Query 000592
Match_columns 1402
No_of_seqs 305 out of 1713
Neff 4.4
Searched_HMMs 46136
Date Mon Apr 1 20:15:31 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000592.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000592hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1802 RNA helicase nonsense 100.0 3.4E-32 7.3E-37 319.9 26.6 350 857-1402 227-586 (935)
2 KOG1803 DNA helicase [Replicat 100.0 1.2E-32 2.6E-37 324.6 20.8 358 870-1401 3-375 (649)
3 TIGR00376 DNA helicase, putati 100.0 9.8E-31 2.1E-35 321.0 31.5 336 907-1402 33-379 (637)
4 PF13086 AAA_11: AAA domain; P 100.0 1.2E-29 2.6E-34 266.6 14.1 208 1062-1401 1-209 (236)
5 KOG1805 DNA replication helica 99.8 1.1E-19 2.4E-24 222.9 13.3 99 1053-1224 660-758 (1100)
6 KOG1807 Helicases [Replication 99.7 1.6E-15 3.4E-20 182.8 22.0 265 861-1212 154-461 (1025)
7 KOG1801 tRNA-splicing endonucl 99.3 2.2E-12 4.8E-17 163.7 8.6 277 828-1191 6-300 (827)
8 PF13245 AAA_19: Part of AAA d 99.2 6.1E-11 1.3E-15 110.2 7.8 61 1070-1189 2-62 (76)
9 COG1112 Superfamily I DNA and 99.2 2.3E-10 5E-15 143.2 15.1 230 1061-1402 273-506 (767)
10 PF13604 AAA_30: AAA domain; P 98.9 3.3E-09 7.3E-14 114.1 9.3 66 1062-1189 1-66 (196)
11 PRK10875 recD exonuclease V su 98.5 3.2E-07 7E-12 114.1 9.7 66 1065-1190 155-220 (615)
12 PF00580 UvrD-helicase: UvrD/R 98.4 4.2E-07 9.2E-12 101.0 8.3 67 1063-1191 1-67 (315)
13 TIGR01447 recD exodeoxyribonuc 98.4 6.2E-07 1.3E-11 111.2 8.6 68 1065-1191 148-215 (586)
14 KOG1806 DEAD box containing he 98.4 4.7E-07 1E-11 113.6 7.2 244 1062-1401 738-1008(1320)
15 TIGR01448 recD_rel helicase, p 98.2 2.7E-06 6E-11 107.9 9.7 42 1060-1109 321-362 (720)
16 TIGR02768 TraA_Ti Ti-type conj 98.1 5.8E-06 1.3E-10 105.3 8.6 42 1061-1109 351-392 (744)
17 PRK10919 ATP-dependent DNA hel 98.0 9.3E-06 2E-10 102.5 7.4 68 1062-1191 2-69 (672)
18 PRK14712 conjugal transfer nic 98.0 1.6E-05 3.5E-10 106.7 9.4 44 1061-1110 834-877 (1623)
19 TIGR01075 uvrD DNA helicase II 97.9 1.2E-05 2.6E-10 102.0 7.2 68 1062-1191 4-71 (715)
20 KOG1804 RNA helicase [RNA proc 97.9 6.7E-06 1.4E-10 103.7 4.1 71 1058-1190 307-377 (775)
21 PRK11773 uvrD DNA-dependent he 97.9 1.8E-05 3.8E-10 100.7 7.7 69 1061-1191 8-76 (721)
22 PRK13889 conjugal transfer rel 97.9 2.2E-05 4.8E-10 102.2 8.4 39 1062-1107 346-384 (988)
23 PRK11054 helD DNA helicase IV; 97.9 1.9E-05 4.1E-10 99.8 7.6 69 1061-1191 195-263 (684)
24 PRK13709 conjugal transfer nic 97.9 3E-05 6.5E-10 105.3 9.6 45 1060-1110 965-1009(1747)
25 TIGR01074 rep ATP-dependent DN 97.8 3.3E-05 7.1E-10 97.1 7.9 68 1062-1191 1-68 (664)
26 smart00487 DEXDc DEAD-like hel 97.8 8.6E-05 1.9E-09 75.5 8.8 72 1061-1193 7-78 (201)
27 cd00046 DEXDc DEAD-like helica 97.8 5.1E-05 1.1E-09 72.7 6.7 52 1087-1192 2-53 (144)
28 PRK13826 Dtr system oriT relax 97.7 7.2E-05 1.6E-09 98.2 8.5 41 1061-1108 380-420 (1102)
29 TIGR02760 TraI_TIGR conjugativ 97.7 6.4E-05 1.4E-09 104.2 8.4 46 1061-1112 1018-1063(1960)
30 TIGR01073 pcrA ATP-dependent D 97.6 7.4E-05 1.6E-09 95.1 7.2 69 1062-1192 4-72 (726)
31 TIGR02760 TraI_TIGR conjugativ 97.6 0.00013 2.9E-09 101.2 9.0 66 1061-1188 428-493 (1960)
32 PF05970 PIF1: PIF1-like helic 97.4 0.00021 4.5E-09 84.3 6.8 46 1062-1109 1-46 (364)
33 PF04851 ResIII: Type III rest 97.2 0.00078 1.7E-08 69.2 7.4 69 1062-1190 3-71 (184)
34 PF00270 DEAD: DEAD/DEAH box h 96.9 0.005 1.1E-07 62.9 9.9 67 1065-1193 2-68 (169)
35 COG0210 UvrD Superfamily I DNA 96.7 0.003 6.5E-08 79.6 7.4 69 1062-1192 2-70 (655)
36 KOG0989 Replication factor C, 96.6 0.0019 4E-08 74.7 4.5 39 1068-1111 45-83 (346)
37 cd00009 AAA The AAA+ (ATPases 96.5 0.0042 9.2E-08 60.1 5.6 42 1064-1110 3-44 (151)
38 cd00268 DEADc DEAD-box helicas 96.5 0.012 2.6E-07 62.7 9.5 70 1062-1191 21-91 (203)
39 PRK06851 hypothetical protein; 96.4 0.014 3E-07 69.6 10.2 59 1086-1198 31-89 (367)
40 smart00382 AAA ATPases associa 96.2 0.003 6.6E-08 60.2 2.9 23 1086-1108 3-25 (148)
41 PF00004 AAA: ATPase family as 96.0 0.0042 9.2E-08 60.8 2.7 22 1088-1109 1-22 (132)
42 PRK07952 DNA replication prote 95.9 0.017 3.6E-07 65.4 7.2 48 1064-1111 78-125 (244)
43 TIGR02785 addA_Gpos recombinat 95.9 0.015 3.3E-07 78.6 7.9 67 1062-1191 1-67 (1232)
44 PTZ00424 helicase 45; Provisio 95.8 0.027 5.8E-07 66.4 8.8 33 1062-1102 50-82 (401)
45 TIGR02928 orc1/cdc6 family rep 95.8 0.01 2.3E-07 69.0 5.0 47 1064-1111 20-66 (365)
46 PHA02558 uvsW UvsW helicase; P 95.8 0.032 6.8E-07 68.8 9.3 69 1062-1193 114-182 (501)
47 PF13191 AAA_16: AAA ATPase do 95.7 0.013 2.8E-07 60.9 5.1 46 1065-1112 6-51 (185)
48 PLN03025 replication factor C 95.7 0.015 3.2E-07 67.4 5.8 45 1063-1112 17-61 (319)
49 TIGR00609 recB exodeoxyribonuc 95.5 0.018 3.9E-07 77.1 6.5 56 1085-1191 9-64 (1087)
50 TIGR02881 spore_V_K stage V sp 95.5 0.018 3.8E-07 65.0 5.5 25 1086-1110 43-67 (261)
51 cd01124 KaiC KaiC is a circadi 95.5 0.027 5.9E-07 59.0 6.5 24 1087-1110 1-24 (187)
52 PRK11192 ATP-dependent RNA hel 95.5 0.051 1.1E-06 65.3 9.5 32 1062-1101 23-54 (434)
53 PRK12377 putative replication 95.4 0.013 2.9E-07 66.4 4.1 27 1086-1112 102-128 (248)
54 PRK05580 primosome assembly pr 95.4 0.047 1E-06 69.8 9.4 70 1061-1191 143-212 (679)
55 PRK10536 hypothetical protein; 95.2 0.041 8.8E-07 63.0 7.2 41 1062-1110 59-99 (262)
56 PF02562 PhoH: PhoH-like prote 95.1 0.04 8.8E-07 61.0 6.6 42 1062-1111 4-45 (205)
57 TIGR00643 recG ATP-dependent D 95.1 0.074 1.6E-06 67.5 9.8 46 1055-1102 228-273 (630)
58 cd01129 PulE-GspE PulE/GspE Th 95.1 0.03 6.4E-07 63.9 5.6 43 1062-1110 63-105 (264)
59 PRK11776 ATP-dependent RNA hel 95.0 0.081 1.8E-06 64.2 9.2 32 1062-1101 26-57 (460)
60 KOG0991 Replication factor C, 94.9 0.036 7.9E-07 62.4 5.5 30 1084-1113 47-76 (333)
61 PRK12402 replication factor C 94.9 0.037 8.1E-07 63.5 5.8 43 1064-1111 20-62 (337)
62 PRK10876 recB exonuclease V su 94.8 0.046 9.9E-07 73.9 6.9 62 1085-1190 17-78 (1181)
63 KOG0744 AAA+-type ATPase [Post 94.8 0.02 4.4E-07 66.8 3.1 23 1085-1107 177-199 (423)
64 PF13401 AAA_22: AAA domain; P 94.7 0.023 5E-07 56.1 3.1 29 1084-1112 3-31 (131)
65 PF07728 AAA_5: AAA domain (dy 94.7 0.023 5E-07 57.3 3.2 22 1088-1109 2-23 (139)
66 PRK10917 ATP-dependent DNA hel 94.7 0.13 2.8E-06 66.0 10.3 47 1055-1103 254-300 (681)
67 PRK08181 transposase; Validate 94.6 0.044 9.5E-07 62.9 5.2 47 1062-1112 87-133 (269)
68 PRK11448 hsdR type I restricti 94.6 0.072 1.6E-06 71.6 7.9 75 1063-1194 414-488 (1123)
69 TIGR00604 rad3 DNA repair heli 94.5 0.11 2.5E-06 66.6 9.3 52 1169-1220 60-115 (705)
70 TIGR02533 type_II_gspE general 94.5 0.042 9.1E-07 67.8 5.1 43 1062-1110 225-267 (486)
71 PRK14974 cell division protein 94.5 0.092 2E-06 62.2 7.7 26 1085-1110 140-165 (336)
72 PRK06893 DNA replication initi 94.4 0.035 7.5E-07 61.7 4.0 28 1085-1112 39-66 (229)
73 PRK00411 cdc6 cell division co 94.4 0.045 9.8E-07 64.5 5.1 26 1086-1111 56-81 (394)
74 cd01120 RecA-like_NTPases RecA 94.3 0.033 7.2E-07 55.8 3.2 24 1087-1110 1-24 (165)
75 PF01695 IstB_IS21: IstB-like 94.3 0.033 7.1E-07 60.0 3.3 28 1085-1112 47-74 (178)
76 TIGR00635 ruvB Holliday juncti 94.3 0.051 1.1E-06 62.0 4.9 24 1086-1109 31-54 (305)
77 PRK08084 DNA replication initi 94.3 0.075 1.6E-06 59.3 6.1 44 1063-1111 28-71 (235)
78 TIGR01650 PD_CobS cobaltochela 94.1 0.064 1.4E-06 63.2 5.4 42 1061-1109 47-88 (327)
79 cd01131 PilT Pilus retraction 94.0 0.045 9.7E-07 59.5 3.6 26 1086-1111 2-27 (198)
80 TIGR00614 recQ_fam ATP-depende 94.0 0.18 3.9E-06 61.7 9.1 32 1061-1100 10-41 (470)
81 PRK00080 ruvB Holliday junctio 93.9 0.06 1.3E-06 62.7 4.7 25 1085-1109 51-75 (328)
82 PRK00254 ski2-like helicase; P 93.9 0.2 4.3E-06 64.6 9.8 68 1061-1191 22-90 (720)
83 PF06745 KaiC: KaiC; InterPro 93.9 0.14 3.1E-06 56.1 7.2 27 1084-1110 18-44 (226)
84 PRK10436 hypothetical protein; 93.8 0.079 1.7E-06 65.1 5.6 43 1062-1110 201-243 (462)
85 PRK11664 ATP-dependent RNA hel 93.8 0.12 2.6E-06 67.6 7.4 21 1170-1190 49-69 (812)
86 PF07652 Flavi_DEAD: Flaviviru 93.8 0.14 2.9E-06 54.4 6.4 22 1169-1190 33-54 (148)
87 TIGR02880 cbbX_cfxQ probable R 93.7 0.05 1.1E-06 62.6 3.5 25 1087-1111 60-84 (284)
88 KOG0743 AAA+-type ATPase [Post 93.7 0.034 7.3E-07 67.4 2.2 22 1087-1108 237-258 (457)
89 PF05729 NACHT: NACHT domain 93.7 0.062 1.3E-06 54.5 3.8 27 1087-1113 2-28 (166)
90 TIGR01587 cas3_core CRISPR-ass 93.7 0.13 2.8E-06 60.0 6.9 24 1169-1192 29-52 (358)
91 PRK11634 ATP-dependent RNA hel 93.7 0.22 4.8E-06 63.4 9.4 32 1062-1101 28-59 (629)
92 TIGR01970 DEAH_box_HrpB ATP-de 93.6 0.16 3.6E-06 66.3 8.3 22 1169-1190 45-66 (819)
93 TIGR01242 26Sp45 26S proteasom 93.6 0.05 1.1E-06 64.3 3.3 21 1087-1107 158-178 (364)
94 PRK08903 DnaA regulatory inact 93.6 0.13 2.8E-06 56.5 6.2 46 1062-1111 23-68 (227)
95 PRK06526 transposase; Provisio 93.6 0.061 1.3E-06 61.2 3.8 46 1062-1112 80-125 (254)
96 PRK04296 thymidine kinase; Pro 93.5 0.094 2E-06 56.8 5.0 26 1086-1111 3-28 (190)
97 PRK00440 rfc replication facto 93.5 0.11 2.3E-06 59.2 5.8 43 1064-1111 22-64 (319)
98 TIGR02538 type_IV_pilB type IV 93.5 0.092 2E-06 65.9 5.6 42 1062-1109 299-340 (564)
99 PRK01172 ski2-like helicase; P 93.4 0.23 5E-06 63.4 9.0 67 1061-1191 21-87 (674)
100 CHL00181 cbbX CbbX; Provisiona 93.4 0.12 2.5E-06 59.8 5.8 24 1087-1110 61-84 (287)
101 PHA02544 44 clamp loader, smal 93.4 0.12 2.5E-06 59.4 5.7 43 1063-1109 25-67 (316)
102 PRK08116 hypothetical protein; 93.3 0.12 2.7E-06 59.0 5.7 26 1087-1112 116-141 (268)
103 TIGR03420 DnaA_homol_Hda DnaA 93.3 0.14 3.1E-06 55.5 6.0 43 1063-1110 21-63 (226)
104 cd01130 VirB11-like_ATPase Typ 93.3 0.12 2.7E-06 55.4 5.3 41 1061-1108 8-48 (186)
105 COG1061 SSL2 DNA or RNA helica 93.3 0.31 6.8E-06 59.5 9.4 71 1061-1194 35-105 (442)
106 PF00448 SRP54: SRP54-type pro 93.1 0.18 3.8E-06 55.3 6.3 25 1086-1110 2-26 (196)
107 TIGR02784 addA_alphas double-s 93.1 0.15 3.2E-06 68.9 6.9 50 1088-1190 13-62 (1141)
108 PF13671 AAA_33: AAA domain; P 93.0 0.066 1.4E-06 53.8 2.7 21 1087-1107 1-21 (143)
109 PRK04195 replication factor C 93.0 0.11 2.4E-06 63.9 5.0 45 1063-1108 18-62 (482)
110 PRK13833 conjugal transfer pro 93.0 0.18 4E-06 59.4 6.6 44 1061-1111 127-170 (323)
111 PRK09183 transposase/IS protei 93.0 0.12 2.6E-06 58.8 4.9 44 1062-1110 84-127 (259)
112 PRK04837 ATP-dependent RNA hel 92.9 0.42 9.2E-06 57.5 9.7 33 1062-1102 30-62 (423)
113 PTZ00361 26 proteosome regulat 92.8 0.13 2.7E-06 63.0 5.2 23 1085-1107 217-239 (438)
114 COG1484 DnaC DNA replication p 92.8 0.1 2.3E-06 59.3 4.2 26 1085-1110 105-130 (254)
115 COG3973 Superfamily I DNA and 92.8 0.28 6.1E-06 61.4 8.0 43 1062-1113 212-254 (747)
116 PRK09401 reverse gyrase; Revie 92.8 0.34 7.5E-06 65.7 9.6 72 1058-1193 76-147 (1176)
117 PRK10416 signal recognition pa 92.8 0.26 5.6E-06 58.0 7.5 27 1084-1110 113-139 (318)
118 PRK10590 ATP-dependent RNA hel 92.8 0.45 9.7E-06 58.1 9.8 74 1062-1191 23-97 (456)
119 PRK08533 flagellar accessory p 92.8 0.22 4.7E-06 55.7 6.6 26 1085-1110 24-49 (230)
120 PRK13767 ATP-dependent helicas 92.8 0.45 9.7E-06 62.9 10.4 73 1062-1190 32-105 (876)
121 TIGR02397 dnaX_nterm DNA polym 92.7 0.16 3.4E-06 59.1 5.6 46 1063-1112 18-63 (355)
122 PRK04537 ATP-dependent RNA hel 92.7 0.42 9.2E-06 60.2 9.7 76 1062-1192 31-107 (572)
123 PRK11057 ATP-dependent DNA hel 92.7 0.41 9E-06 60.7 9.6 38 1055-1100 17-55 (607)
124 PF13207 AAA_17: AAA domain; P 92.6 0.1 2.2E-06 51.1 3.4 21 1087-1107 1-21 (121)
125 PF13481 AAA_25: AAA domain; P 92.6 0.26 5.6E-06 52.2 6.6 28 1085-1112 32-59 (193)
126 TIGR00348 hsdR type I site-spe 92.6 0.27 5.9E-06 63.0 7.9 76 1064-1193 240-317 (667)
127 TIGR00150 HI0065_YjeE ATPase, 92.5 0.19 4.1E-06 52.4 5.2 43 1064-1109 4-46 (133)
128 PF00910 RNA_helicase: RNA hel 92.5 0.11 2.4E-06 51.1 3.4 25 1089-1113 2-26 (107)
129 TIGR02640 gas_vesic_GvpN gas v 92.5 0.14 3E-06 58.1 4.7 22 1086-1107 22-43 (262)
130 PRK06851 hypothetical protein; 92.5 0.53 1.2E-05 56.5 9.6 27 1086-1112 215-241 (367)
131 PRK11331 5-methylcytosine-spec 92.4 0.17 3.7E-06 62.0 5.5 40 1063-1109 179-218 (459)
132 PHA00729 NTP-binding motif con 92.4 0.1 2.2E-06 58.7 3.3 24 1087-1110 19-42 (226)
133 TIGR03015 pepcterm_ATPase puta 92.4 0.1 2.2E-06 58.2 3.3 25 1085-1109 43-67 (269)
134 TIGR00064 ftsY signal recognit 92.4 0.34 7.5E-06 55.7 7.7 24 1086-1109 73-96 (272)
135 PRK06067 flagellar accessory p 92.4 0.33 7.1E-06 53.7 7.3 24 1084-1107 24-47 (234)
136 PRK13894 conjugal transfer ATP 92.3 0.2 4.3E-06 59.0 5.8 42 1062-1110 132-173 (319)
137 COG2805 PilT Tfp pilus assembl 92.3 0.11 2.4E-06 60.6 3.5 29 1084-1112 124-152 (353)
138 PTZ00112 origin recognition co 92.3 0.15 3.2E-06 66.5 5.0 48 1064-1111 760-807 (1164)
139 COG2804 PulE Type II secretory 92.3 0.19 4.1E-06 62.0 5.7 122 1062-1194 241-376 (500)
140 PF03215 Rad17: Rad17 cell cyc 92.3 0.17 3.7E-06 63.1 5.4 25 1085-1109 45-69 (519)
141 PRK06921 hypothetical protein; 92.3 0.12 2.7E-06 59.1 3.9 27 1086-1112 118-144 (266)
142 PF01443 Viral_helicase1: Vira 92.2 0.091 2E-06 57.1 2.7 21 1089-1109 2-22 (234)
143 cd01122 GP4d_helicase GP4d_hel 92.2 0.29 6.2E-06 55.0 6.7 26 1085-1110 30-55 (271)
144 TIGR03880 KaiC_arch_3 KaiC dom 92.2 0.33 7.1E-06 53.3 7.0 24 1085-1108 16-39 (224)
145 smart00488 DEXDc2 DEAD-like he 92.2 0.4 8.6E-06 55.5 7.9 20 1086-1105 28-47 (289)
146 smart00489 DEXDc3 DEAD-like he 92.2 0.4 8.6E-06 55.5 7.9 20 1086-1105 28-47 (289)
147 TIGR00580 mfd transcription-re 92.2 0.55 1.2E-05 62.4 10.1 46 1055-1102 444-489 (926)
148 PF13476 AAA_23: AAA domain; P 92.1 0.12 2.6E-06 54.1 3.4 27 1085-1111 19-45 (202)
149 PF05496 RuvB_N: Holliday junc 92.1 0.15 3.3E-06 57.5 4.2 27 1170-1196 102-131 (233)
150 PRK00771 signal recognition pa 92.0 0.36 7.8E-06 59.2 7.6 28 1084-1111 94-121 (437)
151 PRK14962 DNA polymerase III su 92.0 0.21 4.6E-06 61.6 5.7 26 1086-1111 37-62 (472)
152 cd03115 SRP The signal recogni 92.0 0.22 4.8E-06 52.3 5.1 24 1087-1110 2-25 (173)
153 TIGR03877 thermo_KaiC_1 KaiC d 91.9 0.31 6.7E-06 54.4 6.5 25 1084-1108 20-44 (237)
154 PRK05973 replicative DNA helic 91.9 0.35 7.6E-06 54.9 6.8 27 1084-1110 63-89 (237)
155 TIGR01389 recQ ATP-dependent D 91.8 0.57 1.2E-05 59.0 9.3 39 1055-1101 5-44 (591)
156 TIGR01420 pilT_fam pilus retra 91.7 0.13 2.8E-06 60.7 3.4 26 1085-1110 122-147 (343)
157 PF00308 Bac_DnaA: Bacterial d 91.6 0.35 7.5E-06 53.7 6.4 50 1061-1113 13-62 (219)
158 PLN00206 DEAD-box ATP-dependen 91.6 0.69 1.5E-05 57.6 9.6 32 1062-1101 143-174 (518)
159 PRK06835 DNA replication prote 91.5 0.15 3.3E-06 60.2 3.6 27 1086-1112 184-210 (329)
160 PF13238 AAA_18: AAA domain; P 91.5 0.15 3.2E-06 49.8 3.0 21 1089-1109 2-22 (129)
161 TIGR03689 pup_AAA proteasome A 91.4 0.14 3E-06 63.7 3.3 26 1085-1110 216-241 (512)
162 PRK14961 DNA polymerase III su 91.3 0.26 5.6E-06 58.6 5.3 26 1086-1111 39-64 (363)
163 TIGR03158 cas3_cyano CRISPR-as 91.3 0.6 1.3E-05 55.4 8.3 29 1067-1101 2-30 (357)
164 TIGR00603 rad25 DNA repair hel 91.3 0.54 1.2E-05 60.8 8.4 67 1062-1192 255-321 (732)
165 PRK03992 proteasome-activating 91.3 0.16 3.4E-06 61.0 3.6 22 1086-1107 166-187 (389)
166 PRK14722 flhF flagellar biosyn 91.3 0.19 4.1E-06 60.4 4.1 30 1083-1112 135-164 (374)
167 COG1199 DinG Rad3-related DNA 91.3 0.46 1E-05 60.3 7.8 24 1169-1192 63-86 (654)
168 PF13555 AAA_29: P-loop contai 91.2 0.21 4.5E-06 45.9 3.4 26 1087-1112 25-50 (62)
169 PF01078 Mg_chelatase: Magnesi 91.2 0.21 4.5E-06 55.6 4.0 36 1065-1107 9-44 (206)
170 TIGR01054 rgy reverse gyrase. 91.2 0.68 1.5E-05 62.9 9.6 35 1061-1103 77-111 (1171)
171 PRK06620 hypothetical protein; 91.1 0.2 4.4E-06 55.5 4.0 20 1086-1105 45-64 (214)
172 TIGR02782 TrbB_P P-type conjug 91.0 0.33 7.1E-06 56.6 5.7 42 1062-1110 116-157 (299)
173 TIGR00362 DnaA chromosomal rep 91.0 0.24 5.2E-06 59.4 4.7 27 1086-1112 137-163 (405)
174 PRK09361 radB DNA repair and r 90.9 0.23 5E-06 54.5 4.1 29 1084-1112 22-50 (225)
175 PRK08727 hypothetical protein; 90.9 0.4 8.6E-06 53.6 6.0 27 1086-1112 42-68 (233)
176 PRK10689 transcription-repair 90.9 0.82 1.8E-05 62.1 9.8 47 1055-1103 593-639 (1147)
177 PF03266 NTPase_1: NTPase; In 90.8 0.18 3.9E-06 54.1 3.1 25 1088-1112 2-26 (168)
178 TIGR00595 priA primosomal prot 90.8 0.33 7.1E-06 60.4 5.8 23 1169-1191 25-47 (505)
179 TIGR02524 dot_icm_DotB Dot/Icm 90.8 0.27 6E-06 58.7 4.9 28 1085-1112 134-161 (358)
180 PRK02362 ski2-like helicase; P 90.8 0.73 1.6E-05 59.7 9.0 68 1062-1192 23-90 (737)
181 PF09848 DUF2075: Uncharacteri 90.8 0.41 8.9E-06 56.5 6.3 24 1086-1109 2-25 (352)
182 smart00763 AAA_PrkA PrkA AAA d 90.7 0.34 7.3E-06 58.0 5.5 25 1085-1109 78-102 (361)
183 TIGR03878 thermo_KaiC_2 KaiC d 90.6 0.23 5E-06 56.4 3.9 27 1084-1110 35-61 (259)
184 COG0470 HolB ATPase involved i 90.6 0.18 3.8E-06 57.4 3.0 27 1086-1112 25-51 (325)
185 PTZ00454 26S protease regulato 90.6 0.19 4.2E-06 60.7 3.4 23 1085-1107 179-201 (398)
186 COG1474 CDC6 Cdc6-related prot 90.6 0.32 6.9E-06 58.3 5.1 26 1088-1113 45-70 (366)
187 PTZ00110 helicase; Provisional 90.5 0.93 2E-05 56.9 9.3 75 1062-1193 152-227 (545)
188 TIGR01241 FtsH_fam ATP-depende 90.5 0.18 3.8E-06 62.3 3.0 21 1087-1107 90-110 (495)
189 PRK14701 reverse gyrase; Provi 90.3 0.87 1.9E-05 63.7 9.6 38 1055-1100 72-109 (1638)
190 PF07726 AAA_3: ATPase family 90.3 0.12 2.7E-06 53.7 1.3 21 1088-1108 2-22 (131)
191 cd01394 radB RadB. The archaea 90.2 0.26 5.7E-06 53.7 3.7 28 1084-1111 18-45 (218)
192 PRK06645 DNA polymerase III su 90.2 0.4 8.7E-06 59.8 5.7 28 1085-1112 43-70 (507)
193 PRK00149 dnaA chromosomal repl 90.2 0.44 9.6E-06 58.1 6.0 27 1086-1112 149-175 (450)
194 PRK14963 DNA polymerase III su 90.1 0.41 8.9E-06 59.6 5.7 26 1086-1111 37-62 (504)
195 PRK11889 flhF flagellar biosyn 90.0 1.1 2.4E-05 54.7 8.9 26 1085-1110 241-266 (436)
196 PRK14956 DNA polymerase III su 90.0 0.38 8.3E-06 59.5 5.3 27 1086-1112 41-67 (484)
197 PLN00020 ribulose bisphosphate 90.0 0.24 5.2E-06 59.6 3.4 26 1083-1108 146-171 (413)
198 PRK08939 primosomal protein Dn 90.0 0.24 5.2E-06 57.9 3.4 27 1086-1112 157-183 (306)
199 TIGR01360 aden_kin_iso1 adenyl 89.9 0.29 6.2E-06 51.5 3.7 23 1086-1108 4-26 (188)
200 PRK14970 DNA polymerase III su 89.9 0.46 1E-05 56.1 5.7 45 1063-1111 21-65 (367)
201 TIGR03881 KaiC_arch_4 KaiC dom 89.9 0.76 1.6E-05 50.5 7.1 27 1084-1110 19-45 (229)
202 TIGR00602 rad24 checkpoint pro 89.9 0.46 1E-05 60.7 6.0 47 1063-1109 88-134 (637)
203 TIGR03499 FlhF flagellar biosy 89.8 0.28 6.2E-06 56.5 3.8 28 1084-1111 193-220 (282)
204 PHA02624 large T antigen; Prov 89.7 0.38 8.1E-06 60.9 5.0 25 1085-1109 431-455 (647)
205 TIGR02237 recomb_radB DNA repa 89.7 0.34 7.3E-06 52.4 4.1 28 1084-1111 11-38 (209)
206 KOG0651 26S proteasome regulat 89.7 0.26 5.5E-06 57.9 3.2 22 1083-1104 164-185 (388)
207 COG0467 RAD55 RecA-superfamily 89.7 0.32 6.9E-06 54.8 4.0 29 1084-1112 22-50 (260)
208 cd01393 recA_like RecA is a b 89.7 0.31 6.7E-06 53.1 3.7 27 1084-1110 18-44 (226)
209 TIGR01425 SRP54_euk signal rec 89.6 0.58 1.3E-05 57.3 6.3 26 1085-1110 100-125 (429)
210 PRK13342 recombination factor 89.5 0.29 6.4E-06 59.0 3.8 22 1086-1107 37-58 (413)
211 TIGR02655 circ_KaiC circadian 89.5 0.61 1.3E-05 57.7 6.5 27 1085-1111 263-289 (484)
212 KOG0733 Nuclear AAA ATPase (VC 89.5 0.2 4.4E-06 62.6 2.4 23 1085-1107 223-245 (802)
213 PF13173 AAA_14: AAA domain 89.4 0.34 7.4E-06 48.9 3.6 26 1085-1110 2-27 (128)
214 PRK05642 DNA replication initi 89.4 0.35 7.6E-06 54.1 4.0 26 1086-1111 46-71 (234)
215 PRK12723 flagellar biosynthesi 89.4 0.88 1.9E-05 55.1 7.5 28 1084-1111 173-200 (388)
216 TIGR02525 plasmid_TraJ plasmid 89.3 0.3 6.6E-06 58.6 3.6 26 1086-1111 150-175 (372)
217 PF00437 T2SE: Type II/IV secr 89.2 0.22 4.8E-06 56.1 2.4 25 1085-1109 127-151 (270)
218 PRK14957 DNA polymerase III su 89.2 0.48 1.1E-05 59.5 5.4 27 1085-1111 38-64 (546)
219 PRK13531 regulatory ATPase Rav 89.2 0.32 7E-06 60.2 3.8 24 1086-1109 40-63 (498)
220 PF00931 NB-ARC: NB-ARC domain 89.1 0.53 1.2E-05 52.8 5.2 41 1065-1108 2-42 (287)
221 PRK10867 signal recognition pa 89.1 0.51 1.1E-05 57.8 5.4 28 1085-1112 100-127 (433)
222 PHA02244 ATPase-like protein 89.1 0.52 1.1E-05 56.8 5.3 22 1087-1108 121-142 (383)
223 TIGR01359 UMP_CMP_kin_fam UMP- 89.1 0.3 6.5E-06 51.5 3.1 20 1087-1106 1-20 (183)
224 TIGR00678 holB DNA polymerase 89.0 0.51 1.1E-05 50.4 4.7 29 1084-1112 13-41 (188)
225 PRK14958 DNA polymerase III su 89.0 0.53 1.1E-05 58.7 5.5 41 1068-1112 25-65 (509)
226 PRK01297 ATP-dependent RNA hel 88.9 1.5 3.3E-05 53.8 9.2 75 1062-1191 109-184 (475)
227 PRK04328 hypothetical protein; 88.9 0.92 2E-05 51.3 6.9 24 1085-1108 23-46 (249)
228 PRK14955 DNA polymerase III su 88.9 0.52 1.1E-05 56.8 5.2 27 1086-1112 39-65 (397)
229 TIGR00959 ffh signal recogniti 88.8 0.99 2.1E-05 55.3 7.5 26 1085-1110 99-124 (428)
230 PHA02653 RNA helicase NPH-II; 88.7 1.3 2.7E-05 57.3 8.7 23 1169-1191 222-244 (675)
231 COG4096 HsdR Type I site-speci 88.6 0.57 1.2E-05 60.5 5.5 70 1064-1190 167-236 (875)
232 PRK08233 hypothetical protein; 88.6 0.32 7E-06 50.8 2.8 24 1086-1109 4-27 (182)
233 CHL00195 ycf46 Ycf46; Provisio 88.6 0.32 7E-06 60.3 3.2 23 1086-1108 260-282 (489)
234 cd00984 DnaB_C DnaB helicase C 88.5 0.41 8.9E-06 52.7 3.7 27 1086-1112 14-40 (242)
235 PF06309 Torsin: Torsin; Inte 88.5 0.8 1.7E-05 47.7 5.5 43 1068-1112 38-80 (127)
236 COG1223 Predicted ATPase (AAA+ 88.4 0.29 6.4E-06 56.2 2.5 21 1086-1106 152-172 (368)
237 COG5192 BMS1 GTP-binding prote 88.3 0.36 7.9E-06 59.6 3.3 27 1087-1113 71-97 (1077)
238 COG2256 MGS1 ATPase related to 88.3 0.34 7.3E-06 58.5 3.0 16 1086-1101 49-64 (436)
239 PRK05541 adenylylsulfate kinas 88.2 0.53 1.1E-05 49.7 4.2 28 1083-1110 5-32 (176)
240 PRK00131 aroK shikimate kinase 88.2 0.49 1.1E-05 48.8 3.9 22 1086-1107 5-26 (175)
241 PRK13766 Hef nuclease; Provisi 88.1 1.4 3.1E-05 57.2 8.7 63 1065-1191 18-80 (773)
242 COG0714 MoxR-like ATPases [Gen 88.1 0.63 1.4E-05 54.4 5.1 38 1064-1108 29-66 (329)
243 PRK11823 DNA repair protein Ra 88.0 0.96 2.1E-05 55.6 6.8 26 1085-1110 80-105 (446)
244 PRK14952 DNA polymerase III su 88.0 0.64 1.4E-05 58.9 5.4 27 1086-1112 36-62 (584)
245 cd01121 Sms Sms (bacterial rad 87.9 0.99 2.2E-05 54.3 6.7 27 1085-1111 82-108 (372)
246 PF13521 AAA_28: AAA domain; P 87.7 0.29 6.4E-06 51.0 1.9 19 1089-1107 3-21 (163)
247 PRK14969 DNA polymerase III su 87.7 0.68 1.5E-05 58.0 5.4 44 1064-1111 21-64 (527)
248 PRK12724 flagellar biosynthesi 87.5 0.74 1.6E-05 56.3 5.3 25 1086-1110 224-248 (432)
249 KOG2028 ATPase related to the 87.5 0.49 1.1E-05 56.5 3.6 27 1086-1117 163-189 (554)
250 cd02019 NK Nucleoside/nucleoti 87.4 0.55 1.2E-05 42.9 3.3 22 1088-1109 2-23 (69)
251 PRK03918 chromosome segregatio 87.4 5.7 0.00012 52.3 13.7 27 1085-1111 23-49 (880)
252 TIGR01618 phage_P_loop phage n 87.4 0.4 8.7E-06 53.8 2.8 23 1083-1105 10-32 (220)
253 PRK05480 uridine/cytidine kina 87.4 0.53 1.2E-05 51.1 3.7 26 1084-1109 5-30 (209)
254 PRK05896 DNA polymerase III su 87.4 0.79 1.7E-05 58.2 5.6 27 1086-1112 39-65 (605)
255 PF02492 cobW: CobW/HypB/UreG, 87.3 0.43 9.4E-06 51.0 2.9 22 1086-1107 1-22 (178)
256 PRK14964 DNA polymerase III su 87.2 0.85 1.8E-05 56.8 5.7 27 1086-1112 36-62 (491)
257 PRK14960 DNA polymerase III su 87.1 0.79 1.7E-05 58.8 5.4 40 1068-1111 24-63 (702)
258 PF12774 AAA_6: Hydrolytic ATP 87.1 0.55 1.2E-05 53.0 3.7 31 1070-1107 24-54 (231)
259 cd01123 Rad51_DMC1_radA Rad51_ 87.0 0.48 1E-05 52.0 3.1 26 1083-1108 17-42 (235)
260 COG1222 RPT1 ATP-dependent 26S 86.9 0.39 8.4E-06 57.3 2.5 20 1085-1104 185-204 (406)
261 PRK05703 flhF flagellar biosyn 86.9 0.56 1.2E-05 57.3 3.9 26 1085-1110 221-246 (424)
262 PRK13851 type IV secretion sys 86.8 0.78 1.7E-05 54.7 4.9 38 1064-1108 148-185 (344)
263 PRK09694 helicase Cas3; Provis 86.8 1.8 3.9E-05 57.4 8.6 67 1062-1190 286-352 (878)
264 PRK14949 DNA polymerase III su 86.8 0.75 1.6E-05 60.6 5.1 28 1085-1112 38-65 (944)
265 PRK13909 putative recombinatio 86.6 1 2.2E-05 59.9 6.3 49 1090-1191 3-51 (910)
266 PRK12323 DNA polymerase III su 86.6 0.88 1.9E-05 58.3 5.4 41 1068-1112 25-65 (700)
267 TIGR02655 circ_KaiC circadian 86.5 1.2 2.6E-05 55.2 6.5 25 1084-1108 20-44 (484)
268 PF01637 Arch_ATPase: Archaeal 86.5 0.65 1.4E-05 49.6 3.7 25 1085-1109 20-44 (234)
269 PRK14088 dnaA chromosomal repl 86.5 0.99 2.1E-05 55.3 5.7 26 1087-1112 132-157 (440)
270 PRK09302 circadian clock prote 86.4 1.4 3E-05 54.7 7.0 25 1085-1109 273-297 (509)
271 PF00176 SNF2_N: SNF2 family N 86.4 1.9 4.1E-05 48.3 7.5 46 1067-1112 2-52 (299)
272 PRK13900 type IV secretion sys 86.4 0.78 1.7E-05 54.3 4.6 23 1086-1108 161-183 (332)
273 TIGR01313 therm_gnt_kin carboh 86.4 0.49 1.1E-05 49.2 2.6 18 1089-1106 2-19 (163)
274 TIGR02322 phosphon_PhnN phosph 86.3 0.58 1.3E-05 49.4 3.2 23 1086-1108 2-24 (179)
275 CHL00176 ftsH cell division pr 86.3 0.51 1.1E-05 60.4 3.2 22 1086-1107 217-238 (638)
276 PRK13341 recombination factor 86.3 0.57 1.2E-05 60.7 3.7 22 1086-1107 53-74 (725)
277 PRK09111 DNA polymerase III su 86.1 0.9 2E-05 57.8 5.2 45 1064-1112 29-73 (598)
278 COG0464 SpoVK ATPases of the A 86.1 0.54 1.2E-05 57.9 3.2 23 1084-1106 275-297 (494)
279 PRK14527 adenylate kinase; Pro 86.1 0.74 1.6E-05 49.5 3.9 23 1084-1106 5-27 (191)
280 TIGR00750 lao LAO/AO transport 86.1 0.73 1.6E-05 53.5 4.1 30 1083-1112 32-61 (300)
281 PRK14087 dnaA chromosomal repl 86.1 2.4 5.2E-05 52.3 8.7 27 1086-1112 142-168 (450)
282 PRK07133 DNA polymerase III su 86.0 0.99 2.1E-05 58.5 5.5 44 1065-1112 24-67 (725)
283 PRK12726 flagellar biosynthesi 85.9 1.7 3.6E-05 52.9 7.0 28 1084-1111 205-232 (407)
284 TIGR01967 DEAH_box_HrpA ATP-de 85.8 1.3 2.9E-05 60.4 6.9 31 1068-1105 72-102 (1283)
285 PF12775 AAA_7: P-loop contain 85.7 0.6 1.3E-05 53.8 3.1 22 1086-1107 34-55 (272)
286 PRK13407 bchI magnesium chelat 85.7 0.53 1.1E-05 55.9 2.7 23 1087-1109 31-53 (334)
287 PRK06647 DNA polymerase III su 85.6 1 2.3E-05 56.9 5.4 43 1066-1112 23-65 (563)
288 PRK14950 DNA polymerase III su 85.5 1.1 2.3E-05 56.8 5.5 26 1086-1111 39-64 (585)
289 PRK09112 DNA polymerase III su 85.5 1.1 2.5E-05 53.4 5.4 44 1065-1112 29-72 (351)
290 PRK06762 hypothetical protein; 85.5 0.75 1.6E-05 48.0 3.5 22 1086-1107 3-24 (166)
291 PRK08691 DNA polymerase III su 85.2 1.1 2.4E-05 57.7 5.4 44 1065-1112 22-65 (709)
292 TIGR00763 lon ATP-dependent pr 85.2 0.67 1.5E-05 60.5 3.6 24 1086-1109 348-371 (775)
293 PRK04040 adenylate kinase; Pro 85.2 0.74 1.6E-05 50.2 3.4 24 1086-1109 3-26 (188)
294 KOG0731 AAA+-type ATPase conta 85.2 0.78 1.7E-05 59.3 4.0 43 1055-1106 323-365 (774)
295 COG0552 FtsY Signal recognitio 85.1 1.2 2.5E-05 53.0 5.1 29 1084-1112 138-166 (340)
296 cd02023 UMPK Uridine monophosp 85.1 0.71 1.5E-05 49.7 3.2 23 1087-1109 1-23 (198)
297 PRK14951 DNA polymerase III su 85.1 1.1 2.5E-05 57.1 5.5 40 1069-1112 26-65 (618)
298 cd02021 GntK Gluconate kinase 85.1 0.66 1.4E-05 47.5 2.8 19 1087-1105 1-19 (150)
299 PRK12422 chromosomal replicati 85.0 0.69 1.5E-05 56.8 3.4 26 1087-1112 143-168 (445)
300 TIGR02012 tigrfam_recA protein 85.0 1.2 2.7E-05 52.6 5.3 28 1084-1111 54-81 (321)
301 COG1224 TIP49 DNA helicase TIP 85.0 0.69 1.5E-05 55.2 3.2 25 1085-1109 65-89 (450)
302 PF04665 Pox_A32: Poxvirus A32 85.0 1 2.2E-05 51.4 4.4 24 1086-1109 13-37 (241)
303 TIGR00416 sms DNA repair prote 85.0 1.7 3.6E-05 53.7 6.6 27 1085-1111 94-120 (454)
304 TIGR01243 CDC48 AAA family ATP 84.9 0.73 1.6E-05 59.7 3.8 22 1086-1107 213-234 (733)
305 PRK10865 protein disaggregatio 84.8 1.2 2.5E-05 59.1 5.5 26 1086-1111 599-624 (857)
306 TIGR02030 BchI-ChlI magnesium 84.8 1.2 2.5E-05 53.1 5.0 24 1086-1109 26-49 (337)
307 PRK14965 DNA polymerase III su 84.8 1.2 2.5E-05 56.5 5.3 44 1065-1112 22-65 (576)
308 KOG0741 AAA+-type ATPase [Post 84.8 0.71 1.5E-05 57.3 3.2 31 1081-1113 253-283 (744)
309 PRK13764 ATPase; Provisional 84.7 0.75 1.6E-05 58.5 3.6 26 1086-1111 258-283 (602)
310 TIGR02236 recomb_radA DNA repa 84.6 0.83 1.8E-05 52.9 3.6 25 1084-1108 94-118 (310)
311 PHA02774 E1; Provisional 84.6 0.7 1.5E-05 58.3 3.2 24 1086-1109 435-458 (613)
312 PF06414 Zeta_toxin: Zeta toxi 84.5 0.76 1.7E-05 49.9 3.1 27 1083-1109 13-39 (199)
313 KOG0738 AAA+-type ATPase [Post 84.5 0.59 1.3E-05 56.3 2.4 19 1087-1105 247-265 (491)
314 PRK04301 radA DNA repair and r 84.5 0.83 1.8E-05 53.3 3.6 26 1084-1109 101-126 (317)
315 PRK00889 adenylylsulfate kinas 84.4 1 2.2E-05 47.6 3.9 25 1085-1109 4-28 (175)
316 TIGR03117 cas_csf4 CRISPR-asso 84.4 2.8 6.1E-05 53.8 8.4 22 1169-1190 46-67 (636)
317 PF01580 FtsK_SpoIIIE: FtsK/Sp 84.4 0.82 1.8E-05 49.5 3.3 27 1087-1113 40-66 (205)
318 cd02027 APSK Adenosine 5'-phos 84.4 0.86 1.9E-05 47.5 3.3 24 1087-1110 1-24 (149)
319 cd01428 ADK Adenylate kinase ( 84.3 0.74 1.6E-05 48.8 2.8 18 1088-1105 2-19 (194)
320 PRK07003 DNA polymerase III su 84.2 1.3 2.9E-05 57.5 5.5 28 1085-1112 38-65 (830)
321 PF05673 DUF815: Protein of un 84.2 0.81 1.8E-05 52.4 3.2 27 1086-1112 53-79 (249)
322 PLN02200 adenylate kinase fami 84.0 0.96 2.1E-05 50.9 3.7 22 1085-1106 43-64 (234)
323 PRK13768 GTPase; Provisional 83.9 0.94 2E-05 51.5 3.6 26 1087-1112 4-29 (253)
324 PRK14531 adenylate kinase; Pro 83.9 0.84 1.8E-05 48.9 3.1 19 1087-1105 4-22 (183)
325 TIGR00235 udk uridine kinase. 83.8 0.97 2.1E-05 49.3 3.6 25 1084-1108 5-29 (207)
326 PRK06305 DNA polymerase III su 83.8 0.97 2.1E-05 55.6 4.0 28 1085-1112 39-66 (451)
327 PF06068 TIP49: TIP49 C-termin 83.8 0.9 2E-05 54.7 3.5 25 1085-1109 50-74 (398)
328 PRK14948 DNA polymerase III su 83.8 1.4 3.1E-05 56.3 5.5 27 1086-1112 39-65 (620)
329 PRK05563 DNA polymerase III su 83.5 1.5 3.3E-05 55.4 5.6 27 1086-1112 39-65 (559)
330 PRK06696 uridine kinase; Valid 83.5 1.8 3.9E-05 47.9 5.5 26 1084-1109 21-46 (223)
331 PRK12727 flagellar biosynthesi 83.5 2.5 5.5E-05 53.2 7.3 29 1083-1111 348-376 (559)
332 PF12846 AAA_10: AAA-like doma 83.4 0.99 2.2E-05 50.3 3.5 27 1087-1113 3-29 (304)
333 COG2255 RuvB Holliday junction 83.4 1.4 3E-05 51.5 4.7 39 1065-1108 35-74 (332)
334 PRK08118 topology modulation p 83.3 0.89 1.9E-05 48.5 3.0 15 1088-1102 4-18 (167)
335 TIGR00176 mobB molybdopterin-g 83.3 1 2.2E-05 47.7 3.3 25 1088-1112 2-26 (155)
336 PF00485 PRK: Phosphoribulokin 83.2 1 2.2E-05 48.7 3.4 24 1087-1110 1-24 (194)
337 CHL00081 chlI Mg-protoporyphyr 83.1 1.6 3.5E-05 52.3 5.2 25 1086-1110 39-63 (350)
338 TIGR02903 spore_lon_C ATP-depe 83.0 1.5 3.3E-05 56.0 5.3 22 1086-1107 176-197 (615)
339 PF00005 ABC_tran: ABC transpo 83.0 0.75 1.6E-05 46.1 2.2 23 1085-1107 11-33 (137)
340 PRK07667 uridine kinase; Provi 83.0 1.8 3.9E-05 47.0 5.2 25 1085-1109 17-41 (193)
341 PF14532 Sigma54_activ_2: Sigm 83.0 0.69 1.5E-05 47.3 1.9 16 1086-1101 22-37 (138)
342 PF03205 MobB: Molybdopterin g 82.9 1.2 2.7E-05 46.4 3.7 28 1086-1113 1-28 (140)
343 PRK07994 DNA polymerase III su 82.9 1.7 3.8E-05 55.8 5.7 27 1086-1112 39-65 (647)
344 cd01125 repA Hexameric Replica 82.8 1 2.2E-05 50.2 3.3 25 1086-1110 2-26 (239)
345 cd01983 Fer4_NifH The Fer4_Nif 82.8 1.2 2.7E-05 40.6 3.3 24 1088-1111 2-25 (99)
346 PRK03839 putative kinase; Prov 82.7 1.1 2.4E-05 47.5 3.4 17 1088-1104 3-19 (180)
347 COG1936 Predicted nucleotide k 82.7 0.92 2E-05 49.6 2.8 14 1087-1100 2-15 (180)
348 PRK14954 DNA polymerase III su 82.7 0.81 1.7E-05 58.5 2.7 27 1086-1112 39-65 (620)
349 cd00983 recA RecA is a bacter 82.7 1.8 4E-05 51.3 5.4 28 1084-1111 54-81 (325)
350 PRK09435 membrane ATPase/prote 82.5 1.9 4.1E-05 51.4 5.5 29 1084-1112 55-83 (332)
351 PRK13947 shikimate kinase; Pro 82.5 1 2.2E-05 47.0 3.0 17 1088-1104 4-20 (171)
352 PRK08451 DNA polymerase III su 82.3 1.8 3.9E-05 54.6 5.4 27 1086-1112 37-63 (535)
353 TIGR01407 dinG_rel DnaQ family 82.2 3.7 8.1E-05 54.3 8.6 33 1061-1100 244-279 (850)
354 PRK09087 hypothetical protein; 82.2 1.5 3.2E-05 49.2 4.2 22 1085-1106 44-65 (226)
355 PRK07940 DNA polymerase III su 82.2 0.89 1.9E-05 55.1 2.7 27 1086-1112 37-63 (394)
356 TIGR00764 lon_rel lon-related 82.2 1.4 3E-05 56.3 4.5 25 1086-1110 38-62 (608)
357 PRK06547 hypothetical protein; 82.1 1.6 3.5E-05 47.0 4.4 25 1084-1108 14-38 (172)
358 PRK14532 adenylate kinase; Pro 82.1 0.97 2.1E-05 48.2 2.7 17 1088-1104 3-19 (188)
359 COG1198 PriA Primosomal protei 82.1 3.6 7.9E-05 53.6 8.1 48 1061-1112 197-244 (730)
360 PRK12608 transcription termina 82.0 2.2 4.8E-05 51.6 5.9 26 1087-1112 135-160 (380)
361 PRK01184 hypothetical protein; 82.0 1.1 2.4E-05 47.6 3.0 15 1087-1101 3-17 (184)
362 COG1074 RecB ATP-dependent exo 81.9 2.1 4.6E-05 58.3 6.3 54 1086-1190 17-70 (1139)
363 COG0419 SbcC ATPase involved i 81.9 1.1 2.3E-05 59.6 3.5 30 1084-1113 24-53 (908)
364 PRK14528 adenylate kinase; Pro 81.8 1.1 2.4E-05 48.4 3.1 19 1087-1105 3-21 (186)
365 PRK05342 clpX ATP-dependent pr 81.8 1.1 2.3E-05 54.7 3.3 21 1086-1106 109-129 (412)
366 KOG1942 DNA helicase, TBP-inte 81.8 0.93 2E-05 52.9 2.5 24 1086-1109 65-88 (456)
367 PRK06995 flhF flagellar biosyn 81.8 2 4.4E-05 53.4 5.6 28 1085-1112 256-283 (484)
368 PRK08074 bifunctional ATP-depe 81.7 3.9 8.5E-05 54.7 8.5 33 1061-1100 256-291 (928)
369 PF05127 Helicase_RecD: Helica 81.7 0.4 8.6E-06 52.3 -0.4 21 1170-1190 27-47 (177)
370 PLN03137 ATP-dependent DNA hel 81.7 4.4 9.6E-05 54.9 8.8 38 1055-1100 452-490 (1195)
371 COG0507 RecD ATP-dependent exo 81.6 2.6 5.6E-05 54.3 6.7 44 1061-1112 318-361 (696)
372 TIGR02902 spore_lonB ATP-depen 81.6 1.7 3.7E-05 54.5 5.0 21 1086-1106 87-107 (531)
373 PF07088 GvpD: GvpD gas vesicl 81.6 0.65 1.4E-05 56.1 1.3 28 1086-1113 11-38 (484)
374 PTZ00202 tuzin; Provisional 81.6 1.8 4E-05 53.4 5.0 41 1066-1108 269-309 (550)
375 PF08477 Miro: Miro-like prote 81.6 1.3 2.8E-05 43.0 3.1 21 1088-1108 2-22 (119)
376 PRK02496 adk adenylate kinase; 81.5 1.3 2.7E-05 47.2 3.3 18 1088-1105 4-21 (184)
377 PRK07261 topology modulation p 81.4 1.2 2.6E-05 47.5 3.1 18 1088-1105 3-20 (171)
378 cd02020 CMPK Cytidine monophos 81.4 1.3 2.9E-05 44.5 3.2 19 1088-1106 2-20 (147)
379 PRK07471 DNA polymerase III su 81.3 2.3 5.1E-05 51.1 5.7 41 1069-1113 29-69 (365)
380 PRK10463 hydrogenase nickel in 81.1 2.2 4.8E-05 49.9 5.3 44 1063-1111 87-130 (290)
381 PRK10865 protein disaggregatio 81.1 1.2 2.6E-05 58.9 3.6 27 1085-1111 199-225 (857)
382 PF13177 DNA_pol3_delta2: DNA 81.1 2.5 5.3E-05 45.0 5.3 30 1084-1113 18-47 (162)
383 cd00227 CPT Chloramphenicol (C 81.1 1.5 3.3E-05 46.5 3.7 23 1086-1108 3-25 (175)
384 PF02399 Herpes_ori_bp: Origin 80.9 3.4 7.3E-05 54.1 7.2 56 1084-1194 48-103 (824)
385 cd03112 CobW_like The function 80.9 1.3 2.8E-05 46.8 3.1 23 1086-1108 1-23 (158)
386 cd02025 PanK Pantothenate kina 80.9 1.3 2.8E-05 49.4 3.2 22 1088-1109 2-23 (220)
387 PF13479 AAA_24: AAA domain 80.9 1 2.2E-05 49.7 2.4 19 1087-1105 5-23 (213)
388 cd03114 ArgK-like The function 80.6 2.4 5.3E-05 44.5 4.9 23 1088-1110 2-24 (148)
389 PRK00300 gmk guanylate kinase; 80.6 1.6 3.4E-05 47.1 3.6 24 1084-1107 4-27 (205)
390 PRK14530 adenylate kinase; Pro 80.6 1.5 3.3E-05 48.1 3.6 19 1087-1105 5-23 (215)
391 TIGR01243 CDC48 AAA family ATP 80.6 1.1 2.4E-05 58.0 3.0 20 1088-1107 490-509 (733)
392 COG1102 Cmk Cytidylate kinase 80.4 1 2.2E-05 49.0 2.1 21 1088-1113 3-23 (179)
393 PF00406 ADK: Adenylate kinase 80.4 1.3 2.7E-05 45.8 2.8 17 1090-1106 1-17 (151)
394 TIGR03817 DECH_helic helicase/ 80.4 6.1 0.00013 51.8 9.4 77 1055-1193 25-105 (742)
395 TIGR03346 chaperone_ClpB ATP-d 80.2 2.2 4.7E-05 56.5 5.4 27 1085-1111 595-621 (852)
396 PRK14959 DNA polymerase III su 80.1 2.2 4.9E-05 54.5 5.3 28 1085-1112 38-65 (624)
397 PRK09302 circadian clock prote 80.1 3.4 7.4E-05 51.3 6.8 27 1085-1111 31-57 (509)
398 PRK13765 ATP-dependent proteas 80.0 2.1 4.5E-05 55.0 5.0 24 1086-1109 51-74 (637)
399 PRK08699 DNA polymerase III su 79.9 2.5 5.4E-05 50.0 5.3 27 1086-1112 22-48 (325)
400 cd02028 UMPK_like Uridine mono 79.8 1.6 3.4E-05 47.1 3.3 23 1087-1109 1-23 (179)
401 PRK15455 PrkA family serine pr 79.8 2.3 4.9E-05 54.1 5.0 26 1084-1109 102-127 (644)
402 TIGR03345 VI_ClpV1 type VI sec 79.5 2.5 5.5E-05 56.0 5.7 28 1084-1111 595-622 (852)
403 KOG1970 Checkpoint RAD17-RFC c 79.3 1.5 3.2E-05 55.0 3.2 22 1086-1107 111-132 (634)
404 PRK10751 molybdopterin-guanine 79.3 1.9 4E-05 47.0 3.7 27 1085-1111 6-32 (173)
405 COG1618 Predicted nucleotide k 79.2 1.6 3.4E-05 47.5 3.0 25 1088-1112 8-32 (179)
406 PRK10078 ribose 1,5-bisphospho 79.2 1.5 3.2E-05 47.2 2.8 20 1086-1105 3-22 (186)
407 PRK05439 pantothenate kinase; 79.1 3.1 6.7E-05 49.2 5.6 28 1083-1111 84-111 (311)
408 COG3854 SpoIIIAA ncharacterize 79.1 1.6 3.4E-05 49.9 3.1 20 1088-1107 140-159 (308)
409 PF02463 SMC_N: RecF/RecN/SMC 79.1 1.6 3.5E-05 47.6 3.2 25 1085-1109 24-48 (220)
410 TIGR00554 panK_bact pantothena 79.0 2.9 6.4E-05 48.9 5.4 30 1082-1112 59-88 (290)
411 PRK09354 recA recombinase A; P 79.0 1.9 4.2E-05 51.6 4.0 28 1084-1111 59-86 (349)
412 TIGR00455 apsK adenylylsulfate 78.9 2 4.4E-05 45.8 3.8 26 1085-1110 18-43 (184)
413 TIGR03574 selen_PSTK L-seryl-t 78.9 1.6 3.6E-05 48.9 3.2 22 1088-1109 2-23 (249)
414 PRK14953 DNA polymerase III su 78.8 2.8 6.1E-05 52.2 5.5 25 1086-1110 39-63 (486)
415 TIGR03263 guanyl_kin guanylate 78.8 1.6 3.5E-05 46.0 3.0 22 1086-1107 2-23 (180)
416 KOG0734 AAA+-type ATPase conta 78.8 1.2 2.6E-05 55.5 2.2 22 1085-1106 337-358 (752)
417 CHL00206 ycf2 Ycf2; Provisiona 78.8 1.3 2.9E-05 61.9 2.9 21 1087-1107 1632-1652(2281)
418 TIGR00382 clpX endopeptidase C 78.8 1.6 3.5E-05 53.3 3.3 21 1086-1106 117-137 (413)
419 cd00464 SK Shikimate kinase (S 78.7 1.7 3.7E-05 44.2 3.0 17 1089-1105 3-19 (154)
420 TIGR00041 DTMP_kinase thymidyl 78.7 1.9 4.1E-05 46.0 3.5 23 1086-1108 4-26 (195)
421 PRK14738 gmk guanylate kinase; 78.6 1.8 3.8E-05 47.6 3.3 23 1084-1106 12-34 (206)
422 PRK05564 DNA polymerase III su 78.6 3.1 6.7E-05 48.4 5.5 43 1066-1112 11-53 (313)
423 KOG3347 Predicted nucleotide k 78.5 1.6 3.5E-05 46.9 2.8 21 1086-1106 8-28 (176)
424 PRK13975 thymidylate kinase; P 78.4 1.9 4.1E-05 46.0 3.4 22 1086-1107 3-24 (196)
425 KOG2108 3'-5' DNA helicase [Re 78.2 1.2 2.6E-05 57.8 2.2 78 1057-1197 8-85 (853)
426 TIGR00665 DnaB replicative DNA 78.2 4.2 9E-05 49.4 6.6 26 1085-1110 195-220 (434)
427 TIGR02788 VirB11 P-type DNA tr 78.1 2.3 5.1E-05 49.6 4.3 22 1086-1107 145-166 (308)
428 PRK13695 putative NTPase; Prov 77.9 2 4.3E-05 45.5 3.4 23 1088-1110 3-25 (174)
429 KOG0990 Replication factor C, 77.8 0.98 2.1E-05 53.4 1.1 26 1086-1111 63-88 (360)
430 PRK07764 DNA polymerase III su 77.8 2.9 6.2E-05 55.3 5.4 27 1086-1112 38-64 (824)
431 PHA02530 pseT polynucleotide k 77.8 1.6 3.5E-05 49.8 2.9 22 1086-1107 3-24 (300)
432 TIGR03346 chaperone_ClpB ATP-d 77.8 1.8 3.9E-05 57.2 3.6 26 1086-1111 195-220 (852)
433 TIGR02639 ClpA ATP-dependent C 77.8 1.7 3.6E-05 56.6 3.3 25 1088-1112 206-230 (731)
434 PRK11131 ATP-dependent RNA hel 77.8 4.1 8.9E-05 55.9 6.9 31 1068-1105 79-109 (1294)
435 CHL00095 clpC Clp protease ATP 77.8 2.9 6.2E-05 55.2 5.4 43 1064-1111 184-226 (821)
436 PRK07246 bifunctional ATP-depe 77.7 6.8 0.00015 51.9 8.7 32 1062-1100 245-279 (820)
437 PRK11034 clpA ATP-dependent Cl 77.7 3 6.4E-05 54.7 5.4 23 1085-1107 488-510 (758)
438 KOG0727 26S proteasome regulat 77.7 1.5 3.3E-05 50.4 2.5 21 1085-1105 189-209 (408)
439 PRK14086 dnaA chromosomal repl 77.6 4.2 9E-05 52.1 6.5 26 1087-1112 316-341 (617)
440 PF03029 ATP_bind_1: Conserved 77.6 1.5 3.3E-05 49.6 2.5 22 1090-1111 1-22 (238)
441 PRK00279 adk adenylate kinase; 77.5 1.8 3.9E-05 47.5 3.0 16 1088-1103 3-18 (215)
442 TIGR00101 ureG urease accessor 77.5 2 4.4E-05 47.2 3.4 23 1087-1109 3-25 (199)
443 cd03275 ABC_SMC1_euk Eukaryoti 77.4 2.1 4.6E-05 48.1 3.6 24 1086-1109 23-46 (247)
444 PRK05707 DNA polymerase III su 77.4 1.6 3.5E-05 51.6 2.8 27 1086-1112 23-49 (328)
445 cd04163 Era Era subfamily. Er 77.4 1.7 3.7E-05 43.3 2.5 22 1086-1107 4-25 (168)
446 PF07724 AAA_2: AAA domain (Cd 77.3 2.4 5.1E-05 45.7 3.8 25 1086-1110 4-28 (171)
447 PLN03187 meiotic recombination 77.3 1.8 3.9E-05 51.7 3.1 23 1083-1105 124-146 (344)
448 cd03272 ABC_SMC3_euk Eukaryoti 77.1 2.2 4.8E-05 47.2 3.6 24 1086-1109 24-47 (243)
449 TIGR00073 hypB hydrogenase acc 77.1 2.3 4.9E-05 46.5 3.6 25 1085-1109 22-46 (207)
450 TIGR01351 adk adenylate kinase 77.1 1.8 3.8E-05 47.4 2.8 18 1088-1105 2-19 (210)
451 TIGR00368 Mg chelatase-related 77.1 2.4 5.2E-05 53.0 4.2 35 1066-1107 199-233 (499)
452 COG0378 HypB Ni2+-binding GTPa 76.9 1.7 3.8E-05 48.3 2.6 25 1088-1112 16-40 (202)
453 TIGR02238 recomb_DMC1 meiotic 76.9 1.8 4E-05 50.9 3.0 23 1084-1106 95-117 (313)
454 KOG0736 Peroxisome assembly fa 76.8 2.5 5.4E-05 54.7 4.3 25 1083-1107 429-453 (953)
455 CHL00095 clpC Clp protease ATP 76.6 3.1 6.6E-05 54.9 5.2 26 1086-1111 540-565 (821)
456 TIGR02621 cas3_GSU0051 CRISPR- 76.5 5.5 0.00012 52.7 7.3 40 1056-1102 9-48 (844)
457 TIGR00390 hslU ATP-dependent p 76.4 2.2 4.9E-05 52.3 3.6 22 1086-1107 48-69 (441)
458 PRK10646 ADP-binding protein; 76.4 4.2 9.2E-05 43.6 5.3 43 1064-1109 10-52 (153)
459 cd00876 Ras Ras family. The R 75.8 2 4.3E-05 43.1 2.6 20 1088-1107 2-21 (160)
460 KOG0962 DNA repair protein RAD 75.7 1.8 3.8E-05 58.7 2.7 24 1086-1109 28-51 (1294)
461 cd03273 ABC_SMC2_euk Eukaryoti 75.7 2.6 5.7E-05 47.3 3.7 25 1085-1109 25-49 (251)
462 PTZ00035 Rad51 protein; Provis 75.7 2.4 5.1E-05 50.5 3.5 25 1083-1107 116-140 (337)
463 PF03308 ArgK: ArgK protein; 75.7 2.9 6.3E-05 48.4 4.0 27 1086-1112 30-56 (266)
464 PRK06761 hypothetical protein; 75.6 2.2 4.8E-05 49.7 3.2 24 1086-1109 4-27 (282)
465 COG0606 Predicted ATPase with 75.6 2.3 4.9E-05 52.7 3.3 19 1088-1106 201-219 (490)
466 PRK14723 flhF flagellar biosyn 75.5 6.2 0.00013 51.8 7.4 26 1085-1110 185-210 (767)
467 cd03116 MobB Molybdenum is an 75.4 2.6 5.7E-05 45.0 3.5 26 1087-1112 3-28 (159)
468 PRK14737 gmk guanylate kinase; 75.4 2.5 5.5E-05 46.0 3.4 23 1085-1107 4-26 (186)
469 PRK09825 idnK D-gluconate kina 75.4 2.7 5.7E-05 45.4 3.5 22 1086-1107 4-25 (176)
470 KOG0979 Structural maintenance 75.3 2.2 4.7E-05 56.3 3.2 28 1082-1109 39-66 (1072)
471 PRK13949 shikimate kinase; Pro 75.3 2.2 4.7E-05 45.7 2.8 16 1088-1103 4-19 (169)
472 TIGR02688 conserved hypothetic 75.3 2.5 5.3E-05 52.0 3.5 21 1088-1108 212-232 (449)
473 smart00173 RAS Ras subfamily o 75.2 2.3 5.1E-05 43.3 2.9 19 1089-1107 4-22 (164)
474 PF01745 IPT: Isopentenyl tran 75.2 2.1 4.5E-05 48.4 2.7 21 1086-1106 2-22 (233)
475 TIGR02639 ClpA ATP-dependent C 75.0 3.8 8.3E-05 53.4 5.4 24 1086-1109 485-508 (731)
476 COG0802 Predicted ATPase or ki 75.0 5 0.00011 43.0 5.3 46 1063-1111 6-51 (149)
477 KOG0652 26S proteasome regulat 74.9 2.1 4.6E-05 49.4 2.7 22 1084-1105 204-225 (424)
478 KOG1533 Predicted GTPase [Gene 74.9 1.9 4.1E-05 49.3 2.3 25 1088-1113 5-29 (290)
479 PRK12339 2-phosphoglycerate ki 74.9 2.5 5.5E-05 46.6 3.3 22 1086-1107 4-25 (197)
480 cd03240 ABC_Rad50 The catalyti 74.8 2.9 6.4E-05 45.9 3.7 26 1086-1111 23-48 (204)
481 PRK08058 DNA polymerase III su 74.7 3.1 6.8E-05 49.1 4.2 29 1084-1112 27-55 (329)
482 PRK09270 nucleoside triphospha 74.7 3 6.4E-05 46.4 3.8 26 1084-1109 32-57 (229)
483 TIGR03819 heli_sec_ATPase heli 74.7 3.8 8.3E-05 48.9 4.9 39 1062-1107 162-200 (340)
484 cd01918 HprK_C HprK/P, the bif 74.7 2.5 5.3E-05 45.1 3.0 22 1086-1107 15-36 (149)
485 PRK14712 conjugal transfer nic 74.3 7.6 0.00016 54.6 8.1 65 1062-1188 281-346 (1623)
486 PTZ00301 uridine kinase; Provi 74.3 3 6.6E-05 46.5 3.7 27 1086-1112 4-30 (210)
487 cd01672 TMPK Thymidine monopho 74.3 3 6.4E-05 43.9 3.5 23 1087-1109 2-24 (200)
488 PRK04220 2-phosphoglycerate ki 74.2 2.9 6.4E-05 49.2 3.7 25 1085-1109 92-116 (301)
489 TIGR03600 phage_DnaB phage rep 74.2 6.3 0.00014 47.9 6.6 26 1084-1109 193-218 (421)
490 cd00820 PEPCK_HprK Phosphoenol 74.2 2.7 5.9E-05 42.5 3.0 22 1085-1106 15-36 (107)
491 cd03255 ABC_MJ0796_Lo1CDE_FtsE 74.0 2.5 5.5E-05 46.0 3.0 23 1085-1107 30-52 (218)
492 PRK10733 hflB ATP-dependent me 74.0 2.3 4.9E-05 54.7 3.0 20 1088-1107 188-207 (644)
493 PRK11034 clpA ATP-dependent Cl 74.0 2.5 5.3E-05 55.4 3.3 25 1088-1112 210-234 (758)
494 TIGR00634 recN DNA repair prot 73.8 35 0.00075 43.4 13.2 23 1085-1107 22-44 (563)
495 COG1136 SalX ABC-type antimicr 73.8 2.3 4.9E-05 48.3 2.6 27 1084-1111 30-56 (226)
496 PF01926 MMR_HSR1: 50S ribosom 73.7 2.6 5.6E-05 41.3 2.7 19 1088-1106 2-20 (116)
497 PF00158 Sigma54_activat: Sigm 73.7 3.9 8.4E-05 44.0 4.2 16 1086-1101 23-38 (168)
498 cd04155 Arl3 Arl3 subfamily. 73.6 2.4 5.1E-05 43.8 2.5 22 1086-1107 15-36 (173)
499 cd03278 ABC_SMC_barmotin Barmo 73.5 3.2 6.9E-05 45.4 3.6 23 1086-1108 23-45 (197)
500 PRK12337 2-phosphoglycerate ki 73.5 2.7 5.9E-05 52.1 3.3 26 1084-1109 254-279 (475)
No 1
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=100.00 E-value=3.4e-32 Score=319.93 Aligned_cols=350 Identities=24% Similarity=0.266 Sum_probs=220.2
Q ss_pred ccccccCcccCChhHHHHhhhHHHHHHHHHHHHhhhhhcCccccccccceEEEeeeeeCCeEEEEEeecCCCCccccCCC
Q 000592 857 CKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDMYYGSLSVLSVERVDDFHLVRFVHDDNDSVTSKIFS 936 (1402)
Q Consensus 857 ~kLkkIP~TF~S~eEYi~tFePLLLEE~wAQL~SS~eEiss~E~~~~g~IsVlS~erVDdF~~V~f~~~~~~~~~~~~fs 936 (1402)
.+...|-.+|.+..+|.++|.||+-.|+...- .+.|. .....+.|.+---.+.-+...|..... .....+.
T Consensus 227 ~~~~hv~~ry~da~~y~~vf~pliklea~ydk--~~Kes-----~~q~~~tvRW~~gLnkk~~a~f~~~k~--~~e~kl~ 297 (935)
T KOG1802|consen 227 EEPPHVQLRYEDAYEYQNVFSPLIKLEADYDK--RLKES-----QTQENGTVRWDIGLNKKRLAYFTLPKL--DSELKLA 297 (935)
T ss_pred cCCCcccccccchHHHhhhcchhhhhhhhhhh--hhhhh-----cccccceEEeeeccccceEEEEecCCC--cchhccc
Confidence 35667888999999999999999999986543 22221 112223343322233334444544432 2345788
Q ss_pred CCcEEEEEecCCCCCCCceeEEEEEEeeeccCCCCceEEEEEEEecCCccchhHHHhhhhcccceeeeeeccccHHHHHH
Q 000592 937 ENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLREF 1016 (1402)
Q Consensus 937 EGDLVLLSk~~P~~s~~~~~~LGkVer~e~d~~k~~~iL~LR~~l~n~ssrLnq~~~~Lt~~S~w~~~KL~SLTTilREy 1016 (1402)
.||-+.|+.+...... ..-+|.|.+.-.. ......+.+++... .+. ..++.+.+..+-+-+++.|++
T Consensus 298 ~GdE~~L~y~~~~~~~--w~~~g~v~~~pd~-~~dE~~lEl~~~~~---~p~-------e~~~~Ftvd~vwk~ts~drm~ 364 (935)
T KOG1802|consen 298 IGDEIRLTYSGGLVLP--WNGIGSVLKIPDN-NGDEVKLELEFSQD---PPI-------EVTHGFTVDFVWKSTSFDRMQ 364 (935)
T ss_pred cCCeeEEEecCCcCCc--ccccceEEecCCC-CcceeEEEeecCCC---CCc-------ccccceEEEEEEcCccHHHHH
Confidence 9999999876543221 3447888766432 22233344444321 111 123446666777889999999
Q ss_pred HhhccCCC-------CCCcccccCCCCCCCCCCCcccccccchhH-HHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceE
Q 000592 1017 HALSSLKS-------IPLLPIILNPVNVSRGYNESRELDLGKLSQ-LQQILKTSFNESQLQAISVAIGLSSSWKKDCELS 1088 (1402)
Q Consensus 1017 ~AL~sL~~-------lPL~~~ILsP~~~~~~~~e~~~~~l~ki~~-L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfs 1088 (1402)
.||..|.. |-+...+-.|...... ...+|. +-..--.+||.||..|+..+|++ +++
T Consensus 365 ~alk~la~D~~~vs~y~y~klLgh~~~~~~~--------k~~LP~~~s~~~lpkLN~SQ~~AV~~VL~r--------pls 428 (935)
T KOG1802|consen 365 LALKLLAVDEKKVSGYLYHKLLGHPVEDSSL--------KKLLPRRFSVPNLPKLNASQSNAVKHVLQR--------PLS 428 (935)
T ss_pred HHHHHhhhccccchhhhhhHHhcCcchhhhh--------cccCchhhcCCCchhhchHHHHHHHHHHcC--------Cce
Confidence 99987642 2222222223222100 011221 10000137999999999999976 699
Q ss_pred EEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhccccccccccccccC
Q 000592 1089 LIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSV 1168 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~ 1168 (1402)
|||||||||||.|+..||..|....
T Consensus 429 LIQGPPGTGKTvtsa~IVyhl~~~~------------------------------------------------------- 453 (935)
T KOG1802|consen 429 LIQGPPGTGKTVTSATIVYHLARQH------------------------------------------------------- 453 (935)
T ss_pred eeecCCCCCceehhHHHHHHHHHhc-------------------------------------------------------
Confidence 9999999999999999999887652
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEeccccc--ccCCCccccHHHHHHHHHHHhhhccCCCcccc
Q 000592 1169 RARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKT--VHPNSLPFFIDTLVDHRLAEERMHLTDPKNEF 1246 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~~a--v~s~v~~vsLD~LVeqrLs~~~~~~~~sk~~~ 1246 (1402)
..+||||||||.|||+|+++|.+.|+ +|||+-...+ +.++|..++|.++++.. .
T Consensus 454 ~~~VLvcApSNiAVDqLaeKIh~tgL----------KVvRl~aksRE~~~S~vs~L~lh~~~~~~------~-------- 509 (935)
T KOG1802|consen 454 AGPVLVCAPSNIAVDQLAEKIHKTGL----------KVVRLCAKSREDIESDVSFLSLHEQLRNM------D-------- 509 (935)
T ss_pred CCceEEEcccchhHHHHHHHHHhcCc----------eEeeeehhhhhhccCCccHHHHHHHHhcc------C--------
Confidence 46899999999999999999999887 7999998654 34445555555554311 0
Q ss_pred cccchHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCccccccccCCCCcCchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 000592 1247 CTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQ 1326 (1402)
Q Consensus 1247 ~~~ss~Lrs~Le~L~~ei~~~ea~R~~l~~~~~~~k~~l~~e~~g~d~~~ls~~el~~kL~~L~eqR~qL~~eL~~~~~~ 1326 (1402)
..+|+++.+. +.+ + ++++..
T Consensus 510 -------~pELq~l~kl-------kde-----------------~---gelS~s-------------------------- 529 (935)
T KOG1802|consen 510 -------KPELQKLLKL-------KDE-----------------G---GELSSS-------------------------- 529 (935)
T ss_pred -------cHHHHHHHhh-------hhh-----------------c---ccccch--------------------------
Confidence 0122222110 000 0 011000
Q ss_pred HhhHHHHHHHHHHHHHHHHhccCcEEEEeCCCCCcCccccccccccccccCCCCCCCCCCEEEEecCcccccccCC
Q 000592 1327 EKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHEL 1402 (1402)
Q Consensus 1327 ek~~~~e~~~lRrrir~~IL~eAdIVCSTLSGSG~dll~~c~et~aa~kf~~~~~~~~FDtVIIDEAAQAvElStL 1402 (1402)
-....+.+.++...++|..|||||||+.|+|...|. ..+|.+||||||+||.||++|
T Consensus 530 ---D~~k~~~lk~~~e~ell~~AdVIccTcv~Agd~rl~----------------~~kfr~VLiDEaTQatEpe~L 586 (935)
T KOG1802|consen 530 ---DEKKYRKLKRAAEKELLNQADVICCTCVGAGDRRLS----------------KFKFRTVLIDEATQATEPECL 586 (935)
T ss_pred ---hhHHHHHHHHHHHHHHHhhcCEEEEecccccchhhc----------------cccccEEEEecccccCCcchh
Confidence 001233456778899999999999999999986653 368999999999999999986
No 2
>KOG1803 consensus DNA helicase [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-32 Score=324.60 Aligned_cols=358 Identities=27% Similarity=0.363 Sum_probs=221.2
Q ss_pred hHHHHhhhHHHHHHHHHHHHhhhhhcC--ccccccccceEEEeee----e--eCCeEEEEEeecCCCCccccCCCCCcEE
Q 000592 870 EQFVSIFRPLVLEEFKAQLHSSFLEMS--SWEDMYYGSLSVLSVE----R--VDDFHLVRFVHDDNDSVTSKIFSENDLV 941 (1402)
Q Consensus 870 eEYi~tFePLLLEE~wAQL~SS~eEis--s~E~~~~g~IsVlS~e----r--VDdF~~V~f~~~~~~~~~~~~fsEGDLV 941 (1402)
+++...+.+||-+|..+.+.-...... ..+.......++.... + ..+.+++.|.... ...+...|++||+|
T Consensus 3 ~~f~sk~~~ll~~er~~ei~~t~~~~~~~~ie~l~~~g~~i~nl~~v~~~tGl~g~~li~f~~~~-~~lp~~~~~~gd~v 81 (649)
T KOG1803|consen 3 EEFVSKMSELLDHERKAEISVTEKSLDNVPIEALQRKGLAILNLWLVSVRTGLGGKSLIVFSKNR-EVLPSNSFGPGDVV 81 (649)
T ss_pred hHHHHHHHHHHHhhhhcchhhhhHhhhcCCHHHHHhccceeeeEEEEEEeecccceEEEEeccCc-cccCcCCCCCCcEE
Confidence 678889999999999888763211111 1111111122222221 1 2245667776554 45667789999999
Q ss_pred EEEecCCCCCCCceeEEEEEEeeeccCCCCceEEEEEEEecCCccchhHHHhhhhcccceeeeeeccccHHHHHHHhhcc
Q 000592 942 LLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLREFHALSS 1021 (1402)
Q Consensus 942 LLSk~~P~~s~~~~~~LGkVer~e~d~~k~~~iL~LR~~l~n~ssrLnq~~~~Lt~~S~w~~~KL~SLTTilREy~AL~s 1021 (1402)
.|.. ++......+.+-|.|++...+ .+.+.+.-.. .... ..+...+.++.+-.|+.|+..++..
T Consensus 82 ~lr~-~~~~~~~~~~~~GvV~~~~~~------~i~~a~ee~~-d~~~--------~~~~l~l~kl~n~vty~R~~~~~i~ 145 (649)
T KOG1803|consen 82 WLRT-DKLNNKSKPCTEGVVYRVAED------SIDVAFEEEV-DKPL--------TLSSLRLLKLENKVTYRRMKDTMIC 145 (649)
T ss_pred EEEc-ccccccCcccccceeEeeccc------hhhHhHHhhh-cccc--------hhhHHHHHHhhhhhhheecHHHHhh
Confidence 9983 333333444677888876543 1222111000 0000 0012345567788899999988877
Q ss_pred CCC--CC-----CcccccCCCCCCCCCCCcccccccchhHHHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCC
Q 000592 1022 LKS--IP-----LLPIILNPVNVSRGYNESRELDLGKLSQLQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPP 1094 (1402)
Q Consensus 1022 L~~--lP-----L~~~ILsP~~~~~~~~e~~~~~l~ki~~L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPP 1094 (1402)
+.. .| +...++........ .+....-..++..++|.||.+||..++... .+.+|||||
T Consensus 146 l~~~~~~~~~~~vv~~l~~~~~~~~~--------~~~~~~~~~~~~~~ln~SQk~Av~~~~~~k-------~l~~I~GPP 210 (649)
T KOG1803|consen 146 LSKFSNPGPSSDVVETLFGDRKPIPS--------PNIEIKKITFFNKNLNSSQKAAVSFAINNK-------DLLIIHGPP 210 (649)
T ss_pred HhhhcCccchhhhHHHHhccccCCCC--------chhhhcccccCCccccHHHHHHHHHHhccC-------CceEeeCCC
Confidence 653 22 22222221111100 000000223456789999999999987542 699999999
Q ss_pred CCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhccccccccccccccCCCeEEE
Q 000592 1095 GTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRARVLI 1174 (1402)
Q Consensus 1095 GTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILV 1174 (1402)
|||||+|++.||..++.. ++||||
T Consensus 211 GTGKT~TlvEiI~qlvk~--------------------------------------------------------~k~VLV 234 (649)
T KOG1803|consen 211 GTGKTRTLVEIISQLVKQ--------------------------------------------------------KKRVLV 234 (649)
T ss_pred CCCceeeHHHHHHHHHHc--------------------------------------------------------CCeEEE
Confidence 999999999999988764 579999
Q ss_pred EeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEecccccccCCCccccHHHHHHHHHHHhhhccCCCcccccccchHHH
Q 000592 1175 CAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKTVHPNSLPFFIDTLVDHRLAEERMHLTDPKNEFCTRSSTLR 1254 (1402)
Q Consensus 1175 CAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~~av~s~v~~vsLD~LVeqrLs~~~~~~~~sk~~~~~~ss~Lr 1254 (1402)
|||||.|||+|+.||.-.|+ ++||+|.+.+..+.+.+.+||.++....+... ...++
T Consensus 235 caPSn~AVdNiverl~~~~~----------~l~R~g~paRl~~~~~~~sld~~~~t~d~~~~-------------~~~~s 291 (649)
T KOG1803|consen 235 CAPSNVAVDNIVERLTHLKL----------NLVRVGHPARLLESVADHSLDLLSNTKDNSQN-------------AKDIS 291 (649)
T ss_pred EcCchHHHHHHHHHhccccc----------chhhcCchhhhhhhhhhhHHHHHHhcCchhhh-------------hhhhH
Confidence 99999999999999984443 79999999999999999999988764321110 01112
Q ss_pred HHHHHHHHHHHHHHHhhhcccCCCCCCCCccccccccCCCCcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Q 000592 1255 SNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKKSYEET 1334 (1402)
Q Consensus 1255 s~Le~L~~ei~~~ea~R~~l~~~~~~~k~~l~~e~~g~d~~~ls~~el~~kL~~L~eqR~qL~~eL~~~~~~ek~~~~e~ 1334 (1402)
+.++..... ...+ + + ...|+.+.+++..+ +++.
T Consensus 292 k~~d~~~~~-------~~~t----------------k-------~----------~~~~~~~~~~i~~l-------rkdl 324 (649)
T KOG1803|consen 292 KDIDILFQK-------NTKT----------------K-------N----------DKLRKGIRKEIKLL-------RKDL 324 (649)
T ss_pred HHHHHHhhh-------hhcc----------------c-------c----------hHHHHHHHHHHHHH-------HHHH
Confidence 222222110 0000 0 0 01122222223222 2333
Q ss_pred HHHHHHHHHHHhccCcEEEEeCCCCCcCccccccccccccccCCCCCCCCCCEEEEecCcccccccC
Q 000592 1335 KALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1401 (1402)
Q Consensus 1335 ~~lRrrir~~IL~eAdIVCSTLSGSG~dll~~c~et~aa~kf~~~~~~~~FDtVIIDEAAQAvElSt 1401 (1402)
++.+++.-.+|+.+|+||++||-||...++ .+..||+|||||||||+|++|
T Consensus 325 ~kre~~~v~eii~n~~VVfaTl~ga~~~~~----------------~~~~fD~vIIDEaaQamE~~c 375 (649)
T KOG1803|consen 325 RKRERKTVKEIISNSRVVFATLGGALDRLL----------------RKRTFDLVIIDEAAQAMEPQC 375 (649)
T ss_pred HHHHHHHHHHhhcccceEEEeccchhhhhh----------------cccCCCEEEEehhhhhccchh
Confidence 444567788999999999999999997443 346799999999999999987
No 3
>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=99.98 E-value=9.8e-31 Score=320.98 Aligned_cols=336 Identities=27% Similarity=0.358 Sum_probs=212.7
Q ss_pred EEEeeeeeCCeEEEEEeecCCCCccccCCCCCcEEEEEecCCCCCCCceeEEEEEEeeeccCCCCceEEEEEEEecCCcc
Q 000592 907 SVLSVERVDDFHLVRFVHDDNDSVTSKIFSENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSV 986 (1402)
Q Consensus 907 sVlS~erVDdF~~V~f~~~~~~~~~~~~fsEGDLVLLSk~~P~~s~~~~~~LGkVer~e~d~~k~~~iL~LR~~l~n~ss 986 (1402)
.+.......+.++++|..... ....|..||+|+++..++.. ..+-|+|.++... .+++.+.. . .
T Consensus 33 ~~~~~~~~~g~~~~~f~~~~~---~~~~~~~GD~v~i~~~~~~~----~~~~g~V~~v~~~------~i~v~~~~--~-~ 96 (637)
T TIGR00376 33 QGKIRGGLLGFLLVRFGRRKA---IATEISVGDIVLVSRGNPLQ----SDLTGVVTRVGKR------FITVALEE--S-V 96 (637)
T ss_pred EEEEEeCCCCeEEEEEecCCC---CCCcCCCCCEEEEecCCCCC----CCcEEEEEEEcCc------EEEEEECC--C-C
Confidence 334333445688899985432 24588999999999765432 3468999988642 34455431 1 0
Q ss_pred chhHHHhhhhcccceeeeeeccccHHHHHHHhhccCCCC--CCcccccCCCCCCCCCCCcccccccchhHHHHHhhcCCC
Q 000592 987 RLNQARRNLLERSKWHATLIMSITPQLREFHALSSLKSI--PLLPIILNPVNVSRGYNESRELDLGKLSQLQQILKTSFN 1064 (1402)
Q Consensus 987 rLnq~~~~Lt~~S~w~~~KL~SLTTilREy~AL~sL~~l--PL~~~ILsP~~~~~~~~e~~~~~l~ki~~L~~~Lk~~lN 1064 (1402)
. . .....|.+.++.|-+|+.|++.||..+... ++.+.||+....... .+. ..+ ..+...+|
T Consensus 97 ~------~-~~~~~~~i~~~~~~~t~~rm~~aL~~l~~~~~~l~~~llg~~~p~~~-~~~--------~~~-~~~~~~ln 159 (637)
T TIGR00376 97 P------Q-WSLKRVRIDLYANDVTFKRMKEALRALTENHSRLLEFILGREAPSKA-SEI--------HDF-QFFDPNLN 159 (637)
T ss_pred C------c-ccCceEEEEEecCccHHHHHHHHHHHHHhchhhHHHHHhCCCCCCcc-ccc--------ccc-cccCCCCC
Confidence 0 0 012348888999999999999999988653 566777764322110 000 001 12335799
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHH
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAW 1144 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W 1144 (1402)
.+|.+||..++... +++|||||||||||+||++++..++..
T Consensus 160 ~~Q~~Av~~~l~~~-------~~~lI~GpPGTGKT~t~~~ii~~~~~~-------------------------------- 200 (637)
T TIGR00376 160 ESQKEAVSFALSSK-------DLFLIHGPPGTGKTRTLVELIRQLVKR-------------------------------- 200 (637)
T ss_pred HHHHHHHHHHhcCC-------CeEEEEcCCCCCHHHHHHHHHHHHHHc--------------------------------
Confidence 99999999987643 599999999999999999999876643
Q ss_pred HHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEecccccccCCCccccH
Q 000592 1145 QDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKTVHPNSLPFFI 1224 (1402)
Q Consensus 1145 ~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~~av~s~v~~vsL 1224 (1402)
+.+||||||||.|||+|+.||.+.| .++||+|+..++.+.+..++|
T Consensus 201 ------------------------g~~VLv~a~sn~Avd~l~e~l~~~~----------~~vvRlg~~~r~~~~~~~~sl 246 (637)
T TIGR00376 201 ------------------------GLRVLVTAPSNIAVDNLLERLALCD----------QKIVRLGHPARLLKSNKQHSL 246 (637)
T ss_pred ------------------------CCCEEEEcCcHHHHHHHHHHHHhCC----------CcEEEeCCchhcchhHHhccH
Confidence 3599999999999999999999654 379999999999999999999
Q ss_pred HHHHHHHHHHhhhccCCCcccccccchHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCccccccccCCCCcCchHHHHH
Q 000592 1225 DTLVDHRLAEERMHLTDPKNEFCTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDVELEA 1304 (1402)
Q Consensus 1225 D~LVeqrLs~~~~~~~~sk~~~~~~ss~Lrs~Le~L~~ei~~~ea~R~~l~~~~~~~k~~l~~e~~g~d~~~ls~~el~~ 1304 (1402)
|++++..-. ......++.+++++.++.. ....+. +.....+++..+
T Consensus 247 ~~~~~~~~~-------------~~~~~~~~~~i~~~~~~~~---~~~~~~----------------~~~~~~~~~~~~-- 292 (637)
T TIGR00376 247 DYLIENHPK-------------YQIVADIREKIDELIEERN---KKLKPS----------------PQKRRGLSDIKI-- 292 (637)
T ss_pred HHHHhcChh-------------HHHHHHHHHHHHHHHHHHH---hhccch----------------HhHhhccchHHH--
Confidence 988763210 0111224444444433211 000000 000011122111
Q ss_pred HHHHHHHHH--HHHHH-------HHHHHHHHHhhHHHHHHHHHHHHHHHHhccCcEEEEeCCCCCcCccccccccccccc
Q 000592 1305 KLRKLYEQK--KQIYR-------ELGVAQVQEKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFK 1375 (1402)
Q Consensus 1305 kL~~L~eqR--~qL~~-------eL~~~~~~ek~~~~e~~~lRrrir~~IL~eAdIVCSTLSGSG~dll~~c~et~aa~k 1375 (1402)
+++..++| +.+.. .........+....+++..+.++..+||++|+|+|+|+ |+..|
T Consensus 293 -l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~a~v~~st~---~~~~l----------- 357 (637)
T TIGR00376 293 -LRKALKKREARGIESLKIASMAEWIETNKSIDRLLKLLPEIEERIENEILAESDVVQSTN---SSAGL----------- 357 (637)
T ss_pred -HHHHHhhhhhcccchhhhHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhCCEEEecc---CcHhh-----------
Confidence 11111111 11111 11112223333445566667889999999999998874 45444
Q ss_pred cCCCCCCCCCCEEEEecCcccccccCC
Q 000592 1376 FGNPSENTLFDAVVIDEAAQVVLVHEL 1402 (1402)
Q Consensus 1376 f~~~~~~~~FDtVIIDEAAQAvElStL 1402 (1402)
....||+||||||+||+|+++|
T Consensus 358 -----~~~~Fd~vIIDEAsQ~~ep~~l 379 (637)
T TIGR00376 358 -----KGWEFDVAVIDEASQAMEPSCL 379 (637)
T ss_pred -----ccCCCCEEEEECccccchHHHH
Confidence 2468999999999999999864
No 4
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A.
Probab=99.96 E-value=1.2e-29 Score=266.60 Aligned_cols=208 Identities=35% Similarity=0.568 Sum_probs=116.1
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
+||++|.+||..++... .+++||||||||||+||++++..++.....
T Consensus 1 ~ln~~Q~~Ai~~~~~~~-------~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~-------------------------- 47 (236)
T PF13086_consen 1 KLNESQREAIQSALSSN-------GITLIQGPPGTGKTTTLASIIAQLLQRFKS-------------------------- 47 (236)
T ss_dssp ---HHHHHHHHHHCTSS-------E-EEEE-STTSSHHHHHHHHHHHH--------------------------------
T ss_pred CCCHHHHHHHHHHHcCC-------CCEEEECCCCCChHHHHHHHHHHhccchhh--------------------------
Confidence 48999999999987653 379999999999999999999887542100
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEecccc-cccCCCc
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVK-TVHPNSL 1220 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~~-av~s~v~ 1220 (1402)
.....+.+||||||||+|||+++.||.+ +.+..+..+.+.++|+|+.. ..++.+.
T Consensus 48 ----------------------~~~~~~~~il~~~~sN~avd~~~~~l~~--~~~~~~~~~~~~~ir~~~~~~~~~~~~~ 103 (236)
T PF13086_consen 48 ----------------------RSADRGKKILVVSPSNAAVDNILERLKK--LLDEDGKVYKPKIIRLGSEEEKIHEDLQ 103 (236)
T ss_dssp -----------------------HCCCSS-EEEEESSHHHHHHHHHHHHC----------TT--EEE---GGTTS--TTG
T ss_pred ----------------------hhhhccccceeecCCchhHHHHHHHHHh--hccccccccccchhhhcccccccccccc
Confidence 0012478999999999999999999995 66777888889999999988 6788888
Q ss_pred cccHHHHHHHHHHHhhhccCCCcccccccchHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCccccccccCCCCcCchH
Q 000592 1221 PFFIDTLVDHRLAEERMHLTDPKNEFCTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNMLDDEVHKGDDVKLSDV 1300 (1402)
Q Consensus 1221 ~vsLD~LVeqrLs~~~~~~~~sk~~~~~~ss~Lrs~Le~L~~ei~~~ea~R~~l~~~~~~~k~~l~~e~~g~d~~~ls~~ 1300 (1402)
++++++.++++..... ..++++++++.+.+..... +
T Consensus 104 ~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~-~----------------------------- 139 (236)
T PF13086_consen 104 KFSLESKLEQRFESKL--------------KRLREQLEELQQKIRLSEL-K----------------------------- 139 (236)
T ss_dssp GGBHHHHHHTTT-------------------------THHHCHHHHHHH-H-----------------------------
T ss_pred cccccccccccccccc--------------hhhhHHHHHHHHhhhhhhh-h-----------------------------
Confidence 8988877665432100 0112222222211100000 0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhccCcEEEEeCCCCCcCccccccccccccccCCCC
Q 000592 1301 ELEAKLRKLYEQKKQIYRELGVAQVQEKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKFGNPS 1380 (1402)
Q Consensus 1301 el~~kL~~L~eqR~qL~~eL~~~~~~ek~~~~e~~~lRrrir~~IL~eAdIVCSTLSGSG~dll~~c~et~aa~kf~~~~ 1380 (1402)
.+............+..+..++.+...++++++||++|+++|++..+..
T Consensus 140 -----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~vi~~T~~~~~~~~~~~-------------- 188 (236)
T PF13086_consen 140 -----------------EEKKKLKKSIKRLRKELEKIREELRRFILKEADVIFTTLSSAASPFLSN-------------- 188 (236)
T ss_dssp -----------------HHHCCSSCHHHHHHHHHHHHHHHHHHHHHHT-SEEEEETCGGG-CCGTT--------------
T ss_pred -----------------hhhhhcchhcccccccccccccchhhhhcccccccccccccchhhHhhh--------------
Confidence 0000000011112233444566777999999999999999998776532
Q ss_pred CCCCCCEEEEecCcccccccC
Q 000592 1381 ENTLFDAVVIDEAAQVVLVHE 1401 (1402)
Q Consensus 1381 ~~~~FDtVIIDEAAQAvElSt 1401 (1402)
....||+||||||+|+.|+++
T Consensus 189 ~~~~~d~vIvDEAsq~~e~~~ 209 (236)
T PF13086_consen 189 FKEKFDVVIVDEASQITEPEA 209 (236)
T ss_dssp -----SEEEETTGGGS-HHHH
T ss_pred hcccCCEEEEeCCCCcchHHH
Confidence 112799999999999999875
No 5
>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]
Probab=99.81 E-value=1.1e-19 Score=222.91 Aligned_cols=99 Identities=31% Similarity=0.584 Sum_probs=84.7
Q ss_pred hHHHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCC
Q 000592 1053 SQLQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRP 1132 (1402)
Q Consensus 1053 ~~L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp 1132 (1402)
|.........||..|++|+..|+... .+.||.|-||||||+||+.||-.|+..
T Consensus 660 p~~~~~~~~~LN~dQr~A~~k~L~ae-------dy~LI~GMPGTGKTTtI~~LIkiL~~~-------------------- 712 (1100)
T KOG1805|consen 660 PKIKKIILLRLNNDQRQALLKALAAE-------DYALILGMPGTGKTTTISLLIKILVAL-------------------- 712 (1100)
T ss_pred chhhHHHHhhcCHHHHHHHHHHHhcc-------chheeecCCCCCchhhHHHHHHHHHHc--------------------
Confidence 33334344689999999999998765 499999999999999999999988765
Q ss_pred ccchhHHHHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEeccc
Q 000592 1133 KIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNV 1212 (1402)
Q Consensus 1133 ~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~ 1212 (1402)
+++||+.|+||.|||+|+.+|...|+ .++|+|..
T Consensus 713 ------------------------------------gkkVLLtsyThsAVDNILiKL~~~~i----------~~lRLG~~ 746 (1100)
T KOG1805|consen 713 ------------------------------------GKKVLLTSYTHSAVDNILIKLKGFGI----------YILRLGSE 746 (1100)
T ss_pred ------------------------------------CCeEEEEehhhHHHHHHHHHHhccCc----------ceeecCCc
Confidence 58999999999999999999996665 59999999
Q ss_pred ccccCCCccccH
Q 000592 1213 KTVHPNSLPFFI 1224 (1402)
Q Consensus 1213 ~av~s~v~~vsL 1224 (1402)
.++|+.++.+++
T Consensus 747 ~kih~~v~e~~~ 758 (1100)
T KOG1805|consen 747 EKIHPDVEEFTL 758 (1100)
T ss_pred cccchHHHHHhc
Confidence 999998866553
No 6
>KOG1807 consensus Helicases [Replication, recombination and repair]
Probab=99.68 E-value=1.6e-15 Score=182.84 Aligned_cols=265 Identities=23% Similarity=0.278 Sum_probs=156.1
Q ss_pred ccCcccCChhHHHHhhhHHHHHHHHHHHHhhhhhcCc-c-------ccccccceEEEeeeeeCCeEE---------EEEe
Q 000592 861 EVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSS-W-------EDMYYGSLSVLSVERVDDFHL---------VRFV 923 (1402)
Q Consensus 861 kIP~TF~S~eEYi~tFePLLLEE~wAQL~SS~eEiss-~-------E~~~~g~IsVlS~erVDdF~~---------V~f~ 923 (1402)
.|-..|+|+.+|+++-.-||-|.+-.-+..+...... . ....|..++|....++|+... +.|.
T Consensus 154 ~i~gkyds~~~yld~hfrllrEdfVsplregilllkkn~n~~g~r~~~akcddisiy~~~ridg~~~ss~sgi~~k~qf~ 233 (1025)
T KOG1807|consen 154 RIGGKYDSLWSYLDLHFRLLREDFVSPLREGILLLKKNKNLLGARAAVAKCDDISIYILSRIDGMLLSSHSGILLKHQFY 233 (1025)
T ss_pred ccccchhHHHHHHHHHHhhHHHHhhhHHHHHHHHHhhCchhhhhhhccCCCccceeeeeecccceEeecccceEEEEeeh
Confidence 4556899999999999999999988877766544321 1 122344566666666665432 2222
Q ss_pred ec---CCCCccccCCCCCcEEEEEecCCCCCCCceeEEEEEEeeeccCCCCceEEEEEEEecCCccchhHHHhhhhcccc
Q 000592 924 HD---DNDSVTSKIFSENDLVLLTRVSPQKTPHDVHMVGKVERRERDNNRRSSILLIRFYLQNGSVRLNQARRNLLERSK 1000 (1402)
Q Consensus 924 ~~---~~~~~~~~~fsEGDLVLLSk~~P~~s~~~~~~LGkVer~e~d~~k~~~iL~LR~~l~n~ssrLnq~~~~Lt~~S~ 1000 (1402)
.. ...+..+.....|++|.++.++.... ..+|.|-. ++ .++ +..+.+.+. .....+.++..
T Consensus 234 ~~~~k~kklansrrl~~gslV~ls~dnF~et----f~~gtv~~-s~-L~r-~le~~~~~~---------~~~ap~~p~de 297 (1025)
T KOG1807|consen 234 ELVEKYKKLANSRRLDMGSLVELSTDNFSET----FKGGTVPT-SG-LNR-PLETLLGKD---------ATKAPNEPEDE 297 (1025)
T ss_pred HHHHHHHHhccchhccccceEEEecCchhhh----eeeeeecc-hh-ccc-cchhhhhhh---------hhcCCCCCccc
Confidence 11 11234456788999999999876432 45777755 22 222 112211111 00111112221
Q ss_pred eeeeeeccccH---------HHHHHHhhccCCCCCCcccccCCCCCCCCC---CCcccc----cccchhH-HHHHhh---
Q 000592 1001 WHATLIMSITP---------QLREFHALSSLKSIPLLPIILNPVNVSRGY---NESREL----DLGKLSQ-LQQILK--- 1060 (1402)
Q Consensus 1001 w~~~KL~SLTT---------ilREy~AL~sL~~lPL~~~ILsP~~~~~~~---~e~~~~----~l~ki~~-L~~~Lk--- 1060 (1402)
.+|+-.| .+|+..-+....-.|+.+++.......... ..+... .+.+.++ ..+.+.
T Consensus 298 ----ylm~e~t~~Y~eayrhVLr~lqr~s~~~~vpf~rylvhc~s~~~~pr~L~~~~rytinp~~~n~s~~~~n~lePp~ 373 (1025)
T KOG1807|consen 298 ----YLMSEKTVKYVEAYRHVLRELQRASLVEFVPFLRYLVHCDSLKQQPRLLWSDVRYTINPQFANASRHIVNALEPPG 373 (1025)
T ss_pred ----eeehhhHHHHHHHHHHHHHHhhhcccccccchhhhhccchhhhhchHHhhcCCceecCccccCchhhhhhhcCCCC
Confidence 2233333 445554444444467666655422110000 000000 0011111 112221
Q ss_pred ---cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchh
Q 000592 1061 ---TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQS 1137 (1402)
Q Consensus 1061 ---~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~ 1137 (1402)
..+..||+.|..+++.. ..+|||||||||||.+-+-+|-.||...-.
T Consensus 374 ~g~~ildsSq~~A~qs~lty--------elsliqgppGTgkt~vtlkav~tLL~n~s~---------------------- 423 (1025)
T KOG1807|consen 374 PGLVILDSSQQFAKQSKLTY--------ELSLIQGPPGTGKTLVTLKAVDTLLLNSSG---------------------- 423 (1025)
T ss_pred CCceeecHHHHHHHHHHhhh--------hhheeecCCCCCceeehHHHHHHHHhcccc----------------------
Confidence 24788999999998765 599999999999999999999999986310
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEeccc
Q 000592 1138 AAIARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNV 1212 (1402)
Q Consensus 1138 ~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~ 1212 (1402)
-..+.+|||.+.||+|||+++.|+... .+|+|+|+|..
T Consensus 424 ----------------------------~~~~epIlvvC~Tnhavdq~ligiy~~---------qrpsImr~gsr 461 (1025)
T KOG1807|consen 424 ----------------------------YTEPEPILVVCLTNHAVDQYLIGIYYH---------QRPSIMRQGSR 461 (1025)
T ss_pred ----------------------------cccccceeeeehhhHHHHHHHHHHHhc---------CCceEEEeccc
Confidence 123679999999999999999999842 25899999975
No 7
>KOG1801 consensus tRNA-splicing endonuclease positive effector (SEN1) [RNA processing and modification]
Probab=99.31 E-value=2.2e-12 Score=163.74 Aligned_cols=277 Identities=18% Similarity=0.192 Sum_probs=150.4
Q ss_pred chhhhhhceeecCcccCCCCCCcccccccccccccCcccCChhHHHHhhhHHHHHHHHHHHHhhhhhcCccccc---ccc
Q 000592 828 DDWYKPILEIDYFATVGLASSREDENRVHCKLKEVPVCFQSPEQFVSIFRPLVLEEFKAQLHSSFLEMSSWEDM---YYG 904 (1402)
Q Consensus 828 d~L~k~ILSWDy~~il~~~~~~~d~~l~~~kLkkIP~TF~S~eEYi~tFePLLLEE~wAQL~SS~eEiss~E~~---~~g 904 (1402)
.++....++|.+.+..+ . ..+|.+|.+.++|+..|.|.|+||+++++.++.......... ...
T Consensus 6 ~~~~~~~~~~~~~~~~~---------~-----~~~~~~~~~~~~~~~~~~p~~~ee~~~~l~~s~~~~~~~~~~~~~~~~ 71 (827)
T KOG1801|consen 6 TDLLDSSLSWSLRDVEN---------E-----ETEPETFQSMEEYIREFFPPLLEECRSSLVSSSRKLKAPFLLEKPEQE 71 (827)
T ss_pred ccHHHHhHHHHhhhhhh---------h-----hccchhhhhHHHHHHHhhhhhhHHHHHHHhhhhhhhccchhhhhhhhh
Confidence 46778889999876631 1 789999999999999999999999999999886655421100 000
Q ss_pred ceEEEeeee--eCCeEEEEE---eec-CCCCccccCCCCCcEEEEEecCCCCC-CCceeEEEEEEeeeccCCCCceEEEE
Q 000592 905 SLSVLSVER--VDDFHLVRF---VHD-DNDSVTSKIFSENDLVLLTRVSPQKT-PHDVHMVGKVERRERDNNRRSSILLI 977 (1402)
Q Consensus 905 ~IsVlS~er--VDdF~~V~f---~~~-~~~~~~~~~fsEGDLVLLSk~~P~~s-~~~~~~LGkVer~e~d~~k~~~iL~L 977 (1402)
.+.+....+ .+.++.... ... .............|++-++...+... ...+..+.++..-... ++
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~------ 143 (827)
T KOG1801|consen 72 QIAITKNNPTSKDLRQLTNEKNIFTKEKSEKTASSVEKHLDNIRHSDAIGFAASDHIPGLLPYLASPDLE--KG------ 143 (827)
T ss_pred hhhcccCCCCchhhhcchhHHHHHhhhhccccccccccccchhhhcccCCccccccChhhhhhhcccccc--cc------
Confidence 000110000 111111110 000 11111122345677776663332211 1112222222221110 00
Q ss_pred EEEecCCccchhHHHhhhhcccceeeeeeccccHHHHHHHhhccCCCCCCcccccCCCCCCC----CCCCcccccccchh
Q 000592 978 RFYLQNGSVRLNQARRNLLERSKWHATLIMSITPQLREFHALSSLKSIPLLPIILNPVNVSR----GYNESRELDLGKLS 1053 (1402)
Q Consensus 978 R~~l~n~ssrLnq~~~~Lt~~S~w~~~KL~SLTTilREy~AL~sL~~lPL~~~ILsP~~~~~----~~~e~~~~~l~ki~ 1053 (1402)
.+...........+...+...++..|++..++|.+++..... ...+..+..... ....+.........
T Consensus 144 ------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (827)
T KOG1801|consen 144 ------PSVDLSLAATKSLPSLICAGAFLRVLVENKNEYILIACHANN--HGLHRPDLRFNEVNERTVHKVFENFSVIGS 215 (827)
T ss_pred ------cccccccchhccccccchHHHHHHHHhhcchhhhhccccccc--cccccccccccccccccccccccccccccc
Confidence 000000000000111122245677899999999999876541 111111100000 00000000000000
Q ss_pred -HHHHHhh-cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCC--ChhhHHHHHHHHHHHhcCCCCcccccCcccccC
Q 000592 1054 -QLQQILK-TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGT--GKTRTIVAIVSALLATRTSPKSHLKQNYSSCIN 1129 (1402)
Q Consensus 1054 -~L~~~Lk-~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGT--GKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~ 1129 (1402)
...+++. ..+|.+|..++...+...+ |.+...+++|+||||| |||+|...+...++..
T Consensus 216 ~~~~d~~~~~~l~~~~~~~~~~~l~~~~-~~~~~~~~~v~~~~~~~~~~~~t~~~~~~~~~~~----------------- 277 (827)
T KOG1801|consen 216 LFVGDVIRFTKLSRDQEPLIRGVLSQRN-CEWEVSISLVVGRPGTASGKFKTVAQLLNVLLGL----------------- 277 (827)
T ss_pred cchhhhhhhcccchhhHHHHhhccCccc-cccccceeeeeCCCCccccceeccchHHHHHHhc-----------------
Confidence 1222332 4799999999999888766 8888899999999999 9999888877766554
Q ss_pred CCCccchhHHHHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1130 SRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1130 ~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
..++++|+|||.++=+...|+..
T Consensus 278 ---------------------------------------~~~~~~~s~~~~~~~~~~~r~~~ 300 (827)
T KOG1801|consen 278 ---------------------------------------DCQMLVCSLSNSNILLLTSRLYK 300 (827)
T ss_pred ---------------------------------------ccceeEeeccccchhhhHHHHHh
Confidence 46889999999999888888884
No 8
>PF13245 AAA_19: Part of AAA domain
Probab=99.17 E-value=6.1e-11 Score=110.23 Aligned_cols=61 Identities=46% Similarity=0.681 Sum_probs=50.6
Q ss_pred HHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHH
Q 000592 1070 AISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAAL 1149 (1402)
Q Consensus 1070 AI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~ 1149 (1402)
||..|+. . .++.+|+||||||||+|++.++..++....
T Consensus 2 av~~al~-~------~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~----------------------------------- 39 (76)
T PF13245_consen 2 AVRRALA-G------SPLFVVQGPPGTGKTTTLAARIAELLAARA----------------------------------- 39 (76)
T ss_pred HHHHHHh-h------CCeEEEECCCCCCHHHHHHHHHHHHHHHhc-----------------------------------
Confidence 6666665 2 379999999999999999999998885420
Q ss_pred HhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHH
Q 000592 1150 ARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1189 (1402)
Q Consensus 1150 arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RL 1189 (1402)
. ++++|||++|+|+|+|+|..||
T Consensus 40 ----------------~-~~~~vlv~a~t~~aa~~l~~rl 62 (76)
T PF13245_consen 40 ----------------D-PGKRVLVLAPTRAAADELRERL 62 (76)
T ss_pred ----------------C-CCCeEEEECCCHHHHHHHHHHH
Confidence 1 2579999999999999999999
No 9
>COG1112 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]
Probab=99.16 E-value=2.3e-10 Score=143.19 Aligned_cols=230 Identities=25% Similarity=0.298 Sum_probs=131.5
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..++..|..++..+... ...+.+.+||||||||..+ .++..+....
T Consensus 273 ~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~--------------------------- 318 (767)
T COG1112 273 KELDNEQKLAVKRLLSL------NDLFLIHQGPFGTGKTRSV-TILELIIELL--------------------------- 318 (767)
T ss_pred hhccchhHHHHHHHhcc------cceeEeecCCCCCCcchHH-HHHHHHHHHH---------------------------
Confidence 46788888888877654 2367777799999999966 3222222221
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEecccccccCCCc
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKTVHPNSL 1220 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~~av~s~v~ 1220 (1402)
...+.++|.|+|+|.++|+++.|+.+... . ...+|+|..........
T Consensus 319 -------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-------~~~~~~~~~~~~~~~~~ 365 (767)
T COG1112 319 -------------------------ENNKLKILPTAESNAAVDNLLRRLKRTVI-K-------VELLRIGHPSRVLKKLK 365 (767)
T ss_pred -------------------------HhcccceEEecCcccchhhHHHHHHhhcc-c-------cceEEcCCcchhhhhhh
Confidence 01267999999999999999999995432 1 23899999887777666
Q ss_pred cccHHHHHHHHHHHhhhccCCCcccccccchHHHHHHHHHHHHHHH----HHHhhhcccCCCCCCCCccccccccCCCCc
Q 000592 1221 PFFIDTLVDHRLAEERMHLTDPKNEFCTRSSTLRSNLEKLVDRIRF----FEAKRANTKDGNSDPKNMLDDEVHKGDDVK 1296 (1402)
Q Consensus 1221 ~vsLD~LVeqrLs~~~~~~~~sk~~~~~~ss~Lrs~Le~L~~ei~~----~ea~R~~l~~~~~~~k~~l~~e~~g~d~~~ 1296 (1402)
..++...+...... .+ ....+...+..+..+... ....+... . ....
T Consensus 366 ~~~l~~~~~~~~~~--------~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~--~~~~---- 416 (767)
T COG1112 366 LDTLEELLEKHEIP--------GN----KIAALDKVIRELREEGERIIREIAKLRERL-----------E--RKRL---- 416 (767)
T ss_pred hhHHHHHHHhcccc--------cc----hhHHHHHHHHHHhhhhhccceecHHHHhhh-----------h--hhHH----
Confidence 66666554332100 00 111111222222111000 00000000 0 0000
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhccCcEEEEeCCCCCcCcccccccccccccc
Q 000592 1297 LSDVELEAKLRKLYEQKKQIYRELGVAQVQEKKSYEETKALKHKLRKSILKEAEIVVTTLSGCGGDLYGVCSESVSGFKF 1376 (1402)
Q Consensus 1297 ls~~el~~kL~~L~eqR~qL~~eL~~~~~~ek~~~~e~~~lRrrir~~IL~eAdIVCSTLSGSG~dll~~c~et~aa~kf 1376 (1402)
..........+.+.......................+.+..+......+...+++||+|+++|++..+..
T Consensus 417 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~a~~~~~~~---------- 486 (767)
T COG1112 417 DKISHLNVALRGILPALNKSEALWISLEEKQKKILKELRRLKKKAVTKILEAADVVLSTLSIAGFSILKK---------- 486 (767)
T ss_pred HHHHHhhhhhcchhHHHHHHHHHHHhhhhhHHhHHHHHhHhHHHHHHHHHHhcCeEEEeccchhHHHhcc----------
Confidence 0000000001111111112222222333334455566677788888999999999999999999877642
Q ss_pred CCCCCCCCCCEEEEecCcccccccCC
Q 000592 1377 GNPSENTLFDAVVIDEAAQVVLVHEL 1402 (1402)
Q Consensus 1377 ~~~~~~~~FDtVIIDEAAQAvElStL 1402 (1402)
..||+||||||+|+.|+.++
T Consensus 487 ------~~fd~viiDEAsQ~~~~~~~ 506 (767)
T COG1112 487 ------YEFDYVIIDEASQATEPSAL 506 (767)
T ss_pred ------cccCEEEEcchhcccchhHH
Confidence 37999999999999998764
No 10
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=98.91 E-value=3.3e-09 Score=114.07 Aligned_cols=66 Identities=36% Similarity=0.483 Sum_probs=52.3
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
+||+.|.+|+..++... ..+++||||||||||+++..++.++...
T Consensus 1 ~L~~~Q~~a~~~~l~~~------~~~~~l~G~aGtGKT~~l~~~~~~~~~~----------------------------- 45 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSG------DRVSVLQGPAGTGKTTLLKALAEALEAA----------------------------- 45 (196)
T ss_dssp -S-HHHHHHHHHHHHCT------CSEEEEEESTTSTHHHHHHHHHHHHHHT-----------------------------
T ss_pred CCCHHHHHHHHHHHhcC------CeEEEEEECCCCCHHHHHHHHHHHHHhC-----------------------------
Confidence 48999999999987653 3799999999999999988766554332
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHH
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRI 1189 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RL 1189 (1402)
+.+|++|||||.|++++..++
T Consensus 46 ---------------------------g~~v~~~apT~~Aa~~L~~~~ 66 (196)
T PF13604_consen 46 ---------------------------GKRVIGLAPTNKAAKELREKT 66 (196)
T ss_dssp ---------------------------T--EEEEESSHHHHHHHHHHH
T ss_pred ---------------------------CCeEEEECCcHHHHHHHHHhh
Confidence 479999999999999988885
No 11
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=98.48 E-value=3.2e-07 Score=114.12 Aligned_cols=66 Identities=32% Similarity=0.485 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHH
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAW 1144 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W 1144 (1402)
+.|+.|+..|+.. +|++|.||||||||+||..++..++....
T Consensus 155 d~Qk~Av~~a~~~--------~~~vItGgpGTGKTt~v~~ll~~l~~~~~------------------------------ 196 (615)
T PRK10875 155 DWQKVAAAVALTR--------RISVISGGPGTGKTTTVAKLLAALIQLAD------------------------------ 196 (615)
T ss_pred HHHHHHHHHHhcC--------CeEEEEeCCCCCHHHHHHHHHHHHHHhcC------------------------------
Confidence 7899999988753 69999999999999999999998876420
Q ss_pred HHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1145 QDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1145 ~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
.+..+|++||||+.|..++.+++.
T Consensus 197 ----------------------~~~~~i~l~APTgkAA~rL~e~~~ 220 (615)
T PRK10875 197 ----------------------GERCRIRLAAPTGKAAARLTESLG 220 (615)
T ss_pred ----------------------CCCcEEEEECCcHHHHHHHHHHHH
Confidence 124689999999999999988775
No 12
>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=98.44 E-value=4.2e-07 Score=101.00 Aligned_cols=67 Identities=27% Similarity=0.359 Sum_probs=55.1
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIAR 1142 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar 1142 (1402)
+|+.|.++|.. ..+..+|+|+||||||+|++..+..++....
T Consensus 1 l~~eQ~~~i~~----------~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~---------------------------- 42 (315)
T PF00580_consen 1 LTDEQRRIIRS----------TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG---------------------------- 42 (315)
T ss_dssp S-HHHHHHHHS-----------SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS----------------------------
T ss_pred CCHHHHHHHhC----------CCCCEEEEeCCCCCchHHHHHHHHHhhcccc----------------------------
Confidence 68899999975 2379999999999999999999998887630
Q ss_pred HHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1143 AWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1143 ~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.++.+||+.++||+|.+|+-.||.+
T Consensus 43 ------------------------~~~~~Il~lTft~~aa~e~~~ri~~ 67 (315)
T PF00580_consen 43 ------------------------VPPERILVLTFTNAAAQEMRERIRE 67 (315)
T ss_dssp ------------------------STGGGEEEEESSHHHHHHHHHHHHH
T ss_pred ------------------------CChHHheecccCHHHHHHHHHHHHH
Confidence 1246899999999999999999985
No 13
>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=98.38 E-value=6.2e-07 Score=111.23 Aligned_cols=68 Identities=31% Similarity=0.461 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHH
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAW 1144 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W 1144 (1402)
+.|+.|+..++.. +|++|+|+||||||+|+..|+..++....
T Consensus 148 ~~Qk~A~~~al~~--------~~~vitGgpGTGKTt~v~~ll~~l~~~~~------------------------------ 189 (586)
T TIGR01447 148 NWQKVAVALALKS--------NFSLITGGPGTGKTTTVARLLLALVKQSP------------------------------ 189 (586)
T ss_pred HHHHHHHHHHhhC--------CeEEEEcCCCCCHHHHHHHHHHHHHHhcc------------------------------
Confidence 6899999988764 69999999999999999999988876420
Q ss_pred HHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1145 QDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1145 ~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
...+.+|++||||+.|.+++.+.+..
T Consensus 190 ---------------------~~~~~~I~l~APTGkAA~rL~e~~~~ 215 (586)
T TIGR01447 190 ---------------------KQGKLRIALAAPTGKAAARLAESLRK 215 (586)
T ss_pred ---------------------ccCCCcEEEECCcHHHHHHHHHHHHh
Confidence 00135899999999999999887753
No 14
>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair]
Probab=98.37 E-value=4.7e-07 Score=113.65 Aligned_cols=244 Identities=22% Similarity=0.257 Sum_probs=133.4
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.+|..|.+||.+.. .+|.+.+-||||||||-+.+-||+.+-+..
T Consensus 738 ~ft~~qveai~sg~--------qpgltmvvgppgtgktd~avqil~~lyhn~---------------------------- 781 (1320)
T KOG1806|consen 738 KFTPTQVEAILSGM--------QPGLTMVVGPPGTGKTDVAVQILSVLYHNS---------------------------- 781 (1320)
T ss_pred ccCHHHHHHHHhcC--------CCCceeeecCCCCCCcchhhhhhhhhhhcC----------------------------
Confidence 48899999998732 358999999999999999999999887652
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCCCCCCCCccCCcEEEecccccccCCCcc
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGLYGSDGKTYKPYLVRVGNVKTVHPNSLP 1221 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~dGk~y~P~VVRVG~~~av~s~v~~ 1221 (1402)
+..|.||.+.||+|...+-+++++..+ +.+ .+.|+|..+.--..-++
T Consensus 782 --------------------------p~qrTlivthsnqaln~lfeKi~~~d~---d~r----hLlrlg~ge~eletd~d 828 (1320)
T KOG1806|consen 782 --------------------------PNQRTLIVTHSNQALNQLFEKIMALDV---DER----HLLRLGHGEEELETDKD 828 (1320)
T ss_pred --------------------------CCcceEEEEecccchhHHHHHHHhccc---chh----hHHHhcccHHhhhcccc
Confidence 357999999999999999999985433 111 36777754332111111
Q ss_pred cc------------HHHHHHH-HHHHhhhccCCCcccccccchHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCcc---
Q 000592 1222 FF------------IDTLVDH-RLAEERMHLTDPKNEFCTRSSTLRSNLEKLVDRIRFFEAKRANTKDGNSDPKNML--- 1285 (1402)
Q Consensus 1222 vs------------LD~LVeq-rLs~~~~~~~~sk~~~~~~ss~Lrs~Le~L~~ei~~~ea~R~~l~~~~~~~k~~l--- 1285 (1402)
++ +..|-+. |+........ +.+...--.-+.....-++.+|.++++.+ ++-+.+...
T Consensus 829 fsrygrvn~~l~~r~~ll~ev~rla~sl~~pg------dv~ytcetagyf~~~~V~~~wee~l~~v~-~~~~~~~~~~~~ 901 (1320)
T KOG1806|consen 829 FSRYGRVNYVLSRRLELLREVERLAKSLQAPG------DVDYTCETAGYFFLAYVKRRWEEYLAKVD-KGCDKDSVDIVS 901 (1320)
T ss_pred hhheeeEeeeeccchHHHHHHHHhhhhhcCcc------ccccccchhhhhhhhHHHhhhHHHHHHhc-cCCCchhhhhHh
Confidence 11 1111111 1211111100 01110000111111112455677776665 222111111
Q ss_pred ----ccc--cccCCC--CcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhccCcEEEEeCC
Q 000592 1286 ----DDE--VHKGDD--VKLSDVELEAKLRKLYEQKKQIYRELGVAQVQEKKSYEETKALKHKLRKSILKEAEIVVTTLS 1357 (1402)
Q Consensus 1286 ----~~e--~~g~d~--~~ls~~el~~kL~~L~eqR~qL~~eL~~~~~~ek~~~~e~~~lRrrir~~IL~eAdIVCSTLS 1357 (1402)
... ..+.++ .+.+-..-..-.....+.-.++.++|.+.+.- .-++..+++.-...-++|.||-+|+.
T Consensus 902 ~~fpf~~~f~d~p~~vfeg~n~~~d~~~a~~cf~hl~~ifqqLee~raf-----ellr~~~dr~~Yll~kqakiiamtct 976 (1320)
T KOG1806|consen 902 NRFPFHSYFGDKPKPPFEGYNKENDMDYATGCFRHLEYIFQQLEEFRAF-----ELLRSGEDRELYLLVKQAKIIAMTCT 976 (1320)
T ss_pred hhCcchhhhhcCCCccccccchhhhhhhhhhhHHHHHHHHHHHHhcccc-----cccccchhHhhccCcccceeeecccC
Confidence 011 011110 01111111111233444455666666654321 11222344555567799999999988
Q ss_pred CCCc---CccccccccccccccCCCCCCCCCCEEEEecCcccccccC
Q 000592 1358 GCGG---DLYGVCSESVSGFKFGNPSENTLFDAVVIDEAAQVVLVHE 1401 (1402)
Q Consensus 1358 GSG~---dll~~c~et~aa~kf~~~~~~~~FDtVIIDEAAQAvElSt 1401 (1402)
.+.- |++ -.+..||-.+..||||..|.++
T Consensus 977 haalkr~el~---------------~lgf~ydnl~mEesaqile~et 1008 (1320)
T KOG1806|consen 977 HAALRRGDLV---------------KLGFKYDNLLMEESAQILEIET 1008 (1320)
T ss_pred ChhhChhhHh---------------hhceeechhhhhhccCCccccc
Confidence 7763 222 1357899999999999999876
No 15
>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=98.23 E-value=2.7e-06 Score=107.89 Aligned_cols=42 Identities=36% Similarity=0.540 Sum_probs=35.9
Q ss_pred hcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1060 KTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1060 k~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
...||+.|.+||..++.. ++++|+|+||||||+++.+++.++
T Consensus 321 ~~~l~~~Q~~Ai~~~~~~--------~~~iitGgpGTGKTt~l~~i~~~~ 362 (720)
T TIGR01448 321 RKGLSEEQKQALDTAIQH--------KVVILTGGPGTGKTTITRAIIELA 362 (720)
T ss_pred CCCCCHHHHHHHHHHHhC--------CeEEEECCCCCCHHHHHHHHHHHH
Confidence 357999999999988532 699999999999999998887754
No 16
>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=98.10 E-value=5.8e-06 Score=105.35 Aligned_cols=42 Identities=26% Similarity=0.418 Sum_probs=35.1
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..||+.|.+||..++.. .+|++|+||||||||+++.+++.++
T Consensus 351 ~~Ls~~Q~~Av~~i~~s-------~~~~il~G~aGTGKTtll~~i~~~~ 392 (744)
T TIGR02768 351 YRLSEEQYEAVRHVTGS-------GDIAVVVGRAGTGKSTMLKAAREAW 392 (744)
T ss_pred CCCCHHHHHHHHHHhcC-------CCEEEEEecCCCCHHHHHHHHHHHH
Confidence 47999999999987753 2599999999999999988876543
No 17
>PRK10919 ATP-dependent DNA helicase Rep; Provisional
Probab=97.99 E-value=9.3e-06 Score=102.48 Aligned_cols=68 Identities=24% Similarity=0.309 Sum_probs=57.0
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.||+.|.+||.. ..|-.||-++||||||+||+.-+..|+....
T Consensus 2 ~Ln~~Q~~av~~----------~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~--------------------------- 44 (672)
T PRK10919 2 RLNPGQQQAVEF----------VTGPCLVLAGAGSGKTRVITNKIAHLIRGCG--------------------------- 44 (672)
T ss_pred CCCHHHHHHHhC----------CCCCEEEEecCCCCHHHHHHHHHHHHHHhcC---------------------------
Confidence 489999999864 1356789999999999999999999986420
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.++.+||+.+.||.|.+|+..||.+
T Consensus 45 -------------------------v~p~~IL~lTFT~kAA~em~~Rl~~ 69 (672)
T PRK10919 45 -------------------------YQARHIAAVTFTNKAAREMKERVAQ 69 (672)
T ss_pred -------------------------CCHHHeeeEechHHHHHHHHHHHHH
Confidence 1247999999999999999999984
No 18
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.97 E-value=1.6e-05 Score=106.71 Aligned_cols=44 Identities=27% Similarity=0.400 Sum_probs=38.2
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..||+.|.+||..++...+ .|++|||+||||||+++.+++.++-
T Consensus 834 ~~Lt~~Qr~Av~~iLts~d------r~~~IqG~AGTGKTT~l~~i~~~~~ 877 (1623)
T PRK14712 834 EKLTSGQRAATRMILETSD------RFTVVQGYAGVGKTTQFRAVMSAVN 877 (1623)
T ss_pred cccCHHHHHHHHHHHhCCC------ceEEEEeCCCCCHHHHHHHHHHHHH
Confidence 4799999999999987543 7999999999999999988887654
No 19
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=97.94 E-value=1.2e-05 Score=101.96 Aligned_cols=68 Identities=24% Similarity=0.342 Sum_probs=57.5
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.||+.|.+||.. ..+-.||-|.||||||+|++.-+..|+....
T Consensus 4 ~Ln~~Q~~av~~----------~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~--------------------------- 46 (715)
T TIGR01075 4 GLNDKQREAVAA----------PPGNLLVLAGAGSGKTRVLTHRIAWLLSVEN--------------------------- 46 (715)
T ss_pred ccCHHHHHHHcC----------CCCCEEEEecCCCCHHHHHHHHHHHHHHcCC---------------------------
Confidence 699999999864 2356899999999999999999999987520
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.++.+||+.+.||.|.+|+-.||.+
T Consensus 47 -------------------------v~p~~IL~lTFTnkAA~em~~Rl~~ 71 (715)
T TIGR01075 47 -------------------------ASPHSIMAVTFTNKAAAEMRHRIGA 71 (715)
T ss_pred -------------------------CCHHHeEeeeccHHHHHHHHHHHHH
Confidence 1256999999999999999999984
No 20
>KOG1804 consensus RNA helicase [RNA processing and modification]
Probab=97.91 E-value=6.7e-06 Score=103.73 Aligned_cols=71 Identities=30% Similarity=0.359 Sum_probs=50.0
Q ss_pred HhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchh
Q 000592 1058 ILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQS 1137 (1402)
Q Consensus 1058 ~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~ 1137 (1402)
++....++.|..+ +++.. ...--.|+||||||||-|+.+-+..+--.
T Consensus 307 ~l~s~~~~~~~~~---~~~~~-----~~~~y~~~~p~~~g~~~n~~~a~~~v~~~------------------------- 353 (775)
T KOG1804|consen 307 FLNSVAREEQALH---LLLCR-----LPEPYIVFGPPGTGKTENYREAIAIVSFT------------------------- 353 (775)
T ss_pred chhhhhhhhhhhh---hcccc-----cccccccccCCCcCCccchHHHHHHHHhc-------------------------
Confidence 3434455555555 33322 24677899999999999988655543221
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1138 AAIARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1138 ~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
.+..+||+|||||+|-|.+..||.
T Consensus 354 -----------------------------~~~~~il~~~p~~a~~k~~~~rl~ 377 (775)
T KOG1804|consen 354 -----------------------------SPHFYILVCAPSNASGKQPAHRLH 377 (775)
T ss_pred -----------------------------chHHHhhccccccccccccccccc
Confidence 135799999999999999999995
No 21
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=97.90 E-value=1.8e-05 Score=100.71 Aligned_cols=69 Identities=25% Similarity=0.363 Sum_probs=57.9
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..||+.|++||.. ..|-.||-|.||||||+||+.-+..|+....
T Consensus 8 ~~Ln~~Q~~av~~----------~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~-------------------------- 51 (721)
T PRK11773 8 DSLNDKQREAVAA----------PLGNMLVLAGAGSGKTRVLVHRIAWLMQVEN-------------------------- 51 (721)
T ss_pred HhcCHHHHHHHhC----------CCCCEEEEecCCCCHHHHHHHHHHHHHHcCC--------------------------
Confidence 3799999999864 2357889999999999999999999986420
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.++.+||+.+.||.|.+|+-.||.+
T Consensus 52 --------------------------v~p~~IL~lTFT~kAA~Em~~Rl~~ 76 (721)
T PRK11773 52 --------------------------ASPYSIMAVTFTNKAAAEMRHRIEQ 76 (721)
T ss_pred --------------------------CChhHeEeeeccHHHHHHHHHHHHH
Confidence 1257999999999999999999985
No 22
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=97.89 E-value=2.2e-05 Score=102.20 Aligned_cols=39 Identities=21% Similarity=0.288 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.||+.|.+||..+++.. ++++|+|+||||||+++..++.
T Consensus 346 ~Ls~eQr~Av~~il~s~-------~v~vv~G~AGTGKTT~l~~~~~ 384 (988)
T PRK13889 346 VLSGEQADALAHVTDGR-------DLGVVVGYAGTGKSAMLGVARE 384 (988)
T ss_pred CCCHHHHHHHHHHhcCC-------CeEEEEeCCCCCHHHHHHHHHH
Confidence 69999999999887542 5999999999999998655433
No 23
>PRK11054 helD DNA helicase IV; Provisional
Probab=97.89 E-value=1.9e-05 Score=99.82 Aligned_cols=69 Identities=29% Similarity=0.366 Sum_probs=57.9
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..||+.|.+||... .+-.||.|.||||||+|+++-+..|+....
T Consensus 195 ~~L~~~Q~~av~~~----------~~~~lV~agaGSGKT~vl~~r~ayLl~~~~-------------------------- 238 (684)
T PRK11054 195 SPLNPSQARAVVNG----------EDSLLVLAGAGSGKTSVLVARAGWLLARGQ-------------------------- 238 (684)
T ss_pred CCCCHHHHHHHhCC----------CCCeEEEEeCCCCHHHHHHHHHHHHHHhCC--------------------------
Confidence 47999999998642 235699999999999999999999987531
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
..+.+||+.|.||.|.+|+-.||.+
T Consensus 239 --------------------------~~~~~IL~ltft~~AA~em~eRL~~ 263 (684)
T PRK11054 239 --------------------------AQPEQILLLAFGRQAAEEMDERIRE 263 (684)
T ss_pred --------------------------CCHHHeEEEeccHHHHHHHHHHHHH
Confidence 1247999999999999999999984
No 24
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=97.88 E-value=3e-05 Score=105.35 Aligned_cols=45 Identities=24% Similarity=0.345 Sum_probs=38.2
Q ss_pred hcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1060 KTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1060 k~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...||+.|.+||..++... +.|++|||+||||||+++.+++.++-
T Consensus 965 ~~~Lt~~Q~~Av~~il~s~------dr~~~I~G~AGTGKTT~l~~v~~~~~ 1009 (1747)
T PRK13709 965 MEGLTSGQRAATRMILEST------DRFTVVQGYAGVGKTTQFRAVMSAVN 1009 (1747)
T ss_pred cCCCCHHHHHHHHHHHhCC------CcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 3469999999999998653 37999999999999999888877654
No 25
>TIGR01074 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily.
Probab=97.81 E-value=3.3e-05 Score=97.05 Aligned_cols=68 Identities=24% Similarity=0.323 Sum_probs=56.9
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.||+.|.+||... .+-.+|-|+||||||+|++.-+..++....
T Consensus 1 ~Ln~~Q~~av~~~----------~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~--------------------------- 43 (664)
T TIGR01074 1 KLNPQQQEAVEYV----------TGPCLVLAGAGSGKTRVITNKIAYLIQNCG--------------------------- 43 (664)
T ss_pred CCCHHHHHHHhCC----------CCCEEEEecCCCCHHHHHHHHHHHHHHhcC---------------------------
Confidence 3899999998641 256899999999999999999999986420
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.++.+||+.+.||.|..|+-.||.+
T Consensus 44 -------------------------~~p~~IL~vTFt~~Aa~em~~Rl~~ 68 (664)
T TIGR01074 44 -------------------------YKARNIAAVTFTNKAAREMKERVAK 68 (664)
T ss_pred -------------------------CCHHHeEEEeccHHHHHHHHHHHHH
Confidence 1257999999999999999999984
No 26
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=97.77 E-value=8.6e-05 Score=75.55 Aligned_cols=72 Identities=19% Similarity=0.254 Sum_probs=57.0
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
.++++-|.+++..++... ...+|.||+|||||.++...+...+...
T Consensus 7 ~~~~~~Q~~~~~~~~~~~-------~~~~i~~~~GsGKT~~~~~~~~~~~~~~--------------------------- 52 (201)
T smart00487 7 EPLRPYQKEAIEALLSGL-------RDVILAAPTGSGKTLAALLPALEALKRG--------------------------- 52 (201)
T ss_pred CCCCHHHHHHHHHHHcCC-------CcEEEECCCCCchhHHHHHHHHHHhccc---------------------------
Confidence 368999999999876531 4789999999999998777665544321
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcC
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEG 1193 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~G 1193 (1402)
...++||++|++++++++..++...+
T Consensus 53 ---------------------------~~~~~l~~~p~~~~~~~~~~~~~~~~ 78 (201)
T smart00487 53 ---------------------------KGKRVLVLVPTRELAEQWAEELKKLG 78 (201)
T ss_pred ---------------------------CCCcEEEEeCCHHHHHHHHHHHHHHh
Confidence 14689999999999999999998543
No 27
>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=97.77 E-value=5.1e-05 Score=72.68 Aligned_cols=52 Identities=23% Similarity=0.367 Sum_probs=43.3
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhccccccccccccc
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSES 1166 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~ 1166 (1402)
-.+|+||||||||.++..++..++...
T Consensus 2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~----------------------------------------------------- 28 (144)
T cd00046 2 DVLLAAPTGSGKTLAALLPILELLDSL----------------------------------------------------- 28 (144)
T ss_pred CEEEECCCCCchhHHHHHHHHHHHhcc-----------------------------------------------------
Confidence 468999999999999998877655431
Q ss_pred cCCCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1167 SVRARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1167 ~~k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
..++++|++|++..+++...++.+.
T Consensus 29 -~~~~~lv~~p~~~l~~~~~~~~~~~ 53 (144)
T cd00046 29 -KGGQVLVLAPTRELANQVAERLKEL 53 (144)
T ss_pred -cCCCEEEEcCcHHHHHHHHHHHHHH
Confidence 2579999999999999999988853
No 28
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=97.69 E-value=7.2e-05 Score=98.17 Aligned_cols=41 Identities=27% Similarity=0.391 Sum_probs=33.7
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
..||+.|.+||..+.+. .+|++|+|+||||||+++..++.+
T Consensus 380 ~~Ls~eQ~~Av~~i~~~-------~r~~~v~G~AGTGKTt~l~~~~~~ 420 (1102)
T PRK13826 380 ARLSDEQKTAIEHVAGP-------ARIAAVVGRAGAGKTTMMKAAREA 420 (1102)
T ss_pred CCCCHHHHHHHHHHhcc-------CCeEEEEeCCCCCHHHHHHHHHHH
Confidence 36999999999976532 369999999999999988776543
No 29
>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=97.69 E-value=6.4e-05 Score=104.18 Aligned_cols=46 Identities=26% Similarity=0.371 Sum_probs=38.6
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..||+.|.+||..++...+ .|++|||+||||||+++..++.++...
T Consensus 1018 ~~Lt~~Q~~Ai~~il~~~~------~~~~i~G~AGtGKTt~l~~~~~~i~~~ 1063 (1960)
T TIGR02760 1018 ERLTHGQKQAIHLIISTKD------RFVAVQGLAGVGKTTMLESRYKPVLQA 1063 (1960)
T ss_pred CCCCHHHHHHHHHHHhCCC------cEEEEEeCCCCCHHHhHHHHHHHHHHH
Confidence 4799999999999876543 799999999999999998877766544
No 30
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=97.64 E-value=7.4e-05 Score=95.10 Aligned_cols=69 Identities=26% Similarity=0.340 Sum_probs=57.8
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.||+.|.+||.. ..|-.||-|.||||||+|++.-+..|+....
T Consensus 4 ~Ln~~Q~~av~~----------~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~--------------------------- 46 (726)
T TIGR01073 4 HLNPEQREAVKT----------TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKN--------------------------- 46 (726)
T ss_pred ccCHHHHHHHhC----------CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCC---------------------------
Confidence 699999999964 2356899999999999999999999986420
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
-.+.+||+.+.||.|.+|+..||.+.
T Consensus 47 -------------------------i~P~~IL~lTFT~kAA~em~~Rl~~~ 72 (726)
T TIGR01073 47 -------------------------VAPWNILAITFTNKAAREMKERVEKL 72 (726)
T ss_pred -------------------------CCHHHeeeeeccHHHHHHHHHHHHHH
Confidence 12469999999999999999999843
No 31
>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=97.58 E-value=0.00013 Score=101.15 Aligned_cols=66 Identities=18% Similarity=0.225 Sum_probs=54.6
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..||+.|.+||..++... +.|.+|+|+||||||+++.+++..+ ..
T Consensus 428 ~~Ls~~Q~~Av~~il~s~------~~v~ii~G~aGTGKTt~l~~l~~~~-~~---------------------------- 472 (1960)
T TIGR02760 428 FALSPSNKDAVSTLFTST------KRFIIINGFGGTGSTEIAQLLLHLA-SE---------------------------- 472 (1960)
T ss_pred CCCCHHHHHHHHHHHhCC------CCeEEEEECCCCCHHHHHHHHHHHH-Hh----------------------------
Confidence 369999999999988654 3799999999999999988877542 11
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHH
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSR 1188 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~R 1188 (1402)
.+.+|.+||||+.|...+...
T Consensus 473 ---------------------------~G~~V~~lAPTgrAA~~L~e~ 493 (1960)
T TIGR02760 473 ---------------------------QGYEIQIITAGSLSAQELRQK 493 (1960)
T ss_pred ---------------------------cCCeEEEEeCCHHHHHHHHHH
Confidence 257999999999999988765
No 32
>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=97.43 E-value=0.00021 Score=84.31 Aligned_cols=46 Identities=30% Similarity=0.418 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+||+.|.+++..++..-. ...+....|.||+|||||++|-+|...+
T Consensus 1 ~Ln~eQ~~~~~~v~~~~~--~~~~~~~fv~G~~GtGKs~l~~~i~~~~ 46 (364)
T PF05970_consen 1 KLNEEQRRVFDTVIEAIE--NEEGLNFFVTGPAGTGKSFLIKAIIDYL 46 (364)
T ss_pred CCCHHHHHHHHHHHHHHH--ccCCcEEEEEcCCCCChhHHHHHHHHHh
Confidence 489999999766644321 2345788999999999999988887643
No 33
>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=97.22 E-value=0.00078 Score=69.19 Aligned_cols=69 Identities=28% Similarity=0.371 Sum_probs=51.8
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
++.+.|.+||..++..-. .....+-.||++|+|||||.+++.++..+.
T Consensus 3 ~lr~~Q~~ai~~i~~~~~-~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~------------------------------- 50 (184)
T PF04851_consen 3 KLRPYQQEAIARIINSLE-NKKEERRVLLNAPTGSGKTIIALALILELA------------------------------- 50 (184)
T ss_dssp EE-HHHHHHHHHHHHHHH-TTSGCSEEEEEESTTSSHHHHHHHHHHHHH-------------------------------
T ss_pred CCCHHHHHHHHHHHHHHH-hcCCCCCEEEEECCCCCcChhhhhhhhccc-------------------------------
Confidence 578899999998875311 001247899999999999998886544221
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
+ ++|+++|+..-++.....+.
T Consensus 51 ---------------------------~-~~l~~~p~~~l~~Q~~~~~~ 71 (184)
T PF04851_consen 51 ---------------------------R-KVLIVAPNISLLEQWYDEFD 71 (184)
T ss_dssp ---------------------------C-EEEEEESSHHHHHHHHHHHH
T ss_pred ---------------------------c-ceeEecCHHHHHHHHHHHHH
Confidence 1 89999999999999998884
No 34
>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=96.91 E-value=0.005 Score=62.94 Aligned_cols=67 Identities=30% Similarity=0.291 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHH
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAW 1144 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W 1144 (1402)
+-|.+++..+++. .-.+|+||+|+|||..+...+...+...
T Consensus 2 ~~Q~~~~~~i~~~--------~~~li~aptGsGKT~~~~~~~l~~~~~~------------------------------- 42 (169)
T PF00270_consen 2 PLQQEAIEAIISG--------KNVLISAPTGSGKTLAYILPALNRLQEG------------------------------- 42 (169)
T ss_dssp HHHHHHHHHHHTT--------SEEEEECSTTSSHHHHHHHHHHHHHHTT-------------------------------
T ss_pred HHHHHHHHHHHcC--------CCEEEECCCCCccHHHHHHHHHhhhccC-------------------------------
Confidence 4699999988732 3489999999999997665444333321
Q ss_pred HHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcC
Q 000592 1145 QDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEG 1193 (1402)
Q Consensus 1145 ~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~G 1193 (1402)
...++|+.+|+.+-+++...++.+.+
T Consensus 43 -----------------------~~~~~lii~P~~~l~~q~~~~~~~~~ 68 (169)
T PF00270_consen 43 -----------------------KDARVLIIVPTRALAEQQFERLRKFF 68 (169)
T ss_dssp -----------------------SSSEEEEEESSHHHHHHHHHHHHHHT
T ss_pred -----------------------CCceEEEEeecccccccccccccccc
Confidence 23599999999999999999998554
No 35
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]
Probab=96.68 E-value=0.003 Score=79.59 Aligned_cols=69 Identities=25% Similarity=0.284 Sum_probs=57.2
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.+|+.|.+|+... .|-.||-..||||||+||..-|..|+....
T Consensus 2 ~Ln~~Q~~av~~~----------~gp~lV~AGaGsGKT~vlt~Ria~li~~~~--------------------------- 44 (655)
T COG0210 2 KLNPEQREAVLHP----------DGPLLVLAGAGSGKTRVLTERIAYLIAAGG--------------------------- 44 (655)
T ss_pred CCCHHHHHHHhcC----------CCCeEEEECCCCCchhhHHHHHHHHHHcCC---------------------------
Confidence 5899999998752 357777788999999999999999988631
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
-.+.+||+.+-||.|+.|+..|+.+.
T Consensus 45 -------------------------v~p~~Il~vTFTnkAA~em~~Rl~~~ 70 (655)
T COG0210 45 -------------------------VDPEQILAITFTNKAAAEMRERLLKL 70 (655)
T ss_pred -------------------------cChHHeeeeechHHHHHHHHHHHHHH
Confidence 02356999999999999999999853
No 36
>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]
Probab=96.62 E-value=0.0019 Score=74.71 Aligned_cols=39 Identities=38% Similarity=0.462 Sum_probs=30.0
Q ss_pred HHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1068 LQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1068 ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+++..++.. ...+..|.+||||||||.||.++-.+|.-
T Consensus 45 V~~L~~a~~~-----~~lp~~LFyGPpGTGKTStalafar~L~~ 83 (346)
T KOG0989|consen 45 VQVLKNALLR-----RILPHYLFYGPPGTGKTSTALAFARALNC 83 (346)
T ss_pred HHHHHHHHhh-----cCCceEEeeCCCCCcHhHHHHHHHHHhcC
Confidence 3444455443 24589999999999999999999888876
No 37
>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=96.50 E-value=0.0042 Score=60.13 Aligned_cols=42 Identities=38% Similarity=0.559 Sum_probs=30.1
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
++.+.++|..++... .....+|.||||||||+++..+...+.
T Consensus 3 ~~~~~~~i~~~~~~~-----~~~~v~i~G~~G~GKT~l~~~i~~~~~ 44 (151)
T cd00009 3 QEEAIEALREALELP-----PPKNLLLYGPPGTGKTTLARAIANELF 44 (151)
T ss_pred hHHHHHHHHHHHhCC-----CCCeEEEECCCCCCHHHHHHHHHHHhh
Confidence 455666776665431 246899999999999988777766554
No 38
>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=96.50 E-value=0.012 Score=62.65 Aligned_cols=70 Identities=20% Similarity=0.177 Sum_probs=51.6
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH-HHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI-VAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI-vgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
.++.-|.+|+...+.. .-.||.+|+|+|||.++ ..++..+....
T Consensus 21 ~~~~~Q~~~~~~~~~~--------~~~li~~~TG~GKT~~~~~~~l~~~~~~~--------------------------- 65 (203)
T cd00268 21 KPTPIQARAIPPLLSG--------RDVIGQAQTGSGKTAAFLIPILEKLDPSP--------------------------- 65 (203)
T ss_pred CCCHHHHHHHHHHhcC--------CcEEEECCCCCcHHHHHHHHHHHHHHhhc---------------------------
Confidence 5899999999887652 24899999999999873 33333332210
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
...+.+++|++|+.+-+.++...+.+
T Consensus 66 -------------------------~~~~~~viii~p~~~L~~q~~~~~~~ 91 (203)
T cd00268 66 -------------------------KKDGPQALILAPTRELALQIAEVARK 91 (203)
T ss_pred -------------------------ccCCceEEEEcCCHHHHHHHHHHHHH
Confidence 01367999999999999999887764
No 39
>PRK06851 hypothetical protein; Provisional
Probab=96.41 E-value=0.014 Score=69.62 Aligned_cols=59 Identities=22% Similarity=0.406 Sum_probs=48.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhcccccccccccc
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSE 1165 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~ 1165 (1402)
.+.+|.||||||||+++..++..+....
T Consensus 31 ~~~il~G~pGtGKStl~~~i~~~~~~~g---------------------------------------------------- 58 (367)
T PRK06851 31 RIFILKGGPGTGKSTLMKKIGEEFLEKG---------------------------------------------------- 58 (367)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcC----------------------------------------------------
Confidence 5899999999999999998887765531
Q ss_pred ccCCCeEEEEeCchHHHHHHHHHHHhcCCCCCC
Q 000592 1166 SSVRARVLICAQSNAAVDELVSRISKEGLYGSD 1198 (1402)
Q Consensus 1166 ~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~d 1198 (1402)
..-..++|++.|-+||-|+.+=++.+|.|..
T Consensus 59 --~~Ve~~~~~~d~~slDgviip~l~~aivDgt 89 (367)
T PRK06851 59 --YDVEFLHCSSDNDSLDGVIIPELKIAILDGT 89 (367)
T ss_pred --CeEEEEEcCCCCCceeeEEecCCCEEEEcCC
Confidence 1346899999999999998887777887754
No 40
>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=96.24 E-value=0.003 Score=60.22 Aligned_cols=23 Identities=48% Similarity=0.770 Sum_probs=19.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
...+|.||||||||++...+...
T Consensus 3 ~~~~l~G~~G~GKTtl~~~l~~~ 25 (148)
T smart00382 3 EVILIVGPPGSGKTTLARALARE 25 (148)
T ss_pred CEEEEECCCCCcHHHHHHHHHhc
Confidence 58899999999999987777553
No 41
>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=96.01 E-value=0.0042 Score=60.77 Aligned_cols=22 Identities=50% Similarity=0.794 Sum_probs=18.1
Q ss_pred EEEEcCCCCChhhHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.||.||||||||+++..+...+
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 3899999999999887776653
No 42
>PRK07952 DNA replication protein DnaC; Validated
Probab=95.91 E-value=0.017 Score=65.42 Aligned_cols=48 Identities=31% Similarity=0.428 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
++.|..|+..+..-...-.......++.||||||||+++.+|...+..
T Consensus 78 ~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~ 125 (244)
T PRK07952 78 CEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLL 125 (244)
T ss_pred CchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence 455666665554321101111246799999999999999998887654
No 43
>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=95.87 E-value=0.015 Score=78.60 Aligned_cols=67 Identities=27% Similarity=0.351 Sum_probs=53.2
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
++++.|.+||.. . ..-.||-+.+|||||+|++.-+..++...
T Consensus 1 ~~t~~Q~~ai~~---~-------~~~~lv~A~AGsGKT~~lv~r~~~~~~~~---------------------------- 42 (1232)
T TIGR02785 1 QWTDEQWQAIYT---R-------GQNILVSASAGSGKTAVLVERIIKKILRG---------------------------- 42 (1232)
T ss_pred CCCHHHHHHHhC---C-------CCCEEEEecCCCcHHHHHHHHHHHHHhcC----------------------------
Confidence 478999999973 1 13579999999999999998877666531
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
....+|||.+-||+|..|+-.||.+
T Consensus 43 -------------------------~~~~~il~~tFt~~aa~e~~~ri~~ 67 (1232)
T TIGR02785 43 -------------------------VDIDRLLVVTFTNAAAREMKERIEE 67 (1232)
T ss_pred -------------------------CCHhhEEEEeccHHHHHHHHHHHHH
Confidence 0135899999999999999999874
No 44
>PTZ00424 helicase 45; Provisional
Probab=95.84 E-value=0.027 Score=66.41 Aligned_cols=33 Identities=27% Similarity=0.205 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI 1102 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI 1102 (1402)
.+|+-|.+||..++... =.+|++|+|||||.+.
T Consensus 50 ~~~~~Q~~ai~~i~~~~--------d~ii~apTGsGKT~~~ 82 (401)
T PTZ00424 50 KPSAIQQRGIKPILDGY--------DTIGQAQSGTGKTATF 82 (401)
T ss_pred CCCHHHHHHHHHHhCCC--------CEEEECCCCChHHHHH
Confidence 57999999999987643 2679999999999743
No 45
>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=95.75 E-value=0.01 Score=69.01 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+.|.++|..++...- .....+..+|.||||||||+++..++..+-.
T Consensus 20 Re~e~~~l~~~l~~~~-~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~ 66 (365)
T TIGR02928 20 RDEQIEELAKALRPIL-RGSRPSNVFIYGKTGTGKTAVTKYVMKELEE 66 (365)
T ss_pred cHHHHHHHHHHHHHHH-cCCCCCcEEEECCCCCCHHHHHHHHHHHHHH
Confidence 4566666665554210 0123467899999999999999998887653
No 46
>PHA02558 uvsW UvsW helicase; Provisional
Probab=95.75 E-value=0.032 Score=68.82 Aligned_cols=69 Identities=16% Similarity=0.181 Sum_probs=53.1
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.+.+-|.+||..++... -.+++.|+|+|||.++..++..++..
T Consensus 114 ~~r~~Q~~av~~~l~~~--------~~il~apTGsGKT~i~~~l~~~~~~~----------------------------- 156 (501)
T PHA02558 114 EPHWYQYDAVYEGLKNN--------RRLLNLPTSAGKSLIQYLLSRYYLEN----------------------------- 156 (501)
T ss_pred CCCHHHHHHHHHHHhcC--------ceEEEeCCCCCHHHHHHHHHHHHHhc-----------------------------
Confidence 57789999999887542 35899999999998765544333221
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcC
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEG 1193 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~G 1193 (1402)
.+.++||++||.+-++++..++.+.+
T Consensus 157 --------------------------~~~~vLilvpt~eL~~Q~~~~l~~~~ 182 (501)
T PHA02558 157 --------------------------YEGKVLIIVPTTSLVTQMIDDFVDYR 182 (501)
T ss_pred --------------------------CCCeEEEEECcHHHHHHHHHHHHHhc
Confidence 13489999999999999999998654
No 47
>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A.
Probab=95.74 E-value=0.013 Score=60.86 Aligned_cols=46 Identities=20% Similarity=0.307 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+.|.+.+...+... ........+|.||||+|||+++..+...+-..
T Consensus 6 ~~e~~~l~~~l~~~--~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~ 51 (185)
T PF13191_consen 6 EEEIERLRDLLDAA--QSGSPRNLLLTGESGSGKTSLLRALLDRLAER 51 (185)
T ss_dssp HHHHHHHHHTTGGT--SS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH--HcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 46677777777422 23455899999999999999988877666554
No 48
>PLN03025 replication factor C subunit; Provisional
Probab=95.68 E-value=0.015 Score=67.42 Aligned_cols=45 Identities=33% Similarity=0.516 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-|+...+.+...+... ..+..|++||||||||+++.++...++..
T Consensus 17 g~~~~~~~L~~~~~~~-----~~~~lll~Gp~G~GKTtla~~la~~l~~~ 61 (319)
T PLN03025 17 GNEDAVSRLQVIARDG-----NMPNLILSGPPGTGKTTSILALAHELLGP 61 (319)
T ss_pred CcHHHHHHHHHHHhcC-----CCceEEEECCCCCCHHHHHHHHHHHHhcc
Confidence 4555666666655432 22457999999999999999998887653
No 49
>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=95.53 E-value=0.018 Score=77.05 Aligned_cols=56 Identities=34% Similarity=0.388 Sum_probs=47.3
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhccccccccccc
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSS 1164 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~ 1164 (1402)
.|..||-.-+|||||+||.+++-.|+....
T Consensus 9 ~G~~lieAsAGtGKT~ti~~~~lrll~~~~-------------------------------------------------- 38 (1087)
T TIGR00609 9 NGTFLIEASAGTGKTFTIAQLYLRLLLEGG-------------------------------------------------- 38 (1087)
T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHhcCC--------------------------------------------------
Confidence 479999999999999999999988777520
Q ss_pred cccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1165 ESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1165 ~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.....+|||.+-||+|.-|+-.|+.+
T Consensus 39 -~~~~~~iLvvTFT~aAt~el~~RIr~ 64 (1087)
T TIGR00609 39 -PLTVEEILVVTFTNAATEELKTRIRG 64 (1087)
T ss_pred -CCChhhEEEEehhHHHHHHHHHHHHH
Confidence 01247999999999999999999984
No 50
>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=95.52 E-value=0.018 Score=64.96 Aligned_cols=25 Identities=28% Similarity=0.380 Sum_probs=20.4
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.-.|+.||||||||++...+...+.
T Consensus 43 ~~vll~GppGtGKTtlA~~ia~~l~ 67 (261)
T TIGR02881 43 LHMIFKGNPGTGKTTVARILGKLFK 67 (261)
T ss_pred ceEEEEcCCCCCHHHHHHHHHHHHH
Confidence 4578999999999998888766554
No 51
>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=95.51 E-value=0.027 Score=59.04 Aligned_cols=24 Identities=42% Similarity=0.580 Sum_probs=19.3
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
++||-||||||||.....++...+
T Consensus 1 ~~li~G~~G~GKT~l~~~~~~~~~ 24 (187)
T cd01124 1 STLLSGGPGTGKTTFALQFLYAGL 24 (187)
T ss_pred CEEEEcCCCCCHHHHHHHHHHHHH
Confidence 378999999999998777766544
No 52
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=95.47 E-value=0.051 Score=65.26 Aligned_cols=32 Identities=34% Similarity=0.292 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkT 1101 (1402)
....-|.+||..++... =.|+++|+|||||.+
T Consensus 23 ~p~~iQ~~ai~~~~~g~--------d~l~~apTGsGKT~~ 54 (434)
T PRK11192 23 RPTAIQAEAIPPALDGR--------DVLGSAPTGTGKTAA 54 (434)
T ss_pred CCCHHHHHHHHHHhCCC--------CEEEECCCCChHHHH
Confidence 45689999999988542 389999999999975
No 53
>PRK12377 putative replication protein; Provisional
Probab=95.43 E-value=0.013 Score=66.35 Aligned_cols=27 Identities=41% Similarity=0.527 Sum_probs=23.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.+|.||||||||++..+|...++..
T Consensus 102 ~~l~l~G~~GtGKThLa~AIa~~l~~~ 128 (248)
T PRK12377 102 TNFVFSGKPGTGKNHLAAAIGNRLLAK 128 (248)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHc
Confidence 467999999999999999999888754
No 54
>PRK05580 primosome assembly protein PriA; Validated
Probab=95.41 E-value=0.047 Score=69.85 Aligned_cols=70 Identities=20% Similarity=0.324 Sum_probs=53.2
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..++..|.+|+...+... .....|++||+|+|||.+.+.++...+..
T Consensus 143 ~~Lt~~Q~~ai~~i~~~~-----~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---------------------------- 189 (679)
T PRK05580 143 PTLNPEQAAAVEAIRAAA-----GFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---------------------------- 189 (679)
T ss_pred CCCCHHHHHHHHHHHhcc-----CCCcEEEECCCCChHHHHHHHHHHHHHHc----------------------------
Confidence 368999999999876531 12469999999999998766544433321
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
++++||.+|+-+=+++++.++.+
T Consensus 190 ----------------------------g~~vLvLvPt~~L~~Q~~~~l~~ 212 (679)
T PRK05580 190 ----------------------------GKQALVLVPEIALTPQMLARFRA 212 (679)
T ss_pred ----------------------------CCeEEEEeCcHHHHHHHHHHHHH
Confidence 46899999999999999999974
No 55
>PRK10536 hypothetical protein; Provisional
Probab=95.24 E-value=0.041 Score=63.00 Aligned_cols=41 Identities=27% Similarity=0.281 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..|..|..++.+... ..+++|.||+|||||++.+++....+
T Consensus 59 p~n~~Q~~~l~al~~--------~~lV~i~G~aGTGKT~La~a~a~~~l 99 (262)
T PRK10536 59 ARNEAQAHYLKAIES--------KQLIFATGEAGCGKTWISAAKAAEAL 99 (262)
T ss_pred CCCHHHHHHHHHHhc--------CCeEEEECCCCCCHHHHHHHHHHHHH
Confidence 689999999885432 25999999999999999888776443
No 56
>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=95.15 E-value=0.04 Score=61.01 Aligned_cols=42 Identities=33% Similarity=0.455 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
..|..|..++.+.+.. .++.+.||+|||||.+.++.-..++.
T Consensus 4 p~~~~Q~~~~~al~~~--------~~v~~~G~AGTGKT~LA~a~Al~~v~ 45 (205)
T PF02562_consen 4 PKNEEQKFALDALLNN--------DLVIVNGPAGTGKTFLALAAALELVK 45 (205)
T ss_dssp --SHHHHHHHHHHHH---------SEEEEE--TTSSTTHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhC--------CeEEEECCCCCcHHHHHHHHHHHHHH
Confidence 5799999999987732 59999999999999877665544444
No 57
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=95.12 E-value=0.074 Score=67.49 Aligned_cols=46 Identities=20% Similarity=0.166 Sum_probs=32.3
Q ss_pred HHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH
Q 000592 1055 LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI 1102 (1402)
Q Consensus 1055 L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI 1102 (1402)
+...+...+.+.|.+||...+.... ...+.-.|||||.|||||-+.
T Consensus 228 ~~~~lpf~lt~~Q~~ai~~I~~~~~--~~~~~~~Ll~g~TGSGKT~va 273 (630)
T TIGR00643 228 FLASLPFKLTRAQKRVVKEILQDLK--SDVPMNRLLQGDVGSGKTLVA 273 (630)
T ss_pred HHHhCCCCCCHHHHHHHHHHHHHhc--cCCCccEEEECCCCCcHHHHH
Confidence 3344556899999999998775421 111234799999999999754
No 58
>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=95.10 E-value=0.03 Score=63.87 Aligned_cols=43 Identities=26% Similarity=0.441 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.+.+.|.+++..++... .++.+|-||+|+|||||+.+++..+.
T Consensus 63 g~~~~~~~~l~~~~~~~------~GlilisG~tGSGKTT~l~all~~i~ 105 (264)
T cd01129 63 GLKPENLEIFRKLLEKP------HGIILVTGPTGSGKTTTLYSALSELN 105 (264)
T ss_pred CCCHHHHHHHHHHHhcC------CCEEEEECCCCCcHHHHHHHHHhhhC
Confidence 47788999888877543 38999999999999999988887653
No 59
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=94.98 E-value=0.081 Score=64.19 Aligned_cols=32 Identities=22% Similarity=0.282 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkT 1101 (1402)
.+++-|.+||..++... =.++++|.|||||.+
T Consensus 26 ~~t~iQ~~ai~~~l~g~--------dvi~~a~TGsGKT~a 57 (460)
T PRK11776 26 EMTPIQAQSLPAILAGK--------DVIAQAKTGSGKTAA 57 (460)
T ss_pred CCCHHHHHHHHHHhcCC--------CEEEECCCCCcHHHH
Confidence 57899999999887542 489999999999953
No 60
>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]
Probab=94.92 E-value=0.036 Score=62.44 Aligned_cols=30 Identities=40% Similarity=0.717 Sum_probs=25.7
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
+-+=-+|-||||||||+.|..|-..||...
T Consensus 47 nmP~liisGpPG~GKTTsi~~LAr~LLG~~ 76 (333)
T KOG0991|consen 47 NMPNLIISGPPGTGKTTSILCLARELLGDS 76 (333)
T ss_pred CCCceEeeCCCCCchhhHHHHHHHHHhChh
Confidence 446789999999999999999998888753
No 61
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=94.89 E-value=0.037 Score=63.47 Aligned_cols=43 Identities=30% Similarity=0.550 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
|+...+.+..++... ..+..||.||||||||+++.++...+..
T Consensus 20 ~~~~~~~L~~~~~~~-----~~~~lll~Gp~GtGKT~la~~~~~~l~~ 62 (337)
T PRK12402 20 QDEVVERLSRAVDSP-----NLPHLLVQGPPGSGKTAAVRALARELYG 62 (337)
T ss_pred CHHHHHHHHHHHhCC-----CCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence 555666666665432 2246899999999999999888776653
No 62
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=94.76 E-value=0.046 Score=73.90 Aligned_cols=62 Identities=32% Similarity=0.358 Sum_probs=46.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhccccccccccc
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSS 1164 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~ 1164 (1402)
.|..||----|||||.||.++.-.|+-.......+. +
T Consensus 17 ~G~~LIEASAGTGKTyTIa~lyLrLlL~~g~~~~~~----------~--------------------------------- 53 (1181)
T PRK10876 17 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFP----------R--------------------------------- 53 (1181)
T ss_pred CCCEEEEeCCCCcHHHHHHHHHHHHHccCCcccccc----------C---------------------------------
Confidence 479999999999999999999887765421000000 0
Q ss_pred cccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1165 ESSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1165 ~~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
.-....|||.+-||||..|+-.||.
T Consensus 54 -~L~~~~ILvvTFT~aAt~Elr~RIr 78 (1181)
T PRK10876 54 -PLTVEEILVVTFTEAATEELRGRIR 78 (1181)
T ss_pred -CCChhhEEEEechHHHHHHHHHHHH
Confidence 0124699999999999999999996
No 63
>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=94.76 E-value=0.02 Score=66.83 Aligned_cols=23 Identities=48% Similarity=0.771 Sum_probs=18.9
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+.+.|++||||||||+.-.||..
T Consensus 177 NRliLlhGPPGTGKTSLCKaLaQ 199 (423)
T KOG0744|consen 177 NRLILLHGPPGTGKTSLCKALAQ 199 (423)
T ss_pred eeEEEEeCCCCCChhHHHHHHHH
Confidence 36999999999999997666543
No 64
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=94.74 E-value=0.023 Score=56.09 Aligned_cols=29 Identities=38% Similarity=0.614 Sum_probs=20.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..++.+|.||||+|||+++..+...+...
T Consensus 3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~ 31 (131)
T PF13401_consen 3 SQRILVISGPPGSGKTTLIKRLARQLNAE 31 (131)
T ss_dssp ----EEEEE-TTSSHHHHHHHHHHHHHHH
T ss_pred CCcccEEEcCCCCCHHHHHHHHHHHhHHh
Confidence 34799999999999999988887766543
No 65
>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=94.73 E-value=0.023 Score=57.29 Aligned_cols=22 Identities=45% Similarity=0.758 Sum_probs=18.7
Q ss_pred EEEEcCCCCChhhHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.||.||||||||+++..+...+
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 5899999999999888876655
No 66
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=94.67 E-value=0.13 Score=65.96 Aligned_cols=47 Identities=19% Similarity=0.198 Sum_probs=33.2
Q ss_pred HHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHH
Q 000592 1055 LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIV 1103 (1402)
Q Consensus 1055 L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIv 1103 (1402)
+...+...+.+.|.+||........ ...+.-.|||||.|||||-+..
T Consensus 254 ~~~~l~f~lt~~Q~~ai~~I~~d~~--~~~~~~~Ll~~~TGSGKT~va~ 300 (681)
T PRK10917 254 FLASLPFELTGAQKRVVAEILADLA--SPKPMNRLLQGDVGSGKTVVAA 300 (681)
T ss_pred HHHhCCCCCCHHHHHHHHHHHHhhh--ccCCceEEEECCCCCcHHHHHH
Confidence 4455566899999999998765321 1112357999999999996543
No 67
>PRK08181 transposase; Validated
Probab=94.57 E-value=0.044 Score=62.91 Aligned_cols=47 Identities=30% Similarity=0.373 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+|..|..|+..+-.- .....-.+|.||||||||+...++...++..
T Consensus 87 ~~~~~~~~~L~~~~~~----~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~ 133 (269)
T PRK08181 87 MVSKAQVMAIAAGDSW----LAKGANLLLFGPPGGGKSHLAAAIGLALIEN 133 (269)
T ss_pred CCCHHHHHHHHHHHHH----HhcCceEEEEecCCCcHHHHHHHHHHHHHHc
Confidence 5788888887654211 1122358999999999999999988877654
No 68
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=94.55 E-value=0.072 Score=71.61 Aligned_cols=75 Identities=23% Similarity=0.230 Sum_probs=56.7
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIAR 1142 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar 1142 (1402)
+=.-|.+||.++...-. +...=.||+.|.|||||.|.++++..|+...
T Consensus 414 lR~YQ~~AI~ai~~a~~---~g~r~~Ll~maTGSGKT~tai~li~~L~~~~----------------------------- 461 (1123)
T PRK11448 414 LRYYQEDAIQAVEKAIV---EGQREILLAMATGTGKTRTAIALMYRLLKAK----------------------------- 461 (1123)
T ss_pred CCHHHHHHHHHHHHHHH---hccCCeEEEeCCCCCHHHHHHHHHHHHHhcC-----------------------------
Confidence 45689999977653210 1123489999999999999999888776542
Q ss_pred HHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 000592 1143 AWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGL 1194 (1402)
Q Consensus 1143 ~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI 1194 (1402)
..+|||+.+|.++=++.....+.+.|+
T Consensus 462 -------------------------~~~rVLfLvDR~~L~~Qa~~~F~~~~~ 488 (1123)
T PRK11448 462 -------------------------RFRRILFLVDRSALGEQAEDAFKDTKI 488 (1123)
T ss_pred -------------------------ccCeEEEEecHHHHHHHHHHHHHhccc
Confidence 136999999999999999998886554
No 69
>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=94.52 E-value=0.11 Score=66.63 Aligned_cols=52 Identities=10% Similarity=0.157 Sum_probs=33.4
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcC--CCCCCCCccCCcEEEeccccc--ccCCCc
Q 000592 1169 RARVLICAQSNAAVDELVSRISKEG--LYGSDGKTYKPYLVRVGNVKT--VHPNSL 1220 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl~~G--I~d~dGk~y~P~VVRVG~~~a--v~s~v~ 1220 (1402)
..||..|+.|++-+..++.-|.+.. .....|..-....|=+|..+. +|+.+.
T Consensus 60 ~~kIiy~sRThsQl~q~i~Elk~~~~~~~~~~~~~~~i~~v~L~SR~~lCin~~v~ 115 (705)
T TIGR00604 60 VRKIIYASRTHSQLEQATEELRKLMSYRTPRIGEESPVSGLSLASRKNLCLHPEVS 115 (705)
T ss_pred cccEEEEcccchHHHHHHHHHHhhhhccccccccCCceeEEEechHhhcccChHHH
Confidence 3699999999999999999888532 211112111245677787665 355543
No 70
>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=94.47 E-value=0.042 Score=67.80 Aligned_cols=43 Identities=30% Similarity=0.424 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.+.+.|.+.+..++... .|+.||-||+|+|||||+.+++..+.
T Consensus 225 g~~~~~~~~l~~~~~~~------~GlilitGptGSGKTTtL~a~L~~l~ 267 (486)
T TIGR02533 225 GMSPELLSRFERLIRRP------HGIILVTGPTGSGKTTTLYAALSRLN 267 (486)
T ss_pred CCCHHHHHHHHHHHhcC------CCEEEEEcCCCCCHHHHHHHHHhccC
Confidence 57889999998877654 38999999999999999988776653
No 71
>PRK14974 cell division protein FtsY; Provisional
Probab=94.46 E-value=0.092 Score=62.16 Aligned_cols=26 Identities=35% Similarity=0.364 Sum_probs=22.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.+.++-||||+|||||+..+...+.
T Consensus 140 ~~vi~~~G~~GvGKTTtiakLA~~l~ 165 (336)
T PRK14974 140 PVVIVFVGVNGTGKTTTIAKLAYYLK 165 (336)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 46899999999999999999886553
No 72
>PRK06893 DNA replication initiation factor; Validated
Probab=94.45 E-value=0.035 Score=61.68 Aligned_cols=28 Identities=21% Similarity=0.281 Sum_probs=24.2
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.++.+|.||||||||+...++...+...
T Consensus 39 ~~~l~l~G~~G~GKThL~~ai~~~~~~~ 66 (229)
T PRK06893 39 QPFFYIWGGKSSGKSHLLKAVSNHYLLN 66 (229)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHHHHc
Confidence 3688999999999999999998877654
No 73
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=94.44 E-value=0.045 Score=64.52 Aligned_cols=26 Identities=46% Similarity=0.649 Sum_probs=22.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+..+|.||||||||+++..++..+-.
T Consensus 56 ~~~lI~G~~GtGKT~l~~~v~~~l~~ 81 (394)
T PRK00411 56 LNVLIYGPPGTGKTTTVKKVFEELEE 81 (394)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHH
Confidence 56799999999999999888876644
No 74
>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=94.33 E-value=0.033 Score=55.82 Aligned_cols=24 Identities=33% Similarity=0.595 Sum_probs=20.4
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+++|.||||||||+++..+...+.
T Consensus 1 ~~~i~G~~G~GKT~l~~~i~~~~~ 24 (165)
T cd01120 1 LILVFGPTGSGKTTLALQLALNIA 24 (165)
T ss_pred CeeEeCCCCCCHHHHHHHHHHHHH
Confidence 478999999999999888877653
No 75
>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=94.31 E-value=0.033 Score=59.96 Aligned_cols=28 Identities=43% Similarity=0.643 Sum_probs=23.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..=.+|+||||||||++.++|...++..
T Consensus 47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~ 74 (178)
T PF01695_consen 47 GENLILYGPPGTGKTHLAVAIANEAIRK 74 (178)
T ss_dssp --EEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred CeEEEEEhhHhHHHHHHHHHHHHHhccC
Confidence 3458899999999999999999888774
No 76
>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=94.27 E-value=0.051 Score=61.99 Aligned_cols=24 Identities=38% Similarity=0.638 Sum_probs=19.4
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+-.+|.||||||||++...+...+
T Consensus 31 ~~~ll~Gp~G~GKT~la~~ia~~~ 54 (305)
T TIGR00635 31 DHLLLYGPPGLGKTTLAHIIANEM 54 (305)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHh
Confidence 458999999999999888765543
No 77
>PRK08084 DNA replication initiation factor; Provisional
Probab=94.25 E-value=0.075 Score=59.33 Aligned_cols=44 Identities=20% Similarity=0.243 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
-|.....++....... ..+..+|.||||||||+...++...+..
T Consensus 28 ~n~~a~~~l~~~~~~~-----~~~~l~l~Gp~G~GKThLl~a~~~~~~~ 71 (235)
T PRK08084 28 DNDSLLAALQNALRQE-----HSGYIYLWSREGAGRSHLLHAACAELSQ 71 (235)
T ss_pred ccHHHHHHHHHHHhCC-----CCCeEEEECCCCCCHHHHHHHHHHHHHh
Confidence 6766666666554322 2357899999999999998888776654
No 78
>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=94.12 E-value=0.064 Score=63.21 Aligned_cols=42 Identities=29% Similarity=0.441 Sum_probs=32.5
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+.+|..-.++|..++... +-.||.||||||||+++..+...+
T Consensus 47 y~f~~~~~~~vl~~l~~~-------~~ilL~G~pGtGKTtla~~lA~~l 88 (327)
T TIGR01650 47 YLFDKATTKAICAGFAYD-------RRVMVQGYHGTGKSTHIEQIAARL 88 (327)
T ss_pred ccCCHHHHHHHHHHHhcC-------CcEEEEeCCCChHHHHHHHHHHHH
Confidence 457888888888887543 358999999999999877765443
No 79
>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=93.99 E-value=0.045 Score=59.53 Aligned_cols=26 Identities=35% Similarity=0.691 Sum_probs=22.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
|+.+|-||+|+|||||+.+++..+..
T Consensus 2 GlilI~GptGSGKTTll~~ll~~~~~ 27 (198)
T cd01131 2 GLVLVTGPTGSGKSTTLAAMIDYINK 27 (198)
T ss_pred cEEEEECCCCCCHHHHHHHHHHHhhh
Confidence 79999999999999999888776653
No 80
>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=93.96 E-value=0.18 Score=61.71 Aligned_cols=32 Identities=28% Similarity=0.370 Sum_probs=27.0
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhh
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTk 1100 (1402)
..+..-|.+||.+++... =.+|+.|.|+|||-
T Consensus 10 ~~~r~~Q~~ai~~~l~g~--------dvlv~apTGsGKTl 41 (470)
T TIGR00614 10 SSFRPVQLEVINAVLLGR--------DCFVVMPTGGGKSL 41 (470)
T ss_pred CCCCHHHHHHHHHHHcCC--------CEEEEcCCCCcHhH
Confidence 368899999999988642 37999999999994
No 81
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=93.95 E-value=0.06 Score=62.69 Aligned_cols=25 Identities=36% Similarity=0.604 Sum_probs=20.2
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+-.||.||||||||+++..+...+
T Consensus 51 ~~~~ll~GppG~GKT~la~~ia~~l 75 (328)
T PRK00080 51 LDHVLLYGPPGLGKTTLANIIANEM 75 (328)
T ss_pred CCcEEEECCCCccHHHHHHHHHHHh
Confidence 4578999999999999888765543
No 82
>PRK00254 ski2-like helicase; Provisional
Probab=93.94 E-value=0.2 Score=64.60 Aligned_cols=68 Identities=16% Similarity=0.206 Sum_probs=49.9
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH-HHHHHHHHHhcCCCCcccccCcccccCCCCccchhHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI-VAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAA 1139 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI-vgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~ 1139 (1402)
..+|+-|.+||...+... .=.+|+.|+|+|||.+. +.++..++.
T Consensus 22 ~~l~~~Q~~ai~~~~~~g-------~nvlv~apTGsGKT~~~~l~il~~l~~---------------------------- 66 (720)
T PRK00254 22 EELYPPQAEALKSGVLEG-------KNLVLAIPTASGKTLVAEIVMVNKLLR---------------------------- 66 (720)
T ss_pred CCCCHHHHHHHHHHHhCC-------CcEEEECCCCcHHHHHHHHHHHHHHHh----------------------------
Confidence 379999999998643321 34799999999999755 222222211
Q ss_pred HHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1140 IARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1140 ~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.+.++|+++|+-+=+++...++.+
T Consensus 67 ----------------------------~~~~~l~l~P~~aLa~q~~~~~~~ 90 (720)
T PRK00254 67 ----------------------------EGGKAVYLVPLKALAEEKYREFKD 90 (720)
T ss_pred ----------------------------cCCeEEEEeChHHHHHHHHHHHHH
Confidence 146899999999999999999874
No 83
>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=93.86 E-value=0.14 Score=56.05 Aligned_cols=27 Identities=37% Similarity=0.610 Sum_probs=21.4
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...++||.||||||||.....++..-+
T Consensus 18 ~gs~~li~G~~GsGKT~l~~q~l~~~~ 44 (226)
T PF06745_consen 18 KGSVVLISGPPGSGKTTLALQFLYNGL 44 (226)
T ss_dssp TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred CCcEEEEEeCCCCCcHHHHHHHHHHhh
Confidence 447999999999999997777665433
No 84
>PRK10436 hypothetical protein; Provisional
Probab=93.83 E-value=0.079 Score=65.14 Aligned_cols=43 Identities=30% Similarity=0.455 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.+.+.|.+.+..++... .|+.||-||.|+|||||+.+++..+.
T Consensus 201 G~~~~~~~~l~~~~~~~------~GliLvtGpTGSGKTTtL~a~l~~~~ 243 (462)
T PRK10436 201 GMTPAQLAQFRQALQQP------QGLILVTGPTGSGKTVTLYSALQTLN 243 (462)
T ss_pred CcCHHHHHHHHHHHHhc------CCeEEEECCCCCChHHHHHHHHHhhC
Confidence 47778888888877554 38999999999999999988887653
No 85
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=93.80 E-value=0.12 Score=67.59 Aligned_cols=21 Identities=10% Similarity=0.360 Sum_probs=19.6
Q ss_pred CeEEEEeCchHHHHHHHHHHH
Q 000592 1170 ARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1170 ~RILVCAPSNAAVDEIV~RLl 1190 (1402)
.+|||+.|+-.|.-+++.|+.
T Consensus 49 ~~ilvlqPrR~aA~qia~rva 69 (812)
T PRK11664 49 GKIIMLEPRRLAARNVAQRLA 69 (812)
T ss_pred CeEEEECChHHHHHHHHHHHH
Confidence 489999999999999999996
No 86
>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=93.75 E-value=0.14 Score=54.38 Aligned_cols=22 Identities=27% Similarity=0.486 Sum_probs=19.0
Q ss_pred CCeEEEEeCchHHHHHHHHHHH
Q 000592 1169 RARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
+.|+||.+||-+.++|+..-|.
T Consensus 33 ~~rvLvL~PTRvva~em~~aL~ 54 (148)
T PF07652_consen 33 RLRVLVLAPTRVVAEEMYEALK 54 (148)
T ss_dssp T--EEEEESSHHHHHHHHHHTT
T ss_pred cCeEEEecccHHHHHHHHHHHh
Confidence 6899999999999999999987
No 87
>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=93.74 E-value=0.05 Score=62.60 Aligned_cols=25 Identities=32% Similarity=0.454 Sum_probs=19.7
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
-.||.||||||||++..++...+..
T Consensus 60 ~vll~G~pGTGKT~lA~~ia~~l~~ 84 (284)
T TIGR02880 60 HMSFTGNPGTGKTTVALRMAQILHR 84 (284)
T ss_pred eEEEEcCCCCCHHHHHHHHHHHHHH
Confidence 4789999999999987776555543
No 88
>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=93.72 E-value=0.034 Score=67.36 Aligned_cols=22 Identities=45% Similarity=0.703 Sum_probs=19.0
Q ss_pred eEEEEcCCCCChhhHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
=-|+-||||||||+.|.||-+.
T Consensus 237 GYLLYGPPGTGKSS~IaAmAn~ 258 (457)
T KOG0743|consen 237 GYLLYGPPGTGKSSFIAAMANY 258 (457)
T ss_pred cceeeCCCCCCHHHHHHHHHhh
Confidence 4689999999999999998653
No 89
>PF05729 NACHT: NACHT domain
Probab=93.72 E-value=0.062 Score=54.46 Aligned_cols=27 Identities=26% Similarity=0.509 Sum_probs=23.7
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
+.+|.|+||+|||++...++..+....
T Consensus 2 ~l~I~G~~G~GKStll~~~~~~~~~~~ 28 (166)
T PF05729_consen 2 VLWISGEPGSGKSTLLRKLAQQLAEEE 28 (166)
T ss_pred EEEEECCCCCChHHHHHHHHHHHHhcC
Confidence 689999999999999999888877764
No 90
>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=93.71 E-value=0.13 Score=59.96 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=21.6
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1169 RARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
..|+++++|+.+.++++..|+.+.
T Consensus 29 ~~~ii~v~P~~~L~~q~~~~l~~~ 52 (358)
T TIGR01587 29 ADRVIIALPTRATINAMYRRAKEL 52 (358)
T ss_pred CCeEEEEeehHHHHHHHHHHHHHH
Confidence 469999999999999999999853
No 91
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=93.68 E-value=0.22 Score=63.41 Aligned_cols=32 Identities=22% Similarity=0.141 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkT 1101 (1402)
..++-|.+||...+.. .-.|+|+|+|||||.+
T Consensus 28 ~ptpiQ~~ai~~ll~g--------~dvl~~ApTGsGKT~a 59 (629)
T PRK11634 28 KPSPIQAECIPHLLNG--------RDVLGMAQTGSGKTAA 59 (629)
T ss_pred CCCHHHHHHHHHHHcC--------CCEEEEcCCCCcHHHH
Confidence 5778999999987753 2589999999999975
No 92
>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=93.65 E-value=0.16 Score=66.33 Aligned_cols=22 Identities=9% Similarity=0.273 Sum_probs=20.1
Q ss_pred CCeEEEEeCchHHHHHHHHHHH
Q 000592 1169 RARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
+.+|+|+.|+-.|.-.+..|+.
T Consensus 45 ~~~ilvlqPrR~aA~qiA~rva 66 (819)
T TIGR01970 45 GGKIIMLEPRRLAARSAAQRLA 66 (819)
T ss_pred CCeEEEEeCcHHHHHHHHHHHH
Confidence 3589999999999999999996
No 93
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=93.58 E-value=0.05 Score=64.27 Aligned_cols=21 Identities=48% Similarity=0.672 Sum_probs=17.9
Q ss_pred eEEEEcCCCCChhhHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVs 1107 (1402)
-.||.||||||||+++.++..
T Consensus 158 gvLL~GppGtGKT~lakaia~ 178 (364)
T TIGR01242 158 GVLLYGPPGTGKTLLAKAVAH 178 (364)
T ss_pred eEEEECCCCCCHHHHHHHHHH
Confidence 489999999999998877754
No 94
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=93.55 E-value=0.13 Score=56.51 Aligned_cols=46 Identities=13% Similarity=0.135 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.-|.....++...... .......+|.||||||||+...++...+..
T Consensus 23 ~~~~~~~~~l~~~~~~----~~~~~~~~l~G~~G~GKT~La~ai~~~~~~ 68 (227)
T PRK08903 23 GENAELVARLRELAAG----PVADRFFYLWGEAGSGRSHLLQALVADASY 68 (227)
T ss_pred CCcHHHHHHHHHHHhc----cCCCCeEEEECCCCCCHHHHHHHHHHHHHh
Confidence 3455566666654331 123467899999999999988887776544
No 95
>PRK06526 transposase; Provisional
Probab=93.55 E-value=0.061 Score=61.19 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+|..|...+..+ . ..+...-.+|.||||||||++..+|...+...
T Consensus 80 ~~~~~~~~~l~~~-~----fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~ 125 (254)
T PRK06526 80 SLKRDTIAHLGTL-D----FVTGKENVVFLGPPGTGKTHLAIGLGIRACQA 125 (254)
T ss_pred CcchHHHHHHhcC-c----hhhcCceEEEEeCCCCchHHHHHHHHHHHHHC
Confidence 4566665554321 1 12233467999999999999999998776654
No 96
>PRK04296 thymidine kinase; Provisional
Probab=93.54 E-value=0.094 Score=56.75 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=21.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+.||-||||+|||+.+++++..+..
T Consensus 3 ~i~litG~~GsGKTT~~l~~~~~~~~ 28 (190)
T PRK04296 3 KLEFIYGAMNSGKSTELLQRAYNYEE 28 (190)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHH
Confidence 38999999999999988888765544
No 97
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=93.54 E-value=0.11 Score=59.16 Aligned_cols=43 Identities=28% Similarity=0.468 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
++.+.+.+..++... ..+..||.||||||||+++..+...+..
T Consensus 22 ~~~~~~~l~~~i~~~-----~~~~~ll~G~~G~GKt~~~~~l~~~l~~ 64 (319)
T PRK00440 22 QEEIVERLKSYVKEK-----NMPHLLFAGPPGTGKTTAALALARELYG 64 (319)
T ss_pred cHHHHHHHHHHHhCC-----CCCeEEEECCCCCCHHHHHHHHHHHHcC
Confidence 455666676666432 2234699999999999998888777654
No 98
>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=93.51 E-value=0.092 Score=65.93 Aligned_cols=42 Identities=29% Similarity=0.438 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+.+.|.+.+..++... .|+.||-||+|+|||||+.+++..+
T Consensus 299 g~~~~~~~~l~~~~~~~------~Glilv~G~tGSGKTTtl~a~l~~~ 340 (564)
T TIGR02538 299 GFEPDQKALFLEAIHKP------QGMVLVTGPTGSGKTVSLYTALNIL 340 (564)
T ss_pred CCCHHHHHHHHHHHHhc------CCeEEEECCCCCCHHHHHHHHHHhh
Confidence 47788888888876554 3899999999999999998888765
No 99
>PRK01172 ski2-like helicase; Provisional
Probab=93.41 E-value=0.23 Score=63.40 Aligned_cols=67 Identities=19% Similarity=0.124 Sum_probs=48.8
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..+++.|.+||...... .-.+|++|.|+|||.... .+++...
T Consensus 21 ~~l~~~Q~~ai~~l~~~--------~nvlv~apTGSGKTl~a~---lail~~l--------------------------- 62 (674)
T PRK01172 21 FELYDHQRMAIEQLRKG--------ENVIVSVPTAAGKTLIAY---SAIYETF--------------------------- 62 (674)
T ss_pred CCCCHHHHHHHHHHhcC--------CcEEEECCCCchHHHHHH---HHHHHHH---------------------------
Confidence 35899999999986432 358999999999997432 1122211
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
..+.++++++|+.+=+++...++.+
T Consensus 63 --------------------------~~~~k~v~i~P~raLa~q~~~~~~~ 87 (674)
T PRK01172 63 --------------------------LAGLKSIYIVPLRSLAMEKYEELSR 87 (674)
T ss_pred --------------------------HhCCcEEEEechHHHHHHHHHHHHH
Confidence 0135899999999999999988874
No 100
>CHL00181 cbbX CbbX; Provisional
Probab=93.40 E-value=0.12 Score=59.82 Aligned_cols=24 Identities=33% Similarity=0.533 Sum_probs=19.2
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
-.|+.||||||||++..++...+.
T Consensus 61 ~ill~G~pGtGKT~lAr~la~~~~ 84 (287)
T CHL00181 61 HMSFTGSPGTGKTTVALKMADILY 84 (287)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHH
Confidence 378999999999998887755543
No 101
>PHA02544 44 clamp loader, small subunit; Provisional
Probab=93.36 E-value=0.12 Score=59.45 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.|+...+.+...+... +.+...||.||||||||+++.++...+
T Consensus 25 ~~~~~~~~l~~~~~~~----~~~~~lll~G~~G~GKT~la~~l~~~~ 67 (316)
T PHA02544 25 LPAADKETFKSIVKKG----RIPNMLLHSPSPGTGKTTVAKALCNEV 67 (316)
T ss_pred CcHHHHHHHHHHHhcC----CCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence 5666666666665432 234688889999999999988875543
No 102
>PRK08116 hypothetical protein; Validated
Probab=93.30 E-value=0.12 Score=59.04 Aligned_cols=26 Identities=35% Similarity=0.422 Sum_probs=23.2
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-.+|.||||||||++..++...++..
T Consensus 116 gl~l~G~~GtGKThLa~aia~~l~~~ 141 (268)
T PRK08116 116 GLLLWGSVGTGKTYLAACIANELIEK 141 (268)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHHHc
Confidence 47999999999999999998888765
No 103
>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=93.28 E-value=0.14 Score=55.48 Aligned_cols=43 Identities=23% Similarity=0.209 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
-|..-.+++...+.. ...+..+|.||||||||++...+.....
T Consensus 21 ~~~~~~~~l~~~~~~-----~~~~~lll~G~~G~GKT~la~~~~~~~~ 63 (226)
T TIGR03420 21 GNAELLAALRQLAAG-----KGDRFLYLWGESGSGKSHLLQAACAAAE 63 (226)
T ss_pred CcHHHHHHHHHHHhc-----CCCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence 344444555543321 2347899999999999998888776554
No 104
>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=93.26 E-value=0.12 Score=55.44 Aligned_cols=41 Identities=27% Similarity=0.362 Sum_probs=33.4
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
..+++.|.+.+..++... .+.+|-||+|+|||+++.+|++.
T Consensus 8 g~~~~~~~~~l~~~v~~g-------~~i~I~G~tGSGKTTll~aL~~~ 48 (186)
T cd01130 8 GTFSPLQAAYLWLAVEAR-------KNILISGGTGSGKTTLLNALLAF 48 (186)
T ss_pred CCCCHHHHHHHHHHHhCC-------CEEEEECCCCCCHHHHHHHHHhh
Confidence 357888888888877543 69999999999999998877654
No 105
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=93.25 E-value=0.31 Score=59.51 Aligned_cols=71 Identities=18% Similarity=0.226 Sum_probs=54.6
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..++.-|.+|+.+...... . ..-.+|.-|+|+|||.+.+.++..+
T Consensus 35 ~~lr~yQ~~al~a~~~~~~---~-~~~gvivlpTGaGKT~va~~~~~~~------------------------------- 79 (442)
T COG1061 35 FELRPYQEEALDALVKNRR---T-ERRGVIVLPTGAGKTVVAAEAIAEL------------------------------- 79 (442)
T ss_pred CCCcHHHHHHHHHHHhhcc---c-CCceEEEeCCCCCHHHHHHHHHHHh-------------------------------
Confidence 4688999999998776421 1 4678899999999999766654321
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGL 1194 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI 1194 (1402)
+.++||++|+..-+++-..++.+...
T Consensus 80 ----------------------------~~~~Lvlv~~~~L~~Qw~~~~~~~~~ 105 (442)
T COG1061 80 ----------------------------KRSTLVLVPTKELLDQWAEALKKFLL 105 (442)
T ss_pred ----------------------------cCCEEEEECcHHHHHHHHHHHHHhcC
Confidence 23499999999999999988885544
No 106
>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=93.07 E-value=0.18 Score=55.35 Aligned_cols=25 Identities=36% Similarity=0.611 Sum_probs=20.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.+.++-||+|.|||||+.-|-..+.
T Consensus 2 ~vi~lvGptGvGKTTt~aKLAa~~~ 26 (196)
T PF00448_consen 2 KVIALVGPTGVGKTTTIAKLAARLK 26 (196)
T ss_dssp EEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred EEEEEECCCCCchHhHHHHHHHHHh
Confidence 4678889999999999999866553
No 107
>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=93.06 E-value=0.15 Score=68.90 Aligned_cols=50 Identities=24% Similarity=0.357 Sum_probs=42.6
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhcccccccccccccc
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESS 1167 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~ 1167 (1402)
.+|.+++|||||++++.-+..+|... .
T Consensus 13 ~~~~a~agsgkt~~l~~~~~~~~~~~-----------------------------------------------------~ 39 (1141)
T TIGR02784 13 AWVSANAGSGKTHVLTQRVIRLLLNG-----------------------------------------------------V 39 (1141)
T ss_pred EEEEEECCCCHHHHHHHHHHHHHHcC-----------------------------------------------------C
Confidence 56999999999999998888777541 1
Q ss_pred CCCeEEEEeCchHHHHHHHHHHH
Q 000592 1168 VRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1168 ~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
...+||+.+.||+|.-|+-.||.
T Consensus 40 ~~~~i~~~t~t~~aa~em~~Ri~ 62 (1141)
T TIGR02784 40 PPSKILCLTYTKAAAAEMQNRVF 62 (1141)
T ss_pred CCCeEEEEecCHHHHHHHHHHHH
Confidence 24699999999999999999997
No 108
>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=93.02 E-value=0.066 Score=53.78 Aligned_cols=21 Identities=33% Similarity=0.714 Sum_probs=17.4
Q ss_pred eEEEEcCCCCChhhHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+.++-||||+||||.+-.+..
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 468899999999998777653
No 109
>PRK04195 replication factor C large subunit; Provisional
Probab=92.98 E-value=0.11 Score=63.89 Aligned_cols=45 Identities=29% Similarity=0.259 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.|+.+.+.+...+.... ........||.||||||||+++.++...
T Consensus 18 g~~~~~~~l~~~l~~~~-~g~~~~~lLL~GppG~GKTtla~ala~e 62 (482)
T PRK04195 18 GNEKAKEQLREWIESWL-KGKPKKALLLYGPPGVGKTSLAHALAND 62 (482)
T ss_pred CCHHHHHHHHHHHHHHh-cCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence 45555555555443211 0012468999999999999988776554
No 110
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=92.96 E-value=0.18 Score=59.42 Aligned_cols=44 Identities=30% Similarity=0.380 Sum_probs=35.1
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
..++..|.+.+..|+... +-.||-||+|+|||+++-+|+..+..
T Consensus 127 g~~~~~~~~~L~~~v~~~-------~nilI~G~tGSGKTTll~aL~~~i~~ 170 (323)
T PRK13833 127 KIMTEAQASVIRSAIDSR-------LNIVISGGTGSGKTTLANAVIAEIVA 170 (323)
T ss_pred CCCCHHHHHHHHHHHHcC-------CeEEEECCCCCCHHHHHHHHHHHHhc
Confidence 357888998888887643 35699999999999999888776643
No 111
>PRK09183 transposase/IS protein; Provisional
Probab=92.96 E-value=0.12 Score=58.83 Aligned_cols=44 Identities=25% Similarity=0.351 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..|..|...+..+- ........+|.||||||||+...+|...+.
T Consensus 84 ~~~~~~i~~L~~~~-----~i~~~~~v~l~Gp~GtGKThLa~al~~~a~ 127 (259)
T PRK09183 84 GAPQKQLQSLRSLS-----FIERNENIVLLGPSGVGKTHLAIALGYEAV 127 (259)
T ss_pred CCCHHHHHHHhcCC-----chhcCCeEEEEeCCCCCHHHHHHHHHHHHH
Confidence 56777776664320 122335788999999999999998855443
No 112
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=92.89 E-value=0.42 Score=57.48 Aligned_cols=33 Identities=24% Similarity=0.190 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI 1102 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI 1102 (1402)
..+.-|.+||..++... =.++|+|.|||||.+.
T Consensus 30 ~pt~iQ~~aip~il~g~--------dvi~~ApTGsGKTla~ 62 (423)
T PRK04837 30 NCTPIQALALPLTLAGR--------DVAGQAQTGTGKTMAF 62 (423)
T ss_pred CCCHHHHHHHHHHhCCC--------cEEEECCCCchHHHHH
Confidence 56899999999987643 3799999999999764
No 113
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=92.84 E-value=0.13 Score=63.04 Aligned_cols=23 Identities=39% Similarity=0.585 Sum_probs=19.0
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+...||.||||||||.++-++..
T Consensus 217 p~gVLL~GPPGTGKT~LAraIA~ 239 (438)
T PTZ00361 217 PKGVILYGPPGTGKTLLAKAVAN 239 (438)
T ss_pred CcEEEEECCCCCCHHHHHHHHHH
Confidence 34688999999999998877655
No 114
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=92.83 E-value=0.1 Score=59.27 Aligned_cols=26 Identities=46% Similarity=0.690 Sum_probs=23.1
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..-.++-||||||||+..++|-..++
T Consensus 105 ~~nl~l~G~~G~GKThLa~Ai~~~l~ 130 (254)
T COG1484 105 GENLVLLGPPGVGKTHLAIAIGNELL 130 (254)
T ss_pred CCcEEEECCCCCcHHHHHHHHHHHHH
Confidence 35678999999999999999988888
No 115
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]
Probab=92.81 E-value=0.28 Score=61.39 Aligned_cols=43 Identities=26% Similarity=0.376 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
+.-..|-++|.. ...++.+|||-||||||+..+.-|..||...
T Consensus 212 TIQkEQneIIR~---------ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~ 254 (747)
T COG3973 212 TIQKEQNEIIRF---------EKNKILVVQGAAGSGKTTIALHRVAYLLYGY 254 (747)
T ss_pred HhhHhHHHHHhc---------cCCCeEEEecCCCCCchhHHHHHHHHHHhcc
Confidence 566788888874 2347999999999999999999999999874
No 116
>PRK09401 reverse gyrase; Reviewed
Probab=92.80 E-value=0.34 Score=65.68 Aligned_cols=72 Identities=19% Similarity=0.108 Sum_probs=51.5
Q ss_pred HhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchh
Q 000592 1058 ILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQS 1137 (1402)
Q Consensus 1058 ~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~ 1137 (1402)
.+......-|..+|..++... =.+|++|.|||||...+ +.++...
T Consensus 76 ~~G~~pt~iQ~~~i~~il~g~--------dv~i~ApTGsGKT~f~l--~~~~~l~------------------------- 120 (1176)
T PRK09401 76 KTGSKPWSLQRTWAKRLLLGE--------SFAIIAPTGVGKTTFGL--VMSLYLA------------------------- 120 (1176)
T ss_pred hcCCCCcHHHHHHHHHHHCCC--------cEEEEcCCCCCHHHHHH--HHHHHHH-------------------------
Confidence 333467889999999887543 46889999999995322 2111111
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcC
Q 000592 1138 AAIARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEG 1193 (1402)
Q Consensus 1138 ~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~G 1193 (1402)
..+.++||.+||-.=++++..++.+.|
T Consensus 121 -----------------------------~~g~~alIL~PTreLa~Qi~~~l~~l~ 147 (1176)
T PRK09401 121 -----------------------------KKGKKSYIIFPTRLLVEQVVEKLEKFG 147 (1176)
T ss_pred -----------------------------hcCCeEEEEeccHHHHHHHHHHHHHHh
Confidence 014689999999999999999998654
No 117
>PRK10416 signal recognition particle-docking protein FtsY; Provisional
Probab=92.80 E-value=0.26 Score=57.98 Aligned_cols=27 Identities=30% Similarity=0.306 Sum_probs=22.4
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...+.++-||||.|||||+..|...+.
T Consensus 113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~ 139 (318)
T PRK10416 113 KPFVILVVGVNGVGKTTTIGKLAHKYK 139 (318)
T ss_pred CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence 346888889999999999999876653
No 118
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=92.79 E-value=0.45 Score=58.06 Aligned_cols=74 Identities=18% Similarity=0.226 Sum_probs=51.0
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHH-HHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIV-AIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIv-gLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..+.-|.+||..++... =.|+++|.|||||.+.+ .++..+......
T Consensus 23 ~pt~iQ~~ai~~il~g~--------dvlv~apTGsGKTla~~lpil~~l~~~~~~------------------------- 69 (456)
T PRK10590 23 EPTPIQQQAIPAVLEGR--------DLMASAQTGTGKTAGFTLPLLQHLITRQPH------------------------- 69 (456)
T ss_pred CCCHHHHHHHHHHhCCC--------CEEEECCCCCcHHHHHHHHHHHHhhhcccc-------------------------
Confidence 67899999999987542 28999999999997633 233332221100
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.......++||.+||-+-+.++...+..
T Consensus 70 -----------------------~~~~~~~~aLil~PtreLa~Qi~~~~~~ 97 (456)
T PRK10590 70 -----------------------AKGRRPVRALILTPTRELAAQIGENVRD 97 (456)
T ss_pred -----------------------cccCCCceEEEEeCcHHHHHHHHHHHHH
Confidence 0011246899999999999999888764
No 119
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=92.79 E-value=0.22 Score=55.71 Aligned_cols=26 Identities=31% Similarity=0.381 Sum_probs=21.2
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..+++|-||||||||++...++..++
T Consensus 24 g~~~~i~G~~G~GKTtl~~~~~~~~~ 49 (230)
T PRK08533 24 GSLILIEGDESTGKSILSQRLAYGFL 49 (230)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence 36999999999999998777666544
No 120
>PRK13767 ATP-dependent helicase; Provisional
Probab=92.78 E-value=0.45 Score=62.90 Aligned_cols=73 Identities=23% Similarity=0.300 Sum_probs=51.0
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH-HHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI-VAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI-vgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
.+++-|.+||..++... =+||+.|.|||||-.. +.++..++.... +
T Consensus 32 ~~tpiQ~~Ai~~il~g~--------nvli~APTGSGKTlaa~Lpil~~l~~~~~-------~------------------ 78 (876)
T PRK13767 32 TFTPPQRYAIPLIHEGK--------NVLISSPTGSGKTLAAFLAIIDELFRLGR-------E------------------ 78 (876)
T ss_pred CCCHHHHHHHHHHHcCC--------CEEEECCCCCcHHHHHHHHHHHHHHhhcc-------c------------------
Confidence 58999999999876532 4899999999999753 234444433210 0
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
.....+.++|+++|+-+-..++..+|.
T Consensus 79 -----------------------~~~~~~~~~LyIsPtraLa~di~~~L~ 105 (876)
T PRK13767 79 -----------------------GELEDKVYCLYVSPLRALNNDIHRNLE 105 (876)
T ss_pred -----------------------cCCCCCeEEEEEcCHHHHHHHHHHHHH
Confidence 000135689999999999988887764
No 121
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=92.73 E-value=0.16 Score=59.05 Aligned_cols=46 Identities=30% Similarity=0.312 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-|+...+.+..++... +-+...|+.||||||||+++..+...++..
T Consensus 18 g~~~~~~~l~~~~~~~----~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~ 63 (355)
T TIGR02397 18 GQEHIVQTLKNAIKNG----RIAHAYLFSGPRGTGKTSIARIFAKALNCQ 63 (355)
T ss_pred CcHHHHHHHHHHHHcC----CCCeEEEEECCCCCCHHHHHHHHHHHhcCC
Confidence 3556666666655432 223567999999999999999888887654
No 122
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=92.73 E-value=0.42 Score=60.25 Aligned_cols=76 Identities=22% Similarity=0.212 Sum_probs=52.5
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHH-HHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIV-AIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIv-gLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
..++-|.++|-.++... =.+||+|.|||||.+.+ .++..++.... ..
T Consensus 31 ~ptpiQ~~~ip~~l~G~--------Dvi~~ApTGSGKTlafllpil~~l~~~~~-------------------~~----- 78 (572)
T PRK04537 31 RCTPIQALTLPVALPGG--------DVAGQAQTGTGKTLAFLVAVMNRLLSRPA-------------------LA----- 78 (572)
T ss_pred CCCHHHHHHHHHHhCCC--------CEEEEcCCCCcHHHHHHHHHHHHHHhccc-------------------cc-----
Confidence 57899999999988643 38999999999997643 23333332210 00
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
.......++||++||.+-+.++..++.+.
T Consensus 79 -----------------------~~~~~~~raLIl~PTreLa~Qi~~~~~~l 107 (572)
T PRK04537 79 -----------------------DRKPEDPRALILAPTRELAIQIHKDAVKF 107 (572)
T ss_pred -----------------------ccccCCceEEEEeCcHHHHHHHHHHHHHH
Confidence 00112469999999999999998887754
No 123
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=92.69 E-value=0.41 Score=60.66 Aligned_cols=38 Identities=26% Similarity=0.352 Sum_probs=29.8
Q ss_pred HHHHhhc-CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhh
Q 000592 1055 LQQILKT-SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1055 L~~~Lk~-~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTk 1100 (1402)
+++++.. .+.+-|.+||.+++... =+|+.+|.|+|||-
T Consensus 17 l~~~fG~~~~r~~Q~~ai~~il~g~--------dvlv~apTGsGKTl 55 (607)
T PRK11057 17 LQETFGYQQFRPGQQEIIDAVLSGR--------DCLVVMPTGGGKSL 55 (607)
T ss_pred HHHHcCCCCCCHHHHHHHHHHHcCC--------CEEEEcCCCchHHH
Confidence 5555543 68899999999987643 36889999999994
No 124
>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=92.63 E-value=0.1 Score=51.11 Aligned_cols=21 Identities=33% Similarity=0.751 Sum_probs=16.2
Q ss_pred eEEEEcCCCCChhhHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+.+|.||||+||||+...|..
T Consensus 1 vI~I~G~~gsGKST~a~~La~ 21 (121)
T PF13207_consen 1 VIIISGPPGSGKSTLAKELAE 21 (121)
T ss_dssp EEEEEESTTSSHHHHHHHHHH
T ss_pred CEEEECCCCCCHHHHHHHHHH
Confidence 357999999999996555544
No 125
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=92.59 E-value=0.26 Score=52.24 Aligned_cols=28 Identities=46% Similarity=0.775 Sum_probs=24.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..+++|-||||+|||+.+..+..++...
T Consensus 32 g~l~~i~g~~g~GKT~~~~~l~~~~~~g 59 (193)
T PF13481_consen 32 GELTLIAGPPGSGKTTLALQLAAALATG 59 (193)
T ss_dssp TSEEEEEECSTSSHHHHHHHHHHHHHT-
T ss_pred CeEEEEEeCCCCCHHHHHHHHHHHHHhC
Confidence 3699999999999999999999888754
No 126
>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=92.56 E-value=0.27 Score=62.99 Aligned_cols=76 Identities=20% Similarity=0.219 Sum_probs=56.5
Q ss_pred CHHHHHHHHHHHccCCC--CcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1064 NESQLQAISVAIGLSSS--WKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~--~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
...|..||..++..... ......-.||+-|.|||||.|++.++..|+...
T Consensus 240 r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~---------------------------- 291 (667)
T TIGR00348 240 RYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELL---------------------------- 291 (667)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhc----------------------------
Confidence 35688898877654210 011234688999999999999999988776431
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcC
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEG 1193 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~G 1193 (1402)
...||||.+|.+.=++++...+.+.|
T Consensus 292 --------------------------~~~~vl~lvdR~~L~~Q~~~~f~~~~ 317 (667)
T TIGR00348 292 --------------------------KNPKVFFVVDRRELDYQLMKEFQSLQ 317 (667)
T ss_pred --------------------------CCCeEEEEECcHHHHHHHHHHHHhhC
Confidence 24699999999999999999888655
No 127
>TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.
Probab=92.52 E-value=0.19 Score=52.40 Aligned_cols=43 Identities=21% Similarity=0.307 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
|..+.+++...++. +.+...+.++.||.|+|||+.+.+++..|
T Consensus 4 s~~~t~~l~~~l~~---~l~~~~~i~l~G~lGaGKTtl~~~l~~~l 46 (133)
T TIGR00150 4 DEKAMDKFGKAFAK---PLDFGTVVLLKGDLGAGKTTLVQGLLQGL 46 (133)
T ss_pred CHHHHHHHHHHHHH---hCCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence 34444455444443 23345699999999999999998888765
No 128
>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=92.51 E-value=0.11 Score=51.15 Aligned_cols=25 Identities=36% Similarity=0.591 Sum_probs=22.3
Q ss_pred EEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1089 LIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
.|.||||+|||++.-.|...++...
T Consensus 2 ~i~G~~G~GKS~l~~~l~~~l~~~~ 26 (107)
T PF00910_consen 2 WIYGPPGIGKSTLAKELAKDLLKHI 26 (107)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHHh
Confidence 5899999999999999998888764
No 129
>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=92.48 E-value=0.14 Score=58.10 Aligned_cols=22 Identities=32% Similarity=0.513 Sum_probs=18.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.-.||.||||||||+++..+-.
T Consensus 22 ~~vLL~G~~GtGKT~lA~~la~ 43 (262)
T TIGR02640 22 YPVHLRGPAGTGKTTLAMHVAR 43 (262)
T ss_pred CeEEEEcCCCCCHHHHHHHHHH
Confidence 4678999999999998777643
No 130
>PRK06851 hypothetical protein; Provisional
Probab=92.45 E-value=0.53 Score=56.53 Aligned_cols=27 Identities=30% Similarity=0.484 Sum_probs=22.7
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...+|-||||||||+++..+...+...
T Consensus 215 ~~~~i~G~pG~GKstl~~~i~~~a~~~ 241 (367)
T PRK06851 215 NRYFLKGRPGTGKSTMLKKIAKAAEER 241 (367)
T ss_pred eEEEEeCCCCCcHHHHHHHHHHHHHhC
Confidence 589999999999999888887766544
No 131
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=92.39 E-value=0.17 Score=62.00 Aligned_cols=40 Identities=28% Similarity=0.477 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..+...+.+..++... +..+++||||||||+++..+-..+
T Consensus 179 i~e~~le~l~~~L~~~-------~~iil~GppGtGKT~lA~~la~~l 218 (459)
T PRK11331 179 IPETTIETILKRLTIK-------KNIILQGPPGVGKTFVARRLAYLL 218 (459)
T ss_pred CCHHHHHHHHHHHhcC-------CCEEEECCCCCCHHHHHHHHHHHh
Confidence 4566677777766542 578889999999999887765544
No 132
>PHA00729 NTP-binding motif containing protein
Probab=92.39 E-value=0.1 Score=58.75 Aligned_cols=24 Identities=25% Similarity=0.465 Sum_probs=21.0
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
-.+|.||||||||+...+|...+.
T Consensus 19 nIlItG~pGvGKT~LA~aLa~~l~ 42 (226)
T PHA00729 19 SAVIFGKQGSGKTTYALKVARDVF 42 (226)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHH
Confidence 478999999999999999887765
No 133
>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=92.38 E-value=0.1 Score=58.16 Aligned_cols=25 Identities=36% Similarity=0.488 Sum_probs=20.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.++.+|.||||+|||+++..+...+
T Consensus 43 ~~~~~l~G~~G~GKTtl~~~l~~~l 67 (269)
T TIGR03015 43 EGFILITGEVGAGKTTLIRNLLKRL 67 (269)
T ss_pred CCEEEEEcCCCCCHHHHHHHHHHhc
Confidence 4799999999999999888775543
No 134
>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=92.37 E-value=0.34 Score=55.68 Aligned_cols=24 Identities=38% Similarity=0.565 Sum_probs=19.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+.++-||||.|||+|+..|...+
T Consensus 73 ~vi~l~G~~G~GKTTt~akLA~~l 96 (272)
T TIGR00064 73 NVILFVGVNGVGKTTTIAKLANKL 96 (272)
T ss_pred eEEEEECCCCCcHHHHHHHHHHHH
Confidence 466666999999999999987655
No 135
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=92.36 E-value=0.33 Score=53.72 Aligned_cols=24 Identities=38% Similarity=0.354 Sum_probs=20.1
Q ss_pred CCceEEEEcCCCCChhhHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
...+++|.||||||||+....++.
T Consensus 24 ~g~~~~i~G~~GsGKt~l~~~~~~ 47 (234)
T PRK06067 24 FPSLILIEGDHGTGKSVLSQQFVY 47 (234)
T ss_pred CCcEEEEECCCCCChHHHHHHHHH
Confidence 457999999999999998776654
No 136
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=92.33 E-value=0.2 Score=58.96 Aligned_cols=42 Identities=29% Similarity=0.415 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.++..|.+.+..|+... +-.+|-||||+|||+++.+|+..+.
T Consensus 132 ~~~~~~~~~L~~~v~~~-------~~ilI~G~tGSGKTTll~aL~~~~~ 173 (319)
T PRK13894 132 IMTAAQREAIIAAVRAH-------RNILVIGGTGSGKTTLVNAIINEMV 173 (319)
T ss_pred CCCHHHHHHHHHHHHcC-------CeEEEECCCCCCHHHHHHHHHHhhh
Confidence 57888888888876543 5789999999999999888877654
No 137
>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=92.33 E-value=0.11 Score=60.63 Aligned_cols=29 Identities=31% Similarity=0.574 Sum_probs=25.7
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..|+.|+.||.|+|||||+.+||..+=..
T Consensus 124 ~~GLILVTGpTGSGKSTTlAamId~iN~~ 152 (353)
T COG2805 124 PRGLILVTGPTGSGKSTTLAAMIDYINKH 152 (353)
T ss_pred CCceEEEeCCCCCcHHHHHHHHHHHHhcc
Confidence 45999999999999999999999987554
No 138
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=92.33 E-value=0.15 Score=66.49 Aligned_cols=48 Identities=23% Similarity=0.366 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
=+.|.+.|..+|...-.......+.+|-||||||||.|+..++..|-.
T Consensus 760 REeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqe 807 (1164)
T PTZ00112 760 REKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQH 807 (1164)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHH
Confidence 467777777665431000112234569999999999999998876643
No 139
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=92.32 E-value=0.19 Score=62.02 Aligned_cols=122 Identities=23% Similarity=0.260 Sum_probs=70.1
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.++..|.+.+..++..++ |+.|+-||-|+|||+|.-+++..+......--+..-|. .+.-|++.|..-..
T Consensus 241 g~~~~~~~~~~~~~~~p~------GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPV----E~~~~gI~Q~qVN~ 310 (500)
T COG2804 241 GMSPFQLARLLRLLNRPQ------GLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPV----EYQLPGINQVQVNP 310 (500)
T ss_pred CCCHHHHHHHHHHHhCCC------eEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCe----eeecCCcceeeccc
Confidence 578889999998887654 99999999999999999888887765532111111121 22223443311000
Q ss_pred H---HHH--HHHHHhhhcc--------cccccccc-ccccCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 000592 1142 R---AWQ--DAALARQINE--------DSERDKKS-SESSVRARVLICAQSNAAVDELVSRISKEGL 1194 (1402)
Q Consensus 1142 r---~W~--d~a~arq~~~--------d~~~~~~~-~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI 1194 (1402)
+ .+. -.++-||-.+ |.++.... .....+.=||-.=++|.|..-| .||.+.|+
T Consensus 311 k~gltfa~~LRa~LRqDPDvImVGEIRD~ETAeiavqAalTGHLVlSTlHtnda~~ai-~RL~~mGv 376 (500)
T COG2804 311 KIGLTFARALRAILRQDPDVIMVGEIRDLETAEIAVQAALTGHLVLSTLHTNDAPGAI-TRLLEMGV 376 (500)
T ss_pred ccCCCHHHHHHHHhccCCCeEEEeccCCHHHHHHHHHHHhcCCeEeeecccCchHHHH-HHHHHcCC
Confidence 0 010 0122233211 22211110 1123567888889999999865 57777887
No 140
>PF03215 Rad17: Rad17 cell cycle checkpoint protein
Probab=92.26 E-value=0.17 Score=63.14 Aligned_cols=25 Identities=36% Similarity=0.652 Sum_probs=20.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..+-|+.||||+|||+||..|...+
T Consensus 45 ~~iLlLtGP~G~GKtttv~~La~el 69 (519)
T PF03215_consen 45 KRILLLTGPSGCGKTTTVKVLAKEL 69 (519)
T ss_pred cceEEEECCCCCCHHHHHHHHHHHh
Confidence 4599999999999999987765543
No 141
>PRK06921 hypothetical protein; Provisional
Probab=92.25 E-value=0.12 Score=59.05 Aligned_cols=27 Identities=30% Similarity=0.524 Sum_probs=23.9
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.++.||||||||+++.+|...++..
T Consensus 118 ~~l~l~G~~G~GKThLa~aia~~l~~~ 144 (266)
T PRK06921 118 NSIALLGQPGSGKTHLLTAAANELMRK 144 (266)
T ss_pred CeEEEECCCCCcHHHHHHHHHHHHhhh
Confidence 568999999999999999999888764
No 142
>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases. Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity
Probab=92.21 E-value=0.091 Score=57.10 Aligned_cols=21 Identities=29% Similarity=0.643 Sum_probs=19.0
Q ss_pred EEEcCCCCChhhHHHHHHHHH
Q 000592 1089 LIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+|+||||+|||+.|..++...
T Consensus 2 vv~G~pGsGKSt~i~~~~~~~ 22 (234)
T PF01443_consen 2 VVHGVPGSGKSTLIKKLLKDR 22 (234)
T ss_pred EEEcCCCCCHHHHHHHHHHhc
Confidence 799999999999999998874
No 143
>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=92.21 E-value=0.29 Score=55.04 Aligned_cols=26 Identities=27% Similarity=0.379 Sum_probs=21.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..+++|.||||+|||+++..+...+.
T Consensus 30 g~~~~i~g~~G~GKT~l~~~~~~~~~ 55 (271)
T cd01122 30 GELIILTAGTGVGKTTFLREYALDLI 55 (271)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 36999999999999999888766543
No 144
>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=92.20 E-value=0.33 Score=53.29 Aligned_cols=24 Identities=25% Similarity=0.333 Sum_probs=19.6
Q ss_pred CceEEEEcCCCCChhhHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
..+++|.||||+|||.....++..
T Consensus 16 g~~~li~G~~G~GKt~~~~~~~~~ 39 (224)
T TIGR03880 16 GHVIVVIGEYGTGKTTFSLQFLYQ 39 (224)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHH
Confidence 479999999999999976666543
No 145
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=92.16 E-value=0.4 Score=55.53 Aligned_cols=20 Identities=30% Similarity=0.806 Sum_probs=16.4
Q ss_pred ceEEEEcCCCCChhhHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgL 1105 (1402)
+..+|+.|.|||||-.++..
T Consensus 28 ~~~~~eapTGtGKTl~~L~~ 47 (289)
T smart00488 28 KIGILESPTGTGKTLSLLCL 47 (289)
T ss_pred CcEEEECCCCcchhHHHHHH
Confidence 68999999999999665543
No 146
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=92.16 E-value=0.4 Score=55.53 Aligned_cols=20 Identities=30% Similarity=0.806 Sum_probs=16.4
Q ss_pred ceEEEEcCCCCChhhHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgL 1105 (1402)
+..+|+.|.|||||-.++..
T Consensus 28 ~~~~~eapTGtGKTl~~L~~ 47 (289)
T smart00489 28 KIGILESPTGTGKTLSLLCL 47 (289)
T ss_pred CcEEEECCCCcchhHHHHHH
Confidence 68999999999999665543
No 147
>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=92.15 E-value=0.55 Score=62.38 Aligned_cols=46 Identities=22% Similarity=0.140 Sum_probs=31.8
Q ss_pred HHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH
Q 000592 1055 LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI 1102 (1402)
Q Consensus 1055 L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI 1102 (1402)
+.+.+...+.+.|.+||..++.... ...+.=.|||||.|+|||-+.
T Consensus 444 ~~~~~~f~~T~~Q~~aI~~I~~d~~--~~~~~d~Ll~adTGsGKT~va 489 (926)
T TIGR00580 444 FEDSFPFEETPDQLKAIEEIKADME--SPRPMDRLVCGDVGFGKTEVA 489 (926)
T ss_pred HHHhCCCCCCHHHHHHHHHHHhhhc--ccCcCCEEEECCCCccHHHHH
Confidence 4444556788999999998875321 011123699999999999753
No 148
>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A.
Probab=92.15 E-value=0.12 Score=54.08 Aligned_cols=27 Identities=41% Similarity=0.530 Sum_probs=22.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+|+++|-||-|||||+++-+|..+|-.
T Consensus 19 ~g~~vi~G~Ng~GKStil~ai~~~L~~ 45 (202)
T PF13476_consen 19 PGLNVIYGPNGSGKSTILEAIRYALGG 45 (202)
T ss_dssp SEEEEEEESTTSSHHHHHHHHHHHHHS
T ss_pred CCcEEEECCCCCCHHHHHHHHHHHHcC
Confidence 489999999999999988777665543
No 149
>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=92.05 E-value=0.15 Score=57.45 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=17.0
Q ss_pred CeEEEEeC---chHHHHHHHHHHHhcCCCC
Q 000592 1170 ARVLICAQ---SNAAVDELVSRISKEGLYG 1196 (1402)
Q Consensus 1170 ~RILVCAP---SNAAVDEIV~RLl~~GI~d 1196 (1402)
..||..=- =|.++.|++.-.++.|..+
T Consensus 102 ~~ILFIDEIHRlnk~~qe~LlpamEd~~id 131 (233)
T PF05496_consen 102 GDILFIDEIHRLNKAQQEILLPAMEDGKID 131 (233)
T ss_dssp T-EEEECTCCC--HHHHHHHHHHHHCSEEE
T ss_pred CcEEEEechhhccHHHHHHHHHHhccCeEE
Confidence 44666532 3788899999888777543
No 150
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=91.99 E-value=0.36 Score=59.15 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=23.6
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+.+.++-||||+|||+|+..|...+..
T Consensus 94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~ 121 (437)
T PRK00771 94 KPQTIMLVGLQGSGKTTTAAKLARYFKK 121 (437)
T ss_pred CCeEEEEECCCCCcHHHHHHHHHHHHHH
Confidence 3578899999999999999998876543
No 151
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=91.97 E-value=0.21 Score=61.61 Aligned_cols=26 Identities=31% Similarity=0.480 Sum_probs=21.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.-.|+.||||||||+++..+...+..
T Consensus 37 ~~~Lf~GPpGtGKTTlA~~lA~~l~~ 62 (472)
T PRK14962 37 HAYIFAGPRGTGKTTVARILAKSLNC 62 (472)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHhcc
Confidence 34699999999999998888777654
No 152
>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=91.96 E-value=0.22 Score=52.29 Aligned_cols=24 Identities=33% Similarity=0.418 Sum_probs=19.7
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.+|-||||+|||+++..+...+.
T Consensus 2 ~~~~~G~~G~GKTt~~~~la~~~~ 25 (173)
T cd03115 2 VILLVGLQGVGKTTTAAKLALYLK 25 (173)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHH
Confidence 578889999999999888766543
No 153
>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=91.93 E-value=0.31 Score=54.41 Aligned_cols=25 Identities=28% Similarity=0.445 Sum_probs=20.1
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
...++||-||||||||.....++..
T Consensus 20 ~gs~~lI~G~pGsGKT~la~~~l~~ 44 (237)
T TIGR03877 20 ERNVVLLSGGPGTGKSIFSQQFLWN 44 (237)
T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence 3479999999999999976665543
No 154
>PRK05973 replicative DNA helicase; Provisional
Probab=91.90 E-value=0.35 Score=54.85 Aligned_cols=27 Identities=26% Similarity=0.395 Sum_probs=21.9
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...++||.|+||+|||...+.++....
T Consensus 63 ~Gsl~LIaG~PG~GKT~lalqfa~~~a 89 (237)
T PRK05973 63 PGDLVLLGARPGHGKTLLGLELAVEAM 89 (237)
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHHH
Confidence 346999999999999998877765544
No 155
>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=91.78 E-value=0.57 Score=59.03 Aligned_cols=39 Identities=26% Similarity=0.320 Sum_probs=30.4
Q ss_pred HHHHhh-cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhH
Q 000592 1055 LQQILK-TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1055 L~~~Lk-~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkT 1101 (1402)
|++++. ..|+.-|.+||.+++... =+|+..|.|+|||-.
T Consensus 5 l~~~fg~~~fr~~Q~~~i~~il~g~--------dvlv~~PTG~GKTl~ 44 (591)
T TIGR01389 5 LKRTFGYDDFRPGQEEIISHVLDGR--------DVLVVMPTGGGKSLC 44 (591)
T ss_pred HHHhcCCCCCCHHHHHHHHHHHcCC--------CEEEEcCCCccHhHH
Confidence 445554 368999999999988643 378999999999964
No 156
>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=91.71 E-value=0.13 Score=60.71 Aligned_cols=26 Identities=31% Similarity=0.641 Sum_probs=22.9
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.++.||.||+|+|||||+.+++..+.
T Consensus 122 ~g~ili~G~tGSGKTT~l~al~~~i~ 147 (343)
T TIGR01420 122 RGLILVTGPTGSGKSTTLASMIDYIN 147 (343)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHhhC
Confidence 48999999999999999998887654
No 157
>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=91.63 E-value=0.35 Score=53.74 Aligned_cols=50 Identities=22% Similarity=0.242 Sum_probs=34.2
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
...|+-=..|+.......+ .......|.||+|+|||+.+.++...+....
T Consensus 13 g~~N~~a~~~~~~ia~~~~---~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~ 62 (219)
T PF00308_consen 13 GESNELAYAAAKAIAENPG---ERYNPLFLYGPSGLGKTHLLQAIANEAQKQH 62 (219)
T ss_dssp TTTTHHHHHHHHHHHHSTT---TSSSEEEEEESTTSSHHHHHHHHHHHHHHHC
T ss_pred CCcHHHHHHHHHHHHhcCC---CCCCceEEECCCCCCHHHHHHHHHHHHHhcc
Confidence 3456655555555444432 1223468999999999999999988887753
No 158
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=91.60 E-value=0.69 Score=57.57 Aligned_cols=32 Identities=31% Similarity=0.335 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkT 1101 (1402)
..+.-|.+||..++... =.+++.|.|||||-.
T Consensus 143 ~ptpiQ~~aip~il~g~--------dviv~ApTGSGKTla 174 (518)
T PLN00206 143 FPTPIQMQAIPAALSGR--------SLLVSADTGSGKTAS 174 (518)
T ss_pred CCCHHHHHHHHHHhcCC--------CEEEEecCCCCccHH
Confidence 57899999999988543 389999999999964
No 159
>PRK06835 DNA replication protein DnaC; Validated
Probab=91.51 E-value=0.15 Score=60.19 Aligned_cols=27 Identities=41% Similarity=0.405 Sum_probs=24.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.+|.||||||||++..+|...++..
T Consensus 184 ~~Lll~G~~GtGKThLa~aIa~~l~~~ 210 (329)
T PRK06835 184 ENLLFYGNTGTGKTFLSNCIAKELLDR 210 (329)
T ss_pred CcEEEECCCCCcHHHHHHHHHHHHHHC
Confidence 568999999999999999999888765
No 160
>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=91.50 E-value=0.15 Score=49.79 Aligned_cols=21 Identities=38% Similarity=0.556 Sum_probs=17.5
Q ss_pred EEEcCCCCChhhHHHHHHHHH
Q 000592 1089 LIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+|.|+|||||||++-.|...+
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 689999999999877776653
No 161
>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=91.40 E-value=0.14 Score=63.71 Aligned_cols=26 Identities=38% Similarity=0.553 Sum_probs=21.1
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.-.||.||||||||.++.++...+-
T Consensus 216 p~GILLyGPPGTGKT~LAKAlA~eL~ 241 (512)
T TIGR03689 216 PKGVLLYGPPGCGKTLIAKAVANSLA 241 (512)
T ss_pred CcceEEECCCCCcHHHHHHHHHHhhc
Confidence 34589999999999998888776653
No 162
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=91.31 E-value=0.26 Score=58.57 Aligned_cols=26 Identities=27% Similarity=0.365 Sum_probs=22.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...|+.||||||||+++..+...+..
T Consensus 39 h~~L~~Gp~G~GKTtla~~la~~l~c 64 (363)
T PRK14961 39 HAWLLSGTRGVGKTTIARLLAKSLNC 64 (363)
T ss_pred eEEEEecCCCCCHHHHHHHHHHHhcC
Confidence 45699999999999999988877763
No 163
>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=91.30 E-value=0.6 Score=55.43 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=23.3
Q ss_pred HHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhH
Q 000592 1067 QLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1067 Q~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkT 1101 (1402)
|.+|+.++.... .++.+|.+|+|+|||..
T Consensus 2 Q~~~~~~~~~~~------~~~~~i~apTGsGKT~~ 30 (357)
T TIGR03158 2 QVATFEALQSKD------ADIIFNTAPTGAGKTLA 30 (357)
T ss_pred HHHHHHHHHcCC------CCEEEEECCCCCCHHHH
Confidence 888888876542 36899999999999963
No 164
>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=91.29 E-value=0.54 Score=60.83 Aligned_cols=67 Identities=19% Similarity=0.233 Sum_probs=50.4
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.+=.-|.+||...++.. ..+-.+|.-|+|+|||.+.++++..
T Consensus 255 ~LRpYQ~eAl~~~~~~g-----r~r~GIIvLPtGaGKTlvai~aa~~--------------------------------- 296 (732)
T TIGR00603 255 QIRPYQEKSLSKMFGNG-----RARSGIIVLPCGAGKSLVGVTAACT--------------------------------- 296 (732)
T ss_pred CcCHHHHHHHHHHHhcC-----CCCCcEEEeCCCCChHHHHHHHHHH---------------------------------
Confidence 45578999998876432 1135788999999999987654321
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
.++++||.+||...|++....+.+-
T Consensus 297 --------------------------l~k~tLILvps~~Lv~QW~~ef~~~ 321 (732)
T TIGR00603 297 --------------------------VKKSCLVLCTSAVSVEQWKQQFKMW 321 (732)
T ss_pred --------------------------hCCCEEEEeCcHHHHHHHHHHHHHh
Confidence 1357999999999999999999853
No 165
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=91.29 E-value=0.16 Score=61.00 Aligned_cols=22 Identities=45% Similarity=0.659 Sum_probs=18.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.-.|+.||||||||.+..++..
T Consensus 166 ~gvLL~GppGtGKT~lAkaia~ 187 (389)
T PRK03992 166 KGVLLYGPPGTGKTLLAKAVAH 187 (389)
T ss_pred CceEEECCCCCChHHHHHHHHH
Confidence 4579999999999998777654
No 166
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=91.28 E-value=0.19 Score=60.41 Aligned_cols=30 Identities=23% Similarity=0.391 Sum_probs=25.4
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...++.++-||+|+|||+|+..|...+...
T Consensus 135 ~~g~ii~lvGptGvGKTTtiakLA~~~~~~ 164 (374)
T PRK14722 135 ERGGVFALMGPTGVGKTTTTAKLAARCVMR 164 (374)
T ss_pred cCCcEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence 445799999999999999999998876543
No 167
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=91.25 E-value=0.46 Score=60.31 Aligned_cols=24 Identities=17% Similarity=0.242 Sum_probs=21.7
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1169 RARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
+++|.||++|++..|+++.+....
T Consensus 63 ~~~viist~t~~lq~q~~~~~~~~ 86 (654)
T COG1199 63 GKKVIISTRTKALQEQLLEEDLPI 86 (654)
T ss_pred CCcEEEECCCHHHHHHHHHhhcch
Confidence 589999999999999999999843
No 168
>PF13555 AAA_29: P-loop containing region of AAA domain
Probab=91.20 E-value=0.21 Score=45.89 Aligned_cols=26 Identities=38% Similarity=0.691 Sum_probs=22.8
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
++||.||.|+|||+.+=++..+|...
T Consensus 25 ~tli~G~nGsGKSTllDAi~~~L~~~ 50 (62)
T PF13555_consen 25 VTLITGPNGSGKSTLLDAIQTVLYGN 50 (62)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHcCC
Confidence 89999999999999988887777654
No 169
>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.
Probab=91.18 E-value=0.21 Score=55.64 Aligned_cols=36 Identities=36% Similarity=0.472 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHH
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+.-+.|+..|.... .=.||.||||||||.+...+-+
T Consensus 9 e~aKrAL~iAAaG~-------h~lLl~GppGtGKTmlA~~l~~ 44 (206)
T PF01078_consen 9 EEAKRALEIAAAGG-------HHLLLIGPPGTGKTMLARRLPS 44 (206)
T ss_dssp HHHHHHHHHHHHCC---------EEEES-CCCTHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCC-------CCeEEECCCCCCHHHHHHHHHH
Confidence 34455655444322 2479999999999987666543
No 170
>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=91.18 E-value=0.68 Score=62.94 Aligned_cols=35 Identities=20% Similarity=0.022 Sum_probs=26.8
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHH
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIV 1103 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIv 1103 (1402)
...-.-|..+|..++... =.+|++|+|||||.+.+
T Consensus 77 ~~p~~iQ~~~i~~il~G~--------d~vi~ApTGsGKT~f~l 111 (1171)
T TIGR01054 77 SEPWSIQKMWAKRVLRGD--------SFAIIAPTGVGKTTFGL 111 (1171)
T ss_pred CCCcHHHHHHHHHHhCCC--------eEEEECCCCCCHHHHHH
Confidence 356688999999887543 35689999999996443
No 171
>PRK06620 hypothetical protein; Validated
Probab=91.14 E-value=0.2 Score=55.48 Aligned_cols=20 Identities=35% Similarity=0.385 Sum_probs=16.8
Q ss_pred ceEEEEcCCCCChhhHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgL 1105 (1402)
...+|.||||+|||+...++
T Consensus 45 ~~l~l~Gp~G~GKThLl~a~ 64 (214)
T PRK06620 45 FTLLIKGPSSSGKTYLTKIW 64 (214)
T ss_pred ceEEEECCCCCCHHHHHHHH
Confidence 45899999999999977653
No 172
>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=91.03 E-value=0.33 Score=56.55 Aligned_cols=42 Identities=21% Similarity=0.287 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.+.+.|.+.+..++... +-.||-||+|+|||+++.+|+..+-
T Consensus 116 ~~~~~~~~~L~~~v~~~-------~~ilI~G~tGSGKTTll~al~~~i~ 157 (299)
T TIGR02782 116 IMTAAQRDVLREAVLAR-------KNILVVGGTGSGKTTLANALLAEIA 157 (299)
T ss_pred CCCHHHHHHHHHHHHcC-------CeEEEECCCCCCHHHHHHHHHHHhh
Confidence 57777888888877532 5789999999999999888776543
No 173
>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=90.99 E-value=0.24 Score=59.39 Aligned_cols=27 Identities=33% Similarity=0.409 Sum_probs=22.9
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...+|.||||||||++..++...+...
T Consensus 137 n~l~l~G~~G~GKThL~~ai~~~l~~~ 163 (405)
T TIGR00362 137 NPLFIYGGVGLGKTHLLHAIGNEILEN 163 (405)
T ss_pred CeEEEECCCCCcHHHHHHHHHHHHHHh
Confidence 357899999999999999988877654
No 174
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=90.93 E-value=0.23 Score=54.46 Aligned_cols=29 Identities=28% Similarity=0.513 Sum_probs=24.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...+++|.||||||||+....++...+..
T Consensus 22 ~g~i~~i~G~~GsGKT~l~~~la~~~~~~ 50 (225)
T PRK09361 22 RGTITQIYGPPGSGKTNICLQLAVEAAKN 50 (225)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence 44799999999999999999888776654
No 175
>PRK08727 hypothetical protein; Validated
Probab=90.90 E-value=0.4 Score=53.59 Aligned_cols=27 Identities=33% Similarity=0.546 Sum_probs=23.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...+|.||||||||+...++...+...
T Consensus 42 ~~l~l~G~~G~GKThL~~a~~~~~~~~ 68 (233)
T PRK08727 42 DWLYLSGPAGTGKTHLALALCAAAEQA 68 (233)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHc
Confidence 468999999999999999988876554
No 176
>PRK10689 transcription-repair coupling factor; Provisional
Probab=90.88 E-value=0.82 Score=62.09 Aligned_cols=47 Identities=21% Similarity=0.171 Sum_probs=33.0
Q ss_pred HHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHH
Q 000592 1055 LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIV 1103 (1402)
Q Consensus 1055 L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIv 1103 (1402)
+...+.....+.|.+||..++.... ...+.=.||+||.|+|||-+.+
T Consensus 593 ~~~~~~~~~T~~Q~~aI~~il~d~~--~~~~~d~Ll~a~TGsGKT~val 639 (1147)
T PRK10689 593 FCDSFPFETTPDQAQAINAVLSDMC--QPLAMDRLVCGDVGFGKTEVAM 639 (1147)
T ss_pred HHHhCCCCCCHHHHHHHHHHHHHhh--cCCCCCEEEEcCCCcCHHHHHH
Confidence 3444556788999999998876421 1112347999999999998643
No 177
>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=90.84 E-value=0.18 Score=54.06 Aligned_cols=25 Identities=36% Similarity=0.695 Sum_probs=19.8
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+|.||||+||||.+..++..+-..
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 3799999999999999988766443
No 178
>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=90.83 E-value=0.33 Score=60.42 Aligned_cols=23 Identities=17% Similarity=0.244 Sum_probs=18.9
Q ss_pred CCeEEEEeCchHHHHHHHHHHHh
Q 000592 1169 RARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
++++||.+|+.+=+.+++.||.+
T Consensus 25 g~~vLvlvP~i~L~~Q~~~~l~~ 47 (505)
T TIGR00595 25 GKSVLVLVPEIALTPQMIQRFKY 47 (505)
T ss_pred CCeEEEEeCcHHHHHHHHHHHHH
Confidence 45788999998888888888874
No 179
>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=90.82 E-value=0.27 Score=58.65 Aligned_cols=28 Identities=29% Similarity=0.530 Sum_probs=24.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.++.||-||+|+|||||+.+|+..+...
T Consensus 134 ~glilI~GpTGSGKTTtL~aLl~~i~~~ 161 (358)
T TIGR02524 134 EGIVFITGATGSGKSTLLAAIIRELAEA 161 (358)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHhhc
Confidence 4899999999999999999988877543
No 180
>PRK02362 ski2-like helicase; Provisional
Probab=90.81 E-value=0.73 Score=59.71 Aligned_cols=68 Identities=18% Similarity=0.152 Sum_probs=49.9
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
.+++.|.+||...+... .=.||+.|+|+|||.... + +++...
T Consensus 23 ~l~p~Q~~ai~~~~~~g-------~nvlv~APTGSGKTlia~--l-ail~~l---------------------------- 64 (737)
T PRK02362 23 ELYPPQAEAVEAGLLDG-------KNLLAAIPTASGKTLIAE--L-AMLKAI---------------------------- 64 (737)
T ss_pred cCCHHHHHHHHHHHhCC-------CcEEEECCCcchHHHHHH--H-HHHHHH----------------------------
Confidence 68999999998754322 348999999999997432 1 122210
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhc
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKE 1192 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~ 1192 (1402)
.++.++|+++|+-+=++|...++.+.
T Consensus 65 -------------------------~~~~kal~i~P~raLa~q~~~~~~~~ 90 (737)
T PRK02362 65 -------------------------ARGGKALYIVPLRALASEKFEEFERF 90 (737)
T ss_pred -------------------------hcCCcEEEEeChHHHHHHHHHHHHHh
Confidence 01468999999999999999999854
No 181
>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=90.79 E-value=0.41 Score=56.54 Aligned_cols=24 Identities=38% Similarity=0.567 Sum_probs=20.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+.+|+|.||||||-+.+.++..+
T Consensus 2 ~v~~I~G~aGTGKTvla~~l~~~l 25 (352)
T PF09848_consen 2 QVILITGGAGTGKTVLALNLAKEL 25 (352)
T ss_pred eEEEEEecCCcCHHHHHHHHHHHh
Confidence 378999999999999888777766
No 182
>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=90.75 E-value=0.34 Score=58.01 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=21.0
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..+.+|.||||||||++.-.|...+
T Consensus 78 r~il~L~GPPGsGKStla~~La~~l 102 (361)
T smart00763 78 KQILYLLGPVGGGKSSLVECLKRGL 102 (361)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHH
Confidence 4799999999999999877766655
No 183
>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=90.65 E-value=0.23 Score=56.40 Aligned_cols=27 Identities=19% Similarity=0.195 Sum_probs=21.8
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...++||.||||||||+....++...+
T Consensus 35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a 61 (259)
T TIGR03878 35 AYSVINITGVSDTGKSLMVEQFAVTQA 61 (259)
T ss_pred CCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 347999999999999998777665543
No 184
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=90.63 E-value=0.18 Score=57.42 Aligned_cols=27 Identities=41% Similarity=0.695 Sum_probs=23.9
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||||||+++.++-..|+..
T Consensus 25 halL~~Gp~G~Gktt~a~~lA~~l~~~ 51 (325)
T COG0470 25 HALLFYGPPGVGKTTAALALAKELLCE 51 (325)
T ss_pred ceeeeeCCCCCCHHHHHHHHHHHHhCC
Confidence 368999999999999999999888854
No 185
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=90.62 E-value=0.19 Score=60.72 Aligned_cols=23 Identities=43% Similarity=0.582 Sum_probs=18.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+.-.|+.||||||||+++.++..
T Consensus 179 pkgvLL~GppGTGKT~LAkalA~ 201 (398)
T PTZ00454 179 PRGVLLYGPPGTGKTMLAKAVAH 201 (398)
T ss_pred CceEEEECCCCCCHHHHHHHHHH
Confidence 34588999999999998776644
No 186
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=90.57 E-value=0.32 Score=58.30 Aligned_cols=26 Identities=38% Similarity=0.608 Sum_probs=22.8
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
.+|-||||||||.|+.-+...+-...
T Consensus 45 ~~iyG~~GTGKT~~~~~v~~~l~~~~ 70 (366)
T COG1474 45 IIIYGPTGTGKTATVKFVMEELEESS 70 (366)
T ss_pred EEEECCCCCCHhHHHHHHHHHHHhhh
Confidence 78889999999999999888877763
No 187
>PTZ00110 helicase; Provisional
Probab=90.51 E-value=0.93 Score=56.91 Aligned_cols=75 Identities=17% Similarity=0.172 Sum_probs=50.5
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH-HHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI-VAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI-vgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
....-|.+||-.++...+ .++++|.|||||.+- +.++..++....
T Consensus 152 ~pt~iQ~~aip~~l~G~d--------vI~~ApTGSGKTlaylLP~l~~i~~~~~-------------------------- 197 (545)
T PTZ00110 152 EPTPIQVQGWPIALSGRD--------MIGIAETGSGKTLAFLLPAIVHINAQPL-------------------------- 197 (545)
T ss_pred CCCHHHHHHHHHHhcCCC--------EEEEeCCCChHHHHHHHHHHHHHHhccc--------------------------
Confidence 467899999999886532 578999999999752 222222222100
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcC
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEG 1193 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~G 1193 (1402)
.....++.+||.+||.+-+.++...+.+.+
T Consensus 198 -----------------------~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~ 227 (545)
T PTZ00110 198 -----------------------LRYGDGPIVLVLAPTRELAEQIREQCNKFG 227 (545)
T ss_pred -----------------------ccCCCCcEEEEECChHHHHHHHHHHHHHHh
Confidence 001125689999999999988888777543
No 188
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=90.47 E-value=0.18 Score=62.28 Aligned_cols=21 Identities=48% Similarity=0.684 Sum_probs=18.1
Q ss_pred eEEEEcCCCCChhhHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVs 1107 (1402)
=.|+.||||||||+++.++..
T Consensus 90 giLL~GppGtGKT~la~alA~ 110 (495)
T TIGR01241 90 GVLLVGPPGTGKTLLAKAVAG 110 (495)
T ss_pred cEEEECCCCCCHHHHHHHHHH
Confidence 489999999999998887754
No 189
>PRK14701 reverse gyrase; Provisional
Probab=90.33 E-value=0.87 Score=63.68 Aligned_cols=38 Identities=21% Similarity=0.163 Sum_probs=29.8
Q ss_pred HHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhh
Q 000592 1055 LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1055 L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTk 1100 (1402)
+++.+...+..-|.++|..++... =.++++|.|||||.
T Consensus 72 f~~~~G~~pt~iQ~~~i~~il~G~--------d~li~APTGsGKTl 109 (1638)
T PRK14701 72 FEKITGFEFWSIQKTWAKRILRGK--------SFSIVAPTGMGKST 109 (1638)
T ss_pred HHHhhCCCCCHHHHHHHHHHHcCC--------CEEEEEcCCCCHHH
Confidence 344444578899999999988643 35899999999998
No 190
>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model. AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.
Probab=90.33 E-value=0.12 Score=53.71 Aligned_cols=21 Identities=38% Similarity=0.651 Sum_probs=14.2
Q ss_pred EEEEcCCCCChhhHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.||.|+||+|||+++.++-.+
T Consensus 2 vLleg~PG~GKT~la~~lA~~ 22 (131)
T PF07726_consen 2 VLLEGVPGVGKTTLAKALARS 22 (131)
T ss_dssp EEEES---HHHHHHHHHHHHH
T ss_pred EeeECCCccHHHHHHHHHHHH
Confidence 589999999999987765443
No 191
>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=90.21 E-value=0.26 Score=53.67 Aligned_cols=28 Identities=29% Similarity=0.544 Sum_probs=23.6
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+++|.||||||||+....+...+..
T Consensus 18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~~ 45 (218)
T cd01394 18 RGTVTQVYGPPGTGKTNIAIQLAVETAG 45 (218)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence 3479999999999999999888776654
No 192
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=90.18 E-value=0.4 Score=59.77 Aligned_cols=28 Identities=29% Similarity=0.326 Sum_probs=23.9
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+..|++||||||||+++..+..++...
T Consensus 43 ~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~ 70 (507)
T PRK06645 43 AGGYLLTGIRGVGKTTSARIIAKAVNCS 70 (507)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHhcCc
Confidence 4578999999999999999988877654
No 193
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=90.15 E-value=0.44 Score=58.13 Aligned_cols=27 Identities=33% Similarity=0.377 Sum_probs=23.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.+|.||||||||++..++...+...
T Consensus 149 ~~l~l~G~~G~GKThL~~ai~~~~~~~ 175 (450)
T PRK00149 149 NPLFIYGGVGLGKTHLLHAIGNYILEK 175 (450)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHh
Confidence 357999999999999999988877654
No 194
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=90.11 E-value=0.41 Score=59.63 Aligned_cols=26 Identities=38% Similarity=0.480 Sum_probs=22.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...|+.||||||||+++..+..++..
T Consensus 37 ha~Lf~GppGtGKTTlA~~lA~~l~c 62 (504)
T PRK14963 37 HAYLFSGPRGVGKTTTARLIAMAVNC 62 (504)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHhc
Confidence 34599999999999999988887764
No 195
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=90.04 E-value=1.1 Score=54.67 Aligned_cols=26 Identities=27% Similarity=0.456 Sum_probs=22.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.+.+|-||+|+|||||+..|...+.
T Consensus 241 ~~vI~LVGptGvGKTTTiaKLA~~L~ 266 (436)
T PRK11889 241 VQTIALIGPTGVGKTTTLAKMAWQFH 266 (436)
T ss_pred CcEEEEECCCCCcHHHHHHHHHHHHH
Confidence 46889999999999999999877654
No 196
>PRK14956 DNA polymerase III subunits gamma and tau; Provisional
Probab=90.03 E-value=0.38 Score=59.52 Aligned_cols=27 Identities=26% Similarity=0.373 Sum_probs=22.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...|+.||||||||+++..+...+...
T Consensus 41 ha~Lf~GP~GtGKTTlAriLAk~Lnce 67 (484)
T PRK14956 41 HAYIFFGPRGVGKTTIARILAKRLNCE 67 (484)
T ss_pred eEEEEECCCCCCHHHHHHHHHHhcCcc
Confidence 357999999999999988887776543
No 197
>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional
Probab=89.99 E-value=0.24 Score=59.59 Aligned_cols=26 Identities=23% Similarity=0.128 Sum_probs=20.8
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
+.+-+.||+||||||||...-++...
T Consensus 146 k~PlgllL~GPPGcGKTllAraiA~e 171 (413)
T PLN00020 146 KVPLILGIWGGKGQGKSFQCELVFKK 171 (413)
T ss_pred CCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence 45678999999999999976666543
No 198
>PRK08939 primosomal protein DnaI; Reviewed
Probab=89.97 E-value=0.24 Score=57.92 Aligned_cols=27 Identities=26% Similarity=0.316 Sum_probs=23.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.+|.||||||||+.+.+|...+...
T Consensus 157 ~gl~L~G~~G~GKThLa~Aia~~l~~~ 183 (306)
T PRK08939 157 KGLYLYGDFGVGKSYLLAAIANELAKK 183 (306)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHc
Confidence 357899999999999999998888754
No 199
>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=89.94 E-value=0.29 Score=51.47 Aligned_cols=23 Identities=35% Similarity=0.576 Sum_probs=19.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
++.+|-||||+||||++..|...
T Consensus 4 ~ii~i~G~~GsGKsTl~~~l~~~ 26 (188)
T TIGR01360 4 KIIFIVGGPGSGKGTQCEKIVEK 26 (188)
T ss_pred cEEEEECCCCCCHHHHHHHHHHH
Confidence 68999999999999977666543
No 200
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=89.94 E-value=0.46 Score=56.12 Aligned_cols=45 Identities=20% Similarity=0.176 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.++...+.+..++... +-++..|+.||||+|||+++..+...+..
T Consensus 21 g~~~~~~~l~~~i~~~----~~~~~~L~~G~~G~GKt~~a~~la~~l~~ 65 (367)
T PRK14970 21 GQSHITNTLLNAIENN----HLAQALLFCGPRGVGKTTCARILARKINQ 65 (367)
T ss_pred CcHHHHHHHHHHHHcC----CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence 3455566666666432 23458899999999999998888655544
No 201
>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=89.94 E-value=0.76 Score=50.49 Aligned_cols=27 Identities=30% Similarity=0.316 Sum_probs=21.8
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...+.+|-||||||||++...++...+
T Consensus 19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~ 45 (229)
T TIGR03881 19 RGFFVAVTGEPGTGKTIFCLHFAYKGL 45 (229)
T ss_pred CCeEEEEECCCCCChHHHHHHHHHHHH
Confidence 347999999999999998887765443
No 202
>TIGR00602 rad24 checkpoint protein rad24. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.89 E-value=0.46 Score=60.70 Aligned_cols=47 Identities=21% Similarity=0.351 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.|+.+.+.+..++....-......+.+|.||||||||+|+..+...+
T Consensus 88 ~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l 134 (637)
T TIGR00602 88 VHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKEL 134 (637)
T ss_pred CcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence 45555555555543321011233589999999999999988776543
No 203
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=89.82 E-value=0.28 Score=56.45 Aligned_cols=28 Identities=25% Similarity=0.503 Sum_probs=23.6
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+.+|-||+|+|||||+..|...+..
T Consensus 193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~ 220 (282)
T TIGR03499 193 QGGVIALVGPTGVGKTTTLAKLAARFVL 220 (282)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 3468889999999999999998877654
No 204
>PHA02624 large T antigen; Provisional
Probab=89.75 E-value=0.38 Score=60.88 Aligned_cols=25 Identities=28% Similarity=0.409 Sum_probs=22.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
....||.||||||||+.+.+|+..|
T Consensus 431 k~~il~~GPpnTGKTtf~~sLl~~L 455 (647)
T PHA02624 431 RRYWLFKGPVNSGKTTLAAALLDLC 455 (647)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHc
Confidence 4599999999999999999988866
No 205
>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=89.73 E-value=0.34 Score=52.42 Aligned_cols=28 Identities=29% Similarity=0.510 Sum_probs=23.1
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+++|-||||||||+....++.....
T Consensus 11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~ 38 (209)
T TIGR02237 11 RGTITQIYGPPGSGKTNICMILAVNAAR 38 (209)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence 3479999999999999998877766554
No 206
>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]
Probab=89.70 E-value=0.26 Score=57.86 Aligned_cols=22 Identities=50% Similarity=0.584 Sum_probs=17.5
Q ss_pred CCCceEEEEcCCCCChhhHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVA 1104 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvg 1104 (1402)
+.+...||+||||||||...-+
T Consensus 164 k~Pkg~ll~GppGtGKTlla~~ 185 (388)
T KOG0651|consen 164 KPPKGLLLYGPPGTGKTLLARA 185 (388)
T ss_pred CCCceeEEeCCCCCchhHHHHH
Confidence 3457899999999999975443
No 207
>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]
Probab=89.70 E-value=0.32 Score=54.80 Aligned_cols=29 Identities=34% Similarity=0.469 Sum_probs=25.0
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...++||.||||||||......+...+..
T Consensus 22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ 50 (260)
T COG0467 22 RGSVVLITGPPGTGKTIFALQFLYEGARE 50 (260)
T ss_pred CCcEEEEEcCCCCcHHHHHHHHHHHHHhc
Confidence 34799999999999999988888877765
No 208
>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=89.66 E-value=0.31 Score=53.15 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=22.8
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...+++|.||||+|||++...++...+
T Consensus 18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~ 44 (226)
T cd01393 18 TGRITEIFGEFGSGKTQLCLQLAVEAQ 44 (226)
T ss_pred CCcEEEEeCCCCCChhHHHHHHHHHhh
Confidence 447999999999999999888776554
No 209
>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=89.58 E-value=0.58 Score=57.26 Aligned_cols=26 Identities=23% Similarity=0.300 Sum_probs=22.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.+.++-||||+|||||+..|...+-
T Consensus 100 ~~vi~lvG~~GvGKTTtaaKLA~~l~ 125 (429)
T TIGR01425 100 QNVIMFVGLQGSGKTTTCTKLAYYYQ 125 (429)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence 57999999999999999999876553
No 210
>PRK13342 recombination factor protein RarA; Reviewed
Probab=89.52 E-value=0.29 Score=59.04 Aligned_cols=22 Identities=41% Similarity=0.640 Sum_probs=17.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+-.||.||||||||+++..+..
T Consensus 37 ~~ilL~GppGtGKTtLA~~ia~ 58 (413)
T PRK13342 37 SSMILWGPPGTGKTTLARIIAG 58 (413)
T ss_pred ceEEEECCCCCCHHHHHHHHHH
Confidence 4578899999999998777644
No 211
>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=89.49 E-value=0.61 Score=57.67 Aligned_cols=27 Identities=30% Similarity=0.374 Sum_probs=21.9
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
..++||-||||||||+....++...+.
T Consensus 263 gs~~li~G~~G~GKt~l~~~f~~~~~~ 289 (484)
T TIGR02655 263 DSIILATGATGTGKTLLVSKFLENACA 289 (484)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 479999999999999977777665543
No 212
>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=89.48 E-value=0.2 Score=62.64 Aligned_cols=23 Identities=43% Similarity=0.616 Sum_probs=18.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+.=.|+|||||||||...-++-+
T Consensus 223 prGvLlHGPPGCGKT~lA~AiAg 245 (802)
T KOG0733|consen 223 PRGVLLHGPPGCGKTSLANAIAG 245 (802)
T ss_pred CCceeeeCCCCccHHHHHHHHhh
Confidence 34579999999999997766654
No 213
>PF13173 AAA_14: AAA domain
Probab=89.45 E-value=0.34 Score=48.87 Aligned_cols=26 Identities=31% Similarity=0.615 Sum_probs=22.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.++.+|-||.|+|||+++..++..+.
T Consensus 2 ~~~~~l~G~R~vGKTtll~~~~~~~~ 27 (128)
T PF13173_consen 2 RKIIILTGPRGVGKTTLLKQLAKDLL 27 (128)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHhc
Confidence 46999999999999999888887666
No 214
>PRK05642 DNA replication initiation factor; Validated
Probab=89.40 E-value=0.35 Score=54.12 Aligned_cols=26 Identities=19% Similarity=0.305 Sum_probs=21.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+|.||+|||||+...++...+..
T Consensus 46 ~~l~l~G~~G~GKTHLl~a~~~~~~~ 71 (234)
T PRK05642 46 SLIYLWGKDGVGRSHLLQAACLRFEQ 71 (234)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHh
Confidence 46789999999999998888766553
No 215
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=89.36 E-value=0.88 Score=55.11 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.3
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+.+.++-||+|+|||||+..|...+..
T Consensus 173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~ 200 (388)
T PRK12723 173 KKRVFILVGPTGVGKTTTIAKLAAIYGI 200 (388)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence 3579999999999999999998765543
No 216
>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=89.31 E-value=0.3 Score=58.62 Aligned_cols=26 Identities=31% Similarity=0.387 Sum_probs=23.7
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
|..||-||+|+|||||+.+++..+..
T Consensus 150 GlilI~G~TGSGKTT~l~al~~~i~~ 175 (372)
T TIGR02525 150 GLGLICGETGSGKSTLAASIYQHCGE 175 (372)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHh
Confidence 79999999999999999998887765
No 217
>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=89.25 E-value=0.22 Score=56.11 Aligned_cols=25 Identities=36% Similarity=0.590 Sum_probs=21.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+..||-||+|+|||+++.+++..+
T Consensus 127 ~~~ili~G~tGSGKTT~l~all~~i 151 (270)
T PF00437_consen 127 RGNILISGPTGSGKTTLLNALLEEI 151 (270)
T ss_dssp TEEEEEEESTTSSHHHHHHHHHHHC
T ss_pred ceEEEEECCCccccchHHHHHhhhc
Confidence 4799999999999999988876643
No 218
>PRK14957 DNA polymerase III subunits gamma and tau; Provisional
Probab=89.18 E-value=0.48 Score=59.54 Aligned_cols=27 Identities=26% Similarity=0.267 Sum_probs=22.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+...|+.||||||||++...+...|+.
T Consensus 38 ~ha~Lf~Gp~GvGKTTlAr~lAk~L~c 64 (546)
T PRK14957 38 HHAYLFTGTRGVGKTTLGRLLAKCLNC 64 (546)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 346899999999999998888777764
No 219
>PRK13531 regulatory ATPase RavA; Provisional
Probab=89.17 E-value=0.32 Score=60.21 Aligned_cols=24 Identities=29% Similarity=0.462 Sum_probs=20.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+=.||.||||||||++..+|-.++
T Consensus 40 ~hVLL~GpPGTGKT~LAraLa~~~ 63 (498)
T PRK13531 40 ESVFLLGPPGIAKSLIARRLKFAF 63 (498)
T ss_pred CCEEEECCCChhHHHHHHHHHHHh
Confidence 679999999999999887766543
No 220
>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []. This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.
Probab=89.13 E-value=0.53 Score=52.82 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
+...+.|...|... ....++..|+|+||+|||++...+...
T Consensus 2 e~~~~~l~~~L~~~---~~~~~~v~I~G~~G~GKT~LA~~~~~~ 42 (287)
T PF00931_consen 2 EKEIEKLKDWLLDN---SNEVRVVAIVGMGGIGKTTLARQVARD 42 (287)
T ss_dssp HHHHHHHHHHHHTT---TTSSEEEEEEESTTSSHHHHHHHHHCH
T ss_pred HHHHHHHHHHhhCC---CCCeEEEEEEcCCcCCcceeeeecccc
Confidence 34566676666542 145689999999999999988776644
No 221
>PRK10867 signal recognition particle protein; Provisional
Probab=89.12 E-value=0.51 Score=57.83 Aligned_cols=28 Identities=25% Similarity=0.292 Sum_probs=23.9
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+.+.++-||||+|||||+..|...+...
T Consensus 100 p~vI~~vG~~GsGKTTtaakLA~~l~~~ 127 (433)
T PRK10867 100 PTVIMMVGLQGAGKTTTAGKLAKYLKKK 127 (433)
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHh
Confidence 4688999999999999999988776554
No 222
>PHA02244 ATPase-like protein
Probab=89.11 E-value=0.52 Score=56.76 Aligned_cols=22 Identities=27% Similarity=0.463 Sum_probs=18.3
Q ss_pred eEEEEcCCCCChhhHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
-.||.||||||||+.+.+|...
T Consensus 121 PVLL~GppGtGKTtLA~aLA~~ 142 (383)
T PHA02244 121 PVFLKGGAGSGKNHIAEQIAEA 142 (383)
T ss_pred CEEEECCCCCCHHHHHHHHHHH
Confidence 4688999999999988877554
No 223
>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=89.10 E-value=0.3 Score=51.50 Aligned_cols=20 Identities=35% Similarity=0.659 Sum_probs=15.4
Q ss_pred eEEEEcCCCCChhhHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLV 1106 (1402)
+.+|-||||+||||....|.
T Consensus 1 ~i~i~G~pGsGKst~a~~la 20 (183)
T TIGR01359 1 VVFVLGGPGSGKGTQCAKIV 20 (183)
T ss_pred CEEEECCCCCCHHHHHHHHH
Confidence 35889999999999555543
No 224
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=88.96 E-value=0.51 Score=50.43 Aligned_cols=29 Identities=34% Similarity=0.487 Sum_probs=24.9
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-+..-|+.||||+|||+++..+...++..
T Consensus 13 ~~~~~L~~G~~G~gkt~~a~~~~~~l~~~ 41 (188)
T TIGR00678 13 LAHAYLFAGPEGVGKELLALALAKALLCE 41 (188)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHcCC
Confidence 34679999999999999999998888764
No 225
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=88.95 E-value=0.53 Score=58.73 Aligned_cols=41 Identities=24% Similarity=0.258 Sum_probs=28.9
Q ss_pred HHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1068 LQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1068 ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+++..++... +-+.-.|+.||||||||++...+...|...
T Consensus 25 ~~~L~~~~~~~----~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~ 65 (509)
T PRK14958 25 VRALSNALDQQ----YLHHAYLFTGTRGVGKTTISRILAKCLNCE 65 (509)
T ss_pred HHHHHHHHHhC----CCCeeEEEECCCCCCHHHHHHHHHHHhcCC
Confidence 34555555432 223467999999999999988888777654
No 226
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=88.87 E-value=1.5 Score=53.79 Aligned_cols=75 Identities=21% Similarity=0.235 Sum_probs=49.9
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH-HHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI-VAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI-vgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
.++.-|.+||..++... =.+|+.|.|||||..- +.++..++... ...
T Consensus 109 ~~~~iQ~~ai~~~~~G~--------dvi~~apTGSGKTlay~lpil~~l~~~~---------~~~--------------- 156 (475)
T PRK01297 109 YCTPIQAQVLGYTLAGH--------DAIGRAQTGTGKTAAFLISIINQLLQTP---------PPK--------------- 156 (475)
T ss_pred CCCHHHHHHHHHHhCCC--------CEEEECCCCChHHHHHHHHHHHHHHhcC---------ccc---------------
Confidence 57899999999887643 2678999999999542 22233333221 000
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
.......++||.+||.+-+-++...+..
T Consensus 157 -----------------------~~~~~~~~aLil~PtreLa~Q~~~~~~~ 184 (475)
T PRK01297 157 -----------------------ERYMGEPRALIIAPTRELVVQIAKDAAA 184 (475)
T ss_pred -----------------------ccccCCceEEEEeCcHHHHHHHHHHHHH
Confidence 0001246899999999999998887764
No 227
>PRK04328 hypothetical protein; Provisional
Probab=88.86 E-value=0.92 Score=51.29 Aligned_cols=24 Identities=29% Similarity=0.426 Sum_probs=19.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
..++||-||||||||.....++..
T Consensus 23 gs~ili~G~pGsGKT~l~~~fl~~ 46 (249)
T PRK04328 23 RNVVLLSGGPGTGKSIFSQQFLWN 46 (249)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHH
Confidence 479999999999999976666544
No 228
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=88.86 E-value=0.52 Score=56.76 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=22.7
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||||||++...+...|+..
T Consensus 39 ha~lf~Gp~G~GKtt~A~~~a~~l~c~ 65 (397)
T PRK14955 39 HGYIFSGLRGVGKTTAARVFAKAVNCQ 65 (397)
T ss_pred eeEEEECCCCCCHHHHHHHHHHHhcCC
Confidence 457899999999999988887777653
No 229
>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=88.77 E-value=0.99 Score=55.31 Aligned_cols=26 Identities=31% Similarity=0.316 Sum_probs=23.1
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.+.++-||||+|||+|+..+...+.
T Consensus 99 p~vi~~vG~~GsGKTTtaakLA~~l~ 124 (428)
T TIGR00959 99 PTVILMVGLQGSGKTTTCGKLAYYLK 124 (428)
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHH
Confidence 46899999999999999999988765
No 230
>PHA02653 RNA helicase NPH-II; Provisional
Probab=88.71 E-value=1.3 Score=57.28 Aligned_cols=23 Identities=13% Similarity=0.052 Sum_probs=20.3
Q ss_pred CCeEEEEeCchHHHHHHHHHHHh
Q 000592 1169 RARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
..+|+|.+|+-+|+-++..++.+
T Consensus 222 ~~~ilvt~PrreLa~qi~~~i~~ 244 (675)
T PHA02653 222 ERPIVLSLPRVALVRLHSITLLK 244 (675)
T ss_pred CcEEEEECcHHHHHHHHHHHHHH
Confidence 46899999999999999998864
No 231
>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=88.63 E-value=0.57 Score=60.54 Aligned_cols=70 Identities=36% Similarity=0.384 Sum_probs=54.2
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARA 1143 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~ 1143 (1402)
-.-|..||......-. ...+. .||+=-+|||||+|..+|+..|+...
T Consensus 167 RyyQ~~AI~rv~Eaf~--~g~~r-aLlvMATGTGKTrTAiaii~rL~r~~------------------------------ 213 (875)
T COG4096 167 RYYQIIAIRRVIEAFS--KGQNR-ALLVMATGTGKTRTAIAIIDRLIKSG------------------------------ 213 (875)
T ss_pred hHHHHHHHHHHHHHHh--cCCce-EEEEEecCCCcceeHHHHHHHHHhcc------------------------------
Confidence 3468888876654431 22233 99999999999999999999998873
Q ss_pred HHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1144 WQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1144 W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
-.+|||.-|-.|+=||+-.....
T Consensus 214 ------------------------~~KRVLFLaDR~~Lv~QA~~af~ 236 (875)
T COG4096 214 ------------------------WVKRVLFLADRNALVDQAYGAFE 236 (875)
T ss_pred ------------------------hhheeeEEechHHHHHHHHHHHH
Confidence 15799999999999998886655
No 232
>PRK08233 hypothetical protein; Provisional
Probab=88.59 E-value=0.32 Score=50.84 Aligned_cols=24 Identities=25% Similarity=0.324 Sum_probs=19.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+..|-||||+||||+...|...+
T Consensus 4 ~iI~I~G~~GsGKtTla~~L~~~l 27 (182)
T PRK08233 4 KIITIAAVSGGGKTTLTERLTHKL 27 (182)
T ss_pred eEEEEECCCCCCHHHHHHHHHhhC
Confidence 578899999999999776666543
No 233
>CHL00195 ycf46 Ycf46; Provisional
Probab=88.57 E-value=0.32 Score=60.35 Aligned_cols=23 Identities=39% Similarity=0.411 Sum_probs=18.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.-.|+.||||||||.+.-++-..
T Consensus 260 kGILL~GPpGTGKTllAkaiA~e 282 (489)
T CHL00195 260 RGLLLVGIQGTGKSLTAKAIAND 282 (489)
T ss_pred ceEEEECCCCCcHHHHHHHHHHH
Confidence 45799999999999988776543
No 234
>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=88.50 E-value=0.41 Score=52.72 Aligned_cols=27 Identities=26% Similarity=0.421 Sum_probs=23.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+++|-||||||||+....++..+...
T Consensus 14 ~l~lI~G~~G~GKT~~~~~~~~~~~~~ 40 (242)
T cd00984 14 DLIIIAARPSMGKTAFALNIAENIAKK 40 (242)
T ss_pred eEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence 599999999999999999888776654
No 235
>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor
Probab=88.48 E-value=0.8 Score=47.66 Aligned_cols=43 Identities=21% Similarity=0.192 Sum_probs=25.2
Q ss_pred HHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1068 LQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1068 ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..||..=+...+ .+.+=+--.+||||||||.+.--|..+|...
T Consensus 38 ~~ai~~~l~~~~--p~KpLVlSfHG~tGtGKn~v~~liA~~ly~~ 80 (127)
T PF06309_consen 38 VNAIKGHLANPN--PRKPLVLSFHGWTGTGKNFVSRLIAEHLYKS 80 (127)
T ss_pred HHHHHHHHcCCC--CCCCEEEEeecCCCCcHHHHHHHHHHHHHhc
Confidence 445555454432 2222334489999999999655555555544
No 236
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=88.36 E-value=0.29 Score=56.23 Aligned_cols=21 Identities=48% Similarity=0.702 Sum_probs=17.6
Q ss_pred ceEEEEcCCCCChhhHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
.=+|..||||||||.+..++-
T Consensus 152 knVLFyGppGTGKTm~Akala 172 (368)
T COG1223 152 KNVLFYGPPGTGKTMMAKALA 172 (368)
T ss_pred ceeEEECCCCccHHHHHHHHh
Confidence 468999999999999877653
No 237
>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=88.28 E-value=0.36 Score=59.58 Aligned_cols=27 Identities=33% Similarity=0.636 Sum_probs=22.7
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
|+-|-||||||||++|..||..+-...
T Consensus 71 IvavvGPpGtGKsTLirSlVrr~tk~t 97 (1077)
T COG5192 71 IVAVVGPPGTGKSTLIRSLVRRFTKQT 97 (1077)
T ss_pred EEEeecCCCCChhHHHHHHHHHHHHhh
Confidence 455999999999999999998776654
No 238
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=88.25 E-value=0.34 Score=58.47 Aligned_cols=16 Identities=50% Similarity=0.864 Sum_probs=13.2
Q ss_pred ceEEEEcCCCCChhhH
Q 000592 1086 ELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkT 1101 (1402)
+=.+.+||||||||+.
T Consensus 49 ~SmIl~GPPG~GKTTl 64 (436)
T COG2256 49 HSMILWGPPGTGKTTL 64 (436)
T ss_pred ceeEEECCCCCCHHHH
Confidence 4567899999999983
No 239
>PRK05541 adenylylsulfate kinase; Provisional
Probab=88.22 E-value=0.53 Score=49.72 Aligned_cols=28 Identities=29% Similarity=0.329 Sum_probs=22.1
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+...+.+|.||||+|||+....|...|-
T Consensus 5 ~~~~~I~i~G~~GsGKst~a~~l~~~l~ 32 (176)
T PRK05541 5 PNGYVIWITGLAGSGKTTIAKALYERLK 32 (176)
T ss_pred CCCCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 4456899999999999988777666553
No 240
>PRK00131 aroK shikimate kinase; Reviewed
Probab=88.18 E-value=0.49 Score=48.84 Aligned_cols=22 Identities=18% Similarity=0.166 Sum_probs=17.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
...+|.||||||||++...|-.
T Consensus 5 ~~i~l~G~~GsGKstla~~La~ 26 (175)
T PRK00131 5 PNIVLIGFMGAGKSTIGRLLAK 26 (175)
T ss_pred CeEEEEcCCCCCHHHHHHHHHH
Confidence 5788999999999986555543
No 241
>PRK13766 Hef nuclease; Provisional
Probab=88.12 E-value=1.4 Score=57.17 Aligned_cols=63 Identities=24% Similarity=0.260 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHH
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAW 1144 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W 1144 (1402)
.-|.+++..++.. =+||..|.|+|||.+.+.++..++..
T Consensus 18 ~yQ~~~~~~~l~~---------n~lv~~ptG~GKT~~a~~~i~~~l~~-------------------------------- 56 (773)
T PRK13766 18 LYQQLLAATALKK---------NTLVVLPTGLGKTAIALLVIAERLHK-------------------------------- 56 (773)
T ss_pred HHHHHHHHHHhcC---------CeEEEcCCCccHHHHHHHHHHHHHHh--------------------------------
Confidence 3477777777643 36999999999998655444444321
Q ss_pred HHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHh
Q 000592 1145 QDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1145 ~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
++.++||.+|+.+-+++...++.+
T Consensus 57 -----------------------~~~~vLvl~Pt~~L~~Q~~~~~~~ 80 (773)
T PRK13766 57 -----------------------KGGKVLILAPTKPLVEQHAEFFRK 80 (773)
T ss_pred -----------------------CCCeEEEEeCcHHHHHHHHHHHHH
Confidence 246899999998888887777764
No 242
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=88.10 E-value=0.63 Score=54.42 Aligned_cols=38 Identities=32% Similarity=0.469 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.+....++..|+-.. +-.|+-||||||||..+-.+-..
T Consensus 29 ~~~~~~~~l~a~~~~-------~~vll~G~PG~gKT~la~~lA~~ 66 (329)
T COG0714 29 DEEVIELALLALLAG-------GHVLLEGPPGVGKTLLARALARA 66 (329)
T ss_pred cHHHHHHHHHHHHcC-------CCEEEECCCCccHHHHHHHHHHH
Confidence 344445554444332 57999999999999977665443
No 243
>PRK11823 DNA repair protein RadA; Provisional
Probab=88.02 E-value=0.96 Score=55.59 Aligned_cols=26 Identities=31% Similarity=0.593 Sum_probs=22.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..++||.||||+|||+....+...+.
T Consensus 80 Gs~~lI~G~pG~GKTtL~lq~a~~~a 105 (446)
T PRK11823 80 GSVVLIGGDPGIGKSTLLLQVAARLA 105 (446)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHH
Confidence 36999999999999999888877655
No 244
>PRK14952 DNA polymerase III subunits gamma and tau; Provisional
Probab=87.99 E-value=0.64 Score=58.93 Aligned_cols=27 Identities=30% Similarity=0.468 Sum_probs=23.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...|+.||||||||++...+...|+..
T Consensus 36 ha~Lf~Gp~G~GKTt~A~~lAk~l~c~ 62 (584)
T PRK14952 36 HAYLFSGPRGCGKTSSARILARSLNCA 62 (584)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHhccc
Confidence 467999999999999999988887753
No 245
>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=87.93 E-value=0.99 Score=54.32 Aligned_cols=27 Identities=30% Similarity=0.556 Sum_probs=22.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
..++||.||||+|||++...+...+..
T Consensus 82 GslvLI~G~pG~GKStLllq~a~~~a~ 108 (372)
T cd01121 82 GSVILIGGDPGIGKSTLLLQVAARLAK 108 (372)
T ss_pred CeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence 369999999999999998888766544
No 246
>PF13521 AAA_28: AAA domain; PDB: 1LW7_A.
Probab=87.74 E-value=0.29 Score=50.99 Aligned_cols=19 Identities=47% Similarity=0.712 Sum_probs=13.8
Q ss_pred EEEcCCCCChhhHHHHHHH
Q 000592 1089 LIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgLVs 1107 (1402)
.|.|+|||||||++-.|-.
T Consensus 3 ~i~G~~stGKTTL~~~L~~ 21 (163)
T PF13521_consen 3 VITGGPSTGKTTLIEALAA 21 (163)
T ss_dssp EEE--TTSHHHHHHHHHHH
T ss_pred EEECCCCCCHHHHHHHHHH
Confidence 6889999999998777654
No 247
>PRK14969 DNA polymerase III subunits gamma and tau; Provisional
Probab=87.71 E-value=0.68 Score=57.97 Aligned_cols=44 Identities=23% Similarity=0.292 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
++.-.+++..++... +-+...|+.||||||||++...+...|+.
T Consensus 21 q~~v~~~L~~~i~~~----~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c 64 (527)
T PRK14969 21 QEHVVRALTNALEQQ----RLHHAYLFTGTRGVGKTTLARILAKSLNC 64 (527)
T ss_pred cHHHHHHHHHHHHcC----CCCEEEEEECCCCCCHHHHHHHHHHHhcC
Confidence 344444555555432 22346799999999999988887777654
No 248
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=87.55 E-value=0.74 Score=56.32 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=21.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.+.+|.||+|+|||||+..|...+.
T Consensus 224 ~vi~lvGptGvGKTTtaaKLA~~~~ 248 (432)
T PRK12724 224 KVVFFVGPTGSGKTTSIAKLAAKYF 248 (432)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHH
Confidence 5788999999999999999987653
No 249
>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]
Probab=87.49 E-value=0.49 Score=56.49 Aligned_cols=27 Identities=37% Similarity=0.695 Sum_probs=18.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHhcCCCC
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLATRTSPK 1117 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~ 1117 (1402)
+-.+++||||||||+ +..++.......
T Consensus 163 pSmIlWGppG~GKTt-----lArlia~tsk~~ 189 (554)
T KOG2028|consen 163 PSMILWGPPGTGKTT-----LARLIASTSKKH 189 (554)
T ss_pred CceEEecCCCCchHH-----HHHHHHhhcCCC
Confidence 467889999999998 444555443333
No 250
>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=87.42 E-value=0.55 Score=42.94 Aligned_cols=22 Identities=27% Similarity=0.450 Sum_probs=17.4
Q ss_pred EEEEcCCCCChhhHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..|-||||+|||+....+...+
T Consensus 2 i~i~G~~gsGKst~~~~l~~~l 23 (69)
T cd02019 2 IAITGGSGSGKSTVAKKLAEQL 23 (69)
T ss_pred EEEECCCCCCHHHHHHHHHHHh
Confidence 3578999999998777766655
No 251
>PRK03918 chromosome segregation protein; Provisional
Probab=87.40 E-value=5.7 Score=52.27 Aligned_cols=27 Identities=33% Similarity=0.481 Sum_probs=23.1
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+|+++|.||.|||||+++-+|..+|..
T Consensus 23 ~g~~~i~G~nG~GKStil~ai~~~l~~ 49 (880)
T PRK03918 23 DGINLIIGQNGSGKSSILEAILVGLYW 49 (880)
T ss_pred CCcEEEEcCCCCCHHHHHHHHHHHhcC
Confidence 479999999999999988888776663
No 252
>TIGR01618 phage_P_loop phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.
Probab=87.39 E-value=0.4 Score=53.84 Aligned_cols=23 Identities=48% Similarity=0.639 Sum_probs=18.6
Q ss_pred CCCceEEEEcCCCCChhhHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgL 1105 (1402)
+.+...||-||||||||++...+
T Consensus 10 ~~~~~~liyG~~G~GKtt~a~~~ 32 (220)
T TIGR01618 10 RIPNMYLIYGKPGTGKTSTIKYL 32 (220)
T ss_pred CCCcEEEEECCCCCCHHHHHHhc
Confidence 34578999999999999966554
No 253
>PRK05480 uridine/cytidine kinase; Provisional
Probab=87.39 E-value=0.53 Score=51.13 Aligned_cols=26 Identities=31% Similarity=0.342 Sum_probs=20.8
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
...+..|.||||+||||+...|...+
T Consensus 5 ~~~iI~I~G~sGsGKTTl~~~l~~~l 30 (209)
T PRK05480 5 KPIIIGIAGGSGSGKTTVASTIYEEL 30 (209)
T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence 45689999999999998776665544
No 254
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=87.35 E-value=0.79 Score=58.22 Aligned_cols=27 Identities=26% Similarity=0.389 Sum_probs=23.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||||||++...+..+|+..
T Consensus 39 hA~Lf~GP~GvGKTTlA~~lAk~L~C~ 65 (605)
T PRK05896 39 HAYIFSGPRGIGKTSIAKIFAKAINCL 65 (605)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHhcCC
Confidence 467999999999999999888887653
No 255
>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=87.27 E-value=0.43 Score=51.01 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=19.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
|+++|-|..|+|||++|..++.
T Consensus 1 Pv~ii~GfLGsGKTTli~~ll~ 22 (178)
T PF02492_consen 1 PVIIITGFLGSGKTTLINHLLK 22 (178)
T ss_dssp -EEEEEESTTSSHHHHHHHHHH
T ss_pred CEEEEEcCCCCCHHHHHHHHHH
Confidence 5899999999999999888886
No 256
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=87.23 E-value=0.85 Score=56.76 Aligned_cols=27 Identities=30% Similarity=0.364 Sum_probs=21.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||||||++...+-.+|...
T Consensus 36 ha~Lf~Gp~G~GKTT~ArilAk~LnC~ 62 (491)
T PRK14964 36 QSILLVGASGVGKTTCARIISLCLNCS 62 (491)
T ss_pred ceEEEECCCCccHHHHHHHHHHHHcCc
Confidence 468999999999999887776666543
No 257
>PRK14960 DNA polymerase III subunits gamma and tau; Provisional
Probab=87.08 E-value=0.79 Score=58.79 Aligned_cols=40 Identities=25% Similarity=0.280 Sum_probs=28.2
Q ss_pred HHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1068 LQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1068 ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+++..++... +-....|+.||||||||++...+..++..
T Consensus 24 v~~L~~aI~~g----rl~HAyLF~GPpGvGKTTlAriLAK~LnC 63 (702)
T PRK14960 24 SRALSSALERG----RLHHAYLFTGTRGVGKTTIARILAKCLNC 63 (702)
T ss_pred HHHHHHHHHcC----CCCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 34455555432 22357899999999999998888777654
No 258
>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A.
Probab=87.07 E-value=0.55 Score=53.01 Aligned_cols=31 Identities=35% Similarity=0.564 Sum_probs=22.8
Q ss_pred HHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHH
Q 000592 1070 AISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1070 AI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
++..|+... -...+.||+|||||.||..+-.
T Consensus 24 ~l~~al~~~-------~~~~~~GpagtGKtetik~La~ 54 (231)
T PF12774_consen 24 TLTQALSLN-------LGGALSGPAGTGKTETIKDLAR 54 (231)
T ss_dssp HHHHHHCTT-------TEEEEESSTTSSHHHHHHHHHH
T ss_pred HHHHHhccC-------CCCCCcCCCCCCchhHHHHHHH
Confidence 455555432 3567899999999999988744
No 259
>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=86.99 E-value=0.48 Score=51.98 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=21.5
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
....+++|.||||||||+....++..
T Consensus 17 ~~g~i~~i~G~~GsGKT~l~~~l~~~ 42 (235)
T cd01123 17 ETGSITEIFGEFGSGKTQLCHQLAVT 42 (235)
T ss_pred CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence 34579999999999999988777654
No 260
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=86.92 E-value=0.39 Score=57.29 Aligned_cols=20 Identities=50% Similarity=0.624 Sum_probs=15.6
Q ss_pred CceEEEEcCCCCChhhHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVA 1104 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvg 1104 (1402)
+.=+|..||||||||-...+
T Consensus 185 PKGVLLYGPPGTGKTLLAkA 204 (406)
T COG1222 185 PKGVLLYGPPGTGKTLLAKA 204 (406)
T ss_pred CCceEeeCCCCCcHHHHHHH
Confidence 34579999999999975444
No 261
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=86.86 E-value=0.56 Score=57.26 Aligned_cols=26 Identities=27% Similarity=0.492 Sum_probs=22.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.++.++-||+|+|||||+..|...+.
T Consensus 221 ~~~i~~vGptGvGKTTt~~kLA~~~~ 246 (424)
T PRK05703 221 GGVVALVGPTGVGKTTTLAKLAARYA 246 (424)
T ss_pred CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence 35888889999999999999887765
No 262
>PRK13851 type IV secretion system protein VirB11; Provisional
Probab=86.83 E-value=0.78 Score=54.67 Aligned_cols=38 Identities=26% Similarity=0.295 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
+....+.+..|+.. .+-.||-||+|+||||++.+|+..
T Consensus 148 ~~~~~~~l~~~v~~-------~~nilI~G~tGSGKTTll~aLl~~ 185 (344)
T PRK13851 148 NGDLEAFLHACVVG-------RLTMLLCGPTGSGKTTMSKTLISA 185 (344)
T ss_pred cHHHHHHHHHHHHc-------CCeEEEECCCCccHHHHHHHHHcc
Confidence 34444445554432 368999999999999998776653
No 263
>PRK09694 helicase Cas3; Provisional
Probab=86.83 E-value=1.8 Score=57.39 Aligned_cols=67 Identities=19% Similarity=0.326 Sum_probs=46.5
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIA 1141 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~a 1141 (1402)
..|.-|..+... . ..+++.+|..|.|+|||-..+.....++...
T Consensus 286 ~p~p~Q~~~~~~--~------~~pgl~ileApTGsGKTEAAL~~A~~l~~~~---------------------------- 329 (878)
T PRK09694 286 QPRQLQTLVDAL--P------LQPGLTIIEAPTGSGKTEAALAYAWRLIDQG---------------------------- 329 (878)
T ss_pred CChHHHHHHHhh--c------cCCCeEEEEeCCCCCHHHHHHHHHHHHHHhC----------------------------
Confidence 456777765322 1 1358999999999999997655544433321
Q ss_pred HHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1142 RAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1142 r~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
...+|.++.|+-+.+|++..|+.
T Consensus 330 --------------------------~~~gi~~aLPT~Atan~m~~Rl~ 352 (878)
T PRK09694 330 --------------------------LADSIIFALPTQATANAMLSRLE 352 (878)
T ss_pred --------------------------CCCeEEEECcHHHHHHHHHHHHH
Confidence 13588888888888888888876
No 264
>PRK14949 DNA polymerase III subunits gamma and tau; Provisional
Probab=86.80 E-value=0.75 Score=60.56 Aligned_cols=28 Identities=25% Similarity=0.279 Sum_probs=23.2
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
....|+.||||||||+++..+...|...
T Consensus 38 ~HAyLFtGPpGtGKTTLARiLAk~Lnce 65 (944)
T PRK14949 38 HHAYLFTGTRGVGKTSLARLFAKGLNCE 65 (944)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHhccCc
Confidence 3567999999999999998888777653
No 265
>PRK13909 putative recombination protein RecB; Provisional
Probab=86.61 E-value=1 Score=59.85 Aligned_cols=49 Identities=24% Similarity=0.336 Sum_probs=39.6
Q ss_pred EEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhccccccccccccccCC
Q 000592 1090 IQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVR 1169 (1402)
Q Consensus 1090 IQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k 1169 (1402)
+.-+-|||||.|++...-.||... ...
T Consensus 3 ~~AsAGsGKT~~L~~~yl~ll~~~-----------------------------------------------------~~~ 29 (910)
T PRK13909 3 LKASAGSGKTFALSVRFLALLFKG-----------------------------------------------------ANP 29 (910)
T ss_pred eecCCCCchhHHHHHHHHHHHhcC-----------------------------------------------------CCc
Confidence 456789999999998877776642 013
Q ss_pred CeEEEEeCchHHHHHHHHHHHh
Q 000592 1170 ARVLICAQSNAAVDELVSRISK 1191 (1402)
Q Consensus 1170 ~RILVCAPSNAAVDEIV~RLl~ 1191 (1402)
..||+.+-||+|..|+-.|+.+
T Consensus 30 ~~IlavTFT~kAa~Emk~Ri~~ 51 (910)
T PRK13909 30 SEILALTFTKKAANEMKERIID 51 (910)
T ss_pred ceEEEEeehHHHHHHHHHHHHH
Confidence 5999999999999999999983
No 266
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=86.56 E-value=0.88 Score=58.30 Aligned_cols=41 Identities=24% Similarity=0.306 Sum_probs=29.5
Q ss_pred HHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1068 LQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1068 ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+.+..++... +-....|+.||||||||++...+...|+..
T Consensus 25 v~~L~~al~~g----RLpHA~LFtGP~GvGKTTLAriLAkaLnC~ 65 (700)
T PRK12323 25 VRALTHALEQQ----RLHHAYLFTGTRGVGKTTLSRILAKSLNCT 65 (700)
T ss_pred HHHHHHHHHhC----CCceEEEEECCCCCCHHHHHHHHHHHhcCC
Confidence 33455555432 233577999999999999999988888753
No 267
>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=86.55 E-value=1.2 Score=55.19 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=20.4
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
...++||.||||||||+....++..
T Consensus 20 ~g~~~Li~G~pGsGKT~la~qfl~~ 44 (484)
T TIGR02655 20 IGRSTLVSGTSGTGKTLFSIQFLYN 44 (484)
T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence 3479999999999999977776543
No 268
>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP.; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.
Probab=86.51 E-value=0.65 Score=49.58 Aligned_cols=25 Identities=32% Similarity=0.607 Sum_probs=21.0
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
....+|.||.|+|||+++..++..+
T Consensus 20 ~~~~~l~G~rg~GKTsLl~~~~~~~ 44 (234)
T PF01637_consen 20 SQHILLYGPRGSGKTSLLKEFINEL 44 (234)
T ss_dssp SSEEEEEESTTSSHHHHHHHHHHHC
T ss_pred CcEEEEEcCCcCCHHHHHHHHHHHh
Confidence 3689999999999999877776654
No 269
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=86.47 E-value=0.99 Score=55.33 Aligned_cols=26 Identities=27% Similarity=0.331 Sum_probs=22.5
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-.+|.||||||||+...++...+...
T Consensus 132 ~l~lyG~~G~GKTHLl~ai~~~l~~~ 157 (440)
T PRK14088 132 PLFIYGGVGLGKTHLLQSIGNYVVQN 157 (440)
T ss_pred eEEEEcCCCCcHHHHHHHHHHHHHHh
Confidence 38999999999999999888877664
No 270
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=86.42 E-value=1.4 Score=54.72 Aligned_cols=25 Identities=32% Similarity=0.424 Sum_probs=20.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..++||-||||||||.....++...
T Consensus 273 g~~~li~G~~G~GKT~l~~~~~~~~ 297 (509)
T PRK09302 273 GSIILVSGATGTGKTLLASKFAEAA 297 (509)
T ss_pred CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence 4699999999999999877776543
No 271
>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.
Probab=86.42 E-value=1.9 Score=48.27 Aligned_cols=46 Identities=26% Similarity=0.268 Sum_probs=27.4
Q ss_pred HHHHHHHHHccC-----CCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1067 QLQAISVAIGLS-----SSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1067 Q~qAI~sAL~~~-----~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
|++||...+... .......+=.||-=.+|+|||-+.++++..+...
T Consensus 2 Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~~l~~~ 52 (299)
T PF00176_consen 2 QLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALISYLKNE 52 (299)
T ss_dssp HHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhhhhhhc
Confidence 777777665542 0011233455666679999999999988866654
No 272
>PRK13900 type IV secretion system ATPase VirB11; Provisional
Probab=86.41 E-value=0.78 Score=54.34 Aligned_cols=23 Identities=30% Similarity=0.316 Sum_probs=19.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
+-.||-||+|+||||++-+|+..
T Consensus 161 ~nili~G~tgSGKTTll~aL~~~ 183 (332)
T PRK13900 161 KNIIISGGTSTGKTTFTNAALRE 183 (332)
T ss_pred CcEEEECCCCCCHHHHHHHHHhh
Confidence 57999999999999998777654
No 273
>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family. This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.
Probab=86.40 E-value=0.49 Score=49.20 Aligned_cols=18 Identities=28% Similarity=0.571 Sum_probs=13.4
Q ss_pred EEEcCCCCChhhHHHHHH
Q 000592 1089 LIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgLV 1106 (1402)
+|.||||+|||++...|.
T Consensus 2 ~l~G~~GsGKSTla~~l~ 19 (163)
T TIGR01313 2 VLMGVAGSGKSTIASALA 19 (163)
T ss_pred EEECCCCCCHHHHHHHHH
Confidence 477999999997544443
No 274
>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN. Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.
Probab=86.32 E-value=0.58 Score=49.38 Aligned_cols=23 Identities=26% Similarity=0.432 Sum_probs=18.7
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.+.+|-||||+|||+++-.|...
T Consensus 2 ~~~~i~G~sGsGKttl~~~l~~~ 24 (179)
T TIGR02322 2 RLIYVVGPSGAGKDTLLDYARAR 24 (179)
T ss_pred cEEEEECCCCCCHHHHHHHHHHH
Confidence 37889999999999988766444
No 275
>CHL00176 ftsH cell division protein; Validated
Probab=86.30 E-value=0.51 Score=60.38 Aligned_cols=22 Identities=50% Similarity=0.685 Sum_probs=18.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.-.|+.||||||||++..++..
T Consensus 217 ~gVLL~GPpGTGKT~LAralA~ 238 (638)
T CHL00176 217 KGVLLVGPPGTGKTLLAKAIAG 238 (638)
T ss_pred ceEEEECCCCCCHHHHHHHHHH
Confidence 3489999999999998888754
No 276
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=86.29 E-value=0.57 Score=60.74 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=18.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+-.||.||||||||+++..+-.
T Consensus 53 ~slLL~GPpGtGKTTLA~aIA~ 74 (725)
T PRK13341 53 GSLILYGPPGVGKTTLARIIAN 74 (725)
T ss_pred ceEEEECCCCCCHHHHHHHHHH
Confidence 3569999999999998777654
No 277
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=86.12 E-value=0.9 Score=57.79 Aligned_cols=45 Identities=22% Similarity=0.299 Sum_probs=32.7
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
++...+.+..++... +-..-.|++||||||||++...+...|+..
T Consensus 29 q~~~v~~L~~~~~~g----ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~ 73 (598)
T PRK09111 29 QEAMVRTLTNAFETG----RIAQAFMLTGVRGVGKTTTARILARALNYE 73 (598)
T ss_pred cHHHHHHHHHHHHcC----CCCceEEEECCCCCCHHHHHHHHHHhhCcC
Confidence 455555666666542 223467999999999999999988887754
No 278
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=86.12 E-value=0.54 Score=57.88 Aligned_cols=23 Identities=43% Similarity=0.579 Sum_probs=18.8
Q ss_pred CCceEEEEcCCCCChhhHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
.....|+.||||||||.+..++-
T Consensus 275 ~~~giLl~GpPGtGKT~lAkava 297 (494)
T COG0464 275 PPKGVLLYGPPGTGKTLLAKAVA 297 (494)
T ss_pred CCCeeEEECCCCCCHHHHHHHHH
Confidence 44589999999999999766653
No 279
>PRK14527 adenylate kinase; Provisional
Probab=86.06 E-value=0.74 Score=49.48 Aligned_cols=23 Identities=26% Similarity=0.580 Sum_probs=18.4
Q ss_pred CCceEEEEcCCCCChhhHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
...+.+|-||||+|||+....|.
T Consensus 5 ~~~~i~i~G~pGsGKsT~a~~La 27 (191)
T PRK14527 5 KNKVVIFLGPPGAGKGTQAERLA 27 (191)
T ss_pred CCcEEEEECCCCCCHHHHHHHHH
Confidence 34799999999999998655553
No 280
>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=86.06 E-value=0.73 Score=53.47 Aligned_cols=30 Identities=27% Similarity=0.358 Sum_probs=24.9
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
....+..|-||||+|||+++..+...+...
T Consensus 32 ~~~~~i~i~G~~G~GKttl~~~l~~~~~~~ 61 (300)
T TIGR00750 32 GNAHRVGITGTPGAGKSTLLEALGMELRRR 61 (300)
T ss_pred CCceEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence 345788888999999999999998876554
No 281
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=86.05 E-value=2.4 Score=52.26 Aligned_cols=27 Identities=26% Similarity=0.325 Sum_probs=22.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...+|.||||||||+++.++...+...
T Consensus 142 npl~i~G~~G~GKTHLl~Ai~~~l~~~ 168 (450)
T PRK14087 142 NPLFIYGESGMGKTHLLKAAKNYIESN 168 (450)
T ss_pred CceEEECCCCCcHHHHHHHHHHHHHHh
Confidence 346899999999999998887766554
No 282
>PRK07133 DNA polymerase III subunits gamma and tau; Validated
Probab=85.95 E-value=0.99 Score=58.46 Aligned_cols=44 Identities=30% Similarity=0.364 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+...+.+..++... +-....|+.||||||||+++..+..+|+..
T Consensus 24 e~~v~~L~~aI~~~----rl~HAYLF~GP~GtGKTt~AriLAk~LnC~ 67 (725)
T PRK07133 24 DHIVQTLKNIIKSN----KISHAYLFSGPRGTGKTSVAKIFANALNCS 67 (725)
T ss_pred HHHHHHHHHHHHcC----CCCeEEEEECCCCCcHHHHHHHHHHHhccc
Confidence 33344555555432 223567999999999999999988887764
No 283
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=85.88 E-value=1.7 Score=52.89 Aligned_cols=28 Identities=32% Similarity=0.456 Sum_probs=23.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+.+|-||.|+|||+|+..|-..+..
T Consensus 205 ~~~ii~lvGptGvGKTTt~akLA~~l~~ 232 (407)
T PRK12726 205 NHRIISLIGQTGVGKTTTLVKLGWQLLK 232 (407)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 4579999999999999999998765533
No 284
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=85.85 E-value=1.3 Score=60.41 Aligned_cols=31 Identities=32% Similarity=0.512 Sum_probs=22.8
Q ss_pred HHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHH
Q 000592 1068 LQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1068 ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgL 1105 (1402)
.+.|..++... .+++|+||||+||||-|--+
T Consensus 72 ~~~Il~~l~~~-------~vvii~g~TGSGKTTqlPq~ 102 (1283)
T TIGR01967 72 REDIAEAIAEN-------QVVIIAGETGSGKTTQLPKI 102 (1283)
T ss_pred HHHHHHHHHhC-------ceEEEeCCCCCCcHHHHHHH
Confidence 35566666442 59999999999999965433
No 285
>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=85.69 E-value=0.6 Score=53.77 Aligned_cols=22 Identities=45% Similarity=0.668 Sum_probs=18.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.=.|+-||||||||.+|...+.
T Consensus 34 ~pvLl~G~~GtGKT~li~~~l~ 55 (272)
T PF12775_consen 34 RPVLLVGPSGTGKTSLIQNFLS 55 (272)
T ss_dssp EEEEEESSTTSSHHHHHHHHHH
T ss_pred CcEEEECCCCCchhHHHHhhhc
Confidence 3569999999999998777654
No 286
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=85.67 E-value=0.53 Score=55.88 Aligned_cols=23 Identities=35% Similarity=0.511 Sum_probs=18.7
Q ss_pred eEEEEcCCCCChhhHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
=.||.||||||||++..++-..|
T Consensus 31 ~vLl~G~pG~gKT~lar~la~ll 53 (334)
T PRK13407 31 GVLVFGDRGTGKSTAVRALAALL 53 (334)
T ss_pred cEEEEcCCCCCHHHHHHHHHHHC
Confidence 48999999999999877765543
No 287
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=85.64 E-value=1 Score=56.86 Aligned_cols=43 Identities=23% Similarity=0.323 Sum_probs=30.2
Q ss_pred HHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1066 SQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1066 SQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.+.+..++... +-....|+.||||||||+++..+..+|+..
T Consensus 23 ~iv~~L~~~i~~~----~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~ 65 (563)
T PRK06647 23 FVVETLKHSIESN----KIANAYIFSGPRGVGKTSSARAFARCLNCV 65 (563)
T ss_pred HHHHHHHHHHHcC----CCCeEEEEECCCCCCHHHHHHHHHHhhccc
Confidence 3333455544432 233578999999999999999998888754
No 288
>PRK14950 DNA polymerase III subunits gamma and tau; Provisional
Probab=85.49 E-value=1.1 Score=56.84 Aligned_cols=26 Identities=35% Similarity=0.487 Sum_probs=22.4
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...|+.||||||||+++..+...|+.
T Consensus 39 ~a~Lf~Gp~G~GKTtlA~~lA~~l~c 64 (585)
T PRK14950 39 HAYLFTGPRGVGKTSTARILAKAVNC 64 (585)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHhcC
Confidence 35699999999999999998887764
No 289
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=85.49 E-value=1.1 Score=53.36 Aligned_cols=44 Identities=23% Similarity=0.292 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+.-.+.+..++... +-+..-||.||+|+|||+++..+...|+..
T Consensus 29 ~~a~~~L~~a~~~g----rl~ha~L~~G~~G~GKttlA~~lA~~Llc~ 72 (351)
T PRK09112 29 EEAEAFLAQAYREG----KLHHALLFEGPEGIGKATLAFHLANHILSH 72 (351)
T ss_pred HHHHHHHHHHHHcC----CCCeeEeeECCCCCCHHHHHHHHHHHHcCC
Confidence 33444555655432 234589999999999999999999988874
No 290
>PRK06762 hypothetical protein; Provisional
Probab=85.47 E-value=0.75 Score=47.96 Aligned_cols=22 Identities=32% Similarity=0.530 Sum_probs=17.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+.+|-||||+||||....|..
T Consensus 3 ~li~i~G~~GsGKST~A~~L~~ 24 (166)
T PRK06762 3 TLIIIRGNSGSGKTTIAKQLQE 24 (166)
T ss_pred eEEEEECCCCCCHHHHHHHHHH
Confidence 4789999999999986554433
No 291
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=85.21 E-value=1.1 Score=57.72 Aligned_cols=44 Identities=23% Similarity=0.294 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+.-.+.+..++... +-..-.|+.||||||||+++..+...|+..
T Consensus 22 e~vv~~L~~ai~~~----rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~ 65 (709)
T PRK08691 22 EHVVKALQNALDEG----RLHHAYLLTGTRGVGKTTIARILAKSLNCE 65 (709)
T ss_pred HHHHHHHHHHHHcC----CCCeEEEEECCCCCcHHHHHHHHHHHhccc
Confidence 33344455555432 223467999999999999999888877654
No 292
>TIGR00763 lon ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
Probab=85.20 E-value=0.67 Score=60.48 Aligned_cols=24 Identities=42% Similarity=0.621 Sum_probs=20.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
++.|+.||||||||+++.+|...+
T Consensus 348 ~~lll~GppG~GKT~lAk~iA~~l 371 (775)
T TIGR00763 348 PILCLVGPPGVGKTSLGKSIAKAL 371 (775)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHh
Confidence 578999999999999888876665
No 293
>PRK04040 adenylate kinase; Provisional
Probab=85.18 E-value=0.74 Score=50.15 Aligned_cols=24 Identities=29% Similarity=0.598 Sum_probs=18.9
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+.+|.|+||+|||+..-.+...+
T Consensus 3 ~~i~v~G~pG~GKtt~~~~l~~~l 26 (188)
T PRK04040 3 KVVVVTGVPGVGKTTVLNKALEKL 26 (188)
T ss_pred eEEEEEeCCCCCHHHHHHHHHHHh
Confidence 478999999999999766655543
No 294
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=85.17 E-value=0.78 Score=59.35 Aligned_cols=43 Identities=40% Similarity=0.438 Sum_probs=29.1
Q ss_pred HHHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHH
Q 000592 1055 LQQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1055 L~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
++++.+.==|..|-+..=+ +-+.=.|+.||||||||-...++-
T Consensus 323 l~E~V~fLKNP~~Y~~lGA---------KiPkGvLL~GPPGTGKTLLAKAiA 365 (774)
T KOG0731|consen 323 LMEFVKFLKNPEQYQELGA---------KIPKGVLLVGPPGTGKTLLAKAIA 365 (774)
T ss_pred HHHHHHHhcCHHHHHHcCC---------cCcCceEEECCCCCcHHHHHHHHh
Confidence 4444433348888887532 234558999999999998766653
No 295
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=85.13 E-value=1.2 Score=53.03 Aligned_cols=29 Identities=31% Similarity=0.327 Sum_probs=24.1
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+-+.|+-|..||||||||.-|-..+...
T Consensus 138 ~p~Vil~vGVNG~GKTTTIaKLA~~l~~~ 166 (340)
T COG0552 138 KPFVILFVGVNGVGKTTTIAKLAKYLKQQ 166 (340)
T ss_pred CcEEEEEEecCCCchHhHHHHHHHHHHHC
Confidence 35688999999999999999987766543
No 296
>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
Probab=85.11 E-value=0.71 Score=49.67 Aligned_cols=23 Identities=35% Similarity=0.499 Sum_probs=18.6
Q ss_pred eEEEEcCCCCChhhHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+..|-||+|+||||++-.|...+
T Consensus 1 iigi~G~~GsGKSTl~~~l~~~l 23 (198)
T cd02023 1 IIGIAGGSGSGKTTVAEEIIEQL 23 (198)
T ss_pred CEEEECCCCCCHHHHHHHHHHHh
Confidence 35688999999999887776654
No 297
>PRK14951 DNA polymerase III subunits gamma and tau; Provisional
Probab=85.11 E-value=1.1 Score=57.07 Aligned_cols=40 Identities=25% Similarity=0.294 Sum_probs=28.8
Q ss_pred HHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1069 QAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1069 qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+++..++... +-+...|+.||||||||++...+...|+..
T Consensus 26 ~~L~~~l~~~----rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~ 65 (618)
T PRK14951 26 QALTNALTQQ----RLHHAYLFTGTRGVGKTTVSRILAKSLNCQ 65 (618)
T ss_pred HHHHHHHHcC----CCCeEEEEECCCCCCHHHHHHHHHHHhcCC
Confidence 3455555432 233567999999999999999988877753
No 298
>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
Probab=85.09 E-value=0.66 Score=47.49 Aligned_cols=19 Identities=26% Similarity=0.497 Sum_probs=14.6
Q ss_pred eEEEEcCCCCChhhHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgL 1105 (1402)
+.+|-||||+||||+...|
T Consensus 1 li~l~G~~GsGKST~a~~l 19 (150)
T cd02021 1 IIVVMGVSGSGKSTVGKAL 19 (150)
T ss_pred CEEEEcCCCCCHHHHHHHH
Confidence 3578899999999854444
No 299
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=85.05 E-value=0.69 Score=56.84 Aligned_cols=26 Identities=38% Similarity=0.526 Sum_probs=22.2
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-.+|.||||||||++..++...+...
T Consensus 143 pl~L~G~~G~GKTHLl~Ai~~~l~~~ 168 (445)
T PRK12422 143 PIYLFGPEGSGKTHLMQAAVHALRES 168 (445)
T ss_pred eEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence 46899999999999999988887653
No 300
>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=85.00 E-value=1.2 Score=52.64 Aligned_cols=28 Identities=21% Similarity=0.304 Sum_probs=23.3
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+++|-||||||||++.+.++.....
T Consensus 54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~ 81 (321)
T TIGR02012 54 RGRIIEIYGPESSGKTTLALHAIAEAQK 81 (321)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 3469999999999999998887776654
No 301
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=84.98 E-value=0.69 Score=55.25 Aligned_cols=25 Identities=48% Similarity=0.656 Sum_probs=20.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..-.||-||||||||-..+||---|
T Consensus 65 GrgiLi~GppgTGKTAlA~gIa~eL 89 (450)
T COG1224 65 GRGILIVGPPGTGKTALAMGIAREL 89 (450)
T ss_pred ccEEEEECCCCCcHHHHHHHHHHHh
Confidence 3578999999999999888875543
No 302
>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=84.97 E-value=1 Score=51.41 Aligned_cols=24 Identities=33% Similarity=0.548 Sum_probs=19.2
Q ss_pred ceEE-EEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSL-IQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsL-IQGPPGTGKTkTIvgLVsaL 1109 (1402)
+|.+ |-||+|||||++|..|+..+
T Consensus 13 ~fr~viIG~sGSGKT~li~~lL~~~ 37 (241)
T PF04665_consen 13 PFRMVIIGKSGSGKTTLIKSLLYYL 37 (241)
T ss_pred CceEEEECCCCCCHHHHHHHHHHhh
Confidence 4444 78999999999999987543
No 303
>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=84.97 E-value=1.7 Score=53.72 Aligned_cols=27 Identities=33% Similarity=0.576 Sum_probs=22.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
..++||-|+||+|||++...+...+..
T Consensus 94 GsvilI~G~pGsGKTTL~lq~a~~~a~ 120 (454)
T TIGR00416 94 GSLILIGGDPGIGKSTLLLQVACQLAK 120 (454)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence 469999999999999998887766544
No 304
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=84.94 E-value=0.73 Score=59.68 Aligned_cols=22 Identities=45% Similarity=0.676 Sum_probs=17.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.-.||.||||||||+++.+|..
T Consensus 213 ~giLL~GppGtGKT~laraia~ 234 (733)
T TIGR01243 213 KGVLLYGPPGTGKTLLAKAVAN 234 (733)
T ss_pred ceEEEECCCCCChHHHHHHHHH
Confidence 4689999999999987666544
No 305
>PRK10865 protein disaggregation chaperone; Provisional
Probab=84.85 E-value=1.2 Score=59.07 Aligned_cols=26 Identities=31% Similarity=0.457 Sum_probs=21.9
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+..|+.||||||||++...|...++.
T Consensus 599 ~~~Lf~Gp~G~GKT~lA~aLa~~l~~ 624 (857)
T PRK10865 599 GSFLFLGPTGVGKTELCKALANFMFD 624 (857)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHhhc
Confidence 57899999999999998887766653
No 306
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=84.79 E-value=1.2 Score=53.11 Aligned_cols=24 Identities=29% Similarity=0.484 Sum_probs=19.7
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+=.||.||||||||+++.++-+.+
T Consensus 26 g~vli~G~~G~gKttl~r~~~~~~ 49 (337)
T TIGR02030 26 GGVMVMGDRGTGKSTAVRALAALL 49 (337)
T ss_pred CeEEEEcCCCCCHHHHHHHHHHhh
Confidence 568899999999999888775544
No 307
>PRK14965 DNA polymerase III subunits gamma and tau; Provisional
Probab=84.78 E-value=1.2 Score=56.51 Aligned_cols=44 Identities=27% Similarity=0.308 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1065 ESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1065 eSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+...+.+..++... +-+...|+.||||||||+++..+..++...
T Consensus 22 ~~v~~~L~~~i~~~----~~~hayLf~Gp~G~GKtt~A~~lak~l~c~ 65 (576)
T PRK14965 22 EHVSRTLQNAIDTG----RVAHAFLFTGARGVGKTSTARILAKALNCE 65 (576)
T ss_pred HHHHHHHHHHHHcC----CCCeEEEEECCCCCCHHHHHHHHHHhhcCC
Confidence 33344455554432 223567999999999999999988887654
No 308
>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=84.76 E-value=0.71 Score=57.33 Aligned_cols=31 Identities=42% Similarity=0.655 Sum_probs=23.0
Q ss_pred CcCCCceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1081 WKKDCELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1081 ~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
+.|-.|+ |+-||||||||- |..=|+-+|..+
T Consensus 253 i~HVKGi-LLyGPPGTGKTL-iARqIGkMLNAr 283 (744)
T KOG0741|consen 253 IKHVKGI-LLYGPPGTGKTL-IARQIGKMLNAR 283 (744)
T ss_pred ccceeeE-EEECCCCCChhH-HHHHHHHHhcCC
Confidence 4555555 678999999994 555678888875
No 309
>PRK13764 ATPase; Provisional
Probab=84.73 E-value=0.75 Score=58.47 Aligned_cols=26 Identities=35% Similarity=0.452 Sum_probs=22.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+-.||-||||+||||++.+|+..+..
T Consensus 258 ~~ILIsG~TGSGKTTll~AL~~~i~~ 283 (602)
T PRK13764 258 EGILIAGAPGAGKSTFAQALAEFYAD 283 (602)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHhh
Confidence 45799999999999999998877753
No 310
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=84.56 E-value=0.83 Score=52.90 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=20.9
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
...+++|-||||||||+....+...
T Consensus 94 ~g~i~ei~G~~g~GKT~l~~~~~~~ 118 (310)
T TIGR02236 94 TQAITEVFGEFGSGKTQICHQLAVN 118 (310)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHH
Confidence 4579999999999999988877543
No 311
>PHA02774 E1; Provisional
Probab=84.56 E-value=0.7 Score=58.33 Aligned_cols=24 Identities=33% Similarity=0.591 Sum_probs=21.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.-.+|.||||||||+...+|+..|
T Consensus 435 nciv~~GPP~TGKS~fa~sL~~~L 458 (613)
T PHA02774 435 NCLVIYGPPDTGKSMFCMSLIKFL 458 (613)
T ss_pred cEEEEECCCCCCHHHHHHHHHHHh
Confidence 478999999999999999988875
No 312
>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.
Probab=84.54 E-value=0.76 Score=49.87 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=20.4
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..+-+.+|-||||+|||+++..++..+
T Consensus 13 ~~P~~~i~aG~~GsGKSt~~~~~~~~~ 39 (199)
T PF06414_consen 13 EKPTLIIIAGQPGSGKSTLARQLLEEF 39 (199)
T ss_dssp SS-EEEEEES-TTSTTHHHHHHHHHHT
T ss_pred cCCEEEEEeCCCCCCHHHHHHHhhhhc
Confidence 345788999999999999888776655
No 313
>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=84.51 E-value=0.59 Score=56.29 Aligned_cols=19 Identities=53% Similarity=0.742 Sum_probs=15.5
Q ss_pred eEEEEcCCCCChhhHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgL 1105 (1402)
=.|..||||||||-+..++
T Consensus 247 gvLm~GPPGTGKTlLAKAv 265 (491)
T KOG0738|consen 247 GVLMVGPPGTGKTLLAKAV 265 (491)
T ss_pred eeeeeCCCCCcHHHHHHHH
Confidence 4788999999999766555
No 314
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=84.45 E-value=0.83 Score=53.32 Aligned_cols=26 Identities=19% Similarity=0.288 Sum_probs=21.8
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
...+++|.||||||||++...+....
T Consensus 101 ~g~vtei~G~~GsGKT~l~~~~~~~~ 126 (317)
T PRK04301 101 TQSITEFYGEFGSGKTQICHQLAVNV 126 (317)
T ss_pred CCcEEEEECCCCCCHhHHHHHHHHHh
Confidence 35799999999999999988876543
No 315
>PRK00889 adenylylsulfate kinase; Provisional
Probab=84.43 E-value=1 Score=47.61 Aligned_cols=25 Identities=28% Similarity=0.319 Sum_probs=20.2
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..+..|-|+||+|||++...|...+
T Consensus 4 g~~i~~~G~~GsGKST~a~~la~~l 28 (175)
T PRK00889 4 GVTVWFTGLSGAGKTTIARALAEKL 28 (175)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHH
Confidence 4588889999999998777766655
No 316
>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
Probab=84.38 E-value=2.8 Score=53.83 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=19.1
Q ss_pred CCeEEEEeCchHHHHHHHHHHH
Q 000592 1169 RARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1169 k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
++||||.+||.+=.++++..+.
T Consensus 46 ~~rvlIstpT~~Lq~Ql~~~l~ 67 (636)
T TIGR03117 46 DQKIAIAVPTLALMGQLWSELE 67 (636)
T ss_pred CceEEEECCcHHHHHHHHHHHH
Confidence 5799999999999999987554
No 317
>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies.The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.
Probab=84.38 E-value=0.82 Score=49.45 Aligned_cols=27 Identities=30% Similarity=0.445 Sum_probs=21.8
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
=.||.|+||+|||.++..++..++...
T Consensus 40 h~li~G~tgsGKS~~l~~ll~~l~~~~ 66 (205)
T PF01580_consen 40 HLLIAGATGSGKSTLLRTLLLSLALTY 66 (205)
T ss_dssp SEEEE--TTSSHHHHHHHHHHHHHTT-
T ss_pred eEEEEcCCCCCccHHHHHHHHHHHHHh
Confidence 579999999999999999999888753
No 318
>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.
Probab=84.37 E-value=0.86 Score=47.55 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=19.0
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.+|.|+||+|||+.+..|...+.
T Consensus 1 ~i~i~G~~GsGKSTla~~L~~~l~ 24 (149)
T cd02027 1 VIWLTGLSGSGKSTIARALEEKLF 24 (149)
T ss_pred CEEEEcCCCCCHHHHHHHHHHHHH
Confidence 468899999999987777766553
No 319
>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
Probab=84.30 E-value=0.74 Score=48.77 Aligned_cols=18 Identities=39% Similarity=0.765 Sum_probs=13.9
Q ss_pred EEEEcCCCCChhhHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgL 1105 (1402)
.+|-||||+|||+....|
T Consensus 2 I~i~G~pGsGKst~a~~L 19 (194)
T cd01428 2 ILLLGPPGSGKGTQAERL 19 (194)
T ss_pred EEEECCCCCCHHHHHHHH
Confidence 478899999999854443
No 320
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=84.25 E-value=1.3 Score=57.54 Aligned_cols=28 Identities=29% Similarity=0.294 Sum_probs=23.2
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
....|+.||||||||+++..+...|+..
T Consensus 38 ~HAyLFtGPpGvGKTTlAriLAKaLnCe 65 (830)
T PRK07003 38 HHAYLFTGTRGVGKTTLSRIFAKALNCE 65 (830)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHhcCc
Confidence 3467999999999999988888777643
No 321
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=84.23 E-value=0.81 Score=52.37 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=22.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.=+|++|+.|||||.+|.+++..+...
T Consensus 53 nnvLL~G~rGtGKSSlVkall~~y~~~ 79 (249)
T PF05673_consen 53 NNVLLWGARGTGKSSLVKALLNEYADQ 79 (249)
T ss_pred cceEEecCCCCCHHHHHHHHHHHHhhc
Confidence 358999999999999999988766554
No 322
>PLN02200 adenylate kinase family protein
Probab=83.96 E-value=0.96 Score=50.94 Aligned_cols=22 Identities=32% Similarity=0.516 Sum_probs=17.2
Q ss_pred CceEEEEcCCCCChhhHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
+.+.+|-||||+|||+....|.
T Consensus 43 ~~ii~I~G~PGSGKsT~a~~La 64 (234)
T PLN02200 43 PFITFVLGGPGSGKGTQCEKIV 64 (234)
T ss_pred CEEEEEECCCCCCHHHHHHHHH
Confidence 4578999999999998555443
No 323
>PRK13768 GTPase; Provisional
Probab=83.90 E-value=0.94 Score=51.45 Aligned_cols=26 Identities=27% Similarity=0.374 Sum_probs=22.8
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+.+|.||||+|||+++.++..++...
T Consensus 4 ~i~v~G~~G~GKTt~~~~~~~~l~~~ 29 (253)
T PRK13768 4 IVFFLGTAGSGKTTLTKALSDWLEEQ 29 (253)
T ss_pred EEEEECCCCccHHHHHHHHHHHHHhc
Confidence 78899999999999999998887653
No 324
>PRK14531 adenylate kinase; Provisional
Probab=83.89 E-value=0.84 Score=48.91 Aligned_cols=19 Identities=37% Similarity=0.669 Sum_probs=14.7
Q ss_pred eEEEEcCCCCChhhHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgL 1105 (1402)
-.+|-||||+|||+....|
T Consensus 4 ~i~i~G~pGsGKsT~~~~l 22 (183)
T PRK14531 4 RLLFLGPPGAGKGTQAARL 22 (183)
T ss_pred EEEEECCCCCCHHHHHHHH
Confidence 4688999999999854433
No 325
>TIGR00235 udk uridine kinase. Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below
Probab=83.84 E-value=0.97 Score=49.30 Aligned_cols=25 Identities=28% Similarity=0.278 Sum_probs=19.1
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
...+..|.||+|+||||+.-.|...
T Consensus 5 ~g~vi~I~G~sGsGKSTl~~~l~~~ 29 (207)
T TIGR00235 5 KGIIIGIGGGSGSGKTTVARKIYEQ 29 (207)
T ss_pred CeEEEEEECCCCCCHHHHHHHHHHH
Confidence 4467789999999999866665543
No 326
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=83.82 E-value=0.97 Score=55.60 Aligned_cols=28 Identities=32% Similarity=0.329 Sum_probs=24.1
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
....|+.||||||||+++..+..+++..
T Consensus 39 ~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~ 66 (451)
T PRK06305 39 AHAYLFSGIRGTGKTTLARIFAKALNCQ 66 (451)
T ss_pred ceEEEEEcCCCCCHHHHHHHHHHHhcCC
Confidence 3568999999999999999998888764
No 327
>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.
Probab=83.79 E-value=0.9 Score=54.71 Aligned_cols=25 Identities=52% Similarity=0.745 Sum_probs=19.0
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..-.||-||||||||-+.+||-..|
T Consensus 50 Gr~iLiaGppGtGKTAlA~~ia~eL 74 (398)
T PF06068_consen 50 GRAILIAGPPGTGKTALAMAIAKEL 74 (398)
T ss_dssp T-EEEEEE-TTSSHHHHHHHHHHHC
T ss_pred CcEEEEeCCCCCCchHHHHHHHHHh
Confidence 3678999999999999888875543
No 328
>PRK14948 DNA polymerase III subunits gamma and tau; Provisional
Probab=83.76 E-value=1.4 Score=56.33 Aligned_cols=27 Identities=33% Similarity=0.471 Sum_probs=23.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||||||+++..+...|+..
T Consensus 39 ~a~Lf~Gp~G~GKttlA~~lAk~L~c~ 65 (620)
T PRK14948 39 PAYLFTGPRGTGKTSSARILAKSLNCL 65 (620)
T ss_pred ceEEEECCCCCChHHHHHHHHHHhcCC
Confidence 456999999999999999998888764
No 329
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=83.55 E-value=1.5 Score=55.37 Aligned_cols=27 Identities=33% Similarity=0.444 Sum_probs=23.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...|+.||||||||++...+..++...
T Consensus 39 hayLf~Gp~GtGKTt~Ak~lAkal~c~ 65 (559)
T PRK05563 39 HAYLFSGPRGTGKTSAAKIFAKAVNCL 65 (559)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHhcCC
Confidence 578899999999999998888877654
No 330
>PRK06696 uridine kinase; Validated
Probab=83.52 E-value=1.8 Score=47.91 Aligned_cols=26 Identities=19% Similarity=0.162 Sum_probs=21.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+-+..|-||||+||||+.-.|...|
T Consensus 21 ~~~iI~I~G~sgsGKSTlA~~L~~~l 46 (223)
T PRK06696 21 RPLRVAIDGITASGKTTFADELAEEI 46 (223)
T ss_pred CceEEEEECCCCCCHHHHHHHHHHHH
Confidence 45699999999999999877776655
No 331
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=83.51 E-value=2.5 Score=53.25 Aligned_cols=29 Identities=31% Similarity=0.503 Sum_probs=23.8
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...++..|-||+|+|||+|+..|...+..
T Consensus 348 ~~G~vIaLVGPtGvGKTTtaakLAa~la~ 376 (559)
T PRK12727 348 ERGGVIALVGPTGAGKTTTIAKLAQRFAA 376 (559)
T ss_pred cCCCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 34578888899999999999998776554
No 332
>PF12846 AAA_10: AAA-like domain
Probab=83.40 E-value=0.99 Score=50.29 Aligned_cols=27 Identities=30% Similarity=0.512 Sum_probs=23.7
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
=++|-|++|+|||+++..++..++...
T Consensus 3 h~~i~G~tGsGKT~~~~~l~~~~~~~g 29 (304)
T PF12846_consen 3 HTLILGKTGSGKTTLLKNLLEQLIRRG 29 (304)
T ss_pred eEEEECCCCCcHHHHHHHHHHHHHHcC
Confidence 478999999999999999998877763
No 333
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=83.40 E-value=1.4 Score=51.53 Aligned_cols=39 Identities=36% Similarity=0.515 Sum_probs=24.0
Q ss_pred HHHHHH-HHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1065 ESQLQA-ISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1065 eSQ~qA-I~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
..|++- |++|-.+. ..-.=+|+.||||+|||+. ..|+..
T Consensus 35 k~~L~ifI~AAk~r~----e~lDHvLl~GPPGlGKTTL-A~IIA~ 74 (332)
T COG2255 35 KEQLQIFIKAAKKRG----EALDHVLLFGPPGLGKTTL-AHIIAN 74 (332)
T ss_pred HHHHHHHHHHHHhcC----CCcCeEEeeCCCCCcHHHH-HHHHHH
Confidence 345554 55554332 2345789999999999973 344443
No 334
>PRK08118 topology modulation protein; Reviewed
Probab=83.34 E-value=0.89 Score=48.47 Aligned_cols=15 Identities=27% Similarity=0.543 Sum_probs=12.6
Q ss_pred EEEEcCCCCChhhHH
Q 000592 1088 SLIQGPPGTGKTRTI 1102 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTI 1102 (1402)
.+|-||||+||||..
T Consensus 4 I~I~G~~GsGKSTla 18 (167)
T PRK08118 4 IILIGSGGSGKSTLA 18 (167)
T ss_pred EEEECCCCCCHHHHH
Confidence 578899999999743
No 335
>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=83.31 E-value=1 Score=47.74 Aligned_cols=25 Identities=44% Similarity=0.526 Sum_probs=21.0
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..|.||+|+|||+++..|+..+-..
T Consensus 2 i~i~G~~gsGKTtl~~~l~~~l~~~ 26 (155)
T TIGR00176 2 LQIVGPKNSGKTTLIERLVKALKAR 26 (155)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHhc
Confidence 4577999999999999999977543
No 336
>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2.7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....
Probab=83.23 E-value=1 Score=48.66 Aligned_cols=24 Identities=33% Similarity=0.475 Sum_probs=18.3
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+.-|.||||+||||+...|...|-
T Consensus 1 IIgI~G~sgSGKTTla~~L~~~L~ 24 (194)
T PF00485_consen 1 IIGIAGPSGSGKTTLAKRLAQILN 24 (194)
T ss_dssp EEEEEESTTSSHHHHHHHHHHHHT
T ss_pred CEEEECCCCCCHHHHHHHHHHHhC
Confidence 356899999999987776655543
No 337
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=83.07 E-value=1.6 Score=52.27 Aligned_cols=25 Identities=44% Similarity=0.519 Sum_probs=20.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+=.||.||+|||||+++-++...+-
T Consensus 39 ~~vli~G~~GtGKs~~ar~~~~~l~ 63 (350)
T CHL00081 39 GGVMIMGDRGTGKSTTIRALVDLLP 63 (350)
T ss_pred CeEEEEcCCCCCHHHHHHHHHHHHh
Confidence 5578999999999998877765544
No 338
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=83.04 E-value=1.5 Score=55.95 Aligned_cols=22 Identities=32% Similarity=0.610 Sum_probs=18.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
...+|.||||||||+++..+..
T Consensus 176 ~~vlL~Gp~GtGKTTLAr~i~~ 197 (615)
T TIGR02903 176 QHIILYGPPGVGKTTAARLALE 197 (615)
T ss_pred CeEEEECCCCCCHHHHHHHHHH
Confidence 5799999999999997666543
No 339
>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....
Probab=83.00 E-value=0.75 Score=46.06 Aligned_cols=23 Identities=35% Similarity=0.619 Sum_probs=18.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
..+..|.||+|+|||+.+..|.+
T Consensus 11 g~~~~i~G~nGsGKStLl~~l~g 33 (137)
T PF00005_consen 11 GEIVAIVGPNGSGKSTLLKALAG 33 (137)
T ss_dssp TSEEEEEESTTSSHHHHHHHHTT
T ss_pred CCEEEEEccCCCccccceeeecc
Confidence 46999999999999997665543
No 340
>PRK07667 uridine kinase; Provisional
Probab=82.97 E-value=1.8 Score=47.02 Aligned_cols=25 Identities=20% Similarity=0.227 Sum_probs=20.0
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.-+..|-||||+||||+.-.|...|
T Consensus 17 ~~iIgI~G~~gsGKStla~~L~~~l 41 (193)
T PRK07667 17 RFILGIDGLSRSGKTTFVANLKENM 41 (193)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHH
Confidence 3588999999999999776665554
No 341
>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H.
Probab=82.95 E-value=0.69 Score=47.26 Aligned_cols=16 Identities=50% Similarity=0.740 Sum_probs=13.4
Q ss_pred ceEEEEcCCCCChhhH
Q 000592 1086 ELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkT 1101 (1402)
.-.||+|+|||||+.+
T Consensus 22 ~pvli~GE~GtGK~~~ 37 (138)
T PF14532_consen 22 SPVLITGEPGTGKSLL 37 (138)
T ss_dssp S-EEEECCTTSSHHHH
T ss_pred CcEEEEcCCCCCHHHH
Confidence 4679999999999983
No 342
>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A.
Probab=82.95 E-value=1.2 Score=46.39 Aligned_cols=28 Identities=25% Similarity=0.419 Sum_probs=24.4
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
++..|.||.|+|||+.+..|+..|....
T Consensus 1 pvv~VvG~~~sGKTTl~~~Li~~l~~~g 28 (140)
T PF03205_consen 1 PVVQVVGPKNSGKTTLIRKLINELKRRG 28 (140)
T ss_dssp -EEEEEESTTSSHHHHHHHHHHHHHHTT
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHhHcC
Confidence 3678999999999999999999988664
No 343
>PRK07994 DNA polymerase III subunits gamma and tau; Validated
Probab=82.87 E-value=1.7 Score=55.76 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=23.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...|+.||||||||+++..+...|+..
T Consensus 39 hAyLf~Gp~GvGKTTlAr~lAk~L~c~ 65 (647)
T PRK07994 39 HAYLFSGTRGVGKTTIARLLAKGLNCE 65 (647)
T ss_pred eEEEEECCCCCCHHHHHHHHHHhhhhc
Confidence 457999999999999999888887764
No 344
>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=82.83 E-value=1 Score=50.19 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=20.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
-+++|-||||||||+..+.+..++.
T Consensus 2 ~~~ll~g~~G~GKS~lal~la~~va 26 (239)
T cd01125 2 YVSALVAPGGTGKSSLLLVLALAMA 26 (239)
T ss_pred ceeEEEcCCCCCHHHHHHHHHHHHh
Confidence 3789999999999998888766543
No 345
>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=82.80 E-value=1.2 Score=40.65 Aligned_cols=24 Identities=29% Similarity=0.455 Sum_probs=19.6
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+|.|.+|+|||++...+...+-.
T Consensus 2 ~~~~g~~G~Gktt~~~~l~~~l~~ 25 (99)
T cd01983 2 IVVTGKGGVGKTTLAANLAAALAK 25 (99)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHH
Confidence 578899999999998888776644
No 346
>PRK03839 putative kinase; Provisional
Probab=82.74 E-value=1.1 Score=47.51 Aligned_cols=17 Identities=41% Similarity=0.575 Sum_probs=13.1
Q ss_pred EEEEcCCCCChhhHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVA 1104 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvg 1104 (1402)
.+|-||||+||||....
T Consensus 3 I~l~G~pGsGKsT~~~~ 19 (180)
T PRK03839 3 IAITGTPGVGKTTVSKL 19 (180)
T ss_pred EEEECCCCCCHHHHHHH
Confidence 56779999999984333
No 347
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=82.72 E-value=0.92 Score=49.57 Aligned_cols=14 Identities=57% Similarity=0.904 Sum_probs=12.3
Q ss_pred eEEEEcCCCCChhh
Q 000592 1087 LSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1087 fsLIQGPPGTGKTk 1100 (1402)
.-+|.|.||||||+
T Consensus 2 ~I~ITGTPGvGKTT 15 (180)
T COG1936 2 LIAITGTPGVGKTT 15 (180)
T ss_pred eEEEeCCCCCchHH
Confidence 35799999999997
No 348
>PRK14954 DNA polymerase III subunits gamma and tau; Provisional
Probab=82.71 E-value=0.81 Score=58.45 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=23.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||||||++...+..+|+..
T Consensus 39 ha~Lf~Gp~GvGKttlA~~lAk~L~c~ 65 (620)
T PRK14954 39 HGYIFSGLRGVGKTTAARVFAKAVNCQ 65 (620)
T ss_pred eeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 458899999999999999888887763
No 349
>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=82.68 E-value=1.8 Score=51.34 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=22.9
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+++|-||||||||++.+.++.....
T Consensus 54 ~G~iteI~Gp~GsGKTtLal~~~~~~~~ 81 (325)
T cd00983 54 KGRIIEIYGPESSGKTTLALHAIAEAQK 81 (325)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 3469999999999999988887766544
No 350
>PRK09435 membrane ATPase/protein kinase; Provisional
Probab=82.53 E-value=1.9 Score=51.37 Aligned_cols=29 Identities=31% Similarity=0.369 Sum_probs=24.4
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..-+.-|.||||+||||++-.++..+-..
T Consensus 55 ~~~~igi~G~~GaGKSTl~~~l~~~l~~~ 83 (332)
T PRK09435 55 NALRIGITGVPGVGKSTFIEALGMHLIEQ 83 (332)
T ss_pred CcEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence 34688899999999999999988877643
No 351
>PRK13947 shikimate kinase; Provisional
Probab=82.49 E-value=1 Score=47.02 Aligned_cols=17 Identities=35% Similarity=0.309 Sum_probs=13.1
Q ss_pred EEEEcCCCCChhhHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVA 1104 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvg 1104 (1402)
-+|.||||+|||++...
T Consensus 4 I~l~G~~GsGKst~a~~ 20 (171)
T PRK13947 4 IVLIGFMGTGKTTVGKR 20 (171)
T ss_pred EEEEcCCCCCHHHHHHH
Confidence 46789999999984433
No 352
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=82.26 E-value=1.8 Score=54.55 Aligned_cols=27 Identities=30% Similarity=0.415 Sum_probs=23.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..-|+.||||||||+++..+..+++..
T Consensus 37 hayLf~Gp~G~GKTt~Ar~LAk~L~c~ 63 (535)
T PRK08451 37 HAYLFSGLRGSGKTSSARIFARALVCE 63 (535)
T ss_pred eeEEEECCCCCcHHHHHHHHHHHhcCC
Confidence 466999999999999999998888754
No 353
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=82.23 E-value=3.7 Score=54.33 Aligned_cols=33 Identities=36% Similarity=0.502 Sum_probs=24.2
Q ss_pred cCCCHHHHHH---HHHHHccCCCCcCCCceEEEEcCCCCChhh
Q 000592 1061 TSFNESQLQA---ISVAIGLSSSWKKDCELSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1061 ~~lNeSQ~qA---I~sAL~~~~~~~k~~gfsLIQGPPGTGKTk 1100 (1402)
..+.+.|.+. |..++.. ....+|+.|+|||||-
T Consensus 244 ~~~r~~Q~~~~~~i~~~~~~-------~~~~~~eA~TG~GKT~ 279 (850)
T TIGR01407 244 LEYRPEQLKLAELVLDQLTH-------SEKSLIEAPTGTGKTL 279 (850)
T ss_pred CccCHHHHHHHHHHHHHhcc-------CCcEEEECCCCCchhH
Confidence 4577899974 4455432 2578899999999995
No 354
>PRK09087 hypothetical protein; Validated
Probab=82.19 E-value=1.5 Score=49.23 Aligned_cols=22 Identities=27% Similarity=0.463 Sum_probs=18.3
Q ss_pred CceEEEEcCCCCChhhHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
.+...|.||+|+||||..-++.
T Consensus 44 ~~~l~l~G~~GsGKThLl~~~~ 65 (226)
T PRK09087 44 SPVVVLAGPVGSGKTHLASIWR 65 (226)
T ss_pred CCeEEEECCCCCCHHHHHHHHH
Confidence 3678999999999999777544
No 355
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=82.18 E-value=0.89 Score=55.11 Aligned_cols=27 Identities=37% Similarity=0.615 Sum_probs=23.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||+|||++...+..+++..
T Consensus 37 ha~Lf~Gp~G~GKt~lA~~lA~~l~c~ 63 (394)
T PRK07940 37 HAWLFTGPPGSGRSVAARAFAAALQCT 63 (394)
T ss_pred eEEEEECCCCCcHHHHHHHHHHHhCCC
Confidence 468899999999999999988887764
No 356
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=82.18 E-value=1.4 Score=56.32 Aligned_cols=25 Identities=32% Similarity=0.442 Sum_probs=20.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...++.||||||||+...++...+-
T Consensus 38 ~~~ll~G~pG~GKT~la~~la~~l~ 62 (608)
T TIGR00764 38 RNVLLIGEPGVGKSMLAKAMAELLP 62 (608)
T ss_pred CCEEEECCCCCCHHHHHHHHHHHcC
Confidence 4888999999999998888776553
No 357
>PRK06547 hypothetical protein; Provisional
Probab=82.15 E-value=1.6 Score=47.00 Aligned_cols=25 Identities=32% Similarity=0.399 Sum_probs=19.6
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
...+.+|-||||+|||++.-.|...
T Consensus 14 ~~~~i~i~G~~GsGKTt~a~~l~~~ 38 (172)
T PRK06547 14 GMITVLIDGRSGSGKTTLAGALAAR 38 (172)
T ss_pred CCEEEEEECCCCCCHHHHHHHHHHH
Confidence 4568999999999999976655443
No 358
>PRK14532 adenylate kinase; Provisional
Probab=82.13 E-value=0.97 Score=48.18 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=13.2
Q ss_pred EEEEcCCCCChhhHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVA 1104 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvg 1104 (1402)
.+|-||||+||||....
T Consensus 3 i~~~G~pGsGKsT~a~~ 19 (188)
T PRK14532 3 LILFGPPAAGKGTQAKR 19 (188)
T ss_pred EEEECCCCCCHHHHHHH
Confidence 46789999999994333
No 359
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=82.07 E-value=3.6 Score=53.55 Aligned_cols=48 Identities=23% Similarity=0.357 Sum_probs=37.5
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..||..|..|+..+.+.- ....-.|++|.+|+|||-.-+.+|...|..
T Consensus 197 ~~Ln~~Q~~a~~~i~~~~----~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~ 244 (730)
T COG1198 197 LALNQEQQAAVEAILSSL----GGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ 244 (730)
T ss_pred cccCHHHHHHHHHHHHhc----ccccceeEeCCCCCcHHHHHHHHHHHHHHc
Confidence 369999999998876542 123579999999999998877777766654
No 360
>PRK12608 transcription termination factor Rho; Provisional
Probab=82.03 E-value=2.2 Score=51.61 Aligned_cols=26 Identities=38% Similarity=0.529 Sum_probs=21.1
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
=.||-||||||||+.+..|+..+...
T Consensus 135 R~LIvG~pGtGKTTLl~~la~~i~~~ 160 (380)
T PRK12608 135 RGLIVAPPRAGKTVLLQQIAAAVAAN 160 (380)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 35999999999999888877766554
No 361
>PRK01184 hypothetical protein; Provisional
Probab=81.97 E-value=1.1 Score=47.62 Aligned_cols=15 Identities=33% Similarity=0.556 Sum_probs=13.3
Q ss_pred eEEEEcCCCCChhhH
Q 000592 1087 LSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkT 1101 (1402)
+.+|-||||+||||.
T Consensus 3 ~i~l~G~~GsGKsT~ 17 (184)
T PRK01184 3 IIGVVGMPGSGKGEF 17 (184)
T ss_pred EEEEECCCCCCHHHH
Confidence 678899999999994
No 362
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=81.89 E-value=2.1 Score=58.30 Aligned_cols=54 Identities=28% Similarity=0.335 Sum_probs=45.4
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhcccccccccccc
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKSSE 1165 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~ 1165 (1402)
+..||----|||||+||...+-.+|-... |
T Consensus 17 ~~~lveASAGSGKT~vL~~r~lrlLl~~~-------~------------------------------------------- 46 (1139)
T COG1074 17 QSVLVEASAGTGKTFVLAERVLRLLLEGG-------P------------------------------------------- 46 (1139)
T ss_pred CcEEEEEcCCCCchhHHHHHHHHHHhhcC-------C-------------------------------------------
Confidence 68899999999999999999888876520 0
Q ss_pred ccCCCeEEEEeCchHHHHHHHHHHH
Q 000592 1166 SSVRARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1166 ~~~k~RILVCAPSNAAVDEIV~RLl 1190 (1402)
....+|||.+.||+|--|+-.||.
T Consensus 47 -~~v~~ILvvTFT~aAa~Emk~RI~ 70 (1139)
T COG1074 47 -LDVDEILVVTFTKAAAAEMKERIR 70 (1139)
T ss_pred -CChhHeeeeeccHHHHHHHHHHHH
Confidence 024699999999999999999997
No 363
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=81.89 E-value=1.1 Score=59.57 Aligned_cols=30 Identities=40% Similarity=0.576 Sum_probs=27.0
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
..|++||.||.|+|||+.+=+|..||....
T Consensus 24 ~~gi~lI~G~nGsGKSSIldAI~~ALyG~~ 53 (908)
T COG0419 24 DSGIFLIVGPNGAGKSSILDAITFALYGKT 53 (908)
T ss_pred CCCeEEEECCCCCcHHHHHHHHHHHHcCCC
Confidence 348999999999999999999999998774
No 364
>PRK14528 adenylate kinase; Provisional
Probab=81.84 E-value=1.1 Score=48.37 Aligned_cols=19 Identities=32% Similarity=0.614 Sum_probs=15.0
Q ss_pred eEEEEcCCCCChhhHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgL 1105 (1402)
..+|-||||+|||++...|
T Consensus 3 ~i~i~G~pGsGKtt~a~~l 21 (186)
T PRK14528 3 NIIFMGPPGAGKGTQAKIL 21 (186)
T ss_pred EEEEECCCCCCHHHHHHHH
Confidence 4688999999999865444
No 365
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=81.82 E-value=1.1 Score=54.72 Aligned_cols=21 Identities=33% Similarity=0.520 Sum_probs=17.3
Q ss_pred ceEEEEcCCCCChhhHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
+-.||.||||||||++...|-
T Consensus 109 ~~iLl~Gp~GtGKT~lAr~lA 129 (412)
T PRK05342 109 SNILLIGPTGSGKTLLAQTLA 129 (412)
T ss_pred ceEEEEcCCCCCHHHHHHHHH
Confidence 458999999999999766654
No 366
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=81.79 E-value=0.93 Score=52.94 Aligned_cols=24 Identities=50% Similarity=0.787 Sum_probs=19.8
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.-.||-||||||||-..++|-.-|
T Consensus 65 ravLlaGppgtGKTAlAlaisqEL 88 (456)
T KOG1942|consen 65 RAVLLAGPPGTGKTALALAISQEL 88 (456)
T ss_pred cEEEEecCCCCchhHHHHHHHHHh
Confidence 578999999999999888875433
No 367
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=81.78 E-value=2 Score=53.42 Aligned_cols=28 Identities=25% Similarity=0.408 Sum_probs=24.0
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.++.++-||+|.||||||..|.+.+...
T Consensus 256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~ 283 (484)
T PRK06995 256 GGVFALMGPTGVGKTTTTAKLAARCVMR 283 (484)
T ss_pred CcEEEEECCCCccHHHHHHHHHHHHHHh
Confidence 4699999999999999999998877543
No 368
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=81.69 E-value=3.9 Score=54.72 Aligned_cols=33 Identities=33% Similarity=0.359 Sum_probs=25.6
Q ss_pred cCCCHHHHH---HHHHHHccCCCCcCCCceEEEEcCCCCChhh
Q 000592 1061 TSFNESQLQ---AISVAIGLSSSWKKDCELSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1061 ~~lNeSQ~q---AI~sAL~~~~~~~k~~gfsLIQGPPGTGKTk 1100 (1402)
..+-+.|.+ +|..++... ...+|+.|+|||||.
T Consensus 256 ~e~R~~Q~~m~~~v~~~l~~~-------~~~~iEA~TGtGKTl 291 (928)
T PRK08074 256 YEKREGQQEMMKEVYTALRDS-------EHALIEAGTGTGKSL 291 (928)
T ss_pred CcCCHHHHHHHHHHHHHHhcC-------CCEEEECCCCCchhH
Confidence 357788888 677776532 578999999999995
No 369
>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase. This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.
Probab=81.66 E-value=0.4 Score=52.30 Aligned_cols=21 Identities=29% Similarity=0.343 Sum_probs=13.1
Q ss_pred CeEEEEeCchHHHHHHHHHHH
Q 000592 1170 ARVLICAQSNAAVDELVSRIS 1190 (1402)
Q Consensus 1170 ~RILVCAPSNAAVDEIV~RLl 1190 (1402)
.+|+||||+-.++..+...+.
T Consensus 27 ~~I~vtAP~~~~~~~lf~~~~ 47 (177)
T PF05127_consen 27 IRILVTAPSPENVQTLFEFAE 47 (177)
T ss_dssp --EEEE-SS--S-HHHHHCC-
T ss_pred ceEEEecCCHHHHHHHHHHHH
Confidence 699999999999999988776
No 370
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=81.66 E-value=4.4 Score=54.92 Aligned_cols=38 Identities=21% Similarity=0.304 Sum_probs=29.9
Q ss_pred HHHHhh-cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhh
Q 000592 1055 LQQILK-TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1055 L~~~Lk-~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTk 1100 (1402)
++.++. ..|..-|.+||.+++... =+|+.-|.|+|||-
T Consensus 452 lk~~FG~~sFRp~Q~eaI~aiL~Gr--------DVLVimPTGSGKSL 490 (1195)
T PLN03137 452 NKKVFGNHSFRPNQREIINATMSGY--------DVFVLMPTGGGKSL 490 (1195)
T ss_pred HHHHcCCCCCCHHHHHHHHHHHcCC--------CEEEEcCCCccHHH
Confidence 444443 478999999999988653 28899999999994
No 371
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]
Probab=81.65 E-value=2.6 Score=54.33 Aligned_cols=44 Identities=34% Similarity=0.451 Sum_probs=38.1
Q ss_pred cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1061 TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1061 ~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..|++.|.+|+..++.. +++.+-||||||||+++.+++..+...
T Consensus 318 ~~~~~~q~~a~~vl~~d--------e~smlt~~~~~~~~~~~~~~~~l~~~~ 361 (696)
T COG0507 318 LRLSLEQKEALDVLVVD--------EVSMLTGGPGTGKTTAIKAIARLIKEG 361 (696)
T ss_pred CCcCcccHHHHHHHhcC--------CeeEEeccCCcchHHHHHHHHHHHHhc
Confidence 46899999999988754 699999999999999999998766654
No 372
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=81.64 E-value=1.7 Score=54.51 Aligned_cols=21 Identities=38% Similarity=0.722 Sum_probs=16.9
Q ss_pred ceEEEEcCCCCChhhHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
.-.||.||||||||+..-.+.
T Consensus 87 ~~vLi~Ge~GtGKt~lAr~i~ 107 (531)
T TIGR02902 87 QHVIIYGPPGVGKTAAARLVL 107 (531)
T ss_pred ceEEEECCCCCCHHHHHHHHH
Confidence 456999999999999666554
No 373
>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins. GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding
Probab=81.62 E-value=0.65 Score=56.10 Aligned_cols=28 Identities=36% Similarity=0.577 Sum_probs=24.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
.--||+|-||||||+..+.++..|-...
T Consensus 11 ~TLLIKG~PGTGKTtfaLelL~~l~~~~ 38 (484)
T PF07088_consen 11 QTLLIKGEPGTGKTTFALELLNSLKDHG 38 (484)
T ss_pred cEEEEecCCCCCceeeehhhHHHHhccC
Confidence 4679999999999999999999887653
No 374
>PTZ00202 tuzin; Provisional
Probab=81.59 E-value=1.8 Score=53.40 Aligned_cols=41 Identities=12% Similarity=0.131 Sum_probs=27.0
Q ss_pred HHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHH
Q 000592 1066 SQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1066 SQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.+..++..++.... ...+.|.+|-||+|+|||+++..++..
T Consensus 269 aEla~Lr~VL~~~d--~~~privvLtG~~G~GKTTLlR~~~~~ 309 (550)
T PTZ00202 269 AEESWVRQVLRRLD--TAHPRIVVFTGFRGCGKSSLCRSAVRK 309 (550)
T ss_pred HHHHHHHHHHhccC--CCCceEEEEECCCCCCHHHHHHHHHhc
Confidence 34444555553221 122359999999999999988777643
No 375
>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.
Probab=81.55 E-value=1.3 Score=43.03 Aligned_cols=21 Identities=29% Similarity=0.482 Sum_probs=17.1
Q ss_pred EEEEcCCCCChhhHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.+|-|++|+|||+.|..+++.
T Consensus 2 I~V~G~~g~GKTsLi~~l~~~ 22 (119)
T PF08477_consen 2 IVVLGDSGVGKTSLIRRLCGG 22 (119)
T ss_dssp EEEECSTTSSHHHHHHHHHHS
T ss_pred EEEECcCCCCHHHHHHHHhcC
Confidence 367899999999987777653
No 376
>PRK02496 adk adenylate kinase; Provisional
Probab=81.45 E-value=1.3 Score=47.24 Aligned_cols=18 Identities=39% Similarity=0.798 Sum_probs=14.2
Q ss_pred EEEEcCCCCChhhHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgL 1105 (1402)
.+|-||||+|||++...|
T Consensus 4 i~i~G~pGsGKst~a~~l 21 (184)
T PRK02496 4 LIFLGPPGAGKGTQAVVL 21 (184)
T ss_pred EEEECCCCCCHHHHHHHH
Confidence 578899999999854444
No 377
>PRK07261 topology modulation protein; Provisional
Probab=81.44 E-value=1.2 Score=47.52 Aligned_cols=18 Identities=28% Similarity=0.381 Sum_probs=15.0
Q ss_pred EEEEcCCCCChhhHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgL 1105 (1402)
.+|-||||+||||....|
T Consensus 3 i~i~G~~GsGKSTla~~l 20 (171)
T PRK07261 3 IAIIGYSGSGKSTLARKL 20 (171)
T ss_pred EEEEcCCCCCHHHHHHHH
Confidence 578999999999976554
No 378
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=81.36 E-value=1.3 Score=44.48 Aligned_cols=19 Identities=32% Similarity=0.611 Sum_probs=14.7
Q ss_pred EEEEcCCCCChhhHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLV 1106 (1402)
-.|-||||+|||++...|.
T Consensus 2 I~i~G~~GsGKst~a~~la 20 (147)
T cd02020 2 IAIDGPAGSGKSTVAKLLA 20 (147)
T ss_pred EEEECCCCCCHHHHHHHHH
Confidence 4688999999998655443
No 379
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=81.27 E-value=2.3 Score=51.07 Aligned_cols=41 Identities=32% Similarity=0.309 Sum_probs=30.8
Q ss_pred HHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1069 QAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1069 qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
+.+..++... +-+.--|++||+|+||+++...+...||...
T Consensus 29 ~~L~~~~~~~----rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~ 69 (365)
T PRK07471 29 AALLDAYRSG----RLHHAWLIGGPQGIGKATLAYRMARFLLATP 69 (365)
T ss_pred HHHHHHHHcC----CCCceEEEECCCCCCHHHHHHHHHHHHhCCC
Confidence 3455555442 2334689999999999999999999999753
No 380
>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional
Probab=81.13 E-value=2.2 Score=49.92 Aligned_cols=44 Identities=16% Similarity=0.156 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
-|+..++....-+... .-.+.=|-|+||.|||+++..++..|-.
T Consensus 87 ~n~~~a~~~r~~~~~~-----~~~~v~l~G~pGsGKTTLl~~l~~~l~~ 130 (290)
T PRK10463 87 KNNRLAERNRARFAAR-----KQLVLNLVSSPGSGKTTLLTETLMRLKD 130 (290)
T ss_pred HhHHHHHHHHHHHHhc-----CCeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence 5777777776655432 2356678899999999999998887643
No 381
>PRK10865 protein disaggregation chaperone; Provisional
Probab=81.12 E-value=1.2 Score=58.85 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=22.3
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+..|+.||||||||+++-++...+..
T Consensus 199 ~~n~lL~G~pGvGKT~l~~~la~~i~~ 225 (857)
T PRK10865 199 KNNPVLIGEPGVGKTAIVEGLAQRIIN 225 (857)
T ss_pred cCceEEECCCCCCHHHHHHHHHHHhhc
Confidence 457788899999999999888776654
No 382
>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A ....
Probab=81.12 E-value=2.5 Score=44.96 Aligned_cols=30 Identities=33% Similarity=0.493 Sum_probs=24.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
-+..-|+.||+|+||++++..++..++...
T Consensus 18 l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~ 47 (162)
T PF13177_consen 18 LPHALLFHGPSGSGKKTLALAFARALLCSN 47 (162)
T ss_dssp --SEEEEECSTTSSHHHHHHHHHHHHC-TT
T ss_pred cceeEEEECCCCCCHHHHHHHHHHHHcCCC
Confidence 345789999999999999999999888764
No 383
>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.
Probab=81.11 E-value=1.5 Score=46.51 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=18.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.+.+|.||||+|||+....|...
T Consensus 3 ~~i~l~G~~gsGKst~a~~l~~~ 25 (175)
T cd00227 3 RIIILNGGSSAGKSSIARALQSV 25 (175)
T ss_pred CEEEEECCCCCCHHHHHHHHHHh
Confidence 48899999999999976666543
No 384
>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein. It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication
Probab=80.93 E-value=3.4 Score=54.05 Aligned_cols=56 Identities=25% Similarity=0.442 Sum_probs=44.4
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHHHHHHHHHHHHhhhcccccccccc
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAIARAWQDAALARQINEDSERDKKS 1163 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~ 1163 (1402)
..++.+|..|=|||||+-+...+...+.
T Consensus 48 ~~~V~vVRSpMGTGKTtaLi~wLk~~l~---------------------------------------------------- 75 (824)
T PF02399_consen 48 KRGVLVVRSPMGTGKTTALIRWLKDALK---------------------------------------------------- 75 (824)
T ss_pred CCCeEEEECCCCCCcHHHHHHHHHHhcc----------------------------------------------------
Confidence 4589999999999999965544432221
Q ss_pred ccccCCCeEEEEeCchHHHHHHHHHHHhcCC
Q 000592 1164 SESSVRARVLICAQSNAAVDELVSRISKEGL 1194 (1402)
Q Consensus 1164 ~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI 1194 (1402)
.+..+|||.+.-.+=+.++..|+...|+
T Consensus 76 ---~~~~~VLvVShRrSL~~sL~~rf~~~~l 103 (824)
T PF02399_consen 76 ---NPDKSVLVVSHRRSLTKSLAERFKKAGL 103 (824)
T ss_pred ---CCCCeEEEEEhHHHHHHHHHHHHhhcCC
Confidence 1367999999999999999999987765
No 385
>cd03112 CobW_like The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.
Probab=80.88 E-value=1.3 Score=46.75 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=19.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
++++|-|++|+|||+++..++..
T Consensus 1 p~~~l~G~~GsGKTtl~~~l~~~ 23 (158)
T cd03112 1 PVTVLTGFLGAGKTTLLNHILTE 23 (158)
T ss_pred CEEEEEECCCCCHHHHHHHHHhc
Confidence 47899999999999998876643
No 386
>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
Probab=80.86 E-value=1.3 Score=49.44 Aligned_cols=22 Identities=27% Similarity=0.296 Sum_probs=17.6
Q ss_pred EEEEcCCCCChhhHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.-|-||+|+||||+...|...|
T Consensus 2 igI~G~sGSGKTTla~~L~~~l 23 (220)
T cd02025 2 IGIAGSVAVGKSTTARVLQALL 23 (220)
T ss_pred EEeeCCCCCCHHHHHHHHHHHH
Confidence 4577999999999987766654
No 387
>PF13479 AAA_24: AAA domain
Probab=80.86 E-value=1 Score=49.67 Aligned_cols=19 Identities=47% Similarity=0.812 Sum_probs=15.9
Q ss_pred eEEEEcCCCCChhhHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgL 1105 (1402)
-.||.||||+|||+++..+
T Consensus 5 ~~lIyG~~G~GKTt~a~~~ 23 (213)
T PF13479_consen 5 KILIYGPPGSGKTTLAASL 23 (213)
T ss_pred EEEEECCCCCCHHHHHHhC
Confidence 5799999999999965554
No 388
>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=80.59 E-value=2.4 Score=44.47 Aligned_cols=23 Identities=43% Similarity=0.613 Sum_probs=18.3
Q ss_pred EEEEcCCCCChhhHHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..+-||+|+|||+++..+...+.
T Consensus 2 i~~~G~~GsGKTt~~~~l~~~~~ 24 (148)
T cd03114 2 IGITGVPGAGKSTLIDALITALR 24 (148)
T ss_pred EEEECCCCCcHHHHHHHHHHHHH
Confidence 35669999999999888876553
No 389
>PRK00300 gmk guanylate kinase; Provisional
Probab=80.58 E-value=1.6 Score=47.10 Aligned_cols=24 Identities=29% Similarity=0.585 Sum_probs=18.7
Q ss_pred CCceEEEEcCCCCChhhHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
...+..|-||+|+|||+++..|..
T Consensus 4 ~g~~i~i~G~sGsGKstl~~~l~~ 27 (205)
T PRK00300 4 RGLLIVLSGPSGAGKSTLVKALLE 27 (205)
T ss_pred CCCEEEEECCCCCCHHHHHHHHHh
Confidence 346899999999999986555544
No 390
>PRK14530 adenylate kinase; Provisional
Probab=80.57 E-value=1.5 Score=48.09 Aligned_cols=19 Identities=32% Similarity=0.546 Sum_probs=14.7
Q ss_pred eEEEEcCCCCChhhHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgL 1105 (1402)
..+|-||||+||||....|
T Consensus 5 ~I~i~G~pGsGKsT~~~~L 23 (215)
T PRK14530 5 RILLLGAPGAGKGTQSSNL 23 (215)
T ss_pred EEEEECCCCCCHHHHHHHH
Confidence 5678899999999854443
No 391
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=80.55 E-value=1.1 Score=58.05 Aligned_cols=20 Identities=50% Similarity=0.792 Sum_probs=16.7
Q ss_pred EEEEcCCCCChhhHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVs 1107 (1402)
.|+.||||||||.+..++-.
T Consensus 490 iLL~GppGtGKT~lakalA~ 509 (733)
T TIGR01243 490 VLLFGPPGTGKTLLAKAVAT 509 (733)
T ss_pred EEEECCCCCCHHHHHHHHHH
Confidence 68899999999998777644
No 392
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=80.45 E-value=1 Score=48.96 Aligned_cols=21 Identities=48% Similarity=0.654 Sum_probs=15.5
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
--|-||||+|||| |+..|+..
T Consensus 3 ItIsG~pGsG~TT-----va~~lAe~ 23 (179)
T COG1102 3 ITISGLPGSGKTT-----VARELAEH 23 (179)
T ss_pred EEeccCCCCChhH-----HHHHHHHH
Confidence 3578999999998 55555554
No 393
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=80.41 E-value=1.3 Score=45.82 Aligned_cols=17 Identities=41% Similarity=0.796 Sum_probs=13.3
Q ss_pred EEcCCCCChhhHHHHHH
Q 000592 1090 IQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1090 IQGPPGTGKTkTIvgLV 1106 (1402)
|-||||+|||+....|.
T Consensus 1 i~G~PgsGK~t~~~~la 17 (151)
T PF00406_consen 1 ILGPPGSGKGTQAKRLA 17 (151)
T ss_dssp EEESTTSSHHHHHHHHH
T ss_pred CcCCCCCChHHHHHHHH
Confidence 56999999998655553
No 394
>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=80.41 E-value=6.1 Score=51.76 Aligned_cols=77 Identities=17% Similarity=0.124 Sum_probs=53.8
Q ss_pred HHHHhh----cCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCC
Q 000592 1055 LQQILK----TSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINS 1130 (1402)
Q Consensus 1055 L~~~Lk----~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~ 1130 (1402)
+.+.++ ..+..-|.+||..++... =.+|+-|.|||||-. .++.+|-...
T Consensus 25 l~~~L~~~g~~~p~~~Q~~ai~~il~G~--------nvvv~apTGSGKTla--~~LPiL~~l~----------------- 77 (742)
T TIGR03817 25 VVAALEAAGIHRPWQHQARAAELAHAGR--------HVVVATGTASGKSLA--YQLPVLSALA----------------- 77 (742)
T ss_pred HHHHHHHcCCCcCCHHHHHHHHHHHCCC--------CEEEECCCCCcHHHH--HHHHHHHHHh-----------------
Confidence 445553 257899999999987653 288999999999953 2222221110
Q ss_pred CCccchhHHHHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcC
Q 000592 1131 RPKIGQSAAIARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEG 1193 (1402)
Q Consensus 1131 rp~~s~~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~G 1193 (1402)
..++.++|+-+|+.+=..++..++.+.+
T Consensus 78 -----------------------------------~~~~~~aL~l~PtraLa~q~~~~l~~l~ 105 (742)
T TIGR03817 78 -----------------------------------DDPRATALYLAPTKALAADQLRAVRELT 105 (742)
T ss_pred -----------------------------------hCCCcEEEEEcChHHHHHHHHHHHHHhc
Confidence 0124689999999999999999988654
No 395
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=80.20 E-value=2.2 Score=56.50 Aligned_cols=27 Identities=33% Similarity=0.437 Sum_probs=22.0
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+..|+.||||||||++..+|-..+..
T Consensus 595 ~~~~Lf~Gp~GvGKt~lA~~La~~l~~ 621 (852)
T TIGR03346 595 IGSFLFLGPTGVGKTELAKALAEFLFD 621 (852)
T ss_pred CeEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence 467899999999999988887766543
No 396
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=80.15 E-value=2.2 Score=54.54 Aligned_cols=28 Identities=29% Similarity=0.328 Sum_probs=23.4
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..-.|+.||||||||+++..+...|+..
T Consensus 38 ~ha~Lf~GPpG~GKTtiArilAk~L~C~ 65 (624)
T PRK14959 38 APAYLFSGTRGVGKTTIARIFAKALNCE 65 (624)
T ss_pred CceEEEECCCCCCHHHHHHHHHHhcccc
Confidence 3578899999999999998888777653
No 397
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=80.08 E-value=3.4 Score=51.33 Aligned_cols=27 Identities=26% Similarity=0.362 Sum_probs=21.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
..++||-||||||||.....++..-+.
T Consensus 31 Gs~~li~G~pGsGKT~l~~qf~~~~~~ 57 (509)
T PRK09302 31 GRPTLVSGTAGTGKTLFALQFLVNGIK 57 (509)
T ss_pred CcEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence 479999999999999987777654443
No 398
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=80.02 E-value=2.1 Score=55.03 Aligned_cols=24 Identities=33% Similarity=0.534 Sum_probs=20.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+.||.||||||||++...+...+
T Consensus 51 ~~~l~~G~~G~GKttla~~l~~~l 74 (637)
T PRK13765 51 RHVMMIGSPGTGKSMLAKAMAELL 74 (637)
T ss_pred CeEEEECCCCCcHHHHHHHHHHHc
Confidence 589999999999999988876544
No 399
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=79.86 E-value=2.5 Score=50.02 Aligned_cols=27 Identities=33% Similarity=0.338 Sum_probs=24.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-.|+.||||+|||+++..+..+++-.
T Consensus 22 hA~Lf~G~~G~GK~~la~~~a~~llC~ 48 (325)
T PRK08699 22 NAWLFAGKKGIGKTAFARFAAQALLCE 48 (325)
T ss_pred eEEEeECCCCCCHHHHHHHHHHHHcCC
Confidence 568899999999999999999988864
No 400
>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
Probab=79.76 E-value=1.6 Score=47.10 Aligned_cols=23 Identities=35% Similarity=0.528 Sum_probs=18.1
Q ss_pred eEEEEcCCCCChhhHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+..|-|+||+|||++.-.|...+
T Consensus 1 ii~i~G~sgsGKttla~~l~~~l 23 (179)
T cd02028 1 VVGIAGPSGSGKTTFAKKLSNQL 23 (179)
T ss_pred CEEEECCCCCCHHHHHHHHHHHH
Confidence 35789999999999877666554
No 401
>PRK15455 PrkA family serine protein kinase; Provisional
Probab=79.75 E-value=2.3 Score=54.11 Aligned_cols=26 Identities=23% Similarity=0.394 Sum_probs=20.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
...+.++.||||+|||+..-.|-.++
T Consensus 102 ~~~IL~LvGPpG~GKSsLa~~la~~l 127 (644)
T PRK15455 102 KKQILYLLGPVGGGKSSLAERLKSLM 127 (644)
T ss_pred CCceEEEecCCCCCchHHHHHHHHHH
Confidence 34799999999999998766665543
No 402
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=79.49 E-value=2.5 Score=55.96 Aligned_cols=28 Identities=36% Similarity=0.566 Sum_probs=22.8
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
..+..|+.||||||||.+..+|-..|+.
T Consensus 595 p~~~~lf~Gp~GvGKT~lA~~La~~l~~ 622 (852)
T TIGR03345 595 PLGVFLLVGPSGVGKTETALALAELLYG 622 (852)
T ss_pred CceEEEEECCCCCCHHHHHHHHHHHHhC
Confidence 3457899999999999999888766653
No 403
>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=79.31 E-value=1.5 Score=54.97 Aligned_cols=22 Identities=32% Similarity=0.691 Sum_probs=19.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+.||.||+|+||||||--|-.
T Consensus 111 ~iLLltGPsGcGKSTtvkvLsk 132 (634)
T KOG1970|consen 111 RILLLTGPSGCGKSTTVKVLSK 132 (634)
T ss_pred eEEEEeCCCCCCchhHHHHHHH
Confidence 5999999999999999877644
No 404
>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
Probab=79.28 E-value=1.9 Score=47.02 Aligned_cols=27 Identities=37% Similarity=0.409 Sum_probs=23.2
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.++.-|-||+|+|||++|..|+..|-.
T Consensus 6 ~~ii~ivG~sgsGKTTLi~~li~~l~~ 32 (173)
T PRK10751 6 IPLLAIAAWSGTGKTTLLKKLIPALCA 32 (173)
T ss_pred ceEEEEECCCCChHHHHHHHHHHHHhh
Confidence 468889999999999999999987644
No 405
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=79.17 E-value=1.6 Score=47.54 Aligned_cols=25 Identities=36% Similarity=0.603 Sum_probs=20.9
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..|.||||.|||+.+.-+...|-..
T Consensus 8 i~ITG~PGvGKtTl~~ki~e~L~~~ 32 (179)
T COG1618 8 IFITGRPGVGKTTLVLKIAEKLREK 32 (179)
T ss_pred EEEeCCCCccHHHHHHHHHHHHHhc
Confidence 4789999999999988887766554
No 406
>PRK10078 ribose 1,5-bisphosphokinase; Provisional
Probab=79.17 E-value=1.5 Score=47.16 Aligned_cols=20 Identities=35% Similarity=0.727 Sum_probs=16.6
Q ss_pred ceEEEEcCCCCChhhHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgL 1105 (1402)
.+..|-||+|+||||++-.|
T Consensus 3 ~~i~l~G~sGsGKsTl~~~l 22 (186)
T PRK10078 3 KLIWLMGPSGSGKDSLLAAL 22 (186)
T ss_pred cEEEEECCCCCCHHHHHHHH
Confidence 37889999999999966655
No 407
>PRK05439 pantothenate kinase; Provisional
Probab=79.10 E-value=3.1 Score=49.22 Aligned_cols=28 Identities=29% Similarity=0.246 Sum_probs=20.9
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+.+-+..|-||||+||||+.-.|.. ++.
T Consensus 84 ~~~~iIgIaG~~gsGKSTla~~L~~-~l~ 111 (311)
T PRK05439 84 KVPFIIGIAGSVAVGKSTTARLLQA-LLS 111 (311)
T ss_pred CCCEEEEEECCCCCCHHHHHHHHHH-HHH
Confidence 3445788999999999998766554 444
No 408
>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]
Probab=79.09 E-value=1.6 Score=49.86 Aligned_cols=20 Identities=45% Similarity=0.727 Sum_probs=16.8
Q ss_pred EEEEcCCCCChhhHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVs 1107 (1402)
+||-||||+||||.+.-|--
T Consensus 140 tLiigpP~~GKTTlLRdiaR 159 (308)
T COG3854 140 TLIIGPPQVGKTTLLRDIAR 159 (308)
T ss_pred eEEecCCCCChHHHHHHHHH
Confidence 89999999999997766543
No 409
>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []. The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....
Probab=79.09 E-value=1.6 Score=47.55 Aligned_cols=25 Identities=40% Similarity=0.592 Sum_probs=21.1
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+++++|.||.|+|||..+-+|-.+|
T Consensus 24 ~~~~~i~G~NGsGKS~ileAi~~~l 48 (220)
T PF02463_consen 24 PGLNVIVGPNGSGKSNILEAIEFVL 48 (220)
T ss_dssp SSEEEEEESTTSSHHHHHHHHHHHT
T ss_pred CCCEEEEcCCCCCHHHHHHHHHHHH
Confidence 4799999999999999888875544
No 410
>TIGR00554 panK_bact pantothenate kinase, bacterial type. Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.
Probab=79.03 E-value=2.9 Score=48.89 Aligned_cols=30 Identities=33% Similarity=0.347 Sum_probs=22.2
Q ss_pred cCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1082 KKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1082 ~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+.+-+.-|-||+|+||||+. .++..++..
T Consensus 59 ~~~p~IIGIaG~~GSGKSTla-r~L~~ll~~ 88 (290)
T TIGR00554 59 AKIPYIISIAGSVAVGKSTTA-RILQALLSR 88 (290)
T ss_pred CCCCEEEEEECCCCCCHHHHH-HHHHHHHhh
Confidence 345678889999999999977 445555553
No 411
>PRK09354 recA recombinase A; Provisional
Probab=79.01 E-value=1.9 Score=51.64 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=22.9
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...+++|-||||||||+..+.++.....
T Consensus 59 ~G~IteI~G~~GsGKTtLal~~~~~~~~ 86 (349)
T PRK09354 59 RGRIVEIYGPESSGKTTLALHAIAEAQK 86 (349)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 3469999999999999988877765544
No 412
>TIGR00455 apsK adenylylsulfate kinase (apsK). Important residue (active site in E.coli) is residue 100 of the seed alignment.
Probab=78.94 E-value=2 Score=45.79 Aligned_cols=26 Identities=23% Similarity=0.293 Sum_probs=21.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..+..|-|+||+|||++...|...+.
T Consensus 18 ~~~i~i~G~~GsGKstla~~l~~~l~ 43 (184)
T TIGR00455 18 GVVIWLTGLSGSGKSTIANALEKKLE 43 (184)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence 46999999999999998877776654
No 413
>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.
Probab=78.87 E-value=1.6 Score=48.89 Aligned_cols=22 Identities=27% Similarity=0.520 Sum_probs=17.8
Q ss_pred EEEEcCCCCChhhHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+|-|+||+|||+....|...+
T Consensus 2 Ivl~G~pGSGKST~a~~La~~l 23 (249)
T TIGR03574 2 IILTGLPGVGKSTFSKELAKKL 23 (249)
T ss_pred EEEEcCCCCCHHHHHHHHHHHH
Confidence 5788999999999877766544
No 414
>PRK14953 DNA polymerase III subunits gamma and tau; Provisional
Probab=78.83 E-value=2.8 Score=52.24 Aligned_cols=25 Identities=32% Similarity=0.472 Sum_probs=19.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
...|+.||||||||++...+...+.
T Consensus 39 hayLf~Gp~G~GKTtlAr~lAk~L~ 63 (486)
T PRK14953 39 HAYIFAGPRGTGKTTIARILAKVLN 63 (486)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHhc
Confidence 4678999999999877666655554
No 415
>TIGR03263 guanyl_kin guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.
Probab=78.79 E-value=1.6 Score=45.95 Aligned_cols=22 Identities=36% Similarity=0.682 Sum_probs=17.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+.+|-||+|+|||+.+..|..
T Consensus 2 ~ii~l~G~~GsGKsTl~~~L~~ 23 (180)
T TIGR03263 2 LLIVISGPSGVGKSTLVKALLE 23 (180)
T ss_pred cEEEEECCCCCCHHHHHHHHHc
Confidence 4788999999999996555443
No 416
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=78.79 E-value=1.2 Score=55.49 Aligned_cols=22 Identities=45% Similarity=0.614 Sum_probs=17.0
Q ss_pred CceEEEEcCCCCChhhHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
+.=.|+-||||||||-...++-
T Consensus 337 PKGVLLvGPPGTGKTlLARAvA 358 (752)
T KOG0734|consen 337 PKGVLLVGPPGTGKTLLARAVA 358 (752)
T ss_pred CCceEEeCCCCCchhHHHHHhh
Confidence 3457888999999997666654
No 417
>CHL00206 ycf2 Ycf2; Provisional
Probab=78.77 E-value=1.3 Score=61.90 Aligned_cols=21 Identities=24% Similarity=0.379 Sum_probs=17.4
Q ss_pred eEEEEcCCCCChhhHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVs 1107 (1402)
=.|+.||||||||.++.++.+
T Consensus 1632 GILLiGPPGTGKTlLAKALA~ 1652 (2281)
T CHL00206 1632 GILVIGSIGTGRSYLVKYLAT 1652 (2281)
T ss_pred ceEEECCCCCCHHHHHHHHHH
Confidence 457789999999998888754
No 418
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=78.77 E-value=1.6 Score=53.34 Aligned_cols=21 Identities=33% Similarity=0.520 Sum_probs=17.8
Q ss_pred ceEEEEcCCCCChhhHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
+-.||.||||||||.+...|-
T Consensus 117 ~~iLL~GP~GsGKT~lAraLA 137 (413)
T TIGR00382 117 SNILLIGPTGSGKTLLAQTLA 137 (413)
T ss_pred ceEEEECCCCcCHHHHHHHHH
Confidence 568999999999999777664
No 419
>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.
Probab=78.73 E-value=1.7 Score=44.23 Aligned_cols=17 Identities=29% Similarity=0.372 Sum_probs=13.6
Q ss_pred EEEcCCCCChhhHHHHH
Q 000592 1089 LIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgL 1105 (1402)
+|-||||+|||+....|
T Consensus 3 ~l~G~~GsGKstla~~l 19 (154)
T cd00464 3 VLIGMMGAGKTTVGRLL 19 (154)
T ss_pred EEEcCCCCCHHHHHHHH
Confidence 67799999999855544
No 420
>TIGR00041 DTMP_kinase thymidylate kinase. Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
Probab=78.71 E-value=1.9 Score=46.03 Aligned_cols=23 Identities=26% Similarity=0.351 Sum_probs=18.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.+..|.||||+||||.+-.|...
T Consensus 4 ~~IvieG~~GsGKsT~~~~L~~~ 26 (195)
T TIGR00041 4 MFIVIEGIDGAGKTTQANLLKKL 26 (195)
T ss_pred eEEEEECCCCCCHHHHHHHHHHH
Confidence 47899999999999866555444
No 421
>PRK14738 gmk guanylate kinase; Provisional
Probab=78.63 E-value=1.8 Score=47.58 Aligned_cols=23 Identities=30% Similarity=0.534 Sum_probs=18.3
Q ss_pred CCceEEEEcCCCCChhhHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
...+.+|-||||+|||+++-.|.
T Consensus 12 ~~~~ivi~GpsG~GK~tl~~~L~ 34 (206)
T PRK14738 12 KPLLVVISGPSGVGKDAVLARMR 34 (206)
T ss_pred CCeEEEEECcCCCCHHHHHHHHH
Confidence 44688899999999999765553
No 422
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=78.59 E-value=3.1 Score=48.40 Aligned_cols=43 Identities=21% Similarity=0.208 Sum_probs=30.8
Q ss_pred HHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1066 SQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1066 SQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...+.+..++... +-+..-|+.||+|+|||+++..+..+++..
T Consensus 11 ~~~~~l~~~~~~~----~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~ 53 (313)
T PRK05564 11 NIKNRIKNSIIKN----RFSHAHIIVGEDGIGKSLLAKEIALKILGK 53 (313)
T ss_pred HHHHHHHHHHHcC----CCCceEEeECCCCCCHHHHHHHHHHHHcCC
Confidence 3344455555432 234578999999999999999999888764
No 423
>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]
Probab=78.46 E-value=1.6 Score=46.92 Aligned_cols=21 Identities=33% Similarity=0.550 Sum_probs=16.8
Q ss_pred ceEEEEcCCCCChhhHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
+=-||.|-||||||+|.-.|-
T Consensus 8 PNILvtGTPG~GKstl~~~la 28 (176)
T KOG3347|consen 8 PNILVTGTPGTGKSTLAERLA 28 (176)
T ss_pred CCEEEeCCCCCCchhHHHHHH
Confidence 446999999999999765553
No 424
>PRK13975 thymidylate kinase; Provisional
Probab=78.38 E-value=1.9 Score=46.02 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=17.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.|-.|.||||+||||..-.|-.
T Consensus 3 ~~I~ieG~~GsGKtT~~~~L~~ 24 (196)
T PRK13975 3 KFIVFEGIDGSGKTTQAKLLAE 24 (196)
T ss_pred eEEEEECCCCCCHHHHHHHHHH
Confidence 3889999999999986555443
No 425
>KOG2108 consensus 3'-5' DNA helicase [Replication, recombination and repair]
Probab=78.24 E-value=1.2 Score=57.79 Aligned_cols=78 Identities=26% Similarity=0.249 Sum_probs=57.3
Q ss_pred HHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccch
Q 000592 1057 QILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQ 1136 (1402)
Q Consensus 1057 ~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~ 1136 (1402)
+.+...+|.+|..+... +.+..-+|.| ||+|||.++..=|..++....
T Consensus 8 ds~~~~l~~~q~~~~~~---------~~~~~rviag-pgsgkt~~lt~~v~yli~~~~---------------------- 55 (853)
T KOG2108|consen 8 DSLYSLLNKSQRFSALS---------PLRRKRVIAG-PGSGKTLVLTERVAYLINFNN---------------------- 55 (853)
T ss_pred HHhhhhhhhhhhhhhcC---------CCcccceeec-CCCCccchhhHHHHHHHhccC----------------------
Confidence 33445688888877542 1346889999 999999999998888877631
Q ss_pred hHHHHHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHHHHhcCCCCC
Q 000592 1137 SAAIARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSRISKEGLYGS 1197 (1402)
Q Consensus 1137 ~~~~ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~RLl~~GI~d~ 1197 (1402)
.+..-|++-+-+|.|+|++.+|+. .++.+.
T Consensus 56 ------------------------------ik~~eI~~~t~tnka~~~~~~~l~-~il~~~ 85 (853)
T KOG2108|consen 56 ------------------------------IKPDEILINTGTNKAADSIKLNLI-AILRTS 85 (853)
T ss_pred ------------------------------CCHHHHHHHhcCCccHHHHHHhHH-HHhcCC
Confidence 123456777799999999999998 455444
No 426
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=78.21 E-value=4.2 Score=49.45 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=21.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
..+++|-|+||+|||...+.++..+.
T Consensus 195 G~l~vi~g~pg~GKT~~~l~~a~~~a 220 (434)
T TIGR00665 195 SDLIILAARPSMGKTAFALNIAENAA 220 (434)
T ss_pred CeEEEEEeCCCCChHHHHHHHHHHHH
Confidence 36999999999999998888765443
No 427
>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.
Probab=78.12 E-value=2.3 Score=49.61 Aligned_cols=22 Identities=32% Similarity=0.537 Sum_probs=19.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
...+|-||+|+|||+++.+|+.
T Consensus 145 ~~ili~G~tGsGKTTll~al~~ 166 (308)
T TIGR02788 145 KNIIISGGTGSGKTTFLKSLVD 166 (308)
T ss_pred CEEEEECCCCCCHHHHHHHHHc
Confidence 6899999999999998777654
No 428
>PRK13695 putative NTPase; Provisional
Probab=77.94 E-value=2 Score=45.53 Aligned_cols=23 Identities=43% Similarity=0.674 Sum_probs=18.5
Q ss_pred EEEEcCCCCChhhHHHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.+|.|+||+|||+++..+...+.
T Consensus 3 i~ltG~~G~GKTTll~~i~~~l~ 25 (174)
T PRK13695 3 IGITGPPGVGKTTLVLKIAELLK 25 (174)
T ss_pred EEEECCCCCCHHHHHHHHHHHHH
Confidence 57889999999998887666543
No 429
>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]
Probab=77.84 E-value=0.98 Score=53.38 Aligned_cols=26 Identities=46% Similarity=0.672 Sum_probs=20.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+=.|--||||||||.||.+.-..|..
T Consensus 63 Ph~L~YgPPGtGktsti~a~a~~ly~ 88 (360)
T KOG0990|consen 63 PHLLFYGPPGTGKTSTILANARDFYS 88 (360)
T ss_pred CcccccCCCCCCCCCchhhhhhhhcC
Confidence 46788899999999999987654433
No 430
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=77.83 E-value=2.9 Score=55.28 Aligned_cols=27 Identities=30% Similarity=0.460 Sum_probs=23.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
...|+.||||||||++...|...|+..
T Consensus 38 Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~ 64 (824)
T PRK07764 38 HAYLFSGPRGCGKTSSARILARSLNCV 64 (824)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHhCcc
Confidence 467999999999999999988887753
No 431
>PHA02530 pseT polynucleotide kinase; Provisional
Probab=77.83 E-value=1.6 Score=49.79 Aligned_cols=22 Identities=27% Similarity=0.480 Sum_probs=17.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+.++-|||||||||....|..
T Consensus 3 ~liil~G~pGSGKSTla~~L~~ 24 (300)
T PHA02530 3 KIILTVGVPGSGKSTWAREFAA 24 (300)
T ss_pred EEEEEEcCCCCCHHHHHHHHHH
Confidence 3778899999999986666543
No 432
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=77.81 E-value=1.8 Score=57.24 Aligned_cols=26 Identities=23% Similarity=0.525 Sum_probs=21.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...++.||||||||+++-++...+..
T Consensus 195 ~n~lL~G~pGvGKT~l~~~la~~i~~ 220 (852)
T TIGR03346 195 NNPVLIGEPGVGKTAIVEGLAQRIVN 220 (852)
T ss_pred CceEEEcCCCCCHHHHHHHHHHHHhc
Confidence 46678899999999999888776644
No 433
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=77.78 E-value=1.7 Score=56.57 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=20.7
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.|+.||||||||+++-++...+...
T Consensus 206 ~lL~G~pG~GKT~l~~~la~~~~~~ 230 (731)
T TIGR02639 206 PLLVGEPGVGKTAIAEGLALRIAEG 230 (731)
T ss_pred eEEECCCCCCHHHHHHHHHHHHHhC
Confidence 4788999999999988887776554
No 434
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=77.78 E-value=4.1 Score=55.94 Aligned_cols=31 Identities=32% Similarity=0.427 Sum_probs=22.1
Q ss_pred HHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHH
Q 000592 1068 LQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1068 ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgL 1105 (1402)
.+.|..++.. +.+++|.|++|||||+-|-.+
T Consensus 79 r~~Il~ai~~-------~~VviI~GeTGSGKTTqlPq~ 109 (1294)
T PRK11131 79 KQDILEAIRD-------HQVVIVAGETGSGKTTQLPKI 109 (1294)
T ss_pred HHHHHHHHHh-------CCeEEEECCCCCCHHHHHHHH
Confidence 3446665543 259999999999999965433
No 435
>CHL00095 clpC Clp protease ATP binding subunit
Probab=77.76 E-value=2.9 Score=55.20 Aligned_cols=43 Identities=21% Similarity=0.463 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
.+.+.+.+...|.... ++ =.|+.||||||||.++-++...+..
T Consensus 184 r~~ei~~~~~~L~r~~---~~--n~lL~G~pGvGKTal~~~la~~i~~ 226 (821)
T CHL00095 184 REKEIERVIQILGRRT---KN--NPILIGEPGVGKTAIAEGLAQRIVN 226 (821)
T ss_pred cHHHHHHHHHHHcccc---cC--CeEEECCCCCCHHHHHHHHHHHHHh
Confidence 4666666776665532 22 2378999999999999888776654
No 436
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=77.75 E-value=6.8 Score=51.91 Aligned_cols=32 Identities=22% Similarity=0.159 Sum_probs=25.5
Q ss_pred CCCHHHHH---HHHHHHccCCCCcCCCceEEEEcCCCCChhh
Q 000592 1062 SFNESQLQ---AISVAIGLSSSWKKDCELSLIQGPPGTGKTR 1100 (1402)
Q Consensus 1062 ~lNeSQ~q---AI~sAL~~~~~~~k~~gfsLIQGPPGTGKTk 1100 (1402)
.+.+.|.+ +|..++.. ....+||.|+|||||.
T Consensus 245 e~R~~Q~~ma~~V~~~l~~-------~~~~~~eA~tGtGKT~ 279 (820)
T PRK07246 245 EERPKQESFAKLVGEDFHD-------GPASFIEAQTGIGKTY 279 (820)
T ss_pred ccCHHHHHHHHHHHHHHhC-------CCcEEEECCCCCcHHH
Confidence 56788888 77777753 2589999999999995
No 437
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=77.72 E-value=3 Score=54.69 Aligned_cols=23 Identities=35% Similarity=0.540 Sum_probs=18.6
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+..|+.||||||||.+...+-.
T Consensus 488 ~~~~Lf~GP~GvGKT~lAk~LA~ 510 (758)
T PRK11034 488 VGSFLFAGPTGVGKTEVTVQLSK 510 (758)
T ss_pred cceEEEECCCCCCHHHHHHHHHH
Confidence 35689999999999998776543
No 438
>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]
Probab=77.66 E-value=1.5 Score=50.37 Aligned_cols=21 Identities=48% Similarity=0.638 Sum_probs=16.2
Q ss_pred CceEEEEcCCCCChhhHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgL 1105 (1402)
+.=+|.-||||||||-...+.
T Consensus 189 prgvllygppg~gktml~kav 209 (408)
T KOG0727|consen 189 PRGVLLYGPPGTGKTMLAKAV 209 (408)
T ss_pred CcceEEeCCCCCcHHHHHHHH
Confidence 345789999999999865543
No 439
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=77.58 E-value=4.2 Score=52.11 Aligned_cols=26 Identities=31% Similarity=0.252 Sum_probs=22.5
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
..+|.||+|||||+++.+|...+...
T Consensus 316 pL~LyG~sGsGKTHLL~AIa~~a~~~ 341 (617)
T PRK14086 316 PLFIYGESGLGKTHLLHAIGHYARRL 341 (617)
T ss_pred cEEEECCCCCCHHHHHHHHHHHHHHh
Confidence 47999999999999999988877653
No 440
>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=77.57 E-value=1.5 Score=49.58 Aligned_cols=22 Identities=32% Similarity=0.487 Sum_probs=16.8
Q ss_pred EEcCCCCChhhHHHHHHHHHHH
Q 000592 1090 IQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1090 IQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
|-||||+||||.+.++-..+-.
T Consensus 1 ViGpaGSGKTT~~~~~~~~~~~ 22 (238)
T PF03029_consen 1 VIGPAGSGKTTFCKGLSEWLES 22 (238)
T ss_dssp -EESTTSSHHHHHHHHHHHHTT
T ss_pred CCCCCCCCHHHHHHHHHHHHHh
Confidence 4699999999988887665533
No 441
>PRK00279 adk adenylate kinase; Reviewed
Probab=77.52 E-value=1.8 Score=47.50 Aligned_cols=16 Identities=38% Similarity=0.769 Sum_probs=13.1
Q ss_pred EEEEcCCCCChhhHHH
Q 000592 1088 SLIQGPPGTGKTRTIV 1103 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIv 1103 (1402)
.+|-||||+|||+...
T Consensus 3 I~v~G~pGsGKsT~a~ 18 (215)
T PRK00279 3 LILLGPPGAGKGTQAK 18 (215)
T ss_pred EEEECCCCCCHHHHHH
Confidence 5789999999998433
No 442
>TIGR00101 ureG urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.
Probab=77.47 E-value=2 Score=47.18 Aligned_cols=23 Identities=43% Similarity=0.566 Sum_probs=18.7
Q ss_pred eEEEEcCCCCChhhHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
...|-||+|+|||+++..++..+
T Consensus 3 ~i~i~G~~GsGKTTll~~l~~~l 25 (199)
T TIGR00101 3 KIGVAGPVGSGKTALIEALTRAL 25 (199)
T ss_pred EEEEECCCCCCHHHHHHHHHHhh
Confidence 45678999999999988877643
No 443
>cd03275 ABC_SMC1_euk Eukaryotic SMC1 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for
Probab=77.42 E-value=2.1 Score=48.08 Aligned_cols=24 Identities=38% Similarity=0.591 Sum_probs=21.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
++++|-||.|+|||+++-+|..++
T Consensus 23 ~~~~i~G~NGsGKStll~ai~~~l 46 (247)
T cd03275 23 RFTCIIGPNGSGKSNLMDAISFVL 46 (247)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHh
Confidence 699999999999999888877665
No 444
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=77.40 E-value=1.6 Score=51.61 Aligned_cols=27 Identities=33% Similarity=0.556 Sum_probs=24.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.--|+.||||+|||++...+..+|+-.
T Consensus 23 ha~Lf~G~~G~GK~~~A~~~A~~llC~ 49 (328)
T PRK05707 23 HAYLLHGPAGIGKRALAERLAAALLCE 49 (328)
T ss_pred eeeeeECCCCCCHHHHHHHHHHHHcCC
Confidence 568999999999999999999999875
No 445
>cd04163 Era Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
Probab=77.37 E-value=1.7 Score=43.26 Aligned_cols=22 Identities=32% Similarity=0.525 Sum_probs=18.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
....+-||||.|||+++-.+.+
T Consensus 4 ~~i~~~G~~g~GKttl~~~l~~ 25 (168)
T cd04163 4 GFVAIVGRPNVGKSTLLNALVG 25 (168)
T ss_pred eEEEEECCCCCCHHHHHHHHhC
Confidence 4678889999999998777653
No 446
>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 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 ATPase AAA-2 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 []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....
Probab=77.32 E-value=2.4 Score=45.73 Aligned_cols=25 Identities=36% Similarity=0.553 Sum_probs=19.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
+..|+-||+|+|||.+...|-..|.
T Consensus 4 ~~~ll~GpsGvGKT~la~~la~~l~ 28 (171)
T PF07724_consen 4 SNFLLAGPSGVGKTELAKALAELLF 28 (171)
T ss_dssp EEEEEESSTTSSHHHHHHHHHHHHT
T ss_pred EEEEEECCCCCCHHHHHHHHHHHhc
Confidence 5678999999999997776655444
No 447
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=77.32 E-value=1.8 Score=51.74 Aligned_cols=23 Identities=17% Similarity=0.147 Sum_probs=19.0
Q ss_pred CCCceEEEEcCCCCChhhHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgL 1105 (1402)
....+++|-||||||||+...-+
T Consensus 124 ~~G~ItEI~G~~GsGKTql~lql 146 (344)
T PLN03187 124 ETRCITEAFGEFRSGKTQLAHTL 146 (344)
T ss_pred CCCeEEEEecCCCCChhHHHHHH
Confidence 34579999999999999976554
No 448
>cd03272 ABC_SMC3_euk Eukaryotic SMC3 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (fo
Probab=77.13 E-value=2.2 Score=47.22 Aligned_cols=24 Identities=29% Similarity=0.455 Sum_probs=20.7
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+|++|-||.|+|||+++-+|...+
T Consensus 24 ~~~~i~GpNGsGKStll~ai~~~l 47 (243)
T cd03272 24 KHNVVVGRNGSGKSNFFAAIRFVL 47 (243)
T ss_pred CcEEEECCCCCCHHHHHHHHHHHH
Confidence 699999999999999888877543
No 449
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=77.10 E-value=2.3 Score=46.52 Aligned_cols=25 Identities=28% Similarity=0.433 Sum_probs=20.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+...+-||+|+|||++|..++..+
T Consensus 22 ~~~i~~~G~~gsGKTTli~~l~~~~ 46 (207)
T TIGR00073 22 LVVLNFMSSPGSGKTTLIEKLIDNL 46 (207)
T ss_pred cEEEEEECCCCCCHHHHHHHHHHHH
Confidence 3566688999999999999988764
No 450
>TIGR01351 adk adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
Probab=77.09 E-value=1.8 Score=47.39 Aligned_cols=18 Identities=39% Similarity=0.744 Sum_probs=13.6
Q ss_pred EEEEcCCCCChhhHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgL 1105 (1402)
.+|-||||+|||+....|
T Consensus 2 I~i~G~pGsGKsT~a~~L 19 (210)
T TIGR01351 2 LVLLGPPGSGKGTQAKRI 19 (210)
T ss_pred EEEECCCCCCHHHHHHHH
Confidence 368899999999854433
No 451
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=77.07 E-value=2.4 Score=53.01 Aligned_cols=35 Identities=29% Similarity=0.394 Sum_probs=24.4
Q ss_pred HHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHH
Q 000592 1066 SQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1066 SQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.-.+|+..++.. ....+|.||||||||+++..|-+
T Consensus 199 ~~~~al~~aa~~-------g~~vlliG~pGsGKTtlar~l~~ 233 (499)
T TIGR00368 199 HAKRALEIAAAG-------GHNLLLFGPPGSGKTMLASRLQG 233 (499)
T ss_pred HHHhhhhhhccC-------CCEEEEEecCCCCHHHHHHHHhc
Confidence 335556555432 25899999999999998766543
No 452
>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]
Probab=76.92 E-value=1.7 Score=48.30 Aligned_cols=25 Identities=40% Similarity=0.571 Sum_probs=21.2
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.-|-||||+|||..|..++..|-..
T Consensus 16 i~v~Gp~GSGKTaLie~~~~~L~~~ 40 (202)
T COG0378 16 IGVGGPPGSGKTALIEKTLRALKDE 40 (202)
T ss_pred EEecCCCCcCHHHHHHHHHHHHHhh
Confidence 3456999999999999999988665
No 453
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=76.86 E-value=1.8 Score=50.89 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=18.9
Q ss_pred CCceEEEEcCCCCChhhHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
...+++|-||||||||+...-+.
T Consensus 95 ~G~iteI~G~~GsGKTql~lqla 117 (313)
T TIGR02238 95 SMSITEVFGEFRCGKTQLSHTLC 117 (313)
T ss_pred CCeEEEEECCCCCCcCHHHHHHH
Confidence 45799999999999999765543
No 454
>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]
Probab=76.81 E-value=2.5 Score=54.72 Aligned_cols=25 Identities=40% Similarity=0.662 Sum_probs=19.7
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+-.++.|+|||||+|||+.+...-+
T Consensus 429 ~~~~~vLLhG~~g~GK~t~V~~vas 453 (953)
T KOG0736|consen 429 TLNPSVLLHGPPGSGKTTVVRAVAS 453 (953)
T ss_pred ccceEEEEeCCCCCChHHHHHHHHH
Confidence 3457999999999999987665433
No 455
>CHL00095 clpC Clp protease ATP binding subunit
Probab=76.60 E-value=3.1 Score=54.93 Aligned_cols=26 Identities=35% Similarity=0.515 Sum_probs=21.2
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
+..|+.||||||||++...|...++.
T Consensus 540 ~~~lf~Gp~GvGKt~lA~~LA~~l~~ 565 (821)
T CHL00095 540 ASFLFSGPTGVGKTELTKALASYFFG 565 (821)
T ss_pred eEEEEECCCCCcHHHHHHHHHHHhcC
Confidence 45689999999999988888766653
No 456
>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.
Probab=76.50 E-value=5.5 Score=52.69 Aligned_cols=40 Identities=25% Similarity=0.111 Sum_probs=29.6
Q ss_pred HHHhhcCCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHH
Q 000592 1056 QQILKTSFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTI 1102 (1402)
Q Consensus 1056 ~~~Lk~~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTI 1102 (1402)
.+.....-.+-|.++|..++... ...++|-|.|||||-++
T Consensus 9 ~~~~G~~PtpiQ~~~i~~il~G~-------~~v~~~apTGSGKTaa~ 48 (844)
T TIGR02621 9 QGLHGYSPFPWQLSLAERFVAGQ-------PPESCSTPTGLGKTSII 48 (844)
T ss_pred HHHhCCCCCHHHHHHHHHHHcCC-------CcceEecCCCCcccHHH
Confidence 33344457789999999887432 25888999999999755
No 457
>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit. This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.
Probab=76.44 E-value=2.2 Score=52.32 Aligned_cols=22 Identities=32% Similarity=0.510 Sum_probs=17.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.-.|+.||||||||++...|-.
T Consensus 48 ~~ILLiGppG~GKT~lAraLA~ 69 (441)
T TIGR00390 48 KNILMIGPTGVGKTEIARRLAK 69 (441)
T ss_pred ceEEEECCCCCCHHHHHHHHHH
Confidence 4578999999999987666544
No 458
>PRK10646 ADP-binding protein; Provisional
Probab=76.41 E-value=4.2 Score=43.59 Aligned_cols=43 Identities=19% Similarity=0.229 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1064 NESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1064 NeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
|+.+.+++...++. +.+...+.+..|+=|+|||+.+.+++.+|
T Consensus 10 s~~~t~~l~~~la~---~l~~g~vi~L~GdLGaGKTtf~rgl~~~L 52 (153)
T PRK10646 10 DEQATLDLGARVAK---ACDGATVIYLYGDLGAGKTTFSRGFLQAL 52 (153)
T ss_pred CHHHHHHHHHHHHH---hCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence 55555555555543 23444699999999999999999998876
No 459
>cd00876 Ras Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m
Probab=75.82 E-value=2 Score=43.08 Aligned_cols=20 Identities=25% Similarity=0.519 Sum_probs=16.1
Q ss_pred EEEEcCCCCChhhHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+|-||||+|||+.+-.++.
T Consensus 2 i~i~G~~~~GKTsli~~l~~ 21 (160)
T cd00876 2 VVVLGAGGVGKSAITIQFVK 21 (160)
T ss_pred EEEECCCCCCHHHHHHHHHh
Confidence 36889999999997776654
No 460
>KOG0962 consensus DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]
Probab=75.74 E-value=1.8 Score=58.66 Aligned_cols=24 Identities=46% Similarity=0.570 Sum_probs=20.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
|+|||-||.||||||+|=.+=.+.
T Consensus 28 PlTLIvG~NG~GKTTiIEcLKyat 51 (1294)
T KOG0962|consen 28 PLTLIVGANGTGKTTIIECLKYAT 51 (1294)
T ss_pred CeeeEecCCCCCchhHHHHHHHHh
Confidence 899999999999999887765443
No 461
>cd03273 ABC_SMC2_euk Eukaryotic SMC2 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (fo
Probab=75.71 E-value=2.6 Score=47.34 Aligned_cols=25 Identities=32% Similarity=0.460 Sum_probs=21.5
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
++++.|-||-|+|||+++-+|...|
T Consensus 25 ~~~~~IvG~NGsGKStll~Ai~~ll 49 (251)
T cd03273 25 PQFNAITGLNGSGKSNILDAICFVL 49 (251)
T ss_pred CCeEEEECCCCCCHHHHHHHHHHHh
Confidence 4799999999999999888876655
No 462
>PTZ00035 Rad51 protein; Provisional
Probab=75.68 E-value=2.4 Score=50.47 Aligned_cols=25 Identities=20% Similarity=0.225 Sum_probs=20.1
Q ss_pred CCCceEEEEcCCCCChhhHHHHHHH
Q 000592 1083 KDCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1083 k~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
....++.|.||||||||+....+..
T Consensus 116 ~~G~iteI~G~~GsGKT~l~~~l~~ 140 (337)
T PTZ00035 116 ETGSITELFGEFRTGKTQLCHTLCV 140 (337)
T ss_pred CCCeEEEEECCCCCchhHHHHHHHH
Confidence 3457999999999999998765543
No 463
>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=75.66 E-value=2.9 Score=48.40 Aligned_cols=27 Identities=37% Similarity=0.613 Sum_probs=22.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.+.=|.||||.||+++|-.++..+...
T Consensus 30 ~~iGiTG~PGaGKSTli~~l~~~~~~~ 56 (266)
T PF03308_consen 30 HVIGITGPPGAGKSTLIDALIRELRER 56 (266)
T ss_dssp EEEEEEE-TTSSHHHHHHHHHHHHHHT
T ss_pred eEEEeeCCCCCcHHHHHHHHHHHHhhc
Confidence 456689999999999999999988765
No 464
>PRK06761 hypothetical protein; Provisional
Probab=75.64 E-value=2.2 Score=49.72 Aligned_cols=24 Identities=38% Similarity=0.596 Sum_probs=19.9
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+.+|-||||+||||++..+...+
T Consensus 4 ~lIvI~G~~GsGKTTla~~L~~~L 27 (282)
T PRK06761 4 KLIIIEGLPGFGKSTTAKMLNDIL 27 (282)
T ss_pred cEEEEECCCCCCHHHHHHHHHHhc
Confidence 488999999999999877766554
No 465
>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=75.55 E-value=2.3 Score=52.69 Aligned_cols=19 Identities=47% Similarity=0.737 Sum_probs=15.6
Q ss_pred EEEEcCCCCChhhHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLV 1106 (1402)
-|+-||||||||-++..|-
T Consensus 201 Ll~~GpPGtGKTmla~Rl~ 219 (490)
T COG0606 201 LLLVGPPGTGKTMLASRLP 219 (490)
T ss_pred EEEecCCCCchHHhhhhhc
Confidence 5777999999999877663
No 466
>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=75.51 E-value=6.2 Score=51.76 Aligned_cols=26 Identities=27% Similarity=0.454 Sum_probs=22.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSALL 1110 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaLL 1110 (1402)
.++.++-||.|+|||||+..|.+.+.
T Consensus 185 g~Vi~lVGpnGvGKTTTiaKLA~~~~ 210 (767)
T PRK14723 185 GGVLALVGPTGVGKTTTTAKLAARCV 210 (767)
T ss_pred CeEEEEECCCCCcHHHHHHHHHhhHH
Confidence 46999999999999999999887664
No 467
>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.
Probab=75.44 E-value=2.6 Score=45.00 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=22.1
Q ss_pred eEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
+.-|-|++|+|||+++..|+..|-..
T Consensus 3 vi~i~G~~gsGKTTli~~L~~~l~~~ 28 (159)
T cd03116 3 VIGFVGYSGSGKTTLLEKLIPALSAR 28 (159)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence 67789999999999999999876543
No 468
>PRK14737 gmk guanylate kinase; Provisional
Probab=75.37 E-value=2.5 Score=46.00 Aligned_cols=23 Identities=30% Similarity=0.449 Sum_probs=18.8
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
..+.+|-||+|+|||+++-.|+.
T Consensus 4 ~~~ivl~GpsG~GK~tl~~~l~~ 26 (186)
T PRK14737 4 PKLFIISSVAGGGKSTIIQALLE 26 (186)
T ss_pred CeEEEEECCCCCCHHHHHHHHHh
Confidence 35889999999999997666654
No 469
>PRK09825 idnK D-gluconate kinase; Provisional
Probab=75.36 E-value=2.7 Score=45.36 Aligned_cols=22 Identities=27% Similarity=0.385 Sum_probs=17.6
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+..|.||+|+|||++...|..
T Consensus 4 e~i~l~G~sGsGKSTl~~~la~ 25 (176)
T PRK09825 4 ESYILMGVSGSGKSLIGSKIAA 25 (176)
T ss_pred cEEEEECCCCCCHHHHHHHHHH
Confidence 5889999999999986655444
No 470
>KOG0979 consensus Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=75.28 E-value=2.2 Score=56.27 Aligned_cols=28 Identities=36% Similarity=0.573 Sum_probs=24.0
Q ss_pred cCCCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1082 KKDCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1082 ~k~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
...+.+-+|-||.||||++.++||+-+|
T Consensus 39 ~pgpsLNmIiGpNGSGKSSiVcAIcLgl 66 (1072)
T KOG0979|consen 39 LPGPSLNMIIGPNGSGKSSIVCAICLGL 66 (1072)
T ss_pred cCCCceeeEECCCCCCchHHHHHHHHHc
Confidence 3456799999999999999999998765
No 471
>PRK13949 shikimate kinase; Provisional
Probab=75.27 E-value=2.2 Score=45.68 Aligned_cols=16 Identities=31% Similarity=0.301 Sum_probs=12.7
Q ss_pred EEEEcCCCCChhhHHH
Q 000592 1088 SLIQGPPGTGKTRTIV 1103 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIv 1103 (1402)
.+|-||||+|||++..
T Consensus 4 I~liG~~GsGKstl~~ 19 (169)
T PRK13949 4 IFLVGYMGAGKTTLGK 19 (169)
T ss_pred EEEECCCCCCHHHHHH
Confidence 4667999999998544
No 472
>TIGR02688 conserved hypothetical protein TIGR02688. Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.
Probab=75.27 E-value=2.5 Score=52.03 Aligned_cols=21 Identities=29% Similarity=0.395 Sum_probs=17.0
Q ss_pred EEEEcCCCCChhhHHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsa 1108 (1402)
.++-||||||||++..++-..
T Consensus 212 li~lGp~GTGKThla~~l~~~ 232 (449)
T TIGR02688 212 LIELGPKGTGKSYIYNNLSPY 232 (449)
T ss_pred EEEECCCCCCHHHHHHHHhHH
Confidence 456699999999999886554
No 473
>smart00173 RAS Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades
Probab=75.24 E-value=2.3 Score=43.30 Aligned_cols=19 Identities=26% Similarity=0.555 Sum_probs=16.0
Q ss_pred EEEcCCCCChhhHHHHHHH
Q 000592 1089 LIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1089 LIQGPPGTGKTkTIvgLVs 1107 (1402)
+|-||||+|||+++..++.
T Consensus 4 ~v~G~~~~GKTsli~~~~~ 22 (164)
T smart00173 4 VVLGSGGVGKSALTIQFVQ 22 (164)
T ss_pred EEECCCCCCHHHHHHHHHh
Confidence 4569999999998888764
No 474
>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid [].; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.
Probab=75.16 E-value=2.1 Score=48.43 Aligned_cols=21 Identities=48% Similarity=0.778 Sum_probs=16.5
Q ss_pred ceEEEEcCCCCChhhHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
.+.+|.||+|||||.+.+.+-
T Consensus 2 ~v~~i~GpT~tGKt~~ai~lA 22 (233)
T PF01745_consen 2 KVYLIVGPTGTGKTALAIALA 22 (233)
T ss_dssp EEEEEE-STTSSHHHHHHHHH
T ss_pred cEEEEECCCCCChhHHHHHHH
Confidence 478999999999999766653
No 475
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=75.00 E-value=3.8 Score=53.37 Aligned_cols=24 Identities=38% Similarity=0.534 Sum_probs=19.1
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+..|+.||||||||.+...|-..+
T Consensus 485 ~~~lf~Gp~GvGKT~lA~~la~~l 508 (731)
T TIGR02639 485 GSFLFTGPTGVGKTELAKQLAEAL 508 (731)
T ss_pred eeEEEECCCCccHHHHHHHHHHHh
Confidence 457999999999998877765544
No 476
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=74.97 E-value=5 Score=43.01 Aligned_cols=46 Identities=24% Similarity=0.297 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1063 FNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1063 lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
-|+.+..++...++.. .+...+.+++|+=|.|||+...||+.+|-.
T Consensus 6 ~~~~~t~~lg~~l~~~---l~~g~Vv~L~GdLGAGKTtf~rgi~~~Lg~ 51 (149)
T COG0802 6 PDEEATLALGERLAEA---LKAGDVVLLSGDLGAGKTTLVRGIAKGLGV 51 (149)
T ss_pred CCHHHHHHHHHHHHhh---CCCCCEEEEEcCCcCChHHHHHHHHHHcCC
Confidence 3555666666555542 345589999999999999999999988764
No 477
>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]
Probab=74.90 E-value=2.1 Score=49.38 Aligned_cols=22 Identities=45% Similarity=0.542 Sum_probs=16.6
Q ss_pred CCceEEEEcCCCCChhhHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAI 1105 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgL 1105 (1402)
.+.=+|.-||||||||-...+.
T Consensus 204 pPKGvLmYGPPGTGKTlmARAc 225 (424)
T KOG0652|consen 204 PPKGVLMYGPPGTGKTLMARAC 225 (424)
T ss_pred CCCceEeeCCCCCcHHHHHHHH
Confidence 3456799999999999755443
No 478
>KOG1533 consensus Predicted GTPase [General function prediction only]
Probab=74.89 E-value=1.9 Score=49.31 Aligned_cols=25 Identities=32% Similarity=0.658 Sum_probs=19.5
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHhc
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLATR 1113 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~~ 1113 (1402)
.+|-||||+||||-..|+ +.+++..
T Consensus 5 qvVIGPPgSGKsTYc~g~-~~fls~~ 29 (290)
T KOG1533|consen 5 QVVIGPPGSGKSTYCNGM-SQFLSAI 29 (290)
T ss_pred eEEEcCCCCCccchhhhH-HHHHHHh
Confidence 478899999999887776 5566654
No 479
>PRK12339 2-phosphoglycerate kinase; Provisional
Probab=74.85 E-value=2.5 Score=46.57 Aligned_cols=22 Identities=36% Similarity=0.513 Sum_probs=17.5
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+.+|-|+||+|||+....+..
T Consensus 4 ~~i~i~G~~G~GKst~a~~l~~ 25 (197)
T PRK12339 4 TIHFIGGIPGVGKTSISGYIAR 25 (197)
T ss_pred eEEEEECCCCCCHHHHHHHHHH
Confidence 4889999999999986555443
No 480
>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.
Probab=74.75 E-value=2.9 Score=45.88 Aligned_cols=26 Identities=46% Similarity=0.577 Sum_probs=20.9
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
++++|.||.|+|||+++-+|-.++..
T Consensus 23 g~~~i~G~NGsGKTTLl~ai~~~l~G 48 (204)
T cd03240 23 PLTLIVGQNGAGKTTIIEALKYALTG 48 (204)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHcC
Confidence 69999999999999988766555433
No 481
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=74.73 E-value=3.1 Score=49.06 Aligned_cols=29 Identities=28% Similarity=0.392 Sum_probs=25.2
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-+..-|+.||||+|||+++..+..+++..
T Consensus 27 l~ha~Lf~G~~G~gk~~~a~~la~~l~c~ 55 (329)
T PRK08058 27 LSHAYLFEGAKGTGKKATALWLAKSLFCL 55 (329)
T ss_pred CCceEEEECCCCCCHHHHHHHHHHHHCCC
Confidence 34678999999999999999998888765
No 482
>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed
Probab=74.72 E-value=3 Score=46.42 Aligned_cols=26 Identities=31% Similarity=0.478 Sum_probs=20.7
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
..-+..|-||+|+||||++-.|...+
T Consensus 32 ~~~iigi~G~~GsGKTTl~~~L~~~l 57 (229)
T PRK09270 32 RRTIVGIAGPPGAGKSTLAEFLEALL 57 (229)
T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence 34688899999999999877766544
No 483
>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase. Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.
Probab=74.72 E-value=3.8 Score=48.86 Aligned_cols=39 Identities=23% Similarity=0.365 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCCCChhhHHHHHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.+++.+.+.+..++.. .+-.+|-||+|+|||+++.+++.
T Consensus 162 ~~~~~~~~~L~~~v~~-------~~~ili~G~tGsGKTTll~al~~ 200 (340)
T TIGR03819 162 TFPPGVARLLRAIVAA-------RLAFLISGGTGSGKTTLLSALLA 200 (340)
T ss_pred CCCHHHHHHHHHHHhC-------CCeEEEECCCCCCHHHHHHHHHc
Confidence 4667777777766543 36899999999999998777654
No 484
>cd01918 HprK_C HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.
Probab=74.69 E-value=2.5 Score=45.15 Aligned_cols=22 Identities=32% Similarity=0.575 Sum_probs=18.4
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
.=.||.||+|.|||++...++.
T Consensus 15 ~gvLi~G~sG~GKStlal~L~~ 36 (149)
T cd01918 15 IGVLITGPSGIGKSELALELIK 36 (149)
T ss_pred EEEEEEcCCCCCHHHHHHHHHH
Confidence 3579999999999998877665
No 485
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=74.34 E-value=7.6 Score=54.58 Aligned_cols=65 Identities=18% Similarity=0.192 Sum_probs=51.0
Q ss_pred CCCHHHHHHHHHHHccCCCCcCCCceEEEEcCCC-CChhhHHHHHHHHHHHhcCCCCcccccCcccccCCCCccchhHHH
Q 000592 1062 SFNESQLQAISVAIGLSSSWKKDCELSLIQGPPG-TGKTRTIVAIVSALLATRTSPKSHLKQNYSSCINSRPKIGQSAAI 1140 (1402)
Q Consensus 1062 ~lNeSQ~qAI~sAL~~~~~~~k~~gfsLIQGPPG-TGKTkTIvgLVsaLL~~~~~~~s~~~p~~Ss~~~~rp~~s~~~~~ 1140 (1402)
.+|..|..|+...+... +.|.+|+|+-| ||||+++..++..+ ..
T Consensus 281 ~~~~~q~~Av~~il~dr------~~v~iv~~~GgAtGKtt~l~~l~~~a-~~---------------------------- 325 (1623)
T PRK14712 281 PRTAGYSDAVSVLAQDR------PSLAIVSGQGGAAGQRERVAELVMMA-RE---------------------------- 325 (1623)
T ss_pred ccchhHHHHHHHHhcCC------CceEEEEecccccccHHHHHHHHHHH-Hh----------------------------
Confidence 46889999999988543 47999999888 89999888665432 11
Q ss_pred HHHHHHHHHHhhhccccccccccccccCCCeEEEEeCchHHHHHHHHH
Q 000592 1141 ARAWQDAALARQINEDSERDKKSSESSVRARVLICAQSNAAVDELVSR 1188 (1402)
Q Consensus 1141 ar~W~d~a~arq~~~d~~~~~~~~~~~~k~RILVCAPSNAAVDEIV~R 1188 (1402)
.+.+|-+-||++.|+..+...
T Consensus 326 ---------------------------~G~~V~~lApt~~a~~~L~e~ 346 (1623)
T PRK14712 326 ---------------------------QGREVQIIAADRRSQMNLKQD 346 (1623)
T ss_pred ---------------------------CCcEEEEEeCCHHHHHHHHhc
Confidence 368999999999999988654
No 486
>PTZ00301 uridine kinase; Provisional
Probab=74.33 E-value=3 Score=46.47 Aligned_cols=27 Identities=37% Similarity=0.511 Sum_probs=22.3
Q ss_pred ceEEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
-+..|-||||+||||....|+..|...
T Consensus 4 ~iIgIaG~SgSGKTTla~~l~~~l~~~ 30 (210)
T PTZ00301 4 TVIGISGASGSGKSSLSTNIVSELMAH 30 (210)
T ss_pred EEEEEECCCcCCHHHHHHHHHHHHHhh
Confidence 478899999999999888887777643
No 487
>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
Probab=74.30 E-value=3 Score=43.90 Aligned_cols=23 Identities=30% Similarity=0.485 Sum_probs=18.6
Q ss_pred eEEEEcCCCCChhhHHHHHHHHH
Q 000592 1087 LSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1087 fsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
|..|-||+|+||||.+-.|...+
T Consensus 2 ~I~ieG~~GsGKtT~~~~L~~~l 24 (200)
T cd01672 2 FIVFEGIDGAGKTTLIELLAERL 24 (200)
T ss_pred EEEEECCCCCCHHHHHHHHHHHH
Confidence 56788999999999777766655
No 488
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=74.24 E-value=2.9 Score=49.19 Aligned_cols=25 Identities=28% Similarity=0.418 Sum_probs=19.3
Q ss_pred CceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
+-+.||+||+|+|||++...|...|
T Consensus 92 p~iIlI~G~sgsGKStlA~~La~~l 116 (301)
T PRK04220 92 PIIILIGGASGVGTSTIAFELASRL 116 (301)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHh
Confidence 4588999999999999666655433
No 489
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=74.16 E-value=6.3 Score=47.86 Aligned_cols=26 Identities=27% Similarity=0.418 Sum_probs=21.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
...+++|-|+||+|||...+.+...+
T Consensus 193 ~g~liviag~pg~GKT~~al~ia~~~ 218 (421)
T TIGR03600 193 KGDLIVIGARPSMGKTTLALNIAENV 218 (421)
T ss_pred CCceEEEEeCCCCCHHHHHHHHHHHH
Confidence 34699999999999999988886443
No 490
>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural
Probab=74.16 E-value=2.7 Score=42.53 Aligned_cols=22 Identities=32% Similarity=0.433 Sum_probs=18.6
Q ss_pred CceEEEEcCCCCChhhHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLV 1106 (1402)
..+..|-||.|+|||+++..+.
T Consensus 15 ge~v~I~GpSGsGKSTLl~~l~ 36 (107)
T cd00820 15 KVGVLITGDSGIGKTELALELI 36 (107)
T ss_pred CEEEEEEcCCCCCHHHHHHHhh
Confidence 3689999999999999877654
No 491
>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.
Probab=74.05 E-value=2.5 Score=46.00 Aligned_cols=23 Identities=30% Similarity=0.524 Sum_probs=18.7
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
..++.|-||.|+||||++-.|.+
T Consensus 30 G~~~~l~G~nGsGKSTLl~~i~G 52 (218)
T cd03255 30 GEFVAIVGPSGSGKSTLLNILGG 52 (218)
T ss_pred CCEEEEEcCCCCCHHHHHHHHhC
Confidence 36999999999999986666544
No 492
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=73.97 E-value=2.3 Score=54.69 Aligned_cols=20 Identities=55% Similarity=0.802 Sum_probs=17.5
Q ss_pred EEEEcCCCCChhhHHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVs 1107 (1402)
.||.||||||||+++.++..
T Consensus 188 ill~G~~G~GKt~~~~~~a~ 207 (644)
T PRK10733 188 VLMVGPPGTGKTLLAKAIAG 207 (644)
T ss_pred EEEECCCCCCHHHHHHHHHH
Confidence 89999999999998777654
No 493
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=73.96 E-value=2.5 Score=55.40 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=20.8
Q ss_pred EEEEcCCCCChhhHHHHHHHHHHHh
Q 000592 1088 SLIQGPPGTGKTRTIVAIVSALLAT 1112 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLVsaLL~~ 1112 (1402)
.|+.||||||||.++-++...+...
T Consensus 210 ~LLvGppGvGKT~lae~la~~i~~~ 234 (758)
T PRK11034 210 PLLVGESGVGKTAIAEGLAWRIVQG 234 (758)
T ss_pred eEEECCCCCCHHHHHHHHHHHHHhc
Confidence 4789999999999988887766554
No 494
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=73.83 E-value=35 Score=43.44 Aligned_cols=23 Identities=30% Similarity=0.475 Sum_probs=19.3
Q ss_pred CceEEEEcCCCCChhhHHHHHHH
Q 000592 1085 CELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1085 ~gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
+|+++|.||.|+|||.++-+|-.
T Consensus 22 ~g~~vitG~nGaGKS~ll~al~~ 44 (563)
T TIGR00634 22 RGLTVLTGETGAGKSMIIDALSL 44 (563)
T ss_pred CCeEEEECCCCCCHHHHHHHHHH
Confidence 48999999999999987766544
No 495
>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=73.79 E-value=2.3 Score=48.26 Aligned_cols=27 Identities=30% Similarity=0.578 Sum_probs=20.7
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSALLA 1111 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaLL~ 1111 (1402)
...|+-|.||-|+|||| .+.+++.|..
T Consensus 30 ~Ge~vaI~GpSGSGKST-LLniig~ld~ 56 (226)
T COG1136 30 AGEFVAIVGPSGSGKST-LLNLLGGLDK 56 (226)
T ss_pred CCCEEEEECCCCCCHHH-HHHHHhcccC
Confidence 34799999999999996 5566665544
No 496
>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....
Probab=73.68 E-value=2.6 Score=41.28 Aligned_cols=19 Identities=37% Similarity=0.534 Sum_probs=15.8
Q ss_pred EEEEcCCCCChhhHHHHHH
Q 000592 1088 SLIQGPPGTGKTRTIVAIV 1106 (1402)
Q Consensus 1088 sLIQGPPGTGKTkTIvgLV 1106 (1402)
.+|-|+||+|||+.|-+|+
T Consensus 2 V~iiG~~~~GKSTlin~l~ 20 (116)
T PF01926_consen 2 VAIIGRPNVGKSTLINALT 20 (116)
T ss_dssp EEEEESTTSSHHHHHHHHH
T ss_pred EEEECCCCCCHHHHHHHHh
Confidence 3677999999999877765
No 497
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=73.65 E-value=3.9 Score=44.00 Aligned_cols=16 Identities=44% Similarity=0.488 Sum_probs=13.6
Q ss_pred ceEEEEcCCCCChhhH
Q 000592 1086 ELSLIQGPPGTGKTRT 1101 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkT 1101 (1402)
.-.||+|++||||+..
T Consensus 23 ~pVlI~GE~GtGK~~l 38 (168)
T PF00158_consen 23 LPVLITGETGTGKELL 38 (168)
T ss_dssp S-EEEECSTTSSHHHH
T ss_pred CCEEEEcCCCCcHHHH
Confidence 5789999999999984
No 498
>cd04155 Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.
Probab=73.55 E-value=2.4 Score=43.75 Aligned_cols=22 Identities=32% Similarity=0.365 Sum_probs=18.0
Q ss_pred ceEEEEcCCCCChhhHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVS 1107 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVs 1107 (1402)
--.+|-||||+|||+.+..+.+
T Consensus 15 ~~v~i~G~~g~GKStLl~~l~~ 36 (173)
T cd04155 15 PRILILGLDNAGKTTILKQLAS 36 (173)
T ss_pred cEEEEEccCCCCHHHHHHHHhc
Confidence 3488899999999998777654
No 499
>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w
Probab=73.54 E-value=3.2 Score=45.44 Aligned_cols=23 Identities=43% Similarity=0.590 Sum_probs=19.4
Q ss_pred ceEEEEcCCCCChhhHHHHHHHH
Q 000592 1086 ELSLIQGPPGTGKTRTIVAIVSA 1108 (1402)
Q Consensus 1086 gfsLIQGPPGTGKTkTIvgLVsa 1108 (1402)
|+++|.||-|+|||+++-+|.+.
T Consensus 23 g~~~i~G~nGsGKStll~al~~l 45 (197)
T cd03278 23 GLTAIVGPNGSGKSNIIDAIRWV 45 (197)
T ss_pred CcEEEECCCCCCHHHHHHHHHHH
Confidence 59999999999999988776443
No 500
>PRK12337 2-phosphoglycerate kinase; Provisional
Probab=73.50 E-value=2.7 Score=52.13 Aligned_cols=26 Identities=31% Similarity=0.293 Sum_probs=21.5
Q ss_pred CCceEEEEcCCCCChhhHHHHHHHHH
Q 000592 1084 DCELSLIQGPPGTGKTRTIVAIVSAL 1109 (1402)
Q Consensus 1084 ~~gfsLIQGPPGTGKTkTIvgLVsaL 1109 (1402)
.+.+.+|-|+||+|||+++..|-..+
T Consensus 254 ~p~vil~~G~~G~GKSt~a~~LA~~l 279 (475)
T PRK12337 254 RPLHVLIGGVSGVGKSVLASALAYRL 279 (475)
T ss_pred CCeEEEEECCCCCCHHHHHHHHHHHc
Confidence 35799999999999999988776543
Done!