816-883 1-68 (315)
21 TIGR01447 recD exodeoxyribonuc 98.7 4.2E-08 9.2E-13 119.4 8.9 66 180-245 148-216 (586)
22 PRK10875 recD exonuclease V su 98.6 6.3E-08 1.4E-12 118.3 9.1 67 178-244 153-221 (615)
23 TIGR01447 recD exodeoxyribonuc 98.6 1.3E-07 2.7E-12 115.3 9.2 65 818-882 148-215 (586)
24 PRK10875 recD exonuclease V su 98.5 1.7E-07 3.6E-12 114.6 9.2 66 817-882 154-221 (615)
25 TIGR01448 recD_rel helicase, p 98.5 2.2E-07 4.7E-12 116.1 8.7 68 174-241 320-387 (720)
26 PRK10919 ATP-dependent DNA hel 98.4 3.8E-07 8.3E-12 113.2 8.1 67 177-245 2-70 (672)
27 TIGR01448 recD_rel helicase, p 98.4 6.4E-07 1.4E-11 111.9 9.0 68 813-880 321-388 (720)
28 PRK10919 ATP-dependent DNA hel 98.3 6.8E-07 1.5E-11 111.0 7.9 67 815-883 2-70 (672)
29 PRK11773 uvrD DNA-dependent he 98.3 6.7E-07 1.5E-11 112.0 7.8 67 177-245 9-77 (721)
30 TIGR01075 uvrD DNA helicase II 98.3 6.3E-07 1.4E-11 112.2 7.4 67 177-245 4-72 (715)
31 TIGR02768 TraA_Ti Ti-type conj 98.3 1.1E-06 2.4E-11 110.2 9.3 64 175-240 350-414 (744)
32 PRK11773 uvrD DNA-dependent he 98.3 9.5E-07 2.1E-11 110.7 7.7 67 815-883 9-77 (721)
33 TIGR01075 uvrD DNA helicase II 98.3 1E-06 2.2E-11 110.4 7.6 67 815-883 4-72 (715)
34 smart00487 DEXDc DEAD-like hel 98.3 3.4E-06 7.3E-11 85.6 9.7 72 175-246 6-78 (201)
35 PRK11054 helD DNA helicase IV; 98.2 1.7E-06 3.7E-11 107.3 8.2 70 812-883 193-264 (684)
36 PRK11054 helD DNA helicase IV; 98.2 1.8E-06 3.9E-11 107.1 8.1 68 176-245 195-264 (684)
37 TIGR01074 rep ATP-dependent DN 98.2 1.9E-06 4E-11 107.1 8.2 67 177-245 1-69 (664)
38 smart00487 DEXDc DEAD-like hel 98.2 4.9E-06 1.1E-10 84.4 9.5 72 813-884 6-78 (201)
39 TIGR02768 TraA_Ti Ti-type conj 98.2 2.6E-06 5.5E-11 107.0 9.0 65 813-879 350-415 (744)
40 PRK13889 conjugal transfer rel 98.2 2.9E-06 6.2E-11 108.3 8.9 64 175-240 344-408 (988)
41 TIGR01073 pcrA ATP-dependent D 98.2 2.3E-06 5.1E-11 107.3 7.6 67 177-245 4-72 (726)
42 TIGR01074 rep ATP-dependent DN 98.2 3E-06 6.4E-11 105.3 8.1 67 815-883 1-69 (664)
43 TIGR01073 pcrA ATP-dependent D 98.1 3.8E-06 8.2E-11 105.4 7.7 67 815-883 4-72 (726)
44 PRK13889 conjugal transfer rel 98.1 6.8E-06 1.5E-10 104.9 8.6 63 814-878 345-408 (988)
45 PRK13826 Dtr system oriT relax 98.0 1E-05 2.3E-10 103.8 9.2 65 175-241 379-444 (1102)
46 PRK14712 conjugal transfer nic 98.0 1.4E-05 3.1E-10 105.3 8.6 65 176-240 834-902 (1623)
47 PF04851 ResIII: Type III rest 97.9 2.1E-05 4.5E-10 80.1 7.6 65 176-245 2-73 (184)
48 PRK13826 Dtr system oriT relax 97.9 2E-05 4.4E-10 101.2 9.0 65 813-879 379-444 (1102)
49 PF05970 PIF1: PIF1-like helic 97.9 1.6E-05 3.4E-10 92.1 7.3 60 177-238 1-66 (364)
50 PF00270 DEAD: DEAD/DEAH box h 97.9 4.8E-05 1E-09 76.9 9.7 69 179-247 1-69 (169)
51 PF04851 ResIII: Type III rest 97.9 2.3E-05 5E-10 79.8 7.3 65 814-883 2-73 (184)
52 cd00046 DEXDc DEAD-like helica 97.9 3E-05 6.4E-10 74.0 7.1 53 194-246 2-54 (144)
53 PF05970 PIF1: PIF1-like helic 97.9 2.4E-05 5.1E-10 90.7 7.2 60 815-876 1-66 (364)
54 PRK13709 conjugal transfer nic 97.9 2.9E-05 6.3E-10 103.8 8.7 65 176-240 966-1034(1747)
55 PF00270 DEAD: DEAD/DEAH box h 97.8 8.6E-05 1.9E-09 75.1 9.5 69 817-885 1-69 (169)
56 TIGR02760 TraI_TIGR conjugativ 97.8 4E-05 8.7E-10 104.6 9.2 67 174-242 426-494 (1960)
57 cd00046 DEXDc DEAD-like helica 97.8 4.5E-05 9.8E-10 72.7 7.1 53 832-884 2-54 (144)
58 COG0210 UvrD Superfamily I DNA 97.8 3.8E-05 8.2E-10 95.3 7.3 68 177-246 2-71 (655)
59 PRK14712 conjugal transfer nic 97.8 5.1E-05 1.1E-09 100.4 8.6 64 815-878 835-902 (1623)
60 COG0210 UvrD Superfamily I DNA 97.7 5.7E-05 1.2E-09 93.8 7.4 68 815-884 2-71 (655)
61 PRK13709 conjugal transfer nic 97.7 8E-05 1.7E-09 99.7 8.5 65 814-878 966-1034(1747)
62 TIGR02760 TraI_TIGR conjugativ 97.6 9.2E-05 2E-09 101.2 8.9 66 813-880 427-494 (1960)
63 cd00268 DEADc DEAD-box helicas 97.5 0.00049 1.1E-08 72.2 10.0 69 177-245 21-92 (203)
64 PTZ00252 histone H2A; Provisio 97.4 8.7E-05 1.9E-09 73.3 3.3 90 848-937 28-121 (134)
65 PF02562 PhoH: PhoH-like prote 97.4 0.00023 5E-09 76.3 6.4 58 815-872 4-61 (205)
66 cd01124 KaiC KaiC is a circadi 97.4 0.00021 4.6E-09 73.8 6.0 60 832-894 1-60 (187)
67 cd00268 DEADc DEAD-box helicas 97.4 0.0006 1.3E-08 71.5 9.3 69 815-883 21-92 (203)
68 PLN00153 histone H2A; Provisio 97.4 9.7E-05 2.1E-09 72.9 2.8 45 894-938 75-119 (129)
69 TIGR02785 addA_Gpos recombinat 97.4 0.00036 7.8E-09 92.5 9.0 67 177-245 1-68 (1232)
70 PLN00156 histone H2AX; Provisi 97.4 0.0001 2.2E-09 73.5 2.9 45 894-938 80-124 (139)
71 cd01124 KaiC KaiC is a circadi 97.4 0.0002 4.3E-09 74.1 5.1 53 194-249 1-53 (187)
72 PTZ00017 histone H2A; Provisio 97.4 9.3E-05 2E-09 73.5 2.5 67 871-938 56-122 (134)
73 PF02562 PhoH: PhoH-like prote 97.3 0.00031 6.6E-09 75.3 6.1 58 177-234 4-61 (205)
74 PLN00157 histone H2A; Provisio 97.3 0.00013 2.9E-09 72.2 2.9 45 894-938 77-121 (132)
75 TIGR02785 addA_Gpos recombinat 97.3 0.00056 1.2E-08 90.7 8.7 67 815-883 1-68 (1232)
76 smart00414 H2A Histone 2A. 97.2 0.00018 3.8E-09 69.3 2.6 66 872-938 39-104 (106)
77 cd00009 AAA The AAA+ (ATPases 97.2 0.0011 2.5E-08 63.7 7.8 55 819-875 5-62 (151)
78 PHA02558 uvsW UvsW helicase; P 97.2 0.0012 2.6E-08 79.9 9.4 71 175-246 112-182 (501)
79 cd00009 AAA The AAA+ (ATPases 97.1 0.0013 2.8E-08 63.4 7.6 54 180-235 4-60 (151)
80 cd00074 H2A Histone 2A; H2A is 97.1 0.00023 5E-09 69.4 2.3 65 872-937 50-114 (115)
81 PLN00154 histone H2A; Provisio 97.1 0.00035 7.5E-09 69.4 3.5 88 849-938 42-133 (136)
82 PRK10536 hypothetical protein; 97.1 0.0012 2.5E-08 73.1 7.4 56 814-869 58-113 (262)
83 PHA02558 uvsW UvsW helicase; P 97.1 0.0016 3.4E-08 78.8 9.1 70 814-884 113-182 (501)
84 PRK05580 primosome assembly pr 97.0 0.0017 3.7E-08 81.2 9.3 70 812-883 141-213 (679)
85 PRK10536 hypothetical protein; 97.0 0.0012 2.7E-08 72.9 7.0 57 176-233 58-114 (262)
86 TIGR00643 recG ATP-dependent D 97.0 0.0017 3.6E-08 80.7 8.6 70 812-883 232-307 (630)
87 KOG1756|consensus 97.0 0.00045 9.7E-09 67.4 2.7 46 894-939 78-123 (131)
88 PRK10917 ATP-dependent DNA hel 97.0 0.0019 4.2E-08 80.9 9.1 70 812-883 258-333 (681)
89 PRK05580 primosome assembly pr 97.0 0.0024 5.2E-08 80.0 9.7 69 175-245 142-213 (679)
90 PRK07952 DNA replication prote 97.0 0.0016 3.5E-08 71.7 7.2 49 817-867 78-134 (244)
91 PRK07952 DNA replication prote 96.9 0.0023 5E-08 70.5 8.2 60 178-244 77-144 (244)
92 PRK08181 transposase; Validate 96.9 0.0024 5.2E-08 71.3 8.4 51 815-867 87-141 (269)
93 COG1061 SSL2 DNA or RNA helica 96.9 0.0025 5.5E-08 75.9 9.0 80 176-260 35-118 (442)
94 PTZ00424 helicase 45; Provisio 96.9 0.0025 5.3E-08 74.2 8.7 70 177-246 50-120 (401)
95 smart00382 AAA ATPases associa 96.9 0.00078 1.7E-08 64.0 3.6 42 830-873 2-43 (148)
96 COG1061 SSL2 DNA or RNA helica 96.8 0.0025 5.3E-08 76.0 8.0 68 812-884 33-104 (442)
97 PRK08181 transposase; Validate 96.8 0.0035 7.5E-08 70.0 8.6 52 176-229 86-141 (269)
98 smart00382 AAA ATPases associa 96.8 0.00089 1.9E-08 63.6 3.3 40 192-233 2-41 (148)
99 PTZ00424 helicase 45; Provisio 96.8 0.0033 7.1E-08 73.2 8.6 69 815-883 50-119 (401)
100 PF06745 KaiC: KaiC; InterPro 96.8 0.0016 3.5E-08 70.1 5.6 58 830-890 19-77 (226)
101 PRK12377 putative replication 96.8 0.0021 4.6E-08 70.9 6.5 43 831-876 102-144 (248)
102 TIGR00643 recG ATP-dependent D 96.8 0.0027 5.9E-08 78.9 8.2 70 174-245 232-307 (630)
103 PRK10917 ATP-dependent DNA hel 96.8 0.0032 7E-08 78.9 8.9 70 174-245 258-333 (681)
104 TIGR00609 recB exodeoxyribonuc 96.8 0.0018 4E-08 85.0 6.8 53 192-244 9-64 (1087)
105 PF00448 SRP54: SRP54-type pro 96.8 0.0031 6.7E-08 67.2 7.2 60 192-256 1-63 (196)
106 PRK11776 ATP-dependent RNA hel 96.8 0.0043 9.3E-08 74.0 9.3 70 176-245 25-95 (460)
107 PF00448 SRP54: SRP54-type pro 96.7 0.0026 5.6E-08 67.8 6.2 54 830-885 1-57 (196)
108 COG1112 Superfamily I DNA and 96.7 0.0063 1.4E-07 76.7 10.7 93 175-269 272-368 (767)
109 PRK11192 ATP-dependent RNA hel 96.7 0.0055 1.2E-07 72.5 9.5 70 176-245 22-96 (434)
110 PRK05973 replicative DNA helic 96.7 0.0034 7.5E-08 68.8 7.2 61 824-887 57-118 (237)
111 PRK08533 flagellar accessory p 96.7 0.0028 6.1E-08 69.1 6.5 54 830-886 24-77 (230)
112 COG3973 Superfamily I DNA and 96.7 0.004 8.6E-08 74.8 7.9 69 816-885 213-285 (747)
113 PRK08116 hypothetical protein; 96.7 0.0059 1.3E-07 68.1 9.0 35 831-867 115-149 (268)
114 COG5262 HTA1 Histone H2A [Chro 96.6 0.002 4.3E-08 61.9 4.2 88 849-938 30-121 (132)
115 PRK12377 putative replication 96.6 0.0058 1.3E-07 67.5 8.4 57 179-238 80-144 (248)
116 TIGR00609 recB exodeoxyribonuc 96.6 0.0026 5.6E-08 83.6 6.6 54 830-883 9-65 (1087)
117 PRK01172 ski2-like helicase; P 96.6 0.0056 1.2E-07 76.6 9.3 68 175-244 20-87 (674)
118 PRK05973 replicative DNA helic 96.6 0.0044 9.5E-08 68.0 7.2 61 186-249 57-118 (237)
119 PRK11192 ATP-dependent RNA hel 96.6 0.006 1.3E-07 72.1 8.9 69 815-883 23-96 (434)
120 KOG1757|consensus 96.6 0.00094 2E-08 63.5 1.7 65 872-938 61-125 (131)
121 TIGR03877 thermo_KaiC_1 KaiC d 96.6 0.0035 7.5E-08 68.4 6.4 54 192-248 21-74 (237)
122 PRK13833 conjugal transfer pro 96.6 0.0036 7.7E-08 71.7 6.6 53 177-229 128-181 (323)
123 PF01695 IstB_IS21: IstB-like 96.6 0.0033 7.1E-08 66.0 5.8 46 830-882 47-92 (178)
124 TIGR03877 thermo_KaiC_1 KaiC d 96.6 0.0039 8.4E-08 68.1 6.6 54 830-886 21-74 (237)
125 PF01695 IstB_IS21: IstB-like 96.6 0.0062 1.3E-07 63.9 7.7 60 178-244 30-92 (178)
126 PRK11776 ATP-dependent RNA hel 96.6 0.0066 1.4E-07 72.5 8.9 69 815-883 26-95 (460)
127 PRK01172 ski2-like helicase; P 96.5 0.0072 1.6E-07 75.7 9.4 68 813-882 20-87 (674)
128 PRK06526 transposase; Provisio 96.5 0.0029 6.2E-08 70.1 5.0 52 815-868 80-134 (254)
129 PF06745 KaiC: KaiC; InterPro 96.5 0.0052 1.1E-07 66.2 6.7 55 192-248 19-73 (226)
130 PRK08533 flagellar accessory p 96.5 0.005 1.1E-07 67.2 6.6 53 192-247 24-76 (230)
131 KOG0989|consensus 96.5 0.0028 6E-08 71.0 4.5 36 183-218 45-83 (346)
132 PRK14974 cell division protein 96.4 0.0067 1.4E-07 69.8 7.7 54 192-247 140-196 (336)
133 TIGR00580 mfd transcription-re 96.4 0.008 1.7E-07 77.5 9.2 70 812-883 448-523 (926)
134 PRK11634 ATP-dependent RNA hel 96.4 0.0099 2.1E-07 73.9 9.7 70 176-245 27-97 (629)
135 PRK13894 conjugal transfer ATP 96.4 0.0053 1.2E-07 70.2 6.7 55 178-232 133-188 (319)
136 KOG0989|consensus 96.4 0.0027 5.9E-08 71.1 4.2 27 830-856 57-83 (346)
137 PF09848 DUF2075: Uncharacteri 96.4 0.0053 1.1E-07 70.9 6.7 53 193-245 2-54 (352)
138 PRK06526 transposase; Provisio 96.4 0.0069 1.5E-07 67.2 7.1 51 176-228 79-132 (254)
139 PRK06893 DNA replication initi 96.4 0.0052 1.1E-07 66.8 6.1 37 830-868 39-75 (229)
140 PRK14974 cell division protein 96.4 0.0071 1.5E-07 69.6 7.4 54 830-885 140-196 (336)
141 PRK10689 transcription-repair 96.4 0.0084 1.8E-07 78.9 9.0 69 812-882 597-671 (1147)
142 TIGR00603 rad25 DNA repair hel 96.4 0.013 2.8E-07 73.4 10.1 78 176-258 254-335 (732)
143 PRK08116 hypothetical protein; 96.4 0.0089 1.9E-07 66.7 7.9 34 194-229 116-149 (268)
144 PF07652 Flavi_DEAD: Flaviviru 96.4 0.0062 1.4E-07 61.8 6.0 53 830-884 4-57 (148)
145 PRK06067 flagellar accessory p 96.4 0.0074 1.6E-07 65.5 7.1 56 830-888 25-80 (234)
146 cd01120 RecA-like_NTPases RecA 96.4 0.0055 1.2E-07 60.8 5.6 39 194-234 1-39 (165)
147 PF13401 AAA_22: AAA domain; P 96.4 0.0029 6.4E-08 61.4 3.5 53 192-244 4-60 (131)
148 COG1484 DnaC DNA replication p 96.3 0.0043 9.3E-08 68.7 5.2 38 829-868 104-141 (254)
149 PF13191 AAA_16: AAA ATPase do 96.3 0.0086 1.9E-07 61.4 7.1 40 180-219 6-51 (185)
150 cd01120 RecA-like_NTPases RecA 96.3 0.0056 1.2E-07 60.7 5.5 40 832-873 1-40 (165)
151 TIGR02782 TrbB_P P-type conjug 96.3 0.0065 1.4E-07 68.9 6.6 56 177-232 116-172 (299)
152 TIGR00064 ftsY signal recognit 96.3 0.012 2.5E-07 65.9 8.6 54 192-247 72-128 (272)
153 TIGR03878 thermo_KaiC_2 KaiC d 96.3 0.0048 1E-07 68.4 5.4 38 192-231 36-73 (259)
154 cd01129 PulE-GspE PulE/GspE Th 96.3 0.0062 1.3E-07 67.8 6.2 52 814-867 62-115 (264)
155 PF00004 AAA: ATPase family as 96.3 0.0028 6E-08 61.2 3.0 22 195-216 1-22 (132)
156 TIGR03878 thermo_KaiC_2 KaiC d 96.3 0.005 1.1E-07 68.3 5.5 39 830-870 36-74 (259)
157 COG3973 Superfamily I DNA and 96.3 0.0094 2E-07 71.7 7.9 69 178-247 213-285 (747)
158 PRK13833 conjugal transfer pro 96.3 0.0069 1.5E-07 69.4 6.7 53 815-867 128-181 (323)
159 COG0467 RAD55 RecA-superfamily 96.3 0.0065 1.4E-07 67.1 6.3 55 830-887 23-77 (260)
160 TIGR02655 circ_KaiC circadian 96.3 0.0058 1.3E-07 73.7 6.4 58 830-890 263-320 (484)
161 PRK11448 hsdR type I restricti 96.3 0.011 2.4E-07 77.6 9.3 72 814-885 412-488 (1123)
162 PRK11634 ATP-dependent RNA hel 96.3 0.012 2.5E-07 73.3 9.1 69 815-883 28-97 (629)
163 PRK08084 DNA replication initi 96.3 0.0085 1.8E-07 65.5 7.0 53 816-870 28-83 (235)
164 cd01129 PulE-GspE PulE/GspE Th 96.3 0.0063 1.4E-07 67.7 6.1 54 175-230 61-116 (264)
165 PF00004 AAA: ATPase family as 96.3 0.0029 6.2E-08 61.1 3.0 22 833-854 1-22 (132)
166 TIGR03880 KaiC_arch_3 KaiC dom 96.3 0.0091 2E-07 64.3 7.0 53 192-247 16-68 (224)
167 PRK10689 transcription-repair 96.2 0.0049 1.1E-07 81.0 5.8 71 173-245 596-672 (1147)
168 TIGR00603 rad25 DNA repair hel 96.2 0.013 2.9E-07 73.3 9.2 67 812-883 252-321 (732)
169 PRK09401 reverse gyrase; Revie 96.2 0.012 2.6E-07 77.7 9.2 70 176-247 79-148 (1176)
170 PRK13894 conjugal transfer ATP 96.2 0.008 1.7E-07 68.8 6.8 56 815-870 132-188 (319)
171 PRK06067 flagellar accessory p 96.2 0.0092 2E-07 64.7 7.0 54 192-248 25-78 (234)
172 TIGR03880 KaiC_arch_3 KaiC dom 96.2 0.0093 2E-07 64.2 6.9 54 830-886 16-69 (224)
173 PRK10876 recB exonuclease V su 96.2 0.0065 1.4E-07 80.4 6.8 53 192-244 17-79 (1181)
174 PRK04328 hypothetical protein; 96.2 0.0079 1.7E-07 66.3 6.5 54 192-248 23-76 (249)
175 TIGR02655 circ_KaiC circadian 96.2 0.0048 1E-07 74.4 5.1 54 192-248 263-316 (484)
176 TIGR02525 plasmid_TraJ plasmid 96.2 0.01 2.2E-07 69.3 7.5 51 176-228 135-185 (372)
177 TIGR00580 mfd transcription-re 96.2 0.013 2.9E-07 75.5 9.2 69 175-245 449-523 (926)
178 TIGR00064 ftsY signal recognit 96.2 0.01 2.2E-07 66.4 7.3 54 830-885 72-128 (272)
179 PRK11448 hsdR type I restricti 96.2 0.017 3.6E-07 76.0 10.2 72 176-247 412-488 (1123)
180 PRK04837 ATP-dependent RNA hel 96.2 0.016 3.5E-07 68.4 9.3 70 176-245 29-106 (423)
181 COG0467 RAD55 RecA-superfamily 96.2 0.0063 1.4E-07 67.2 5.5 53 192-247 23-75 (260)
182 smart00488 DEXDc2 DEAD-like he 96.2 0.02 4.4E-07 64.5 9.6 72 811-883 4-84 (289)
183 smart00489 DEXDc3 DEAD-like he 96.2 0.02 4.4E-07 64.5 9.6 72 811-883 4-84 (289)
184 PRK09183 transposase/IS protei 96.2 0.011 2.3E-07 65.8 7.2 51 815-867 84-137 (259)
185 PF13401 AAA_22: AAA domain; P 96.2 0.0041 9E-08 60.4 3.5 54 830-883 4-61 (131)
186 PRK10590 ATP-dependent RNA hel 96.2 0.019 4E-07 68.7 9.7 70 176-245 22-98 (456)
187 PF07652 Flavi_DEAD: Flaviviru 96.2 0.0085 1.8E-07 60.9 5.7 52 192-245 4-56 (148)
188 PF09848 DUF2075: Uncharacteri 96.2 0.0085 1.8E-07 69.2 6.5 53 831-883 2-54 (352)
189 KOG0743|consensus 96.1 0.0052 1.1E-07 72.0 4.7 43 174-216 201-259 (457)
190 PRK04328 hypothetical protein; 96.1 0.01 2.2E-07 65.4 6.7 54 830-886 23-76 (249)
191 PRK08084 DNA replication initi 96.1 0.011 2.3E-07 64.7 6.8 52 178-231 28-82 (235)
192 TIGR01054 rgy reverse gyrase. 96.1 0.016 3.4E-07 76.6 9.4 68 176-245 77-144 (1171)
193 PRK00254 ski2-like helicase; P 96.1 0.021 4.5E-07 72.2 10.2 67 176-244 22-90 (720)
194 PRK14722 flhF flagellar biosyn 96.1 0.015 3.3E-07 67.7 8.2 56 192-247 137-195 (374)
195 PRK06893 DNA replication initi 96.1 0.007 1.5E-07 65.8 5.2 37 192-230 39-75 (229)
196 PRK09401 reverse gyrase; Revie 96.1 0.016 3.5E-07 76.5 9.1 68 815-884 80-147 (1176)
197 PRK08903 DnaA regulatory inact 96.0 0.022 4.8E-07 61.4 8.7 51 178-230 24-78 (227)
198 PF13191 AAA_16: AAA ATPase do 96.0 0.013 2.9E-07 60.0 6.7 39 819-857 7-51 (185)
199 cd03115 SRP The signal recogni 96.0 0.0087 1.9E-07 61.7 5.3 34 194-229 2-35 (173)
200 PRK10416 signal recognition pa 96.0 0.014 3E-07 66.8 7.4 54 192-247 114-170 (318)
201 PRK10590 ATP-dependent RNA hel 96.0 0.021 4.5E-07 68.3 9.2 69 815-883 23-98 (456)
202 PRK10867 signal recognition pa 96.0 0.017 3.8E-07 68.6 8.4 55 830-885 100-157 (433)
203 TIGR01587 cas3_core CRISPR-ass 96.0 0.013 2.8E-07 67.3 7.2 51 195-245 2-52 (358)
204 TIGR02928 orc1/cdc6 family rep 96.0 0.0086 1.9E-07 68.9 5.7 41 179-219 20-67 (365)
205 TIGR01650 PD_CobS cobaltochela 96.0 0.0093 2E-07 68.2 5.9 45 810-854 43-88 (327)
206 TIGR01970 DEAH_box_HrpB ATP-de 96.0 0.014 3.1E-07 74.4 8.1 62 181-244 5-67 (819)
207 COG1484 DnaC DNA replication p 96.0 0.0075 1.6E-07 66.8 5.0 38 191-230 104-141 (254)
208 TIGR02782 TrbB_P P-type conjug 96.0 0.012 2.5E-07 66.8 6.7 55 815-869 116-171 (299)
209 TIGR01054 rgy reverse gyrase. 96.0 0.018 4E-07 76.0 9.3 67 815-883 78-144 (1171)
210 KOG0744|consensus 96.0 0.0044 9.6E-08 69.7 3.1 26 192-217 177-202 (423)
211 PRK04837 ATP-dependent RNA hel 96.0 0.021 4.6E-07 67.4 9.0 68 815-882 30-105 (423)
212 PRK04296 thymidine kinase; Pro 96.0 0.0089 1.9E-07 63.2 5.2 36 193-230 3-38 (190)
213 PRK09183 transposase/IS protei 96.0 0.015 3.3E-07 64.5 7.2 51 177-229 84-137 (259)
214 PRK14722 flhF flagellar biosyn 96.0 0.016 3.4E-07 67.6 7.6 56 830-885 137-195 (374)
215 PRK06835 DNA replication prote 96.0 0.014 2.9E-07 67.2 7.0 37 830-868 183-219 (329)
216 PRK10416 signal recognition pa 96.0 0.015 3.3E-07 66.5 7.3 54 830-885 114-170 (318)
217 TIGR03881 KaiC_arch_4 KaiC dom 96.0 0.014 3E-07 63.0 6.6 54 830-886 20-73 (229)
218 PRK08903 DnaA regulatory inact 96.0 0.017 3.7E-07 62.2 7.3 51 816-868 24-78 (227)
219 TIGR03420 DnaA_homol_Hda DnaA 96.0 0.015 3.4E-07 62.0 7.0 40 830-871 38-77 (226)
220 PRK00771 signal recognition pa 96.0 0.015 3.3E-07 69.2 7.5 54 830-885 95-151 (437)
221 cd03115 SRP The signal recogni 95.9 0.01 2.2E-07 61.1 5.4 34 832-867 2-35 (173)
222 TIGR02784 addA_alphas double-s 95.9 0.012 2.6E-07 78.0 7.1 53 193-245 11-64 (1141)
223 PRK04296 thymidine kinase; Pro 95.9 0.0098 2.1E-07 62.9 5.2 36 831-868 3-38 (190)
224 PRK00771 signal recognition pa 95.9 0.017 3.8E-07 68.7 7.7 54 192-247 95-151 (437)
225 PRK11664 ATP-dependent RNA hel 95.9 0.013 2.9E-07 74.6 7.2 62 181-244 8-70 (812)
226 TIGR02928 orc1/cdc6 family rep 95.9 0.017 3.6E-07 66.5 7.4 40 817-856 20-66 (365)
227 KOG0744|consensus 95.9 0.0054 1.2E-07 69.1 3.1 54 830-883 177-244 (423)
228 TIGR01650 PD_CobS cobaltochela 95.9 0.014 3E-07 66.9 6.5 44 174-217 45-89 (327)
229 PRK04537 ATP-dependent RNA hel 95.9 0.027 5.9E-07 69.4 9.5 71 176-246 30-108 (572)
230 PRK09361 radB DNA repair and r 95.9 0.011 2.4E-07 63.6 5.4 38 830-869 23-60 (225)
231 PLN03025 replication factor C 95.9 0.017 3.7E-07 65.8 7.2 64 179-242 18-85 (319)
232 PRK06851 hypothetical protein; 95.8 0.0071 1.5E-07 70.3 4.1 47 191-239 29-77 (367)
233 PRK08727 hypothetical protein; 95.8 0.027 5.8E-07 61.5 8.3 38 830-869 41-78 (233)
234 PRK02362 ski2-like helicase; P 95.8 0.032 7E-07 70.7 10.2 68 176-245 22-90 (737)
235 TIGR02237 recomb_radB DNA repa 95.8 0.013 2.8E-07 62.2 5.4 39 830-870 12-50 (209)
236 cd01394 radB RadB. The archaea 95.8 0.013 2.7E-07 62.8 5.3 37 830-868 19-55 (218)
237 PRK00254 ski2-like helicase; P 95.8 0.026 5.6E-07 71.4 9.0 66 815-882 23-90 (720)
238 PF13207 AAA_17: AAA domain; P 95.8 0.0085 1.8E-07 57.6 3.7 23 194-216 1-23 (121)
239 TIGR01587 cas3_core CRISPR-ass 95.8 0.018 4E-07 66.1 7.0 51 833-883 2-52 (358)
240 cd00984 DnaB_C DnaB helicase C 95.7 0.013 2.8E-07 63.5 5.4 53 827-881 9-62 (242)
241 TIGR01970 DEAH_box_HrpB ATP-de 95.7 0.022 4.7E-07 72.8 8.1 61 820-882 6-67 (819)
242 PLN03025 replication factor C 95.7 0.021 4.6E-07 65.1 7.3 38 819-856 20-60 (319)
243 TIGR03420 DnaA_homol_Hda DnaA 95.7 0.017 3.8E-07 61.6 6.3 52 179-232 22-76 (226)
244 TIGR02533 type_II_gspE general 95.7 0.01 2.2E-07 71.6 4.9 54 172-227 220-275 (486)
245 PF00308 Bac_DnaA: Bacterial d 95.7 0.021 4.7E-07 61.8 7.0 38 193-230 35-72 (219)
246 PF13481 AAA_25: AAA domain; P 95.7 0.021 4.5E-07 59.6 6.7 53 192-245 32-92 (193)
247 PRK09361 radB DNA repair and r 95.7 0.014 3E-07 62.9 5.5 38 192-231 23-60 (225)
248 TIGR02237 recomb_radB DNA repa 95.7 0.014 3E-07 62.0 5.4 39 192-232 12-50 (209)
249 TIGR03881 KaiC_arch_4 KaiC dom 95.7 0.019 4.1E-07 61.9 6.5 53 192-247 20-72 (229)
250 PRK10876 recB exonuclease V su 95.7 0.015 3.2E-07 77.2 6.7 54 830-883 17-80 (1181)
251 PRK09694 helicase Cas3; Provis 95.7 0.032 7E-07 71.5 9.5 69 176-244 285-353 (878)
252 COG1198 PriA Primosomal protei 95.7 0.031 6.7E-07 70.1 9.1 69 174-244 195-267 (730)
253 KOG0743|consensus 95.7 0.011 2.3E-07 69.5 4.7 24 830-853 235-258 (457)
254 TIGR01425 SRP54_euk signal rec 95.7 0.021 4.5E-07 67.8 7.2 54 830-885 100-156 (429)
255 TIGR02881 spore_V_K stage V sp 95.7 0.011 2.5E-07 65.3 4.8 26 193-218 43-68 (261)
256 TIGR01425 SRP54_euk signal rec 95.7 0.03 6.5E-07 66.4 8.4 54 192-247 100-156 (429)
257 TIGR02525 plasmid_TraJ plasmid 95.7 0.023 5E-07 66.4 7.4 50 815-866 136-185 (372)
258 cd01394 radB RadB. The archaea 95.7 0.014 3.1E-07 62.3 5.3 36 192-229 19-54 (218)
259 PF05729 NACHT: NACHT domain 95.7 0.018 3.9E-07 57.7 5.7 29 193-221 1-29 (166)
260 TIGR03499 FlhF flagellar biosy 95.7 0.028 6.1E-07 63.2 7.8 50 192-241 194-246 (282)
261 TIGR02784 addA_alphas double-s 95.7 0.015 3.3E-07 77.1 6.5 53 831-883 11-64 (1141)
262 PRK00411 cdc6 cell division co 95.7 0.023 4.9E-07 66.2 7.3 41 180-220 36-83 (394)
263 cd00984 DnaB_C DnaB helicase C 95.7 0.018 3.8E-07 62.4 6.0 53 189-243 9-62 (242)
264 KOG1804|consensus 95.6 0.0046 1E-07 77.1 1.6 64 180-243 314-377 (775)
265 TIGR02533 type_II_gspE general 95.6 0.014 3.1E-07 70.4 5.7 51 813-865 223-275 (486)
266 cd01131 PilT Pilus retraction 95.6 0.015 3.3E-07 61.8 5.3 38 192-230 1-38 (198)
267 TIGR00348 hsdR type I site-spe 95.6 0.021 4.5E-07 71.6 7.3 69 817-885 240-318 (667)
268 PRK04537 ATP-dependent RNA hel 95.6 0.035 7.7E-07 68.4 9.2 69 815-883 31-107 (572)
269 TIGR00348 hsdR type I site-spe 95.6 0.022 4.8E-07 71.3 7.6 69 179-247 240-318 (667)
270 PRK06835 DNA replication prote 95.6 0.022 4.7E-07 65.6 6.8 37 192-230 183-219 (329)
271 PHA00729 NTP-binding motif con 95.6 0.023 5E-07 61.9 6.7 24 832-855 19-42 (226)
272 PRK10436 hypothetical protein; 95.6 0.013 2.8E-07 70.2 5.2 53 173-227 197-251 (462)
273 TIGR03817 DECH_helic helicase/ 95.6 0.082 1.8E-06 67.2 12.5 70 176-246 35-105 (742)
274 TIGR00614 recQ_fam ATP-depende 95.6 0.041 8.9E-07 66.1 9.5 74 176-257 10-83 (470)
275 PRK11664 ATP-dependent RNA hel 95.6 0.021 4.5E-07 72.9 7.2 61 820-882 9-70 (812)
276 PF13671 AAA_33: AAA domain; P 95.6 0.0084 1.8E-07 59.2 3.0 21 194-214 1-21 (143)
277 TIGR03499 FlhF flagellar biosy 95.6 0.03 6.5E-07 63.0 7.7 49 830-878 194-245 (282)
278 PF00308 Bac_DnaA: Bacterial d 95.6 0.017 3.7E-07 62.5 5.5 38 831-868 35-72 (219)
279 TIGR00614 recQ_fam ATP-depende 95.6 0.036 7.9E-07 66.6 8.7 67 815-886 11-77 (470)
280 PRK02362 ski2-like helicase; P 95.5 0.034 7.4E-07 70.5 8.9 67 815-883 23-90 (737)
281 KOG0991|consensus 95.5 0.013 2.7E-07 63.6 4.1 66 179-244 32-101 (333)
282 PRK06921 hypothetical protein; 95.5 0.016 3.4E-07 64.7 5.1 38 830-868 117-154 (266)
283 PRK12723 flagellar biosynthesi 95.5 0.03 6.6E-07 65.7 7.6 56 192-247 174-234 (388)
284 PRK10436 hypothetical protein; 95.5 0.019 4.1E-07 68.9 6.0 44 813-856 199-244 (462)
285 COG0552 FtsY Signal recognitio 95.5 0.039 8.5E-07 62.9 8.2 69 830-903 139-210 (340)
286 TIGR02881 spore_V_K stage V sp 95.5 0.015 3.3E-07 64.3 4.9 26 831-856 43-68 (261)
287 PRK13766 Hef nuclease; Provisi 95.5 0.065 1.4E-06 68.2 11.2 82 174-257 12-94 (773)
288 PF07728 AAA_5: AAA domain (dy 95.5 0.016 3.6E-07 57.3 4.6 22 195-216 2-23 (139)
289 cd01122 GP4d_helicase GP4d_hel 95.5 0.024 5.3E-07 62.6 6.4 55 827-883 26-81 (271)
290 PRK00411 cdc6 cell division co 95.5 0.03 6.5E-07 65.2 7.5 28 830-857 55-82 (394)
291 PRK08727 hypothetical protein; 95.5 0.029 6.4E-07 61.2 6.9 37 192-230 41-77 (233)
292 PRK09694 helicase Cas3; Provis 95.5 0.044 9.5E-07 70.4 9.4 70 813-882 284-353 (878)
293 PRK01297 ATP-dependent RNA hel 95.4 0.048 1E-06 65.5 9.3 70 176-245 108-185 (475)
294 TIGR00959 ffh signal recogniti 95.4 0.041 8.8E-07 65.4 8.4 55 830-885 99-156 (428)
295 PF07728 AAA_5: AAA domain (dy 95.4 0.016 3.5E-07 57.3 4.4 42 833-878 2-43 (139)
296 PF13207 AAA_17: AAA domain; P 95.4 0.012 2.7E-07 56.5 3.4 23 832-854 1-23 (121)
297 PRK06851 hypothetical protein; 95.4 0.013 2.8E-07 68.2 4.1 48 829-878 29-78 (367)
298 PRK12402 replication factor C 95.4 0.021 4.6E-07 64.7 5.8 41 179-219 20-63 (337)
299 PRK14701 reverse gyrase; Provi 95.4 0.041 8.9E-07 74.7 9.3 68 176-245 78-145 (1638)
300 PF13481 AAA_25: AAA domain; P 95.4 0.03 6.5E-07 58.3 6.4 53 830-883 32-92 (193)
301 TIGR00959 ffh signal recogniti 95.4 0.044 9.4E-07 65.2 8.4 55 192-247 99-156 (428)
302 TIGR00604 rad3 DNA repair heli 95.4 0.037 8.1E-07 69.8 8.4 67 817-883 12-83 (705)
303 COG0552 FtsY Signal recognitio 95.4 0.037 8E-07 63.1 7.4 58 192-254 139-199 (340)
304 TIGR00362 DnaA chromosomal rep 95.4 0.032 7E-07 65.6 7.2 38 831-868 137-174 (405)
305 PRK14088 dnaA chromosomal repl 95.3 0.028 6E-07 67.2 6.7 37 832-868 132-168 (440)
306 PRK12402 replication factor C 95.3 0.025 5.5E-07 64.1 6.1 40 817-856 20-62 (337)
307 cd01130 VirB11-like_ATPase Typ 95.3 0.028 6.1E-07 59.0 6.0 49 815-866 9-58 (186)
308 PF13671 AAA_33: AAA domain; P 95.3 0.011 2.3E-07 58.5 2.7 22 832-853 1-22 (143)
309 PRK09302 circadian clock prote 95.3 0.028 6.2E-07 68.1 6.8 55 830-887 273-327 (509)
310 smart00489 DEXDc3 DEAD-like he 95.3 0.066 1.4E-06 60.5 9.2 68 178-245 9-84 (289)
311 smart00488 DEXDc2 DEAD-like he 95.3 0.066 1.4E-06 60.5 9.2 68 178-245 9-84 (289)
312 TIGR02538 type_IV_pilB type IV 95.3 0.021 4.5E-07 70.3 5.5 45 173-217 295-341 (564)
313 PF13173 AAA_14: AAA domain 95.3 0.031 6.8E-07 55.0 5.7 43 191-236 1-43 (128)
314 PHA02653 RNA helicase NPH-II; 95.3 0.032 6.9E-07 69.8 7.1 65 180-244 167-244 (675)
315 TIGR03015 pepcterm_ATPase puta 95.3 0.032 7E-07 61.2 6.4 41 177-217 23-68 (269)
316 PRK00149 dnaA chromosomal repl 95.3 0.032 6.9E-07 66.7 6.8 39 831-869 149-187 (450)
317 PLN00206 DEAD-box ATP-dependen 95.3 0.06 1.3E-06 65.6 9.3 70 176-245 142-219 (518)
318 TIGR00604 rad3 DNA repair heli 95.2 0.035 7.5E-07 70.1 7.5 67 179-245 12-83 (705)
319 PRK05642 DNA replication initi 95.2 0.026 5.5E-07 61.7 5.5 36 831-868 46-81 (234)
320 PTZ00110 helicase; Provisional 95.2 0.055 1.2E-06 66.4 9.0 71 176-246 151-227 (545)
321 COG2804 PulE Type II secretory 95.2 0.025 5.5E-07 67.4 5.8 48 172-219 236-285 (500)
322 PRK11823 DNA repair protein Ra 95.2 0.037 8E-07 66.2 7.3 54 192-248 80-133 (446)
323 PF00910 RNA_helicase: RNA hel 95.2 0.026 5.7E-07 54.1 4.9 24 834-857 2-25 (107)
324 PRK13767 ATP-dependent helicas 95.2 0.052 1.1E-06 70.1 9.1 67 177-243 32-105 (876)
325 PF05729 NACHT: NACHT domain 95.2 0.031 6.8E-07 55.9 5.7 28 832-859 2-29 (166)
326 PRK11889 flhF flagellar biosyn 95.2 0.039 8.5E-07 64.7 7.2 54 192-247 241-297 (436)
327 cd01122 GP4d_helicase GP4d_hel 95.2 0.036 7.8E-07 61.2 6.7 54 189-244 26-80 (271)
328 COG1474 CDC6 Cdc6-related prot 95.2 0.033 7.2E-07 64.9 6.7 67 178-244 21-95 (366)
329 cd01130 VirB11-like_ATPase Typ 95.2 0.029 6.3E-07 58.9 5.6 49 177-228 9-58 (186)
330 PRK14701 reverse gyrase; Provi 95.2 0.047 1E-06 74.2 8.8 67 815-883 79-145 (1638)
331 PRK08939 primosomal protein Dn 95.2 0.023 5E-07 64.7 5.2 36 831-868 157-192 (306)
332 PRK11889 flhF flagellar biosyn 95.2 0.041 8.9E-07 64.5 7.2 54 830-885 241-297 (436)
333 PF02492 cobW: CobW/HypB/UreG, 95.2 0.044 9.5E-07 57.2 6.8 59 193-259 1-61 (178)
334 PRK00149 dnaA chromosomal repl 95.1 0.034 7.4E-07 66.4 6.7 39 193-231 149-187 (450)
335 PRK01297 ATP-dependent RNA hel 95.1 0.069 1.5E-06 64.2 9.2 69 815-883 109-185 (475)
336 PHA02653 RNA helicase NPH-II; 95.1 0.05 1.1E-06 68.1 8.1 64 819-882 168-244 (675)
337 TIGR02538 type_IV_pilB type IV 95.1 0.029 6.4E-07 68.9 6.1 44 812-855 296-341 (564)
338 cd01131 PilT Pilus retraction 95.1 0.028 6E-07 59.8 5.1 38 830-868 1-38 (198)
339 PRK11823 DNA repair protein Ra 95.1 0.039 8.5E-07 66.0 6.8 54 830-886 80-133 (446)
340 TIGR00362 DnaA chromosomal rep 95.0 0.029 6.3E-07 66.0 5.6 38 193-230 137-174 (405)
341 PRK05703 flhF flagellar biosyn 95.0 0.048 1E-06 64.8 7.4 56 830-885 221-279 (424)
342 PF13173 AAA_14: AAA domain 95.0 0.04 8.6E-07 54.3 5.6 42 830-874 2-43 (128)
343 PRK05703 flhF flagellar biosyn 95.0 0.052 1.1E-06 64.5 7.6 56 192-247 221-279 (424)
344 TIGR02640 gas_vesic_GvpN gas v 95.0 0.029 6.2E-07 62.3 5.1 24 829-852 20-43 (262)
345 cd01121 Sms Sms (bacterial rad 95.0 0.052 1.1E-06 63.5 7.4 53 192-247 82-134 (372)
346 PRK12723 flagellar biosynthesi 95.0 0.049 1.1E-06 64.0 7.2 57 829-885 173-234 (388)
347 PRK05642 DNA replication initi 95.0 0.033 7.1E-07 60.9 5.4 36 193-230 46-81 (234)
348 PRK10867 signal recognition pa 95.0 0.046 9.9E-07 65.1 7.0 55 192-247 100-157 (433)
349 PRK09302 circadian clock prote 95.0 0.042 9.1E-07 66.7 6.9 54 192-248 273-326 (509)
350 PTZ00110 helicase; Provisional 95.0 0.071 1.5E-06 65.4 8.8 70 815-884 152-227 (545)
351 KOG2028|consensus 95.0 0.026 5.6E-07 64.6 4.5 50 193-244 163-212 (554)
352 TIGR02524 dot_icm_DotB Dot/Icm 94.9 0.051 1.1E-06 63.3 7.1 42 177-220 121-162 (358)
353 TIGR02640 gas_vesic_GvpN gas v 94.9 0.042 9E-07 61.1 6.2 24 191-214 20-43 (262)
354 PRK11331 5-methylcytosine-spec 94.9 0.041 8.9E-07 65.5 6.3 64 176-239 177-242 (459)
355 PRK13767 ATP-dependent helicas 94.9 0.073 1.6E-06 68.8 9.1 67 815-881 32-105 (876)
356 PF05496 RuvB_N: Holliday junc 94.9 0.018 3.8E-07 62.7 2.9 24 831-855 51-74 (233)
357 PRK06921 hypothetical protein; 94.9 0.045 9.7E-07 61.1 6.3 38 192-230 117-154 (266)
358 KOG2028|consensus 94.9 0.028 6.1E-07 64.3 4.6 59 820-880 149-210 (554)
359 PRK11331 5-methylcytosine-spec 94.9 0.04 8.6E-07 65.6 6.1 64 817-880 180-245 (459)
360 PHA00729 NTP-binding motif con 94.9 0.033 7.1E-07 60.8 5.0 24 194-217 19-42 (226)
361 PF05496 RuvB_N: Holliday junc 94.9 0.018 3.9E-07 62.7 2.9 24 193-217 51-74 (233)
362 COG4096 HsdR Type I site-speci 94.9 0.04 8.6E-07 68.7 6.2 69 815-883 165-238 (875)
363 cd01121 Sms Sms (bacterial rad 94.8 0.055 1.2E-06 63.3 7.0 54 830-886 82-135 (372)
364 KOG0991|consensus 94.8 0.031 6.7E-07 60.7 4.5 57 826-882 44-101 (333)
365 PRK14088 dnaA chromosomal repl 94.8 0.036 7.8E-07 66.2 5.6 37 194-230 132-168 (440)
366 TIGR00635 ruvB Holliday juncti 94.8 0.029 6.3E-07 63.0 4.5 25 192-216 30-54 (305)
367 TIGR00635 ruvB Holliday juncti 94.8 0.031 6.7E-07 62.8 4.7 24 831-854 31-54 (305)
368 TIGR02012 tigrfam_recA protein 94.8 0.051 1.1E-06 62.3 6.5 40 827-868 51-91 (321)
369 COG2804 PulE Type II secretory 94.8 0.048 1E-06 65.2 6.4 43 814-856 240-284 (500)
370 TIGR02880 cbbX_cfxQ probable R 94.8 0.024 5.1E-07 63.9 3.7 26 194-219 60-85 (284)
371 PRK13909 putative recombinatio 94.8 0.039 8.5E-07 71.6 6.2 50 196-245 2-52 (910)
372 PF03205 MobB: Molybdopterin g 94.8 0.037 8.1E-07 55.9 4.8 39 831-871 1-39 (140)
373 TIGR03015 pepcterm_ATPase puta 94.8 0.041 8.8E-07 60.5 5.5 38 817-854 25-67 (269)
374 cd01393 recA_like RecA is a b 94.8 0.035 7.6E-07 59.5 4.9 39 830-870 19-63 (226)
375 PRK08939 primosomal protein Dn 94.8 0.036 7.8E-07 63.2 5.1 36 193-230 157-192 (306)
376 COG2805 PilT Tfp pilus assembl 94.7 0.062 1.3E-06 60.5 6.7 48 176-226 111-158 (353)
377 PF03205 MobB: Molybdopterin g 94.7 0.038 8.3E-07 55.8 4.8 39 193-233 1-39 (140)
378 PF00437 T2SE: Type II/IV secr 94.7 0.029 6.4E-07 62.1 4.3 50 180-231 114-164 (270)
379 PRK12726 flagellar biosynthesi 94.7 0.065 1.4E-06 62.7 7.1 54 830-885 206-262 (407)
380 PRK12724 flagellar biosynthesi 94.7 0.063 1.4E-06 63.5 7.1 55 830-885 223-280 (432)
381 PF13238 AAA_18: AAA domain; P 94.7 0.027 5.9E-07 54.1 3.5 21 196-216 2-22 (129)
382 TIGR02880 cbbX_cfxQ probable R 94.7 0.025 5.3E-07 63.7 3.7 25 832-856 60-84 (284)
383 PLN00206 DEAD-box ATP-dependen 94.7 0.094 2E-06 63.9 8.9 69 815-883 143-219 (518)
384 COG1074 RecB ATP-dependent exo 94.7 0.042 9.2E-07 72.8 6.2 53 192-244 16-71 (1139)
385 TIGR02012 tigrfam_recA protein 94.7 0.055 1.2E-06 62.0 6.4 55 189-248 51-106 (321)
386 COG1474 CDC6 Cdc6-related prot 94.7 0.067 1.4E-06 62.5 7.1 65 818-882 23-95 (366)
387 KOG0354|consensus 94.6 0.12 2.5E-06 64.5 9.4 77 809-886 56-132 (746)
388 COG2805 PilT Tfp pilus assembl 94.6 0.044 9.6E-07 61.6 5.2 34 830-864 125-158 (353)
389 TIGR00416 sms DNA repair prote 94.6 0.066 1.4E-06 64.2 7.1 54 192-248 94-147 (454)
390 PRK12724 flagellar biosynthesi 94.6 0.075 1.6E-06 62.8 7.4 55 192-247 223-280 (432)
391 KOG0354|consensus 94.6 0.12 2.6E-06 64.4 9.4 74 174-248 59-132 (746)
392 TIGR00595 priA primosomal prot 94.6 0.048 1E-06 66.2 6.0 48 196-245 1-48 (505)
393 cd00983 recA RecA is a bacter 94.6 0.077 1.7E-06 60.9 7.3 37 830-868 55-91 (325)
394 PF02492 cobW: CobW/HypB/UreG, 94.6 0.04 8.8E-07 57.5 4.7 35 831-868 1-35 (178)
395 PRK11057 ATP-dependent DNA hel 94.6 0.098 2.1E-06 65.0 8.7 67 815-886 25-91 (607)
396 COG1198 PriA Primosomal protei 94.5 0.075 1.6E-06 66.7 7.6 68 813-882 196-267 (730)
397 PF05673 DUF815: Protein of un 94.5 0.17 3.6E-06 55.9 9.4 64 180-245 33-104 (249)
398 COG2256 MGS1 ATPase related to 94.5 0.056 1.2E-06 62.8 5.9 45 193-242 49-93 (436)
399 PRK12726 flagellar biosynthesi 94.5 0.082 1.8E-06 61.8 7.2 54 192-247 206-262 (407)
400 PRK13768 GTPase; Provisional 94.5 0.045 9.7E-07 60.6 4.9 34 194-229 4-37 (253)
401 PRK14087 dnaA chromosomal repl 94.5 0.1 2.2E-06 62.6 8.3 38 831-868 142-179 (450)
402 TIGR00416 sms DNA repair prote 94.5 0.067 1.4E-06 64.2 6.7 54 830-886 94-147 (454)
403 PRK13766 Hef nuclease; Provisi 94.5 0.11 2.4E-06 66.2 9.1 67 815-883 15-81 (773)
404 cd01983 Fer4_NifH The Fer4_Nif 94.5 0.063 1.4E-06 48.4 5.1 33 195-229 2-34 (99)
405 PRK13768 GTPase; Provisional 94.5 0.047 1E-06 60.5 5.0 34 832-867 4-37 (253)
406 COG2256 MGS1 ATPase related to 94.5 0.062 1.3E-06 62.5 6.1 20 831-850 49-68 (436)
407 PF00437 T2SE: Type II/IV secr 94.4 0.037 8.1E-07 61.3 4.3 49 818-868 114-163 (270)
408 PHA02544 44 clamp loader, smal 94.4 0.064 1.4E-06 60.6 6.2 41 176-216 23-67 (316)
409 TIGR03817 DECH_helic helicase/ 94.4 0.12 2.6E-06 65.6 9.2 69 815-884 36-105 (742)
410 COG0507 RecD ATP-dependent exo 94.4 0.076 1.6E-06 66.9 7.3 69 172-242 314-382 (696)
411 PRK11057 ATP-dependent DNA hel 94.4 0.1 2.2E-06 64.9 8.2 66 177-247 25-90 (607)
412 PRK09354 recA recombinase A; P 94.3 0.062 1.4E-06 62.2 5.9 35 830-866 60-94 (349)
413 TIGR00750 lao LAO/AO transport 94.3 0.056 1.2E-06 61.3 5.5 36 830-867 34-69 (300)
414 TIGR00595 priA primosomal prot 94.3 0.058 1.3E-06 65.5 5.8 48 834-883 1-48 (505)
415 CHL00181 cbbX CbbX; Provisiona 94.3 0.036 7.7E-07 62.6 3.8 24 195-218 62-85 (287)
416 TIGR01242 26Sp45 26S proteasom 94.3 0.039 8.4E-07 64.1 4.2 23 194-216 158-180 (364)
417 cd01983 Fer4_NifH The Fer4_Nif 94.3 0.071 1.5E-06 48.0 5.1 33 833-867 2-34 (99)
418 TIGR03158 cas3_cyano CRISPR-as 94.2 0.13 2.7E-06 59.9 8.2 59 820-883 2-62 (357)
419 PRK12608 transcription termina 94.2 0.068 1.5E-06 62.3 5.9 61 184-244 122-187 (380)
420 PRK06995 flhF flagellar biosyn 94.2 0.059 1.3E-06 64.9 5.6 48 192-239 256-306 (484)
421 CHL00181 cbbX CbbX; Provisiona 94.2 0.038 8.3E-07 62.4 3.7 24 833-856 62-85 (287)
422 PF13238 AAA_18: AAA domain; P 94.2 0.038 8.2E-07 53.1 3.2 22 833-854 1-22 (129)
423 TIGR01242 26Sp45 26S proteasom 94.2 0.044 9.5E-07 63.6 4.4 24 831-854 157-180 (364)
424 COG5192 BMS1 GTP-binding prote 94.2 0.059 1.3E-06 64.1 5.3 27 192-218 68-95 (1077)
425 cd00983 recA RecA is a bacter 94.2 0.078 1.7E-06 60.9 6.2 51 192-247 55-105 (325)
426 TIGR03158 cas3_cyano CRISPR-as 94.2 0.13 2.8E-06 59.7 8.2 59 182-245 2-62 (357)
427 cd02019 NK Nucleoside/nucleoti 94.2 0.076 1.7E-06 46.9 4.8 22 195-216 2-23 (69)
428 PRK13909 putative recombinatio 94.2 0.069 1.5E-06 69.3 6.5 50 834-883 2-52 (910)
429 PRK14087 dnaA chromosomal repl 94.2 0.098 2.1E-06 62.7 7.3 38 193-230 142-179 (450)
430 PRK03992 proteasome-activating 94.2 0.055 1.2E-06 63.6 5.0 24 830-853 165-188 (389)
431 TIGR00750 lao LAO/AO transport 94.2 0.065 1.4E-06 60.8 5.5 36 192-229 34-69 (300)
432 PRK03992 proteasome-activating 94.2 0.053 1.1E-06 63.8 4.9 24 192-215 165-188 (389)
433 PRK04195 replication factor C 94.2 0.078 1.7E-06 64.0 6.4 41 176-216 16-63 (482)
434 cd01393 recA_like RecA is a b 94.2 0.058 1.3E-06 57.8 4.8 28 192-219 19-46 (226)
435 TIGR01359 UMP_CMP_kin_fam UMP- 94.1 0.038 8.2E-07 57.3 3.2 23 194-216 1-23 (183)
436 PF03308 ArgK: ArgK protein; 94.1 0.052 1.1E-06 60.2 4.4 34 832-867 31-64 (266)
437 PRK13342 recombination factor 94.1 0.12 2.5E-06 61.3 7.7 43 192-239 36-78 (413)
438 PF04665 Pox_A32: Poxvirus A32 94.1 0.056 1.2E-06 59.6 4.6 40 189-230 9-49 (241)
439 PRK12727 flagellar biosynthesi 94.1 0.1 2.2E-06 63.3 7.1 50 192-241 350-402 (559)
440 cd01123 Rad51_DMC1_radA Rad51_ 94.1 0.065 1.4E-06 57.8 5.1 41 830-870 19-63 (235)
441 PRK00440 rfc replication facto 94.1 0.082 1.8E-06 59.4 6.1 41 179-219 22-65 (319)
442 PRK00080 ruvB Holliday junctio 94.1 0.051 1.1E-06 62.2 4.4 25 192-216 51-75 (328)
443 TIGR02524 dot_icm_DotB Dot/Icm 94.0 0.11 2.3E-06 60.6 7.1 28 829-856 133-160 (358)
444 TIGR00176 mobB molybdopterin-g 94.0 0.057 1.2E-06 55.5 4.3 38 833-872 2-39 (155)
445 PRK12727 flagellar biosynthesi 94.0 0.1 2.2E-06 63.3 7.0 49 830-878 350-401 (559)
446 COG1074 RecB ATP-dependent exo 94.0 0.07 1.5E-06 70.8 6.1 54 830-883 16-72 (1139)
447 TIGR01389 recQ ATP-dependent D 94.0 0.21 4.6E-06 61.8 10.0 73 177-257 13-85 (591)
448 PF00910 RNA_helicase: RNA hel 94.0 0.049 1.1E-06 52.2 3.6 25 196-220 2-26 (107)
449 TIGR03689 pup_AAA proteasome A 94.0 0.054 1.2E-06 65.7 4.7 26 192-217 216-241 (512)
450 TIGR01360 aden_kin_iso1 adenyl 94.0 0.047 1E-06 56.5 3.6 25 192-216 3-27 (188)
451 PRK14962 DNA polymerase III su 94.0 0.053 1.2E-06 65.3 4.5 26 193-218 37-62 (472)
452 TIGR00176 mobB molybdopterin-g 94.0 0.085 1.8E-06 54.2 5.4 36 195-232 2-37 (155)
453 cd02019 NK Nucleoside/nucleoti 93.9 0.091 2E-06 46.4 4.8 22 833-854 2-23 (69)
454 PRK06995 flhF flagellar biosyn 93.9 0.074 1.6E-06 64.1 5.6 49 830-878 256-307 (484)
455 cd01125 repA Hexameric Replica 93.9 0.094 2E-06 57.2 6.0 52 193-245 2-63 (239)
456 PTZ00301 uridine kinase; Provi 93.9 0.081 1.7E-06 57.2 5.3 36 193-228 4-39 (210)
457 PRK10751 molybdopterin-guanine 93.9 0.071 1.5E-06 56.0 4.7 42 829-872 5-46 (173)
458 PRK12608 transcription termina 93.9 0.089 1.9E-06 61.4 5.9 59 822-880 122-185 (380)
459 PHA02544 44 clamp loader, smal 93.9 0.096 2.1E-06 59.2 6.1 39 816-854 25-67 (316)
460 PRK04195 replication factor C 93.8 0.058 1.2E-06 65.1 4.5 39 816-854 18-63 (482)
461 TIGR03689 pup_AAA proteasome A 93.8 0.063 1.4E-06 65.1 4.8 27 830-856 216-242 (512)
462 PRK00440 rfc replication facto 93.8 0.1 2.2E-06 58.7 6.2 39 818-856 23-64 (319)
463 TIGR01420 pilT_fam pilus retra 93.8 0.066 1.4E-06 61.9 4.8 39 191-230 121-159 (343)
464 cd03114 ArgK-like The function 93.8 0.089 1.9E-06 53.6 5.2 33 195-229 2-34 (148)
465 PRK04301 radA DNA repair and r 93.8 0.083 1.8E-06 60.3 5.4 56 830-885 102-162 (317)
466 PTZ00361 26 proteosome regulat 93.8 0.071 1.5E-06 63.6 5.0 23 193-215 218-240 (438)
467 COG0556 UvrB Helicase subunit 93.7 0.097 2.1E-06 62.6 5.9 64 815-883 12-80 (663)
468 TIGR01359 UMP_CMP_kin_fam UMP- 93.7 0.049 1.1E-06 56.4 3.2 22 832-853 1-22 (183)
469 COG1201 Lhr Lhr-like helicases 93.7 0.35 7.5E-06 61.5 11.0 118 815-938 22-166 (814)
470 PF12846 AAA_10: AAA-like doma 93.7 0.18 3.9E-06 55.6 7.7 59 192-259 1-59 (304)
471 PF03029 ATP_bind_1: Conserved 93.6 0.054 1.2E-06 59.6 3.5 30 197-228 1-30 (238)
472 PRK14962 DNA polymerase III su 93.6 0.064 1.4E-06 64.6 4.4 26 831-856 37-62 (472)
473 cd00544 CobU Adenosylcobinamid 93.6 0.087 1.9E-06 55.0 4.8 47 832-883 1-47 (169)
474 PRK08233 hypothetical protein; 93.6 0.054 1.2E-06 55.7 3.3 24 193-216 4-27 (182)
475 smart00763 AAA_PrkA PrkA AAA d 93.6 0.075 1.6E-06 61.6 4.7 25 830-854 78-102 (361)
476 TIGR01360 aden_kin_iso1 adenyl 93.6 0.06 1.3E-06 55.7 3.6 24 830-853 3-26 (188)
477 PRK08233 hypothetical protein; 93.6 0.053 1.1E-06 55.8 3.2 25 830-854 3-27 (182)
478 PTZ00301 uridine kinase; Provi 93.6 0.096 2.1E-06 56.6 5.2 37 831-867 4-40 (210)
479 TIGR01389 recQ ATP-dependent D 93.6 0.2 4.3E-06 62.0 8.7 67 815-886 13-79 (591)
480 PF03266 NTPase_1: NTPase; In 93.6 0.069 1.5E-06 55.7 4.0 25 195-219 2-26 (168)
481 smart00763 AAA_PrkA PrkA AAA d 93.6 0.075 1.6E-06 61.6 4.6 26 192-217 78-103 (361)
482 cd01125 repA Hexameric Replica 93.6 0.098 2.1E-06 57.1 5.3 52 831-883 2-63 (239)
483 PRK00080 ruvB Holliday junctio 93.5 0.055 1.2E-06 61.9 3.5 25 830-854 51-75 (328)
484 PRK13342 recombination factor 93.5 0.17 3.7E-06 59.9 7.7 24 830-853 36-59 (413)
485 PTZ00361 26 proteosome regulat 93.5 0.086 1.9E-06 62.9 5.1 25 830-854 217-241 (438)
486 COG1199 DinG Rad3-related DNA 93.5 0.19 4.2E-06 62.7 8.5 72 810-883 10-86 (654)
487 PRK00131 aroK shikimate kinase 93.5 0.074 1.6E-06 54.1 4.0 25 192-216 4-28 (175)
488 PRK08118 topology modulation p 93.5 0.061 1.3E-06 55.8 3.4 22 195-216 4-25 (167)
489 COG3854 SpoIIIAA ncharacterize 93.5 0.095 2.1E-06 57.1 4.8 40 833-872 140-182 (308)
490 PRK05541 adenylylsulfate kinas 93.5 0.12 2.6E-06 53.5 5.5 35 830-866 7-41 (176)
491 cd01123 Rad51_DMC1_radA Rad51_ 93.4 0.1 2.2E-06 56.3 5.2 40 192-231 19-62 (235)
492 PRK14963 DNA polymerase III su 93.4 0.083 1.8E-06 64.2 4.9 27 192-218 36-62 (504)
493 PRK14961 DNA polymerase III su 93.4 0.076 1.7E-06 61.8 4.4 26 192-217 38-63 (363)
494 PRK13531 regulatory ATPase Rav 93.4 0.077 1.7E-06 63.7 4.5 31 187-217 34-64 (498)
495 PRK12422 chromosomal replicati 93.4 0.093 2E-06 62.8 5.2 36 831-868 142-177 (445)
496 KOG1804|consensus 93.4 0.02 4.4E-07 71.6 -0.4 63 818-880 314-376 (775)
497 PF13555 AAA_29: P-loop contai 93.4 0.085 1.8E-06 46.3 3.6 27 193-219 24-50 (62)
498 PRK06762 hypothetical protein; 93.4 0.07 1.5E-06 54.5 3.6 25 192-216 2-26 (166)
499 PF03266 NTPase_1: NTPase; In 93.4 0.084 1.8E-06 55.0 4.2 24 833-856 2-25 (168)
500 COG1224 TIP49 DNA helicase TIP 93.3 0.089 1.9E-06 60.4 4.6 28 828-855 63-90 (450)
No 1
>KOG1806|consensus
Probab=100.00 E-value=2.5e-88 Score=797.73 Aligned_cols=475 Identities=54% Similarity=0.879 Sum_probs=445.8
Q ss_pred cccccccccHHHhhcCCCCCCChhhhccCCCCCCcccCCcccccCcCccccccChhhHHHhhhhhhhhhhhcccccchhh
Q psy12659 451 ISRHEKRSSQLEALNSMPLYPTQEIIWNENIVPTEYFSGEGCLALPKLNLQFLTLHDYLLRNFNLFRLESTCRVNYVLAK 530 (1051)
Q Consensus 451 IS~~Err~s~~~~~~~~~~~p~e~~~~~~~~~~~~~~~~~~~~~l~klnlq~l~~~D~l~r~~~l~r~es~~~i~~~~~~ 530 (1051)
|+.+||++||.|..|.+|+||+|++|||++.+|.++|. ++||||||||||||||+||+.|||++||+|++|+|
T Consensus 373 Vm~nEK~rs~ve~~~~~~l~p~~~i~wd~~v~~~e~~l-e~cl~l~kl~lq~ltL~~~er~all~F~~~~f~si------ 445 (1320)
T KOG1806|consen 373 VMTNEKTRSQVEDYNEIPLYPLEDILWDESVMPSENYL-EGCLALPKLNLQFLTLHDYERRALLLFRLESFYSI------ 445 (1320)
T ss_pred hhhhHHHHHHHHHHHhhhcCchhhhccccccchhhhhh-hhhhcchhhHHHHhHHHHHHHHHHHHHHHHHHHHH------
Confidence 45789999999999999999999999999999999999 99999999999999999999999999999999999
Q ss_pred hhhHHHHHHHhccccCCCCCeeEeeccCCcchhhhhhhhhHhhhccccccCCCcccccccCCCcccccCCCeEEEEEEEE
Q psy12659 531 RLDLLQEVERLQKSLDVSGDVAYTCETAGHFFLYQVLARWEKFLATVRQRKQDRRKPAVSRTNIIREKQPSRVRADVIVN 610 (1051)
Q Consensus 531 r~d~e~~i~rl~p~~~~~~~~~f~~~~~~~~~~~~~~~g~srm~~~~a~~i~~~~i~~v~~p~~ig~~~p~~v~a~~~~~ 610 (1051)
|.||.+.+.|+.| .+|++.| +||+|| |.|+..|.|.+|++|+ ||++.|.+|+|+++++
T Consensus 446 e~ei~~~~~~~l~---~~~~vs~--------------~~W~~l----~~~r~~f~v~eV~~p~-ige~~p~kv~ad~~~~ 503 (1320)
T KOG1806|consen 446 EAEILNFVERYLR---LSGKVAF--------------KGWARL----AFPRNDFKVTEVAPPN-IGENLPQKVTADVTLS 503 (1320)
T ss_pred HHHHHHHHHHHhh---hccchhh--------------hhhhhc----cchhhhheeeecCCcc-hhhhhhhhhhhhcccc
Confidence 9999999999998 6889999 999999 9999999999999999 9999999999999999
Q ss_pred cC-CchhHHHHHhhcCCCceEEEEeecCCCCCCCCCCCCCCcccccCccceecchhhhhhcccCcccCCCCCCCCCCCCC
Q psy12659 611 LN-VKREIKGEWESLRKHDVCFLITLKPPLPIGTKISYKGPFLEQTGLTYVRGCEIEGMLDVNGRIIEDGPEPRPVLPGD 689 (1051)
Q Consensus 611 ~~-~~~~~r~ew~~lr~~dv~fL~~v~~~~~~~~~~~~~~~~~~~~gi~~vR~~Ei~~~~de~g~~~~~~~~~~~~~~~~ 689 (1051)
+. .++.++++|+.+++||||||++++|..+.+.+.+...+...+.|+++||+||+..|+|.+|..+.+ +
T Consensus 504 ~~~eRh~~~nli~~f~k~~~~~Li~i~P~e~~~~~~~~~~~~eg~vp~~~v~yCErf~~f~idlesild----------t 573 (1320)
T KOG1806|consen 504 RPGERHSILNLIENFKKHDVLFLIYIRPMEPKGLEGNALDPLEGRVPLTYVRYCERFGMFDIDLESILD----------T 573 (1320)
T ss_pred CcchHHHHHHHHHHhhhcCeeEEEEeccCcccCcccccccccccccCcccchhhhhhhhhhhhhhhccC----------C
Confidence 97 799999999999999999999999988888888888888899999999999999999999999874 2
Q ss_pred CceEEEecChhhHhhchhh-hhcCCCcceeeeEEEEecCCCccchHHHHHHHHHhhccCCCCChhhhhhhcccCCCCCCc
Q psy12659 690 TRTFRVMLDCNQYKEDLDN-VAQGNEDVYETFNVLMRRKPKENNFKAVLETIRDLMNTECVVPDWLHDIILGYGDPGAAH 768 (1051)
Q Consensus 690 ~r~l~v~LD~~qy~~d~~~-~~~~~~dvy~~fNllirr~~~ennfk~vl~~i~~ll~~~~~lP~wl~difLG~gdp~~a~ 768 (1051)
.|++.|.||+.+|+.++.. .+.+.+++|.+||++++++|++|+|+.+++.|++++|..|.+|.|+++++||||+|+.++
T Consensus 574 rRffnvvLd~~h~~~lLs~li~~~ag~lf~qF~~~l~~~~~~n~~~~~l~~l~~l~n~~~~~p~wl~~~~Lg~g~pS~~~ 653 (1320)
T KOG1806|consen 574 RRFFNVVLDPFHYHHLLSGLIEYGAGDLFFQFNLLLRRKPEENNFKAILEIIRSLMNRACEVPKWLHDLFLGYGTPSIAH 653 (1320)
T ss_pred cceEEEecchHHHHHHhhHHhhcCchhhhhhhhheeeeccCcchhHhHHHHHHHHHHhhhccchhhhccccccCCcchhh
Confidence 3899999999999999988 577899999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhhcccccCccccccccccccCCCcccccccCC-------------------CCC---------CC---CCC---
Q psy12659 769 YTEMPNEIATMDFNDTFLNMDHLRSSFPQAEIRVKTDN-------------------PTK---------LV---PPF--- 814 (1051)
Q Consensus 769 y~~m~~~l~~ld~~dtfl~~~hl~~sfp~~~i~~~~~~-------------------~~~---------~~---~~~--- 814 (1051)
|.+|++.+...+ ++|++..|+.++||++.+.+..+. +.+ .. -||
T Consensus 654 ~~n~~~~~~~~~--~~f~~~~ql~~~f~~~~v~~v~~~~al~~~k~~~~~nki~~~~~ae~~~~~v~~~~lp~~~py~y~ 731 (1320)
T KOG1806|consen 654 YPNMPNLSIYAD--DTFLTVEHLQSSFPNCNVSSNLSTEALQIKKFYTDQNKISADVTAEVPALIVEPFTLPSNGPYPYN 731 (1320)
T ss_pred ccCchhhHHHHH--HhhhhHHHHHHhccCCCccccCccHHHHHHHhhhhccccCccccccchhhccCccccCCCCCCCcC
Confidence 999999998887 899999999999998876542211 000 00 112
Q ss_pred ------CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCcc
Q psy12659 815 ------KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDER 888 (1051)
Q Consensus 815 ------~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~~ 888 (1051)
..|+.|.+||.+++++|+|+|.||||||||.++++||..++++.|++|++|+++||+|++.+++++++.+++.+
T Consensus 732 p~~n~v~ft~~qveai~sg~qpgltmvvgppgtgktd~avqil~~lyhn~p~qrTlivthsnqaln~lfeKi~~~d~d~r 811 (1320)
T KOG1806|consen 732 PKKNQVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMALDVDER 811 (1320)
T ss_pred cccchhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhhhhhhhhhcCCCcceEEEEecccchhHHHHHHHhcccchh
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHHHHhhcCCCCCCCCCCCCccccchhhhhhhh
Q psy12659 889 HLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTLKTLLSPWKSEDGSPFFGGWARMAQPIVNF 968 (1051)
Q Consensus 889 ~llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~~~~ll~P~~~~~~~~~~~~w~~~~~~i~~~ 968 (1051)
+++|+|
T Consensus 812 hLlrlg-------------------------------------------------------------------------- 817 (1320)
T KOG1806|consen 812 HLLRLG-------------------------------------------------------------------------- 817 (1320)
T ss_pred hHHHhc--------------------------------------------------------------------------
Confidence 999999
Q ss_pred hhhhhcccchhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCCCcccchhhhhHHHHHHHHHHHHHHHHHHh
Q psy12659 969 AVVEVAKPNIEEALETEKDFSRYGRVNYVLAKRLDLLQEVERLQKSLDVSGDVAYTCETAGHFFLYQVLARWEKFLATVR 1048 (1051)
Q Consensus 969 ~~~~~~~~~~~~~l~~~~~~s~~grv~~~l~~r~~Ll~eve~L~~~l~~~~~~~~~~e~a~~f~~~~~~~~we~~~~~~~ 1048 (1051)
||+++++++++|++||||++++.+|.+|++||++|++|++++||+.|||+||+|||.++|.++||+|++++.
T Consensus 818 --------~ge~eletd~dfsrygrvn~~l~~r~~ll~ev~rla~sl~~pgdv~ytcetagyf~~~~V~~~wee~l~~v~ 889 (1320)
T KOG1806|consen 818 --------HGEEELETDKDFSRYGRVNYVLSRRLELLREVERLAKSLQAPGDVDYTCETAGYFFLAYVKRRWEEYLAKVD 889 (1320)
T ss_pred --------ccHHhhhcccchhheeeEeeeeccchHHHHHHHHhhhhhcCccccccccchhhhhhhhHHHhhhHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999987
No 2
>KOG1806|consensus
Probab=100.00 E-value=2.5e-63 Score=586.53 Aligned_cols=404 Identities=50% Similarity=0.740 Sum_probs=347.7
Q ss_pred hhhhccccccCCCCCCCchhhhHHhhhhhHHHHHHHhccCchhhhhhhccccccchhhhhhcccCCCCccccccccCCCc
Q psy12659 13 KFYARFEISDETGDPLTDHDMTQIHYQNITSLQKAAFAKFPDLRSFSLANVASVDTRETLTKHFEPLTPLCVLKKRTEEE 92 (1051)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~r~~~~~~~~~l~~~~~~~~~~~~~ 92 (1051)
+||..|++ .||.-+++++|.++|+--+++.|..-|-++++|.=+...|+.+.+.++.+...+ .+- =...+-
T Consensus 604 qF~~~l~~--~~~~n~~~~~l~~l~~l~n~~~~~p~wl~~~~Lg~g~pS~~~~~n~~~~~~~~~--~~f-~~~~ql---- 674 (1320)
T KOG1806|consen 604 QFNLLLRR--KPEENNFKAILEIIRSLMNRACEVPKWLHDLFLGYGTPSIAHYPNMPNLSIYAD--DTF-LTVEHL---- 674 (1320)
T ss_pred hhhheeee--ccCcchhHhHHHHHHHHHHhhhccchhhhccccccCCcchhhccCchhhHHHHH--Hhh-hhHHHH----
Confidence 68888888 899999999999999999999999999999999999999999999998877433 111 000000
Q ss_pred cCCccccccccccccccccCCCcceEEEEEeechhhhHHHHHHHhhhhhcccccCCCCCccccCCCCCCCCCCCCCCCCC
Q psy12659 93 ENEDEDVEMENKDANVLTTTPPRQAIIIGFLLIQVLKKRTEEEENEDEDVEMENKDGKPIITVEPHVIPSRGPYLFNEPR 172 (1051)
Q Consensus 93 ~~~~~~~~~e~~d~~~l~~~~~~~~~~i~~l~~~~~~~R~~~Al~~l~~~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~ 172 (1051)
.+. ....-+.+..+....+|.+.++++..- ....+...+.+.++++.+|..+||+.+ |+
T Consensus 675 ----------------~~~---f~~~~v~~v~~~~al~~~k~~~~~nki-~~~~~ae~~~~~v~~~~lp~~~py~y~-p~ 733 (1320)
T KOG1806|consen 675 ----------------QSS---FPNCNVSSNLSTEALQIKKFYTDQNKI-SADVTAEVPALIVEPFTLPSNGPYPYN-PK 733 (1320)
T ss_pred ----------------HHh---ccCCCccccCccHHHHHHHhhhhcccc-CccccccchhhccCccccCCCCCCCcC-cc
Confidence 000 001111222222222233223322211 112223355677999999999999999 99
Q ss_pred CCCCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCcE
Q psy12659 173 KNTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHL 252 (1051)
Q Consensus 173 ~~~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~l 252 (1051)
+|.+.+|+.|.+||.+++++|++++.||||||||.++++||..++++.|++|+||+++||+|++++++++.+..++.+++
T Consensus 734 ~n~v~ft~~qveai~sg~qpgltmvvgppgtgktd~avqil~~lyhn~p~qrTlivthsnqaln~lfeKi~~~d~d~rhL 813 (1320)
T KOG1806|consen 734 KNQVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMALDVDERHL 813 (1320)
T ss_pred cchhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhhhhhhhhhcCCCcceEEEEecccchhHHHHHHHhcccchhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCccccchhhhhcccchhhhHHHHHHHHHHHHHHHHHHhccCCCccccccccchhHHHHHHHHHHHHHHhhcCCCC
Q psy12659 253 LRLGHGEEALETEKDFSRYGRVNYVLAKRLDLLQEVERLQKSLDVSGDVAYTCETAGHFFLYQVLARWEKFLATVRPSDG 332 (1051)
Q Consensus 253 vRlG~~~~~~~~~~~fs~~~rv~~~l~~r~~ll~ev~~L~k~L~~~~~~~~sce~a~~f~~~~v~~~w~~fl~~~~~~~~ 332 (1051)
+|+|+++...++.++|+++|||++.+.+|..++.++++|+++++.++++.++|++|++|+..+|..+|+.|+.++....+
T Consensus 814 lrlg~ge~eletd~dfsrygrvn~~l~~r~~ll~ev~rla~sl~~pgdv~ytcetagyf~~~~V~~~wee~l~~v~~~~~ 893 (1320)
T KOG1806|consen 814 LRLGHGEEELETDKDFSRYGRVNYVLSRRLELLREVERLAKSLQAPGDVDYTCETAGYFFLAYVKRRWEEYLAKVDKGCD 893 (1320)
T ss_pred HHhcccHHhhhcccchhheeeEeeeeccchHHHHHHHHhhhhhcCccccccccchhhhhhhhHHHhhhHHHHHHhccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999982222
Q ss_pred CccccccccccCCcchhcccCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHhchhHHHhhccccccceeeeccceeee
Q psy12659 333 KTVPVKTIKTEFPFHGFFENAPKPLFKEKSYETDMEIAEGCFRYIEKMFTQLEEFRAFELLRSGLDRSKYLLVKEAKIIA 412 (1051)
Q Consensus 333 ~~~~~~~i~~~FPF~~ff~~~~~~lf~~~~~e~~~~~a~~~~~~i~~iF~~L~e~r~fE~Lr~~~dr~~ylL~keA~IIa 412 (1051)
+ .....+...|||++||++.|+|+|.+-+.+++++.|++||+||+.+|++|+|+||||+||+..||..|+++|+|+|||
T Consensus 894 ~-~~~~~~~~~fpf~~~f~d~p~~vfeg~n~~~d~~~a~~cf~hl~~ifqqLee~rafellr~~~dr~~Yll~kqakiia 972 (1320)
T KOG1806|consen 894 K-DSVDIVSNRFPFHSYFGDKPKPPFEGYNKENDMDYATGCFRHLEYIFQQLEEFRAFELLRSGEDRELYLLVKQAKIIA 972 (1320)
T ss_pred c-hhhhhHhhhCcchhhhhcCCCccccccchhhhhhhhhhhHHHHHHHHHHHHhcccccccccchhHhhccCcccceeee
Confidence 2 234567889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eehhHHhhhhhhHHhcCccccCccceeechhhhhhhhcccccc
Q psy12659 413 MTCTHAALKRKELVDMGFSFSISPIWVSFNTVSDLCSQISRHE 455 (1051)
Q Consensus 413 mTcthaal~r~~l~~lgf~yd~~~~~~~~~~i~eea~qIS~~E 455 (1051)
|||||||+||.+++++||+|| |.+|||++|+...|
T Consensus 973 mtcthaalkr~el~~lgf~yd--------nl~mEesaqile~e 1007 (1320)
T KOG1806|consen 973 MTCTHAALRRGDLVKLGFKYD--------NLLMEESAQILEIE 1007 (1320)
T ss_pred cccCChhhChhhHhhhceeec--------hhhhhhccCCcccc
Confidence 999999999999999999999 99999999665443
No 3
>KOG1802|consensus
Probab=99.90 E-value=1.7e-23 Score=241.79 Aligned_cols=169 Identities=20% Similarity=0.174 Sum_probs=133.5
Q ss_pred CCCccCCccccccccccccccccCCCcceEEEEEeechhhhHHHHHHHhhhhhcccccC-CCCCccccCCCCC-CCCCCC
Q psy12659 89 TEEEENEDEDVEMENKDANVLTTTPPRQAIIIGFLLIQVLKKRTEEEENEDEDVEMENK-DGKPIITVEPHVI-PSRGPY 166 (1051)
Q Consensus 89 ~~~~~~~~~~~~~e~~d~~~l~~~~~~~~~~i~~l~~~~~~~R~~~Al~~l~~~~~~~~-~l~~~l~~~~~~~-~~~~p~ 166 (1051)
.+.|+|+.+++.+|+.-..- ....++++|++.|+|+.+.++|+..|+..|..++.... .+.-.++..+... .-..+.
T Consensus 321 ~~~pd~~~dE~~lEl~~~~~-~p~e~~~~Ftvd~vwk~ts~drm~~alk~la~D~~~vs~y~y~klLgh~~~~~~~k~~L 399 (935)
T KOG1802|consen 321 LKIPDNNGDEVKLELEFSQD-PPIEVTHGFTVDFVWKSTSFDRMQLALKLLAVDEKKVSGYLYHKLLGHPVEDSSLKKLL 399 (935)
T ss_pred EecCCCCcceeEEEeecCCC-CCcccccceEEEEEEcCccHHHHHHHHHHhhhccccchhhhhhHHhcCcchhhhhcccC
Confidence 34789999999999875444 56788999999999999999999999999987653322 2222222221111 111122
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 167 LFNEPRKNTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 167 ~~~~~~~~~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
+......+..+||.+|..||+++|+++++|||||||||||.|++.||.++.... +.+||||||||.|||+|.++|++.|
T Consensus 400 P~~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~-~~~VLvcApSNiAVDqLaeKIh~tg 478 (935)
T KOG1802|consen 400 PRRFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQH-AGPVLVCAPSNIAVDQLAEKIHKTG 478 (935)
T ss_pred chhhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhc-CCceEEEcccchhHHHHHHHHHhcC
Confidence 233344566799999999999999999999999999999999999999999884 6799999999999999999999998
Q ss_pred CCCCcEEEecCCcccc
Q psy12659 247 VDERHLLRLGHGEEAL 262 (1051)
Q Consensus 247 ~~~~~lvRlG~~~~~~ 262 (1051)
+ .++|+....+..
T Consensus 479 L---KVvRl~aksRE~ 491 (935)
T KOG1802|consen 479 L---KVVRLCAKSRED 491 (935)
T ss_pred c---eEeeeehhhhhh
Confidence 7 899999876653
No 4
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=99.87 E-value=2.3e-21 Score=235.98 Aligned_cols=284 Identities=20% Similarity=0.223 Sum_probs=174.5
Q ss_pred ceEEEEEeechhhhHHHHHHHhhhhhcccccCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhcCC-Ce
Q psy12659 116 QAIIIGFLLIQVLKKRTEEEENEDEDVEMENKDGKPIITVEPHVIPSRGPYLFNEPRKNTIPFTPTQIEAIRAGMQP-GL 194 (1051)
Q Consensus 116 ~~~~i~~l~~~~~~~R~~~Al~~l~~~~~~~~~l~~~l~~~~~~~~~~~p~~~~~~~~~~~~ln~~Q~~Ai~~~l~~-~~ 194 (1051)
..|.+.++++.++++|+..||..+..... .+.+++............... ......||++|++||..++.. ++
T Consensus 102 ~~~~i~~~~~~~t~~rm~~aL~~l~~~~~---~l~~~llg~~~p~~~~~~~~~---~~~~~~ln~~Q~~Av~~~l~~~~~ 175 (637)
T TIGR00376 102 KRVRIDLYANDVTFKRMKEALRALTENHS---RLLEFILGREAPSKASEIHDF---QFFDPNLNESQKEAVSFALSSKDL 175 (637)
T ss_pred ceEEEEEecCccHHHHHHHHHHHHHhchh---hHHHHHhCCCCCCcccccccc---cccCCCCCHHHHHHHHHHhcCCCe
Confidence 35899999999999999999999876432 333344332221110111111 112257999999999999975 99
Q ss_pred EEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCcEEEecCCccccchhhhhcccchh
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLRLGHGEEALETEKDFSRYGRV 274 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~lvRlG~~~~~~~~~~~fs~~~rv 274 (1051)
++|+||||||||+|+++++.+++.. +.+||+|||||.|+|+++++|.+.++ .++|+|++.+..+....++....+
T Consensus 176 ~lI~GpPGTGKT~t~~~ii~~~~~~--g~~VLv~a~sn~Avd~l~e~l~~~~~---~vvRlg~~~r~~~~~~~~sl~~~~ 250 (637)
T TIGR00376 176 FLIHGPPGTGKTRTLVELIRQLVKR--GLRVLVTAPSNIAVDNLLERLALCDQ---KIVRLGHPARLLKSNKQHSLDYLI 250 (637)
T ss_pred EEEEcCCCCCHHHHHHHHHHHHHHc--CCCEEEEcCcHHHHHHHHHHHHhCCC---cEEEeCCchhcchhHHhccHHHHH
Confidence 9999999999999999999999987 77999999999999999999998765 799999999987777777765444
Q ss_pred hhH--HHHHHHHHHHHHHHHHHhccCCCccccccccchhHHHHHHHHHHHHHHhhcCCCCCccccccccccCCcchhccc
Q psy12659 275 NYV--LAKRLDLLQEVERLQKSLDVSGDVAYTCETAGHFFLYQVLARWEKFLATVRPSDGKTVPVKTIKTEFPFHGFFEN 352 (1051)
Q Consensus 275 ~~~--l~~r~~ll~ev~~L~k~L~~~~~~~~sce~a~~f~~~~v~~~w~~fl~~~~~~~~~~~~~~~i~~~FPF~~ff~~ 352 (1051)
... .+.-.++.+++.++.+....... . .+.|+..+.+.. .+...+.=.+ +..
T Consensus 251 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~------~---------~~~~~~~~~~~~----------~l~~~~~~~~-~~~ 304 (637)
T TIGR00376 251 ENHPKYQIVADIREKIDELIEERNKKLK------P---------SPQKRRGLSDIK----------ILRKALKKRE-ARG 304 (637)
T ss_pred hcChhHHHHHHHHHHHHHHHHHHHhhcc------c---------hHhHhhccchHH----------HHHHHHhhhh-hcc
Confidence 321 11112233344443333211000 0 001111000000 0000000000 000
Q ss_pred CCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHhchh---HHHhhc-------------cccccceeeeccc-eeeeeeh
Q psy12659 353 APKPLFKEKSYETDMEIAEGCFRYIEKMFTQLEEFRA---FELLRS-------------GLDRSKYLLVKEA-KIIAMTC 415 (1051)
Q Consensus 353 ~~~~lf~~~~~e~~~~~a~~~~~~i~~iF~~L~e~r~---fE~Lr~-------------~~dr~~ylL~keA-~IIamTc 415 (1051)
.+...+ ..+-....|...+++++..+.+.+. -++|++ ...+.+++|++|| ++..+.|
T Consensus 305 i~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~a~v~~st~~~~~l~~~~Fd~vIIDEAsQ~~ep~~ 378 (637)
T TIGR00376 305 IESLKI------ASMAEWIETNKSIDRLLKLLPEIEERIENEILAESDVVQSTNSSAGLKGWEFDVAVIDEASQAMEPSC 378 (637)
T ss_pred cchhhh------HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhCCEEEeccCcHhhccCCCCEEEEECccccchHHH
Confidence 000000 0011112333444554444443310 112211 2358899999999 5999999
Q ss_pred hHHhhhhhhHHhcCccccCccceeech
Q psy12659 416 THAALKRKELVDMGFSFSISPIWVSFN 442 (1051)
Q Consensus 416 thaal~r~~l~~lgf~yd~~~~~~~~~ 442 (1051)
+.++++-++++..|+|.||||+|.+..
T Consensus 379 lipl~~~~~~vLvGD~~QLpP~v~s~~ 405 (637)
T TIGR00376 379 LIPLLKARKLILAGDHKQLPPTILSHD 405 (637)
T ss_pred HHHHhhCCeEEEecChhhcCCcccccc
Confidence 999999999999999999999998874
No 5
>KOG1803|consensus
Probab=99.86 E-value=6e-22 Score=229.73 Aligned_cols=285 Identities=21% Similarity=0.251 Sum_probs=167.3
Q ss_pred EEeechhhhHHHHHHHhhhhhccccc--CCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhcCC-CeEEE
Q psy12659 121 GFLLIQVLKKRTEEEENEDEDVEMEN--KDGKPIITVEPHVIPSRGPYLFNEPRKNTIPFTPTQIEAIRAGMQP-GLTLV 197 (1051)
Q Consensus 121 ~~l~~~~~~~R~~~Al~~l~~~~~~~--~~l~~~l~~~~~~~~~~~p~~~~~~~~~~~~ln~~Q~~Ai~~~l~~-~~~lI 197 (1051)
.-+.+..+++|...++-.+....... ......+..+....|+... .......-+..||.+|++||..+++. .+++|
T Consensus 128 ~kl~n~vty~R~~~~~i~l~~~~~~~~~~~vv~~l~~~~~~~~~~~~-~~~~~~~~~~~ln~SQk~Av~~~~~~k~l~~I 206 (649)
T KOG1803|consen 128 LKLENKVTYRRMKDTMICLSKFSNPGPSSDVVETLFGDRKPIPSPNI-EIKKITFFNKNLNSSQKAAVSFAINNKDLLII 206 (649)
T ss_pred HHhhhhhhheecHHHHhhHhhhcCccchhhhHHHHhccccCCCCchh-hhcccccCCccccHHHHHHHHHHhccCCceEe
Confidence 34566777888887766555421110 1111112233333332210 00111122357999999999999874 99999
Q ss_pred EccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCcEEEecCCccccchhhhhcccchhhhH
Q psy12659 198 VGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLRLGHGEEALETEKDFSRYGRVNYV 277 (1051)
Q Consensus 198 ~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~lvRlG~~~~~~~~~~~fs~~~rv~~~ 277 (1051)
|||||||||+|+++||.+++++ +++||||||||.|||+|.+||...+. .++|+|+..+.++...+.+.+.-++.-
T Consensus 207 ~GPPGTGKT~TlvEiI~qlvk~--~k~VLVcaPSn~AVdNiverl~~~~~---~l~R~g~paRl~~~~~~~sld~~~~t~ 281 (649)
T KOG1803|consen 207 HGPPGTGKTRTLVEIISQLVKQ--KKRVLVCAPSNVAVDNIVERLTHLKL---NLVRVGHPARLLESVADHSLDLLSNTK 281 (649)
T ss_pred eCCCCCCceeeHHHHHHHHHHc--CCeEEEEcCchHHHHHHHHHhccccc---chhhcCchhhhhhhhhhhHHHHHHhcC
Confidence 9999999999999999999998 89999999999999999999997766 799999999998877776664433321
Q ss_pred H-HHHHHHHH-HHHHHHHHhccCCCccccccccchhHHHHHHHHHHHHHHhhcCCCCCccccccccccCCcchhcccCCC
Q psy12659 278 L-AKRLDLLQ-EVERLQKSLDVSGDVAYTCETAGHFFLYQVLARWEKFLATVRPSDGKTVPVKTIKTEFPFHGFFENAPK 355 (1051)
Q Consensus 278 l-~~r~~ll~-ev~~L~k~L~~~~~~~~sce~a~~f~~~~v~~~w~~fl~~~~~~~~~~~~~~~i~~~FPF~~ff~~~~~ 355 (1051)
. ....+... .+. ..+.. .+|..... ....+......+.+++.... .+++. +-++++ .
T Consensus 282 d~~~~~~~~sk~~d---~~~~~-----~~~tk~~~-~~~~~~~~i~~lrkdl~kre-----~~~v~------eii~n~-~ 340 (649)
T KOG1803|consen 282 DNSQNAKDISKDID---ILFQK-----NTKTKNDK-LRKGIRKEIKLLRKDLRKRE-----RKTVK------EIISNS-R 340 (649)
T ss_pred chhhhhhhhHHHHH---HHhhh-----hhcccchH-HHHHHHHHHHHHHHHHHHHH-----HHHHH------Hhhccc-c
Confidence 1 01111111 111 11100 01111100 00001111111111111000 00111 112222 1
Q ss_pred CCCCCCChhhhHHHHHHHHHHHHHHHHHHHhchhHHHhhccccccceeeeccce-eeeeehhHHhhhhhhHHhcCccccC
Q psy12659 356 PLFKEKSYETDMEIAEGCFRYIEKMFTQLEEFRAFELLRSGLDRSKYLLVKEAK-IIAMTCTHAALKRKELVDMGFSFSI 434 (1051)
Q Consensus 356 ~lf~~~~~e~~~~~a~~~~~~i~~iF~~L~e~r~fE~Lr~~~dr~~ylL~keA~-IIamTcthaal~r~~l~~lgf~yd~ 434 (1051)
.+|.... ... . .++++ .+.+++|++||. .++..||.|.++.++|+..|++-||
T Consensus 341 VVfaTl~--ga~---~-------------------~~~~~--~~fD~vIIDEaaQamE~~cWipvlk~kk~ILaGDp~QL 394 (649)
T KOG1803|consen 341 VVFATLG--GAL---D-------------------RLLRK--RTFDLVIIDEAAQAMEPQCWIPVLKGKKFILAGDPKQL 394 (649)
T ss_pred eEEEecc--chh---h-------------------hhhcc--cCCCEEEEehhhhhccchhhhHHhcCCceEEeCCcccC
Confidence 3343210 000 0 11222 556999999976 9999999999999999999999999
Q ss_pred ccceeechhhhhhhhcccccccccc
Q psy12659 435 SPIWVSFNTVSDLCSQISRHEKRSS 459 (1051)
Q Consensus 435 ~~~~~~~~~i~eea~qIS~~Err~s 459 (1051)
||+|.|... +....++|.+||-..
T Consensus 395 pP~v~S~~a-~~~gl~~Sl~erlae 418 (649)
T KOG1803|consen 395 PPTVLSDKA-KRGGLQVSLLERLAE 418 (649)
T ss_pred Ccccccchh-hhccchhhHHHHHHH
Confidence 999998844 233347777776554
No 6
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A.
Probab=99.85 E-value=8.1e-22 Score=207.74 Aligned_cols=94 Identities=33% Similarity=0.502 Sum_probs=67.8
Q ss_pred CCCHHHHHHHHHhcCCCe-EEEEccCCCChHHHHHHHHHHHH------HcCCCCeEEEEeCCHHHHHHHHHHHHh-----
Q psy12659 177 PFTPTQIEAIRAGMQPGL-TLVVGPPGTGKTDVAVQIISNLY------HNFPHQRTLIVTHSNQALNQLFEKIIS----- 244 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~-~lI~GPPGTGKT~ti~~ii~~l~------~~~p~~riLv~a~SN~Avd~l~~rl~~----- 244 (1051)
+||++|.+||..+++.+. ++|+||||||||+|++.++..++ ...++.+||+||+||.|+|++++++.+
T Consensus 1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~~~~~~ 80 (236)
T PF13086_consen 1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKKLLDED 80 (236)
T ss_dssp ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC-----
T ss_pred CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHhhcccc
Confidence 489999999999998775 99999999999999999999994 356789999999999999999999998
Q ss_pred CCCCCCcEEEecCCc-cccchhhhhcc
Q psy12659 245 LDVDERHLLRLGHGE-EALETEKDFSR 270 (1051)
Q Consensus 245 ~~~~~~~lvRlG~~~-~~~~~~~~fs~ 270 (1051)
.......++|+|+.. ...+....++.
T Consensus 81 ~~~~~~~~ir~~~~~~~~~~~~~~~~~ 107 (236)
T PF13086_consen 81 GKVYKPKIIRLGSEEEKIHEDLQKFSL 107 (236)
T ss_dssp ---TT--EEE---GGTTS--TTGGGBH
T ss_pred ccccccchhhhcccccccccccccccc
Confidence 234456899999987 34444444553
No 7
>KOG1805|consensus
Probab=99.80 E-value=9.2e-20 Score=219.17 Aligned_cols=184 Identities=23% Similarity=0.344 Sum_probs=153.2
Q ss_pred CCCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCcEEE
Q psy12659 176 IPFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLR 254 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~lvR 254 (1051)
..||..|++|+..++. .+++||.|.|||||||||+.+|..|+.. |++||++|+||.|||||+-||...++ .++|
T Consensus 668 ~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~--gkkVLLtsyThsAVDNILiKL~~~~i---~~lR 742 (1100)
T KOG1805|consen 668 LRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVAL--GKKVLLTSYTHSAVDNILIKLKGFGI---YILR 742 (1100)
T ss_pred hhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHc--CCeEEEEehhhHHHHHHHHHHhccCc---ceee
Confidence 4899999999999986 8999999999999999999999999988 99999999999999999999999887 6999
Q ss_pred ecCCccccchhhhhcccchhhhHHHHHHHHHHHHHHHHHHhccCCCccccccccchhHHHHHHHHHHHHHHhhcCCCCCc
Q psy12659 255 LGHGEEALETEKDFSRYGRVNYVLAKRLDLLQEVERLQKSLDVSGDVAYTCETAGHFFLYQVLARWEKFLATVRPSDGKT 334 (1051)
Q Consensus 255 lG~~~~~~~~~~~fs~~~rv~~~l~~r~~ll~ev~~L~k~L~~~~~~~~sce~a~~f~~~~v~~~w~~fl~~~~~~~~~~ 334 (1051)
+|.++++.+.+..|+... ..-.+-++.+.+.++-+..++.||-..+|
T Consensus 743 LG~~~kih~~v~e~~~~~---------~~s~ks~~~l~~~~~~~~IVa~TClgi~~------------------------ 789 (1100)
T KOG1805|consen 743 LGSEEKIHPDVEEFTLTN---------ETSEKSYADLKKFLDQTSIVACTCLGINH------------------------ 789 (1100)
T ss_pred cCCccccchHHHHHhccc---------ccchhhHHHHHHHhCCCcEEEEEccCCCc------------------------
Confidence 999999998888887521 11123366777788888888888877665
Q ss_pred cccccccccCCcchhcccCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHhchhHHHhhccccccceeeeccce-eeee
Q psy12659 335 VPVKTIKTEFPFHGFFENAPKPLFKEKSYETDMEIAEGCFRYIEKMFTQLEEFRAFELLRSGLDRSKYLLVKEAK-IIAM 413 (1051)
Q Consensus 335 ~~~~~i~~~FPF~~ff~~~~~~lf~~~~~e~~~~~a~~~~~~i~~iF~~L~e~r~fE~Lr~~~dr~~ylL~keA~-IIam 413 (1051)
|+|. +.+.||.+++||. |--+
T Consensus 790 ---------------------plf~-------------------------------------~R~FD~cIiDEASQI~lP 811 (1100)
T KOG1805|consen 790 ---------------------PLFV-------------------------------------NRQFDYCIIDEASQILLP 811 (1100)
T ss_pred ---------------------hhhh-------------------------------------ccccCEEEEccccccccc
Confidence 4544 1234999999998 7788
Q ss_pred ehhHHhhhhhhHHhcCccccCccceeechhhhhhhhccccccc
Q psy12659 414 TCTHAALKRKELVDMGFSFSISPIWVSFNTVSDLCSQISRHEK 456 (1051)
Q Consensus 414 Tcthaal~r~~l~~lgf~yd~~~~~~~~~~i~eea~qIS~~Er 456 (1051)
+|-++..--.+|+..|+||||||.|.+... -.+.+.+|.|+|
T Consensus 812 ~~LgPL~~s~kFVLVGDh~QLpPLV~s~ea-r~~Gl~~SLFkr 853 (1100)
T KOG1805|consen 812 LCLGPLSFSNKFVLVGDHYQLPPLVRSSEA-RQEGLSESLFKR 853 (1100)
T ss_pred hhhhhhhhcceEEEecccccCCccccchhh-hhcCcchHHHHH
Confidence 999999999999999999999999988733 233366666654
No 8
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=99.66 E-value=2.3e-17 Score=201.18 Aligned_cols=221 Identities=20% Similarity=0.260 Sum_probs=147.1
Q ss_pred ceecchhhhhhcccCcccCC--CCCCCCCCCCCCceEEEecCh-hhHhhc---hhhhhcCCCcceeeeEEEEecCCCccc
Q psy12659 659 YVRGCEIEGMLDVNGRIIED--GPEPRPVLPGDTRTFRVMLDC-NQYKED---LDNVAQGNEDVYETFNVLMRRKPKENN 732 (1051)
Q Consensus 659 ~vR~~Ei~~~~de~g~~~~~--~~~~~~~~~~~~r~l~v~LD~-~qy~~d---~~~~~~~~~dvy~~fNllirr~~~enn 732 (1051)
.+|.+|++.+..+..+++.. +..|+++.+...+ ....+.. ..+... ....+...+|++ ++...++....
T Consensus 1 ~e~~~e~~~~~~~~~~~s~~~~~~~g~~~~~l~~~-~~~~~~g~~~~~f~~~~~~~~~~~~GD~v----~i~~~~~~~~~ 75 (637)
T TIGR00376 1 LEREAEISAMMNEIRRLSLKQRERRGRAILNLQGK-IRGGLLGFLLVRFGRRKAIATEISVGDIV----LVSRGNPLQSD 75 (637)
T ss_pred CchHHHHHHHHHHHHhcCHHHHHhcCceEeceEEE-EEeCCCCeEEEEEecCCCCCCcCCCCCEE----EEecCCCCCCC
Confidence 37899999999988888765 4567776665555 3333221 111111 112355677887 66666666666
Q ss_pred hHHHHHHHHH---hhccCCCCChhhhh-hhcccCCCCCCcccchhhhhcccccCccccccccccccCCCccc-ccccCCC
Q psy12659 733 FKAVLETIRD---LMNTECVVPDWLHD-IILGYGDPGAAHYTEMPNEIATMDFNDTFLNMDHLRSSFPQAEI-RVKTDNP 807 (1051)
Q Consensus 733 fk~vl~~i~~---ll~~~~~lP~wl~d-ifLG~gdp~~a~y~~m~~~l~~ld~~dtfl~~~hl~~sfp~~~i-~~~~~~~ 807 (1051)
..+++..+.+ .+..+..+|.|..+ +.+.. .+++.+|++|..++..+.-... ++..-..|... .+.....
T Consensus 76 ~~g~V~~v~~~~i~v~~~~~~~~~~~~~~~i~~-~~~~~t~~rm~~aL~~l~~~~~-----~l~~~llg~~~p~~~~~~~ 149 (637)
T TIGR00376 76 LTGVVTRVGKRFITVALEESVPQWSLKRVRIDL-YANDVTFKRMKEALRALTENHS-----RLLEFILGREAPSKASEIH 149 (637)
T ss_pred cEEEEEEEcCcEEEEEECCCCCcccCceEEEEE-ecCccHHHHHHHHHHHHHhchh-----hHHHHHhCCCCCCcccccc
Confidence 7777777655 12344457877543 22322 5689999999998887642211 11111111100 0000000
Q ss_pred CCCCCCCCCCHHHHHHHHHhcCC-CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 808 TKLVPPFKLTFHEIEAIRAGMQP-GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 808 ~~~~~~~~Ln~~Q~~Ai~~~l~~-~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
........||.+|++||..++.. ++++|+||||||||+|++++|.+++. .+.+|||||+||.|+|+++++|.+.++
T Consensus 150 ~~~~~~~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~--~g~~VLv~a~sn~Avd~l~e~l~~~~~- 226 (637)
T TIGR00376 150 DFQFFDPNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVK--RGLRVLVTAPSNIAVDNLLERLALCDQ- 226 (637)
T ss_pred cccccCCCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHH--cCCCEEEEcCcHHHHHHHHHHHHhCCC-
Confidence 01112237999999999999985 99999999999999999999999998 678999999999999999999998754
Q ss_pred ccccccccc
Q psy12659 887 ERHLLHKKY 895 (1051)
Q Consensus 887 ~~~llRlgs 895 (1051)
+++|+|.
T Consensus 227 --~vvRlg~ 233 (637)
T TIGR00376 227 --KIVRLGH 233 (637)
T ss_pred --cEEEeCC
Confidence 7899994
No 9
>KOG1803|consensus
Probab=99.62 E-value=5.2e-16 Score=180.88 Aligned_cols=86 Identities=31% Similarity=0.491 Sum_probs=77.1
Q ss_pred CCCCCCCCHHHHHHHHHhcCC-CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCcc
Q psy12659 810 LVPPFKLTFHEIEAIRAGMQP-GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDER 888 (1051)
Q Consensus 810 ~~~~~~Ln~~Q~~Ai~~~l~~-~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~~ 888 (1051)
...+..||.+|++||..+++. .+++||||||||||+|+++||.+++. .+++||||||||.||||+.+||...+.
T Consensus 180 ~~~~~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk--~~k~VLVcaPSn~AVdNiverl~~~~~--- 254 (649)
T KOG1803|consen 180 TFFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVK--QKKRVLVCAPSNVAVDNIVERLTHLKL--- 254 (649)
T ss_pred ccCCccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHH--cCCeEEEEcCchHHHHHHHHHhccccc---
Confidence 345679999999999999995 99999999999999999999999999 889999999999999999999986655
Q ss_pred cccccccccChhhHH
Q psy12659 889 HLLHKKYRITPRYLL 903 (1051)
Q Consensus 889 ~llRlgsritpr~l~ 903 (1051)
.++|+| +|.++.
T Consensus 255 ~l~R~g---~paRl~ 266 (649)
T KOG1803|consen 255 NLVRVG---HPARLL 266 (649)
T ss_pred chhhcC---chhhhh
Confidence 789999 555444
No 10
>KOG1802|consensus
Probab=99.57 E-value=8.6e-15 Score=170.57 Aligned_cols=137 Identities=25% Similarity=0.333 Sum_probs=101.4
Q ss_pred eEEEEecCCCccchHHHHHHHHHhhccCCCCChhhhhhhcccCCCCCCcccchhhhhcccccCccccccccccccCCCcc
Q psy12659 720 FNVLMRRKPKENNFKAVLETIRDLMNTECVVPDWLHDIILGYGDPGAAHYTEMPNEIATMDFNDTFLNMDHLRSSFPQAE 799 (1051)
Q Consensus 720 fNllirr~~~ennfk~vl~~i~~ll~~~~~lP~wl~difLG~gdp~~a~y~~m~~~l~~ld~~dtfl~~~hl~~sfp~~~ 799 (1051)
.+++|+ .+.|...+..++.+...+..+...+....||-.-.+...+. .|+. .
T Consensus 351 vd~vwk----~ts~drm~~alk~la~D~~~vs~y~y~klLgh~~~~~~~k~--------------~LP~-----~----- 402 (935)
T KOG1802|consen 351 VDFVWK----STSFDRMQLALKLLAVDEKKVSGYLYHKLLGHPVEDSSLKK--------------LLPR-----R----- 402 (935)
T ss_pred EEEEEc----CccHHHHHHHHHHhhhccccchhhhhhHHhcCcchhhhhcc--------------cCch-----h-----
Confidence 345554 46677777777777665656777777777774211100000 0111 0
Q ss_pred cccccCCCCCCCCCCCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHH
Q psy12659 800 IRVKTDNPTKLVPPFKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEK 879 (1051)
Q Consensus 800 i~~~~~~~~~~~~~~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~ 879 (1051)
+. . .-+| .||.||..||.++|+.++++||||||||||.|++.||.+|... ...+|||||+||.|+|+|.++
T Consensus 403 --~s--~--~~lp--kLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~-~~~~VLvcApSNiAVDqLaeK 473 (935)
T KOG1802|consen 403 --FS--V--PNLP--KLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ-HAGPVLVCAPSNIAVDQLAEK 473 (935)
T ss_pred --hc--C--CCch--hhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh-cCCceEEEcccchhHHHHHHH
Confidence 00 0 1123 8999999999999999999999999999999999999999986 467999999999999999999
Q ss_pred HHhcCCCcccccccccc
Q psy12659 880 IISLDVDERHLLHKKYR 896 (1051)
Q Consensus 880 l~~~~~~~~~llRlgsr 896 (1051)
|.+.|+ +++|+-++
T Consensus 474 Ih~tgL---KVvRl~ak 487 (935)
T KOG1802|consen 474 IHKTGL---KVVRLCAK 487 (935)
T ss_pred HHhcCc---eEeeeehh
Confidence 999997 78888743
No 11
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A.
Probab=99.55 E-value=9.7e-15 Score=153.96 Aligned_cols=82 Identities=30% Similarity=0.451 Sum_probs=62.1
Q ss_pred CCCHHHHHHHHHhcCCCe-EEEECCCCCChhHHHHHHHHHHH------HhCCCCcEEEEecchHHHHHHHHHHHh-----
Q psy12659 815 KLTFHEIEAIRAGMQPGL-TLVVGPPGTGKTDVAVQIISNLY------HNFPHQRTLIVTHSNQALNQLFEKIIS----- 882 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~-tlIqGPPGTGKT~ti~~iI~~ll------~~~~~~riLV~a~SN~Ald~l~e~l~~----- 882 (1051)
.||++|.+||..++..+. ++|+||||||||+|++.++..++ ...++++|||||+||.|+|++++++.+
T Consensus 1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~~~~~~ 80 (236)
T PF13086_consen 1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKKLLDED 80 (236)
T ss_dssp ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC-----
T ss_pred CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHhhcccc
Confidence 489999999999999765 99999999999999999999994 245789999999999999999999998
Q ss_pred cCCCcccccccccc
Q psy12659 883 LDVDERHLLHKKYR 896 (1051)
Q Consensus 883 ~~~~~~~llRlgsr 896 (1051)
.......++|+|+.
T Consensus 81 ~~~~~~~~ir~~~~ 94 (236)
T PF13086_consen 81 GKVYKPKIIRLGSE 94 (236)
T ss_dssp ---TT--EEE---G
T ss_pred ccccccchhhhccc
Confidence 23345578888843
No 12
>KOG1807|consensus
Probab=99.45 E-value=3.3e-13 Score=159.59 Aligned_cols=87 Identities=26% Similarity=0.350 Sum_probs=76.2
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCC----CCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 172 RKNTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFP----HQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 172 ~~~~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p----~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
.....-|+.+|..|..+++...+++||||||||||.+...++..|+.+.. ..+|||+|.||+|||++++++...+
T Consensus 373 ~~g~~ildsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~ligiy~~q- 451 (1025)
T KOG1807|consen 373 GPGLVILDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYLIGIYYHQ- 451 (1025)
T ss_pred CCCceeecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHHHHHHhcC-
Confidence 33456789999999999999999999999999999999999999998853 3789999999999999999999753
Q ss_pred CCCcEEEecCCcc
Q psy12659 248 DERHLLRLGHGEE 260 (1051)
Q Consensus 248 ~~~~lvRlG~~~~ 260 (1051)
...|+|.|+...
T Consensus 452 -rpsImr~gsr~~ 463 (1025)
T KOG1807|consen 452 -RPSIMRQGSRFF 463 (1025)
T ss_pred -CceEEEeccccC
Confidence 347999997654
No 13
>KOG1805|consensus
Probab=99.32 E-value=3.3e-12 Score=155.07 Aligned_cols=116 Identities=19% Similarity=0.326 Sum_probs=100.3
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCccccccc
Q psy12659 815 KLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLHK 893 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~~~llRl 893 (1051)
.||..|++|+..++. .++++|.|-||||||||++.+|..|+. .|++||++|+||.|||||+-||...++ .++|+
T Consensus 669 ~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~--~gkkVLLtsyThsAVDNILiKL~~~~i---~~lRL 743 (1100)
T KOG1805|consen 669 RLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVA--LGKKVLLTSYTHSAVDNILIKLKGFGI---YILRL 743 (1100)
T ss_pred hcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHH--cCCeEEEEehhhHHHHHHHHHHhccCc---ceeec
Confidence 899999999999999 899999999999999999999999999 899999999999999999999999988 58899
Q ss_pred cc--ccChhhHHHhccC------HHHHHhhhcCceeeccccccccccccc
Q psy12659 894 KY--RITPRYLLLAIKN------DVELSQLLSDVTIAQGGVMPNIQSMKF 935 (1051)
Q Consensus 894 gs--ritpr~l~laVrn------d~eL~~LL~~vtIs~ggvlp~i~k~ll 935 (1051)
|+ +++|.-..+...+ -.++.+.+..+.|..+..+.-.|+...
T Consensus 744 G~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf~ 793 (1100)
T KOG1805|consen 744 GSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLFV 793 (1100)
T ss_pred CCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhhh
Confidence 97 5667666655333 377888888888888877776666543
No 14
>PF13245 AAA_19: Part of AAA domain
Probab=99.27 E-value=8.2e-12 Score=112.70 Aligned_cols=59 Identities=36% Similarity=0.576 Sum_probs=52.8
Q ss_pred HHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHHHH
Q psy12659 184 EAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKI 242 (1051)
Q Consensus 184 ~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~rl 242 (1051)
+||..++. +++++|+||||||||+++++++..++.. .++++||++++||.|+|++.+++
T Consensus 1 ~av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl 62 (76)
T PF13245_consen 1 EAVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL 62 (76)
T ss_pred CHHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence 46776776 8999999999999999999999999953 34789999999999999999999
No 15
>PF13245 AAA_19: Part of AAA domain
Probab=99.25 E-value=1.1e-11 Score=111.82 Aligned_cols=59 Identities=36% Similarity=0.576 Sum_probs=53.1
Q ss_pred HHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHh--CCCCcEEEEecchHHHHHHHHHH
Q psy12659 822 EAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 822 ~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~--~~~~riLV~a~SN~Ald~l~e~l 880 (1051)
+||..++. +++++|+||||||||+|+++++..++.. .++++|||+++||.|+++|.+++
T Consensus 1 ~av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl 62 (76)
T PF13245_consen 1 EAVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL 62 (76)
T ss_pred CHHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence 46777777 8999999999999999999999999953 23899999999999999999999
No 16
>KOG1807|consensus
Probab=98.98 E-value=6.5e-10 Score=132.30 Aligned_cols=84 Identities=26% Similarity=0.346 Sum_probs=74.7
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCC----CCcEEEEecchHHHHHHHHHHHhcCCCccc
Q psy12659 814 FKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFP----HQRTLIVTHSNQALNQLFEKIISLDVDERH 889 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~----~~riLV~a~SN~Ald~l~e~l~~~~~~~~~ 889 (1051)
+.|+.||+.|..+++...+++||||||||||++...+|..|+.|.. ..+|||+|.||+|||++++++...+- ..
T Consensus 377 ~ildsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~ligiy~~qr--ps 454 (1025)
T KOG1807|consen 377 VILDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYLIGIYYHQR--PS 454 (1025)
T ss_pred eeecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHHHHHHhcCC--ce
Confidence 3689999999999999999999999999999999999999998652 47999999999999999999997542 36
Q ss_pred ccccccccCh
Q psy12659 890 LLHKKYRITP 899 (1051)
Q Consensus 890 llRlgsritp 899 (1051)
++|.|++...
T Consensus 455 Imr~gsr~~s 464 (1025)
T KOG1807|consen 455 IMRQGSRFFS 464 (1025)
T ss_pred EEEeccccCC
Confidence 8999987753
No 17
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=98.95 E-value=1.7e-09 Score=114.46 Aligned_cols=64 Identities=30% Similarity=0.413 Sum_probs=54.4
Q ss_pred CCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHH
Q psy12659 177 PFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 242 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl 242 (1051)
.||+.|++|+..+++ .++++|+||||||||+++..++..+... +.+|+++||||.|++++.+++
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~~ 66 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAA--GKRVIGLAPTNKAAKELREKT 66 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHT--T--EEEEESSHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhC--CCeEEEECCcHHHHHHHHHhh
Confidence 489999999999874 4699999999999999999988877776 789999999999999998885
No 18
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=98.89 E-value=3.5e-09 Score=112.02 Aligned_cols=64 Identities=30% Similarity=0.406 Sum_probs=54.5
Q ss_pred CCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHH
Q psy12659 815 KLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l 880 (1051)
.||+.|++|+..++. ..+++|+||||||||+++..++..+.. .+.+|+++|+||.|+++|.+++
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~--~g~~v~~~apT~~Aa~~L~~~~ 66 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEA--AGKRVIGLAPTNKAAKELREKT 66 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHH--TT--EEEEESSHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHh--CCCeEEEECCcHHHHHHHHHhh
Confidence 489999999999976 459999999999999999998877777 5799999999999999999885
No 19
>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....
Probab=98.77 E-value=1.4e-08 Score=112.35 Aligned_cols=66 Identities=33% Similarity=0.434 Sum_probs=57.3
Q ss_pred CCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcC--CCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 178 FTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~--p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
||+.|.++|.. ..+..+|.|+||||||+|++..+..++... +..+||++|+||.|++++.+||...
T Consensus 1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~ 68 (315)
T PF00580_consen 1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIREL 68 (315)
T ss_dssp S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHh
Confidence 68999999998 778899999999999999999998888765 5689999999999999999999763
No 20
>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....
Probab=98.72 E-value=2.5e-08 Score=110.49 Aligned_cols=66 Identities=33% Similarity=0.423 Sum_probs=57.6
Q ss_pred CCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhC--CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 816 LTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 816 Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~--~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
||+.|.++|.. ..+.++|.|+||||||+|++..|..|+... +..+||++|+||.|++.+.++|...
T Consensus 1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~ 68 (315)
T PF00580_consen 1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIREL 68 (315)
T ss_dssp S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHh
Confidence 68999999999 778899999999999999999999998854 5689999999999999999999774
No 21
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.
Probab=98.66 E-value=4.2e-08 Score=119.41 Aligned_cols=66 Identities=24% Similarity=0.390 Sum_probs=59.7
Q ss_pred HHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCC---CeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 180 PTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPH---QRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 180 ~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~---~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
+.|+.|+..++.+++++|.||||||||||+..++..+....+. .+|+++|||++|+.++.+.+...
T Consensus 148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~ 216 (586)
T TIGR01447 148 NWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKA 216 (586)
T ss_pred HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhh
Confidence 6899999999999999999999999999999999988875432 58999999999999999988653
No 22
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=98.63 E-value=6.3e-08 Score=118.28 Aligned_cols=67 Identities=21% Similarity=0.272 Sum_probs=60.2
Q ss_pred CCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcC--CCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 178 FTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~--p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
..+.|++|+..++..++++|.||||||||||+..++..+.+.. +..+|+++|||++|+.++.+.+..
T Consensus 153 ~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~ 221 (615)
T PRK10875 153 EVDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGK 221 (615)
T ss_pred CCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHh
Confidence 3579999999999999999999999999999999999987743 246899999999999999998865
No 23
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.
Probab=98.57 E-value=1.3e-07 Score=115.32 Aligned_cols=65 Identities=23% Similarity=0.399 Sum_probs=58.6
Q ss_pred HHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCC---CcEEEEecchHHHHHHHHHHHh
Q psy12659 818 FHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPH---QRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 818 ~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~---~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
+.|+.|+..++.+++++|+||||||||+|++.++..+....+. .+|+++|||++|+.+|.+.+..
T Consensus 148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~ 215 (586)
T TIGR01447 148 NWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRK 215 (586)
T ss_pred HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHh
Confidence 5799999999999999999999999999999999988764432 5899999999999999998854
No 24
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=98.54 E-value=1.7e-07 Score=114.63 Aligned_cols=66 Identities=20% Similarity=0.285 Sum_probs=59.2
Q ss_pred CHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhC--CCCcEEEEecchHHHHHHHHHHHh
Q psy12659 817 TFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 817 n~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~--~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.+.|++|+..++..++++|+||||||||+|+..++..+.+.. +..+|+++|||++|..+|.+.+..
T Consensus 154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~ 221 (615)
T PRK10875 154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGK 221 (615)
T ss_pred CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHh
Confidence 468999999999999999999999999999999999987643 246899999999999999998853
No 25
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=98.49 E-value=2.2e-07 Score=116.05 Aligned_cols=68 Identities=22% Similarity=0.209 Sum_probs=59.0
Q ss_pred CCCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHH
Q psy12659 174 NTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEK 241 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~r 241 (1051)
....||+.|++|+..+.+.++++|+|+|||||||++..++..+-...+..+|++||||+.|++.+.+.
T Consensus 320 ~~~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~ 387 (720)
T TIGR01448 320 LRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEV 387 (720)
T ss_pred cCCCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHh
Confidence 34689999999999999999999999999999999999988777652227899999999999976544
No 26
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=98.42 E-value=3.8e-07 Score=113.21 Aligned_cols=67 Identities=27% Similarity=0.407 Sum_probs=59.5
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.||++|++||... .+..+|.|+||||||+|++.-|..|+.. .+.++||++|.||.|++++.+|+.+.
T Consensus 2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~ 70 (672)
T PRK10919 2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQT 70 (672)
T ss_pred CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHH
Confidence 6999999999764 4668999999999999999999999964 35689999999999999999999864
No 27
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=98.39 E-value=6.4e-07 Score=111.90 Aligned_cols=68 Identities=22% Similarity=0.205 Sum_probs=59.0
Q ss_pred CCCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHH
Q psy12659 813 PFKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l 880 (1051)
.+.|++.|++|+..+...++++|+|+||||||+++..++..+-...+..+|+++|||+.|...|.+.+
T Consensus 321 ~~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~ 388 (720)
T TIGR01448 321 RKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT 388 (720)
T ss_pred CCCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc
Confidence 34799999999999999999999999999999999998887666322278999999999999887754
No 28
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=98.35 E-value=6.8e-07 Score=111.04 Aligned_cols=67 Identities=25% Similarity=0.371 Sum_probs=59.5
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHh--CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~--~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.||+.|++||... .+-.+|.|+||||||+|++..|.+|+.. .+.++||++|.||.|.+++.+|+.+.
T Consensus 2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~ 70 (672)
T PRK10919 2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQT 70 (672)
T ss_pred CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHH
Confidence 6899999999864 4568899999999999999999999963 35689999999999999999999865
No 29
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=98.34 E-value=6.7e-07 Score=111.99 Aligned_cols=67 Identities=31% Similarity=0.348 Sum_probs=59.9
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.||+.|++||... .+..+|.|+||||||+|++.-|..|+.. .+..+||++|.||.|++++.+|+.+.
T Consensus 9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~ 77 (721)
T PRK11773 9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQL 77 (721)
T ss_pred hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHH
Confidence 6999999999854 4668999999999999999999999964 35689999999999999999999875
No 30
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=98.34 E-value=6.3e-07 Score=112.15 Aligned_cols=67 Identities=31% Similarity=0.371 Sum_probs=60.0
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.||+.|++||... .+..+|.|.||||||+|++.-|..|+.. .+..+||++|.||.|++++.+|+.+.
T Consensus 4 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~ 72 (715)
T TIGR01075 4 GLNDKQREAVAAP--PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGAL 72 (715)
T ss_pred ccCHHHHHHHcCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHH
Confidence 5999999999754 4668999999999999999999999974 35689999999999999999999875
No 31
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=98.33 E-value=1.1e-06 Score=110.22 Aligned_cols=64 Identities=23% Similarity=0.231 Sum_probs=56.7
Q ss_pred CCCCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHH
Q psy12659 175 TIPFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFE 240 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~ 240 (1051)
...||+.|++||..+++ .++++|+||||||||+++..++..+-.. +.+|++||||+.|+..+.+
T Consensus 350 ~~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~~i~~~~~~~--g~~V~~~ApTg~Aa~~L~~ 414 (744)
T TIGR02768 350 HYRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLKAAREAWEAA--GYRVIGAALSGKAAEGLQA 414 (744)
T ss_pred cCCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHHHHHHHHHhC--CCeEEEEeCcHHHHHHHHh
Confidence 36799999999999887 6899999999999999999988777665 7899999999999988754
No 32
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=98.30 E-value=9.5e-07 Score=110.66 Aligned_cols=67 Identities=33% Similarity=0.365 Sum_probs=59.9
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHH--hCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYH--NFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~--~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.||+.|++||... .+-.+|.|+||||||+|++..|.+|+. ..+..+||++|.||.|++++.+|+.+.
T Consensus 9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~ 77 (721)
T PRK11773 9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQL 77 (721)
T ss_pred hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHH
Confidence 6999999999865 455889999999999999999999996 345789999999999999999999875
No 33
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=98.29 E-value=1e-06 Score=110.39 Aligned_cols=67 Identities=31% Similarity=0.362 Sum_probs=60.1
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHh--CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~--~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.||+.|++||... .+..+|.|.||||||+|++..|.+|+.. .+..+||++|.||.|++++.+|+.+.
T Consensus 4 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~ 72 (715)
T TIGR01075 4 GLNDKQREAVAAP--PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGAL 72 (715)
T ss_pred ccCHHHHHHHcCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHH
Confidence 6999999999764 4568999999999999999999999973 35689999999999999999999876
No 34
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=98.27 E-value=3.4e-06 Score=85.63 Aligned_cols=72 Identities=25% Similarity=0.284 Sum_probs=64.3
Q ss_pred CCCCCHHHHHHHHHhcCC-CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 175 TIPFTPTQIEAIRAGMQP-GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~~-~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
...+++.|.+++...... ...+|.||+|||||.++...+...+...+..++|+++|+..++.++..++....
T Consensus 6 ~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~ 78 (201)
T smart00487 6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLG 78 (201)
T ss_pred CCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHh
Confidence 357899999999999887 899999999999999999988888877656899999999999999999988754
No 35
>PRK11054 helD DNA helicase IV; Provisional
Probab=98.25 E-value=1.7e-06 Score=107.29 Aligned_cols=70 Identities=24% Similarity=0.246 Sum_probs=61.1
Q ss_pred CCCCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhC--CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 812 PPFKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~--~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+.+||++|++||.... +-.+|.|.||||||+|++..+..|+... ++.+||++|.|+.|.+++.+||.+.
T Consensus 193 e~~~L~~~Q~~av~~~~--~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~ 264 (684)
T PRK11054 193 ESSPLNPSQARAVVNGE--DSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRER 264 (684)
T ss_pred cCCCCCHHHHHHHhCCC--CCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHh
Confidence 45689999999998764 4479999999999999999999999743 4679999999999999999999764
No 36
>PRK11054 helD DNA helicase IV; Provisional
Probab=98.24 E-value=1.8e-06 Score=107.15 Aligned_cols=68 Identities=28% Similarity=0.357 Sum_probs=59.5
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcC--CCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~--p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.+||++|++||.... +-.+|.|+||||||+|++..+..|+... ++.+||++|+|+.|++++.+||.+.
T Consensus 195 ~~L~~~Q~~av~~~~--~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~ 264 (684)
T PRK11054 195 SPLNPSQARAVVNGE--DSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRER 264 (684)
T ss_pred CCCCHHHHHHHhCCC--CCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHh
Confidence 479999999998654 4469999999999999999999998753 4679999999999999999999863
No 37
>TIGR01074 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily.
Probab=98.23 E-value=1.9e-06 Score=107.05 Aligned_cols=67 Identities=30% Similarity=0.426 Sum_probs=59.1
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.||+.|++||... .+..+|.|+||||||+|++.-|..++.. .+.++||++|.||+|+.++.+|+.+.
T Consensus 1 ~Ln~~Q~~av~~~--~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~ 69 (664)
T TIGR01074 1 KLNPQQQEAVEYV--TGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKT 69 (664)
T ss_pred CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence 4899999999764 4568999999999999999999999964 35689999999999999999999863
No 38
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=98.22 E-value=4.9e-06 Score=84.44 Aligned_cols=72 Identities=22% Similarity=0.183 Sum_probs=64.5
Q ss_pred CCCCCHHHHHHHHHhcCC-CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 813 PFKLTFHEIEAIRAGMQP-GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~~-~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
...+++.|.+++...... ...+|.||+|||||.++...+...+...+..++|+++++..++.++..++....
T Consensus 6 ~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~ 78 (201)
T smart00487 6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLG 78 (201)
T ss_pred CCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHh
Confidence 457899999999999998 999999999999999999999888885556899999999999999999887764
No 39
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=98.22 E-value=2.6e-06 Score=106.95 Aligned_cols=65 Identities=23% Similarity=0.271 Sum_probs=57.9
Q ss_pred CCCCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHH
Q psy12659 813 PFKLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEK 879 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~ 879 (1051)
.+.||+.|++||..++. .++++|+||||||||+++..++..+-. .+.+|+++|||+.|...|.+.
T Consensus 350 ~~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~~i~~~~~~--~g~~V~~~ApTg~Aa~~L~~~ 415 (744)
T TIGR02768 350 HYRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLKAAREAWEA--AGYRVIGAALSGKAAEGLQAE 415 (744)
T ss_pred cCCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHHHHHHHHHh--CCCeEEEEeCcHHHHHHHHhc
Confidence 45899999999999988 689999999999999999998776655 688999999999999998764
No 40
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=98.20 E-value=2.9e-06 Score=108.28 Aligned_cols=64 Identities=20% Similarity=0.115 Sum_probs=54.6
Q ss_pred CCCCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHH
Q psy12659 175 TIPFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFE 240 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~ 240 (1051)
.+.||+.|++||..+++ .++++|+|+|||||||++..++..+-.. +.+|++||||+.|+..+-+
T Consensus 344 g~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l~~~~~~~e~~--G~~V~~~ApTGkAA~~L~e 408 (988)
T PRK13889 344 GLVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAMLGVAREAWEAA--GYEVRGAALSGIAAENLEG 408 (988)
T ss_pred CCCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEecCcHHHHHHHhh
Confidence 46899999999999887 6799999999999999987766655444 7899999999999988653
No 41
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=98.18 E-value=2.3e-06 Score=107.29 Aligned_cols=67 Identities=28% Similarity=0.434 Sum_probs=59.8
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.||+.|++||... .+..+|.|+||||||+|++.-|..|+.. .+..+||++|.||.|+.++.+|+.+.
T Consensus 4 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~ 72 (726)
T TIGR01073 4 HLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKL 72 (726)
T ss_pred ccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHH
Confidence 6999999999853 5668999999999999999999999974 35589999999999999999999865
No 42
>TIGR01074 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily.
Probab=98.17 E-value=3e-06 Score=105.28 Aligned_cols=67 Identities=30% Similarity=0.400 Sum_probs=59.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHh--CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~--~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.||+.|++||... .+-.+|.|+||||||+|++..|..++.. .+.++||++|.||+|..++.++|.+.
T Consensus 1 ~Ln~~Q~~av~~~--~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~ 69 (664)
T TIGR01074 1 KLNPQQQEAVEYV--TGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKT 69 (664)
T ss_pred CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence 4899999999865 4568999999999999999999999963 35689999999999999999999764
No 43
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=98.13 E-value=3.8e-06 Score=105.44 Aligned_cols=67 Identities=27% Similarity=0.393 Sum_probs=59.8
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHh--CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~--~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.||+.|++||... .+-.+|.|+||||||+|++..|.+|+.. .+..+||++|.||.|..++.+|+.+.
T Consensus 4 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~ 72 (726)
T TIGR01073 4 HLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKL 72 (726)
T ss_pred ccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHH
Confidence 6999999999864 4568999999999999999999999974 35689999999999999999999865
No 44
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=98.07 E-value=6.8e-06 Score=104.94 Aligned_cols=63 Identities=21% Similarity=0.111 Sum_probs=54.5
Q ss_pred CCCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHH
Q psy12659 814 FKLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFE 878 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e 878 (1051)
+.||+.|++||..+++ .++++|+|+|||||||++..++..+-. .+.+|+++|+|+.|..+|-+
T Consensus 345 ~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l~~~~~~~e~--~G~~V~~~ApTGkAA~~L~e 408 (988)
T PRK13889 345 LVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAMLGVAREAWEA--AGYEVRGAALSGIAAENLEG 408 (988)
T ss_pred CCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEecCcHHHHHHHhh
Confidence 4799999999999998 679999999999999997665554444 58899999999999999865
No 45
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=98.03 E-value=1e-05 Score=103.85 Aligned_cols=65 Identities=20% Similarity=0.146 Sum_probs=56.9
Q ss_pred CCCCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHH
Q psy12659 175 TIPFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEK 241 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~r 241 (1051)
...||+.|++||..+.. .++++|+|+|||||||++..++..+-.. +.+|+.+|||+.|+..|.+.
T Consensus 379 ~~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~~~~~~~e~~--G~~V~g~ApTgkAA~~L~e~ 444 (1102)
T PRK13826 379 HARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMKAAREAWEAA--GYRVVGGALAGKAAEGLEKE 444 (1102)
T ss_pred CCCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEEcCcHHHHHHHHHh
Confidence 46899999999998754 7899999999999999999988766655 88999999999999988653
No 46
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.96 E-value=1.4e-05 Score=105.33 Aligned_cols=65 Identities=22% Similarity=0.239 Sum_probs=54.9
Q ss_pred CCCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHHH--cCCCCeEEEEeCCHHHHHHHHH
Q psy12659 176 IPFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYH--NFPHQRTLIVTHSNQALNQLFE 240 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~~--~~p~~riLv~a~SN~Avd~l~~ 240 (1051)
..||+.|++||..+++ .++++|+|+|||||||++..++..+-. ..++.+|+.+|||+.|+..|.+
T Consensus 834 ~~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~glAPTgkAa~~L~e 902 (1623)
T PRK14712 834 EKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRS 902 (1623)
T ss_pred cccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEEechHHHHHHHHH
Confidence 4799999999999985 589999999999999999888776543 2246789999999999998853
No 47
>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3.1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....
Probab=97.93 E-value=2.1e-05 Score=80.08 Aligned_cols=65 Identities=29% Similarity=0.414 Sum_probs=56.3
Q ss_pred CCCCHHHHHHHHHhcC-------CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~-------~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
++|.+.|.+|+..... .+..+|+||+|||||.++..++..+.. ++++++|+..-+++..+.+...
T Consensus 2 ~~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~-----~~l~~~p~~~l~~Q~~~~~~~~ 73 (184)
T PF04851_consen 2 YKLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR-----KVLIVAPNISLLEQWYDEFDDF 73 (184)
T ss_dssp -EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC-----EEEEEESSHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc-----ceeEecCHHHHHHHHHHHHHHh
Confidence 4688999999998773 588999999999999999999988886 8999999999999999998543
No 48
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=97.93 E-value=2e-05 Score=101.24 Aligned_cols=65 Identities=20% Similarity=0.144 Sum_probs=57.4
Q ss_pred CCCCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHH
Q psy12659 813 PFKLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEK 879 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~ 879 (1051)
.+.||+.|++||..+.. .++++|+|+|||||||++..++..+-. .+.+|+.+|+|+.|...|.+.
T Consensus 379 ~~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~~~~~~~e~--~G~~V~g~ApTgkAA~~L~e~ 444 (1102)
T PRK13826 379 HARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMKAAREAWEA--AGYRVVGGALAGKAAEGLEKE 444 (1102)
T ss_pred CCCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEcCcHHHHHHHHHh
Confidence 46899999999998765 789999999999999999998876655 688999999999999998654
No 49
>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].
Probab=97.93 E-value=1.6e-05 Score=92.15 Aligned_cols=60 Identities=22% Similarity=0.246 Sum_probs=52.6
Q ss_pred CCCHHHHHHHHHh------cCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHH
Q psy12659 177 PFTPTQIEAIRAG------MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQL 238 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~------l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l 238 (1051)
.||+.|++++..+ ..+....|.||+|||||+++..|+..+-.. +..+++||+|..|+-++
T Consensus 1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~--~~~~~~~a~tg~AA~~i 66 (364)
T PF05970_consen 1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSR--GKKVLVTAPTGIAAFNI 66 (364)
T ss_pred CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccc--cceEEEecchHHHHHhc
Confidence 4899999998877 457788999999999999999999877554 78999999999998876
No 50
>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....
Probab=97.91 E-value=4.8e-05 Score=76.90 Aligned_cols=69 Identities=29% Similarity=0.310 Sum_probs=58.6
Q ss_pred CHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 179 TPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 179 n~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
|+.|.+++..+.+..-.+|.||+|+|||..+.-.+.+.+.+.+..++++++|+..-++++.+++.....
T Consensus 1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~ 69 (169)
T PF00270_consen 1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFS 69 (169)
T ss_dssp -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeeccccccccccccccccc
Confidence 578999999998877799999999999999997776666554456999999999999999999987643
No 51
>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3.1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....
Probab=97.90 E-value=2.3e-05 Score=79.75 Aligned_cols=65 Identities=29% Similarity=0.409 Sum_probs=56.7
Q ss_pred CCCCHHHHHHHHHhcC-------CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 814 FKLTFHEIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~-------~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
+.|.+.|.+|+..+.. .+..+|++|+|||||.++..++..+.. ++++++|+..-+++..+.+...
T Consensus 2 ~~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~-----~~l~~~p~~~l~~Q~~~~~~~~ 73 (184)
T PF04851_consen 2 YKLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR-----KVLIVAPNISLLEQWYDEFDDF 73 (184)
T ss_dssp -EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC-----EEEEEESSHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc-----ceeEecCHHHHHHHHHHHHHHh
Confidence 4678899999999984 689999999999999999999988876 8999999999999999988443
No 52
>cd00046 DEXDc DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Probab=97.88 E-value=3e-05 Score=73.99 Aligned_cols=53 Identities=26% Similarity=0.362 Sum_probs=47.3
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
..+|.||||||||+++...+..+....+..++++++|++..+++..+.+....
T Consensus 2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~ 54 (144)
T cd00046 2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELF 54 (144)
T ss_pred CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHh
Confidence 36899999999999999999998876567899999999999999999887653
No 53
>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].
Probab=97.86 E-value=2.4e-05 Score=90.68 Aligned_cols=60 Identities=23% Similarity=0.249 Sum_probs=53.9
Q ss_pred CCCHHHHHHHHHh------cCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHH
Q psy12659 815 KLTFHEIEAIRAG------MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQL 876 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~------l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l 876 (1051)
.||+.|+.++..+ ..+....|.||+|||||+++..|+..+-. .++.|++||+|..|.-++
T Consensus 1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~--~~~~~~~~a~tg~AA~~i 66 (364)
T PF05970_consen 1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRS--RGKKVLVTAPTGIAAFNI 66 (364)
T ss_pred CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhcc--ccceEEEecchHHHHHhc
Confidence 4899999998888 55888999999999999999999987655 678999999999999988
No 54
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.85 E-value=2.9e-05 Score=103.77 Aligned_cols=65 Identities=22% Similarity=0.219 Sum_probs=55.2
Q ss_pred CCCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHH
Q psy12659 176 IPFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVTHSNQALNQLFE 240 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~ 240 (1051)
..||+.|++||..+++ .++++|+|+|||||||++..++..+-.. ..+.+|+.||||+.|+.++.+
T Consensus 966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~e 1034 (1747)
T PRK13709 966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGLGPTHRAVGEMRS 1034 (1747)
T ss_pred CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEECCcHHHHHHHHh
Confidence 5799999999999987 4799999999999999999988876432 235689999999999998754
No 55
>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....
Probab=97.81 E-value=8.6e-05 Score=75.05 Aligned_cols=69 Identities=26% Similarity=0.247 Sum_probs=58.6
Q ss_pred CHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCC
Q psy12659 817 TFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 885 (1051)
Q Consensus 817 n~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~ 885 (1051)
++.|.+++..+.++.-.+|.||+|+|||..+.-.+.+.+......++++++|+..-+++..+.+.....
T Consensus 1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~ 69 (169)
T PF00270_consen 1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFS 69 (169)
T ss_dssp -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeeccccccccccccccccc
Confidence 467999999999878899999999999999987777666543446999999999999999999987643
No 56
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=97.81 E-value=4e-05 Score=104.60 Aligned_cols=67 Identities=19% Similarity=0.316 Sum_probs=59.5
Q ss_pred CCCCCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHH
Q psy12659 174 NTIPFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 242 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl 242 (1051)
..+.||+.|++||..+++ ..+.+|+|+||||||+++..++..+-.. |.+|.++|||+.|+..+.+.+
T Consensus 426 ~~~~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l~~l~~~~~~~--G~~V~~lAPTgrAA~~L~e~~ 494 (1960)
T TIGR02760 426 SEFALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIAQLLLHLASEQ--GYEIQIITAGSLSAQELRQKI 494 (1960)
T ss_pred ccCCCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHHHHHHHHHHhc--CCeEEEEeCCHHHHHHHHHHh
Confidence 356899999999999886 5899999999999999999998776655 889999999999999988764
No 57
>cd00046 DEXDc DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Probab=97.81 E-value=4.5e-05 Score=72.71 Aligned_cols=53 Identities=26% Similarity=0.362 Sum_probs=47.3
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
..+|.||||||||+++...+..+......++++|++|++..+++..+.+....
T Consensus 2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~ 54 (144)
T cd00046 2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELF 54 (144)
T ss_pred CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHh
Confidence 36899999999999999999998876567899999999999999998887653
No 58
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=97.76 E-value=3.8e-05 Score=95.34 Aligned_cols=68 Identities=29% Similarity=0.382 Sum_probs=60.9
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcC--CCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~--p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
.||+.|++||... .|..+|.+.||||||+|++.-|.+++... ...+||+++.||.|+.++.+|+.+..
T Consensus 2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~ 71 (655)
T COG0210 2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLL 71 (655)
T ss_pred CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHh
Confidence 6899999999877 66789999999999999999999999873 34679999999999999999998863
No 59
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.76 E-value=5.1e-05 Score=100.35 Aligned_cols=64 Identities=23% Similarity=0.264 Sum_probs=54.5
Q ss_pred CCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHH--hCCCCcEEEEecchHHHHHHHH
Q psy12659 815 KLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYH--NFPHQRTLIVTHSNQALNQLFE 878 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~--~~~~~riLV~a~SN~Ald~l~e 878 (1051)
.||+.|++||..++. ..+++|+|+||||||+++..++..+-. ...+.+|+.+|||+.|+..|.+
T Consensus 835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~glAPTgkAa~~L~e 902 (1623)
T PRK14712 835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRS 902 (1623)
T ss_pred ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEEechHHHHHHHHH
Confidence 799999999999996 589999999999999998877765432 2246789999999999999864
No 60
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=97.70 E-value=5.7e-05 Score=93.81 Aligned_cols=68 Identities=29% Similarity=0.352 Sum_probs=60.6
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhC--CCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF--PHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~--~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
.||+.|++||... .+..+|.+.||||||+|++.-|.+|+.+. ...+||+++.||.|+.++.+++.+..
T Consensus 2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~ 71 (655)
T COG0210 2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLL 71 (655)
T ss_pred CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHh
Confidence 6899999999988 56688888999999999999999999853 34689999999999999999998864
No 61
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.67 E-value=8e-05 Score=99.69 Aligned_cols=65 Identities=22% Similarity=0.223 Sum_probs=55.4
Q ss_pred CCCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHH--hCCCCcEEEEecchHHHHHHHH
Q psy12659 814 FKLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYH--NFPHQRTLIVTHSNQALNQLFE 878 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~--~~~~~riLV~a~SN~Ald~l~e 878 (1051)
..||+.|++||..++. ..+++|+|+||||||+++..++..+-. ...+.+|+.+|||+.|+..|.+
T Consensus 966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~e 1034 (1747)
T PRK13709 966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGLGPTHRAVGEMRS 1034 (1747)
T ss_pred CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEECCcHHHHHHHHh
Confidence 3799999999999998 479999999999999999888876542 2235689999999999998765
No 62
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=97.65 E-value=9.2e-05 Score=101.23 Aligned_cols=66 Identities=21% Similarity=0.281 Sum_probs=59.1
Q ss_pred CCCCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHH
Q psy12659 813 PFKLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l 880 (1051)
.+.||+.|++||..+++ ..+.+|+|+||||||+++..++..+-. .|.+|.++|||+.|...|.+.+
T Consensus 427 ~~~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l~~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~~ 494 (1960)
T TIGR02760 427 EFALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIAQLLLHLASE--QGYEIQIITAGSLSAQELRQKI 494 (1960)
T ss_pred cCCCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHHHHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHh
Confidence 45899999999999988 489999999999999999998876555 6899999999999999998864
No 63
>cd00268 DEADc DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
Probab=97.50 E-value=0.00049 Score=72.24 Aligned_cols=69 Identities=23% Similarity=0.215 Sum_probs=57.8
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHH-HHHHHHHHHHc--CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDV-AVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~t-i~~ii~~l~~~--~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.+++.|.+|+...+...-.+|.+|+|+|||.+ +..++..+... .++.++++++|+..-+.++...+.+.
T Consensus 21 ~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~ 92 (203)
T cd00268 21 KPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKL 92 (203)
T ss_pred CCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHH
Confidence 57889999999988877799999999999988 45566666655 35679999999999999998887765
No 64
>PTZ00252 histone H2A; Provisional
Probab=97.45 E-value=8.7e-05 Score=73.29 Aligned_cols=90 Identities=29% Similarity=0.419 Sum_probs=58.9
Q ss_pred HHHHHHHHHhCC-CCcEEEEec--chHHHHHHHHHHHhcCCCccc-ccccccccChhhHHHhccCHHHHHhhhcCceeec
Q psy12659 848 VQIISNLYHNFP-HQRTLIVTH--SNQALNQLFEKIISLDVDERH-LLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQ 923 (1051)
Q Consensus 848 ~~iI~~ll~~~~-~~riLV~a~--SN~Ald~l~e~l~~~~~~~~~-llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~ 923 (1051)
+..|..++.... .+||-..|+ .-..++.|...+.++...... --....||+|+|++++|+||+||+.++.+++|++
T Consensus 28 VgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeEL~~Ll~~vTIa~ 107 (134)
T PTZ00252 28 VGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSR 107 (134)
T ss_pred hHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHHHHHHHcCCccCC
Confidence 345556665221 345444333 223344444444444221110 0013468999999999999999999999999999
Q ss_pred cccccccccccchH
Q psy12659 924 GGVMPNIQSMKFDK 937 (1051)
Q Consensus 924 ggvlp~i~k~ll~k 937 (1051)
||++|++|+.++.+
T Consensus 108 GGVlP~i~~~l~~k 121 (134)
T PTZ00252 108 GGVMPSLNKALAKK 121 (134)
T ss_pred CccCCCccHhhccc
Confidence 99999999999865
No 65
>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli [].; GO: 0005524 ATP binding; PDB: 3B85_A.
Probab=97.42 E-value=0.00023 Score=76.25 Aligned_cols=58 Identities=26% Similarity=0.262 Sum_probs=43.8
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHH
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQA 872 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~A 872 (1051)
+.|..|..++...+..+++++.||+|||||.++++....++.+..-++|+++-+.-.+
T Consensus 4 p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~ 61 (205)
T PF02562_consen 4 PKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEA 61 (205)
T ss_dssp --SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T
T ss_pred CCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCC
Confidence 5799999999999999999999999999999999999988886555788777665433
No 66
>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=97.42 E-value=0.00021 Score=73.84 Aligned_cols=60 Identities=33% Similarity=0.365 Sum_probs=47.1
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCcccccccc
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLHKK 894 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~~~llRlg 894 (1051)
.++|.||||||||+++.+++....+ .+++++.++. ....+++.+++.+.|++...+.+.|
T Consensus 1 ~~li~G~~G~GKT~l~~~~~~~~~~--~g~~v~~~s~-e~~~~~~~~~~~~~g~~~~~l~~~g 60 (187)
T cd01124 1 STLLSGGPGTGKTTFALQFLYAGLA--RGEPGLYVTL-EESPEELIENAESLGWDLERLEDEG 60 (187)
T ss_pred CEEEEcCCCCCHHHHHHHHHHHHHH--CCCcEEEEEC-CCCHHHHHHHHHHcCCChHHHHhcC
Confidence 3789999999999999999999887 6889998875 4557777888877776544444444
No 67
>cd00268 DEADc DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
Probab=97.41 E-value=0.0006 Score=71.55 Aligned_cols=69 Identities=22% Similarity=0.173 Sum_probs=57.7
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHH-HHHHHHHHHHh--CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDV-AVQIISNLYHN--FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~t-i~~iI~~ll~~--~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|.+|+...+.+.-.+|.+|+|+|||.+ +..++..+... ..+.+++|++|+..-+.+..+.+.+.
T Consensus 21 ~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~ 92 (203)
T cd00268 21 KPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKL 92 (203)
T ss_pred CCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHH
Confidence 47888999999999988899999999999988 45556666554 35679999999999999998887665
No 68
>PLN00153 histone H2A; Provisional
Probab=97.39 E-value=9.7e-05 Score=72.87 Aligned_cols=45 Identities=56% Similarity=0.857 Sum_probs=42.1
Q ss_pred ccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHH
Q psy12659 894 KYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKT 938 (1051)
Q Consensus 894 gsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~ 938 (1051)
..||+|+|++++++||+||+.++.+++|++||++|++|+.++.++
T Consensus 75 k~RItPrHi~lAI~nDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk 119 (129)
T PLN00153 75 KNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKK 119 (129)
T ss_pred CCccChHHHHhhccCcHHHHHHHCCCccCCCccCCCcchhhcCcc
Confidence 468999999999999999999999999999999999999998554
No 69
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=97.39 E-value=0.00036 Score=92.51 Aligned_cols=67 Identities=31% Similarity=0.314 Sum_probs=55.2
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcC-CCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF-PHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~-p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.+|+.|.+||.. ...-.+|.+.+|||||+|+++.+..++... +..+|||+|.||.|+.++.+||.+.
T Consensus 1 ~~t~~Q~~ai~~--~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~ 68 (1232)
T TIGR02785 1 QWTDEQWQAIYT--RGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEA 68 (1232)
T ss_pred CCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHH
Confidence 479999999983 344579999999999999999877766532 2357999999999999999999763
No 70
>PLN00156 histone H2AX; Provisional
Probab=97.38 E-value=0.0001 Score=73.49 Aligned_cols=45 Identities=56% Similarity=0.822 Sum_probs=42.2
Q ss_pred ccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHH
Q psy12659 894 KYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKT 938 (1051)
Q Consensus 894 gsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~ 938 (1051)
..||+|+|++++++||+||+.++.+++|++||++|++|+.++.++
T Consensus 80 k~RItPrHi~lAIrnDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk 124 (139)
T PLN00156 80 KNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIHQTLLPKK 124 (139)
T ss_pred CCcCcHHHHHhhccCcHHHHHHHCCCccCCCccCCCccHhhcccc
Confidence 458999999999999999999999999999999999999998665
No 71
>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=97.38 E-value=0.0002 Score=74.10 Aligned_cols=53 Identities=36% Similarity=0.399 Sum_probs=43.6
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCC
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDE 249 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~ 249 (1051)
.++|.||||||||+++.+++....++ ++++++++.. ...+++.+++...|++.
T Consensus 1 ~~li~G~~G~GKT~l~~~~~~~~~~~--g~~v~~~s~e-~~~~~~~~~~~~~g~~~ 53 (187)
T cd01124 1 STLLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLE-ESPEELIENAESLGWDL 53 (187)
T ss_pred CEEEEcCCCCCHHHHHHHHHHHHHHC--CCcEEEEECC-CCHHHHHHHHHHcCCCh
Confidence 37899999999999999999998877 7889988764 44678888887777643
No 72
>PTZ00017 histone H2A; Provisional
Probab=97.37 E-value=9.3e-05 Score=73.52 Aligned_cols=67 Identities=45% Similarity=0.628 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHhcCCCcccccccccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHH
Q psy12659 871 QALNQLFEKIISLDVDERHLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKT 938 (1051)
Q Consensus 871 ~Ald~l~e~l~~~~~~~~~llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~ 938 (1051)
..++.|...+.++......-. -..||+|+|++++++||+||+.++.+++|++||++|++|+.++.++
T Consensus 56 AVLEYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~l~~k~ 122 (134)
T PTZ00017 56 AVLEYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKVLLPKK 122 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccCcHHHHHHHcCCcccCCccCCCccHhhccCC
Confidence 345555555555432221111 2458999999999999999999999999999999999999998554
No 73
>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli [].; GO: 0005524 ATP binding; PDB: 3B85_A.
Probab=97.33 E-value=0.00031 Score=75.31 Aligned_cols=58 Identities=29% Similarity=0.324 Sum_probs=43.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHH
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQA 234 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~A 234 (1051)
+.|..|..++...+..+++.+.||+|||||.++.+....++.+..-.+|+++-|.-.+
T Consensus 4 p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~ 61 (205)
T PF02562_consen 4 PKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEA 61 (205)
T ss_dssp --SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T
T ss_pred CCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCC
Confidence 6799999999999999999999999999999999998888887445678777666544
No 74
>PLN00157 histone H2A; Provisional
Probab=97.32 E-value=0.00013 Score=72.18 Aligned_cols=45 Identities=58% Similarity=0.846 Sum_probs=42.0
Q ss_pred ccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHH
Q psy12659 894 KYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKT 938 (1051)
Q Consensus 894 gsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~ 938 (1051)
..+|+|+|++++++||+||..++.+++|++||++|++|+.++.++
T Consensus 77 k~RItPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~ll~kk 121 (132)
T PLN00157 77 KSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSVLLPKK 121 (132)
T ss_pred CccccHHHHhhcccCcHHHHHHHcCceecCCccCCCcchhhcCCC
Confidence 458999999999999999999999999999999999999998554
No 75
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=97.26 E-value=0.00056 Score=90.69 Aligned_cols=67 Identities=30% Similarity=0.280 Sum_probs=55.5
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhC-CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF-PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~-~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|++||.. .+.-.+|.+.+|||||+|+++.|..++... .-.+|||+|.||.|..++.+||.+.
T Consensus 1 ~~t~~Q~~ai~~--~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~ 68 (1232)
T TIGR02785 1 QWTDEQWQAIYT--RGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEA 68 (1232)
T ss_pred CCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHH
Confidence 368899999984 355689999999999999999888777532 2367999999999999999998653
No 76
>smart00414 H2A Histone 2A.
Probab=97.23 E-value=0.00018 Score=69.33 Aligned_cols=66 Identities=48% Similarity=0.654 Sum_probs=49.4
Q ss_pred HHHHHHHHHHhcCCCcccccccccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHH
Q psy12659 872 ALNQLFEKIISLDVDERHLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKT 938 (1051)
Q Consensus 872 Ald~l~e~l~~~~~~~~~llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~ 938 (1051)
.++.|...+.+.......-. -..+++|+|+.++++||+||..++.+++|++||++|++|+.++.++
T Consensus 39 vLEYLtaEILeLagn~a~~~-k~~rItp~hi~lAi~nD~EL~~L~~~vti~~ggv~p~i~~~l~~~~ 104 (106)
T smart00414 39 VLEYLTAEVLELAGNAARDN-KKRRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHKVLLPKK 104 (106)
T ss_pred HHHHHHHHHHHHHHHHHHhc-CCCccchHHHhhhccCCHHHHHHHcCcccCCCccCCCcchhhcccC
Confidence 44555555544322221111 2458999999999999999999999999999999999999987553
No 77
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=97.18 E-value=0.0011 Score=63.69 Aligned_cols=55 Identities=36% Similarity=0.576 Sum_probs=40.2
Q ss_pred HHHHHHHHhcC---CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHH
Q psy12659 819 HEIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQ 875 (1051)
Q Consensus 819 ~Q~~Ai~~~l~---~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~ 875 (1051)
.+..++...+. ....+|.||||||||+++..+...+.. .+.+++.+..+..+...
T Consensus 5 ~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~--~~~~v~~~~~~~~~~~~ 62 (151)
T cd00009 5 EAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFR--PGAPFLYLNASDLLEGL 62 (151)
T ss_pred HHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhc--CCCCeEEEehhhhhhhh
Confidence 45555555544 578999999999999999988888764 56777777766544443
No 78
>PHA02558 uvsW UvsW helicase; Provisional
Probab=97.17 E-value=0.0012 Score=79.86 Aligned_cols=71 Identities=17% Similarity=0.257 Sum_probs=60.3
Q ss_pred CCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 175 TIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
...+.+.|.+||..++..+-.+++.|+|+|||.++..++..++.. ...++||++||..-+++..+++.+.+
T Consensus 112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~-~~~~vLilvpt~eL~~Q~~~~l~~~~ 182 (501)
T PHA02558 112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN-YEGKVLIIVPTTSLVTQMIDDFVDYR 182 (501)
T ss_pred cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc-CCCeEEEEECcHHHHHHHHHHHHHhc
Confidence 367899999999999987778999999999999988776655554 23499999999999999999998754
No 79
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=97.14 E-value=0.0013 Score=63.37 Aligned_cols=54 Identities=35% Similarity=0.535 Sum_probs=39.0
Q ss_pred HHHHHHHHHhcC---CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHH
Q psy12659 180 PTQIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQAL 235 (1051)
Q Consensus 180 ~~Q~~Ai~~~l~---~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Av 235 (1051)
+.+..++...+. .+..+|.||||||||+++..+...+... +..++.+..+..+.
T Consensus 4 ~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~~~~ 60 (151)
T cd00009 4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP--GAPFLYLNASDLLE 60 (151)
T ss_pred HHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC--CCCeEEEehhhhhh
Confidence 455666665543 5789999999999999999998887743 56677776654443
No 80
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=97.13 E-value=0.00023 Score=69.42 Aligned_cols=65 Identities=46% Similarity=0.644 Sum_probs=48.7
Q ss_pred HHHHHHHHHHhcCCCcccccccccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchH
Q psy12659 872 ALNQLFEKIISLDVDERHLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDK 937 (1051)
Q Consensus 872 Ald~l~e~l~~~~~~~~~llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k 937 (1051)
.++.+...+.+.......-. -..+++|+|+.+++++|+||..++.+++|++||++|++|+.++.+
T Consensus 50 vLEYL~aEIlelA~n~ak~~-k~krItp~hi~lAi~nD~EL~~L~~~vtI~~ggv~p~i~~~l~~~ 114 (115)
T cd00074 50 VLEYLTAEVLELAGNAARDN-KKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIHKVLLPK 114 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCeEcHHHHHHHHhccHHHHHHHcCCcccCCccCCCcchhhcCC
Confidence 44555555544432221111 235899999999999999999999999999999999999998743
No 81
>PLN00154 histone H2A; Provisional
Probab=97.12 E-value=0.00035 Score=69.40 Aligned_cols=88 Identities=33% Similarity=0.415 Sum_probs=57.2
Q ss_pred HHHHHHHHhCC--CCcEEEEec--chHHHHHHHHHHHhcCCCcccccccccccChhhHHHhccCHHHHHhhhcCceeecc
Q psy12659 849 QIISNLYHNFP--HQRTLIVTH--SNQALNQLFEKIISLDVDERHLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQG 924 (1051)
Q Consensus 849 ~iI~~ll~~~~--~~riLV~a~--SN~Ald~l~e~l~~~~~~~~~llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~g 924 (1051)
..|..+++... ..||-..|+ .-..++.|...+.++..+..+-.+ ..||+|+|++++++||+||+.++. .+|++|
T Consensus 42 gRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~k-k~RItPrHi~lAIrnDeEL~~Ll~-~TIa~G 119 (136)
T PLN00154 42 GRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLK-VKRITPRHLQLAIRGDEELDTLIK-GTIAGG 119 (136)
T ss_pred HHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhC-CceecHHHhhhhccCcHHHHHHhc-CCccCC
Confidence 34555555321 235544333 233444455455444322222122 358999999999999999999997 699999
Q ss_pred ccccccccccchHH
Q psy12659 925 GVMPNIQSMKFDKT 938 (1051)
Q Consensus 925 gvlp~i~k~ll~k~ 938 (1051)
|++|++|+.++.++
T Consensus 120 GVlP~i~~~l~~k~ 133 (136)
T PLN00154 120 GVIPHIHKSLINKS 133 (136)
T ss_pred ccCCCcchhhcccc
Confidence 99999999987553
No 82
>PRK10536 hypothetical protein; Provisional
Probab=97.08 E-value=0.0012 Score=73.08 Aligned_cols=56 Identities=14% Similarity=0.139 Sum_probs=44.3
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecc
Q psy12659 814 FKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 869 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~S 869 (1051)
.+.|..|..++......+++++.||+|||||+++..+....+.+..-.+++|+-|+
T Consensus 58 ~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~ 113 (262)
T PRK10536 58 LARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPV 113 (262)
T ss_pred cCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCC
Confidence 36899999999988888999999999999999999998876643233455554443
No 83
>PHA02558 uvsW UvsW helicase; Provisional
Probab=97.07 E-value=0.0016 Score=78.78 Aligned_cols=70 Identities=14% Similarity=0.295 Sum_probs=59.8
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 814 FKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
..+.+.|.+||..++.+.-.+++.|+|+|||.++..++..++.. ...++||++||..-+++..+++.+.+
T Consensus 113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~-~~~~vLilvpt~eL~~Q~~~~l~~~~ 182 (501)
T PHA02558 113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN-YEGKVLIIVPTTSLVTQMIDDFVDYR 182 (501)
T ss_pred CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc-CCCeEEEEECcHHHHHHHHHHHHHhc
Confidence 46888999999999997778999999999999988777666663 23399999999999999999998754
No 84
>PRK05580 primosome assembly protein PriA; Validated
Probab=97.03 E-value=0.0017 Score=81.23 Aligned_cols=70 Identities=21% Similarity=0.256 Sum_probs=62.5
Q ss_pred CCCCCCHHHHHHHHHhcC---CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 812 PPFKLTFHEIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~---~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.++.|++.|++|+..... ....+++||+|+|||.+...++...+. .++++||++|+..-++++.+++.+.
T Consensus 141 ~~~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~--~g~~vLvLvPt~~L~~Q~~~~l~~~ 213 (679)
T PRK05580 141 EPPTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLA--QGKQALVLVPEIALTPQMLARFRAR 213 (679)
T ss_pred CCCCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHH--cCCeEEEEeCcHHHHHHHHHHHHHH
Confidence 466899999999999886 367999999999999999999888887 6789999999999999999999764
No 85
>PRK10536 hypothetical protein; Provisional
Probab=97.02 E-value=0.0012 Score=72.86 Aligned_cols=57 Identities=18% Similarity=0.185 Sum_probs=44.2
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHH
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ 233 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~ 233 (1051)
.+.|..|..++......++.++.||+|||||+++.++....+.+..-.+|+| +.++.
T Consensus 58 ~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI-~RP~v 114 (262)
T PRK10536 58 LARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIV-TRPVL 114 (262)
T ss_pred cCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEE-eCCCC
Confidence 4689999999998888889999999999999999999886654322234444 44443
No 86
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=96.99 E-value=0.0017 Score=80.74 Aligned_cols=70 Identities=23% Similarity=0.273 Sum_probs=58.6
Q ss_pred CCCCCCHHHHHHHHHhcCC------CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 812 PPFKLTFHEIEAIRAGMQP------GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~~------~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
-||.|++.|++||...+.. --.+|+||.|||||.++.-.+...+. .+.++++++||..-+.+..+.+.+.
T Consensus 232 lpf~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~--~g~qvlilaPT~~LA~Q~~~~~~~l 307 (630)
T TIGR00643 232 LPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE--AGYQVALMAPTEILAEQHYNSLRNL 307 (630)
T ss_pred CCCCCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH--cCCcEEEECCHHHHHHHHHHHHHHH
Confidence 4789999999999988762 23699999999999988776666666 5789999999999999998887654
No 87
>KOG1756|consensus
Probab=96.98 E-value=0.00045 Score=67.38 Aligned_cols=46 Identities=63% Similarity=0.876 Sum_probs=42.6
Q ss_pred ccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHHH
Q psy12659 894 KYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTL 939 (1051)
Q Consensus 894 gsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~~ 939 (1051)
..+++|+|++++|+||+||+.++..++|++||++|.+|..+|.++-
T Consensus 78 k~ri~PrH~~lAI~NDeEL~~lL~~vtIa~GGvlPnI~~~lLpKk~ 123 (131)
T KOG1756|consen 78 KTRITPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAILLPKKT 123 (131)
T ss_pred ccccChHHHHHHHhCcHHHHHHhccceeccCCcccccchhhccccc
Confidence 4488999999999999999999999999999999999999987653
No 88
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=96.98 E-value=0.0019 Score=80.88 Aligned_cols=70 Identities=21% Similarity=0.231 Sum_probs=60.1
Q ss_pred CCCCCCHHHHHHHHHhcCC------CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 812 PPFKLTFHEIEAIRAGMQP------GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~~------~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.||.|++.|++|+...... .-.+++||.|||||-++.-.+...+. .+.++++++||..-+.+..+.+.+.
T Consensus 258 l~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~--~g~q~lilaPT~~LA~Q~~~~l~~l 333 (681)
T PRK10917 258 LPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE--AGYQAALMAPTEILAEQHYENLKKL 333 (681)
T ss_pred CCCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH--cCCeEEEEeccHHHHHHHHHHHHHH
Confidence 4789999999999988763 25799999999999998877776666 6789999999999999999888764
No 89
>PRK05580 primosome assembly protein PriA; Validated
Probab=96.96 E-value=0.0024 Score=79.97 Aligned_cols=69 Identities=22% Similarity=0.284 Sum_probs=60.9
Q ss_pred CCCCCHHHHHHHHHhcC---CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 175 TIPFTPTQIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~---~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
...|++.|.+|+..... ....+++||+|+|||.+...++...+.. +.++||++|+..=++++.+++.+.
T Consensus 142 ~~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~--g~~vLvLvPt~~L~~Q~~~~l~~~ 213 (679)
T PRK05580 142 PPTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ--GKQALVLVPEIALTPQMLARFRAR 213 (679)
T ss_pred CCCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc--CCeEEEEeCcHHHHHHHHHHHHHH
Confidence 45799999999998775 4679999999999999999888888876 789999999999999999999763
No 90
>PRK07952 DNA replication protein DnaC; Validated
Probab=96.96 E-value=0.0016 Score=71.70 Aligned_cols=49 Identities=29% Similarity=0.394 Sum_probs=38.9
Q ss_pred CHHHHHHHHHhcC--------CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 817 TFHEIEAIRAGMQ--------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 817 n~~Q~~Ai~~~l~--------~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
+..|..|+..+.. ....++.||||||||+++.++...+.. .+.+|++++
T Consensus 78 ~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~--~g~~v~~it 134 (244)
T PRK07952 78 CEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLL--RGKSVLIIT 134 (244)
T ss_pred CchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEE
Confidence 3457666665543 146899999999999999999999988 678888885
No 91
>PRK07952 DNA replication protein DnaC; Validated
Probab=96.93 E-value=0.0023 Score=70.45 Aligned_cols=60 Identities=25% Similarity=0.375 Sum_probs=44.2
Q ss_pred CCHHHHHHHHHhcC--------CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 178 FTPTQIEAIRAGMQ--------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l~--------~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.++.|..|+..+.. ....++.||||||||+++.++...+... +.++++++ +.++++++..
T Consensus 77 ~~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~--g~~v~~it-----~~~l~~~l~~ 144 (244)
T PRK07952 77 ECEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLR--GKSVLIIT-----VADIMSAMKD 144 (244)
T ss_pred CCchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEE-----HHHHHHHHHH
Confidence 35677777765432 2468999999999999999999999876 77888774 3445555543
No 92
>PRK08181 transposase; Validated
Probab=96.93 E-value=0.0024 Score=71.32 Aligned_cols=51 Identities=31% Similarity=0.412 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHhc----CCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 815 KLTFHEIEAIRAGM----QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l----~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
.++..|..++..+- ...-.++.||||||||+++..+...+.. .+.+|+.+.
T Consensus 87 ~~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~--~g~~v~f~~ 141 (269)
T PRK08181 87 MVSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIE--NGWRVLFTR 141 (269)
T ss_pred CCCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHH--cCCceeeee
Confidence 57888998886652 3566999999999999999999998887 678887776
No 93
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=96.92 E-value=0.0025 Score=75.91 Aligned_cols=80 Identities=29% Similarity=0.375 Sum_probs=64.2
Q ss_pred CCCCHHHHHHHHHhcC----CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCc
Q psy12659 176 IPFTPTQIEAIRAGMQ----PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERH 251 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~----~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~ 251 (1051)
+.+.+-|.+|+..... .+-.+|+-|+|+|||.+++.++..+... +||++|+..-++|-.+++.........
T Consensus 35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~~-----~Lvlv~~~~L~~Qw~~~~~~~~~~~~~ 109 (442)
T COG1061 35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRS-----TLVLVPTKELLDQWAEALKKFLLLNDE 109 (442)
T ss_pred CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcCC-----EEEEECcHHHHHHHHHHHHHhcCCccc
Confidence 5789999999998876 8889999999999999999998876543 999999999999999888765432223
Q ss_pred EEEecCCcc
Q psy12659 252 LLRLGHGEE 260 (1051)
Q Consensus 252 lvRlG~~~~ 260 (1051)
+--+|.+.+
T Consensus 110 ~g~~~~~~~ 118 (442)
T COG1061 110 IGIYGGGEK 118 (442)
T ss_pred cceecCcee
Confidence 444554443
No 94
>PTZ00424 helicase 45; Provisional
Probab=96.91 E-value=0.0025 Score=74.22 Aligned_cols=70 Identities=20% Similarity=0.212 Sum_probs=55.8
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHH-cCCCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYH-NFPHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~-~~p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
.+++.|.+|+..++...-.+|++|+|||||.+..-.+...+. ...+.++|+++|+..-+.++.+.+...+
T Consensus 50 ~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~ 120 (401)
T PTZ00424 50 KPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALG 120 (401)
T ss_pred CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHHHh
Confidence 689999999999998767889999999999876654444443 2246789999999999888888776653
No 95
>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=96.89 E-value=0.00078 Score=63.99 Aligned_cols=42 Identities=29% Similarity=0.474 Sum_probs=31.7
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQAL 873 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Al 873 (1051)
+...+|.||||||||+++..++..+.. ....++.++.+....
T Consensus 2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~--~~~~~~~~~~~~~~~ 43 (148)
T smart00382 2 GEVILIVGPPGSGKTTLARALARELGP--PGGGVIYIDGEDILE 43 (148)
T ss_pred CCEEEEECCCCCcHHHHHHHHHhccCC--CCCCEEEECCEEccc
Confidence 467899999999999999999887665 334577766655433
No 96
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=96.84 E-value=0.0025 Score=76.00 Aligned_cols=68 Identities=29% Similarity=0.344 Sum_probs=60.3
Q ss_pred CCCCCCHHHHHHHHHhcC----CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 812 PPFKLTFHEIEAIRAGMQ----PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~----~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
+.+.|.+.|.+|+..... .+-.+|+-|+|+|||.+++.++..+.. ++||++|+..-+++..+++....
T Consensus 33 ~~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~-----~~Lvlv~~~~L~~Qw~~~~~~~~ 104 (442)
T COG1061 33 FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKR-----STLVLVPTKELLDQWAEALKKFL 104 (442)
T ss_pred cCCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcC-----CEEEEECcHHHHHHHHHHHHHhc
Confidence 455789999999999998 899999999999999999999998655 39999999999999988886653
No 97
>PRK08181 transposase; Validated
Probab=96.83 E-value=0.0035 Score=70.04 Aligned_cols=52 Identities=35% Similarity=0.432 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHhc----CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 176 IPFTPTQIEAIRAGM----QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l----~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
..++..|..++..+- ...-.++.||||||||+++..+...+..+ +.+++.++
T Consensus 86 ~~~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~--g~~v~f~~ 141 (269)
T PRK08181 86 PMVSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIEN--GWRVLFTR 141 (269)
T ss_pred CCCCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHc--CCceeeee
Confidence 467889999986552 34558999999999999999999988876 77777665
No 98
>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=96.81 E-value=0.00089 Score=63.58 Aligned_cols=40 Identities=28% Similarity=0.460 Sum_probs=29.9
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ 233 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~ 233 (1051)
....+|.||||||||+++..++..+... ...++.++.+..
T Consensus 2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~--~~~~~~~~~~~~ 41 (148)
T smart00382 2 GEVILIVGPPGSGKTTLARALARELGPP--GGGVIYIDGEDI 41 (148)
T ss_pred CCEEEEECCCCCcHHHHHHHHHhccCCC--CCCEEEECCEEc
Confidence 4578999999999999999998776654 234666655543
No 99
>PTZ00424 helicase 45; Provisional
Probab=96.81 E-value=0.0033 Score=73.19 Aligned_cols=69 Identities=20% Similarity=0.215 Sum_probs=55.9
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHH-hCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYH-NFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~-~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|.+|+..++.+.-++|++|+|||||.+..-.+...+. ...+.++|+++|+..-+.++.+.+...
T Consensus 50 ~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~ 119 (401)
T PTZ00424 50 KPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLAL 119 (401)
T ss_pred CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHHH
Confidence 578899999999999777899999999999877655544443 224578999999999888888776654
No 100
>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=96.81 E-value=0.0016 Score=70.09 Aligned_cols=58 Identities=29% Similarity=0.501 Sum_probs=44.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCC-CCcEEEEecchHHHHHHHHHHHhcCCCcccc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFP-HQRTLIVTHSNQALNQLFEKIISLDVDERHL 890 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~-~~riLV~a~SN~Ald~l~e~l~~~~~~~~~l 890 (1051)
+.+++|.||||||||..+.+++.+-+. . +++++.++- ....+.+.+.+.+.|.+....
T Consensus 19 gs~~li~G~~GsGKT~l~~q~l~~~~~--~~ge~vlyvs~-ee~~~~l~~~~~s~g~d~~~~ 77 (226)
T PF06745_consen 19 GSVVLISGPPGSGKTTLALQFLYNGLK--NFGEKVLYVSF-EEPPEELIENMKSFGWDLEEY 77 (226)
T ss_dssp TSEEEEEESTTSSHHHHHHHHHHHHHH--HHT--EEEEES-SS-HHHHHHHHHTTTS-HHHH
T ss_pred CcEEEEEeCCCCCcHHHHHHHHHHhhh--hcCCcEEEEEe-cCCHHHHHHHHHHcCCcHHHH
Confidence 678999999999999999999988887 5 789999885 444588888888887654333
No 101
>PRK12377 putative replication protein; Provisional
Probab=96.79 E-value=0.0021 Score=70.90 Aligned_cols=43 Identities=28% Similarity=0.423 Sum_probs=33.8
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQL 876 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l 876 (1051)
...++.||||||||+++..|...+.. .+.+|++++- ...++.+
T Consensus 102 ~~l~l~G~~GtGKThLa~AIa~~l~~--~g~~v~~i~~-~~l~~~l 144 (248)
T PRK12377 102 TNFVFSGKPGTGKNHLAAAIGNRLLA--KGRSVIVVTV-PDVMSRL 144 (248)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHH--cCCCeEEEEH-HHHHHHH
Confidence 56899999999999999999999987 6777766653 4444443
No 102
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=96.79 E-value=0.0027 Score=78.87 Aligned_cols=70 Identities=19% Similarity=0.215 Sum_probs=57.0
Q ss_pred CCCCCCHHHHHHHHHhcCC---C---eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 174 NTIPFTPTQIEAIRAGMQP---G---LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~~---~---~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.++.|++.|.+||...+.. + -.||+||.|||||.++.-.+...+.+ +.++++++||..-+.++.+.+.+.
T Consensus 232 lpf~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~--g~qvlilaPT~~LA~Q~~~~~~~l 307 (630)
T TIGR00643 232 LPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA--GYQVALMAPTEILAEQHYNSLRNL 307 (630)
T ss_pred CCCCCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc--CCcEEEECCHHHHHHHHHHHHHHH
Confidence 4568999999999876541 2 36999999999999887666666655 779999999999999998888764
No 103
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=96.79 E-value=0.0032 Score=78.88 Aligned_cols=70 Identities=19% Similarity=0.171 Sum_probs=58.3
Q ss_pred CCCCCCHHHHHHHHHhcCC------CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 174 NTIPFTPTQIEAIRAGMQP------GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~~------~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
-++.|++.|.+|+...... .-.|++||.|||||-+..-.+...+.+ +.++|+++||..-+.++.+.+.+.
T Consensus 258 l~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~--g~q~lilaPT~~LA~Q~~~~l~~l 333 (681)
T PRK10917 258 LPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA--GYQAALMAPTEILAEQHYENLKKL 333 (681)
T ss_pred CCCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc--CCeEEEEeccHHHHHHHHHHHHHH
Confidence 4568999999999876542 247999999999999988777666655 789999999999999999988765
No 104
>TIGR00609 recB exodeoxyribonuclease V, beta subunit. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.77 E-value=0.0018 Score=84.96 Aligned_cols=53 Identities=30% Similarity=0.330 Sum_probs=47.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcC---CCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNF---PHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~---p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.|..+|..-+|||||+||+.++..|+.+. +.++|||+|.|++|..++.+||.+
T Consensus 9 ~G~~lieAsAGtGKT~ti~~~~lrll~~~~~~~~~~iLvvTFT~aAt~el~~RIr~ 64 (1087)
T TIGR00609 9 NGTFLIEASAGTGKTFTIAQLYLRLLLEGGPLTVEEILVVTFTNAATEELKTRIRG 64 (1087)
T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHhcCCCCChhhEEEEehhHHHHHHHHHHHHH
Confidence 57899999999999999999999888753 347999999999999999999976
No 105
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=96.76 E-value=0.0031 Score=67.23 Aligned_cols=60 Identities=27% Similarity=0.355 Sum_probs=43.6
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeE-EEEeCC--HHHHHHHHHHHHhCCCCCCcEEEec
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRT-LIVTHS--NQALNQLFEKIISLDVDERHLLRLG 256 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~ri-Lv~a~S--N~Avd~l~~rl~~~~~~~~~lvRlG 256 (1051)
|.+.++.||+|+|||||++.+.+.+..+ +.+| ||++-+ ..|++++..--...++ ++....
T Consensus 1 p~vi~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~v---p~~~~~ 63 (196)
T PF00448_consen 1 PKVIALVGPTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGV---PFYVAR 63 (196)
T ss_dssp SEEEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTE---EEEESS
T ss_pred CEEEEEECCCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhcc---ccchhh
Confidence 4578899999999999999999988877 5555 455544 4789988766666665 454444
No 106
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=96.76 E-value=0.0043 Score=74.01 Aligned_cols=70 Identities=19% Similarity=0.222 Sum_probs=54.6
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+|+-|.+|+..++...-.++++|+|||||....- ++..+.......++||++||..-++++.+.+...
T Consensus 25 ~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~ 95 (460)
T PRK11776 25 TEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRL 95 (460)
T ss_pred CCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHH
Confidence 368899999999999877799999999999976443 3444332222457999999999999998877654
No 107
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=96.72 E-value=0.0026 Score=67.82 Aligned_cols=54 Identities=26% Similarity=0.409 Sum_probs=40.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE-ecch--HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSN--QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~-a~SN--~Ald~l~e~l~~~~~ 885 (1051)
|.+.++.||+|+|||||++.+...+..+ +++|.++ +.+. .|+++|..-....++
T Consensus 1 p~vi~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~v 57 (196)
T PF00448_consen 1 PKVIALVGPTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGV 57 (196)
T ss_dssp SEEEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTE
T ss_pred CEEEEEECCCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhcc
Confidence 3567899999999999999999998875 5565554 4444 788888766666665
No 108
>COG1112 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]
Probab=96.71 E-value=0.0063 Score=76.65 Aligned_cols=93 Identities=28% Similarity=0.376 Sum_probs=68.8
Q ss_pred CCCCCHHHHHHHHHhcC-CCeEEEE-ccCCCChHH--HHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCC
Q psy12659 175 TIPFTPTQIEAIRAGMQ-PGLTLVV-GPPGTGKTD--VAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDER 250 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~-~~~~lI~-GPPGTGKT~--ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~ 250 (1051)
...++..|..++..... .+..++. ||||||||. ++.+.+...+... ..+++.+++++.+++....++.+... ..
T Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 349 (767)
T COG1112 272 NKELDNEQKLAVKRLLSLNDLFLIHQGPFGTGKTRSVTILELIIELLENN-KLKILPTAESNAAVDNLLRRLKRTVI-KV 349 (767)
T ss_pred chhccchhHHHHHHHhcccceeEeecCCCCCCcchHHHHHHHHHHHHHhc-ccceEEecCcccchhhHHHHHHhhcc-cc
Confidence 34667788888776543 5555555 999999999 6666666666553 68999999999999999999988543 33
Q ss_pred cEEEecCCccccchhhhhc
Q psy12659 251 HLLRLGHGEEALETEKDFS 269 (1051)
Q Consensus 251 ~lvRlG~~~~~~~~~~~fs 269 (1051)
..+|++++..........+
T Consensus 350 ~~~~~~~~~~~~~~~~~~~ 368 (767)
T COG1112 350 ELLRIGHPSRVLKKLKLDT 368 (767)
T ss_pred ceEEcCCcchhhhhhhhhH
Confidence 5899999887664444333
No 109
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=96.70 E-value=0.0055 Score=72.48 Aligned_cols=70 Identities=27% Similarity=0.256 Sum_probs=54.2
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHc----CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHN----FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~----~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++-|.+||..++...-.++++|+|||||....- ++..+... .++.++||++||..-+.++.+.+...
T Consensus 22 ~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l 96 (434)
T PRK11192 22 TRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQAREL 96 (434)
T ss_pred CCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHH
Confidence 357889999999999876799999999999987544 34444321 12368999999999999988877654
No 110
>PRK05973 replicative DNA helicase; Provisional
Probab=96.70 E-value=0.0034 Score=68.81 Aligned_cols=61 Identities=16% Similarity=0.290 Sum_probs=49.1
Q ss_pred HHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCc
Q psy12659 824 IRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDE 887 (1051)
Q Consensus 824 i~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~ 887 (1051)
+..++. +.+++|.|+||+|||+.+.+++.+... .++++++++--.. -+++.+++.+.|++.
T Consensus 57 l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~--~Ge~vlyfSlEes-~~~i~~R~~s~g~d~ 118 (237)
T PRK05973 57 LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMK--SGRTGVFFTLEYT-EQDVRDRLRALGADR 118 (237)
T ss_pred hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHh--cCCeEEEEEEeCC-HHHHHHHHHHcCCCh
Confidence 445555 569999999999999999999998877 5788888875444 588888988887654
No 111
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=96.70 E-value=0.0028 Score=69.08 Aligned_cols=54 Identities=19% Similarity=0.313 Sum_probs=43.6
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
..+++|.||||||||+++.+++..++. ++.+++.++ +....+++.+.+.+.|.+
T Consensus 24 g~~~~i~G~~G~GKTtl~~~~~~~~~~--~g~~~~yi~-~e~~~~~~~~~~~~~g~~ 77 (230)
T PRK08533 24 GSLILIEGDESTGKSILSQRLAYGFLQ--NGYSVSYVS-TQLTTTEFIKQMMSLGYD 77 (230)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHh--CCCcEEEEe-CCCCHHHHHHHHHHhCCc
Confidence 678999999999999999999999887 678888888 444556777777666653
No 112
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=96.68 E-value=0.004 Score=74.75 Aligned_cols=69 Identities=20% Similarity=0.298 Sum_probs=55.7
Q ss_pred CCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCC----CcEEEEecchHHHHHHHHHHHhcCC
Q psy12659 816 LTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPH----QRTLIVTHSNQALNQLFEKIISLDV 885 (1051)
Q Consensus 816 Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~----~riLV~a~SN~Ald~l~e~l~~~~~ 885 (1051)
+-..|.++|+. -.+++.+|||.||||||+++.+.++.|+-++++ +.|||++|+..-++.+..=|-++|.
T Consensus 213 IQkEQneIIR~-ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe 285 (747)
T COG3973 213 IQKEQNEIIRF-EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGE 285 (747)
T ss_pred hhHhHHHHHhc-cCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhcc
Confidence 33458888876 446789999999999999999999999987654 4699999998888777776666654
No 113
>PRK08116 hypothetical protein; Validated
Probab=96.67 E-value=0.0059 Score=68.12 Aligned_cols=35 Identities=31% Similarity=0.305 Sum_probs=29.8
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
...+++||||||||+++..+...+.. .+.++++++
T Consensus 115 ~gl~l~G~~GtGKThLa~aia~~l~~--~~~~v~~~~ 149 (268)
T PRK08116 115 VGLLLWGSVGTGKTYLAACIANELIE--KGVPVIFVN 149 (268)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHHHH--cCCeEEEEE
Confidence 35899999999999999999999988 467776665
No 114
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=96.65 E-value=0.002 Score=61.90 Aligned_cols=88 Identities=40% Similarity=0.486 Sum_probs=58.4
Q ss_pred HHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh----cCCCcccccccccccChhhHHHhccCHHHHHhhhcCceeecc
Q psy12659 849 QIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS----LDVDERHLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQG 924 (1051)
Q Consensus 849 ~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~----~~~~~~~llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~g 924 (1051)
.-|..+++. ..-+.=|-+-.-.++..+++-|.. ..-+...-. -..|++|+|+++++|||+||+.++.+.+|++|
T Consensus 30 grvkr~lk~-~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~-kkkri~PrHlqlAIrnD~EL~~l~~~~tIa~G 107 (132)
T COG5262 30 GRVKRLLKK-GNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDN-KKKRIIPRHLQLAIRNDEELNKLLGDVTIAQG 107 (132)
T ss_pred HHHHHHHHc-CccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhc-CcceechHHHHHHhcCcHHHHHHhhhheeecC
Confidence 345555551 233444445555555555555432 211111111 12388999999999999999999999999999
Q ss_pred ccccccccccchHH
Q psy12659 925 GVMPNIQSMKFDKT 938 (1051)
Q Consensus 925 gvlp~i~k~ll~k~ 938 (1051)
|+.|++++.++.+.
T Consensus 108 Gvlp~I~~~ll~k~ 121 (132)
T COG5262 108 GVLPNINPGLLPKS 121 (132)
T ss_pred CcccccChhhhhhh
Confidence 99999999987554
No 115
>PRK12377 putative replication protein; Provisional
Probab=96.63 E-value=0.0058 Score=67.53 Aligned_cols=57 Identities=25% Similarity=0.311 Sum_probs=39.9
Q ss_pred CHHHHHHHHHhc--------CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHH
Q psy12659 179 TPTQIEAIRAGM--------QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQL 238 (1051)
Q Consensus 179 n~~Q~~Ai~~~l--------~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l 238 (1051)
++.|..|+..+. .....++.||||||||+++.+|...+... +.++++++ ....++.+
T Consensus 80 ~~~~~~a~~~a~~~a~~~~~~~~~l~l~G~~GtGKThLa~AIa~~l~~~--g~~v~~i~-~~~l~~~l 144 (248)
T PRK12377 80 NDGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAIGNRLLAK--GRSVIVVT-VPDVMSRL 144 (248)
T ss_pred ChhHHHHHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEE-HHHHHHHH
Confidence 456766665432 13568999999999999999999999876 66665543 34444444
No 116
>TIGR00609 recB exodeoxyribonuclease V, beta subunit. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.62 E-value=0.0026 Score=83.58 Aligned_cols=54 Identities=30% Similarity=0.310 Sum_probs=48.2
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhC---CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNF---PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~---~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.|..+|..-+|||||+|++.++..|+.+. +.++|||+|.|++|..+|.+||.+.
T Consensus 9 ~G~~lieAsAGtGKT~ti~~~~lrll~~~~~~~~~~iLvvTFT~aAt~el~~RIr~r 65 (1087)
T TIGR00609 9 NGTFLIEASAGTGKTFTIAQLYLRLLLEGGPLTVEEILVVTFTNAATEELKTRIRGR 65 (1087)
T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHhcCCCCChhhEEEEehhHHHHHHHHHHHHHH
Confidence 47899999999999999999999888853 3489999999999999999999764
No 117
>PRK01172 ski2-like helicase; Provisional
Probab=96.62 E-value=0.0056 Score=76.63 Aligned_cols=68 Identities=16% Similarity=0.155 Sum_probs=57.1
Q ss_pred CCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 175 TIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.+.|++.|.+|+....+..-.+|++|+|+|||.++...+...+.. +.++++++|+..-+++..+.+.+
T Consensus 20 ~~~l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~--~~k~v~i~P~raLa~q~~~~~~~ 87 (674)
T PRK01172 20 DFELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA--GLKSIYIVPLRSLAMEKYEELSR 87 (674)
T ss_pred CCCCCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh--CCcEEEEechHHHHHHHHHHHHH
Confidence 457999999999998887789999999999999877665555544 67899999999988998887764
No 118
>PRK05973 replicative DNA helicase; Provisional
Probab=96.61 E-value=0.0044 Score=68.01 Aligned_cols=61 Identities=16% Similarity=0.293 Sum_probs=48.8
Q ss_pred HHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCC
Q psy12659 186 IRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDE 249 (1051)
Q Consensus 186 i~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~ 249 (1051)
+..++. ..+++|.|+||+|||+++.+++.+...+ ++++++++--.. .+++.+++.+.|++.
T Consensus 57 l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~--Ge~vlyfSlEes-~~~i~~R~~s~g~d~ 118 (237)
T PRK05973 57 LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS--GRTGVFFTLEYT-EQDVRDRLRALGADR 118 (237)
T ss_pred hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEEEeCC-HHHHHHHHHHcCCCh
Confidence 444555 5589999999999999999999988876 788888876544 488999998887653
No 119
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=96.60 E-value=0.006 Score=72.14 Aligned_cols=69 Identities=26% Similarity=0.253 Sum_probs=53.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHH-HHHHHHh----CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQI-ISNLYHN----FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~i-I~~ll~~----~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|.+||..++.+.-.++++|+|||||....-. +..++.. ..+.++||++||..-+.++.+.+...
T Consensus 23 ~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l 96 (434)
T PRK11192 23 RPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQAREL 96 (434)
T ss_pred CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHH
Confidence 456789999999999877999999999999875443 3333321 12358999999999999988776554
No 120
>KOG1757|consensus
Probab=96.60 E-value=0.00094 Score=63.45 Aligned_cols=65 Identities=42% Similarity=0.594 Sum_probs=48.0
Q ss_pred HHHHHHHHHHhcCCCcccccccccccChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHH
Q psy12659 872 ALNQLFEKIISLDVDERHLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKT 938 (1051)
Q Consensus 872 Ald~l~e~l~~~~~~~~~llRlgsritpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~ 938 (1051)
-+..|...+.++..+..+-+... ||+|+|+++++|.|+||+.++. .+|+.||++||+|+.++.+.
T Consensus 61 ileYLTaEVLeLAgNasKdLKvK-RitprHlqLAiRGDeELDtLIk-~TiagGgViPhihk~l~~k~ 125 (131)
T KOG1757|consen 61 ILEYLTAEVLELAGNASKDLKVK-RITPRHLQLAIRGDEELDTLIK-ATIAGGGVIPHIHKSLINKK 125 (131)
T ss_pred HHHHHHHHHHHHcccccccceee-eccchhheeeecCcHHHHHHHH-HhhccCccccchHHHHhccc
Confidence 34444445555433333334444 8899999999999999999985 57899999999999987554
No 121
>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=96.59 E-value=0.0035 Score=68.41 Aligned_cols=54 Identities=22% Similarity=0.279 Sum_probs=44.7
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+++|.||||||||+++.+++..-+.+ +++++.++- ....+++.++..+.|.+
T Consensus 21 gs~~lI~G~pGsGKT~la~~~l~~~~~~--ge~~lyvs~-ee~~~~i~~~~~~~g~~ 74 (237)
T TIGR03877 21 RNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGIYVAL-EEHPVQVRRNMAQFGWD 74 (237)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEEEe-eCCHHHHHHHHHHhCCC
Confidence 5679999999999999999998887766 888998885 44567888888877764
No 122
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=96.59 E-value=0.0036 Score=71.65 Aligned_cols=53 Identities=26% Similarity=0.430 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 177 PFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
.+++.|.+.+..++. +...+|.||+|+||||++.+++..+....|+.||+++=
T Consensus 128 ~~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiE 181 (323)
T PRK13833 128 IMTEAQASVIRSAIDSRLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILE 181 (323)
T ss_pred CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEec
Confidence 467888888888775 56689999999999999999998887665677877643
No 123
>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif. They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.
Probab=96.58 E-value=0.0033 Score=65.97 Aligned_cols=46 Identities=30% Similarity=0.508 Sum_probs=35.4
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
+.-.++.||||||||++++.+...++. .+.+++.+.. ..++++|..
T Consensus 47 ~~~l~l~G~~G~GKThLa~ai~~~~~~--~g~~v~f~~~-----~~L~~~l~~ 92 (178)
T PF01695_consen 47 GENLILYGPPGTGKTHLAVAIANEAIR--KGYSVLFITA-----SDLLDELKQ 92 (178)
T ss_dssp --EEEEEESTTSSHHHHHHHHHHHHHH--TT--EEEEEH-----HHHHHHHHC
T ss_pred CeEEEEEhhHhHHHHHHHHHHHHHhcc--CCcceeEeec-----Cceeccccc
Confidence 566899999999999999999999998 7888888873 456666654
No 124
>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=96.58 E-value=0.0039 Score=68.06 Aligned_cols=54 Identities=22% Similarity=0.278 Sum_probs=45.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
+.+++|.||||||||+.+.+++.+-+. .+++++.++- ....+++.+++.+.+.+
T Consensus 21 gs~~lI~G~pGsGKT~la~~~l~~~~~--~ge~~lyvs~-ee~~~~i~~~~~~~g~~ 74 (237)
T TIGR03877 21 RNVVLLSGGPGTGKSIFSQQFLWNGLQ--MGEPGIYVAL-EEHPVQVRRNMAQFGWD 74 (237)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHHH--cCCcEEEEEe-eCCHHHHHHHHHHhCCC
Confidence 578999999999999999999888776 6889999985 45667788888777664
No 125
>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif. They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.
Probab=96.56 E-value=0.0062 Score=63.90 Aligned_cols=60 Identities=28% Similarity=0.431 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHh---cCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 178 FTPTQIEAIRAG---MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 178 ln~~Q~~Ai~~~---l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.+..|...+... -...-.++.||||||||++++.+...++.. +.+++.+. +.+++++|..
T Consensus 30 ~~~~~~~~l~~~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~--g~~v~f~~-----~~~L~~~l~~ 92 (178)
T PF01695_consen 30 IDKAQIAQLAALEFIENGENLILYGPPGTGKTHLAVAIANEAIRK--GYSVLFIT-----ASDLLDELKQ 92 (178)
T ss_dssp ----HHHHHHHH-S-SC--EEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEE-----HHHHHHHHHC
T ss_pred HHHHHHHHHhcCCCcccCeEEEEEhhHhHHHHHHHHHHHHHhccC--CcceeEee-----cCceeccccc
Confidence 344455444322 124558999999999999999999999986 77888776 3557777764
No 126
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=96.56 E-value=0.0066 Score=72.46 Aligned_cols=69 Identities=14% Similarity=0.123 Sum_probs=54.4
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHH-hCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYH-NFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~-~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++-|.+|+..++++.-.++++|+|||||....-.+.+.+. .....++||++||..-++++.+.+...
T Consensus 26 ~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~ 95 (460)
T PRK11776 26 EMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRL 95 (460)
T ss_pred CCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHH
Confidence 578899999999999888999999999999765444444343 222447999999999999988877654
No 127
>PRK01172 ski2-like helicase; Provisional
Probab=96.53 E-value=0.0072 Score=75.70 Aligned_cols=68 Identities=19% Similarity=0.210 Sum_probs=57.4
Q ss_pred CCCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 813 PFKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
++.|++.|.+|+....++.-.+|++|.|+|||..+...+...+. .+.++++++|+..-+++..+.+.+
T Consensus 20 ~~~l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~--~~~k~v~i~P~raLa~q~~~~~~~ 87 (674)
T PRK01172 20 DFELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFL--AGLKSIYIVPLRSLAMEKYEELSR 87 (674)
T ss_pred CCCCCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHH--hCCcEEEEechHHHHHHHHHHHHH
Confidence 34689999999999888888999999999999988766655555 467899999999888888887754
No 128
>PRK06526 transposase; Provisional
Probab=96.50 E-value=0.0029 Score=70.11 Aligned_cols=52 Identities=27% Similarity=0.373 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHh---cCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 815 KLTFHEIEAIRAG---MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~---l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
.++..|...+..+ -.+.-.++.||||||||+++..+...+.. .+.+|+..+.
T Consensus 80 ~~~~~~~~~l~~~~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~--~g~~v~f~t~ 134 (254)
T PRK06526 80 SLKRDTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQ--AGHRVLFATA 134 (254)
T ss_pred CcchHHHHHHhcCchhhcCceEEEEeCCCCchHHHHHHHHHHHHH--CCCchhhhhH
Confidence 5666666654433 23567899999999999999999988887 6778877543
No 129
>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=96.48 E-value=0.0052 Score=66.18 Aligned_cols=55 Identities=35% Similarity=0.599 Sum_probs=42.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+++|.||||||||.++.+++.+-+.+. +++++.++-... .+++.+.+.+.|++
T Consensus 19 gs~~li~G~~GsGKT~l~~q~l~~~~~~~-ge~vlyvs~ee~-~~~l~~~~~s~g~d 73 (226)
T PF06745_consen 19 GSVVLISGPPGSGKTTLALQFLYNGLKNF-GEKVLYVSFEEP-PEELIENMKSFGWD 73 (226)
T ss_dssp TSEEEEEESTTSSHHHHHHHHHHHHHHHH-T--EEEEESSS--HHHHHHHHHTTTS-
T ss_pred CcEEEEEeCCCCCcHHHHHHHHHHhhhhc-CCcEEEEEecCC-HHHHHHHHHHcCCc
Confidence 67799999999999999999987776653 567888875444 48999999888763
No 130
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=96.47 E-value=0.005 Score=67.16 Aligned_cols=53 Identities=19% Similarity=0.318 Sum_probs=42.4
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
..+++|.||||||||+++.+++..++.+ +.+++.++ +....+++.+.+.+.|.
T Consensus 24 g~~~~i~G~~G~GKTtl~~~~~~~~~~~--g~~~~yi~-~e~~~~~~~~~~~~~g~ 76 (230)
T PRK08533 24 GSLILIEGDESTGKSILSQRLAYGFLQN--GYSVSYVS-TQLTTTEFIKQMMSLGY 76 (230)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHhC--CCcEEEEe-CCCCHHHHHHHHHHhCC
Confidence 5689999999999999999999988865 77888888 44445777777766655
No 131
>KOG0989|consensus
Probab=96.47 E-value=0.0028 Score=71.03 Aligned_cols=36 Identities=31% Similarity=0.517 Sum_probs=28.7
Q ss_pred HHHHHHhcC---CCeEEEEccCCCChHHHHHHHHHHHHH
Q psy12659 183 IEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYH 218 (1051)
Q Consensus 183 ~~Ai~~~l~---~~~~lI~GPPGTGKT~ti~~ii~~l~~ 218 (1051)
++++..++. -+..|.+||||||||+|+..+..+|+-
T Consensus 45 V~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~ 83 (346)
T KOG0989|consen 45 VQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNC 83 (346)
T ss_pred HHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcC
Confidence 444444543 577999999999999999999998875
No 132
>PRK14974 cell division protein FtsY; Provisional
Probab=96.45 E-value=0.0067 Score=69.85 Aligned_cols=54 Identities=31% Similarity=0.371 Sum_probs=42.4
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC-C--HHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-S--NQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~-S--N~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||||+|||||++.+...+... +.+|++++. + ..|++++.......|+
T Consensus 140 ~~vi~~~G~~GvGKTTtiakLA~~l~~~--g~~V~li~~Dt~R~~a~eqL~~~a~~lgv 196 (336)
T PRK14974 140 PVVIVFVGVNGTGKTTTIAKLAYYLKKN--GFSVVIAAGDTFRAGAIEQLEEHAERLGV 196 (336)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHHHc--CCeEEEecCCcCcHHHHHHHHHHHHHcCC
Confidence 4678999999999999999999877654 667766643 3 6788888777777766
No 133
>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=96.45 E-value=0.008 Score=77.47 Aligned_cols=70 Identities=24% Similarity=0.235 Sum_probs=58.3
Q ss_pred CCCCCCHHHHHHHHHhcCC------CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 812 PPFKLTFHEIEAIRAGMQP------GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~~------~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.||.+++.|.+||..+++. .-.+|+||.|+|||.++...+...+. .+.+++|++||..=+.+..+.+.+.
T Consensus 448 ~~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~--~g~qvlvLvPT~~LA~Q~~~~f~~~ 523 (926)
T TIGR00580 448 FPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVL--DGKQVAVLVPTTLLAQQHFETFKER 523 (926)
T ss_pred CCCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHH--hCCeEEEEeCcHHHHHHHHHHHHHH
Confidence 4668899999999998772 34699999999999998877666665 5689999999999999988877654
No 134
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=96.44 E-value=0.0099 Score=73.92 Aligned_cols=70 Identities=20% Similarity=0.234 Sum_probs=55.4
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++-|.+||...+...-.++++|+|||||.+..- ++..+.....+.++||++||..-+.++.+.+...
T Consensus 27 ~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~ 97 (629)
T PRK11634 27 EKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDF 97 (629)
T ss_pred CCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHH
Confidence 367899999999999877799999999999987543 4444444334568999999999999998777654
No 135
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=96.43 E-value=0.0053 Score=70.20 Aligned_cols=55 Identities=33% Similarity=0.481 Sum_probs=44.7
Q ss_pred CCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH
Q psy12659 178 FTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 232 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN 232 (1051)
+++.|.+.+..+.. +...+|.||||+||||++..++..+....|..|++++-.+.
T Consensus 133 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~ 188 (319)
T PRK13894 133 MTAAQREAIIAAVRAHRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTG 188 (319)
T ss_pred CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCC
Confidence 57788888887764 77789999999999999999998876555678888766554
No 136
>KOG0989|consensus
Probab=96.42 E-value=0.0027 Score=71.08 Aligned_cols=27 Identities=41% Similarity=0.544 Sum_probs=24.6
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
.+..+.+||||||||.|+....++|..
T Consensus 57 lp~~LFyGPpGTGKTStalafar~L~~ 83 (346)
T KOG0989|consen 57 LPHYLFYGPPGTGKTSTALAFARALNC 83 (346)
T ss_pred CceEEeeCCCCCcHhHHHHHHHHHhcC
Confidence 578999999999999999999888876
No 137
>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function. It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].
Probab=96.41 E-value=0.0053 Score=70.94 Aligned_cols=53 Identities=25% Similarity=0.357 Sum_probs=44.7
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.+.+|+|.||||||.++..++..+.....+.+++++++++.-.+.+.+.+.+.
T Consensus 2 ~v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~ 54 (352)
T PF09848_consen 2 QVILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKK 54 (352)
T ss_pred eEEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhhh
Confidence 47899999999999999999999943344788999999988888888888754
No 138
>PRK06526 transposase; Provisional
Probab=96.39 E-value=0.0069 Score=67.16 Aligned_cols=51 Identities=24% Similarity=0.352 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHh---cCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE
Q psy12659 176 IPFTPTQIEAIRAG---MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 228 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~---l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~ 228 (1051)
..++..|...+..+ -.+.-.+|.||||||||+++..+...+... +.+++..
T Consensus 79 ~~~~~~~~~~l~~~~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~--g~~v~f~ 132 (254)
T PRK06526 79 RSLKRDTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQA--GHRVLFA 132 (254)
T ss_pred CCcchHHHHHHhcCchhhcCceEEEEeCCCCchHHHHHHHHHHHHHC--CCchhhh
Confidence 35677777665433 235568999999999999999999888876 6777664
No 139
>PRK06893 DNA replication initiation factor; Validated
Probab=96.38 E-value=0.0052 Score=66.77 Aligned_cols=37 Identities=8% Similarity=0.203 Sum_probs=30.2
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
.+..+++|||||||||++..+...+.. .+.++..+..
T Consensus 39 ~~~l~l~G~~G~GKThL~~ai~~~~~~--~~~~~~y~~~ 75 (229)
T PRK06893 39 QPFFYIWGGKSSGKSHLLKAVSNHYLL--NQRTAIYIPL 75 (229)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHHHH--cCCCeEEeeH
Confidence 567899999999999999999998887 4556655554
No 140
>PRK14974 cell division protein FtsY; Provisional
Probab=96.38 E-value=0.0071 Score=69.60 Aligned_cols=54 Identities=30% Similarity=0.342 Sum_probs=42.4
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec-c--hHHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-S--NQALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~-S--N~Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||||+|||||++.+...+.. .+.+|++++- + ..|.+++.......++
T Consensus 140 ~~vi~~~G~~GvGKTTtiakLA~~l~~--~g~~V~li~~Dt~R~~a~eqL~~~a~~lgv 196 (336)
T PRK14974 140 PVVIVFVGVNGTGKTTTIAKLAYYLKK--NGFSVVIAAGDTFRAGAIEQLEEHAERLGV 196 (336)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHHH--cCCeEEEecCCcCcHHHHHHHHHHHHHcCC
Confidence 578999999999999999999987765 5677766653 3 5778888776666665
No 141
>PRK10689 transcription-repair coupling factor; Provisional
Probab=96.38 E-value=0.0084 Score=78.89 Aligned_cols=69 Identities=25% Similarity=0.297 Sum_probs=58.0
Q ss_pred CCCCCCHHHHHHHHHhcCC------CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 812 PPFKLTFHEIEAIRAGMQP------GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~~------~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.||.+++.|.+||..++.. .-.+++||.|+|||-++...+...+. .+.+++|++||..=+.++.+.+.+
T Consensus 597 ~~~~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~--~g~qvlvLvPT~eLA~Q~~~~f~~ 671 (1147)
T PRK10689 597 FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE--NHKQVAVLVPTTLLAQQHYDNFRD 671 (1147)
T ss_pred CCCCCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH--cCCeEEEEeCcHHHHHHHHHHHHH
Confidence 5778999999999998773 45899999999999998766655555 678999999999988888887765
No 142
>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=96.37 E-value=0.013 Score=73.39 Aligned_cols=78 Identities=18% Similarity=0.279 Sum_probs=61.8
Q ss_pred CCCCHHHHHHHHHhcCC---CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC-CCCCCc
Q psy12659 176 IPFTPTQIEAIRAGMQP---GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL-DVDERH 251 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~---~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~-~~~~~~ 251 (1051)
..|=+-|.+|+...... +-.+|+-|+|+|||.++..++..+ ++++||+|||...++|-.+.+.+. .++...
T Consensus 254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l-----~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~ 328 (732)
T TIGR00603 254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV-----KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQ 328 (732)
T ss_pred CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh-----CCCEEEEeCcHHHHHHHHHHHHHhcCCCCce
Confidence 56778999999987753 357999999999999999887654 468999999999999999999875 344445
Q ss_pred EEEecCC
Q psy12659 252 LLRLGHG 258 (1051)
Q Consensus 252 lvRlG~~ 258 (1051)
+.++..+
T Consensus 329 I~~~tg~ 335 (732)
T TIGR00603 329 ICRFTSD 335 (732)
T ss_pred EEEEecC
Confidence 5555543
No 143
>PRK08116 hypothetical protein; Validated
Probab=96.36 E-value=0.0089 Score=66.72 Aligned_cols=34 Identities=32% Similarity=0.360 Sum_probs=29.2
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
..+++||||||||+++..+...+..+ +.++++++
T Consensus 116 gl~l~G~~GtGKThLa~aia~~l~~~--~~~v~~~~ 149 (268)
T PRK08116 116 GLLLWGSVGTGKTYLAACIANELIEK--GVPVIFVN 149 (268)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEE
Confidence 48999999999999999999999877 66776655
No 144
>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain. The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....
Probab=96.36 E-value=0.0062 Score=61.84 Aligned_cols=53 Identities=25% Similarity=0.399 Sum_probs=44.5
Q ss_pred CCeEEEECCCCCChhH-HHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 830 PGLTLVVGPPGTGKTD-VAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~-ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
..+++|.=.||+|||+ ++.+++.+.+. .+.||||++||...++++.+.|....
T Consensus 4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~--~~~rvLvL~PTRvva~em~~aL~~~~ 57 (148)
T PF07652_consen 4 GELTVLDLHPGAGKTRRVLPEIVREAIK--RRLRVLVLAPTRVVAEEMYEALKGLP 57 (148)
T ss_dssp TEEEEEE--TTSSTTTTHHHHHHHHHHH--TT--EEEEESSHHHHHHHHHHTTTSS
T ss_pred CceeEEecCCCCCCcccccHHHHHHHHH--ccCeEEEecccHHHHHHHHHHHhcCC
Confidence 4689999999999999 79999999999 88999999999999999999997654
No 145
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=96.36 E-value=0.0074 Score=65.48 Aligned_cols=56 Identities=23% Similarity=0.438 Sum_probs=46.4
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCcc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDER 888 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~~ 888 (1051)
+.+++|.||||||||+.+.+++...+. .+++++.++-.+ ..+.+.+.+.+.+++..
T Consensus 25 g~~~~i~G~~GsGKt~l~~~~~~~~~~--~g~~~~y~~~e~-~~~~~~~~~~~~g~~~~ 80 (234)
T PRK06067 25 PSLILIEGDHGTGKSVLSQQFVYGALK--QGKKVYVITTEN-TSKSYLKQMESVKIDIS 80 (234)
T ss_pred CcEEEEECCCCCChHHHHHHHHHHHHh--CCCEEEEEEcCC-CHHHHHHHHHHCCCChh
Confidence 678999999999999999999888777 688999999865 45778888887776543
No 146
>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=96.35 E-value=0.0055 Score=60.82 Aligned_cols=39 Identities=33% Similarity=0.545 Sum_probs=32.5
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHH
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQA 234 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~A 234 (1051)
+++|.||||||||+++..++..+... +.++++.+.....
T Consensus 1 ~~~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~e~~~ 39 (165)
T cd01120 1 LILVFGPTGSGKTTLALQLALNIATK--GGKVVYVDIEEEI 39 (165)
T ss_pred CeeEeCCCCCCHHHHHHHHHHHHHhc--CCEEEEEECCcch
Confidence 47899999999999999999988764 7788888775544
No 147
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=96.35 E-value=0.0029 Score=61.41 Aligned_cols=53 Identities=19% Similarity=0.374 Sum_probs=35.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcC----CCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNF----PHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~----p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.++.+|.||||+|||+++..++..+.... +..-+.+.+++......+...+.+
T Consensus 4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 60 (131)
T PF13401_consen 4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILE 60 (131)
T ss_dssp ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHH
T ss_pred CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHH
Confidence 56789999999999999999999887521 133345555555556677777654
No 148
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=96.35 E-value=0.0043 Score=68.73 Aligned_cols=38 Identities=32% Similarity=0.535 Sum_probs=33.6
Q ss_pred CCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 829 QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 829 ~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
++.-.++.||||||||+++++|-..+.. .|.+|++++-
T Consensus 104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~--~g~sv~f~~~ 141 (254)
T COG1484 104 RGENLVLLGPPGVGKTHLAIAIGNELLK--AGISVLFITA 141 (254)
T ss_pred cCCcEEEECCCCCcHHHHHHHHHHHHHH--cCCeEEEEEH
Confidence 3668999999999999999999999996 6889998873
No 149
>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A.
Probab=96.34 E-value=0.0086 Score=61.38 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=29.3
Q ss_pred HHHHHHHHHhc------CCCeEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 180 PTQIEAIRAGM------QPGLTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 180 ~~Q~~Ai~~~l------~~~~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
++|.+.+...+ .+...+|.||||||||+++.++...+...
T Consensus 6 ~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~ 51 (185)
T PF13191_consen 6 EEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER 51 (185)
T ss_dssp HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 46777777766 26789999999999999999999888877
No 150
>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=96.34 E-value=0.0056 Score=60.75 Aligned_cols=40 Identities=33% Similarity=0.497 Sum_probs=33.3
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHH
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQAL 873 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Al 873 (1051)
+++|.||||||||+++.+++..+.. .+.+|++.+......
T Consensus 1 ~~~i~G~~G~GKT~l~~~i~~~~~~--~~~~v~~~~~e~~~~ 40 (165)
T cd01120 1 LILVFGPTGSGKTTLALQLALNIAT--KGGKVVYVDIEEEIE 40 (165)
T ss_pred CeeEeCCCCCCHHHHHHHHHHHHHh--cCCEEEEEECCcchH
Confidence 4789999999999999999998876 678888888755443
No 151
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.
Probab=96.33 E-value=0.0065 Score=68.90 Aligned_cols=56 Identities=29% Similarity=0.465 Sum_probs=44.2
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH
Q psy12659 177 PFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 232 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN 232 (1051)
.+++.|.+.+..++. .+..+|.||+|+||||++..++..+-...|+.||+++-.+.
T Consensus 116 ~~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~ 172 (299)
T TIGR02782 116 IMTAAQRDVLREAVLARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTR 172 (299)
T ss_pred CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCch
Confidence 367778888887765 67789999999999999999988776655678887765443
No 152
>TIGR00064 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
Probab=96.32 E-value=0.012 Score=65.95 Aligned_cols=54 Identities=30% Similarity=0.416 Sum_probs=40.3
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe---CCHHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT---HSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a---~SN~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||||+|||||++.+...+... +.+|++++ +...|.+++.......++
T Consensus 72 ~~vi~l~G~~G~GKTTt~akLA~~l~~~--g~~V~li~~D~~r~~a~~ql~~~~~~~~i 128 (272)
T TIGR00064 72 PNVILFVGVNGVGKTTTIAKLANKLKKQ--GKSVLLAAGDTFRAAAIEQLEEWAKRLGV 128 (272)
T ss_pred CeEEEEECCCCCcHHHHHHHHHHHHHhc--CCEEEEEeCCCCCHHHHHHHHHHHHhCCe
Confidence 4567788999999999999999877655 67887775 344566777666666554
No 153
>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=96.31 E-value=0.0048 Score=68.42 Aligned_cols=38 Identities=21% Similarity=0.175 Sum_probs=33.4
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 231 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~S 231 (1051)
..+++|.||||||||+++.+++.+...+ +++++.++--
T Consensus 36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~--Ge~vlyis~E 73 (259)
T TIGR03878 36 YSVINITGVSDTGKSLMVEQFAVTQASR--GNPVLFVTVE 73 (259)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEec
Confidence 5679999999999999999999888776 7888888854
No 154
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=96.31 E-value=0.0062 Score=67.83 Aligned_cols=52 Identities=31% Similarity=0.535 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 814 FKLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
..+.+.|.+++..++. .++.+|.||+|+||||++..++..+.. ++.+|+.+-
T Consensus 62 lg~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l~all~~i~~--~~~~iitiE 115 (264)
T cd01129 62 LGLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSELNT--PEKNIITVE 115 (264)
T ss_pred cCCCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHHHHHHhhhCC--CCCeEEEEC
Confidence 4678889999988876 689999999999999999999887654 455665553
No 155
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=96.30 E-value=0.0028 Score=61.25 Aligned_cols=22 Identities=50% Similarity=0.806 Sum_probs=19.3
Q ss_pred EEEEccCCCChHHHHHHHHHHH
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.||.||||||||+++..+...+
T Consensus 1 ill~G~~G~GKT~l~~~la~~l 22 (132)
T PF00004_consen 1 ILLHGPPGTGKTTLARALAQYL 22 (132)
T ss_dssp EEEESSTTSSHHHHHHHHHHHT
T ss_pred CEEECcCCCCeeHHHHHHHhhc
Confidence 3899999999999998887765
No 156
>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=96.30 E-value=0.005 Score=68.26 Aligned_cols=39 Identities=21% Similarity=0.168 Sum_probs=33.6
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecch
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 870 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN 870 (1051)
+.+++|.||||||||+.+.+++.+... .+.+++.++--.
T Consensus 36 gs~~lI~G~pGtGKT~l~~qf~~~~a~--~Ge~vlyis~Ee 74 (259)
T TIGR03878 36 YSVINITGVSDTGKSLMVEQFAVTQAS--RGNPVLFVTVES 74 (259)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHHh--CCCcEEEEEecC
Confidence 578999999999999999999988777 578888888643
No 157
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=96.30 E-value=0.0094 Score=71.70 Aligned_cols=69 Identities=22% Similarity=0.314 Sum_probs=53.6
Q ss_pred CCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCC----CCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 178 FTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFP----HQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p----~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
+-++|-++|+.- .+++.+|||.||||||+++.+-++.|+-.+. ++.|||++|+..=++-+..-|-++|.
T Consensus 213 IQkEQneIIR~e-k~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe 285 (747)
T COG3973 213 IQKEQNEIIRFE-KNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGE 285 (747)
T ss_pred hhHhHHHHHhcc-CCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhcc
Confidence 345777777643 3668999999999999999999999987653 35599999998777776666666654
No 158
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=96.30 E-value=0.0069 Score=69.36 Aligned_cols=53 Identities=25% Similarity=0.404 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 815 KLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
.+++.|.+.+..++. +...+|.||+|+||||++..++..+....++.||+++=
T Consensus 128 ~~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiE 181 (323)
T PRK13833 128 IMTEAQASVIRSAIDSRLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILE 181 (323)
T ss_pred CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEec
Confidence 467788888888887 66788999999999999999988876544567766543
No 159
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=96.29 E-value=0.0065 Score=67.08 Aligned_cols=55 Identities=31% Similarity=0.442 Sum_probs=44.2
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDE 887 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~ 887 (1051)
..+++|.||||||||..+.+.+.+... .+.+++.++-...+ ..+.+...+.|.+.
T Consensus 23 g~~~lI~G~pGsGKT~f~~qfl~~~~~--~ge~vlyvs~~e~~-~~l~~~~~~~g~d~ 77 (260)
T COG0467 23 GSVVLITGPPGTGKTIFALQFLYEGAR--EGEPVLYVSTEESP-EELLENARSFGWDL 77 (260)
T ss_pred CcEEEEEcCCCCcHHHHHHHHHHHHHh--cCCcEEEEEecCCH-HHHHHHHHHcCCCH
Confidence 688999999999999999999999998 58999999965554 45555555566544
No 160
>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=96.29 E-value=0.0058 Score=73.69 Aligned_cols=58 Identities=22% Similarity=0.391 Sum_probs=49.6
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCcccc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHL 890 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~~~l 890 (1051)
..+++|.||||||||+++.+.+.+... .+++++.++ .....+++..+..+.|++....
T Consensus 263 gs~~li~G~~G~GKt~l~~~f~~~~~~--~ge~~~y~s-~eEs~~~i~~~~~~lg~~~~~~ 320 (484)
T TIGR02655 263 DSIILATGATGTGKTLLVSKFLENACA--NKERAILFA-YEESRAQLLRNAYSWGIDFEEM 320 (484)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHH--CCCeEEEEE-eeCCHHHHHHHHHHcCCChHHH
Confidence 578999999999999999999999888 688999988 6777889999988888764443
No 161
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=96.29 E-value=0.011 Score=77.59 Aligned_cols=72 Identities=21% Similarity=0.253 Sum_probs=61.1
Q ss_pred CCCCHHHHHHHHHhcC-----CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCC
Q psy12659 814 FKLTFHEIEAIRAGMQ-----PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 885 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~-----~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~ 885 (1051)
+.+=+.|.+||..... ..-.+|+.|.|||||.|++.++..+++....+|||++++++.=+++..+.+...++
T Consensus 412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~ 488 (1123)
T PRK11448 412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKI 488 (1123)
T ss_pred CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhccc
Confidence 3567789999977652 35689999999999999999999998866678999999999999999998877654
No 162
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=96.28 E-value=0.012 Score=73.29 Aligned_cols=69 Identities=19% Similarity=0.209 Sum_probs=54.6
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHH-HHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~-iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|.++|...+...-.++++|+|||||.+..- ++..+.....+.++||++||..-+.++.+.+...
T Consensus 28 ~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~ 97 (629)
T PRK11634 28 KPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDF 97 (629)
T ss_pred CCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHH
Confidence 57788999999999988899999999999987543 3444433334568999999999999987776543
No 163
>PRK08084 DNA replication initiation factor; Provisional
Probab=96.28 E-value=0.0085 Score=65.46 Aligned_cols=53 Identities=11% Similarity=0.154 Sum_probs=40.1
Q ss_pred CCHHHHHHHHHhcC---CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecch
Q psy12659 816 LTFHEIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 870 (1051)
Q Consensus 816 Ln~~Q~~Ai~~~l~---~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN 870 (1051)
-|.....++..... .+..+|.|||||||||++..+...+.. .+.+++.+.-..
T Consensus 28 ~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~--~~~~v~y~~~~~ 83 (235)
T PRK08084 28 DNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQ--RGRAVGYVPLDK 83 (235)
T ss_pred ccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHh--CCCeEEEEEHHH
Confidence 56666666666542 467899999999999999988888776 577887776643
No 164
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=96.28 E-value=0.0063 Score=67.75 Aligned_cols=54 Identities=30% Similarity=0.573 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 175 TIPFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
...+.+.|.+++..++. .++.+|.||+|+||||++..++..+.. ++.+|+.+-.
T Consensus 61 ~lg~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l~all~~i~~--~~~~iitiEd 116 (264)
T cd01129 61 KLGLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSELNT--PEKNIITVED 116 (264)
T ss_pred HcCCCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHHHHHHhhhCC--CCCeEEEECC
Confidence 35688999999987764 689999999999999999999887653 3566766543
No 165
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=96.28 E-value=0.0029 Score=61.12 Aligned_cols=22 Identities=50% Similarity=0.806 Sum_probs=19.3
Q ss_pred EEEECCCCCChhHHHHHHHHHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
.+|.||||||||+++..+...+
T Consensus 1 ill~G~~G~GKT~l~~~la~~l 22 (132)
T PF00004_consen 1 ILLHGPPGTGKTTLARALAQYL 22 (132)
T ss_dssp EEEESSTTSSHHHHHHHHHHHT
T ss_pred CEEECcCCCCeeHHHHHHHhhc
Confidence 4799999999999999888774
No 166
>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=96.25 E-value=0.0091 Score=64.27 Aligned_cols=53 Identities=19% Similarity=0.280 Sum_probs=45.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
..+++|.||||+|||+++.+++...+++ +++++.++... ..+++.++....+.
T Consensus 16 g~~~li~G~~G~GKt~~~~~~~~~~~~~--g~~~~y~s~e~-~~~~l~~~~~~~~~ 68 (224)
T TIGR03880 16 GHVIVVIGEYGTGKTTFSLQFLYQGLKN--GEKAMYISLEE-REERILGYAKSKGW 68 (224)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC-CHHHHHHHHHHcCC
Confidence 5679999999999999999999888877 78898887765 57899999887765
No 167
>PRK10689 transcription-repair coupling factor; Provisional
Probab=96.25 E-value=0.0049 Score=81.01 Aligned_cols=71 Identities=25% Similarity=0.285 Sum_probs=57.1
Q ss_pred CCCCCCCHHHHHHHHHhcCC------CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 173 KNTIPFTPTQIEAIRAGMQP------GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 173 ~~~~~ln~~Q~~Ai~~~l~~------~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.-++.+++.|.+||..++.. .-.||+||.|||||.++...+...+.. +.++||++||..=+.++.+.+.+.
T Consensus 596 ~~~~~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~--g~qvlvLvPT~eLA~Q~~~~f~~~ 672 (1147)
T PRK10689 596 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN--HKQVAVLVPTTLLAQQHYDNFRDR 672 (1147)
T ss_pred hCCCCCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc--CCeEEEEeCcHHHHHHHHHHHHHh
Confidence 34468999999999987652 347999999999999887666555554 789999999999989888887753
No 168
>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=96.24 E-value=0.013 Score=73.32 Aligned_cols=67 Identities=16% Similarity=0.218 Sum_probs=56.9
Q ss_pred CCCCCCHHHHHHHHHhcCC---CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 812 PPFKLTFHEIEAIRAGMQP---GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~~---~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
|.+.|=+.|.+|+...+.. +..+|+-|+|+|||.++..++..+ ++++||++||...+++..+.+.+.
T Consensus 252 ~~~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l-----~k~tLILvps~~Lv~QW~~ef~~~ 321 (732)
T TIGR00603 252 PTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV-----KKSCLVLCTSAVSVEQWKQQFKMW 321 (732)
T ss_pred cCCCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh-----CCCEEEEeCcHHHHHHHHHHHHHh
Confidence 4556778899999998863 367999999999999999887754 478999999999999999988875
No 169
>PRK09401 reverse gyrase; Reviewed
Probab=96.24 E-value=0.012 Score=77.71 Aligned_cols=70 Identities=16% Similarity=0.150 Sum_probs=57.4
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
..+++.|+.++..++...-.++++|.|||||.++.-++..+.. .+.++||++||..=+.++.+++...+.
T Consensus 79 ~~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~~ 148 (1176)
T PRK09401 79 SKPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFGE 148 (1176)
T ss_pred CCCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHhh
Confidence 3678899999999998778899999999999765544433333 378999999999999999999987653
No 170
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=96.24 E-value=0.008 Score=68.78 Aligned_cols=56 Identities=30% Similarity=0.437 Sum_probs=44.1
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecch
Q psy12659 815 KLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 870 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN 870 (1051)
.+++.|.+.+..++. +...+|.||||+|||+++..++..+....+..|++++-.+.
T Consensus 132 ~~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~ 188 (319)
T PRK13894 132 IMTAAQREAIIAAVRAHRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTG 188 (319)
T ss_pred CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCC
Confidence 356778899988877 78899999999999999999998776444667777655443
No 171
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=96.23 E-value=0.0092 Score=64.73 Aligned_cols=54 Identities=24% Similarity=0.477 Sum_probs=45.7
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+++|.||||||||+++.+++...+.+ +++++.++-.+ ..+.+.+++.+.+++
T Consensus 25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~-~~~~~~~~~~~~g~~ 78 (234)
T PRK06067 25 PSLILIEGDHGTGKSVLSQQFVYGALKQ--GKKVYVITTEN-TSKSYLKQMESVKID 78 (234)
T ss_pred CcEEEEECCCCCChHHHHHHHHHHHHhC--CCEEEEEEcCC-CHHHHHHHHHHCCCC
Confidence 6779999999999999999999888776 88999988765 457888888887764
No 172
>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=96.23 E-value=0.0093 Score=64.19 Aligned_cols=54 Identities=19% Similarity=0.275 Sum_probs=45.8
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
+.+++|.||||+|||+.+.+++.+.+. .+++++.++... ..+++.+++.+.+.+
T Consensus 16 g~~~li~G~~G~GKt~~~~~~~~~~~~--~g~~~~y~s~e~-~~~~l~~~~~~~~~~ 69 (224)
T TIGR03880 16 GHVIVVIGEYGTGKTTFSLQFLYQGLK--NGEKAMYISLEE-REERILGYAKSKGWD 69 (224)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHh--CCCeEEEEECCC-CHHHHHHHHHHcCCC
Confidence 578999999999999999999988877 588999888654 678888888877654
No 173
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=96.23 E-value=0.0065 Score=80.41 Aligned_cols=53 Identities=28% Similarity=0.340 Sum_probs=45.9
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCC----------CCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFP----------HQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p----------~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.|..||-.-.|||||.||+.+...|+-..+ -+.|||||.||+|+.++.+||.+
T Consensus 17 ~G~~LIEASAGTGKTyTIa~lyLrLlL~~g~~~~~~~~L~~~~ILvvTFT~aAt~Elr~RIr~ 79 (1181)
T PRK10876 17 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRS 79 (1181)
T ss_pred CCCEEEEeCCCCcHHHHHHHHHHHHHccCCccccccCCCChhhEEEEechHHHHHHHHHHHHH
Confidence 578999999999999999999887775321 15899999999999999999965
No 174
>PRK04328 hypothetical protein; Provisional
Probab=96.22 E-value=0.0079 Score=66.28 Aligned_cols=54 Identities=22% Similarity=0.254 Sum_probs=43.3
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+++|.||||||||+++.+++.+-+.+ +++++.++-.. ..+++.++..+.|.+
T Consensus 23 gs~ili~G~pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee-~~~~i~~~~~~~g~d 76 (249)
T PRK04328 23 RNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGVYVALEE-HPVQVRRNMRQFGWD 76 (249)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEEeeC-CHHHHHHHHHHcCCC
Confidence 5679999999999999999999887766 78888888544 345688887777653
No 175
>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=96.22 E-value=0.0048 Score=74.41 Aligned_cols=54 Identities=26% Similarity=0.451 Sum_probs=47.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..++||.||||||||+++.+++.....+ +++++.++ .....+++..+....|++
T Consensus 263 gs~~li~G~~G~GKt~l~~~f~~~~~~~--ge~~~y~s-~eEs~~~i~~~~~~lg~~ 316 (484)
T TIGR02655 263 DSIILATGATGTGKTLLVSKFLENACAN--KERAILFA-YEESRAQLLRNAYSWGID 316 (484)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEE-eeCCHHHHHHHHHHcCCC
Confidence 5679999999999999999999999887 88999888 455678999999888774
No 176
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).
Probab=96.21 E-value=0.01 Score=69.26 Aligned_cols=51 Identities=22% Similarity=0.494 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 228 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~ 228 (1051)
..+.+...+.+.. ..++.+|.||+|+||||++..++..+..+.++.+|+.+
T Consensus 135 lgl~~~~~~~l~~--~~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~Ivti 185 (372)
T TIGR02525 135 MGIEPDLFNSLLP--AAGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTY 185 (372)
T ss_pred cCCCHHHHHHHHh--cCCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEE
Confidence 4566666555542 57899999999999999999999988876566677765
No 177
>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=96.21 E-value=0.013 Score=75.51 Aligned_cols=69 Identities=25% Similarity=0.250 Sum_probs=56.6
Q ss_pred CCCCCHHHHHHHHHhcCC------CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 175 TIPFTPTQIEAIRAGMQP------GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 175 ~~~ln~~Q~~Ai~~~l~~------~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
++.+++.|.+||..+++. --.+|+||.|||||.++...+...+.+ +.+++|++||..=+.+..+.+.+.
T Consensus 449 ~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~--g~qvlvLvPT~~LA~Q~~~~f~~~ 523 (926)
T TIGR00580 449 PFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD--GKQVAVLVPTTLLAQQHFETFKER 523 (926)
T ss_pred CCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh--CCeEEEEeCcHHHHHHHHHHHHHH
Confidence 467899999999987651 236999999999999887766655555 679999999999999998888764
No 178
>TIGR00064 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
Probab=96.20 E-value=0.01 Score=66.44 Aligned_cols=54 Identities=30% Similarity=0.414 Sum_probs=40.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe-c--chHHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-H--SNQALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a-~--SN~Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||||+|||||++++...+.. .+++|++++ . ...|.+++.......++
T Consensus 72 ~~vi~l~G~~G~GKTTt~akLA~~l~~--~g~~V~li~~D~~r~~a~~ql~~~~~~~~i 128 (272)
T TIGR00064 72 PNVILFVGVNGVGKTTTIAKLANKLKK--QGKSVLLAAGDTFRAAAIEQLEEWAKRLGV 128 (272)
T ss_pred CeEEEEECCCCCcHHHHHHHHHHHHHh--cCCEEEEEeCCCCCHHHHHHHHHHHHhCCe
Confidence 456778899999999999999988765 577887776 2 33456776665555554
No 179
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=96.20 E-value=0.017 Score=75.99 Aligned_cols=72 Identities=21% Similarity=0.202 Sum_probs=61.0
Q ss_pred CCCCHHHHHHHHHhc-----CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 176 IPFTPTQIEAIRAGM-----QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l-----~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
+.+=+-|.+||..+. ..+-.||+.|.|||||.|+..++..+++.....|||++++++.=+++..+.+...+.
T Consensus 412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~ 488 (1123)
T PRK11448 412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKI 488 (1123)
T ss_pred CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhccc
Confidence 567789999997654 234589999999999999999999998876668999999999999999998887643
No 180
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.20 E-value=0.016 Score=68.39 Aligned_cols=70 Identities=21% Similarity=0.170 Sum_probs=54.0
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHcC-------CCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNF-------PHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~~-------p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++-|.+||..+++..=.++++|.|||||....- ++..+.... .+.++||++||..-+.++.+.+...
T Consensus 29 ~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~l 106 (423)
T PRK04837 29 HNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPL 106 (423)
T ss_pred CCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHHH
Confidence 367899999999999877789999999999987544 344444321 2358999999999999987766543
No 181
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=96.19 E-value=0.0063 Score=67.19 Aligned_cols=53 Identities=30% Similarity=0.455 Sum_probs=43.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
..+++|.|+||||||.++.+++...... +.+++.+|-.-.+ .++.+...+.|.
T Consensus 23 g~~~lI~G~pGsGKT~f~~qfl~~~~~~--ge~vlyvs~~e~~-~~l~~~~~~~g~ 75 (260)
T COG0467 23 GSVVLITGPPGTGKTIFALQFLYEGARE--GEPVLYVSTEESP-EELLENARSFGW 75 (260)
T ss_pred CcEEEEEcCCCCcHHHHHHHHHHHHHhc--CCcEEEEEecCCH-HHHHHHHHHcCC
Confidence 6789999999999999999999999988 8889988876555 556666655554
No 182
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=96.17 E-value=0.02 Score=64.54 Aligned_cols=72 Identities=18% Similarity=0.303 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHH---hcC-CCeEEEECCCCCChhHHHHHHH-HHHHHhCCC----CcEEEEecchHHHHHHHHHHH
Q psy12659 811 VPPFKLTFHEIEAIRA---GMQ-PGLTLVVGPPGTGKTDVAVQII-SNLYHNFPH----QRTLIVTHSNQALNQLFEKII 881 (1051)
Q Consensus 811 ~~~~~Ln~~Q~~Ai~~---~l~-~~~tlIqGPPGTGKT~ti~~iI-~~ll~~~~~----~riLV~a~SN~Ald~l~e~l~ 881 (1051)
.+||..-+.|.+.+.. ++. ++..+|..|.|||||..+.-.. ..+.. .+. .+|+++++|+.-..+....+.
T Consensus 4 ~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~-~~~~~~~~kvi~~t~T~~~~~q~i~~l~ 82 (289)
T smart00488 4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRS-FPERIQKIKLIYLSRTVSEIEKRLEELR 82 (289)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHh-CcccccccceeEEeccHHHHHHHHHHHH
Confidence 4677778899994333 343 7889999999999997655444 44443 233 389999999998888777765
Q ss_pred hc
Q psy12659 882 SL 883 (1051)
Q Consensus 882 ~~ 883 (1051)
+.
T Consensus 83 ~~ 84 (289)
T smart00488 83 KL 84 (289)
T ss_pred hc
Confidence 54
No 183
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=96.17 E-value=0.02 Score=64.54 Aligned_cols=72 Identities=18% Similarity=0.303 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHH---hcC-CCeEEEECCCCCChhHHHHHHH-HHHHHhCCC----CcEEEEecchHHHHHHHHHHH
Q psy12659 811 VPPFKLTFHEIEAIRA---GMQ-PGLTLVVGPPGTGKTDVAVQII-SNLYHNFPH----QRTLIVTHSNQALNQLFEKII 881 (1051)
Q Consensus 811 ~~~~~Ln~~Q~~Ai~~---~l~-~~~tlIqGPPGTGKT~ti~~iI-~~ll~~~~~----~riLV~a~SN~Ald~l~e~l~ 881 (1051)
.+||..-+.|.+.+.. ++. ++..+|..|.|||||..+.-.. ..+.. .+. .+|+++++|+.-..+....+.
T Consensus 4 ~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~-~~~~~~~~kvi~~t~T~~~~~q~i~~l~ 82 (289)
T smart00489 4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRS-FPERIQKIKLIYLSRTVSEIEKRLEELR 82 (289)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHh-CcccccccceeEEeccHHHHHHHHHHHH
Confidence 4677778899994333 343 7889999999999997655444 44443 233 389999999998888777765
Q ss_pred hc
Q psy12659 882 SL 883 (1051)
Q Consensus 882 ~~ 883 (1051)
+.
T Consensus 83 ~~ 84 (289)
T smart00489 83 KL 84 (289)
T ss_pred hc
Confidence 54
No 184
>PRK09183 transposase/IS protein; Provisional
Probab=96.17 E-value=0.011 Score=65.79 Aligned_cols=51 Identities=18% Similarity=0.292 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHh---cCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 815 KLTFHEIEAIRAG---MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~---l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
.+|..|...+... -.....+|.||||||||+++..+...+.. .+.+|+.+.
T Consensus 84 ~~~~~~i~~L~~~~~i~~~~~v~l~Gp~GtGKThLa~al~~~a~~--~G~~v~~~~ 137 (259)
T PRK09183 84 GAPQKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIALGYEAVR--AGIKVRFTT 137 (259)
T ss_pred CCCHHHHHHHhcCCchhcCCeEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEe
Confidence 5677777777554 22567889999999999999999776665 677888765
No 185
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=96.16 E-value=0.0041 Score=60.36 Aligned_cols=54 Identities=19% Similarity=0.359 Sum_probs=36.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhC----CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNF----PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~----~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.++.+|.||||+|||+++.++...+.... ...-+.+.+++......+...+.+.
T Consensus 4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 61 (131)
T PF13401_consen 4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEA 61 (131)
T ss_dssp ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHH
T ss_pred CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence 57899999999999999999999876421 2234555555555577777777654
No 186
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=96.16 E-value=0.019 Score=68.71 Aligned_cols=70 Identities=26% Similarity=0.240 Sum_probs=54.5
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHcC------CCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNF------PHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~~------p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++-|.+||..++...-.++++|.|||||.+..- ++..+.... ...++||++||..-+.++.+.+...
T Consensus 22 ~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~ 98 (456)
T PRK10590 22 REPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDY 98 (456)
T ss_pred CCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHH
Confidence 367899999999999866689999999999987544 344443321 1237999999999999999888764
No 187
>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain. The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....
Probab=96.15 E-value=0.0085 Score=60.90 Aligned_cols=52 Identities=25% Similarity=0.418 Sum_probs=43.3
Q ss_pred CCeEEEEccCCCChHH-HHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 192 PGLTLVVGPPGTGKTD-VAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~-ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..++.|.=.||+|||+ ++.+++...+.. +.|+||++||...++++.+.|...
T Consensus 4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~--~~rvLvL~PTRvva~em~~aL~~~ 56 (148)
T PF07652_consen 4 GELTVLDLHPGAGKTRRVLPEIVREAIKR--RLRVLVLAPTRVVAEEMYEALKGL 56 (148)
T ss_dssp TEEEEEE--TTSSTTTTHHHHHHHHHHHT--T--EEEEESSHHHHHHHHHHTTTS
T ss_pred CceeEEecCCCCCCcccccHHHHHHHHHc--cCeEEEecccHHHHHHHHHHHhcC
Confidence 4578999999999999 799999999988 889999999999999999999755
No 188
>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function. It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].
Probab=96.15 E-value=0.0085 Score=69.24 Aligned_cols=53 Identities=25% Similarity=0.357 Sum_probs=44.4
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+.+|+|.||||||-++..++..+.....+.++++++.++.-.+.+.+.+...
T Consensus 2 ~v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~ 54 (352)
T PF09848_consen 2 QVILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKK 54 (352)
T ss_pred eEEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhhh
Confidence 46899999999999999999999933337889999999888888788777654
No 189
>KOG0743|consensus
Probab=96.15 E-value=0.0052 Score=72.02 Aligned_cols=43 Identities=30% Similarity=0.497 Sum_probs=30.9
Q ss_pred CCCCCCHHHHHHHHHhcC----------------CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 174 NTIPFTPTQIEAIRAGMQ----------------PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~----------------~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.++.+++.-++-|..-+. .+-+|+.||||||||++|+++...|
T Consensus 201 ~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L 259 (457)
T KOG0743|consen 201 ETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYL 259 (457)
T ss_pred cccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhc
Confidence 446677766666644221 2458999999999999999987654
No 190
>PRK04328 hypothetical protein; Provisional
Probab=96.13 E-value=0.01 Score=65.42 Aligned_cols=54 Identities=22% Similarity=0.253 Sum_probs=43.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
+.+++|.||||||||+.+.+++.+-+. .+++++.++-.. ..+.+.+...+.|.+
T Consensus 23 gs~ili~G~pGsGKT~l~~~fl~~~~~--~ge~~lyis~ee-~~~~i~~~~~~~g~d 76 (249)
T PRK04328 23 RNVVLLSGGPGTGKSIFSQQFLWNGLQ--MGEPGVYVALEE-HPVQVRRNMRQFGWD 76 (249)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHHh--cCCcEEEEEeeC-CHHHHHHHHHHcCCC
Confidence 578999999999999999999988777 688888888544 444577777777654
No 191
>PRK08084 DNA replication initiation factor; Provisional
Probab=96.13 E-value=0.011 Score=64.66 Aligned_cols=52 Identities=12% Similarity=0.197 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHhc---CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCC
Q psy12659 178 FTPTQIEAIRAGM---QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 231 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l---~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~S 231 (1051)
-|.....++.... ..+..+|.||||||||+++..+...+..+ +.+++.+.-.
T Consensus 28 ~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~--~~~v~y~~~~ 82 (235)
T PRK08084 28 DNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR--GRAVGYVPLD 82 (235)
T ss_pred ccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEEHH
Confidence 4666666666543 24678999999999999999988887765 6777776654
No 192
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=96.11 E-value=0.016 Score=76.62 Aligned_cols=68 Identities=22% Similarity=0.195 Sum_probs=55.9
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++-|+.++..++...-.++++|+|||||.++.-++..+... +.++||++||..-+.++.+.+.+.
T Consensus 77 ~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~l~~~~~l~~~--g~~vLIL~PTreLa~Qi~~~l~~l 144 (1171)
T TIGR01054 77 SEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFGLAMSLFLAKK--GKRCYIILPTTLLVIQVAEKISSL 144 (1171)
T ss_pred CCCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEeCHHHHHHHHHHHHHHH
Confidence 46788999999999987778899999999998665544444333 779999999999999998888764
No 193
>PRK00254 ski2-like helicase; Provisional
Probab=96.11 E-value=0.021 Score=72.21 Aligned_cols=67 Identities=16% Similarity=0.281 Sum_probs=55.2
Q ss_pred CCCCHHHHHHHHH-hcCCCeEEEEccCCCChHHHH-HHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 176 IPFTPTQIEAIRA-GMQPGLTLVVGPPGTGKTDVA-VQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~-~l~~~~~lI~GPPGTGKT~ti-~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
..|++.|.+|+.. .++..-.+|+.|+|+|||.+. ..++..+... +.++|+++|+.+-+++..+++..
T Consensus 22 ~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--~~~~l~l~P~~aLa~q~~~~~~~ 90 (720)
T PRK00254 22 EELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GGKAVYLVPLKALAEEKYREFKD 90 (720)
T ss_pred CCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--CCeEEEEeChHHHHHHHHHHHHH
Confidence 3689999999986 456667899999999999988 4455555544 67999999999999999988875
No 194
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=96.10 E-value=0.015 Score=67.75 Aligned_cols=56 Identities=25% Similarity=0.297 Sum_probs=40.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC-C--HHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-S--NQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~-S--N~Avd~l~~rl~~~~~ 247 (1051)
.++.++.||+|+|||||++.+...+....+..+|.+++. + -.|++++..--...++
T Consensus 137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv 195 (374)
T PRK14722 137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGV 195 (374)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCC
Confidence 568999999999999999999988765543457766653 2 2377776554444454
No 195
>PRK06893 DNA replication initiation factor; Validated
Probab=96.09 E-value=0.007 Score=65.81 Aligned_cols=37 Identities=11% Similarity=0.245 Sum_probs=30.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
.+..+|+||||||||+++..+...+..+ +.++..+..
T Consensus 39 ~~~l~l~G~~G~GKThL~~ai~~~~~~~--~~~~~y~~~ 75 (229)
T PRK06893 39 QPFFYIWGGKSSGKSHLLKAVSNHYLLN--QRTAIYIPL 75 (229)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEeeH
Confidence 5667999999999999999999998877 455655544
No 196
>PRK09401 reverse gyrase; Reviewed
Probab=96.06 E-value=0.016 Score=76.50 Aligned_cols=68 Identities=16% Similarity=0.175 Sum_probs=56.7
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
.+++.|+.++..++.+.-+++++|.|||||..+.-++..+.. .+.++||++||..-+.++.+++...+
T Consensus 80 ~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~ 147 (1176)
T PRK09401 80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFG 147 (1176)
T ss_pred CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHh
Confidence 567889999999999888999999999999765544433333 57899999999999999999997764
No 197
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=96.04 E-value=0.022 Score=61.37 Aligned_cols=51 Identities=8% Similarity=0.167 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHhc----CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 178 FTPTQIEAIRAGM----QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l----~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
-|.....++.... ..+..+|.||||||||+++..+...+... +.++.++.-
T Consensus 24 ~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~--~~~~~~i~~ 78 (227)
T PRK08903 24 ENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG--GRNARYLDA 78 (227)
T ss_pred CcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC--CCcEEEEeh
Confidence 3556666666542 35678999999999999999998887765 555555543
No 198
>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A.
Probab=96.04 E-value=0.013 Score=59.96 Aligned_cols=39 Identities=31% Similarity=0.500 Sum_probs=28.4
Q ss_pred HHHHHHHHhc-----C-CCeEEEECCCCCChhHHHHHHHHHHHHh
Q psy12659 819 HEIEAIRAGM-----Q-PGLTLVVGPPGTGKTDVAVQIISNLYHN 857 (1051)
Q Consensus 819 ~Q~~Ai~~~l-----~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~ 857 (1051)
+|.+.+...+ . +...+|.||||||||+++.++...+-..
T Consensus 7 ~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~ 51 (185)
T PF13191_consen 7 EEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER 51 (185)
T ss_dssp HHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 4677777777 1 6789999999999999999999888874
No 199
>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=96.04 E-value=0.0087 Score=61.68 Aligned_cols=34 Identities=32% Similarity=0.518 Sum_probs=29.0
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
+.++.||||+|||+++..+...+... +.+++++.
T Consensus 2 ~~~~~G~~G~GKTt~~~~la~~~~~~--g~~v~~i~ 35 (173)
T cd03115 2 VILLVGLQGVGKTTTAAKLALYLKKK--GKKVLLVA 35 (173)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHC--CCcEEEEE
Confidence 57899999999999999999888776 67787665
No 200
>PRK10416 signal recognition particle-docking protein FtsY; Provisional
Probab=96.03 E-value=0.014 Score=66.81 Aligned_cols=54 Identities=26% Similarity=0.306 Sum_probs=40.3
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe-CC--HHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HS--NQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a-~S--N~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||||+|||||++.+...+... +.+|++++ .+ ..|++++.......++
T Consensus 114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~~--g~~V~Li~~D~~r~~a~eql~~~a~~~~i 170 (318)
T PRK10416 114 PFVILVVGVNGVGKTTTIGKLAHKYKAQ--GKKVLLAAGDTFRAAAIEQLQVWGERVGV 170 (318)
T ss_pred CeEEEEECCCCCcHHHHHHHHHHHHHhc--CCeEEEEecCccchhhHHHHHHHHHHcCc
Confidence 5678899999999999999998877654 66787765 33 3467777655555554
No 201
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=96.02 E-value=0.021 Score=68.29 Aligned_cols=69 Identities=23% Similarity=0.177 Sum_probs=53.8
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHH-HHHHHhC------CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQII-SNLYHNF------PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI-~~ll~~~------~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++-|.+||..++...-.++++|.|||||.+..-.+ ..+.... ...++||++||..-+.++.+.+...
T Consensus 23 ~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~ 98 (456)
T PRK10590 23 EPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDY 98 (456)
T ss_pred CCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHH
Confidence 5678899999999997779999999999998755443 3333211 1237999999999999998887654
No 202
>PRK10867 signal recognition particle protein; Provisional
Probab=96.02 E-value=0.017 Score=68.57 Aligned_cols=55 Identities=27% Similarity=0.384 Sum_probs=39.4
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe-cch--HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HSN--QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a-~SN--~Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||||+|||||++.+...+... .+.+|++++ .+. .|.+++.......++
T Consensus 100 p~vI~~vG~~GsGKTTtaakLA~~l~~~-~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv 157 (433)
T PRK10867 100 PTVIMMVGLQGAGKTTTAGKLAKYLKKK-KKKKVLLVAADVYRPAAIEQLKTLGEQIGV 157 (433)
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHh-cCCcEEEEEccccchHHHHHHHHHHhhcCC
Confidence 4678999999999999999999988763 267776554 433 456666544444554
No 203
>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=96.02 E-value=0.013 Score=67.30 Aligned_cols=51 Identities=20% Similarity=0.358 Sum_probs=44.9
Q ss_pred EEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.+|+||+|+|||.+....+...+...++.++++++|+...++++.+++.+.
T Consensus 2 vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~ 52 (358)
T TIGR01587 2 LVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKEL 52 (358)
T ss_pred EEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHH
Confidence 689999999999998887776666556789999999999999999999875
No 204
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=96.02 E-value=0.0086 Score=68.87 Aligned_cols=41 Identities=29% Similarity=0.494 Sum_probs=32.0
Q ss_pred CHHHHHHHHHhcC-------CCeEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 179 TPTQIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 179 n~~Q~~Ai~~~l~-------~~~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
-+.|.+.+...+. ++..+|.||||||||+++..++.++...
T Consensus 20 Re~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~ 67 (365)
T TIGR02928 20 RDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEA 67 (365)
T ss_pred cHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHH
Confidence 4567766665532 4678999999999999999999887654
No 205
>TIGR01650 PD_CobS cobaltochelatase, CobS subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=96.02 E-value=0.0093 Score=68.22 Aligned_cols=45 Identities=31% Similarity=0.401 Sum_probs=39.1
Q ss_pred CCCCCCCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 810 LVPPFKLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 810 ~~~~~~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
.-|.|.++++-..+|..++. ++-.+|.||||||||+++.++...+
T Consensus 43 ~d~~y~f~~~~~~~vl~~l~~~~~ilL~G~pGtGKTtla~~lA~~l 88 (327)
T TIGR01650 43 IDPAYLFDKATTKAICAGFAYDRRVMVQGYHGTGKSTHIEQIAARL 88 (327)
T ss_pred CCCCccCCHHHHHHHHHHHhcCCcEEEEeCCCChHHHHHHHHHHHH
Confidence 34678999999999999887 7789999999999999999888765
No 206
>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=96.02 E-value=0.014 Score=74.39 Aligned_cols=62 Identities=15% Similarity=0.255 Sum_probs=49.5
Q ss_pred HHHHHHHHhc-CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 181 TQIEAIRAGM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 181 ~Q~~Ai~~~l-~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
..+..|..++ +++..+|+||||||||+.+...+..... .+.+|+|+.|+..|+.++.+++.+
T Consensus 5 ~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~--~~~~ilvlqPrR~aA~qiA~rva~ 67 (819)
T TIGR01970 5 AVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG--IGGKIIMLEPRRLAARSAAQRLAS 67 (819)
T ss_pred HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc--cCCeEEEEeCcHHHHHHHHHHHHH
Confidence 3455555555 4788999999999999999987654442 356999999999999999999964
No 207
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=96.01 E-value=0.0075 Score=66.82 Aligned_cols=38 Identities=32% Similarity=0.530 Sum_probs=32.1
Q ss_pred CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 191 QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 191 ~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
+..-.++.||||||||+++++|...+... |.+|++++-
T Consensus 104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~--g~sv~f~~~ 141 (254)
T COG1484 104 RGENLVLLGPPGVGKTHLAIAIGNELLKA--GISVLFITA 141 (254)
T ss_pred cCCcEEEECCCCCcHHHHHHHHHHHHHHc--CCeEEEEEH
Confidence 35668999999999999999999999955 778887653
No 208
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.
Probab=96.01 E-value=0.012 Score=66.84 Aligned_cols=55 Identities=27% Similarity=0.452 Sum_probs=42.8
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecc
Q psy12659 815 KLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 869 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~S 869 (1051)
.+++.|.+.+..++. .+..+|.||+|+||||++..++..+-...++.||+++-.+
T Consensus 116 ~~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~ 171 (299)
T TIGR02782 116 IMTAAQRDVLREAVLARKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDT 171 (299)
T ss_pred CCCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCc
Confidence 466778888888877 6789999999999999999988776654356777665443
No 209
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=96.00 E-value=0.018 Score=76.01 Aligned_cols=67 Identities=21% Similarity=0.187 Sum_probs=55.6
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+.+.|+.++..++.+.-.++++|+|||||.++.-++..+.. .+.++||++||..-+.++.+.+...
T Consensus 78 ~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~~l 144 (1171)
T TIGR01054 78 EPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEKISSL 144 (1171)
T ss_pred CCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHHHH
Confidence 467789999999999888999999999999866544444333 5789999999999999999888765
No 210
>KOG0744|consensus
Probab=96.00 E-value=0.0044 Score=69.75 Aligned_cols=26 Identities=42% Similarity=0.699 Sum_probs=22.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
..+.|++||||||||++..++...|-
T Consensus 177 NRliLlhGPPGTGKTSLCKaLaQkLS 202 (423)
T KOG0744|consen 177 NRLILLHGPPGTGKTSLCKALAQKLS 202 (423)
T ss_pred eeEEEEeCCCCCChhHHHHHHHHhhe
Confidence 57899999999999999888877664
No 211
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.99 E-value=0.021 Score=67.44 Aligned_cols=68 Identities=18% Similarity=0.103 Sum_probs=53.0
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHH-HHHHHHHhC-------CCCcEEEEecchHHHHHHHHHHHh
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNF-------PHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~-iI~~ll~~~-------~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.+++-|.+||..++++.=.++++|.|||||.+..- ++..++... .+.++||++||..-+.++.+.+..
T Consensus 30 ~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~ 105 (423)
T PRK04837 30 NCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEP 105 (423)
T ss_pred CCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHH
Confidence 56788999999999988899999999999987643 334444321 235899999999999998776544
No 212
>PRK04296 thymidine kinase; Provisional
Probab=95.99 E-value=0.0089 Score=63.18 Aligned_cols=36 Identities=19% Similarity=0.271 Sum_probs=31.6
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
.+.+|.||||+|||+.+..++..+... +.+++++.|
T Consensus 3 ~i~litG~~GsGKTT~~l~~~~~~~~~--g~~v~i~k~ 38 (190)
T PRK04296 3 KLEFIYGAMNSGKSTELLQRAYNYEER--GMKVLVFKP 38 (190)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHc--CCeEEEEec
Confidence 368999999999999999999988876 789998854
No 213
>PRK09183 transposase/IS protein; Provisional
Probab=95.97 E-value=0.015 Score=64.55 Aligned_cols=51 Identities=20% Similarity=0.297 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHh---cCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 177 PFTPTQIEAIRAG---MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~---l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
.+|..|...+... -.....+|.||||||||+++..+...+... +.+++.+.
T Consensus 84 ~~~~~~i~~L~~~~~i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~--G~~v~~~~ 137 (259)
T PRK09183 84 GAPQKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIALGYEAVRA--GIKVRFTT 137 (259)
T ss_pred CCCHHHHHHHhcCCchhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEEe
Confidence 5677777777543 235568899999999999999997766655 77887664
No 214
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=95.97 E-value=0.016 Score=67.63 Aligned_cols=56 Identities=23% Similarity=0.309 Sum_probs=39.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecch---HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN---QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN---~Ald~l~e~l~~~~~ 885 (1051)
+++.++.||+|+|||||++.+...+.......+|.+++.-. .|.+++..-....++
T Consensus 137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv 195 (374)
T PRK14722 137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGV 195 (374)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCC
Confidence 67999999999999999999999876533335776665322 367776543333444
No 215
>PRK06835 DNA replication protein DnaC; Validated
Probab=95.97 E-value=0.014 Score=67.21 Aligned_cols=37 Identities=27% Similarity=0.248 Sum_probs=32.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
....++.|||||||||++..|...++. .+.+|+.++-
T Consensus 183 ~~~Lll~G~~GtGKThLa~aIa~~l~~--~g~~V~y~t~ 219 (329)
T PRK06835 183 NENLLFYGNTGTGKTFLSNCIAKELLD--RGKSVIYRTA 219 (329)
T ss_pred CCcEEEECCCCCcHHHHHHHHHHHHHH--CCCeEEEEEH
Confidence 467999999999999999999999988 6778877663
No 216
>PRK10416 signal recognition particle-docking protein FtsY; Provisional
Probab=95.96 E-value=0.015 Score=66.51 Aligned_cols=54 Identities=26% Similarity=0.301 Sum_probs=40.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe-cc--hHHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HS--NQALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a-~S--N~Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||||+|||||++.+...+.. .+.+|++++ .+ ..|++++.......++
T Consensus 114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~--~g~~V~Li~~D~~r~~a~eql~~~a~~~~i 170 (318)
T PRK10416 114 PFVILVVGVNGVGKTTTIGKLAHKYKA--QGKKVLLAAGDTFRAAAIEQLQVWGERVGV 170 (318)
T ss_pred CeEEEEECCCCCcHHHHHHHHHHHHHh--cCCeEEEEecCccchhhHHHHHHHHHHcCc
Confidence 568899999999999999999987765 567888765 33 3466776655444444
No 217
>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=95.96 E-value=0.014 Score=62.97 Aligned_cols=54 Identities=20% Similarity=0.301 Sum_probs=41.2
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
..+++|.||||||||+++.+++.+.+. ++++++.++- ....+.+.++..+.+++
T Consensus 20 G~~~~i~G~~G~GKT~l~~~~~~~~~~--~g~~~~~is~-e~~~~~i~~~~~~~g~~ 73 (229)
T TIGR03881 20 GFFVAVTGEPGTGKTIFCLHFAYKGLR--DGDPVIYVTT-EESRESIIRQAAQFGMD 73 (229)
T ss_pred CeEEEEECCCCCChHHHHHHHHHHHHh--cCCeEEEEEc-cCCHHHHHHHHHHhCCC
Confidence 578999999999999999999887776 6778877775 33346666665555543
No 218
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=95.96 E-value=0.017 Score=62.23 Aligned_cols=51 Identities=8% Similarity=0.139 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHhc----CCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 816 LTFHEIEAIRAGM----QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 816 Ln~~Q~~Ai~~~l----~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
-|.....++.... ..+..+|.||||||||+++..+...+.. .+.++.++.-
T Consensus 24 ~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~--~~~~~~~i~~ 78 (227)
T PRK08903 24 ENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASY--GGRNARYLDA 78 (227)
T ss_pred CcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHh--CCCcEEEEeh
Confidence 3455556665542 2567999999999999999998888776 5556666554
No 219
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=95.95 E-value=0.015 Score=62.04 Aligned_cols=40 Identities=10% Similarity=0.176 Sum_probs=32.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ 871 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~ 871 (1051)
++..+|.||||||||+++..+...+.. ++.+++.+.-++.
T Consensus 38 ~~~lll~G~~G~GKT~la~~~~~~~~~--~~~~~~~i~~~~~ 77 (226)
T TIGR03420 38 DRFLYLWGESGSGKSHLLQAACAAAEE--RGKSAIYLPLAEL 77 (226)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHHHh--cCCcEEEEeHHHH
Confidence 678999999999999999999888776 5566666654443
No 220
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=95.95 E-value=0.015 Score=69.15 Aligned_cols=54 Identities=24% Similarity=0.333 Sum_probs=39.8
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec-c--hHHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-S--NQALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~-S--N~Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||||+|||||++.+...+.. .+.+|++++. + ..|.+++.......++
T Consensus 95 p~vI~lvG~~GsGKTTtaakLA~~L~~--~g~kV~lV~~D~~R~aa~eQL~~la~~~gv 151 (437)
T PRK00771 95 PQTIMLVGLQGSGKTTTAAKLARYFKK--KGLKVGLVAADTYRPAAYDQLKQLAEKIGV 151 (437)
T ss_pred CeEEEEECCCCCcHHHHHHHHHHHHHH--cCCeEEEecCCCCCHHHHHHHHHHHHHcCC
Confidence 578899999999999999999988766 5677776654 2 3456666655445454
No 221
>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=95.95 E-value=0.01 Score=61.12 Aligned_cols=34 Identities=32% Similarity=0.505 Sum_probs=29.0
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
+.++.||||+|||+++..+...+.. .+.+|+++.
T Consensus 2 ~~~~~G~~G~GKTt~~~~la~~~~~--~g~~v~~i~ 35 (173)
T cd03115 2 VILLVGLQGVGKTTTAAKLALYLKK--KGKKVLLVA 35 (173)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHH--CCCcEEEEE
Confidence 5789999999999999999988777 577887665
No 222
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=95.92 E-value=0.012 Score=78.03 Aligned_cols=53 Identities=25% Similarity=0.345 Sum_probs=45.3
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHc-CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHN-FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~-~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.-.+|.+++|||||++++.-+..++.. .+.++||+++.||.|+.++.+||.+.
T Consensus 11 ~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~ 64 (1141)
T TIGR02784 11 TSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDR 64 (1141)
T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHH
Confidence 346799999999999999988877754 34689999999999999999999753
No 223
>PRK04296 thymidine kinase; Provisional
Probab=95.92 E-value=0.0098 Score=62.89 Aligned_cols=36 Identities=19% Similarity=0.260 Sum_probs=31.7
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
.+.+|.||||+|||+.+..++..+.. .+++++++.+
T Consensus 3 ~i~litG~~GsGKTT~~l~~~~~~~~--~g~~v~i~k~ 38 (190)
T PRK04296 3 KLEFIYGAMNSGKSTELLQRAYNYEE--RGMKVLVFKP 38 (190)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHH--cCCeEEEEec
Confidence 47899999999999999999998877 6889998854
No 224
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=95.90 E-value=0.017 Score=68.67 Aligned_cols=54 Identities=24% Similarity=0.342 Sum_probs=39.6
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC-C--HHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-S--NQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~-S--N~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||||+|||||++.+...+... +.+|++++. + ..|.+++..-....++
T Consensus 95 p~vI~lvG~~GsGKTTtaakLA~~L~~~--g~kV~lV~~D~~R~aa~eQL~~la~~~gv 151 (437)
T PRK00771 95 PQTIMLVGLQGSGKTTTAAKLARYFKKK--GLKVGLVAADTYRPAAYDQLKQLAEKIGV 151 (437)
T ss_pred CeEEEEECCCCCcHHHHHHHHHHHHHHc--CCeEEEecCCCCCHHHHHHHHHHHHHcCC
Confidence 5678999999999999999999877655 667776643 3 3556666655555555
No 225
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=95.90 E-value=0.013 Score=74.62 Aligned_cols=62 Identities=10% Similarity=0.149 Sum_probs=47.3
Q ss_pred HHHHHHHHhc-CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 181 TQIEAIRAGM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 181 ~Q~~Ai~~~l-~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
+.+..|..++ +++..+|+||||||||+.+...+..-. ..+.+|+|+.|+..|+.++.+++.+
T Consensus 8 ~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~--~~~~~ilvlqPrR~aA~qia~rva~ 70 (812)
T PRK11664 8 AVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHG--GINGKIIMLEPRRLAARNVAQRLAE 70 (812)
T ss_pred HHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcC--CcCCeEEEECChHHHHHHHHHHHHH
Confidence 4455555555 467899999999999999876543221 2245899999999999999999864
No 226
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=95.90 E-value=0.017 Score=66.51 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=30.8
Q ss_pred CHHHHHHHHHhcC-------CCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 817 TFHEIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 817 n~~Q~~Ai~~~l~-------~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
-+.|.+.+...+. ++..+|.||||||||+++..+..++..
T Consensus 20 Re~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~ 66 (365)
T TIGR02928 20 RDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEE 66 (365)
T ss_pred cHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHH
Confidence 3456666555542 467999999999999999999988764
No 227
>KOG0744|consensus
Probab=95.88 E-value=0.0054 Score=69.09 Aligned_cols=54 Identities=33% Similarity=0.511 Sum_probs=37.9
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCC---CCcEEEE-----------ecchHHHHHHHHHHHhc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFP---HQRTLIV-----------THSNQALNQLFEKIISL 883 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~---~~riLV~-----------a~SN~Ald~l~e~l~~~ 883 (1051)
+.+.+++||||||||++..++...|--... .+.+||= +.|.+-+..++.++.+.
T Consensus 177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~EL 244 (423)
T KOG0744|consen 177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQEL 244 (423)
T ss_pred eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 789999999999999998887766532111 1334442 23567788888888765
No 228
>TIGR01650 PD_CobS cobaltochelatase, CobS subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=95.88 E-value=0.014 Score=66.85 Aligned_cols=44 Identities=32% Similarity=0.363 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 174 NTIPFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
..+.|+++-..+|..++. .+-.+|.||||||||+++..+...+-
T Consensus 45 ~~y~f~~~~~~~vl~~l~~~~~ilL~G~pGtGKTtla~~lA~~l~ 89 (327)
T TIGR01650 45 PAYLFDKATTKAICAGFAYDRRVMVQGYHGTGKSTHIEQIAARLN 89 (327)
T ss_pred CCccCCHHHHHHHHHHHhcCCcEEEEeCCCChHHHHHHHHHHHHC
Confidence 357899999998888775 66789999999999999998877663
No 229
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.88 E-value=0.027 Score=69.38 Aligned_cols=71 Identities=20% Similarity=0.256 Sum_probs=56.2
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHcC-------CCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNF-------PHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~~-------p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
..+++-|.++|-.++...=.++++|.|||||.+..- ++..++... .+.++||++||..-+.++.+.+...+
T Consensus 30 ~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~ 108 (572)
T PRK04537 30 TRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFG 108 (572)
T ss_pred CCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHHh
Confidence 468999999999999876689999999999987655 444454321 13589999999999999998887654
No 230
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=95.87 E-value=0.011 Score=63.58 Aligned_cols=38 Identities=24% Similarity=0.541 Sum_probs=32.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 869 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~S 869 (1051)
..+++|.||||||||+++.+++.+... .+.+++.++--
T Consensus 23 g~i~~i~G~~GsGKT~l~~~la~~~~~--~~~~v~yi~~e 60 (225)
T PRK09361 23 GTITQIYGPPGSGKTNICLQLAVEAAK--NGKKVIYIDTE 60 (225)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHH--CCCeEEEEECC
Confidence 568999999999999999999998887 56777776643
No 231
>PLN03025 replication factor C subunit; Provisional
Probab=95.85 E-value=0.017 Score=65.80 Aligned_cols=64 Identities=20% Similarity=0.318 Sum_probs=39.0
Q ss_pred CHHHHHHHHHhcC---CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH-HHHHHHHHHH
Q psy12659 179 TPTQIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN-QALNQLFEKI 242 (1051)
Q Consensus 179 n~~Q~~Ai~~~l~---~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN-~Avd~l~~rl 242 (1051)
++...+.++.... .+..+++||||||||+++..+...++...-...++-...|. .-++.+.+.+
T Consensus 18 ~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~sd~~~~~~vr~~i 85 (319)
T PLN03025 18 NEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVVRNKI 85 (319)
T ss_pred cHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecccccccHHHHHHHH
Confidence 4455555655433 34579999999999999999988886432122344443333 2344444444
No 232
>PRK06851 hypothetical protein; Provisional
Probab=95.85 E-value=0.0071 Score=70.25 Aligned_cols=47 Identities=21% Similarity=0.362 Sum_probs=40.1
Q ss_pred CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCe--EEEEeCCHHHHHHHH
Q psy12659 191 QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQR--TLIVTHSNQALNQLF 239 (1051)
Q Consensus 191 ~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~r--iLv~a~SN~Avd~l~ 239 (1051)
...+++|.||||||||+++.+++..+... +.. .+.|+..|.++|-|.
T Consensus 29 ~~~~~il~G~pGtGKStl~~~i~~~~~~~--g~~Ve~~~~~~d~~slDgvi 77 (367)
T PRK06851 29 ANRIFILKGGPGTGKSTLMKKIGEEFLEK--GYDVEFLHCSSDNDSLDGVI 77 (367)
T ss_pred cceEEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEcCCCCCceeeEE
Confidence 46789999999999999999999999876 444 678888898998765
No 233
>PRK08727 hypothetical protein; Validated
Probab=95.85 E-value=0.027 Score=61.49 Aligned_cols=38 Identities=21% Similarity=0.363 Sum_probs=31.6
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 869 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~S 869 (1051)
....+|.|||||||||++..+...+.. .+.++..++..
T Consensus 41 ~~~l~l~G~~G~GKThL~~a~~~~~~~--~~~~~~y~~~~ 78 (233)
T PRK08727 41 SDWLYLSGPAGTGKTHLALALCAAAEQ--AGRSSAYLPLQ 78 (233)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHHHH--cCCcEEEEeHH
Confidence 456999999999999999999988777 56777777643
No 234
>PRK02362 ski2-like helicase; Provisional
Probab=95.83 E-value=0.032 Score=70.70 Aligned_cols=68 Identities=22% Similarity=0.264 Sum_probs=55.3
Q ss_pred CCCCHHHHHHHHHh-cCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAG-MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~-l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..|++.|.+|+..+ ++..-.+|+.|+|+|||.++.-.+...+.. +.++|+++|+..=+++..+++...
T Consensus 22 ~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~--~~kal~i~P~raLa~q~~~~~~~~ 90 (737)
T PRK02362 22 EELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR--GGKALYIVPLRALASEKFEEFERF 90 (737)
T ss_pred CcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHHHHHHHHh
Confidence 36899999999884 456678999999999999886544444433 779999999999999999988764
No 235
>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=95.78 E-value=0.013 Score=62.23 Aligned_cols=39 Identities=23% Similarity=0.512 Sum_probs=32.8
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecch
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 870 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN 870 (1051)
..++.|.||||||||+++.+++.+... .+.+++.++..+
T Consensus 12 g~i~~i~G~~GsGKT~l~~~~~~~~~~--~g~~v~yi~~e~ 50 (209)
T TIGR02237 12 GTITQIYGPPGSGKTNICMILAVNAAR--QGKKVVYIDTEG 50 (209)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHh--CCCeEEEEECCC
Confidence 578999999999999999999998877 567777776643
No 236
>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=95.77 E-value=0.013 Score=62.78 Aligned_cols=37 Identities=32% Similarity=0.537 Sum_probs=32.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
..+++|.||||||||+++.+++.++.. .+.+++.++-
T Consensus 19 g~i~~i~G~~GsGKT~l~~~~a~~~~~--~g~~v~yi~~ 55 (218)
T cd01394 19 GTVTQVYGPPGTGKTNIAIQLAVETAG--QGKKVAYIDT 55 (218)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEEC
Confidence 578999999999999999999998876 5778877753
No 237
>PRK00254 ski2-like helicase; Provisional
Probab=95.77 E-value=0.026 Score=71.36 Aligned_cols=66 Identities=15% Similarity=0.242 Sum_probs=55.2
Q ss_pred CCCHHHHHHHHH-hcCCCeEEEECCCCCChhHHH-HHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 815 KLTFHEIEAIRA-GMQPGLTLVVGPPGTGKTDVA-VQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~-~l~~~~tlIqGPPGTGKT~ti-~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.+++.|.+|+.. .+++.-.+|++|+|+|||.++ ..++..++. ++.++++++|+..-+++..+.+..
T Consensus 23 ~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~--~~~~~l~l~P~~aLa~q~~~~~~~ 90 (720)
T PRK00254 23 ELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR--EGGKAVYLVPLKALAEEKYREFKD 90 (720)
T ss_pred CCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHHHHHHHH
Confidence 688899999987 566778999999999999988 555666665 578999999999999999887764
No 238
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=95.77 E-value=0.0085 Score=57.63 Aligned_cols=23 Identities=35% Similarity=0.840 Sum_probs=20.0
Q ss_pred eEEEEccCCCChHHHHHHHHHHH
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
+.+|.||||+||||++..+...+
T Consensus 1 vI~I~G~~gsGKST~a~~La~~~ 23 (121)
T PF13207_consen 1 VIIISGPPGSGKSTLAKELAERL 23 (121)
T ss_dssp EEEEEESTTSSHHHHHHHHHHHH
T ss_pred CEEEECCCCCCHHHHHHHHHHHH
Confidence 36899999999999999987765
No 239
>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=95.77 E-value=0.018 Score=66.07 Aligned_cols=51 Identities=20% Similarity=0.358 Sum_probs=45.1
Q ss_pred EEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
++|+||+|+|||.++...+...+....+.++++++|+...++++.+++...
T Consensus 2 vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~ 52 (358)
T TIGR01587 2 LVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKEL 52 (358)
T ss_pred EEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHH
Confidence 689999999999998888777776556789999999999999999998775
No 240
>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=95.75 E-value=0.013 Score=63.49 Aligned_cols=53 Identities=25% Similarity=0.445 Sum_probs=40.7
Q ss_pred hcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHH
Q psy12659 827 GMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKII 881 (1051)
Q Consensus 827 ~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~ 881 (1051)
++. ..+++|.||||||||+++.+++.++..+ .+.+++.++-=..+- ++..++.
T Consensus 9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~-~g~~vly~s~E~~~~-~~~~r~~ 62 (242)
T cd00984 9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKK-QGKPVLFFSLEMSKE-QLLQRLL 62 (242)
T ss_pred CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh-CCCceEEEeCCCCHH-HHHHHHH
Confidence 555 4599999999999999999999998873 278999998654433 4445553
No 241
>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=95.74 E-value=0.022 Score=72.77 Aligned_cols=61 Identities=15% Similarity=0.254 Sum_probs=49.4
Q ss_pred HHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 820 EIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 820 Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.+..|..++. +..++|+||||||||+.+...|..... .+.+|+|+.|+..|+.++.+++.+
T Consensus 6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~--~~~~ilvlqPrR~aA~qiA~rva~ 67 (819)
T TIGR01970 6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG--IGGKIIMLEPRRLAARSAAQRLAS 67 (819)
T ss_pred HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc--cCCeEEEEeCcHHHHHHHHHHHHH
Confidence 4455555655 789999999999999999887665443 456999999999999999999864
No 242
>PLN03025 replication factor C subunit; Provisional
Probab=95.74 E-value=0.021 Score=65.07 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=28.3
Q ss_pred HHHHHHHHhcC---CCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 819 HEIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 819 ~Q~~Ai~~~l~---~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
...+.+..... .+..+++||||||||+++..+...++.
T Consensus 20 ~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~ 60 (319)
T PLN03025 20 DAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLG 60 (319)
T ss_pred HHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhc
Confidence 34444444433 245799999999999999999988875
No 243
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=95.74 E-value=0.017 Score=61.64 Aligned_cols=52 Identities=12% Similarity=0.185 Sum_probs=36.4
Q ss_pred CHHHHHHHHHh---cCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH
Q psy12659 179 TPTQIEAIRAG---MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 232 (1051)
Q Consensus 179 n~~Q~~Ai~~~---l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN 232 (1051)
+..-.++++.. -.++..+|.||||||||+++..+....... +.+++.+.-++
T Consensus 22 ~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~--~~~~~~i~~~~ 76 (226)
T TIGR03420 22 NAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER--GKSAIYLPLAE 76 (226)
T ss_pred cHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc--CCcEEEEeHHH
Confidence 44444555543 236779999999999999999998887754 55666555444
No 244
>TIGR02533 type_II_gspE general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.
Probab=95.74 E-value=0.01 Score=71.63 Aligned_cols=54 Identities=28% Similarity=0.499 Sum_probs=42.0
Q ss_pred CCCCCCCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEE
Q psy12659 172 RKNTIPFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLI 227 (1051)
Q Consensus 172 ~~~~~~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv 227 (1051)
......+++.|.+.+..++. .|+.+|.||+|+|||||+..++..+.. ++.+|+.
T Consensus 220 ~l~~Lg~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL~a~L~~l~~--~~~~iiT 275 (486)
T TIGR02533 220 DLETLGMSPELLSRFERLIRRPHGIILVTGPTGSGKTTTLYAALSRLNT--PERNILT 275 (486)
T ss_pred CHHHcCCCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHhccCC--CCCcEEE
Confidence 33456789999999988765 689999999999999999988776643 2444444
No 245
>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.
Probab=95.73 E-value=0.021 Score=61.77 Aligned_cols=38 Identities=24% Similarity=0.442 Sum_probs=31.9
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
+...|.||+|+|||+++.++...+....|+.+|+.+..
T Consensus 35 ~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~ 72 (219)
T PF00308_consen 35 NPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSA 72 (219)
T ss_dssp SEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEH
T ss_pred CceEEECCCCCCHHHHHHHHHHHHHhccccccceeecH
Confidence 35789999999999999999999998888888877653
No 246
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=95.73 E-value=0.021 Score=59.55 Aligned_cols=53 Identities=32% Similarity=0.528 Sum_probs=38.7
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcC--------CCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNF--------PHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~--------p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++|.||||+|||+++.+++.++.... .+.+||.++.-+. ..++..|+...
T Consensus 32 g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~ 92 (193)
T PF13481_consen 32 GELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRAL 92 (193)
T ss_dssp TSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHH
T ss_pred CeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHH
Confidence 67899999999999999999999998621 2568888877665 46677777654
No 247
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=95.73 E-value=0.014 Score=62.88 Aligned_cols=38 Identities=26% Similarity=0.582 Sum_probs=32.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 231 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~S 231 (1051)
..+++|.||||||||+++.+++.+.... +.+++.++--
T Consensus 23 g~i~~i~G~~GsGKT~l~~~la~~~~~~--~~~v~yi~~e 60 (225)
T PRK09361 23 GTITQIYGPPGSGKTNICLQLAVEAAKN--GKKVIYIDTE 60 (225)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEECC
Confidence 4589999999999999999999988866 6777777643
No 248
>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=95.73 E-value=0.014 Score=61.98 Aligned_cols=39 Identities=23% Similarity=0.520 Sum_probs=32.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 232 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN 232 (1051)
..+++|.||||||||+++.+++.+...+ +.+++.++-.+
T Consensus 12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~--g~~v~yi~~e~ 50 (209)
T TIGR02237 12 GTITQIYGPPGSGKTNICMILAVNAARQ--GKKVVYIDTEG 50 (209)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC
Confidence 5689999999999999999999888876 67777776643
No 249
>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=95.72 E-value=0.019 Score=61.87 Aligned_cols=53 Identities=19% Similarity=0.291 Sum_probs=40.2
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
..+++|.||||||||+++.+++.+.+.+ +++++.++.- ...+++.++..+.++
T Consensus 20 G~~~~i~G~~G~GKT~l~~~~~~~~~~~--g~~~~~is~e-~~~~~i~~~~~~~g~ 72 (229)
T TIGR03881 20 GFFVAVTGEPGTGKTIFCLHFAYKGLRD--GDPVIYVTTE-ESRESIIRQAAQFGM 72 (229)
T ss_pred CeEEEEECCCCCChHHHHHHHHHHHHhc--CCeEEEEEcc-CCHHHHHHHHHHhCC
Confidence 5679999999999999999998877755 7778777653 234677666666554
No 250
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=95.72 E-value=0.015 Score=77.17 Aligned_cols=54 Identities=28% Similarity=0.315 Sum_probs=46.0
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCC----------CCcEEEEecchHHHHHHHHHHHhc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFP----------HQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~----------~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.|..+|-.--|||||+||+.+...|+-... -+.|||||.||+|..+|.+||.+.
T Consensus 17 ~G~~LIEASAGTGKTyTIa~lyLrLlL~~g~~~~~~~~L~~~~ILvvTFT~aAt~Elr~RIr~r 80 (1181)
T PRK10876 17 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEEILVVTFTEAATEELRGRIRSN 80 (1181)
T ss_pred CCCEEEEeCCCCcHHHHHHHHHHHHHccCCccccccCCCChhhEEEEechHHHHHHHHHHHHHH
Confidence 478999999999999999999887775321 158999999999999999999653
No 251
>PRK09694 helicase Cas3; Provisional
Probab=95.72 E-value=0.032 Score=71.52 Aligned_cols=69 Identities=20% Similarity=0.284 Sum_probs=59.2
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
...++-|..+.....++++++|.+|.|+|||..+...+..+.......+|.++.||-..++++++|+.+
T Consensus 285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~Atan~m~~Rl~~ 353 (878)
T PRK09694 285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEA 353 (878)
T ss_pred CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHHHHHHHHHHHHH
Confidence 466888987755445699999999999999999988888887765568999999999999999999875
No 252
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=95.71 E-value=0.031 Score=70.06 Aligned_cols=69 Identities=20% Similarity=0.289 Sum_probs=59.0
Q ss_pred CCCCCCHHHHHHHHHhcC----CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 174 NTIPFTPTQIEAIRAGMQ----PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~----~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
....||+.|..|+..... ...+|++|.+|+|||.+-.++|...+.. |+.+||..|--.=..++.+|+..
T Consensus 195 ~~~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~--GkqvLvLVPEI~Ltpq~~~rf~~ 267 (730)
T COG1198 195 EWLALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ--GKQVLVLVPEIALTPQLLARFKA 267 (730)
T ss_pred cccccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc--CCEEEEEeccccchHHHHHHHHH
Confidence 456899999999987754 3779999999999999999999999998 89999999976666777777654
No 253
>KOG0743|consensus
Probab=95.71 E-value=0.011 Score=69.51 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=20.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISN 853 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ 853 (1051)
..-.|+.||||||||+.|+++...
T Consensus 235 KRGYLLYGPPGTGKSS~IaAmAn~ 258 (457)
T KOG0743|consen 235 KRGYLLYGPPGTGKSSFIAAMANY 258 (457)
T ss_pred hccceeeCCCCCCHHHHHHHHHhh
Confidence 356899999999999999988643
No 254
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=95.71 E-value=0.021 Score=67.76 Aligned_cols=54 Identities=19% Similarity=0.271 Sum_probs=38.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec-ch--HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-SN--QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~-SN--~Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||||+|||||++.+...+.. .+.+|++++- +. .|.+++...-...++
T Consensus 100 ~~vi~lvG~~GvGKTTtaaKLA~~l~~--~G~kV~lV~~D~~R~aA~eQLk~~a~~~~v 156 (429)
T TIGR01425 100 QNVIMFVGLQGSGKTTTCTKLAYYYQR--KGFKPCLVCADTFRAGAFDQLKQNATKARI 156 (429)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEEcCcccchhHHHHHHHHhhccCC
Confidence 468899999999999999999987665 5777766554 43 566666433333333
No 255
>TIGR02881 spore_V_K stage V sporulation protein K. Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.
Probab=95.70 E-value=0.011 Score=65.29 Aligned_cols=26 Identities=35% Similarity=0.342 Sum_probs=21.8
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHH
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYH 218 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~ 218 (1051)
.-.++.||||||||+++..+...+..
T Consensus 43 ~~vll~GppGtGKTtlA~~ia~~l~~ 68 (261)
T TIGR02881 43 LHMIFKGNPGTGKTTVARILGKLFKE 68 (261)
T ss_pred ceEEEEcCCCCCHHHHHHHHHHHHHh
Confidence 34789999999999999888777654
No 256
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=95.69 E-value=0.03 Score=66.43 Aligned_cols=54 Identities=19% Similarity=0.287 Sum_probs=38.4
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe-CCH--HHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HSN--QALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a-~SN--~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||||+|||||++.+...+... +.+|++++ -+. .|++++...-...++
T Consensus 100 ~~vi~lvG~~GvGKTTtaaKLA~~l~~~--G~kV~lV~~D~~R~aA~eQLk~~a~~~~v 156 (429)
T TIGR01425 100 QNVIMFVGLQGSGKTTTCTKLAYYYQRK--GFKPCLVCADTFRAGAFDQLKQNATKARI 156 (429)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHC--CCCEEEEcCcccchhHHHHHHHHhhccCC
Confidence 5688999999999999999998876654 66776654 343 577776443333444
No 257
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).
Probab=95.68 E-value=0.023 Score=66.37 Aligned_cols=50 Identities=20% Similarity=0.421 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 866 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~ 866 (1051)
.+.+...+.+.. ..++.+|.||+|+||||++..++..+..+.++.+|+.+
T Consensus 136 gl~~~~~~~l~~--~~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~Ivti 185 (372)
T TIGR02525 136 GIEPDLFNSLLP--AAGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTY 185 (372)
T ss_pred CCCHHHHHHHHh--cCCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEE
Confidence 455555554432 47899999999999999999999988765455666654
No 258
>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=95.68 E-value=0.014 Score=62.32 Aligned_cols=36 Identities=33% Similarity=0.563 Sum_probs=31.2
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
..+++|.||||||||+++.+++.....+ +.+++.++
T Consensus 19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~--g~~v~yi~ 54 (218)
T cd01394 19 GTVTQVYGPPGTGKTNIAIQLAVETAGQ--GKKVAYID 54 (218)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEE
Confidence 5679999999999999999999988766 77887775
No 259
>PF05729 NACHT: NACHT domain
Probab=95.66 E-value=0.018 Score=57.67 Aligned_cols=29 Identities=24% Similarity=0.504 Sum_probs=25.8
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFP 221 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p 221 (1051)
.+.+|.|+||+|||+++..++..+....+
T Consensus 1 r~l~I~G~~G~GKStll~~~~~~~~~~~~ 29 (166)
T PF05729_consen 1 RVLWISGEPGSGKSTLLRKLAQQLAEEEP 29 (166)
T ss_pred CEEEEECCCCCChHHHHHHHHHHHHhcCc
Confidence 36799999999999999999999988754
No 260
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=95.66 E-value=0.028 Score=63.21 Aligned_cols=50 Identities=24% Similarity=0.422 Sum_probs=35.6
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC-CH--HHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-SN--QALNQLFEK 241 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~-SN--~Avd~l~~r 241 (1051)
+.+.+|.||+|+|||||++.+...+.....+.+|.+++- +. .|++++...
T Consensus 194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~ 246 (282)
T TIGR03499 194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTY 246 (282)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHH
Confidence 347889999999999999999988875433467776653 32 355555443
No 261
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=95.66 E-value=0.015 Score=77.05 Aligned_cols=53 Identities=25% Similarity=0.345 Sum_probs=46.2
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHh-CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHN-FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~-~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
..++|.+++|||||+++++.+..++.. .+.++||++|.||.|+.++.+||.+.
T Consensus 11 ~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~ 64 (1141)
T TIGR02784 11 TSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDR 64 (1141)
T ss_pred CCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHH
Confidence 457899999999999999999888853 34689999999999999999999754
No 262
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=95.66 E-value=0.023 Score=66.21 Aligned_cols=41 Identities=34% Similarity=0.533 Sum_probs=30.6
Q ss_pred HHHHHHHHHhc-------CCCeEEEEccCCCChHHHHHHHHHHHHHcC
Q psy12659 180 PTQIEAIRAGM-------QPGLTLVVGPPGTGKTDVAVQIISNLYHNF 220 (1051)
Q Consensus 180 ~~Q~~Ai~~~l-------~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~ 220 (1051)
+.|.+.+...+ .++..+|.||||||||+++..++..+-...
T Consensus 36 e~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~ 83 (394)
T PRK00411 36 EEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIA 83 (394)
T ss_pred HHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhc
Confidence 45555555443 245689999999999999999998887653
No 263
>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=95.66 E-value=0.018 Score=62.44 Aligned_cols=53 Identities=26% Similarity=0.511 Sum_probs=41.2
Q ss_pred hcCC-CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHH
Q psy12659 189 GMQP-GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKII 243 (1051)
Q Consensus 189 ~l~~-~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~ 243 (1051)
++.+ .+++|.||||||||+++.+++.++..+. +.+++.++.-..+ .++..|+.
T Consensus 9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~-g~~vly~s~E~~~-~~~~~r~~ 62 (242)
T cd00984 9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQ-GKPVLFFSLEMSK-EQLLQRLL 62 (242)
T ss_pred CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC-CCceEEEeCCCCH-HHHHHHHH
Confidence 5554 4899999999999999999999888763 6788888865544 45566664
No 264
>KOG1804|consensus
Probab=95.64 E-value=0.0046 Score=77.14 Aligned_cols=64 Identities=28% Similarity=0.320 Sum_probs=52.4
Q ss_pred HHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHH
Q psy12659 180 PTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKII 243 (1051)
Q Consensus 180 ~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~ 243 (1051)
..|..++-..-......+.||||||||.++++.+..+.-..+...+++|+++|.|.|++..++.
T Consensus 314 ~~~~~~~~~~~~~~~y~~~~p~~~g~~~n~~~a~~~v~~~~~~~~il~~~p~~a~~k~~~~rl~ 377 (775)
T KOG1804|consen 314 EEQALHLLLCRLPEPYIVFGPPGTGKTENYREAIAIVSFTSPHFYILVCAPSNASGKQPAHRLH 377 (775)
T ss_pred hhhhhhhcccccccccccccCCCcCCccchHHHHHHHHhcchHHHhhccccccccccccccccc
Confidence 3444442222336779999999999999999988888888888999999999999999999983
No 265
>TIGR02533 type_II_gspE general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.
Probab=95.64 E-value=0.014 Score=70.40 Aligned_cols=51 Identities=25% Similarity=0.449 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEE
Q psy12659 813 PFKLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLI 865 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV 865 (1051)
...+++.|.+.+..++. .++.+|.||+|+|||||+..++..+.. ++.+|+.
T Consensus 223 ~Lg~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL~a~L~~l~~--~~~~iiT 275 (486)
T TIGR02533 223 TLGMSPELLSRFERLIRRPHGIILVTGPTGSGKTTTLYAALSRLNT--PERNILT 275 (486)
T ss_pred HcCCCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHhccCC--CCCcEEE
Confidence 35788999999998876 689999999999999999988877643 3444443
No 266
>cd01131 PilT Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.
Probab=95.64 E-value=0.015 Score=61.80 Aligned_cols=38 Identities=32% Similarity=0.597 Sum_probs=29.2
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
.|+.+|.||+|+||||++..++..+... .+.+|+.+-.
T Consensus 1 ~GlilI~GptGSGKTTll~~ll~~~~~~-~~~~i~t~e~ 38 (198)
T cd01131 1 RGLVLVTGPTGSGKSTTLAAMIDYINKN-KTHHILTIED 38 (198)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHhhhc-CCcEEEEEcC
Confidence 4789999999999999999988877643 2446665544
No 267
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family. Members of this family are assumed to differ from each other in DNA site specificity.
Probab=95.63 E-value=0.021 Score=71.63 Aligned_cols=69 Identities=16% Similarity=0.195 Sum_probs=58.6
Q ss_pred CHHHHHHHHHhcC----------CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCC
Q psy12659 817 TFHEIEAIRAGMQ----------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 885 (1051)
Q Consensus 817 n~~Q~~Ai~~~l~----------~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~ 885 (1051)
-..|..||..+.. ..-.+|+-|.|||||.|++.++..|+......+||+++++..=++++.+.+...+.
T Consensus 240 r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~ 318 (667)
T TIGR00348 240 RYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQK 318 (667)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCC
Confidence 3458888887633 24689999999999999999999998766778999999999999999999887754
No 268
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.63 E-value=0.035 Score=68.39 Aligned_cols=69 Identities=17% Similarity=0.212 Sum_probs=55.0
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHH-HHHHHHHhC-------CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNF-------PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~-iI~~ll~~~-------~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|.++|..++...=.++++|.|||||.+..- ++..++... .+.++||++||..-+.++.+.+...
T Consensus 31 ~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l 107 (572)
T PRK04537 31 RCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKF 107 (572)
T ss_pred CCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHH
Confidence 56889999999999987899999999999987644 344444321 1358999999999999998887665
No 269
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family. Members of this family are assumed to differ from each other in DNA site specificity.
Probab=95.63 E-value=0.022 Score=71.33 Aligned_cols=69 Identities=17% Similarity=0.164 Sum_probs=58.4
Q ss_pred CHHHHHHHHHhcC----------CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 179 TPTQIEAIRAGMQ----------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 179 n~~Q~~Ai~~~l~----------~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
-..|..||..+.. .+-.+|+-|.|||||.|++.++..++...+..+||+++++..=++++.+.+...+.
T Consensus 240 r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~ 318 (667)
T TIGR00348 240 RYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQK 318 (667)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCC
Confidence 3569889876531 34689999999999999999999998776778999999999999999999987653
No 270
>PRK06835 DNA replication protein DnaC; Validated
Probab=95.63 E-value=0.022 Score=65.56 Aligned_cols=37 Identities=27% Similarity=0.259 Sum_probs=31.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
....++.||||||||+++..+...++.. +.+|+.++-
T Consensus 183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~--g~~V~y~t~ 219 (329)
T PRK06835 183 NENLLFYGNTGTGKTFLSNCIAKELLDR--GKSVIYRTA 219 (329)
T ss_pred CCcEEEECCCCCcHHHHHHHHHHHHHHC--CCeEEEEEH
Confidence 4668999999999999999999999876 677766553
No 271
>PHA00729 NTP-binding motif containing protein
Probab=95.63 E-value=0.023 Score=61.95 Aligned_cols=24 Identities=25% Similarity=0.632 Sum_probs=21.8
Q ss_pred eEEEECCCCCChhHHHHHHHHHHH
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLY 855 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll 855 (1051)
..+|.|||||||||++..+...+.
T Consensus 19 nIlItG~pGvGKT~LA~aLa~~l~ 42 (226)
T PHA00729 19 SAVIFGKQGSGKTTYALKVARDVF 42 (226)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHH
Confidence 588999999999999999988865
No 272
>PRK10436 hypothetical protein; Provisional
Probab=95.62 E-value=0.013 Score=70.24 Aligned_cols=53 Identities=30% Similarity=0.483 Sum_probs=41.9
Q ss_pred CCCCCCCHHHHHHHHHhc--CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEE
Q psy12659 173 KNTIPFTPTQIEAIRAGM--QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLI 227 (1051)
Q Consensus 173 ~~~~~ln~~Q~~Ai~~~l--~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv 227 (1051)
.....+.+.|.+.+..++ ..|+.+|.||+|+|||||+.+++..+.. ++.+|+-
T Consensus 197 L~~LG~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL~a~l~~~~~--~~~~i~T 251 (462)
T PRK10436 197 LETLGMTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTLYSALQTLNT--AQINICS 251 (462)
T ss_pred HHHcCcCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHHHHHHHhhCC--CCCEEEE
Confidence 345678899999998875 4899999999999999999998887643 2455543
No 273
>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=95.61 E-value=0.082 Score=67.17 Aligned_cols=70 Identities=14% Similarity=0.086 Sum_probs=57.9
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
..+++-|.+||..++...=.+++.|.|||||-...- ++..+.. .++.++|+++||.+=+.++...+.+.+
T Consensus 35 ~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~-~~~~~aL~l~PtraLa~q~~~~l~~l~ 105 (742)
T TIGR03817 35 HRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALAD-DPRATALYLAPTKALAADQLRAVRELT 105 (742)
T ss_pred CcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhh-CCCcEEEEEcChHHHHHHHHHHHHHhc
Confidence 368999999999999877789999999999976544 3444443 467799999999999999999988765
No 274
>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=95.61 E-value=0.041 Score=66.10 Aligned_cols=74 Identities=22% Similarity=0.247 Sum_probs=56.5
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCcEEEe
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLRL 255 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~lvRl 255 (1051)
..|++.|.+||..++...-.+|+.|+|+|||.+ .++-.+.. +..+||++|+..=+.+..+++...|+ ...-+
T Consensus 10 ~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~--y~lp~l~~---~~~~lVi~P~~~L~~dq~~~l~~~gi---~~~~l 81 (470)
T TIGR00614 10 SSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLC--YQLPALCS---DGITLVISPLISLMEDQVLQLKASGI---PATFL 81 (470)
T ss_pred CCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHH--HHHHHHHc---CCcEEEEecHHHHHHHHHHHHHHcCC---cEEEE
Confidence 368899999999999876789999999999954 23333332 55799999999888888888888776 34444
Q ss_pred cC
Q psy12659 256 GH 257 (1051)
Q Consensus 256 G~ 257 (1051)
++
T Consensus 82 ~~ 83 (470)
T TIGR00614 82 NS 83 (470)
T ss_pred eC
Confidence 43
No 275
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=95.60 E-value=0.021 Score=72.92 Aligned_cols=61 Identities=10% Similarity=0.154 Sum_probs=46.6
Q ss_pred HHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 820 EIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 820 Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.+..|..++. +...+|+||||||||+.+...+..-. ..+.+|+|+.|+..|+.++.+++.+
T Consensus 9 ~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~--~~~~~ilvlqPrR~aA~qia~rva~ 70 (812)
T PRK11664 9 VLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHG--GINGKIIMLEPRRLAARNVAQRLAE 70 (812)
T ss_pred HHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcC--CcCCeEEEECChHHHHHHHHHHHHH
Confidence 4455555554 78899999999999999876544321 2345899999999999999999854
No 276
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=95.60 E-value=0.0084 Score=59.21 Aligned_cols=21 Identities=38% Similarity=0.877 Sum_probs=18.1
Q ss_pred eEEEEccCCCChHHHHHHHHH
Q psy12659 194 LTLVVGPPGTGKTDVAVQIIS 214 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~ 214 (1051)
+.++.||||+||||++..+..
T Consensus 1 lii~~G~pgsGKSt~a~~l~~ 21 (143)
T PF13671_consen 1 LIILCGPPGSGKSTLAKRLAK 21 (143)
T ss_dssp EEEEEESTTSSHHHHHHHHHH
T ss_pred CEEEECCCCCCHHHHHHHHHH
Confidence 578999999999999887754
No 277
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=95.59 E-value=0.03 Score=62.98 Aligned_cols=49 Identities=24% Similarity=0.451 Sum_probs=35.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecch---HHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN---QALNQLFE 878 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN---~Ald~l~e 878 (1051)
+.+.++.||+|+|||||++.+...+.....+.+|.+++--. .|++++..
T Consensus 194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~ 245 (282)
T TIGR03499 194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKT 245 (282)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHH
Confidence 56899999999999999999998887632236777666432 35555544
No 278
>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.
Probab=95.57 E-value=0.017 Score=62.52 Aligned_cols=38 Identities=24% Similarity=0.442 Sum_probs=31.8
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
....|.||+|+||||++.++...+...+++.+|+.+.-
T Consensus 35 ~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~ 72 (219)
T PF00308_consen 35 NPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSA 72 (219)
T ss_dssp SEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEH
T ss_pred CceEEECCCCCCHHHHHHHHHHHHHhccccccceeecH
Confidence 35799999999999999999999888778888877753
No 279
>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=95.56 E-value=0.036 Score=66.56 Aligned_cols=67 Identities=18% Similarity=0.193 Sum_probs=53.8
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
.+.+.|.+||..++.+.-.+|+.|.|+|||.+. .+..+. .+..+||++|+..=+.+..+++...|++
T Consensus 11 ~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y--~lp~l~---~~~~~lVi~P~~~L~~dq~~~l~~~gi~ 77 (470)
T TIGR00614 11 SFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCY--QLPALC---SDGITLVISPLISLMEDQVLQLKASGIP 77 (470)
T ss_pred CCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHH--HHHHHH---cCCcEEEEecHHHHHHHHHHHHHHcCCc
Confidence 567889999999999778999999999999542 333343 3568999999998888888888877764
No 280
>PRK02362 ski2-like helicase; Provisional
Probab=95.55 E-value=0.034 Score=70.48 Aligned_cols=67 Identities=21% Similarity=0.227 Sum_probs=55.8
Q ss_pred CCCHHHHHHHHHh-cCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAG-MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~-l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.|++.|.+|+..+ +++.-.+|+.|+|+|||.++.-.+...+. ++.++++++|+..=+++..+.+...
T Consensus 23 ~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~--~~~kal~i~P~raLa~q~~~~~~~~ 90 (737)
T PRK02362 23 ELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA--RGGKALYIVPLRALASEKFEEFERF 90 (737)
T ss_pred cCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh--cCCcEEEEeChHHHHHHHHHHHHHh
Confidence 5788999999984 45778999999999999998655555454 5789999999999999999888754
No 281
>KOG0991|consensus
Probab=95.52 E-value=0.013 Score=63.60 Aligned_cols=66 Identities=20% Similarity=0.283 Sum_probs=44.8
Q ss_pred CHHHHHHHHHh---cCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE-eCCHHHHHHHHHHHHh
Q psy12659 179 TPTQIEAIRAG---MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSNQALNQLFEKIIS 244 (1051)
Q Consensus 179 n~~Q~~Ai~~~---l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~-a~SN~Avd~l~~rl~~ 244 (1051)
|+.-.+-+.-. -+-+-.+|.|||||||||.+..+...|+-..-.+-+|=. |...+-+|.+..++..
T Consensus 32 Ne~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~ 101 (333)
T KOG0991|consen 32 NEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKM 101 (333)
T ss_pred CHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHH
Confidence 55444444332 234558999999999999999999988853223445544 4455678888888754
No 282
>PRK06921 hypothetical protein; Provisional
Probab=95.52 E-value=0.016 Score=64.69 Aligned_cols=38 Identities=21% Similarity=0.344 Sum_probs=31.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
....++.||||||||+++..|...+... .+.+|+.++.
T Consensus 117 ~~~l~l~G~~G~GKThLa~aia~~l~~~-~g~~v~y~~~ 154 (266)
T PRK06921 117 KNSIALLGQPGSGKTHLLTAAANELMRK-KGVPVLYFPF 154 (266)
T ss_pred CCeEEEECCCCCcHHHHHHHHHHHHhhh-cCceEEEEEH
Confidence 5678999999999999999999998872 1677777764
No 283
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=95.52 E-value=0.03 Score=65.70 Aligned_cols=56 Identities=20% Similarity=0.182 Sum_probs=40.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHc--CCCCeEEEE-eCC--HHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIV-THS--NQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~--~p~~riLv~-a~S--N~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||+|+|||||++.+...+... ..+.+|.++ +-+ ..|++++.......|+
T Consensus 174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgv 234 (388)
T PRK12723 174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGI 234 (388)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCc
Confidence 5689999999999999999998877643 135667655 444 6688885554444565
No 284
>PRK10436 hypothetical protein; Provisional
Probab=95.52 E-value=0.019 Score=68.89 Aligned_cols=44 Identities=32% Similarity=0.526 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 813 PFKLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
...+.+.|.+.+..++. .|+.+|.||+|+|||||+..++..+..
T Consensus 199 ~LG~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL~a~l~~~~~ 244 (462)
T PRK10436 199 TLGMTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTLYSALQTLNT 244 (462)
T ss_pred HcCcCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHHHHHHHhhCC
Confidence 34778889999998865 799999999999999999998888654
No 285
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=95.51 E-value=0.039 Score=62.90 Aligned_cols=69 Identities=25% Similarity=0.260 Sum_probs=51.6
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec---chHHHHHHHHHHHhcCCCcccccccccccChhhHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH---SNQALNQLFEKIISLDVDERHLLHKKYRITPRYLL 903 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~---SN~Ald~l~e~l~~~~~~~~~llRlgsritpr~l~ 903 (1051)
+-+.++.|..|||||||++.+...+.. .|++|+++|- --.|+++|-.--.+.|+ .++......+|..+.
T Consensus 139 p~Vil~vGVNG~GKTTTIaKLA~~l~~--~g~~VllaA~DTFRAaAiEQL~~w~er~gv---~vI~~~~G~DpAaVa 210 (340)
T COG0552 139 PFVILFVGVNGVGKTTTIAKLAKYLKQ--QGKSVLLAAGDTFRAAAIEQLEVWGERLGV---PVISGKEGADPAAVA 210 (340)
T ss_pred cEEEEEEecCCCchHhHHHHHHHHHHH--CCCeEEEEecchHHHHHHHHHHHHHHHhCC---eEEccCCCCCcHHHH
Confidence 678999999999999999999999888 7888888764 45677887776666666 344422335665543
No 286
>TIGR02881 spore_V_K stage V sporulation protein K. Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.
Probab=95.51 E-value=0.015 Score=64.34 Aligned_cols=26 Identities=35% Similarity=0.342 Sum_probs=21.6
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
.-.++.||||||||+++..+...+..
T Consensus 43 ~~vll~GppGtGKTtlA~~ia~~l~~ 68 (261)
T TIGR02881 43 LHMIFKGNPGTGKTTVARILGKLFKE 68 (261)
T ss_pred ceEEEEcCCCCCHHHHHHHHHHHHHh
Confidence 34789999999999999888777654
No 287
>PRK13766 Hef nuclease; Provisional
Probab=95.50 E-value=0.065 Score=68.22 Aligned_cols=82 Identities=26% Similarity=0.298 Sum_probs=62.9
Q ss_pred CCCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC-CCCCCcE
Q psy12659 174 NTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL-DVDERHL 252 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~-~~~~~~l 252 (1051)
+.+..-+-|.+++..++.. -++|+.|.|+|||.++..++..++. .++.++|+++||..-+++..+.+.+. +++...+
T Consensus 12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~-~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v 89 (773)
T PRK13766 12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH-KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKI 89 (773)
T ss_pred CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH-hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceE
Confidence 3355667899999998887 4799999999999988888877774 46789999999998888888888764 3333345
Q ss_pred EEecC
Q psy12659 253 LRLGH 257 (1051)
Q Consensus 253 vRlG~ 257 (1051)
+.+.+
T Consensus 90 ~~~~g 94 (773)
T PRK13766 90 VVFTG 94 (773)
T ss_pred EEEeC
Confidence 55543
No 288
>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []. The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=95.49 E-value=0.016 Score=57.28 Aligned_cols=22 Identities=55% Similarity=0.915 Sum_probs=19.8
Q ss_pred EEEEccCCCChHHHHHHHHHHH
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.++.||||||||+++..+...+
T Consensus 2 vlL~G~~G~GKt~l~~~la~~~ 23 (139)
T PF07728_consen 2 VLLVGPPGTGKTTLARELAALL 23 (139)
T ss_dssp EEEEESSSSSHHHHHHHHHHHH
T ss_pred EEEECCCCCCHHHHHHHHHHHh
Confidence 5899999999999999987776
No 289
>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=95.48 E-value=0.024 Score=62.57 Aligned_cols=55 Identities=15% Similarity=0.245 Sum_probs=42.2
Q ss_pred hcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 827 GMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 827 ~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
++. ..+++|.||||+|||+++.+++.++... .+.+|++++--. ..+.+..++.+.
T Consensus 26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~-~g~~vl~iS~E~-~~~~~~~r~~~~ 81 (271)
T cd01122 26 GLRKGELIILTAGTGVGKTTFLREYALDLITQ-HGVRVGTISLEE-PVVRTARRLLGQ 81 (271)
T ss_pred EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh-cCceEEEEEccc-CHHHHHHHHHHH
Confidence 344 5699999999999999999999988762 278999988644 446666666543
No 290
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=95.48 E-value=0.03 Score=65.18 Aligned_cols=28 Identities=39% Similarity=0.636 Sum_probs=24.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHh
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHN 857 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~ 857 (1051)
++..+|.||||||||+++..+...+-..
T Consensus 55 ~~~~lI~G~~GtGKT~l~~~v~~~l~~~ 82 (394)
T PRK00411 55 PLNVLIYGPPGTGKTTTVKKVFEELEEI 82 (394)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHHHHh
Confidence 4668999999999999999999887653
No 291
>PRK08727 hypothetical protein; Validated
Probab=95.47 E-value=0.029 Score=61.19 Aligned_cols=37 Identities=22% Similarity=0.365 Sum_probs=30.7
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
....+|.||||||||+++..+...+... +.+++.++-
T Consensus 41 ~~~l~l~G~~G~GKThL~~a~~~~~~~~--~~~~~y~~~ 77 (233)
T PRK08727 41 SDWLYLSGPAGTGKTHLALALCAAAEQA--GRSSAYLPL 77 (233)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEeH
Confidence 4568999999999999999999888766 667776653
No 292
>PRK09694 helicase Cas3; Provisional
Probab=95.47 E-value=0.044 Score=70.37 Aligned_cols=70 Identities=19% Similarity=0.296 Sum_probs=59.2
Q ss_pred CCCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 813 PFKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.+..++-|..+......+++++|.+|.|+|||..+...+..++......+|.++.||....|.+++++.+
T Consensus 284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~Atan~m~~Rl~~ 353 (878)
T PRK09694 284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEA 353 (878)
T ss_pred CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHHHHHHHHHHHHH
Confidence 3467788997755445689999999999999999988888887755568999999999999999999864
No 293
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.45 E-value=0.048 Score=65.50 Aligned_cols=70 Identities=24% Similarity=0.314 Sum_probs=54.8
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHH-HHHHHHHHcCC-------CCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAV-QIISNLYHNFP-------HQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~-~ii~~l~~~~p-------~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++-|.+|+..++...=.+|++|.|||||.... -++..+....+ ..++|+++||..-+.++.+.+...
T Consensus 108 ~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l 185 (475)
T PRK01297 108 PYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAAL 185 (475)
T ss_pred CCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHh
Confidence 46899999999999986667899999999996543 34555554321 358999999999999998888765
No 294
>TIGR00959 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
Probab=95.44 E-value=0.041 Score=65.44 Aligned_cols=55 Identities=27% Similarity=0.338 Sum_probs=38.9
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE-ecch--HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSN--QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~-a~SN--~Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||||+|||||++.+...+... .+.+|+++ +.+. .|.+++.......++
T Consensus 99 p~vi~~vG~~GsGKTTtaakLA~~l~~~-~g~kV~lV~~D~~R~~a~~QL~~~a~~~gv 156 (428)
T TIGR00959 99 PTVILMVGLQGSGKTTTCGKLAYYLKKK-QGKKVLLVACDLYRPAAIEQLKVLGQQVGV 156 (428)
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHh-CCCeEEEEeccccchHHHHHHHHHHHhcCC
Confidence 4689999999999999999999987632 45666555 4444 356666555455555
No 295
>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []. The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=95.44 E-value=0.016 Score=57.30 Aligned_cols=42 Identities=36% Similarity=0.506 Sum_probs=28.8
Q ss_pred EEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFE 878 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e 878 (1051)
.++.||||||||+++..+...+ ...-+.+..+++.-.+.+..
T Consensus 2 vlL~G~~G~GKt~l~~~la~~~----~~~~~~i~~~~~~~~~dl~g 43 (139)
T PF07728_consen 2 VLLVGPPGTGKTTLARELAALL----GRPVIRINCSSDTTEEDLIG 43 (139)
T ss_dssp EEEEESSSSSHHHHHHHHHHHH----TCEEEEEE-TTTSTHHHHHC
T ss_pred EEEECCCCCCHHHHHHHHHHHh----hcceEEEEecccccccccee
Confidence 5899999999999998887766 22334455555555555553
No 296
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=95.44 E-value=0.012 Score=56.52 Aligned_cols=23 Identities=35% Similarity=0.840 Sum_probs=20.0
Q ss_pred eEEEECCCCCChhHHHHHHHHHH
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
+.+|.||||+||||++..+...+
T Consensus 1 vI~I~G~~gsGKST~a~~La~~~ 23 (121)
T PF13207_consen 1 VIIISGPPGSGKSTLAKELAERL 23 (121)
T ss_dssp EEEEEESTTSSHHHHHHHHHHHH
T ss_pred CEEEECCCCCCHHHHHHHHHHHH
Confidence 36899999999999999887765
No 297
>PRK06851 hypothetical protein; Provisional
Probab=95.44 E-value=0.013 Score=68.20 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=40.4
Q ss_pred CCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCc--EEEEecchHHHHHHHH
Q psy12659 829 QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQR--TLIVTHSNQALNQLFE 878 (1051)
Q Consensus 829 ~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~r--iLV~a~SN~Ald~l~e 878 (1051)
...+.+|.||||||||+++.+++..+.. .+.. .+.|+..|.++|-+.-
T Consensus 29 ~~~~~il~G~pGtGKStl~~~i~~~~~~--~g~~Ve~~~~~~d~~slDgvii 78 (367)
T PRK06851 29 ANRIFILKGGPGTGKSTLMKKIGEEFLE--KGYDVEFLHCSSDNDSLDGVII 78 (367)
T ss_pred cceEEEEECCCCCCHHHHHHHHHHHHHH--cCCeEEEEEcCCCCCceeeEEe
Confidence 4678999999999999999999999887 4444 7788989999988653
No 298
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=95.42 E-value=0.021 Score=64.70 Aligned_cols=41 Identities=32% Similarity=0.592 Sum_probs=30.9
Q ss_pred CHHHHHHHHHhcC-C--CeEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 179 TPTQIEAIRAGMQ-P--GLTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 179 n~~Q~~Ai~~~l~-~--~~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
++...+.+..++. + +..++.||||||||+++..+...+...
T Consensus 20 ~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~ 63 (337)
T PRK12402 20 QDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGD 63 (337)
T ss_pred CHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCc
Confidence 4556666666554 2 368999999999999999998877643
No 299
>PRK14701 reverse gyrase; Provisional
Probab=95.42 E-value=0.041 Score=74.70 Aligned_cols=68 Identities=21% Similarity=0.250 Sum_probs=54.2
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
+.+++.|.+++..++...-.++++|+|||||.+..- +...+ ..++.++||++||..=+.++.+++...
T Consensus 78 ~~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~-~al~~-~~~g~~aLVl~PTreLa~Qi~~~l~~l 145 (1638)
T PRK14701 78 FEFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAF-IALFL-ALKGKKCYIILPTTLLVKQTVEKIESF 145 (1638)
T ss_pred CCCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHH-HHHHH-HhcCCeEEEEECHHHHHHHHHHHHHHH
Confidence 357889999999999977789999999999994332 22222 224779999999999999999888764
No 300
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=95.40 E-value=0.03 Score=58.34 Aligned_cols=53 Identities=32% Similarity=0.528 Sum_probs=38.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhC--------CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNF--------PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~--------~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
..+++|.||||+|||+++.+++.++.... .+.+||.++.-+. .+.+..++...
T Consensus 32 g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~ 92 (193)
T PF13481_consen 32 GELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRAL 92 (193)
T ss_dssp TSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHH
T ss_pred CeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHH
Confidence 67999999999999999999999988621 3568888876555 55666676554
No 301
>TIGR00959 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
Probab=95.38 E-value=0.044 Score=65.19 Aligned_cols=55 Identities=27% Similarity=0.323 Sum_probs=38.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE-eCCH--HHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSN--QALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~-a~SN--~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||||+|||||++.+...+.... +.+|+++ +-+. .|.+++...-...++
T Consensus 99 p~vi~~vG~~GsGKTTtaakLA~~l~~~~-g~kV~lV~~D~~R~~a~~QL~~~a~~~gv 156 (428)
T TIGR00959 99 PTVILMVGLQGSGKTTTCGKLAYYLKKKQ-GKKVLLVACDLYRPAAIEQLKVLGQQVGV 156 (428)
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHhC-CCeEEEEeccccchHHHHHHHHHHHhcCC
Confidence 45789999999999999999998876432 5666555 4444 356666555444554
No 302
>TIGR00604 rad3 DNA repair helicase (rad3). All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.38 E-value=0.037 Score=69.80 Aligned_cols=67 Identities=18% Similarity=0.199 Sum_probs=52.9
Q ss_pred CHHHHHHHHHhc---C-CCeEEEECCCCCChh-HHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 817 TFHEIEAIRAGM---Q-PGLTLVVGPPGTGKT-DVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 817 n~~Q~~Ai~~~l---~-~~~tlIqGPPGTGKT-~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
=+.|++.+..+. . ++..++.+|.||||| .++...++...++....+|..|+.||.-+.++.+.|...
T Consensus 12 y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~ 83 (705)
T TIGR00604 12 YPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKL 83 (705)
T ss_pred CHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhh
Confidence 568887766653 3 788999999999999 566666666554322379999999999999999999774
No 303
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=95.37 E-value=0.037 Score=63.11 Aligned_cols=58 Identities=26% Similarity=0.307 Sum_probs=47.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC-C--HHHHHHHHHHHHhCCCCCCcEEE
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-S--NQALNQLFEKIISLDVDERHLLR 254 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~-S--N~Avd~l~~rl~~~~~~~~~lvR 254 (1051)
+-+.|+.|-.||||||||..+...+..+ |.+|++.|- | -.|++|+-.--.+.|+ +++.
T Consensus 139 p~Vil~vGVNG~GKTTTIaKLA~~l~~~--g~~VllaA~DTFRAaAiEQL~~w~er~gv---~vI~ 199 (340)
T COG0552 139 PFVILFVGVNGVGKTTTIAKLAKYLKQQ--GKSVLLAAGDTFRAAAIEQLEVWGERLGV---PVIS 199 (340)
T ss_pred cEEEEEEecCCCchHhHHHHHHHHHHHC--CCeEEEEecchHHHHHHHHHHHHHHHhCC---eEEc
Confidence 6679999999999999999999988877 888888753 4 5678888777777776 4555
No 304
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=95.36 E-value=0.032 Score=65.63 Aligned_cols=38 Identities=24% Similarity=0.376 Sum_probs=32.0
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
...+|.||||||||+++..+...+..+.++.+++.++.
T Consensus 137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~ 174 (405)
T TIGR00362 137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS 174 (405)
T ss_pred CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH
Confidence 35789999999999999999888887666788887764
No 305
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=95.35 E-value=0.028 Score=67.16 Aligned_cols=37 Identities=27% Similarity=0.364 Sum_probs=32.2
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
..+|.||||||||+++..+...+....++.+|+.++.
T Consensus 132 ~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~ 168 (440)
T PRK14088 132 PLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS 168 (440)
T ss_pred eEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence 5899999999999999999988888777788887764
No 306
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=95.34 E-value=0.025 Score=64.07 Aligned_cols=40 Identities=33% Similarity=0.557 Sum_probs=29.9
Q ss_pred CHHHHHHHHHhcC-C--CeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 817 TFHEIEAIRAGMQ-P--GLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 817 n~~Q~~Ai~~~l~-~--~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
++...+.+..++. + +..++.||||||||+++..+...+..
T Consensus 20 ~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~ 62 (337)
T PRK12402 20 QDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYG 62 (337)
T ss_pred CHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence 3445555555555 2 36899999999999999998887764
No 307
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.
Probab=95.34 E-value=0.028 Score=59.02 Aligned_cols=49 Identities=16% Similarity=0.346 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE
Q psy12659 815 KLTFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 866 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~ 866 (1051)
.+++.|.+.+..++. ....+|.||+|+||||++..++. ++. +..+++.+
T Consensus 9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll~aL~~-~i~--~~~~~i~i 58 (186)
T cd01130 9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLLNALLA-FIP--PDERIITI 58 (186)
T ss_pred CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHHHHHHh-hcC--CCCCEEEE
Confidence 467889999999888 78899999999999999977655 444 44555544
No 308
>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B ....
Probab=95.34 E-value=0.011 Score=58.45 Aligned_cols=22 Identities=36% Similarity=0.842 Sum_probs=18.9
Q ss_pred eEEEECCCCCChhHHHHHHHHH
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISN 853 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ 853 (1051)
+.++.||||+||||++.++...
T Consensus 1 lii~~G~pgsGKSt~a~~l~~~ 22 (143)
T PF13671_consen 1 LIILCGPPGSGKSTLAKRLAKR 22 (143)
T ss_dssp EEEEEESTTSSHHHHHHHHHHH
T ss_pred CEEEECCCCCCHHHHHHHHHHH
Confidence 5789999999999998887654
No 309
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=95.32 E-value=0.028 Score=68.13 Aligned_cols=55 Identities=27% Similarity=0.350 Sum_probs=46.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCCc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDE 887 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~~ 887 (1051)
+.+++|.||||||||+++.+++.+.+. .+.+++.++.... .+.+.+.+...|++.
T Consensus 273 g~~~li~G~~G~GKT~l~~~~~~~~~~--~g~~~~yis~e~~-~~~i~~~~~~~g~~~ 327 (509)
T PRK09302 273 GSIILVSGATGTGKTLLASKFAEAACR--RGERCLLFAFEES-RAQLIRNARSWGIDL 327 (509)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHHh--CCCcEEEEEecCC-HHHHHHHHHHcCCCh
Confidence 578999999999999999999998887 6889999987654 777888887777653
No 310
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=95.31 E-value=0.066 Score=60.49 Aligned_cols=68 Identities=19% Similarity=0.338 Sum_probs=48.0
Q ss_pred CCHHHHHHHHH---hc-CCCeEEEEccCCCChHHHHHHHHHHHHHcCCC----CeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 178 FTPTQIEAIRA---GM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPH----QRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 178 ln~~Q~~Ai~~---~l-~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~----~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.-+.|.+-+.. ++ ..+..+|..|+|||||..+.-.+...+...+. .+|+++++|+.-..++...+.+.
T Consensus 9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~ 84 (289)
T smart00489 9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL 84 (289)
T ss_pred CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence 36789885443 33 47789999999999997666554333333333 38999999998888877776554
No 311
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=95.31 E-value=0.066 Score=60.49 Aligned_cols=68 Identities=19% Similarity=0.338 Sum_probs=48.0
Q ss_pred CCHHHHHHHHH---hc-CCCeEEEEccCCCChHHHHHHHHHHHHHcCCC----CeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 178 FTPTQIEAIRA---GM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPH----QRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 178 ln~~Q~~Ai~~---~l-~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~----~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
.-+.|.+-+.. ++ ..+..+|..|+|||||..+.-.+...+...+. .+|+++++|+.-..++...+.+.
T Consensus 9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~ 84 (289)
T smart00488 9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL 84 (289)
T ss_pred CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence 36789885443 33 47789999999999997666554333333333 38999999998888877776554
No 312
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
Probab=95.27 E-value=0.021 Score=70.26 Aligned_cols=45 Identities=29% Similarity=0.490 Sum_probs=38.4
Q ss_pred CCCCCCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 173 KNTIPFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 173 ~~~~~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
.....+.+.|.+.+..++. .|+.+|.||+|+|||||+..++..+.
T Consensus 295 l~~lg~~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl~a~l~~~~ 341 (564)
T TIGR02538 295 IDKLGFEPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSLYTALNILN 341 (564)
T ss_pred HHHcCCCHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHhhC
Confidence 3456789999999998764 79999999999999999999888663
No 313
>PF13173 AAA_14: AAA domain
Probab=95.26 E-value=0.031 Score=54.98 Aligned_cols=43 Identities=23% Similarity=0.470 Sum_probs=34.1
Q ss_pred CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHH
Q psy12659 191 QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALN 236 (1051)
Q Consensus 191 ~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd 236 (1051)
+..+.+|.||.|+||||++.+++..+. ++++++.+.-.+....
T Consensus 1 n~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~ 43 (128)
T PF13173_consen 1 NRKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDR 43 (128)
T ss_pred CCCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHH
Confidence 357899999999999999999998888 3567777766554443
No 314
>PHA02653 RNA helicase NPH-II; Provisional
Probab=95.26 E-value=0.032 Score=69.78 Aligned_cols=65 Identities=14% Similarity=0.166 Sum_probs=49.8
Q ss_pred HHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHH---------HHH----cCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 180 PTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISN---------LYH----NFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 180 ~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~---------l~~----~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
..|.+++...+.+...+++|++|||||+.+-+++.. .+. ...+.+|+|++|+..++.++.+++.+
T Consensus 167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~ 244 (675)
T PHA02653 167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLK 244 (675)
T ss_pred HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHH
Confidence 367777777788888999999999999987665432 111 22346899999999999998888865
No 315
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=95.26 E-value=0.032 Score=61.23 Aligned_cols=41 Identities=22% Similarity=0.314 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHh---cC--CCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 177 PFTPTQIEAIRAG---MQ--PGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~---l~--~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
-.++.+.+|+... +. +++.+|.||||+|||+++..+...+-
T Consensus 23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~ 68 (269)
T TIGR03015 23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLD 68 (269)
T ss_pred CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcC
Confidence 3456667676643 23 56899999999999999998865543
No 316
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=95.25 E-value=0.032 Score=66.68 Aligned_cols=39 Identities=23% Similarity=0.331 Sum_probs=32.8
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecc
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 869 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~S 869 (1051)
+..+|.||||||||+++..+...+..++++.+++.+...
T Consensus 149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~ 187 (450)
T PRK00149 149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSE 187 (450)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHH
Confidence 458999999999999999999998887677888776543
No 317
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=95.25 E-value=0.06 Score=65.56 Aligned_cols=70 Identities=27% Similarity=0.248 Sum_probs=53.9
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHH-HHHHHHHHHc-------CCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVA-VQIISNLYHN-------FPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti-~~ii~~l~~~-------~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
..+++-|.+|+..+++..-.++++|+|||||... .-++.++... ..+.++||++||..-+.++.+.+...
T Consensus 142 ~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l 219 (518)
T PLN00206 142 EFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVL 219 (518)
T ss_pred CCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHH
Confidence 3679999999999998777999999999999753 3345554421 13568999999998888877666544
No 318
>TIGR00604 rad3 DNA repair helicase (rad3). All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.25 E-value=0.035 Score=70.10 Aligned_cols=67 Identities=21% Similarity=0.282 Sum_probs=50.8
Q ss_pred CHHHHHHHHHh---c-CCCeEEEEccCCCChH-HHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 179 TPTQIEAIRAG---M-QPGLTLVVGPPGTGKT-DVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 179 n~~Q~~Ai~~~---l-~~~~~lI~GPPGTGKT-~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
=+.|++.+..+ + ..+..++..|+||||| .+++..++...+.....+|..|+.||.-+.++.+-|...
T Consensus 12 y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~ 83 (705)
T TIGR00604 12 YPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKL 83 (705)
T ss_pred CHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhh
Confidence 36888887654 3 3788999999999999 555555554444422369999999999999999888764
No 319
>PRK05642 DNA replication initiation factor; Validated
Probab=95.25 E-value=0.026 Score=61.73 Aligned_cols=36 Identities=11% Similarity=0.206 Sum_probs=29.0
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
...+|+||+||||||++..+...+.. .+.+++.++.
T Consensus 46 ~~l~l~G~~G~GKTHLl~a~~~~~~~--~~~~v~y~~~ 81 (234)
T PRK05642 46 SLIYLWGKDGVGRSHLLQAACLRFEQ--RGEPAVYLPL 81 (234)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHh--CCCcEEEeeH
Confidence 56899999999999998888766665 4678877765
No 320
>PTZ00110 helicase; Provisional
Probab=95.24 E-value=0.055 Score=66.36 Aligned_cols=71 Identities=15% Similarity=0.165 Sum_probs=55.3
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHH-HHHHHHHHHc-----CCCCeEEEEeCCHHHHHHHHHHHHhCC
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVA-VQIISNLYHN-----FPHQRTLIVTHSNQALNQLFEKIISLD 246 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti-~~ii~~l~~~-----~p~~riLv~a~SN~Avd~l~~rl~~~~ 246 (1051)
..+++-|.+|+-.+++..=.++++|.|||||... .-++.++... ..+..+||++||..-+.++.+.+.+.+
T Consensus 151 ~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~ 227 (545)
T PTZ00110 151 TEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFG 227 (545)
T ss_pred CCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHh
Confidence 4688999999999998666789999999999863 3344444432 124579999999999999998887754
No 321
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=95.24 E-value=0.025 Score=67.44 Aligned_cols=48 Identities=29% Similarity=0.475 Sum_probs=41.6
Q ss_pred CCCCCCCCHHHHHHHHHhcC--CCeEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 172 RKNTIPFTPTQIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 172 ~~~~~~ln~~Q~~Ai~~~l~--~~~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
..+...+++.|.+.+..+++ .|+.||.||.|+|||||+-+++..+...
T Consensus 236 ~l~~Lg~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTLY~~L~~ln~~ 285 (500)
T COG2804 236 DLEKLGMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTLYAALSELNTP 285 (500)
T ss_pred CHHHhCCCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHHHHHHHHhcCC
Confidence 34556789999999999886 7999999999999999999999988754
No 322
>PRK11823 DNA repair protein RadA; Provisional
Probab=95.24 E-value=0.037 Score=66.21 Aligned_cols=54 Identities=22% Similarity=0.360 Sum_probs=43.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+++|.||||+|||+++.++...+..+ +.++|.++.. ...+++..+....+++
T Consensus 80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~--g~~vlYvs~E-es~~qi~~ra~rlg~~ 133 (446)
T PRK11823 80 GSVVLIGGDPGIGKSTLLLQVAARLAAA--GGKVLYVSGE-ESASQIKLRAERLGLP 133 (446)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEcc-ccHHHHHHHHHHcCCC
Confidence 5579999999999999999999988765 6788888754 3457787777666653
No 323
>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5). All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity
Probab=95.23 E-value=0.026 Score=54.06 Aligned_cols=24 Identities=33% Similarity=0.760 Sum_probs=21.8
Q ss_pred EEECCCCCChhHHHHHHHHHHHHh
Q psy12659 834 LVVGPPGTGKTDVAVQIISNLYHN 857 (1051)
Q Consensus 834 lIqGPPGTGKT~ti~~iI~~ll~~ 857 (1051)
.|.||||+|||+++..++..++..
T Consensus 2 ~i~G~~G~GKS~l~~~l~~~l~~~ 25 (107)
T PF00910_consen 2 WIYGPPGIGKSTLAKELAKDLLKH 25 (107)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHH
Confidence 589999999999999999988864
No 324
>PRK13767 ATP-dependent helicase; Provisional
Probab=95.23 E-value=0.052 Score=70.13 Aligned_cols=67 Identities=28% Similarity=0.295 Sum_probs=52.9
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHH-HHHHHHHc------CCCCeEEEEeCCHHHHHHHHHHHH
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHN------FPHQRTLIVTHSNQALNQLFEKII 243 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~-ii~~l~~~------~p~~riLv~a~SN~Avd~l~~rl~ 243 (1051)
.+++-|.+|+..++...-.+|+.|+|||||....- ++..++.. .++.++|+++|+.+-++++..++.
T Consensus 32 ~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~ 105 (876)
T PRK13767 32 TFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLE 105 (876)
T ss_pred CCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHH
Confidence 58999999999998877899999999999987554 45555532 124579999999988888776654
No 325
>PF05729 NACHT: NACHT domain
Probab=95.22 E-value=0.031 Score=55.89 Aligned_cols=28 Identities=25% Similarity=0.534 Sum_probs=25.1
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCC
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFP 859 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~ 859 (1051)
+.+|.|+||+|||+++..++..+.....
T Consensus 2 ~l~I~G~~G~GKStll~~~~~~~~~~~~ 29 (166)
T PF05729_consen 2 VLWISGEPGSGKSTLLRKLAQQLAEEEP 29 (166)
T ss_pred EEEEECCCCCChHHHHHHHHHHHHhcCc
Confidence 6799999999999999999999888554
No 326
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=95.22 E-value=0.039 Score=64.66 Aligned_cols=54 Identities=17% Similarity=0.300 Sum_probs=41.3
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe-CCH--HHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HSN--QALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a-~SN--~Avd~l~~rl~~~~~ 247 (1051)
+...+|.||+|+||||+++.+...+... +.++++++ -+. .|++++.......++
T Consensus 241 ~~vI~LVGptGvGKTTTiaKLA~~L~~~--GkkVglI~aDt~RiaAvEQLk~yae~lgi 297 (436)
T PRK11889 241 VQTIALIGPTGVGKTTTLAKMAWQFHGK--KKTVGFITTDHSRIGTVQQLQDYVKTIGF 297 (436)
T ss_pred CcEEEEECCCCCcHHHHHHHHHHHHHHc--CCcEEEEecCCcchHHHHHHHHHhhhcCC
Confidence 4678999999999999999999887755 66776664 354 488888776555554
No 327
>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=95.22 E-value=0.036 Score=61.24 Aligned_cols=54 Identities=15% Similarity=0.265 Sum_probs=41.5
Q ss_pred hcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 189 GMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 189 ~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
++. ..+++|.||||+|||+++.+++.++.... +.++++++--. ..+++..++..
T Consensus 26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~-g~~vl~iS~E~-~~~~~~~r~~~ 80 (271)
T cd01122 26 GLRKGELIILTAGTGVGKTTFLREYALDLITQH-GVRVGTISLEE-PVVRTARRLLG 80 (271)
T ss_pred EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhc-CceEEEEEccc-CHHHHHHHHHH
Confidence 443 56899999999999999999988887543 67898888654 34667777654
No 328
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=95.22 E-value=0.033 Score=64.94 Aligned_cols=67 Identities=21% Similarity=0.318 Sum_probs=51.6
Q ss_pred CCHHHHHHHHHhcC-------CCeEEEEccCCCChHHHHHHHHHHHHHcCCCC-eEEEEeCCHHHHHHHHHHHHh
Q psy12659 178 FTPTQIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQ-RTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 178 ln~~Q~~Ai~~~l~-------~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~-riLv~a~SN~Avd~l~~rl~~ 244 (1051)
-=++|.+.+..++. +.-.+|-||||||||.++..++..+....++. -+-|=|..+.-..+++.+|.+
T Consensus 21 ~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~ 95 (366)
T COG1474 21 HREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILN 95 (366)
T ss_pred ccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHH
Confidence 34577777765442 44489999999999999999999999876655 456667777777888888876
No 329
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.
Probab=95.21 E-value=0.029 Score=58.93 Aligned_cols=49 Identities=22% Similarity=0.457 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHhcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE
Q psy12659 177 PFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 228 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~ 228 (1051)
.+++.|.+.+..++. ....+|.||+|+||||++..++..+ . +..+++.+
T Consensus 9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll~aL~~~i-~--~~~~~i~i 58 (186)
T cd01130 9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLLNALLAFI-P--PDERIITI 58 (186)
T ss_pred CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHHHHHHhhc-C--CCCCEEEE
Confidence 468899999998876 6789999999999999998876543 2 35566554
No 330
>PRK14701 reverse gyrase; Provisional
Probab=95.21 E-value=0.047 Score=74.17 Aligned_cols=67 Identities=18% Similarity=0.221 Sum_probs=54.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|++++..++++.-.++++|+|||||.... ++...+ ..++.++||++||..=+.++.+.+...
T Consensus 79 ~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~-~~al~~-~~~g~~aLVl~PTreLa~Qi~~~l~~l 145 (1638)
T PRK14701 79 EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGA-FIALFL-ALKGKKCYIILPTTLLVKQTVEKIESF 145 (1638)
T ss_pred CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHH-HHHHHH-HhcCCeEEEEECHHHHHHHHHHHHHHH
Confidence 5778899999999998889999999999999433 333222 225779999999999999999988764
No 331
>PRK08939 primosomal protein DnaI; Reviewed
Probab=95.21 E-value=0.023 Score=64.71 Aligned_cols=36 Identities=17% Similarity=0.184 Sum_probs=30.9
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
.-.++.||||||||+++.++...+.. .+.++.++..
T Consensus 157 ~gl~L~G~~G~GKThLa~Aia~~l~~--~g~~v~~~~~ 192 (306)
T PRK08939 157 KGLYLYGDFGVGKSYLLAAIANELAK--KGVSSTLLHF 192 (306)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHH--cCCCEEEEEH
Confidence 46899999999999999999999987 6777777654
No 332
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=95.19 E-value=0.041 Score=64.52 Aligned_cols=54 Identities=17% Similarity=0.287 Sum_probs=41.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec-ch--HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-SN--QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~-SN--~Ald~l~e~l~~~~~ 885 (1051)
+...++.||+|+||||+++.+...+.. .+.+|++++- +. .|++++.......++
T Consensus 241 ~~vI~LVGptGvGKTTTiaKLA~~L~~--~GkkVglI~aDt~RiaAvEQLk~yae~lgi 297 (436)
T PRK11889 241 VQTIALIGPTGVGKTTTLAKMAWQFHG--KKKTVGFITTDHSRIGTVQQLQDYVKTIGF 297 (436)
T ss_pred CcEEEEECCCCCcHHHHHHHHHHHHHH--cCCcEEEEecCCcchHHHHHHHHHhhhcCC
Confidence 467899999999999999999988775 5777766554 44 488887765555554
No 333
>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.
Probab=95.18 E-value=0.044 Score=57.25 Aligned_cols=59 Identities=19% Similarity=0.333 Sum_probs=38.7
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH--HHHHHHHHHHHhCCCCCCcEEEecCCc
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN--QALNQLFEKIISLDVDERHLLRLGHGE 259 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN--~Avd~l~~rl~~~~~~~~~lvRlG~~~ 259 (1051)
|+++|.|..|+||||++.+++. ....+.|+.|+..=- ..+|. +.+.+.++ .++.++++.
T Consensus 1 Pv~ii~GfLGsGKTTli~~ll~---~~~~~~~~~vI~ne~g~~~iD~--~~l~~~~~---~v~~l~~gc 61 (178)
T PF02492_consen 1 PVIIITGFLGSGKTTLINHLLK---RNRQGERVAVIVNEFGEVNIDA--ELLQEDGV---PVVELNNGC 61 (178)
T ss_dssp -EEEEEESTTSSHHHHHHHHHH---HHTTTS-EEEEECSTTSTHHHH--HHHHTTT----EEEEECTTT
T ss_pred CEEEEEcCCCCCHHHHHHHHHH---HhcCCceeEEEEccccccccch--hhhcccce---EEEEecCCC
Confidence 5799999999999999999988 333478888886422 22332 23333433 588887764
No 334
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=95.14 E-value=0.034 Score=66.42 Aligned_cols=39 Identities=23% Similarity=0.331 Sum_probs=33.0
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 231 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~S 231 (1051)
+..+|.||||||||+++..+...+..+.|+.+++.++..
T Consensus 149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~ 187 (450)
T PRK00149 149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSE 187 (450)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHH
Confidence 458999999999999999999999888777777776543
No 335
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.12 E-value=0.069 Score=64.19 Aligned_cols=69 Identities=22% Similarity=0.272 Sum_probs=54.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHH-HHHHHHHHHhCC-------CCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVA-VQIISNLYHNFP-------HQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti-~~iI~~ll~~~~-------~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++.|.+|+..++++.-.+|++|.|||||... .-++..++.+.+ +.++||++||..-+.++.+.+...
T Consensus 109 ~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l 185 (475)
T PRK01297 109 YCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAAL 185 (475)
T ss_pred CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHh
Confidence 578899999999999877899999999999654 334455554321 358999999999999988877654
No 336
>PHA02653 RNA helicase NPH-II; Provisional
Probab=95.12 E-value=0.05 Score=68.11 Aligned_cols=64 Identities=13% Similarity=0.209 Sum_probs=50.8
Q ss_pred HHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHH------HH-------hCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 819 HEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNL------YH-------NFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 819 ~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~l------l~-------~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
.|.+++...+.+...+++||+|||||+.+-+++... +. ...+.+|+|++|+..++.++.+.+.+
T Consensus 168 iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~ 244 (675)
T PHA02653 168 VQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLK 244 (675)
T ss_pred HHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHH
Confidence 488999999999999999999999998876655321 11 22356899999999999898888865
No 337
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
Probab=95.10 E-value=0.029 Score=68.95 Aligned_cols=44 Identities=23% Similarity=0.360 Sum_probs=37.9
Q ss_pred CCCCCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHH
Q psy12659 812 PPFKLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLY 855 (1051)
Q Consensus 812 ~~~~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll 855 (1051)
....+.+.|.+.+..++. .|+.+|.||+|+|||||+..++..+.
T Consensus 296 ~~lg~~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl~a~l~~~~ 341 (564)
T TIGR02538 296 DKLGFEPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSLYTALNILN 341 (564)
T ss_pred HHcCCCHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHhhC
Confidence 345788899999998876 79999999999999999999888764
No 338
>cd01131 PilT Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.
Probab=95.10 E-value=0.028 Score=59.80 Aligned_cols=38 Identities=32% Similarity=0.597 Sum_probs=28.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
.|+.+|.||+|+||||++..++..+... .+.+|+....
T Consensus 1 ~GlilI~GptGSGKTTll~~ll~~~~~~-~~~~i~t~e~ 38 (198)
T cd01131 1 RGLVLVTGPTGSGKSTTLAAMIDYINKN-KTHHILTIED 38 (198)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHhhhc-CCcEEEEEcC
Confidence 4789999999999999999888877642 2345554443
No 339
>PRK11823 DNA repair protein RadA; Provisional
Probab=95.07 E-value=0.039 Score=66.00 Aligned_cols=54 Identities=22% Similarity=0.364 Sum_probs=42.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
..+++|.||||+|||+++.++..++.. .+.+++.++.- ...+++..+..+.+++
T Consensus 80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~--~g~~vlYvs~E-es~~qi~~ra~rlg~~ 133 (446)
T PRK11823 80 GSVVLIGGDPGIGKSTLLLQVAARLAA--AGGKVLYVSGE-ESASQIKLRAERLGLP 133 (446)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEEcc-ccHHHHHHHHHHcCCC
Confidence 568999999999999999999998776 57788888753 4556777766666553
No 340
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=95.05 E-value=0.029 Score=66.00 Aligned_cols=38 Identities=24% Similarity=0.376 Sum_probs=32.3
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
+..+|.||||||||+++..+...+..+.++.+++.++.
T Consensus 137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~ 174 (405)
T TIGR00362 137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS 174 (405)
T ss_pred CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH
Confidence 45789999999999999999998888777778877754
No 341
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=95.03 E-value=0.048 Score=64.82 Aligned_cols=56 Identities=21% Similarity=0.379 Sum_probs=37.7
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec-chH--HHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH-SNQ--ALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~-SN~--Ald~l~e~l~~~~~ 885 (1051)
+.+.++.||+|+|||||++.+...+.....+.+|.+++- +.. |++++.......++
T Consensus 221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~v 279 (424)
T PRK05703 221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGI 279 (424)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCC
Confidence 468899999999999999999988761124566665554 432 56665544333443
No 342
>PF13173 AAA_14: AAA domain
Probab=95.03 E-value=0.04 Score=54.26 Aligned_cols=42 Identities=24% Similarity=0.476 Sum_probs=33.4
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALN 874 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald 874 (1051)
+.+.+|.||.|+|||+++.+++..+. ++++++.+.-.+....
T Consensus 2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~ 43 (128)
T PF13173_consen 2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDR 43 (128)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHH
Confidence 57899999999999999999999887 4566777766554443
No 343
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=95.03 E-value=0.052 Score=64.55 Aligned_cols=56 Identities=21% Similarity=0.393 Sum_probs=37.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe-CCHH--HHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HSNQ--ALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a-~SN~--Avd~l~~rl~~~~~ 247 (1051)
..+.++.||+|+|||||++.+...+.....+.+|.+++ .+.+ |++++...-...++
T Consensus 221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~v 279 (424)
T PRK05703 221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGI 279 (424)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCC
Confidence 34788999999999999999988876222356676654 4433 56666544443444
No 344
>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).
Probab=95.01 E-value=0.029 Score=62.34 Aligned_cols=24 Identities=33% Similarity=0.490 Sum_probs=20.3
Q ss_pred CCCeEEEECCCCCChhHHHHHHHH
Q psy12659 829 QPGLTLVVGPPGTGKTDVAVQIIS 852 (1051)
Q Consensus 829 ~~~~tlIqGPPGTGKT~ti~~iI~ 852 (1051)
.+.-.++.||||||||+++..+..
T Consensus 20 ~g~~vLL~G~~GtGKT~lA~~la~ 43 (262)
T TIGR02640 20 SGYPVHLRGPAGTGKTTLAMHVAR 43 (262)
T ss_pred cCCeEEEEcCCCCCHHHHHHHHHH
Confidence 366788999999999999987755
No 345
>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=95.01 E-value=0.052 Score=63.51 Aligned_cols=53 Identities=23% Similarity=0.369 Sum_probs=42.4
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
..+++|.||||+|||+++.++..++... +.++|.++... ..+++..+....++
T Consensus 82 GslvLI~G~pG~GKStLllq~a~~~a~~--g~~VlYvs~EE-s~~qi~~Ra~rlg~ 134 (372)
T cd01121 82 GSVILIGGDPGIGKSTLLLQVAARLAKR--GGKVLYVSGEE-SPEQIKLRADRLGI 134 (372)
T ss_pred CeEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCc-CHHHHHHHHHHcCC
Confidence 5689999999999999999999888765 67898887643 45677777666655
No 346
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.99 E-value=0.049 Score=63.97 Aligned_cols=57 Identities=21% Similarity=0.206 Sum_probs=40.5
Q ss_pred CCCeEEEECCCCCChhHHHHHHHHHHHHh--CCCCcEEEEe-cc--hHHHHHHHHHHHhcCC
Q psy12659 829 QPGLTLVVGPPGTGKTDVAVQIISNLYHN--FPHQRTLIVT-HS--NQALNQLFEKIISLDV 885 (1051)
Q Consensus 829 ~~~~tlIqGPPGTGKT~ti~~iI~~ll~~--~~~~riLV~a-~S--N~Ald~l~e~l~~~~~ 885 (1051)
.+.+.++.||+|+|||||++.+...+... ..+.+|.+++ .+ ..|.+++.......++
T Consensus 173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgv 234 (388)
T PRK12723 173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGI 234 (388)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCc
Confidence 35789999999999999999999877643 2456666554 45 5677775544444555
No 347
>PRK05642 DNA replication initiation factor; Validated
Probab=94.99 E-value=0.033 Score=60.89 Aligned_cols=36 Identities=11% Similarity=0.217 Sum_probs=28.8
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
+..+|+||+|||||+++..+...+... +.+++.++.
T Consensus 46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~--~~~v~y~~~ 81 (234)
T PRK05642 46 SLIYLWGKDGVGRSHLLQAACLRFEQR--GEPAVYLPL 81 (234)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHhC--CCcEEEeeH
Confidence 567899999999999988887776654 667776654
No 348
>PRK10867 signal recognition particle protein; Provisional
Probab=94.99 E-value=0.046 Score=65.10 Aligned_cols=55 Identities=27% Similarity=0.387 Sum_probs=39.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE-eCC--HHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THS--NQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~-a~S--N~Avd~l~~rl~~~~~ 247 (1051)
+.+.++.||||+|||||++.+...+... .+.+|+++ +-+ -.|.+++.......++
T Consensus 100 p~vI~~vG~~GsGKTTtaakLA~~l~~~-~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv 157 (433)
T PRK10867 100 PTVIMMVGLQGAGKTTTAGKLAKYLKKK-KKKKVLLVAADVYRPAAIEQLKTLGEQIGV 157 (433)
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHh-cCCcEEEEEccccchHHHHHHHHHHhhcCC
Confidence 5578999999999999999999877655 35666655 444 3456676554445555
No 349
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=94.99 E-value=0.042 Score=66.68 Aligned_cols=54 Identities=28% Similarity=0.382 Sum_probs=45.7
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+++|.||||||||+++.+++...+.+ +++++.++.... .+++.++....|++
T Consensus 273 g~~~li~G~~G~GKT~l~~~~~~~~~~~--g~~~~yis~e~~-~~~i~~~~~~~g~~ 326 (509)
T PRK09302 273 GSIILVSGATGTGKTLLASKFAEAACRR--GERCLLFAFEES-RAQLIRNARSWGID 326 (509)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecCC-HHHHHHHHHHcCCC
Confidence 5679999999999999999999988877 889999987654 67888888877754
No 350
>PTZ00110 helicase; Provisional
Probab=94.95 E-value=0.071 Score=65.38 Aligned_cols=70 Identities=13% Similarity=0.119 Sum_probs=55.0
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHH-HHHHHHHHHh-----CCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVA-VQIISNLYHN-----FPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti-~~iI~~ll~~-----~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
.+++.|.+|+..++...=.++++|.|||||.+. .-++.++... ..+..+||++||..-+.++.+.+...+
T Consensus 152 ~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~ 227 (545)
T PTZ00110 152 EPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFG 227 (545)
T ss_pred CCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHh
Confidence 567889999999999777899999999999863 3344444432 124679999999999999988887654
No 351
>KOG2028|consensus
Probab=94.95 E-value=0.026 Score=64.58 Aligned_cols=50 Identities=28% Similarity=0.313 Sum_probs=34.4
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
+-.++|||||||||+++.-|+..-- .+.-+.+-++-||.-+..+..-+.+
T Consensus 163 pSmIlWGppG~GKTtlArlia~tsk--~~SyrfvelSAt~a~t~dvR~ife~ 212 (554)
T KOG2028|consen 163 PSMILWGPPGTGKTTLARLIASTSK--KHSYRFVELSATNAKTNDVRDIFEQ 212 (554)
T ss_pred CceEEecCCCCchHHHHHHHHhhcC--CCceEEEEEeccccchHHHHHHHHH
Confidence 5578999999999997766554322 2245677777787777766555543
No 352
>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB. Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.
Probab=94.95 E-value=0.051 Score=63.25 Aligned_cols=42 Identities=29% Similarity=0.484 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNF 220 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~ 220 (1051)
.|.+.-.+++. ...++.+|.||+|+||||++..++..+....
T Consensus 121 ~~~~~~~~~~~--~~~glilI~GpTGSGKTTtL~aLl~~i~~~~ 162 (358)
T TIGR02524 121 DLPAAIIDAIA--PQEGIVFITGATGSGKSTLLAAIIRELAEAP 162 (358)
T ss_pred CCCHHHHHHHh--ccCCEEEEECCCCCCHHHHHHHHHHHHhhcC
Confidence 45444444332 2479999999999999999999988776543
No 353
>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).
Probab=94.94 E-value=0.042 Score=61.06 Aligned_cols=24 Identities=33% Similarity=0.490 Sum_probs=20.2
Q ss_pred CCCeEEEEccCCCChHHHHHHHHH
Q psy12659 191 QPGLTLVVGPPGTGKTDVAVQIIS 214 (1051)
Q Consensus 191 ~~~~~lI~GPPGTGKT~ti~~ii~ 214 (1051)
.....++.||||||||+++..+..
T Consensus 20 ~g~~vLL~G~~GtGKT~lA~~la~ 43 (262)
T TIGR02640 20 SGYPVHLRGPAGTGKTTLAMHVAR 43 (262)
T ss_pred cCCeEEEEcCCCCCHHHHHHHHHH
Confidence 355678999999999999988765
No 354
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=94.93 E-value=0.041 Score=65.47 Aligned_cols=64 Identities=25% Similarity=0.359 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHhc-CCCeEEEEccCCCChHHHHHHHHHHHHHcC-CCCeEEEEeCCHHHHHHHH
Q psy12659 176 IPFTPTQIEAIRAGM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNF-PHQRTLIVTHSNQALNQLF 239 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l-~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~-p~~riLv~a~SN~Avd~l~ 239 (1051)
.-..+...+.+..++ ..+..++.||||||||+++..+...+.... +...-.|+.+.+-+...+.
T Consensus 177 ~~i~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI 242 (459)
T PRK11331 177 LFIPETTIETILKRLTIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFI 242 (459)
T ss_pred ccCCHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHh
Confidence 345566666666666 477889999999999999987766654321 1223345555554444433
No 355
>PRK13767 ATP-dependent helicase; Provisional
Probab=94.91 E-value=0.073 Score=68.85 Aligned_cols=67 Identities=24% Similarity=0.202 Sum_probs=52.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHH-HHHHHHHh------CCCCcEEEEecchHHHHHHHHHHH
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHN------FPHQRTLIVTHSNQALNQLFEKII 881 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~-iI~~ll~~------~~~~riLV~a~SN~Ald~l~e~l~ 881 (1051)
.+++.|.+|+..++++.-++|+.|+|||||..+.- ++..++.. .++-++|+++|+..-++++..++.
T Consensus 32 ~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~ 105 (876)
T PRK13767 32 TFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLE 105 (876)
T ss_pred CCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHH
Confidence 58889999999999988899999999999997643 44555532 123479999999888887776543
No 356
>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.
Probab=94.90 E-value=0.018 Score=62.71 Aligned_cols=24 Identities=50% Similarity=0.726 Sum_probs=17.5
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLY 855 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll 855 (1051)
+.++.+||||||||+++. +|++-+
T Consensus 51 ~h~lf~GPPG~GKTTLA~-IIA~e~ 74 (233)
T PF05496_consen 51 DHMLFYGPPGLGKTTLAR-IIANEL 74 (233)
T ss_dssp -EEEEESSTTSSHHHHHH-HHHHHC
T ss_pred ceEEEECCCccchhHHHH-HHHhcc
Confidence 568999999999987654 555433
No 357
>PRK06921 hypothetical protein; Provisional
Probab=94.90 E-value=0.045 Score=61.14 Aligned_cols=38 Identities=21% Similarity=0.321 Sum_probs=30.4
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
....++.||||||||+++.+|...+.... +.+++.++.
T Consensus 117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~-g~~v~y~~~ 154 (266)
T PRK06921 117 KNSIALLGQPGSGKTHLLTAAANELMRKK-GVPVLYFPF 154 (266)
T ss_pred CCeEEEECCCCCcHHHHHHHHHHHHhhhc-CceEEEEEH
Confidence 45689999999999999999999888652 456666654
No 358
>KOG2028|consensus
Probab=94.90 E-value=0.028 Score=64.29 Aligned_cols=59 Identities=25% Similarity=0.312 Sum_probs=37.5
Q ss_pred HHHHHHHhcC---CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHH
Q psy12659 820 EIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 820 Q~~Ai~~~l~---~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l 880 (1051)
|.-.+.+.+. -+..++|||||||||+++.-|+..--. +.-|.+=++-||.-++.+..-+
T Consensus 149 q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~--~SyrfvelSAt~a~t~dvR~if 210 (554)
T KOG2028|consen 149 QDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKK--HSYRFVELSATNAKTNDVRDIF 210 (554)
T ss_pred cchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCC--CceEEEEEeccccchHHHHHHH
Confidence 4444555544 356889999999999887766554222 3345666666776666655444
No 359
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=94.90 E-value=0.04 Score=65.57 Aligned_cols=64 Identities=23% Similarity=0.335 Sum_probs=41.6
Q ss_pred CHHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhC-CCCcEEEEecchHHHHHHHHHH
Q psy12659 817 TFHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNF-PHQRTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 817 n~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~-~~~riLV~a~SN~Ald~l~e~l 880 (1051)
.+...+.+..++. .+..++.||||||||+++..+...+.... ....-.|+.+.+.+...+++.+
T Consensus 180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~ 245 (459)
T PRK11331 180 PETTIETILKRLTIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGY 245 (459)
T ss_pred CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhccc
Confidence 3445555555554 78899999999999999977665554321 2234466666666666655443
No 360
>PHA00729 NTP-binding motif containing protein
Probab=94.89 E-value=0.033 Score=60.75 Aligned_cols=24 Identities=25% Similarity=0.632 Sum_probs=21.7
Q ss_pred eEEEEccCCCChHHHHHHHHHHHH
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
-.+|.||||||||+++..+...+.
T Consensus 19 nIlItG~pGvGKT~LA~aLa~~l~ 42 (226)
T PHA00729 19 SAVIFGKQGSGKTTYALKVARDVF 42 (226)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHH
Confidence 478999999999999999988875
No 361
>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.
Probab=94.88 E-value=0.018 Score=62.65 Aligned_cols=24 Identities=50% Similarity=0.775 Sum_probs=17.4
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
+-.+.+||||+||||++ .+|++-+
T Consensus 51 ~h~lf~GPPG~GKTTLA-~IIA~e~ 74 (233)
T PF05496_consen 51 DHMLFYGPPGLGKTTLA-RIIANEL 74 (233)
T ss_dssp -EEEEESSTTSSHHHHH-HHHHHHC
T ss_pred ceEEEECCCccchhHHH-HHHHhcc
Confidence 56899999999998854 4444444
No 362
>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=94.86 E-value=0.04 Score=68.71 Aligned_cols=69 Identities=28% Similarity=0.352 Sum_probs=58.5
Q ss_pred CCCHHHHHHHHHhcC-----CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQ-----PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~-----~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+=.-|..||.+... +.=.||+=.+|||||.|+.+||-.|++...-+|||..|..|.-+++..+...+.
T Consensus 165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~ 238 (875)
T COG4096 165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDF 238 (875)
T ss_pred cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHh
Confidence 344569999988743 345899999999999999999999999777799999999999999988776554
No 363
>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=94.83 E-value=0.055 Score=63.31 Aligned_cols=54 Identities=22% Similarity=0.363 Sum_probs=41.7
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
..+++|.||||+|||+++.++..++.. .+.+|+.++.- ...+++..+..+.+++
T Consensus 82 GslvLI~G~pG~GKStLllq~a~~~a~--~g~~VlYvs~E-Es~~qi~~Ra~rlg~~ 135 (372)
T cd01121 82 GSVILIGGDPGIGKSTLLLQVAARLAK--RGGKVLYVSGE-ESPEQIKLRADRLGIS 135 (372)
T ss_pred CeEEEEEeCCCCCHHHHHHHHHHHHHh--cCCeEEEEECC-cCHHHHHHHHHHcCCC
Confidence 578999999999999999999988876 56788887754 3356666666555543
No 364
>KOG0991|consensus
Probab=94.82 E-value=0.031 Score=60.69 Aligned_cols=57 Identities=21% Similarity=0.296 Sum_probs=37.6
Q ss_pred HhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE-ecchHHHHHHHHHHHh
Q psy12659 826 AGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSNQALNQLFEKIIS 882 (1051)
Q Consensus 826 ~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~-a~SN~Ald~l~e~l~~ 882 (1051)
.--+-+-.+|.|||||||||.+..+...|+...-.+-+|=. |.....+|.+..++..
T Consensus 44 ~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~ 101 (333)
T KOG0991|consen 44 KEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKM 101 (333)
T ss_pred HcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHH
Confidence 33345668999999999999999998888862212233322 3344566666666643
No 365
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=94.80 E-value=0.036 Score=66.17 Aligned_cols=37 Identities=27% Similarity=0.364 Sum_probs=32.5
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
..+|.||||||||+++..+...+....|+.+++.++.
T Consensus 132 ~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~ 168 (440)
T PRK14088 132 PLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS 168 (440)
T ss_pred eEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence 5899999999999999999999888877888887764
No 366
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=94.80 E-value=0.029 Score=63.03 Aligned_cols=25 Identities=40% Similarity=0.624 Sum_probs=20.6
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.+..++.||||||||+++..+...+
T Consensus 30 ~~~~ll~Gp~G~GKT~la~~ia~~~ 54 (305)
T TIGR00635 30 LDHLLLYGPPGLGKTTLAHIIANEM 54 (305)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHh
Confidence 3458999999999999998876544
No 367
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=94.79 E-value=0.031 Score=62.83 Aligned_cols=24 Identities=42% Similarity=0.682 Sum_probs=20.3
Q ss_pred CeEEEECCCCCChhHHHHHHHHHH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
+..++.||||||||+++..+...+
T Consensus 31 ~~~ll~Gp~G~GKT~la~~ia~~~ 54 (305)
T TIGR00635 31 DHLLLYGPPGLGKTTLAHIIANEM 54 (305)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHh
Confidence 458999999999999998876654
No 368
>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=94.78 E-value=0.051 Score=62.27 Aligned_cols=40 Identities=20% Similarity=0.388 Sum_probs=32.3
Q ss_pred hcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 827 GMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 827 ~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
++. ..++.|.||||||||+++.+++.+... .+.+++.+..
T Consensus 51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~--~g~~v~yId~ 91 (321)
T TIGR02012 51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQK--AGGTAAFIDA 91 (321)
T ss_pred CCcCCeEEEEECCCCCCHHHHHHHHHHHHHH--cCCcEEEEcc
Confidence 444 568999999999999999999999887 5667765543
No 369
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=94.78 E-value=0.048 Score=65.19 Aligned_cols=43 Identities=28% Similarity=0.475 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHHhcC--CCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 814 FKLTFHEIEAIRAGMQ--PGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 814 ~~Ln~~Q~~Ai~~~l~--~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
..+++.|.+.+..+++ .|+.||.||.|+|||+|+-.++..+..
T Consensus 240 Lg~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTLY~~L~~ln~ 284 (500)
T COG2804 240 LGMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTLYAALSELNT 284 (500)
T ss_pred hCCCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHHHHHHHHhcC
Confidence 3678889999999988 799999999999999999999998776
No 370
>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX. Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.
Probab=94.78 E-value=0.024 Score=63.85 Aligned_cols=26 Identities=38% Similarity=0.485 Sum_probs=21.7
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
-.++.||||||||+++..+...+...
T Consensus 60 ~vll~G~pGTGKT~lA~~ia~~l~~~ 85 (284)
T TIGR02880 60 HMSFTGNPGTGKTTVALRMAQILHRL 85 (284)
T ss_pred eEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence 47899999999999998887766654
No 371
>PRK13909 putative recombination protein RecB; Provisional
Probab=94.78 E-value=0.039 Score=71.58 Aligned_cols=50 Identities=24% Similarity=0.248 Sum_probs=41.7
Q ss_pred EEEccCCCChHHHHHHHHHHHHHcC-CCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 196 LVVGPPGTGKTDVAVQIISNLYHNF-PHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 196 lI~GPPGTGKT~ti~~ii~~l~~~~-p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
++..+.|||||.+++...-.|+... ....||++|.||+|+.++.+||.+.
T Consensus 2 ~~~AsAGsGKT~~L~~~yl~ll~~~~~~~~IlavTFT~kAa~Emk~Ri~~~ 52 (910)
T PRK13909 2 ALKASAGSGKTFALSVRFLALLFKGANPSEILALTFTKKAANEMKERIIDT 52 (910)
T ss_pred ceecCCCCchhHHHHHHHHHHHhcCCCcceEEEEeehHHHHHHHHHHHHHH
Confidence 4678999999999999766666542 2369999999999999999999864
No 372
>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A.
Probab=94.77 E-value=0.037 Score=55.92 Aligned_cols=39 Identities=28% Similarity=0.526 Sum_probs=31.7
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ 871 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~ 871 (1051)
+...|.||.|||||+++..+|..|.. .+.++.++-+++.
T Consensus 1 pvv~VvG~~~sGKTTl~~~Li~~l~~--~g~~v~~ik~~~~ 39 (140)
T PF03205_consen 1 PVVQVVGPKNSGKTTLIRKLINELKR--RGYRVAVIKHTDH 39 (140)
T ss_dssp -EEEEEESTTSSHHHHHHHHHHHHHH--TT--EEEEEE-ST
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHhH--cCCceEEEEEccC
Confidence 36789999999999999999999998 7889998887765
No 373
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=94.77 E-value=0.041 Score=60.45 Aligned_cols=38 Identities=24% Similarity=0.390 Sum_probs=27.9
Q ss_pred CHHHHHHHHHh---cC--CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 817 TFHEIEAIRAG---MQ--PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 817 n~~Q~~Ai~~~---l~--~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
+..+.+|+... +. +++.+|.||||+|||+++..+...+
T Consensus 25 ~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l 67 (269)
T TIGR03015 25 SKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRL 67 (269)
T ss_pred CHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhc
Confidence 44455555543 33 5689999999999999999886654
No 374
>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=94.77 E-value=0.035 Score=59.50 Aligned_cols=39 Identities=21% Similarity=0.369 Sum_probs=31.4
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCC------CcEEEEecch
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPH------QRTLIVTHSN 870 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~------~riLV~a~SN 870 (1051)
..++.|.||||+|||+++.+++.+... ++ .+++.++..+
T Consensus 19 g~v~~I~G~~GsGKT~l~~~ia~~~~~--~~~~~g~~~~v~yi~~e~ 63 (226)
T cd01393 19 GRITEIFGEFGSGKTQLCLQLAVEAQL--PGELGGLEGKVVYIDTEG 63 (226)
T ss_pred CcEEEEeCCCCCChhHHHHHHHHHhhc--ccccCCCcceEEEEecCC
Confidence 579999999999999999999988776 43 5666666543
No 375
>PRK08939 primosomal protein DnaI; Reviewed
Probab=94.75 E-value=0.036 Score=63.16 Aligned_cols=36 Identities=17% Similarity=0.197 Sum_probs=29.9
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
.-.+|.||||||||+++.++...+... +.++.++..
T Consensus 157 ~gl~L~G~~G~GKThLa~Aia~~l~~~--g~~v~~~~~ 192 (306)
T PRK08939 157 KGLYLYGDFGVGKSYLLAAIANELAKK--GVSSTLLHF 192 (306)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHc--CCCEEEEEH
Confidence 357899999999999999999999876 667766643
No 376
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=94.75 E-value=0.062 Score=60.52 Aligned_cols=48 Identities=29% Similarity=0.466 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEE
Q psy12659 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTL 226 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riL 226 (1051)
..+.+.-.+ ......|+.||.||.|+|||||++++|..+-++. ...||
T Consensus 111 LglP~i~~~--~~~~~~GLILVTGpTGSGKSTTlAamId~iN~~~-~~HIl 158 (353)
T COG2805 111 LGLPPIVRE--LAESPRGLILVTGPTGSGKSTTLAAMIDYINKHK-AKHIL 158 (353)
T ss_pred cCCCHHHHH--HHhCCCceEEEeCCCCCcHHHHHHHHHHHHhccC-CcceE
Confidence 345544444 1233489999999999999999999999887764 33444
No 377
>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A.
Probab=94.74 E-value=0.038 Score=55.83 Aligned_cols=39 Identities=28% Similarity=0.537 Sum_probs=30.9
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHH
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ 233 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~ 233 (1051)
++..|.||.||||||++..++..|..+ +.++.++-+++.
T Consensus 1 pvv~VvG~~~sGKTTl~~~Li~~l~~~--g~~v~~ik~~~~ 39 (140)
T PF03205_consen 1 PVVQVVGPKNSGKTTLIRKLINELKRR--GYRVAVIKHTDH 39 (140)
T ss_dssp -EEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEE-ST
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHhHc--CCceEEEEEccC
Confidence 467899999999999999999999987 888887766654
No 378
>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]. These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....
Probab=94.73 E-value=0.029 Score=62.07 Aligned_cols=50 Identities=22% Similarity=0.442 Sum_probs=36.7
Q ss_pred HHHHHHHHHhc-CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCC
Q psy12659 180 PTQIEAIRAGM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 231 (1051)
Q Consensus 180 ~~Q~~Ai~~~l-~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~S 231 (1051)
+...+.+..+. ..+..+|.||+|+||||++..++..+-.. ..+|+++--+
T Consensus 114 ~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~~--~~~iv~iEd~ 164 (270)
T PF00437_consen 114 EEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPPE--DERIVTIEDP 164 (270)
T ss_dssp HHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHTT--TSEEEEEESS
T ss_pred HHHHHHHhhccccceEEEEECCCccccchHHHHHhhhcccc--ccceEEeccc
Confidence 44555555553 47889999999999999999998755543 4677776544
No 379
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.72 E-value=0.065 Score=62.65 Aligned_cols=54 Identities=24% Similarity=0.289 Sum_probs=41.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE-ecch--HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSN--QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~-a~SN--~Ald~l~e~l~~~~~ 885 (1051)
+.+.+|.||.|+|||||++.+...+.. .+.+|.++ +.+- .|++++.......++
T Consensus 206 ~~ii~lvGptGvGKTTt~akLA~~l~~--~g~~V~lItaDtyR~gAveQLk~yae~lgv 262 (407)
T PRK12726 206 HRIISLIGQTGVGKTTTLVKLGWQLLK--QNRTVGFITTDTFRSGAVEQFQGYADKLDV 262 (407)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHH--cCCeEEEEeCCccCccHHHHHHHHhhcCCC
Confidence 578999999999999999999988766 46677554 4444 468887776665555
No 380
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.72 E-value=0.063 Score=63.47 Aligned_cols=55 Identities=20% Similarity=0.336 Sum_probs=37.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe-cc--hHHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HS--NQALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a-~S--N~Ald~l~e~l~~~~~ 885 (1051)
+.+.+|.||+|+|||||++++...+... .+.+|++++ .+ ..|.+++.......++
T Consensus 223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~-~G~~V~Lit~Dt~R~aA~eQLk~yAe~lgv 280 (432)
T PRK12724 223 RKVVFFVGPTGSGKTTSIAKLAAKYFLH-MGKSVSLYTTDNYRIAAIEQLKRYADTMGM 280 (432)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHh-cCCeEEEecccchhhhHHHHHHHHHHhcCC
Confidence 4678999999999999999999876332 567776555 33 2345544444444444
No 381
>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C ....
Probab=94.72 E-value=0.027 Score=54.08 Aligned_cols=21 Identities=38% Similarity=0.662 Sum_probs=19.5
Q ss_pred EEEccCCCChHHHHHHHHHHH
Q psy12659 196 LVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 196 lI~GPPGTGKT~ti~~ii~~l 216 (1051)
+|.|+|||||||++..+...+
T Consensus 2 ~i~G~~GsGKtTia~~L~~~~ 22 (129)
T PF13238_consen 2 GISGIPGSGKTTIAKELAERL 22 (129)
T ss_dssp EEEESTTSSHHHHHHHHHHHH
T ss_pred EEECCCCCCHHHHHHHHHHHH
Confidence 799999999999999998877
No 382
>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX. Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.
Probab=94.72 E-value=0.025 Score=63.73 Aligned_cols=25 Identities=40% Similarity=0.545 Sum_probs=20.9
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
-.++.||||||||+++..+...+..
T Consensus 60 ~vll~G~pGTGKT~lA~~ia~~l~~ 84 (284)
T TIGR02880 60 HMSFTGNPGTGKTTVALRMAQILHR 84 (284)
T ss_pred eEEEEcCCCCCHHHHHHHHHHHHHH
Confidence 4889999999999999877776654
No 383
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=94.70 E-value=0.094 Score=63.92 Aligned_cols=69 Identities=25% Similarity=0.207 Sum_probs=53.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHH-HHHHHHHHHh-------CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVA-VQIISNLYHN-------FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti-~~iI~~ll~~-------~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++-|.+||..++++.-.++++|+|||||... .-++.+++.. ..+.++||++||..-+.++.+.+...
T Consensus 143 ~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l 219 (518)
T PLN00206 143 FPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVL 219 (518)
T ss_pred CCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHH
Confidence 578899999999999888999999999999753 3445554421 13568999999998888877665443
No 384
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=94.68 E-value=0.042 Score=72.77 Aligned_cols=53 Identities=28% Similarity=0.273 Sum_probs=46.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcC---CCCeEEEEeCCHHHHHHHHHHHHh
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNF---PHQRTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~---p~~riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.+..+|-.-.|||||.|++..+-.++... .-.+|||+|.||+|..++.+||.+
T Consensus 16 ~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~ 71 (1139)
T COG1074 16 GQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRD 71 (1139)
T ss_pred CCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHH
Confidence 45789999999999999999988887763 347999999999999999999865
No 385
>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=94.67 E-value=0.055 Score=62.00 Aligned_cols=55 Identities=24% Similarity=0.392 Sum_probs=39.3
Q ss_pred hcC-CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 189 GMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 189 ~l~-~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
++. ..+++|.||||||||+++.+++.+.... +.+++.+..-+ +.+.. .....|++
T Consensus 51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~--g~~v~yId~E~-~~~~~--~a~~lGvd 106 (321)
T TIGR02012 51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEH-ALDPV--YARKLGVD 106 (321)
T ss_pred CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEcccc-hhHHH--HHHHcCCC
Confidence 444 4589999999999999999999988876 67777665433 44442 34444553
No 386
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=94.66 E-value=0.067 Score=62.48 Aligned_cols=65 Identities=23% Similarity=0.325 Sum_probs=47.6
Q ss_pred HHHHHHHHHhcC-------CCeEEEECCCCCChhHHHHHHHHHHHHhCCCC-cEEEEecchHHHHHHHHHHHh
Q psy12659 818 FHEIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQ-RTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 818 ~~Q~~Ai~~~l~-------~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~-riLV~a~SN~Ald~l~e~l~~ 882 (1051)
++|.+.+...+. +.-.+|-||||||||.++-.+...+....++. -+-|=|..+....+++.+|.+
T Consensus 23 e~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~ 95 (366)
T COG1474 23 EEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILN 95 (366)
T ss_pred HHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHH
Confidence 456666665443 44489999999999999999999988855444 466667777777777777655
No 387
>KOG0354|consensus
Probab=94.64 E-value=0.12 Score=64.55 Aligned_cols=77 Identities=18% Similarity=0.240 Sum_probs=67.0
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 809 KLVPPFKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 809 ~~~~~~~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
....++.|=..|.+.++.|| ..=++|.-|.|.|||.+++-++.+.++.+|+.+|++.||+---|.+-.......+.+
T Consensus 56 ~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~ 132 (746)
T KOG0354|consen 56 IYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIP 132 (746)
T ss_pred cccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCc
Confidence 34456678889999999999 778999999999999999999999999999999999999999998877666555543
No 388
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=94.62 E-value=0.044 Score=61.63 Aligned_cols=34 Identities=32% Similarity=0.580 Sum_probs=28.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEE
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTL 864 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riL 864 (1051)
.|+.||.||.|+|||||++++|..+-.+. ..+||
T Consensus 125 ~GLILVTGpTGSGKSTTlAamId~iN~~~-~~HIl 158 (353)
T COG2805 125 RGLILVTGPTGSGKSTTLAAMIDYINKHK-AKHIL 158 (353)
T ss_pred CceEEEeCCCCCcHHHHHHHHHHHHhccC-CcceE
Confidence 79999999999999999999999876643 34444
No 389
>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=94.60 E-value=0.066 Score=64.23 Aligned_cols=54 Identities=30% Similarity=0.488 Sum_probs=42.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+++|.|+||+|||+++.+++.++..+ +.++|.++.-. ..+++..|....++.
T Consensus 94 GsvilI~G~pGsGKTTL~lq~a~~~a~~--g~kvlYvs~EE-s~~qi~~ra~rlg~~ 147 (454)
T TIGR00416 94 GSLILIGGDPGIGKSTLLLQVACQLAKN--QMKVLYVSGEE-SLQQIKMRAIRLGLP 147 (454)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEECcC-CHHHHHHHHHHcCCC
Confidence 5689999999999999999999988876 67888887543 356777776665543
No 390
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.60 E-value=0.075 Score=62.85 Aligned_cols=55 Identities=20% Similarity=0.336 Sum_probs=37.3
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe-CC--HHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HS--NQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a-~S--N~Avd~l~~rl~~~~~ 247 (1051)
+.+.+|.||+|+||||+++.+...+... .+.+|++++ -+ ..|.+++.......++
T Consensus 223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~-~G~~V~Lit~Dt~R~aA~eQLk~yAe~lgv 280 (432)
T PRK12724 223 RKVVFFVGPTGSGKTTSIAKLAAKYFLH-MGKSVSLYTTDNYRIAAIEQLKRYADTMGM 280 (432)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHh-cCCeEEEecccchhhhHHHHHHHHHHhcCC
Confidence 4568899999999999999999876432 266776664 33 3355555544444444
No 391
>KOG0354|consensus
Probab=94.60 E-value=0.12 Score=64.37 Aligned_cols=74 Identities=19% Similarity=0.278 Sum_probs=65.5
Q ss_pred CCCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCC
Q psy12659 174 NTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 248 (1051)
Q Consensus 174 ~~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~ 248 (1051)
..+.|=+-|.+.+..|| ..-++|.-|.|.|||.+++.++.+.+.-+|+.+|++.|||---|.+-.+.....+++
T Consensus 59 ~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~ 132 (746)
T KOG0354|consen 59 TNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIP 132 (746)
T ss_pred CcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCc
Confidence 34678889999999999 666999999999999999999999999999999999999988888877777766654
No 392
>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=94.59 E-value=0.048 Score=66.23 Aligned_cols=48 Identities=23% Similarity=0.342 Sum_probs=43.3
Q ss_pred EEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 196 LVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 196 lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
|++||.|+|||.+...++...+.. ++++|+++|+..-+.++.+++.+.
T Consensus 1 LL~g~TGsGKT~v~l~~i~~~l~~--g~~vLvlvP~i~L~~Q~~~~l~~~ 48 (505)
T TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLAL--GKSVLVLVPEIALTPQMIQRFKYR 48 (505)
T ss_pred CccCCCCCCHHHHHHHHHHHHHHc--CCeEEEEeCcHHHHHHHHHHHHHH
Confidence 589999999999999988888876 789999999999999999999764
No 393
>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=94.58 E-value=0.077 Score=60.92 Aligned_cols=37 Identities=19% Similarity=0.308 Sum_probs=30.7
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
..++.|.||||||||+++.+++.+... .+.+++.+..
T Consensus 55 G~iteI~Gp~GsGKTtLal~~~~~~~~--~g~~~vyId~ 91 (325)
T cd00983 55 GRIIEIYGPESSGKTTLALHAIAEAQK--LGGTVAFIDA 91 (325)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHH--cCCCEEEECc
Confidence 468999999999999999999998877 5666666553
No 394
>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.
Probab=94.58 E-value=0.04 Score=57.49 Aligned_cols=35 Identities=20% Similarity=0.423 Sum_probs=28.0
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
|+++|.|..|+|||+++.+++. ....+.|+.|+..
T Consensus 1 Pv~ii~GfLGsGKTTli~~ll~---~~~~~~~~~vI~n 35 (178)
T PF02492_consen 1 PVIIITGFLGSGKTTLINHLLK---RNRQGERVAVIVN 35 (178)
T ss_dssp -EEEEEESTTSSHHHHHHHHHH---HHTTTS-EEEEEC
T ss_pred CEEEEEcCCCCCHHHHHHHHHH---HhcCCceeEEEEc
Confidence 5789999999999999999988 3337888888864
No 395
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=94.57 E-value=0.098 Score=65.01 Aligned_cols=67 Identities=24% Similarity=0.236 Sum_probs=53.9
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
.+.+.|.+||..++.+.-++|.+|.|+|||.+. .+-.++. +..+||++|+..-+.+..+.+...|+.
T Consensus 25 ~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y--~lpal~~---~g~tlVisPl~sL~~dqv~~l~~~gi~ 91 (607)
T PRK11057 25 QFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCY--QIPALVL---DGLTLVVSPLISLMKDQVDQLLANGVA 91 (607)
T ss_pred CCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHH--HHHHHHc---CCCEEEEecHHHHHHHHHHHHHHcCCc
Confidence 466789999999999888999999999999543 3444444 457999999998888888888877664
No 396
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=94.55 E-value=0.075 Score=66.72 Aligned_cols=68 Identities=21% Similarity=0.286 Sum_probs=58.4
Q ss_pred CCCCCHHHHHHHHHhcCC----CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHh
Q psy12659 813 PFKLTFHEIEAIRAGMQP----GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIIS 882 (1051)
Q Consensus 813 ~~~Ln~~Q~~Ai~~~l~~----~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~ 882 (1051)
+..||..|..|+...... ..++++|.+|+|||.+-.++|...+. .|+.+||..|--.=..++.+++..
T Consensus 196 ~~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~--~GkqvLvLVPEI~Ltpq~~~rf~~ 267 (730)
T COG1198 196 WLALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLA--QGKQVLVLVPEIALTPQLLARFKA 267 (730)
T ss_pred ccccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHH--cCCEEEEEeccccchHHHHHHHHH
Confidence 348999999999988664 78999999999999999999999999 889999999966666666666644
No 397
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=94.54 E-value=0.17 Score=55.88 Aligned_cols=64 Identities=22% Similarity=0.349 Sum_probs=47.6
Q ss_pred HHHHHHHHH-------hcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH-HHHHHHHHHHHhC
Q psy12659 180 PTQIEAIRA-------GMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN-QALNQLFEKIISL 245 (1051)
Q Consensus 180 ~~Q~~Ai~~-------~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN-~Avd~l~~rl~~~ 245 (1051)
+.|++++.. +....-+|++|+.|||||+++.+++...... +-|++=+.... ..+..|++.|...
T Consensus 33 e~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~--GLRlIev~k~~L~~l~~l~~~l~~~ 104 (249)
T PF05673_consen 33 ERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ--GLRLIEVSKEDLGDLPELLDLLRDR 104 (249)
T ss_pred HHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc--CceEEEECHHHhccHHHHHHHHhcC
Confidence 467777654 2335568999999999999999998877766 77877777665 4566777777654
No 398
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=94.50 E-value=0.056 Score=62.84 Aligned_cols=45 Identities=29% Similarity=0.380 Sum_probs=27.7
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHH
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 242 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl 242 (1051)
+-++.+|||||||||++.-| +.-. +..+.-++.+..-+.++.+-+
T Consensus 49 ~SmIl~GPPG~GKTTlA~li-A~~~----~~~f~~~sAv~~gvkdlr~i~ 93 (436)
T COG2256 49 HSMILWGPPGTGKTTLARLI-AGTT----NAAFEALSAVTSGVKDLREII 93 (436)
T ss_pred ceeEEECCCCCCHHHHHHHH-HHhh----CCceEEeccccccHHHHHHHH
Confidence 45889999999999966544 3322 334555555544455554444
No 399
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.50 E-value=0.082 Score=61.82 Aligned_cols=54 Identities=24% Similarity=0.294 Sum_probs=41.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE-eCCH--HHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSN--QALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~-a~SN--~Avd~l~~rl~~~~~ 247 (1051)
+.+.+|.||.|+||||+++.+...+... +.+|.++ +-+- .|++++...-...++
T Consensus 206 ~~ii~lvGptGvGKTTt~akLA~~l~~~--g~~V~lItaDtyR~gAveQLk~yae~lgv 262 (407)
T PRK12726 206 HRIISLIGQTGVGKTTTLVKLGWQLLKQ--NRTVGFITTDTFRSGAVEQFQGYADKLDV 262 (407)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEeCCccCccHHHHHHHHhhcCCC
Confidence 5678999999999999999999877665 6677655 4444 468888777666665
No 400
>PRK13768 GTPase; Provisional
Probab=94.48 E-value=0.045 Score=60.62 Aligned_cols=34 Identities=24% Similarity=0.376 Sum_probs=29.8
Q ss_pred eEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
+.+|.||+|+||||++..+...+..+ +.+++++.
T Consensus 4 ~i~v~G~~G~GKTt~~~~~~~~l~~~--g~~v~~i~ 37 (253)
T PRK13768 4 IVFFLGTAGSGKTTLTKALSDWLEEQ--GYDVAIVN 37 (253)
T ss_pred EEEEECCCCccHHHHHHHHHHHHHhc--CCceEEEE
Confidence 57899999999999999999888766 78888874
No 401
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=94.48 E-value=0.1 Score=62.61 Aligned_cols=38 Identities=18% Similarity=0.289 Sum_probs=31.1
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
...+|.|||||||||++..+...+....++.+|+.++.
T Consensus 142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~ 179 (450)
T PRK14087 142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSG 179 (450)
T ss_pred CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence 34789999999999999888777776667888887664
No 402
>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=94.48 E-value=0.067 Score=64.20 Aligned_cols=54 Identities=28% Similarity=0.464 Sum_probs=42.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
..+++|.|+||+|||+++.+++.++.. .+.++|.++.- ...+++..+..+.+++
T Consensus 94 GsvilI~G~pGsGKTTL~lq~a~~~a~--~g~kvlYvs~E-Es~~qi~~ra~rlg~~ 147 (454)
T TIGR00416 94 GSLILIGGDPGIGKSTLLLQVACQLAK--NQMKVLYVSGE-ESLQQIKMRAIRLGLP 147 (454)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHHh--cCCcEEEEECc-CCHHHHHHHHHHcCCC
Confidence 578999999999999999999998877 46788887753 3456777666666554
No 403
>PRK13766 Hef nuclease; Provisional
Probab=94.47 E-value=0.11 Score=66.16 Aligned_cols=67 Identities=24% Similarity=0.286 Sum_probs=56.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
..-+-|++++..++.. -++|+.|.|+|||.++.-++.+++. .++.++||++||..-+++..+.+...
T Consensus 15 ~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~-~~~~~vLvl~Pt~~L~~Q~~~~~~~~ 81 (773)
T PRK13766 15 EARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH-KKGGKVLILAPTKPLVEQHAEFFRKF 81 (773)
T ss_pred CccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH-hCCCeEEEEeCcHHHHHHHHHHHHHH
Confidence 3445699999999887 5799999999999988888888774 46789999999999888888888764
No 404
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=94.47 E-value=0.063 Score=48.39 Aligned_cols=33 Identities=30% Similarity=0.537 Sum_probs=29.2
Q ss_pred EEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
.++.|.+|+|||+++..+...+... +.+++++.
T Consensus 2 ~~~~g~~G~Gktt~~~~l~~~l~~~--g~~v~~~~ 34 (99)
T cd01983 2 IVVTGKGGVGKTTLAANLAAALAKR--GKRVLLID 34 (99)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEC
Confidence 5788999999999999999988875 88898887
No 405
>PRK13768 GTPase; Provisional
Probab=94.45 E-value=0.047 Score=60.46 Aligned_cols=34 Identities=24% Similarity=0.367 Sum_probs=30.0
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
..+|.||+|+||||++.++...+.. .+.+|+++.
T Consensus 4 ~i~v~G~~G~GKTt~~~~~~~~l~~--~g~~v~~i~ 37 (253)
T PRK13768 4 IVFFLGTAGSGKTTLTKALSDWLEE--QGYDVAIVN 37 (253)
T ss_pred EEEEECCCCccHHHHHHHHHHHHHh--cCCceEEEE
Confidence 5789999999999999999998876 678888874
No 406
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=94.45 E-value=0.062 Score=62.51 Aligned_cols=20 Identities=50% Similarity=0.762 Sum_probs=16.3
Q ss_pred CeEEEECCCCCChhHHHHHH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQI 850 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~i 850 (1051)
..++.+||||||||+++.-|
T Consensus 49 ~SmIl~GPPG~GKTTlA~li 68 (436)
T COG2256 49 HSMILWGPPGTGKTTLARLI 68 (436)
T ss_pred ceeEEECCCCCCHHHHHHHH
Confidence 45888999999999876543
No 407
>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]. These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....
Probab=94.45 E-value=0.037 Score=61.26 Aligned_cols=49 Identities=22% Similarity=0.431 Sum_probs=36.0
Q ss_pred HHHHHHHHHhcC-CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 818 FHEIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 818 ~~Q~~Ai~~~l~-~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
....+.+..++. .+..+|.||+|+||||++..++..+-. ...+|+++-.
T Consensus 114 ~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~~i~~--~~~~iv~iEd 163 (270)
T PF00437_consen 114 EEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLEEIPP--EDERIVTIED 163 (270)
T ss_dssp HHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHHHCHT--TTSEEEEEES
T ss_pred HHHHHHHhhccccceEEEEECCCccccchHHHHHhhhccc--cccceEEecc
Confidence 445556666644 789999999999999999998876554 2366666554
No 408
>PHA02544 44 clamp loader, small subunit; Provisional
Probab=94.44 E-value=0.064 Score=60.61 Aligned_cols=41 Identities=27% Similarity=0.434 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHHHhcC----CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 176 IPFTPTQIEAIRAGMQ----PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~----~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
+-.++...+.+..... +.+.++.||||||||+++..+...+
T Consensus 23 ~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~ 67 (316)
T PHA02544 23 CILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV 67 (316)
T ss_pred hcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence 3455666666655432 5677889999999999988886654
No 409
>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=94.41 E-value=0.12 Score=65.63 Aligned_cols=69 Identities=14% Similarity=0.136 Sum_probs=56.7
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHH-HHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLD 884 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~-iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~ 884 (1051)
.+++.|.+||..++.+.-.+++.|.|||||-...- ++..+.. .++.++|+++||..-+.+..+.+.+.+
T Consensus 36 ~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~-~~~~~aL~l~PtraLa~q~~~~l~~l~ 105 (742)
T TIGR03817 36 RPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALAD-DPRATALYLAPTKALAADQLRAVRELT 105 (742)
T ss_pred cCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhh-CCCcEEEEEcChHHHHHHHHHHHHHhc
Confidence 57889999999999988899999999999986543 3444443 467799999999998899999887764
No 410
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]
Probab=94.40 E-value=0.076 Score=66.94 Aligned_cols=69 Identities=23% Similarity=0.311 Sum_probs=60.4
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHH
Q psy12659 172 RKNTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 242 (1051)
Q Consensus 172 ~~~~~~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl 242 (1051)
......+++.|.+|+..+.....++|.||||||||+++..++..+..- +..+++.+++..|+-.+.+.-
T Consensus 314 ~~~~~~~~~~q~~a~~vl~~de~smlt~~~~~~~~~~~~~~~~l~~~~--~~~~l~aa~tG~a~~~l~e~t 382 (696)
T COG0507 314 AKVKLRLSLEQKEALDVLVVDEVSMLTGGPGTGKTTAIKAIARLIKEG--DGDQLLAAPTGKAAKRLNEST 382 (696)
T ss_pred cccCCCcCcccHHHHHHHhcCCeeEEeccCCcchHHHHHHHHHHHHhc--CCcEEeechhhHHHHHHHHhh
Confidence 334478999999999999999999999999999999999998877765 556999999999998887764
No 411
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=94.37 E-value=0.1 Score=64.93 Aligned_cols=66 Identities=29% Similarity=0.321 Sum_probs=53.3
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
.+.+.|.+||..++...-.+|.+|.|+|||.+. .+-.+.. +..+||++|+..=+.+..+.+...|+
T Consensus 25 ~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y--~lpal~~---~g~tlVisPl~sL~~dqv~~l~~~gi 90 (607)
T PRK11057 25 QFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCY--QIPALVL---DGLTLVVSPLISLMKDQVDQLLANGV 90 (607)
T ss_pred CCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHH--HHHHHHc---CCCEEEEecHHHHHHHHHHHHHHcCC
Confidence 688999999999998777899999999999543 3344443 34799999999888888888887765
No 412
>PRK09354 recA recombinase A; Provisional
Probab=94.34 E-value=0.062 Score=62.18 Aligned_cols=35 Identities=20% Similarity=0.369 Sum_probs=28.4
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 866 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~ 866 (1051)
..++.|.||||||||+++.+++.+... .+.+++.+
T Consensus 60 G~IteI~G~~GsGKTtLal~~~~~~~~--~G~~~~yI 94 (349)
T PRK09354 60 GRIVEIYGPESSGKTTLALHAIAEAQK--AGGTAAFI 94 (349)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHH--cCCcEEEE
Confidence 468999999999999999999988876 45554433
No 413
>TIGR00750 lao LAO/AO transport system ATPase. Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.
Probab=94.34 E-value=0.056 Score=61.26 Aligned_cols=36 Identities=17% Similarity=0.295 Sum_probs=30.9
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
..+..|.||||+|||+++..++..+.. .+.+|.|++
T Consensus 34 ~~~i~i~G~~G~GKttl~~~l~~~~~~--~~~~v~~i~ 69 (300)
T TIGR00750 34 AHRVGITGTPGAGKSTLLEALGMELRR--RGLKVAVIA 69 (300)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHHHHH--CCCeEEEEe
Confidence 577889999999999999999998776 577887765
No 414
>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=94.31 E-value=0.058 Score=65.54 Aligned_cols=48 Identities=23% Similarity=0.346 Sum_probs=43.5
Q ss_pred EEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 834 LVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 834 lIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
|++||.|+|||.+...++...+. .++++||++|+..-+.++.+++.+.
T Consensus 1 LL~g~TGsGKT~v~l~~i~~~l~--~g~~vLvlvP~i~L~~Q~~~~l~~~ 48 (505)
T TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLA--LGKSVLVLVPEIALTPQMIQRFKYR 48 (505)
T ss_pred CccCCCCCCHHHHHHHHHHHHHH--cCCeEEEEeCcHHHHHHHHHHHHHH
Confidence 58999999999999999988887 6889999999999999999999764
No 415
>CHL00181 cbbX CbbX; Provisional
Probab=94.31 E-value=0.036 Score=62.58 Aligned_cols=24 Identities=46% Similarity=0.754 Sum_probs=21.0
Q ss_pred EEEEccCCCChHHHHHHHHHHHHH
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNLYH 218 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l~~ 218 (1051)
.++.||||||||+++..+...+..
T Consensus 62 ill~G~pGtGKT~lAr~la~~~~~ 85 (287)
T CHL00181 62 MSFTGSPGTGKTTVALKMADILYK 85 (287)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHH
Confidence 789999999999999998777654
No 416
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=94.30 E-value=0.039 Score=64.08 Aligned_cols=23 Identities=43% Similarity=0.631 Sum_probs=19.3
Q ss_pred eEEEEccCCCChHHHHHHHHHHH
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
-.++.||||||||+++..+...+
T Consensus 158 gvLL~GppGtGKT~lakaia~~l 180 (364)
T TIGR01242 158 GVLLYGPPGTGKTLLAKAVAHET 180 (364)
T ss_pred eEEEECCCCCCHHHHHHHHHHhC
Confidence 37999999999999998886543
No 417
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=94.30 E-value=0.071 Score=48.04 Aligned_cols=33 Identities=30% Similarity=0.525 Sum_probs=29.5
Q ss_pred EEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
.++.|.+|+|||+++..+...+-. .+.+++++.
T Consensus 2 ~~~~g~~G~Gktt~~~~l~~~l~~--~g~~v~~~~ 34 (99)
T cd01983 2 IVVTGKGGVGKTTLAANLAAALAK--RGKRVLLID 34 (99)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHH--CCCeEEEEC
Confidence 578899999999999999998877 788998887
No 418
>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type. subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
Probab=94.24 E-value=0.13 Score=59.85 Aligned_cols=59 Identities=20% Similarity=0.281 Sum_probs=46.5
Q ss_pred HHHHHHHhcCC--CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 820 EIEAIRAGMQP--GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 820 Q~~Ai~~~l~~--~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
|.+|+..+.+. +..+|.+|+|+|||....- ..+ . .+.++++++|++.-+++..+++.+.
T Consensus 2 Q~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~--~~l-~--~~~~~~~~~P~~aL~~~~~~~~~~~ 62 (357)
T TIGR03158 2 QVATFEALQSKDADIIFNTAPTGAGKTLAWLT--PLL-H--GENDTIALYPTNALIEDQTEAIKEF 62 (357)
T ss_pred HHHHHHHHHcCCCCEEEEECCCCCCHHHHHHH--HHH-H--cCCCEEEEeChHHHHHHHHHHHHHH
Confidence 88999999884 4689999999999987642 222 3 3557899999999999888887654
No 419
>PRK12608 transcription termination factor Rho; Provisional
Probab=94.24 E-value=0.068 Score=62.32 Aligned_cols=61 Identities=20% Similarity=0.307 Sum_probs=44.1
Q ss_pred HHHHHhcC---CCeEEEEccCCCChHHHHHHHHHHHHHcCCCC--eEEEEeCCHHHHHHHHHHHHh
Q psy12659 184 EAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQ--RTLIVTHSNQALNQLFEKIIS 244 (1051)
Q Consensus 184 ~Ai~~~l~---~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~--riLv~a~SN~Avd~l~~rl~~ 244 (1051)
.+|..... ..=.+|.||||||||+++..++..+..+.|+- .++++.....-+.++.+.+..
T Consensus 122 RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~EV~df~~~i~~ 187 (380)
T PRK12608 122 RVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKG 187 (380)
T ss_pred hhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCCCHHHHHHHHhh
Confidence 35554432 23379999999999999999999998875543 355566666677788777764
No 420
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=94.23 E-value=0.059 Score=64.88 Aligned_cols=48 Identities=23% Similarity=0.359 Sum_probs=34.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe-CCH--HHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HSN--QALNQLF 239 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a-~SN--~Avd~l~ 239 (1051)
+++.++.||+|+|||||++.+...+....++.+|.+++ -+. .|.+++.
T Consensus 256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr 306 (484)
T PRK06995 256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLR 306 (484)
T ss_pred CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHH
Confidence 46899999999999999999998876554445776664 332 3455554
No 421
>CHL00181 cbbX CbbX; Provisional
Probab=94.22 E-value=0.038 Score=62.36 Aligned_cols=24 Identities=46% Similarity=0.754 Sum_probs=20.8
Q ss_pred EEEECCCCCChhHHHHHHHHHHHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
.++.||||||||+++..+...+..
T Consensus 62 ill~G~pGtGKT~lAr~la~~~~~ 85 (287)
T CHL00181 62 MSFTGSPGTGKTTVALKMADILYK 85 (287)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHH
Confidence 788999999999999988776654
No 422
>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C ....
Probab=94.21 E-value=0.038 Score=53.07 Aligned_cols=22 Identities=36% Similarity=0.623 Sum_probs=19.7
Q ss_pred EEEECCCCCChhHHHHHHHHHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
.+|.|+|||||||++..+...+
T Consensus 1 I~i~G~~GsGKtTia~~L~~~~ 22 (129)
T PF13238_consen 1 IGISGIPGSGKTTIAKELAERL 22 (129)
T ss_dssp EEEEESTTSSHHHHHHHHHHHH
T ss_pred CEEECCCCCCHHHHHHHHHHHH
Confidence 3789999999999999988876
No 423
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=94.21 E-value=0.044 Score=63.64 Aligned_cols=24 Identities=42% Similarity=0.589 Sum_probs=19.9
Q ss_pred CeEEEECCCCCChhHHHHHHHHHH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
.-.++.||||||||+++..+...+
T Consensus 157 ~gvLL~GppGtGKT~lakaia~~l 180 (364)
T TIGR01242 157 KGVLLYGPPGTGKTLLAKAVAHET 180 (364)
T ss_pred ceEEEECCCCCCHHHHHHHHHHhC
Confidence 348999999999999988876653
No 424
>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=94.20 E-value=0.059 Score=64.14 Aligned_cols=27 Identities=37% Similarity=0.791 Sum_probs=22.5
Q ss_pred CCeEE-EEccCCCChHHHHHHHHHHHHH
Q psy12659 192 PGLTL-VVGPPGTGKTDVAVQIISNLYH 218 (1051)
Q Consensus 192 ~~~~l-I~GPPGTGKT~ti~~ii~~l~~ 218 (1051)
+++.+ |.|||||||||+|..++...-+
T Consensus 68 PPfIvavvGPpGtGKsTLirSlVrr~tk 95 (1077)
T COG5192 68 PPFIVAVVGPPGTGKSTLIRSLVRRFTK 95 (1077)
T ss_pred CCeEEEeecCCCCChhHHHHHHHHHHHH
Confidence 44444 9999999999999999988765
No 425
>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=94.19 E-value=0.078 Score=60.87 Aligned_cols=51 Identities=22% Similarity=0.288 Sum_probs=37.9
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 247 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~ 247 (1051)
..++.|.||||||||+++.+++.+.... +.+++.+..-+ +.+. ++....|+
T Consensus 55 G~iteI~Gp~GsGKTtLal~~~~~~~~~--g~~~vyId~E~-~~~~--~~a~~lGv 105 (325)
T cd00983 55 GRIIEIYGPESSGKTTLALHAIAEAQKL--GGTVAFIDAEH-ALDP--VYAKKLGV 105 (325)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHHc--CCCEEEECccc-cHHH--HHHHHcCC
Confidence 4589999999999999999999988876 67777776543 3443 34444454
No 426
>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type. subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
Probab=94.19 E-value=0.13 Score=59.74 Aligned_cols=59 Identities=22% Similarity=0.298 Sum_probs=45.9
Q ss_pred HHHHHHHhcCC--CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 182 QIEAIRAGMQP--GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 182 Q~~Ai~~~l~~--~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
|.+|+..+... +..+|.+|+|+|||....- ..+ .. +.++++++|++.-+++..+++.+.
T Consensus 2 Q~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~--~~l-~~--~~~~~~~~P~~aL~~~~~~~~~~~ 62 (357)
T TIGR03158 2 QVATFEALQSKDADIIFNTAPTGAGKTLAWLT--PLL-HG--ENDTIALYPTNALIEDQTEAIKEF 62 (357)
T ss_pred HHHHHHHHHcCCCCEEEEECCCCCCHHHHHHH--HHH-Hc--CCCEEEEeChHHHHHHHHHHHHHH
Confidence 88999888764 4689999999999986543 222 22 457899999999999988887664
No 427
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=94.18 E-value=0.076 Score=46.93 Aligned_cols=22 Identities=32% Similarity=0.585 Sum_probs=19.5
Q ss_pred EEEEccCCCChHHHHHHHHHHH
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
..|.||||+|||+++..+...+
T Consensus 2 i~i~G~~gsGKst~~~~l~~~l 23 (69)
T cd02019 2 IAITGGSGSGKSTVAKKLAEQL 23 (69)
T ss_pred EEEECCCCCCHHHHHHHHHHHh
Confidence 4689999999999999988877
No 428
>PRK13909 putative recombination protein RecB; Provisional
Probab=94.17 E-value=0.069 Score=69.32 Aligned_cols=50 Identities=24% Similarity=0.248 Sum_probs=41.7
Q ss_pred EEECCCCCChhHHHHHHHHHHHHhC-CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 834 LVVGPPGTGKTDVAVQIISNLYHNF-PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 834 lIqGPPGTGKT~ti~~iI~~ll~~~-~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
++..+-|||||++++.....|+... ....||++|.||+|+.++.+|+.+.
T Consensus 2 ~~~AsAGsGKT~~L~~~yl~ll~~~~~~~~IlavTFT~kAa~Emk~Ri~~~ 52 (910)
T PRK13909 2 ALKASAGSGKTFALSVRFLALLFKGANPSEILALTFTKKAANEMKERIIDT 52 (910)
T ss_pred ceecCCCCchhHHHHHHHHHHHhcCCCcceEEEEeehHHHHHHHHHHHHHH
Confidence 4577899999999998877777632 2479999999999999999999764
No 429
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=94.17 E-value=0.098 Score=62.74 Aligned_cols=38 Identities=18% Similarity=0.289 Sum_probs=31.7
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
+..+|.||||||||+++.++...+....++.+++.++.
T Consensus 142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~ 179 (450)
T PRK14087 142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSG 179 (450)
T ss_pred CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence 45789999999999999988887777677888877655
No 430
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=94.16 E-value=0.055 Score=63.63 Aligned_cols=24 Identities=46% Similarity=0.713 Sum_probs=19.8
Q ss_pred CCeEEEECCCCCChhHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISN 853 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ 853 (1051)
+.-.++.||||||||+++..+...
T Consensus 165 p~gvLL~GppGtGKT~lAkaia~~ 188 (389)
T PRK03992 165 PKGVLLYGPPGTGKTLLAKAVAHE 188 (389)
T ss_pred CCceEEECCCCCChHHHHHHHHHH
Confidence 445899999999999998877654
No 431
>TIGR00750 lao LAO/AO transport system ATPase. Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.
Probab=94.16 E-value=0.065 Score=60.76 Aligned_cols=36 Identities=17% Similarity=0.306 Sum_probs=31.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
..+..|.||||+||||++..++..+... +.++.+++
T Consensus 34 ~~~i~i~G~~G~GKttl~~~l~~~~~~~--~~~v~~i~ 69 (300)
T TIGR00750 34 AHRVGITGTPGAGKSTLLEALGMELRRR--GLKVAVIA 69 (300)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEe
Confidence 5678899999999999999999988766 77888766
No 432
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=94.16 E-value=0.053 Score=63.76 Aligned_cols=24 Identities=46% Similarity=0.713 Sum_probs=19.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISN 215 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~ 215 (1051)
+.-.|+.||||||||+++..+...
T Consensus 165 p~gvLL~GppGtGKT~lAkaia~~ 188 (389)
T PRK03992 165 PKGVLLYGPPGTGKTLLAKAVAHE 188 (389)
T ss_pred CCceEEECCCCCChHHHHHHHHHH
Confidence 344899999999999998887553
No 433
>PRK04195 replication factor C large subunit; Provisional
Probab=94.15 E-value=0.078 Score=64.04 Aligned_cols=41 Identities=27% Similarity=0.438 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHhcC-------CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 176 IPFTPTQIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 176 ~~ln~~Q~~Ai~~~l~-------~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
+-.++.+.+.+...+. +...||.||||||||+++..+...+
T Consensus 16 lvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el 63 (482)
T PRK04195 16 VVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY 63 (482)
T ss_pred hcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence 3456666666655432 5679999999999999998886654
No 434
>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=94.15 E-value=0.058 Score=57.81 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=24.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
..++.|.||||+|||+++.+++......
T Consensus 19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~ 46 (226)
T cd01393 19 GRITEIFGEFGSGKTQLCLQLAVEAQLP 46 (226)
T ss_pred CcEEEEeCCCCCChhHHHHHHHHHhhcc
Confidence 5689999999999999999998887654
No 435
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=94.13 E-value=0.038 Score=57.26 Aligned_cols=23 Identities=35% Similarity=0.755 Sum_probs=19.1
Q ss_pred eEEEEccCCCChHHHHHHHHHHH
Q psy12659 194 LTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 194 ~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
+.+|.|||||||||++..+...+
T Consensus 1 ~i~i~G~pGsGKst~a~~la~~~ 23 (183)
T TIGR01359 1 VVFVLGGPGSGKGTQCAKIVENF 23 (183)
T ss_pred CEEEECCCCCCHHHHHHHHHHHc
Confidence 36899999999999988876543
No 436
>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.
Probab=94.12 E-value=0.052 Score=60.18 Aligned_cols=34 Identities=26% Similarity=0.554 Sum_probs=27.2
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
..=|.||||.||||++-+++..+.. .+++|-|+|
T Consensus 31 ~iGiTG~PGaGKSTli~~l~~~~~~--~g~~VaVlA 64 (266)
T PF03308_consen 31 VIGITGPPGAGKSTLIDALIRELRE--RGKRVAVLA 64 (266)
T ss_dssp EEEEEE-TTSSHHHHHHHHHHHHHH--TT--EEEEE
T ss_pred EEEeeCCCCCcHHHHHHHHHHHHhh--cCCceEEEE
Confidence 4557999999999999999999998 788888876
No 437
>PRK13342 recombination factor protein RarA; Reviewed
Probab=94.11 E-value=0.12 Score=61.30 Aligned_cols=43 Identities=26% Similarity=0.338 Sum_probs=28.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLF 239 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~ 239 (1051)
.+..++.||||||||+++..+...+ +.+...+..+...++.+.
T Consensus 36 ~~~ilL~GppGtGKTtLA~~ia~~~-----~~~~~~l~a~~~~~~~ir 78 (413)
T PRK13342 36 LSSMILWGPPGTGKTTLARIIAGAT-----DAPFEALSAVTSGVKDLR 78 (413)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHh-----CCCEEEEecccccHHHHH
Confidence 4457889999999999988875543 234555555444444443
No 438
>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein. This is thought to be an ATPase involved in viral DNA packaging [].
Probab=94.09 E-value=0.056 Score=59.55 Aligned_cols=40 Identities=23% Similarity=0.516 Sum_probs=32.2
Q ss_pred hcCCCe-EEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 189 GMQPGL-TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 189 ~l~~~~-~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
.+..++ .+|.||+|||||+++..++..+.+.+ ..|.++++
T Consensus 9 l~~~~fr~viIG~sGSGKT~li~~lL~~~~~~f--~~I~l~t~ 49 (241)
T PF04665_consen 9 LLKDPFRMVIIGKSGSGKTTLIKSLLYYLRHKF--DHIFLITP 49 (241)
T ss_pred hcCCCceEEEECCCCCCHHHHHHHHHHhhcccC--CEEEEEec
Confidence 344443 67999999999999999998888775 57888877
No 439
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.08 E-value=0.1 Score=63.29 Aligned_cols=50 Identities=24% Similarity=0.373 Sum_probs=36.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe-C--CHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-H--SNQALNQLFEK 241 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a-~--SN~Avd~l~~r 241 (1051)
.++..|.||+|+||||++..+...+.....+.+|.+++ . ...|.+++...
T Consensus 350 G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~y 402 (559)
T PRK12727 350 GGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSY 402 (559)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHh
Confidence 57888999999999999999998877654456776664 2 33355554443
No 440
>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=94.08 E-value=0.065 Score=57.76 Aligned_cols=41 Identities=17% Similarity=0.307 Sum_probs=30.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCC----CCcEEEEecch
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFP----HQRTLIVTHSN 870 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~----~~riLV~a~SN 870 (1051)
..++.|.||||||||+++.+++.+.....+ +.+++.++.-+
T Consensus 19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~ 63 (235)
T cd01123 19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG 63 (235)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence 678999999999999999999987554211 25666665433
No 441
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=94.08 E-value=0.082 Score=59.40 Aligned_cols=41 Identities=32% Similarity=0.550 Sum_probs=30.8
Q ss_pred CHHHHHHHHHhcC---CCeEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 179 TPTQIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 179 n~~Q~~Ai~~~l~---~~~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
.+.+.+.+...+. .+..+|.||||||||+++..+...+...
T Consensus 22 ~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~ 65 (319)
T PRK00440 22 QEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGE 65 (319)
T ss_pred cHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCC
Confidence 3456666665543 3457999999999999999998887644
No 442
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=94.06 E-value=0.051 Score=62.21 Aligned_cols=25 Identities=40% Similarity=0.639 Sum_probs=20.8
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.+..+|.||||||||+++..+...+
T Consensus 51 ~~~~ll~GppG~GKT~la~~ia~~l 75 (328)
T PRK00080 51 LDHVLLYGPPGLGKTTLANIIANEM 75 (328)
T ss_pred CCcEEEECCCCccHHHHHHHHHHHh
Confidence 4568999999999999998776554
No 443
>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB. Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.
Probab=94.04 E-value=0.11 Score=60.59 Aligned_cols=28 Identities=32% Similarity=0.649 Sum_probs=25.1
Q ss_pred CCCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 829 QPGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 829 ~~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
..++.+|.||+|+||||++..++..+..
T Consensus 133 ~~glilI~GpTGSGKTTtL~aLl~~i~~ 160 (358)
T TIGR02524 133 QEGIVFITGATGSGKSTLLAAIIRELAE 160 (358)
T ss_pred cCCEEEEECCCCCCHHHHHHHHHHHHhh
Confidence 4799999999999999999998887764
No 444
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB. This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.
Probab=94.04 E-value=0.057 Score=55.47 Aligned_cols=38 Identities=24% Similarity=0.435 Sum_probs=32.2
Q ss_pred EEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQA 872 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~A 872 (1051)
..|.||+|+|||+++..++..+-. .|.+|.++-+....
T Consensus 2 i~i~G~~gsGKTtl~~~l~~~l~~--~G~~V~viK~~~~~ 39 (155)
T TIGR00176 2 LQIVGPKNSGKTTLIERLVKALKA--RGYRVATIKHDHHD 39 (155)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEeccccc
Confidence 578999999999999999998866 57899999876543
No 445
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=94.03 E-value=0.1 Score=63.28 Aligned_cols=49 Identities=24% Similarity=0.406 Sum_probs=35.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe-cc--hHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HS--NQALNQLFE 878 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a-~S--N~Ald~l~e 878 (1051)
+++.+|.||+|+||||++..+...+.....+++|.+++ .+ ..|.+++..
T Consensus 350 G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ 401 (559)
T PRK12727 350 GGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHS 401 (559)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHH
Confidence 57889999999999999999998877644456776665 23 234555443
No 446
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=94.02 E-value=0.07 Score=70.78 Aligned_cols=54 Identities=28% Similarity=0.254 Sum_probs=47.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhC---CCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNF---PHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~---~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+..+|..--|||||+|+++.+..++... .-.+|||+|.||+|..+|.+||.+.
T Consensus 16 ~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~ 72 (1139)
T COG1074 16 GQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDR 72 (1139)
T ss_pred CCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHH
Confidence 45799999999999999999998888752 3479999999999999999999653
No 447
>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=94.02 E-value=0.21 Score=61.79 Aligned_cols=73 Identities=22% Similarity=0.249 Sum_probs=57.1
Q ss_pred CCCHHHHHHHHHhcCCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCcEEEec
Q psy12659 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLRLG 256 (1051)
Q Consensus 177 ~ln~~Q~~Ai~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~lvRlG 256 (1051)
.|++-|.+||..++...-.+|..|.|+|||.+.. +-.+.. +..++|++|+..-+.+-.+++.+.|+ .+..++
T Consensus 13 ~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~--lpal~~---~g~~lVisPl~sL~~dq~~~l~~~gi---~~~~~~ 84 (591)
T TIGR01389 13 DFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQ--VPALLL---KGLTVVISPLISLMKDQVDQLRAAGV---AAAYLN 84 (591)
T ss_pred CCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHH--HHHHHc---CCcEEEEcCCHHHHHHHHHHHHHcCC---cEEEEe
Confidence 6899999999999986678999999999997653 333442 45789999999888888888988776 344554
Q ss_pred C
Q psy12659 257 H 257 (1051)
Q Consensus 257 ~ 257 (1051)
+
T Consensus 85 s 85 (591)
T TIGR01389 85 S 85 (591)
T ss_pred C
Confidence 3
No 448
>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5). All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity
Probab=94.02 E-value=0.049 Score=52.20 Aligned_cols=25 Identities=32% Similarity=0.743 Sum_probs=22.4
Q ss_pred EEEccCCCChHHHHHHHHHHHHHcC
Q psy12659 196 LVVGPPGTGKTDVAVQIISNLYHNF 220 (1051)
Q Consensus 196 lI~GPPGTGKT~ti~~ii~~l~~~~ 220 (1051)
.|.||||+|||+++..++..+....
T Consensus 2 ~i~G~~G~GKS~l~~~l~~~l~~~~ 26 (107)
T PF00910_consen 2 WIYGPPGIGKSTLAKELAKDLLKHI 26 (107)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHHh
Confidence 5899999999999999999888753
No 449
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=94.01 E-value=0.054 Score=65.69 Aligned_cols=26 Identities=42% Similarity=0.673 Sum_probs=21.5
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
+.-.|+.||||||||+++..+...+.
T Consensus 216 p~GILLyGPPGTGKT~LAKAlA~eL~ 241 (512)
T TIGR03689 216 PKGVLLYGPPGCGKTLIAKAVANSLA 241 (512)
T ss_pred CcceEEECCCCCcHHHHHHHHHHhhc
Confidence 34589999999999999888877664
No 450
>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
Probab=93.97 E-value=0.047 Score=56.47 Aligned_cols=25 Identities=28% Similarity=0.569 Sum_probs=21.2
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.++.+|.||||+||||++..+...+
T Consensus 3 ~~ii~i~G~~GsGKsTl~~~l~~~~ 27 (188)
T TIGR01360 3 CKIIFIVGGPGSGKGTQCEKIVEKY 27 (188)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHh
Confidence 3578999999999999998887653
No 451
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=93.97 E-value=0.053 Score=65.31 Aligned_cols=26 Identities=38% Similarity=0.506 Sum_probs=21.7
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHH
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYH 218 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~ 218 (1051)
...|+.||||||||+++..+...+..
T Consensus 37 ~~~Lf~GPpGtGKTTlA~~lA~~l~~ 62 (472)
T PRK14962 37 HAYIFAGPRGTGKTTVARILAKSLNC 62 (472)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHhcc
Confidence 44799999999999999888777653
No 452
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB. This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.
Probab=93.95 E-value=0.085 Score=54.23 Aligned_cols=36 Identities=25% Similarity=0.462 Sum_probs=31.1
Q ss_pred EEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCH
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN 232 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN 232 (1051)
..|.||+|+||||++..++..+-.. +.+|.++-+..
T Consensus 2 i~i~G~~gsGKTtl~~~l~~~l~~~--G~~V~viK~~~ 37 (155)
T TIGR00176 2 LQIVGPKNSGKTTLIERLVKALKAR--GYRVATIKHDH 37 (155)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEeccc
Confidence 5689999999999999999988765 77998887764
No 453
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=93.94 E-value=0.091 Score=46.45 Aligned_cols=22 Identities=32% Similarity=0.585 Sum_probs=19.4
Q ss_pred EEEECCCCCChhHHHHHHHHHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
..|.||||+|||+++..+...+
T Consensus 2 i~i~G~~gsGKst~~~~l~~~l 23 (69)
T cd02019 2 IAITGGSGSGKSTVAKKLAEQL 23 (69)
T ss_pred EEEECCCCCCHHHHHHHHHHHh
Confidence 4689999999999999888877
No 454
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=93.93 E-value=0.074 Score=64.08 Aligned_cols=49 Identities=22% Similarity=0.333 Sum_probs=35.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe-cch--HHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT-HSN--QALNQLFE 878 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a-~SN--~Ald~l~e 878 (1051)
+++.++.||+|+|||||++.+...+.....+++|.+++ .+. .|.++|..
T Consensus 256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~ 307 (484)
T PRK06995 256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRI 307 (484)
T ss_pred CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHH
Confidence 57899999999999999999998876533345776655 332 34555543
No 455
>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=93.92 E-value=0.094 Score=57.20 Aligned_cols=52 Identities=13% Similarity=0.291 Sum_probs=37.2
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHH----------cCCCCeEEEEeCCHHHHHHHHHHHHhC
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYH----------NFPHQRTLIVTHSNQALNQLFEKIISL 245 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~----------~~p~~riLv~a~SN~Avd~l~~rl~~~ 245 (1051)
-+++|.||||||||+++.++..++.. ...+.+||+++-=+.+ +++.+|+...
T Consensus 2 ~~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed~~-~~i~~Rl~~i 63 (239)
T cd01125 2 YVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPR-EEIHRRLEAI 63 (239)
T ss_pred ceeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCCCH-HHHHHHHHHH
Confidence 36899999999999999999877642 1135678888754332 4666666554
No 456
>PTZ00301 uridine kinase; Provisional
Probab=93.90 E-value=0.081 Score=57.16 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=27.0
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEE
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 228 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~ 228 (1051)
-+..|-||||+||||++..++..+....+...+.++
T Consensus 4 ~iIgIaG~SgSGKTTla~~l~~~l~~~~~~~~~~vi 39 (210)
T PTZ00301 4 TVIGISGASGSGKSSLSTNIVSELMAHCGPVSIGVI 39 (210)
T ss_pred EEEEEECCCcCCHHHHHHHHHHHHHhhcCCCeEEEe
Confidence 356799999999999999998888765433344333
No 457
>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
Probab=93.89 E-value=0.071 Score=55.98 Aligned_cols=42 Identities=24% Similarity=0.308 Sum_probs=35.4
Q ss_pred CCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHH
Q psy12659 829 QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQA 872 (1051)
Q Consensus 829 ~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~A 872 (1051)
..+++.|.||+|+||||++..++..|-. .+-+|-++-++++.
T Consensus 5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~--~g~~vg~Ik~~~~~ 46 (173)
T PRK10751 5 MIPLLAIAAWSGTGKTTLLKKLIPALCA--RGIRPGLIKHTHHD 46 (173)
T ss_pred CceEEEEECCCCChHHHHHHHHHHHHhh--cCCeEEEEEEcCCC
Confidence 4568999999999999999999998765 57788888886663
No 458
>PRK12608 transcription termination factor Rho; Provisional
Probab=93.86 E-value=0.089 Score=61.38 Aligned_cols=59 Identities=20% Similarity=0.327 Sum_probs=39.9
Q ss_pred HHHHHhcC---CCeEEEECCCCCChhHHHHHHHHHHHHhCCCC--cEEEEecchHHHHHHHHHH
Q psy12659 822 EAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQ--RTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 822 ~Ai~~~l~---~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~--riLV~a~SN~Ald~l~e~l 880 (1051)
.+|..... ..=.+|.||||||||+++..++.++..+.++- .++.+.....-+..+.+.+
T Consensus 122 RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~EV~df~~~i 185 (380)
T PRK12608 122 RVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSV 185 (380)
T ss_pred hhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCCCHHHHHHHH
Confidence 35555543 45579999999999999999999887754443 2444455555555555554
No 459
>PHA02544 44 clamp loader, small subunit; Provisional
Probab=93.86 E-value=0.096 Score=59.21 Aligned_cols=39 Identities=31% Similarity=0.485 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHhcC----CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 816 LTFHEIEAIRAGMQ----PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 816 Ln~~Q~~Ai~~~l~----~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
.++...+.+..... +...++.||||||||+++..+...+
T Consensus 25 ~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~ 67 (316)
T PHA02544 25 LPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV 67 (316)
T ss_pred CcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence 34444445544433 4677779999999999988776653
No 460
>PRK04195 replication factor C large subunit; Provisional
Probab=93.84 E-value=0.058 Score=65.14 Aligned_cols=39 Identities=28% Similarity=0.433 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHhcC-------CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 816 LTFHEIEAIRAGMQ-------PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 816 Ln~~Q~~Ai~~~l~-------~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
.++.+++.+...+. +...+|.||||||||+++..+...+
T Consensus 18 g~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el 63 (482)
T PRK04195 18 GNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY 63 (482)
T ss_pred CCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence 34445555544432 5789999999999999998776543
No 461
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=93.83 E-value=0.063 Score=65.08 Aligned_cols=27 Identities=41% Similarity=0.663 Sum_probs=22.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
+.-.++.||||||||+++..+...+-.
T Consensus 216 p~GILLyGPPGTGKT~LAKAlA~eL~~ 242 (512)
T TIGR03689 216 PKGVLLYGPPGCGKTLIAKAVANSLAQ 242 (512)
T ss_pred CcceEEECCCCCcHHHHHHHHHHhhcc
Confidence 456899999999999988887776643
No 462
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=93.82 E-value=0.1 Score=58.68 Aligned_cols=39 Identities=33% Similarity=0.539 Sum_probs=29.5
Q ss_pred HHHHHHHHHhcC---CCeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 818 FHEIEAIRAGMQ---PGLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 818 ~~Q~~Ai~~~l~---~~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
..+.+.+...+. .+..++.||||||||+++..+...+..
T Consensus 23 ~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~ 64 (319)
T PRK00440 23 EEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYG 64 (319)
T ss_pred HHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcC
Confidence 345566666554 235799999999999999988888765
No 463
>TIGR01420 pilT_fam pilus retraction protein PilT. This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.
Probab=93.81 E-value=0.066 Score=61.87 Aligned_cols=39 Identities=28% Similarity=0.553 Sum_probs=30.1
Q ss_pred CCCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeC
Q psy12659 191 QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 230 (1051)
Q Consensus 191 ~~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~ 230 (1051)
..++.+|.||+|+||||++..++..+... ++.+|+.+-.
T Consensus 121 ~~g~ili~G~tGSGKTT~l~al~~~i~~~-~~~~i~tiEd 159 (343)
T TIGR01420 121 PRGLILVTGPTGSGKSTTLASMIDYINKN-AAGHIITIED 159 (343)
T ss_pred cCcEEEEECCCCCCHHHHHHHHHHhhCcC-CCCEEEEEcC
Confidence 37899999999999999999988776432 2456666544
No 464
>cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
Probab=93.80 E-value=0.089 Score=53.58 Aligned_cols=33 Identities=24% Similarity=0.463 Sum_probs=28.4
Q ss_pred EEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEe
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a 229 (1051)
..+.||+|+|||+++..+...+... +.+++++.
T Consensus 2 i~~~G~~GsGKTt~~~~l~~~~~~~--g~~v~ii~ 34 (148)
T cd03114 2 IGITGVPGAGKSTLIDALITALRAR--GKRVAVLA 34 (148)
T ss_pred EEEECCCCCcHHHHHHHHHHHHHHC--CCEEEEEE
Confidence 4678999999999999999888776 77888876
No 465
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=93.77 E-value=0.083 Score=60.28 Aligned_cols=56 Identities=16% Similarity=0.194 Sum_probs=36.3
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhC----CCCcEEEEecch-HHHHHHHHHHHhcCC
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNF----PHQRTLIVTHSN-QALNQLFEKIISLDV 885 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~----~~~riLV~a~SN-~Ald~l~e~l~~~~~ 885 (1051)
+.++.|.||||||||+++.+++.+..... .+.+++.++.-+ --.+.+.+.....+.
T Consensus 102 g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~~~~~g~ 162 (317)
T PRK04301 102 QSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAEALGL 162 (317)
T ss_pred CcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHHHHHcCC
Confidence 68899999999999999999998765421 123555555322 234555554444443
No 466
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=93.76 E-value=0.071 Score=63.61 Aligned_cols=23 Identities=39% Similarity=0.632 Sum_probs=19.3
Q ss_pred CeEEEEccCCCChHHHHHHHHHH
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISN 215 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~ 215 (1051)
.-.++.||||||||+++..+...
T Consensus 218 ~gVLL~GPPGTGKT~LAraIA~e 240 (438)
T PTZ00361 218 KGVILYGPPGTGKTLLAKAVANE 240 (438)
T ss_pred cEEEEECCCCCCHHHHHHHHHHh
Confidence 45789999999999998887654
No 467
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=93.72 E-value=0.097 Score=62.57 Aligned_cols=64 Identities=23% Similarity=0.345 Sum_probs=51.8
Q ss_pred CCCHHHHHHHHHhcC-----CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 815 KLTFHEIEAIRAGMQ-----PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~-----~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.-.-.|-+||..... ...-++.|-.|||||.|++++|+.+ ++.+||.||+..-..+|...+.+.
T Consensus 12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI~~~-----~rPtLV~AhNKTLAaQLy~Efk~f 80 (663)
T COG0556 12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVIAKV-----QRPTLVLAHNKTLAAQLYSEFKEF 80 (663)
T ss_pred CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHHHHh-----CCCeEEEecchhHHHHHHHHHHHh
Confidence 334457788887654 3467889999999999999999873 567999999999999999988664
No 468
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=93.71 E-value=0.049 Score=56.39 Aligned_cols=22 Identities=36% Similarity=0.759 Sum_probs=18.7
Q ss_pred eEEEECCCCCChhHHHHHHHHH
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISN 853 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ 853 (1051)
+.+|.||||+||||++..+...
T Consensus 1 ~i~i~G~pGsGKst~a~~la~~ 22 (183)
T TIGR01359 1 VVFVLGGPGSGKGTQCAKIVEN 22 (183)
T ss_pred CEEEECCCCCCHHHHHHHHHHH
Confidence 3689999999999999887664
No 469
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=93.67 E-value=0.35 Score=61.51 Aligned_cols=118 Identities=21% Similarity=0.275 Sum_probs=75.6
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHH-HHHHHHHHhCC-----CCcEEEEecchHHHHHHHHHH----HhcC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAV-QIISNLYHNFP-----HQRTLIVTHSNQALNQLFEKI----ISLD 884 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~-~iI~~ll~~~~-----~~riLV~a~SN~Ald~l~e~l----~~~~ 884 (1051)
.+++.|.+|+..+..+.-+||..|.|+|||-++. -++..|+...+ +=.+|-++|=.+=-+.+..+| ...|
T Consensus 22 ~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~~G 101 (814)
T COG1201 22 SLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELG 101 (814)
T ss_pred CCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHHcC
Confidence 5778899999999999999999999999999874 45555665411 236888999555445555555 4445
Q ss_pred CCcccccccccc-----------------cChhhHHHhccCHHHHHhhhcCceeeccccccccccccchHH
Q psy12659 885 VDERHLLHKKYR-----------------ITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKT 938 (1051)
Q Consensus 885 ~~~~~llRlgsr-----------------itpr~l~laVrnd~eL~~LL~~vtIs~ggvlp~i~k~ll~k~ 938 (1051)
++. -+|-|-. .||+.++.-+.+. .+++.+.++.. -++-.+|+.+..|+
T Consensus 102 ~~v--~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~-~~r~~l~~vr~---VIVDEiHel~~sKR 166 (814)
T COG1201 102 IEV--AVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSP-KFRELLRDVRY---VIVDEIHALAESKR 166 (814)
T ss_pred Ccc--ceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCH-HHHHHhcCCcE---EEeehhhhhhcccc
Confidence 543 3555541 2566666655554 55555555442 23344555544443
No 470
>PF12846 AAA_10: AAA-like domain
Probab=93.67 E-value=0.18 Score=55.56 Aligned_cols=59 Identities=19% Similarity=0.289 Sum_probs=0.0
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCCCCeEEEEeCCHHHHHHHHHHHHhCCCCCCcEEEecCCc
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLRLGHGE 259 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~a~SN~Avd~l~~rl~~~~~~~~~lvRlG~~~ 259 (1051)
++-++|.|++|+|||+++..++..++.. +.++++.=+...-.+-+.. ....++.++...
T Consensus 1 n~h~~i~G~tGsGKT~~~~~l~~~~~~~--g~~~~i~D~~g~~~~~~~~-------~~~~~i~~~~~~ 59 (304)
T PF12846_consen 1 NPHTLILGKTGSGKTTLLKNLLEQLIRR--GPRVVIFDPKGDYSPLARA-------LGGQYIDIDPGD 59 (304)
T ss_pred CCeEEEECCCCCcHHHHHHHHHHHHHHc--CCCEEEEcCCchHHHHHHh-------cCceEEEeecCC
No 471
>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.
Probab=93.64 E-value=0.054 Score=59.58 Aligned_cols=30 Identities=37% Similarity=0.545 Sum_probs=21.7
Q ss_pred EEccCCCChHHHHHHHHHHHHHcCCCCeEEEE
Q psy12659 197 VVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 228 (1051)
Q Consensus 197 I~GPPGTGKT~ti~~ii~~l~~~~p~~riLv~ 228 (1051)
|.||||+||||.+..+...+-.. +.++.++
T Consensus 1 ViGpaGSGKTT~~~~~~~~~~~~--~~~~~~v 30 (238)
T PF03029_consen 1 VIGPAGSGKTTFCKGLSEWLESN--GRDVYIV 30 (238)
T ss_dssp -EESTTSSHHHHHHHHHHHHTTT---S-EEEE
T ss_pred CCCCCCCCHHHHHHHHHHHHHhc--cCCceEE
Confidence 68999999999999988766554 5555554
No 472
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=93.64 E-value=0.064 Score=64.63 Aligned_cols=26 Identities=38% Similarity=0.506 Sum_probs=21.6
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHH
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
...+++||||||||+++..+...+..
T Consensus 37 ~~~Lf~GPpGtGKTTlA~~lA~~l~~ 62 (472)
T PRK14962 37 HAYIFAGPRGTGKTTVARILAKSLNC 62 (472)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHhcc
Confidence 44799999999999999888777653
No 473
>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=93.63 E-value=0.087 Score=55.00 Aligned_cols=47 Identities=17% Similarity=0.254 Sum_probs=36.2
Q ss_pred eEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 832 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 832 ~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
+++|.||||+|||+.+.+++.. .+++++.++.....-+++.+++..+
T Consensus 1 ~~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d~em~~rI~~H 47 (169)
T cd00544 1 IILVTGGARSGKSRFAERLAAE-----LGGPVTYIATAEAFDDEMAERIARH 47 (169)
T ss_pred CEEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCCHHHHHHHHHH
Confidence 4799999999999999988754 3567888877665556677777654
No 474
>PRK08233 hypothetical protein; Provisional
Probab=93.61 E-value=0.054 Score=55.70 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=20.4
Q ss_pred CeEEEEccCCCChHHHHHHHHHHH
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.+..|.||||+||||++..+...+
T Consensus 4 ~iI~I~G~~GsGKtTla~~L~~~l 27 (182)
T PRK08233 4 KIITIAAVSGGGKTTLTERLTHKL 27 (182)
T ss_pred eEEEEECCCCCCHHHHHHHHHhhC
Confidence 467899999999999998887654
No 475
>smart00763 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
Probab=93.61 E-value=0.075 Score=61.64 Aligned_cols=25 Identities=24% Similarity=0.477 Sum_probs=21.8
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
..+.++.||||||||+++..+...+
T Consensus 78 r~il~L~GPPGsGKStla~~La~~l 102 (361)
T smart00763 78 KQILYLLGPVGGGKSSLVECLKRGL 102 (361)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHH
Confidence 5789999999999999988877665
No 476
>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
Probab=93.60 E-value=0.06 Score=55.70 Aligned_cols=24 Identities=29% Similarity=0.592 Sum_probs=20.7
Q ss_pred CCeEEEECCCCCChhHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISN 853 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ 853 (1051)
-++.+|.||||+||||++..+...
T Consensus 3 ~~ii~i~G~~GsGKsTl~~~l~~~ 26 (188)
T TIGR01360 3 CKIIFIVGGPGSGKGTQCEKIVEK 26 (188)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHH
Confidence 357899999999999999888765
No 477
>PRK08233 hypothetical protein; Provisional
Probab=93.60 E-value=0.053 Score=55.78 Aligned_cols=25 Identities=20% Similarity=0.385 Sum_probs=21.1
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
..+..|.||||+||||++..+...+
T Consensus 3 ~~iI~I~G~~GsGKtTla~~L~~~l 27 (182)
T PRK08233 3 TKIITIAAVSGGGKTTLTERLTHKL 27 (182)
T ss_pred ceEEEEECCCCCCHHHHHHHHHhhC
Confidence 3567889999999999998887764
No 478
>PTZ00301 uridine kinase; Provisional
Probab=93.58 E-value=0.096 Score=56.57 Aligned_cols=37 Identities=19% Similarity=0.348 Sum_probs=27.8
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEe
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a 867 (1051)
-+..|.||||+||||++..++..+........+.|++
T Consensus 4 ~iIgIaG~SgSGKTTla~~l~~~l~~~~~~~~~~vi~ 40 (210)
T PTZ00301 4 TVIGISGASGSGKSSLSTNIVSELMAHCGPVSIGVIC 40 (210)
T ss_pred EEEEEECCCcCCHHHHHHHHHHHHHhhcCCCeEEEeC
Confidence 4678999999999999999998887644334454443
No 479
>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=93.58 E-value=0.2 Score=61.99 Aligned_cols=67 Identities=18% Similarity=0.192 Sum_probs=54.7
Q ss_pred CCCHHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhcCCC
Q psy12659 815 KLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVD 886 (1051)
Q Consensus 815 ~Ln~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~~~~ 886 (1051)
.+++-|.+||..++.+.-++|..|.|+|||.+.. +..++. +..++|++|+..-+.+-.+++.+.|+.
T Consensus 13 ~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~--lpal~~---~g~~lVisPl~sL~~dq~~~l~~~gi~ 79 (591)
T TIGR01389 13 DFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQ--VPALLL---KGLTVVISPLISLMKDQVDQLRAAGVA 79 (591)
T ss_pred CCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHH--HHHHHc---CCcEEEEcCCHHHHHHHHHHHHHcCCc
Confidence 5778899999999997789999999999997653 344443 457899999998888888888887764
No 480
>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []. It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.
Probab=93.58 E-value=0.069 Score=55.65 Aligned_cols=25 Identities=36% Similarity=0.761 Sum_probs=21.0
Q ss_pred EEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
.+|.|+||+||||++..++..+-..
T Consensus 2 i~iTG~pG~GKTTll~k~i~~l~~~ 26 (168)
T PF03266_consen 2 IFITGPPGVGKTTLLKKVIEELKKK 26 (168)
T ss_dssp EEEES-TTSSHHHHHHHHHHHHHHT
T ss_pred EEEECcCCCCHHHHHHHHHHHhhcc
Confidence 4799999999999999999888653
No 481
>smart00763 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
Probab=93.56 E-value=0.075 Score=61.64 Aligned_cols=26 Identities=23% Similarity=0.424 Sum_probs=22.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
+.+.++.||||||||+++..+...+-
T Consensus 78 r~il~L~GPPGsGKStla~~La~~l~ 103 (361)
T smart00763 78 KQILYLLGPVGGGKSSLVECLKRGLE 103 (361)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHh
Confidence 57889999999999998888766653
No 482
>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=93.56 E-value=0.098 Score=57.05 Aligned_cols=52 Identities=13% Similarity=0.301 Sum_probs=36.2
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHh----------CCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHN----------FPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~----------~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+++|.||||||||+++.++..++... ..+.+||+++-=+ -.+.+.+|+...
T Consensus 2 ~~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed-~~~~i~~Rl~~i 63 (239)
T cd01125 2 YVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED-PREEIHRRLEAI 63 (239)
T ss_pred ceeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC-CHHHHHHHHHHH
Confidence 478999999999999999998775431 1345787777432 234566666554
No 483
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=93.54 E-value=0.055 Score=61.88 Aligned_cols=25 Identities=40% Similarity=0.639 Sum_probs=20.7
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
.+..+|.||||||||+++..+...+
T Consensus 51 ~~~~ll~GppG~GKT~la~~ia~~l 75 (328)
T PRK00080 51 LDHVLLYGPPGLGKTTLANIIANEM 75 (328)
T ss_pred CCcEEEECCCCccHHHHHHHHHHHh
Confidence 4578999999999999998766553
No 484
>PRK13342 recombination factor protein RarA; Reviewed
Probab=93.52 E-value=0.17 Score=59.88 Aligned_cols=24 Identities=42% Similarity=0.614 Sum_probs=19.5
Q ss_pred CCeEEEECCCCCChhHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISN 853 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ 853 (1051)
.+..+++||||||||+++..+...
T Consensus 36 ~~~ilL~GppGtGKTtLA~~ia~~ 59 (413)
T PRK13342 36 LSSMILWGPPGTGKTTLARIIAGA 59 (413)
T ss_pred CceEEEECCCCCCHHHHHHHHHHH
Confidence 346788999999999998877554
No 485
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=93.52 E-value=0.086 Score=62.91 Aligned_cols=25 Identities=40% Similarity=0.666 Sum_probs=20.2
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHH
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNL 854 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~l 854 (1051)
+...++.||||||||+++..+...+
T Consensus 217 p~gVLL~GPPGTGKT~LAraIA~el 241 (438)
T PTZ00361 217 PKGVILYGPPGTGKTLLAKAVANET 241 (438)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHhh
Confidence 3468899999999999988776643
No 486
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=93.51 E-value=0.19 Score=62.73 Aligned_cols=72 Identities=22% Similarity=0.301 Sum_probs=53.1
Q ss_pred CCCCCCCCHHHHHHHHH---hcC-CCeEEEECCCCCChhHHHH-HHHHHHHHhCCCCcEEEEecchHHHHHHHHHHHhc
Q psy12659 810 LVPPFKLTFHEIEAIRA---GMQ-PGLTLVVGPPGTGKTDVAV-QIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISL 883 (1051)
Q Consensus 810 ~~~~~~Ln~~Q~~Ai~~---~l~-~~~tlIqGPPGTGKT~ti~-~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l~~~ 883 (1051)
.+|++..-+.|.+.+.. ++. ....+|++|.|||||--.. ..+....+ .+++|+|++.|+...+++.++....
T Consensus 10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~--~~~~viist~t~~lq~q~~~~~~~~ 86 (654)
T COG1199 10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYARE--EGKKVIISTRTKALQEQLLEEDLPI 86 (654)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHH--cCCcEEEECCCHHHHHHHHHhhcch
Confidence 35666777888876644 455 4559999999999997443 33333333 4699999999999999999987654
No 487
>PRK00131 aroK shikimate kinase; Reviewed
Probab=93.49 E-value=0.074 Score=54.09 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=21.2
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
+...+|.|||||||||++..+...+
T Consensus 4 ~~~i~l~G~~GsGKstla~~La~~l 28 (175)
T PRK00131 4 GPNIVLIGFMGAGKSTIGRLLAKRL 28 (175)
T ss_pred CCeEEEEcCCCCCHHHHHHHHHHHh
Confidence 4568899999999999988887665
No 488
>PRK08118 topology modulation protein; Reviewed
Probab=93.46 E-value=0.061 Score=55.80 Aligned_cols=22 Identities=32% Similarity=0.608 Sum_probs=18.6
Q ss_pred EEEEccCCCChHHHHHHHHHHH
Q psy12659 195 TLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 195 ~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
.+|.||||+||||++..+-..+
T Consensus 4 I~I~G~~GsGKSTlak~L~~~l 25 (167)
T PRK08118 4 IILIGSGGSGKSTLARQLGEKL 25 (167)
T ss_pred EEEECCCCCCHHHHHHHHHHHh
Confidence 5899999999999888876654
No 489
>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]
Probab=93.45 E-value=0.095 Score=57.09 Aligned_cols=40 Identities=30% Similarity=0.509 Sum_probs=32.3
Q ss_pred EEEECCCCCChhHHHHHHHHHHHH---hCCCCcEEEEecchHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNLYH---NFPHQRTLIVTHSNQA 872 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~ll~---~~~~~riLV~a~SN~A 872 (1051)
++|-||||+||||.+..|...+-. ++.++||.|+-.+|.-
T Consensus 140 tLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEI 182 (308)
T COG3854 140 TLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEI 182 (308)
T ss_pred eEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchh
Confidence 899999999999999888776543 3467899988877653
No 490
>PRK05541 adenylylsulfate kinase; Provisional
Probab=93.45 E-value=0.12 Score=53.52 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=27.2
Q ss_pred CCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEE
Q psy12659 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 866 (1051)
Q Consensus 830 ~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~ 866 (1051)
+.+.++.||||+||||++..+...+-. ++..+.++
T Consensus 7 ~~~I~i~G~~GsGKst~a~~l~~~l~~--~~~~~~~~ 41 (176)
T PRK05541 7 GYVIWITGLAGSGKTTIAKALYERLKL--KYSNVIYL 41 (176)
T ss_pred CCEEEEEcCCCCCHHHHHHHHHHHHHH--cCCcEEEE
Confidence 568899999999999999888887765 44445444
No 491
>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=93.44 E-value=0.1 Score=56.26 Aligned_cols=40 Identities=18% Similarity=0.311 Sum_probs=29.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHHcCC----CCeEEEEeCC
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNFP----HQRTLIVTHS 231 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~~~p----~~riLv~a~S 231 (1051)
..++.|.||||||||+++.+++.+.....+ +.+++.++-.
T Consensus 19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e 62 (235)
T cd01123 19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE 62 (235)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC
Confidence 567999999999999999999877543321 2455555543
No 492
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=93.44 E-value=0.083 Score=64.19 Aligned_cols=27 Identities=33% Similarity=0.355 Sum_probs=22.6
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLYH 218 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~~ 218 (1051)
+...|+.||||||||+++..+...+.-
T Consensus 36 ~ha~Lf~GppGtGKTTlA~~lA~~l~c 62 (504)
T PRK14963 36 GHAYLFSGPRGVGKTTTARLIAMAVNC 62 (504)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHhc
Confidence 344699999999999999988887764
No 493
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=93.43 E-value=0.076 Score=61.79 Aligned_cols=26 Identities=31% Similarity=0.383 Sum_probs=22.3
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
+...++.||||||||+++..+...+.
T Consensus 38 ~h~~L~~Gp~G~GKTtla~~la~~l~ 63 (363)
T PRK14961 38 HHAWLLSGTRGVGKTTIARLLAKSLN 63 (363)
T ss_pred CeEEEEecCCCCCHHHHHHHHHHHhc
Confidence 34569999999999999999888776
No 494
>PRK13531 regulatory ATPase RavA; Provisional
Probab=93.43 E-value=0.077 Score=63.74 Aligned_cols=31 Identities=23% Similarity=0.396 Sum_probs=25.1
Q ss_pred HHhcCCCeEEEEccCCCChHHHHHHHHHHHH
Q psy12659 187 RAGMQPGLTLVVGPPGTGKTDVAVQIISNLY 217 (1051)
Q Consensus 187 ~~~l~~~~~lI~GPPGTGKT~ti~~ii~~l~ 217 (1051)
..++..+-.+|.||||||||+++..+-...-
T Consensus 34 ~aalag~hVLL~GpPGTGKT~LAraLa~~~~ 64 (498)
T PRK13531 34 LAALSGESVFLLGPPGIAKSLIARRLKFAFQ 64 (498)
T ss_pred HHHccCCCEEEECCCChhHHHHHHHHHHHhc
Confidence 3456788899999999999999888866543
No 495
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=93.41 E-value=0.093 Score=62.81 Aligned_cols=36 Identities=25% Similarity=0.409 Sum_probs=30.2
Q ss_pred CeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEec
Q psy12659 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTH 868 (1051)
Q Consensus 831 ~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~ 868 (1051)
...+|.|||||||||++..+...+.. .+.+++.++.
T Consensus 142 npl~L~G~~G~GKTHLl~Ai~~~l~~--~~~~v~yi~~ 177 (445)
T PRK12422 142 NPIYLFGPEGSGKTHLMQAAVHALRE--SGGKILYVRS 177 (445)
T ss_pred ceEEEEcCCCCCHHHHHHHHHHHHHH--cCCCEEEeeH
Confidence 45789999999999999999888876 5788877764
No 496
>KOG1804|consensus
Probab=93.41 E-value=0.02 Score=71.65 Aligned_cols=63 Identities=27% Similarity=0.316 Sum_probs=51.6
Q ss_pred HHHHHHHHHhcCCCeEEEECCCCCChhHHHHHHHHHHHHhCCCCcEEEEecchHHHHHHHHHH
Q psy12659 818 FHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 880 (1051)
Q Consensus 818 ~~Q~~Ai~~~l~~~~tlIqGPPGTGKT~ti~~iI~~ll~~~~~~riLV~a~SN~Ald~l~e~l 880 (1051)
..|+.++-..-......+.||||||||.++++.+.++.-.-+..++++|+++|+|.|.+..++
T Consensus 314 ~~~~~~~~~~~~~~~y~~~~p~~~g~~~n~~~a~~~v~~~~~~~~il~~~p~~a~~k~~~~rl 376 (775)
T KOG1804|consen 314 EEQALHLLLCRLPEPYIVFGPPGTGKTENYREAIAIVSFTSPHFYILVCAPSNASGKQPAHRL 376 (775)
T ss_pred hhhhhhhcccccccccccccCCCcCCccchHHHHHHHHhcchHHHhhcccccccccccccccc
Confidence 344555222223788999999999999999988888877667899999999999999999988
No 497
>PF13555 AAA_29: P-loop containing region of AAA domain
Probab=93.38 E-value=0.085 Score=46.28 Aligned_cols=27 Identities=41% Similarity=0.708 Sum_probs=23.8
Q ss_pred CeEEEEccCCCChHHHHHHHHHHHHHc
Q psy12659 193 GLTLVVGPPGTGKTDVAVQIISNLYHN 219 (1051)
Q Consensus 193 ~~~lI~GPPGTGKT~ti~~ii~~l~~~ 219 (1051)
++++|.||.|+||||++-++...|+..
T Consensus 24 ~~tli~G~nGsGKSTllDAi~~~L~~~ 50 (62)
T PF13555_consen 24 DVTLITGPNGSGKSTLLDAIQTVLYGN 50 (62)
T ss_pred cEEEEECCCCCCHHHHHHHHHHHHcCC
Confidence 389999999999999999998877754
No 498
>PRK06762 hypothetical protein; Provisional
Probab=93.36 E-value=0.07 Score=54.52 Aligned_cols=25 Identities=36% Similarity=0.597 Sum_probs=21.1
Q ss_pred CCeEEEEccCCCChHHHHHHHHHHH
Q psy12659 192 PGLTLVVGPPGTGKTDVAVQIISNL 216 (1051)
Q Consensus 192 ~~~~lI~GPPGTGKT~ti~~ii~~l 216 (1051)
+.+.+|.|+||+||||++..+...+
T Consensus 2 ~~li~i~G~~GsGKST~A~~L~~~l 26 (166)
T PRK06762 2 TTLIIIRGNSGSGKTTIAKQLQERL 26 (166)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHh
Confidence 3578899999999999998887665
No 499
>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []. It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.
Probab=93.36 E-value=0.084 Score=55.02 Aligned_cols=24 Identities=38% Similarity=0.782 Sum_probs=20.5
Q ss_pred EEEECCCCCChhHHHHHHHHHHHH
Q psy12659 833 TLVVGPPGTGKTDVAVQIISNLYH 856 (1051)
Q Consensus 833 tlIqGPPGTGKT~ti~~iI~~ll~ 856 (1051)
.+|.|+||+||||++..++..+-.
T Consensus 2 i~iTG~pG~GKTTll~k~i~~l~~ 25 (168)
T PF03266_consen 2 IFITGPPGVGKTTLLKKVIEELKK 25 (168)
T ss_dssp EEEES-TTSSHHHHHHHHHHHHHH
T ss_pred EEEECcCCCCHHHHHHHHHHHhhc
Confidence 479999999999999999988854
No 500
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=93.34 E-value=0.089 Score=60.38 Aligned_cols=28 Identities=50% Similarity=0.698 Sum_probs=23.8
Q ss_pred cCCCeEEEECCCCCChhHHHHHHHHHHH
Q psy12659 828 MQPGLTLVVGPPGTGKTDVAVQIISNLY 855 (1051)
Q Consensus 828 l~~~~tlIqGPPGTGKT~ti~~iI~~ll 855 (1051)
+...-.|+.||||||||-++..|...|=
T Consensus 63 ~aGrgiLi~GppgTGKTAlA~gIa~eLG 90 (450)
T COG1224 63 MAGRGILIVGPPGTGKTALAMGIARELG 90 (450)
T ss_pred ccccEEEEECCCCCcHHHHHHHHHHHhC
Confidence 4567899999999999999998877654
Done!