Query psy3868
Match_columns 69
No_of_seqs 130 out of 1071
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 19:28:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3868.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3868hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0733|consensus 99.9 1.7E-23 3.6E-28 147.5 6.3 66 3-68 559-624 (802)
2 COG1222 RPT1 ATP-dependent 26S 99.9 1.7E-22 3.7E-27 135.6 6.1 66 3-68 199-264 (406)
3 KOG0739|consensus 99.9 2.9E-22 6.3E-27 133.1 6.4 66 3-68 180-245 (439)
4 KOG0738|consensus 99.9 3.6E-22 7.9E-27 135.4 5.8 65 3-67 259-323 (491)
5 KOG0736|consensus 99.9 4.5E-22 9.7E-27 142.6 6.2 65 3-67 719-783 (953)
6 KOG0733|consensus 99.8 1.3E-21 2.8E-26 138.0 5.5 65 3-67 237-301 (802)
7 KOG0730|consensus 99.8 1.6E-21 3.4E-26 137.7 5.6 65 3-67 482-546 (693)
8 PLN00020 ribulose bisphosphate 99.8 8.5E-20 1.8E-24 123.5 7.1 65 3-67 162-231 (413)
9 KOG0734|consensus 99.8 1.1E-19 2.3E-24 127.3 5.1 66 3-68 351-416 (752)
10 COG0464 SpoVK ATPases of the A 99.8 5.2E-19 1.1E-23 121.7 6.8 65 3-67 290-354 (494)
11 KOG0740|consensus 99.7 3.2E-18 7E-23 117.0 6.1 65 3-67 200-264 (428)
12 KOG0735|consensus 99.7 6.1E-18 1.3E-22 121.1 6.3 66 3-68 715-780 (952)
13 COG1223 Predicted ATPase (AAA+ 99.7 4.8E-18 1E-22 111.5 5.2 63 3-65 165-227 (368)
14 KOG0727|consensus 99.7 4.6E-18 9.9E-23 111.7 4.6 66 3-68 203-268 (408)
15 KOG0728|consensus 99.7 1.1E-17 2.3E-22 109.8 6.2 65 3-67 195-259 (404)
16 COG0465 HflB ATP-dependent Zn 99.7 7.7E-18 1.7E-22 118.7 4.9 65 2-66 196-260 (596)
17 KOG0726|consensus 99.7 1.3E-17 2.7E-22 111.0 3.8 66 3-68 233-298 (440)
18 KOG0737|consensus 99.7 1.3E-17 2.9E-22 112.1 3.7 64 3-66 141-204 (386)
19 KOG0731|consensus 99.7 6E-17 1.3E-21 116.4 5.5 63 3-65 358-420 (774)
20 TIGR01243 CDC48 AAA family ATP 99.7 1.6E-16 3.4E-21 113.9 7.3 64 3-66 501-564 (733)
21 CHL00195 ycf46 Ycf46; Provisio 99.7 2.6E-16 5.6E-21 109.3 7.0 63 3-65 273-335 (489)
22 KOG0729|consensus 99.6 3.9E-16 8.5E-21 103.2 5.1 64 3-66 225-288 (435)
23 KOG0652|consensus 99.6 3.3E-16 7.1E-21 103.3 4.2 66 3-68 219-284 (424)
24 KOG0651|consensus 99.6 8.3E-16 1.8E-20 102.5 6.0 64 3-66 180-243 (388)
25 KOG0730|consensus 99.6 9.6E-16 2.1E-20 108.7 5.7 67 2-68 231-298 (693)
26 PTZ00454 26S protease regulato 99.6 1.4E-14 3.1E-19 98.6 7.0 64 3-66 193-256 (398)
27 PRK03992 proteasome-activating 99.5 1.9E-14 4E-19 97.5 7.1 64 3-66 179-242 (389)
28 TIGR01241 FtsH_fam ATP-depende 99.5 9.8E-15 2.1E-19 101.0 5.9 64 3-66 102-165 (495)
29 CHL00206 ycf2 Ycf2; Provisiona 99.5 2.9E-14 6.2E-19 109.5 6.7 63 3-65 1644-1749(2281)
30 PTZ00361 26 proteosome regulat 99.5 4.2E-14 9.1E-19 97.3 5.6 64 3-66 231-294 (438)
31 PF00004 AAA: ATPase family as 99.5 1.7E-13 3.7E-18 78.7 7.3 62 3-64 12-74 (132)
32 CHL00176 ftsH cell division pr 99.5 1.1E-13 2.4E-18 98.6 6.2 64 3-66 230-293 (638)
33 KOG0741|consensus 99.4 1.5E-13 3.3E-18 96.7 4.6 65 3-67 270-343 (744)
34 PRK10733 hflB ATP-dependent me 99.4 4.3E-13 9.4E-18 95.6 6.4 64 3-66 199-262 (644)
35 TIGR03689 pup_AAA proteasome A 99.4 6E-13 1.3E-17 93.1 6.1 64 3-66 230-307 (512)
36 TIGR01243 CDC48 AAA family ATP 99.4 1.1E-12 2.4E-17 94.3 7.2 64 3-66 226-289 (733)
37 TIGR01242 26Sp45 26S proteasom 99.4 1.6E-12 3.4E-17 87.1 6.3 64 3-66 170-233 (364)
38 KOG0732|consensus 99.3 9.9E-13 2.2E-17 97.3 4.5 64 3-66 313-381 (1080)
39 TIGR02639 ClpA ATP-dependent C 99.1 3.6E-10 7.8E-15 81.6 7.0 62 3-64 217-290 (731)
40 KOG0744|consensus 99.0 1.8E-10 3.8E-15 77.7 3.8 64 3-66 191-268 (423)
41 CHL00095 clpC Clp protease ATP 98.9 3.9E-09 8.5E-14 77.1 7.3 63 3-65 214-288 (821)
42 TIGR02881 spore_V_K stage V sp 98.9 4E-09 8.7E-14 67.9 5.8 57 3-62 56-119 (261)
43 CHL00181 cbbX CbbX; Provisiona 98.9 4.4E-09 9.5E-14 69.1 5.3 59 3-64 73-138 (287)
44 TIGR02880 cbbX_cfxQ probable R 98.8 7.4E-09 1.6E-13 67.9 5.5 59 3-64 72-137 (284)
45 PRK10865 protein disaggregatio 98.8 3.3E-08 7.1E-13 72.8 7.0 63 3-65 213-288 (857)
46 COG1219 ClpX ATP-dependent pro 98.7 3.7E-08 7.9E-13 66.6 5.8 66 3-68 111-182 (408)
47 COG2256 MGS1 ATPase related to 98.7 2.3E-08 4.9E-13 68.7 4.8 57 3-66 62-122 (436)
48 PRK11034 clpA ATP-dependent Cl 98.7 5.5E-08 1.2E-12 71.0 6.6 63 3-65 221-295 (758)
49 PRK05342 clpX ATP-dependent pr 98.7 8.3E-08 1.8E-12 66.0 6.2 63 3-65 122-190 (412)
50 TIGR03346 chaperone_ClpB ATP-d 98.6 1.1E-07 2.3E-12 70.0 6.9 62 3-64 208-282 (852)
51 TIGR00382 clpX endopeptidase C 98.6 9.9E-08 2.1E-12 65.7 5.7 64 3-66 130-199 (413)
52 COG0464 SpoVK ATPases of the A 98.6 7.6E-08 1.7E-12 66.7 5.1 64 2-66 31-94 (494)
53 KOG0736|consensus 98.6 1.6E-07 3.5E-12 68.8 6.5 65 3-67 445-509 (953)
54 KOG0742|consensus 98.6 8.4E-08 1.8E-12 66.9 4.0 66 3-69 398-464 (630)
55 TIGR00763 lon ATP-dependent pr 98.5 1.2E-07 2.7E-12 69.0 5.0 61 3-64 361-430 (775)
56 TIGR03345 VI_ClpV1 type VI sec 98.5 2.8E-07 6E-12 68.0 6.8 63 3-65 222-297 (852)
57 KOG0745|consensus 98.5 2.6E-07 5.7E-12 64.5 5.7 63 3-65 240-308 (564)
58 PF05496 RuvB_N: Holliday junc 98.5 1.1E-07 2.3E-12 61.3 2.5 54 3-64 64-117 (233)
59 KOG2028|consensus 98.4 5.6E-07 1.2E-11 62.2 4.9 57 3-66 176-240 (554)
60 COG2255 RuvB Holliday junction 98.2 1.7E-06 3.7E-11 57.7 3.7 53 3-63 66-118 (332)
61 smart00382 AAA ATPases associa 98.0 1.4E-05 3.1E-10 44.7 4.9 62 3-64 16-94 (148)
62 KOG0735|consensus 98.0 1.5E-05 3.2E-10 58.6 5.7 61 3-63 445-509 (952)
63 COG0542 clpA ATP-binding subun 98.0 2.8E-05 6.2E-10 57.2 7.2 52 14-65 226-279 (786)
64 TIGR00390 hslU ATP-dependent p 97.8 1.2E-05 2.7E-10 55.9 2.4 57 3-66 61-119 (441)
65 PRK13342 recombination factor 97.8 6.6E-05 1.4E-09 51.4 5.7 53 3-62 50-106 (413)
66 PRK10787 DNA-binding ATP-depen 97.8 3.8E-05 8.3E-10 56.5 4.6 61 3-64 363-432 (784)
67 cd00009 AAA The AAA+ (ATPases 97.7 0.00018 4E-09 40.6 5.3 58 3-60 33-96 (151)
68 PRK00080 ruvB Holliday junctio 97.6 0.00019 4.1E-09 47.7 4.9 52 3-62 65-116 (328)
69 PRK11034 clpA ATP-dependent Cl 97.5 7.5E-05 1.6E-09 54.9 3.2 60 3-62 502-571 (758)
70 PRK04195 replication factor C 97.5 0.00034 7.4E-09 48.8 5.9 54 3-62 53-112 (482)
71 PRK04132 replication factor C 97.5 0.00032 7E-09 52.2 5.9 54 3-62 580-644 (846)
72 KOG0741|consensus 97.5 0.00034 7.3E-09 50.5 5.4 57 3-61 552-611 (744)
73 PRK05201 hslU ATP-dependent pr 97.4 0.00017 3.8E-09 50.3 3.7 47 3-49 64-112 (443)
74 KOG1969|consensus 97.4 0.00042 9E-09 51.2 5.4 52 3-60 340-399 (877)
75 PRK00149 dnaA chromosomal repl 97.4 0.00031 6.7E-09 48.6 4.6 60 3-64 162-227 (450)
76 KOG2004|consensus 97.3 0.00035 7.5E-09 51.7 4.4 59 3-62 452-519 (906)
77 PF07724 AAA_2: AAA domain (Cd 97.3 0.00056 1.2E-08 42.0 4.7 59 3-63 17-83 (171)
78 TIGR02639 ClpA ATP-dependent C 97.3 0.00059 1.3E-08 49.9 5.5 58 3-62 498-567 (731)
79 TIGR00362 DnaA chromosomal rep 97.3 0.00043 9.4E-09 47.1 4.4 60 3-64 150-215 (405)
80 TIGR00635 ruvB Holliday juncti 97.3 0.00052 1.1E-08 44.7 4.6 53 3-63 44-96 (305)
81 COG0466 Lon ATP-dependent Lon 97.2 0.00076 1.6E-08 49.7 5.0 60 3-63 364-432 (782)
82 TIGR02640 gas_vesic_GvpN gas v 97.2 0.0014 3.1E-08 42.4 5.9 58 3-61 35-118 (262)
83 PRK13341 recombination factor 97.2 0.00097 2.1E-08 49.0 5.5 54 3-63 66-124 (725)
84 PRK14088 dnaA chromosomal repl 97.2 0.00086 1.9E-08 46.5 4.7 61 3-64 144-210 (440)
85 TIGR01650 PD_CobS cobaltochela 97.1 0.00031 6.8E-09 47.4 2.3 59 3-62 78-148 (327)
86 PRK00411 cdc6 cell division co 97.1 0.0018 3.9E-08 43.5 5.8 59 3-61 69-151 (394)
87 PRK14086 dnaA chromosomal repl 97.0 0.0018 3.9E-08 47.0 4.9 61 3-64 328-393 (617)
88 PHA02544 44 clamp loader, smal 96.9 0.0028 6.1E-08 41.5 5.2 56 3-61 57-113 (316)
89 TIGR03345 VI_ClpV1 type VI sec 96.8 0.0028 6.1E-08 47.3 5.0 58 3-62 610-682 (852)
90 PF13173 AAA_14: AAA domain 96.7 0.0042 9E-08 36.0 4.4 57 3-61 16-74 (128)
91 TIGR02928 orc1/cdc6 family rep 96.7 0.0059 1.3E-07 40.6 5.6 60 3-62 54-143 (365)
92 PRK07952 DNA replication prote 96.5 0.0063 1.4E-07 39.5 4.5 57 3-61 113-175 (244)
93 PRK14956 DNA polymerase III su 96.5 0.0091 2E-07 42.3 5.5 54 3-62 54-135 (484)
94 PRK12422 chromosomal replicati 96.5 0.0068 1.5E-07 42.3 4.8 60 3-63 155-217 (445)
95 TIGR03420 DnaA_homol_Hda DnaA 96.4 0.01 2.2E-07 36.8 5.0 51 3-63 52-105 (226)
96 PRK14962 DNA polymerase III su 96.4 0.0099 2.2E-07 41.8 5.4 54 3-62 50-131 (472)
97 PRK14958 DNA polymerase III su 96.4 0.011 2.4E-07 41.9 5.6 54 3-62 52-133 (509)
98 PRK12323 DNA polymerase III su 96.4 0.0076 1.6E-07 44.3 4.7 54 3-62 52-138 (700)
99 PLN03025 replication factor C 96.3 0.015 3.2E-07 38.6 5.5 55 3-63 48-114 (319)
100 PRK07003 DNA polymerase III su 96.1 0.013 2.8E-07 43.8 4.7 54 3-62 52-133 (830)
101 PRK14960 DNA polymerase III su 96.1 0.021 4.6E-07 42.1 5.7 54 3-62 51-132 (702)
102 CHL00095 clpC Clp protease ATP 96.0 0.0096 2.1E-07 44.2 3.9 58 3-62 553-625 (821)
103 PRK06893 DNA replication initi 96.0 0.013 2.9E-07 37.2 4.0 52 3-64 53-107 (229)
104 PRK12402 replication factor C 95.9 0.044 9.5E-07 35.9 6.2 60 3-62 50-139 (337)
105 PRK14087 dnaA chromosomal repl 95.8 0.028 6E-07 39.3 5.3 60 3-64 155-222 (450)
106 COG0714 MoxR-like ATPases [Gen 95.7 0.014 3.1E-07 38.8 3.2 60 3-62 57-126 (329)
107 PRK07940 DNA polymerase III su 95.6 0.035 7.6E-07 38.3 5.2 30 34-63 99-132 (394)
108 PTZ00112 origin recognition co 95.6 0.028 6E-07 43.1 4.9 32 33-64 852-885 (1164)
109 PRK07994 DNA polymerase III su 95.6 0.027 5.8E-07 41.3 4.7 54 3-62 52-133 (647)
110 PHA02244 ATPase-like protein 95.6 0.023 5.1E-07 39.3 4.1 59 3-62 133-194 (383)
111 PRK08181 transposase; Validate 95.5 0.026 5.6E-07 37.1 4.1 60 3-64 120-183 (269)
112 PRK08116 hypothetical protein; 95.5 0.042 9.1E-07 35.9 4.9 55 3-59 128-189 (268)
113 PRK06645 DNA polymerase III su 95.3 0.067 1.5E-06 38.1 5.8 30 33-62 109-142 (507)
114 PF07728 AAA_5: AAA domain (dy 95.3 0.0025 5.5E-08 37.0 -1.1 56 3-61 13-78 (139)
115 PRK14961 DNA polymerase III su 95.2 0.07 1.5E-06 36.1 5.5 54 3-62 52-133 (363)
116 PRK14951 DNA polymerase III su 95.2 0.051 1.1E-06 39.6 5.1 54 3-62 52-138 (618)
117 PRK09183 transposase/IS protei 95.2 0.041 8.9E-07 35.8 4.2 62 3-65 116-181 (259)
118 PRK05642 DNA replication initi 95.2 0.087 1.9E-06 33.6 5.5 52 3-64 59-113 (234)
119 PRK14969 DNA polymerase III su 95.1 0.076 1.6E-06 37.9 5.6 54 3-62 52-133 (527)
120 PRK14957 DNA polymerase III su 95.1 0.088 1.9E-06 37.9 5.9 54 3-62 52-133 (546)
121 PRK08903 DnaA regulatory inact 95.1 0.052 1.1E-06 34.0 4.3 46 3-62 56-104 (227)
122 TIGR03346 chaperone_ClpB ATP-d 95.0 0.038 8.1E-07 41.4 3.9 58 3-62 609-681 (852)
123 PF13401 AAA_22: AAA domain; P 95.0 0.06 1.3E-06 30.5 4.0 28 34-61 73-100 (131)
124 PRK09376 rho transcription ter 94.9 0.065 1.4E-06 37.5 4.6 63 3-65 183-273 (416)
125 PF00158 Sigma54_activat: Sigm 94.8 0.18 3.9E-06 30.8 6.0 54 3-62 36-107 (168)
126 PRK14959 DNA polymerase III su 94.8 0.085 1.8E-06 38.6 5.2 53 3-61 52-132 (624)
127 PRK08691 DNA polymerase III su 94.8 0.12 2.7E-06 38.3 6.0 54 3-62 52-133 (709)
128 PRK14949 DNA polymerase III su 94.7 0.086 1.9E-06 40.2 5.1 54 3-62 52-133 (944)
129 PRK14964 DNA polymerase III su 94.7 0.12 2.6E-06 36.8 5.7 54 3-62 49-130 (491)
130 PRK08727 hypothetical protein; 94.6 0.16 3.5E-06 32.3 5.7 53 3-65 55-110 (233)
131 PF12774 AAA_6: Hydrolytic ATP 94.6 0.081 1.8E-06 34.1 4.3 52 3-61 46-97 (231)
132 COG1220 HslU ATP-dependent pro 94.5 0.046 1E-06 38.0 3.2 18 48-65 250-267 (444)
133 KOG0743|consensus 94.5 0.093 2E-06 37.1 4.7 54 3-64 249-302 (457)
134 COG0542 clpA ATP-binding subun 94.5 0.054 1.2E-06 40.5 3.6 55 3-60 535-605 (786)
135 COG0470 HolB ATPase involved i 94.4 0.14 3E-06 33.2 5.2 59 3-63 38-124 (325)
136 PF00308 Bac_DnaA: Bacterial d 94.4 0.082 1.8E-06 33.5 4.0 60 3-64 48-113 (219)
137 PRK07764 DNA polymerase III su 94.4 0.1 2.2E-06 39.3 4.9 29 34-62 102-134 (824)
138 PRK14948 DNA polymerase III su 94.4 0.17 3.8E-06 36.8 6.0 53 3-61 52-134 (620)
139 PRK12377 putative replication 94.3 0.11 2.4E-06 33.8 4.5 57 3-61 115-176 (248)
140 TIGR00678 holB DNA polymerase 94.3 0.15 3.2E-06 31.1 4.8 29 34-62 78-110 (188)
141 PRK14970 DNA polymerase III su 94.3 0.098 2.1E-06 35.1 4.3 54 3-62 53-122 (367)
142 PRK10865 protein disaggregatio 94.2 0.12 2.7E-06 38.8 5.0 57 3-61 612-683 (857)
143 PRK14963 DNA polymerase III su 94.1 0.18 4E-06 35.9 5.6 53 3-61 50-129 (504)
144 PRK08939 primosomal protein Dn 94.1 0.1 2.2E-06 34.8 4.1 56 3-60 170-229 (306)
145 COG1484 DnaC DNA replication p 94.0 0.14 3.1E-06 33.3 4.5 51 3-61 119-180 (254)
146 PRK14965 DNA polymerase III su 93.9 0.18 3.9E-06 36.4 5.3 54 3-62 52-133 (576)
147 PRK05563 DNA polymerase III su 93.9 0.21 4.7E-06 35.9 5.7 53 3-61 52-132 (559)
148 TIGR00390 hslU ATP-dependent p 93.7 0.1 2.2E-06 36.8 3.5 17 48-64 247-263 (441)
149 PRK05201 hslU ATP-dependent pr 93.6 0.095 2E-06 37.0 3.3 18 48-65 249-266 (443)
150 PRK08084 DNA replication initi 93.6 0.13 2.8E-06 32.8 3.7 52 3-64 59-113 (235)
151 PRK06526 transposase; Provisio 93.5 0.1 2.2E-06 34.0 3.2 60 3-64 112-175 (254)
152 PF05673 DUF815: Protein of un 93.3 0.35 7.5E-06 31.8 5.3 47 3-58 66-116 (249)
153 TIGR02974 phageshock_pspF psp 93.2 0.19 4.1E-06 33.8 4.2 53 3-62 36-107 (329)
154 PF06068 TIP49: TIP49 C-termin 93.2 0.23 5.1E-06 34.6 4.6 41 3-44 64-106 (398)
155 PRK06921 hypothetical protein; 93.2 0.31 6.6E-06 31.9 5.0 54 3-59 131-188 (266)
156 PF14516 AAA_35: AAA-like doma 93.0 0.28 6.1E-06 32.9 4.8 17 47-63 126-142 (331)
157 TIGR02397 dnaX_nterm DNA polym 92.9 0.49 1.1E-05 31.3 5.8 30 33-62 98-131 (355)
158 cd01120 RecA-like_NTPases RecA 92.9 0.69 1.5E-05 26.5 5.9 25 39-63 76-100 (165)
159 KOG1051|consensus 92.7 0.39 8.5E-06 36.6 5.6 56 3-60 605-672 (898)
160 PF01695 IstB_IS21: IstB-like 92.7 0.15 3.3E-06 31.4 3.0 56 3-60 61-120 (178)
161 PRK06835 DNA replication prote 92.7 0.36 7.9E-06 32.6 5.0 57 3-61 197-259 (329)
162 PRK11331 5-methylcytosine-spec 92.6 0.3 6.5E-06 34.7 4.6 62 3-64 208-288 (459)
163 COG1474 CDC6 Cdc6-related prot 92.5 0.6 1.3E-05 32.0 5.9 63 3-65 56-140 (366)
164 COG1224 TIP49 DNA helicase TIP 92.3 0.19 4.2E-06 35.1 3.3 41 3-44 79-121 (450)
165 TIGR01817 nifA Nif-specific re 92.3 0.24 5.2E-06 35.1 3.9 53 3-62 233-304 (534)
166 TIGR00602 rad24 checkpoint pro 92.2 0.18 3.9E-06 37.0 3.2 60 3-62 124-209 (637)
167 KOG0732|consensus 92.2 0.14 3E-06 39.6 2.7 61 4-64 607-669 (1080)
168 COG0593 DnaA ATPase involved i 92.2 0.38 8.3E-06 33.6 4.7 60 3-64 127-191 (408)
169 PRK14953 DNA polymerase III su 92.1 0.6 1.3E-05 33.1 5.6 28 34-61 101-132 (486)
170 PRK05896 DNA polymerase III su 91.8 0.67 1.4E-05 34.0 5.7 53 3-61 52-132 (605)
171 PRK14955 DNA polymerase III su 91.6 0.75 1.6E-05 31.6 5.6 29 34-62 109-141 (397)
172 PRK14952 DNA polymerase III su 91.6 0.62 1.3E-05 33.9 5.4 29 34-62 100-132 (584)
173 PRK15424 propionate catabolism 91.6 0.32 6.9E-06 35.0 3.9 57 3-62 256-336 (538)
174 PRK06647 DNA polymerase III su 91.4 0.77 1.7E-05 33.2 5.6 29 34-62 101-133 (563)
175 PRK05022 anaerobic nitric oxid 91.3 0.4 8.7E-06 33.9 4.2 57 3-62 224-295 (509)
176 PRK09111 DNA polymerase III su 91.2 0.81 1.8E-05 33.4 5.7 29 34-62 114-146 (598)
177 PRK00440 rfc replication facto 91.1 1 2.2E-05 29.2 5.6 54 3-62 52-116 (319)
178 TIGR02903 spore_lon_C ATP-depe 91.0 0.87 1.9E-05 33.2 5.7 23 3-25 189-221 (615)
179 PRK08118 topology modulation p 90.7 1 2.2E-05 27.3 5.0 42 3-44 15-56 (167)
180 PRK11388 DNA-binding transcrip 90.7 0.35 7.6E-06 34.9 3.4 53 3-62 362-430 (638)
181 KOG1051|consensus 90.5 1.3 2.8E-05 34.0 6.2 51 15-65 244-297 (898)
182 COG2607 Predicted ATPase (AAA+ 90.1 1.7 3.7E-05 29.0 5.9 46 3-57 99-148 (287)
183 PRK10365 transcriptional regul 89.9 0.27 5.8E-06 33.5 2.2 53 3-62 176-247 (441)
184 KOG0989|consensus 89.7 0.36 7.7E-06 33.0 2.6 60 3-62 71-143 (346)
185 TIGR02329 propionate_PrpR prop 89.6 0.71 1.5E-05 33.1 4.2 57 3-62 249-321 (526)
186 PRK07133 DNA polymerase III su 89.1 1.6 3.4E-05 32.8 5.7 59 3-61 54-131 (725)
187 COG2204 AtoC Response regulato 88.8 0.47 1E-05 33.7 2.8 51 4-61 179-248 (464)
188 cd01128 rho_factor Transcripti 88.5 2.1 4.5E-05 27.9 5.5 18 47-64 102-119 (249)
189 cd00338 Ser_Recombinase Serine 88.3 1.7 3.7E-05 24.7 4.6 58 7-64 24-81 (137)
190 PRK10820 DNA-binding transcrip 88.3 1.2 2.6E-05 31.8 4.6 57 3-62 241-312 (520)
191 PRK15429 formate hydrogenlyase 88.3 0.85 1.8E-05 33.4 3.9 56 3-62 413-484 (686)
192 PF01637 Arch_ATPase: Archaeal 88.2 0.64 1.4E-05 28.3 2.9 29 33-61 102-131 (234)
193 PRK14950 DNA polymerase III su 88.0 1.9 4.1E-05 31.2 5.5 29 34-62 102-134 (585)
194 PRK11823 DNA repair protein Ra 87.7 1.8 3.9E-05 30.4 5.1 28 36-63 144-171 (446)
195 PRK11608 pspF phage shock prot 87.6 1.2 2.6E-05 29.8 4.1 57 3-62 43-114 (326)
196 TIGR02902 spore_lonB ATP-depen 87.2 0.68 1.5E-05 33.1 2.8 15 48-62 175-189 (531)
197 PF05707 Zot: Zonular occluden 86.9 0.53 1.1E-05 29.1 2.0 19 48-66 79-97 (193)
198 PRK14954 DNA polymerase III su 86.7 2.7 5.9E-05 30.9 5.7 29 34-62 109-141 (620)
199 COG1066 Sms Predicted ATP-depe 86.1 2 4.4E-05 30.5 4.6 63 2-64 107-184 (456)
200 PRK06305 DNA polymerase III su 86.0 2.6 5.6E-05 29.6 5.2 16 47-62 120-135 (451)
201 TIGR01818 ntrC nitrogen regula 85.8 1.1 2.4E-05 30.8 3.2 54 3-62 171-242 (463)
202 PF13304 AAA_21: AAA domain; P 85.6 1.5 3.3E-05 26.1 3.5 31 30-60 237-269 (303)
203 KOG1942|consensus 85.5 0.58 1.3E-05 32.3 1.7 38 23-60 270-308 (456)
204 COG1373 Predicted ATPase (AAA+ 85.5 2.8 6E-05 29.0 5.1 56 3-60 51-106 (398)
205 COG2812 DnaX DNA polymerase II 85.2 0.81 1.8E-05 33.0 2.4 59 3-61 52-132 (515)
206 PRK15115 response regulator Gl 85.0 1.3 2.9E-05 30.3 3.3 55 3-63 171-243 (444)
207 PRK07261 topology modulation p 84.7 3.4 7.3E-05 25.0 4.7 31 3-33 14-44 (171)
208 PF05621 TniB: Bacterial TniB 84.4 2.6 5.6E-05 28.5 4.4 25 38-62 135-159 (302)
209 TIGR02442 Cob-chelat-sub cobal 84.1 0.97 2.1E-05 33.0 2.4 14 49-62 127-140 (633)
210 COG0703 AroK Shikimate kinase 83.6 1.3 2.8E-05 27.6 2.6 36 3-43 16-51 (172)
211 PF07693 KAP_NTPase: KAP famil 83.4 0.92 2E-05 29.6 2.0 17 47-63 171-187 (325)
212 TIGR00764 lon_rel lon-related 83.4 1.8 4E-05 31.6 3.6 48 3-50 51-108 (608)
213 PRK13531 regulatory ATPase Rav 83.4 0.91 2E-05 32.6 2.0 56 3-62 53-121 (498)
214 PF07931 CPT: Chloramphenicol 83.4 8 0.00017 23.9 6.0 26 3-28 15-40 (174)
215 PRK11361 acetoacetate metaboli 82.1 2 4.4E-05 29.4 3.3 54 3-62 180-251 (457)
216 PRK06620 hypothetical protein; 82.0 2.2 4.7E-05 27.0 3.2 12 49-60 86-97 (214)
217 COG4130 Predicted sugar epimer 81.9 6.3 0.00014 26.0 5.2 46 5-50 53-98 (272)
218 PF01202 SKI: Shikimate kinase 81.6 2.6 5.7E-05 25.0 3.3 29 3-33 6-34 (158)
219 PRK10923 glnG nitrogen regulat 81.4 2 4.3E-05 29.7 3.1 54 3-62 175-246 (469)
220 TIGR02915 PEP_resp_reg putativ 80.9 2.1 4.6E-05 29.3 3.1 53 3-62 176-247 (445)
221 PRK13947 shikimate kinase; Pro 80.8 8.6 0.00019 22.7 5.4 28 3-32 15-42 (171)
222 PRK14971 DNA polymerase III su 80.7 7 0.00015 28.7 5.7 29 34-62 103-135 (614)
223 PRK07631 amidophosphoribosyltr 80.7 2.8 6.1E-05 29.9 3.7 53 2-57 294-357 (475)
224 COG1220 HslU ATP-dependent pro 80.3 4.1 9E-05 28.6 4.2 42 3-44 64-107 (444)
225 smart00534 MUTSac ATPase domai 80.2 11 0.00023 23.0 6.3 13 47-59 77-89 (185)
226 PF14532 Sigma54_activ_2: Sigm 80.2 1.1 2.5E-05 25.9 1.4 45 4-62 36-83 (138)
227 cd01121 Sms Sms (bacterial rad 80.2 4.5 9.8E-05 27.9 4.4 29 35-63 145-173 (372)
228 KOG3406|consensus 79.9 2.1 4.5E-05 25.7 2.4 29 4-32 67-95 (134)
229 PRK13946 shikimate kinase; Pro 79.8 8.4 0.00018 23.4 5.2 21 2-22 23-43 (184)
230 PHA00729 NTP-binding motif con 79.8 7.9 0.00017 25.1 5.2 12 3-14 31-42 (226)
231 TIGR03015 pepcterm_ATPase puta 79.7 6.3 0.00014 24.9 4.8 17 45-61 120-136 (269)
232 PRK08451 DNA polymerase III su 79.6 8.3 0.00018 28.0 5.7 29 34-62 99-131 (535)
233 COG1221 PspF Transcriptional r 79.2 0.68 1.5E-05 32.4 0.2 48 9-62 124-187 (403)
234 TIGR02031 BchD-ChlD magnesium 78.2 2.3 5E-05 30.9 2.6 58 3-62 30-98 (589)
235 PRK06781 amidophosphoribosyltr 77.9 1.9 4.2E-05 30.6 2.2 53 2-57 294-357 (471)
236 KOG1514|consensus 77.7 1.1 2.4E-05 33.6 0.9 52 15-66 458-526 (767)
237 PRK00131 aroK shikimate kinase 77.6 12 0.00025 21.8 5.5 27 3-31 18-44 (175)
238 PF06068 TIP49: TIP49 C-termin 77.3 1.2 2.7E-05 31.1 1.0 13 48-60 278-290 (398)
239 KOG2680|consensus 77.1 3 6.5E-05 29.0 2.8 23 38-60 274-300 (454)
240 PF13207 AAA_17: AAA domain; P 76.7 3.7 8.1E-05 22.7 2.8 20 3-22 13-32 (121)
241 PF09820 AAA-ATPase_like: Pred 76.6 5 0.00011 26.4 3.7 28 35-62 128-157 (284)
242 COG4080 SpoU rRNA Methylase fa 76.4 6.4 0.00014 24.0 3.8 45 9-59 22-67 (147)
243 PRK05707 DNA polymerase III su 75.9 7.7 0.00017 26.2 4.5 30 33-62 87-120 (328)
244 PF12846 AAA_10: AAA-like doma 75.7 3.1 6.7E-05 26.3 2.5 17 47-63 219-235 (304)
245 PRK09087 hypothetical protein; 75.4 6.3 0.00014 25.1 3.8 14 3-16 58-71 (226)
246 TIGR00767 rho transcription te 75.3 7.3 0.00016 27.5 4.4 18 47-64 254-271 (415)
247 COG3172 NadR Predicted ATPase/ 75.1 5.8 0.00013 25.0 3.5 54 3-56 22-86 (187)
248 PF06733 DEAD_2: DEAD_2; Inte 75.1 6.3 0.00014 23.7 3.7 40 15-62 120-159 (174)
249 KOG1968|consensus 75.0 2.5 5.3E-05 32.4 2.1 60 3-62 371-442 (871)
250 cd03283 ABC_MutS-like MutS-lik 74.6 3.7 7.9E-05 25.6 2.6 23 35-57 92-114 (199)
251 PRK07272 amidophosphoribosyltr 74.3 3.6 7.8E-05 29.4 2.7 56 2-57 296-359 (484)
252 PRK00109 Holliday junction res 74.3 16 0.00034 21.7 5.4 51 7-57 47-98 (138)
253 cd03281 ABC_MSH5_euk MutS5 hom 74.0 19 0.00042 22.6 6.0 26 34-59 93-119 (213)
254 PF13872 AAA_34: P-loop contai 73.5 3.6 7.9E-05 27.8 2.5 31 33-63 157-187 (303)
255 TIGR00201 comF comF family pro 72.8 3.6 7.7E-05 25.4 2.2 53 3-57 102-161 (190)
256 PF04465 DUF499: Protein of un 72.6 2.3 5E-05 33.1 1.5 25 34-62 89-113 (1035)
257 COG4650 RtcR Sigma54-dependent 72.5 5.2 0.00011 27.9 3.1 49 10-64 235-298 (531)
258 COG1224 TIP49 DNA helicase TIP 72.2 2.3 5E-05 30.0 1.3 14 47-60 290-303 (450)
259 PRK06217 hypothetical protein; 71.9 18 0.00038 21.9 5.1 20 3-22 15-34 (183)
260 PF02075 RuvC: Crossover junct 71.3 5.4 0.00012 23.9 2.7 56 6-61 86-144 (149)
261 cd00983 recA RecA is a bacter 71.2 29 0.00062 23.7 6.4 31 33-63 118-148 (325)
262 KOG2170|consensus 71.2 5.9 0.00013 27.2 3.1 29 34-62 164-192 (344)
263 TIGR00368 Mg chelatase-related 70.4 2.3 4.9E-05 30.5 1.0 15 48-62 295-309 (499)
264 PF03652 UPF0081: Uncharacteri 69.9 13 0.00029 21.9 4.2 51 7-57 44-96 (135)
265 smart00857 Resolvase Resolvase 69.4 18 0.00039 20.8 4.6 58 6-64 24-81 (148)
266 cd01873 RhoBTB RhoBTB subfamil 69.1 7.4 0.00016 24.0 3.0 35 3-46 159-193 (195)
267 PRK11595 DNA utilization prote 68.7 6.6 0.00014 25.0 2.8 54 3-57 135-196 (227)
268 cd03286 ABC_MSH6_euk MutS6 hom 68.4 6.2 0.00013 25.1 2.6 23 35-59 98-120 (218)
269 TIGR01526 nadR_NMN_Atrans nico 68.2 24 0.00051 23.8 5.5 53 3-56 176-240 (325)
270 PRK13948 shikimate kinase; Pro 67.1 9.7 0.00021 23.6 3.2 28 3-32 24-51 (182)
271 KOG2228|consensus 67.0 12 0.00027 26.2 4.0 35 29-63 113-152 (408)
272 cd02027 APSK Adenosine 5'-phos 66.8 24 0.00051 20.7 6.4 55 3-57 13-79 (149)
273 COG1134 TagH ABC-type polysacc 66.6 8 0.00017 25.6 2.9 28 34-61 151-178 (249)
274 cd00464 SK Shikimate kinase (S 66.4 16 0.00035 20.9 4.0 28 3-32 13-40 (154)
275 cd01124 KaiC KaiC is a circadi 66.2 9 0.0002 22.7 3.0 25 38-62 85-109 (187)
276 TIGR01420 pilT_fam pilus retra 66.2 13 0.00029 25.0 4.0 29 30-58 177-205 (343)
277 COG1110 Reverse gyrase [DNA re 65.9 4.4 9.6E-05 31.9 1.8 28 37-64 192-219 (1187)
278 PF14097 SpoVAE: Stage V sporu 65.9 27 0.00059 22.0 5.0 53 5-62 15-67 (180)
279 COG4098 comFA Superfamily II D 65.7 3.3 7.1E-05 29.1 1.0 15 48-62 202-216 (441)
280 PHA00012 I assembly protein 65.3 5.5 0.00012 27.6 2.0 21 47-67 80-100 (361)
281 KOG0991|consensus 65.3 11 0.00025 25.3 3.4 56 3-61 62-126 (333)
282 cd00046 DEXDc DEAD-like helica 64.8 3.6 7.8E-05 22.3 0.9 16 48-63 103-118 (144)
283 cd03770 SR_TndX_transposase Se 64.8 26 0.00056 20.4 4.9 56 7-63 28-83 (140)
284 TIGR02012 tigrfam_recA protein 64.6 40 0.00086 23.0 6.0 31 33-63 118-148 (321)
285 cd03280 ABC_MutS2 MutS2 homolo 64.1 23 0.00051 21.7 4.6 13 47-59 107-119 (200)
286 PRK03731 aroL shikimate kinase 64.1 8.4 0.00018 22.8 2.5 20 2-21 15-34 (171)
287 cd03227 ABC_Class2 ABC-type Cl 64.1 7.4 0.00016 23.2 2.3 13 48-60 99-111 (162)
288 PRK00625 shikimate kinase; Pro 63.5 8.1 0.00018 23.7 2.4 19 3-21 14-32 (173)
289 PRK07471 DNA polymerase III su 63.4 19 0.00041 24.7 4.4 29 34-62 123-155 (365)
290 PF00931 NB-ARC: NB-ARC domain 63.3 18 0.00038 23.0 4.0 26 34-60 88-113 (287)
291 PF07726 AAA_3: ATPase family 63.1 10 0.00022 22.7 2.7 55 3-63 13-77 (131)
292 PHA00350 putative assembly pro 62.7 5.3 0.00011 28.0 1.6 19 48-66 81-99 (399)
293 COG1061 SSL2 DNA or RNA helica 62.4 11 0.00024 26.4 3.1 16 47-62 145-160 (442)
294 PF13191 AAA_16: AAA ATPase do 62.3 3.6 7.8E-05 24.2 0.7 16 47-62 149-164 (185)
295 PRK14021 bifunctional shikimat 61.9 28 0.00062 25.1 5.2 28 3-32 20-47 (542)
296 TIGR03574 selen_PSTK L-seryl-t 61.6 39 0.00084 21.4 5.4 56 3-58 13-77 (249)
297 cd01131 PilT Pilus retraction 61.1 7 0.00015 24.2 1.8 27 31-57 57-83 (198)
298 PF02463 SMC_N: RecF/RecN/SMC 61.0 8.8 0.00019 23.7 2.3 15 47-61 157-171 (220)
299 cd00006 PTS_IIA_man PTS_IIA, P 60.5 19 0.00041 20.5 3.5 27 30-56 40-66 (122)
300 cd02020 CMPK Cytidine monophos 60.5 29 0.00062 19.6 5.4 20 2-21 12-31 (147)
301 PRK05564 DNA polymerase III su 60.4 20 0.00043 23.6 4.0 56 3-62 40-107 (313)
302 cd00227 CPT Chloramphenicol (C 60.2 28 0.0006 20.8 4.3 23 3-25 16-38 (175)
303 smart00763 AAA_PrkA PrkA AAA d 59.9 13 0.00029 25.7 3.1 42 3-44 92-144 (361)
304 TIGR02858 spore_III_AA stage I 59.8 12 0.00027 24.6 2.9 22 37-58 183-204 (270)
305 PRK14484 phosphotransferase ma 59.6 34 0.00074 20.1 4.5 46 5-55 20-65 (124)
306 TIGR02237 recomb_radB DNA repa 59.4 14 0.00031 22.5 3.0 26 37-62 86-111 (209)
307 PF00456 Transketolase_N: Tran 59.2 30 0.00065 23.6 4.7 38 12-58 204-244 (332)
308 PRK06762 hypothetical protein; 58.8 35 0.00075 20.0 6.2 27 3-29 16-42 (166)
309 PF02969 TAF: TATA box binding 58.8 13 0.00028 19.6 2.4 54 3-59 6-63 (66)
310 PF13189 Cytidylate_kin2: Cyti 58.5 8.7 0.00019 23.4 1.9 18 2-19 12-29 (179)
311 COG3412 Uncharacterized protei 58.1 34 0.00074 20.5 4.3 47 5-55 21-67 (129)
312 PF03618 Kinase-PPPase: Kinase 58.0 39 0.00085 22.4 5.0 46 2-54 12-58 (255)
313 PF00270 DEAD: DEAD/DEAH box h 57.9 4.8 0.0001 23.3 0.7 16 48-63 119-134 (169)
314 PRK14532 adenylate kinase; Pro 57.9 22 0.00047 21.4 3.6 24 3-28 14-37 (188)
315 PF00005 ABC_tran: ABC transpo 57.7 23 0.0005 19.9 3.5 18 40-57 118-135 (137)
316 COG1040 ComFC Predicted amidop 57.6 3 6.4E-05 26.8 -0.3 55 3-57 134-193 (225)
317 COG0156 BioF 7-keto-8-aminopel 57.2 13 0.00028 26.0 2.7 27 34-61 187-213 (388)
318 PHA02552 4 head completion pro 56.9 17 0.00036 22.3 2.9 16 5-20 122-137 (151)
319 PF02572 CobA_CobO_BtuR: ATP:c 56.8 17 0.00038 22.5 3.0 25 35-59 79-107 (172)
320 PF02456 Adeno_IVa2: Adenoviru 56.7 8.5 0.00019 26.7 1.8 47 16-65 165-214 (369)
321 PRK13810 orotate phosphoribosy 56.7 9 0.00019 23.9 1.8 46 4-57 86-131 (187)
322 COG0396 sufC Cysteine desulfur 56.5 22 0.00047 23.6 3.5 35 24-59 135-173 (251)
323 cd03287 ABC_MSH3_euk MutS3 hom 56.4 11 0.00024 24.0 2.2 22 35-58 99-120 (222)
324 PRK03839 putative kinase; Prov 56.3 13 0.00027 22.3 2.3 19 3-21 14-32 (180)
325 PRK07414 cob(I)yrinic acid a,c 56.3 22 0.00047 22.3 3.4 27 33-59 96-126 (178)
326 COG3829 RocR Transcriptional r 56.1 5.9 0.00013 29.0 1.0 22 4-25 283-307 (560)
327 COG1127 Ttg2A ABC-type transpo 55.9 14 0.0003 24.6 2.6 18 39-56 154-171 (263)
328 TIGR00223 panD L-aspartate-alp 55.8 11 0.00024 22.5 1.9 19 44-62 98-116 (126)
329 COG1201 Lhr Lhr-like helicases 55.6 13 0.00029 28.4 2.7 44 17-68 126-169 (814)
330 PRK13949 shikimate kinase; Pro 55.5 21 0.00045 21.6 3.2 19 3-21 15-33 (169)
331 PF09895 DUF2122: RecB-family 55.4 17 0.00037 21.0 2.7 22 37-58 8-29 (106)
332 KOG1942|consensus 55.4 17 0.00036 25.4 3.0 41 3-44 78-120 (456)
333 PF13177 DNA_pol3_delta2: DNA 55.1 40 0.00086 20.2 4.4 30 33-62 83-116 (162)
334 cd06919 Asp_decarbox Aspartate 55.0 11 0.00025 21.9 1.9 14 43-56 96-109 (111)
335 cd04102 RabL3 RabL3 (Rab-like3 55.0 25 0.00054 21.9 3.6 41 6-46 156-197 (202)
336 PRK09246 amidophosphoribosyltr 55.0 15 0.00032 26.4 2.8 52 3-57 305-367 (501)
337 PF13481 AAA_25: AAA domain; P 54.7 19 0.00041 21.5 2.9 30 34-63 126-156 (193)
338 PF04851 ResIII: Type III rest 54.7 8.1 0.00018 22.5 1.3 15 48-62 146-160 (184)
339 PF10923 DUF2791: P-loop Domai 54.4 14 0.0003 26.1 2.5 29 37-66 229-257 (416)
340 PF00488 MutS_V: MutS domain V 54.3 19 0.00041 23.1 3.0 23 34-58 110-132 (235)
341 PRK08058 DNA polymerase III su 54.1 38 0.00083 22.7 4.6 29 34-62 92-124 (329)
342 TIGR00708 cobA cob(I)alamin ad 54.0 24 0.00052 21.9 3.3 26 34-59 79-108 (173)
343 COG1922 WecG Teichoic acid bio 54.0 16 0.00034 24.2 2.6 26 27-54 142-167 (253)
344 COG0563 Adk Adenylate kinase a 53.8 21 0.00045 22.0 3.0 25 3-29 14-38 (178)
345 PF07517 SecA_DEAD: SecA DEAD- 53.6 9.6 0.00021 25.2 1.6 19 47-65 196-214 (266)
346 COG0853 PanD Aspartate 1-decar 53.4 12 0.00027 22.2 1.9 17 44-60 97-113 (126)
347 PF05763 DUF835: Protein of un 53.4 25 0.00054 20.9 3.3 29 33-61 56-88 (136)
348 PRK08154 anaerobic benzoate ca 53.3 28 0.0006 23.1 3.8 20 2-21 146-165 (309)
349 cd04131 Rnd Rnd subfamily. Th 53.0 21 0.00045 21.5 3.0 36 3-46 137-173 (178)
350 PF00448 SRP54: SRP54-type pro 52.7 49 0.0011 20.6 4.6 44 7-57 49-92 (196)
351 COG1121 ZnuC ABC-type Mn/Zn tr 52.2 27 0.00057 23.1 3.5 17 40-56 149-165 (254)
352 PTZ00132 GTP-binding nuclear p 52.2 52 0.0011 20.1 4.7 13 46-58 168-180 (215)
353 PRK08558 adenine phosphoribosy 52.0 7 0.00015 25.3 0.8 18 4-21 124-141 (238)
354 PF00071 Ras: Ras family; Int 51.7 32 0.00068 19.6 3.5 34 3-45 124-157 (162)
355 cd00561 CobA_CobO_BtuR ATP:cor 51.6 30 0.00066 21.1 3.5 26 35-60 78-107 (159)
356 cd02016 TPP_E1_OGDC_like Thiam 51.5 46 0.00099 22.1 4.5 49 8-66 201-250 (265)
357 PF09807 DUF2348: Uncharacteri 51.4 15 0.00032 23.9 2.2 28 35-62 115-149 (249)
358 COG4517 Uncharacterized protei 51.4 15 0.00032 21.0 1.9 35 30-64 50-87 (109)
359 COG3959 Transketolase, N-termi 51.1 35 0.00077 22.5 3.9 36 13-57 204-241 (243)
360 PRK12270 kgd alpha-ketoglutara 51.1 49 0.0011 26.6 5.1 54 5-67 705-758 (1228)
361 PRK05788 cobalamin biosynthesi 50.8 45 0.00099 22.5 4.5 51 3-58 16-88 (315)
362 PF05872 DUF853: Bacterial pro 50.6 16 0.00034 26.5 2.3 30 35-64 237-271 (502)
363 PF01656 CbiA: CobQ/CobB/MinD/ 50.6 51 0.0011 19.4 5.7 22 35-56 81-102 (195)
364 COG4619 ABC-type uncharacteriz 50.5 24 0.00052 22.7 2.9 28 33-61 137-164 (223)
365 PRK08099 bifunctional DNA-bind 50.4 58 0.0013 22.7 5.1 18 3-20 233-250 (399)
366 PRK07349 amidophosphoribosyltr 50.4 14 0.00031 26.6 2.1 17 2-18 323-339 (500)
367 PRK05986 cob(I)alamin adenolsy 50.4 30 0.00066 21.8 3.4 28 33-60 96-127 (191)
368 PRK12571 1-deoxy-D-xylulose-5- 50.4 34 0.00074 25.3 4.1 40 9-57 241-283 (641)
369 TIGR01769 GGGP geranylgeranylg 50.0 65 0.0014 20.5 5.0 45 11-61 21-67 (205)
370 PRK09694 helicase Cas3; Provis 49.9 20 0.00044 27.6 3.0 16 46-61 437-452 (878)
371 PF01976 DUF116: Protein of un 49.8 53 0.0012 20.0 4.4 24 7-30 79-102 (158)
372 TIGR02525 plasmid_TraJ plasmid 49.8 46 0.00099 23.1 4.5 29 30-58 207-235 (372)
373 KOG0922|consensus 49.8 21 0.00046 26.8 3.0 57 2-59 108-174 (674)
374 PRK04296 thymidine kinase; Pro 49.6 22 0.00048 21.8 2.7 23 38-60 66-90 (190)
375 cd03112 CobW_like The function 49.3 31 0.00068 20.5 3.3 41 15-55 51-93 (158)
376 cd04121 Rab40 Rab40 subfamily. 49.2 25 0.00055 21.5 2.9 34 3-45 130-163 (189)
377 KOG0058|consensus 49.1 18 0.0004 27.3 2.6 55 6-60 574-634 (716)
378 PRK06067 flagellar accessory p 48.9 27 0.00059 21.8 3.1 27 35-61 107-133 (234)
379 PRK08533 flagellar accessory p 48.9 30 0.00066 22.0 3.3 28 34-61 103-130 (230)
380 cd02012 TPP_TK Thiamine pyroph 48.9 70 0.0015 20.5 5.2 39 8-55 185-225 (255)
381 PF12694 MoCo_carrier: Putativ 48.4 62 0.0013 19.8 5.7 42 2-52 78-119 (145)
382 PF02261 Asp_decarbox: Asparta 48.2 17 0.00037 21.4 1.9 15 44-58 98-112 (116)
383 cd03285 ABC_MSH2_euk MutS2 hom 48.1 56 0.0012 20.7 4.4 11 47-57 108-118 (222)
384 COG3283 TyrR Transcriptional r 47.9 20 0.00043 25.7 2.4 44 14-62 255-307 (511)
385 PF13558 SbcCD_C: Putative exo 47.7 13 0.00029 20.2 1.4 11 47-57 62-72 (90)
386 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 47.5 26 0.00057 21.3 2.8 34 4-46 142-177 (182)
387 TIGR00250 RNAse_H_YqgF RNAse H 47.3 57 0.0012 19.1 5.3 50 8-57 42-92 (130)
388 smart00487 DEXDc DEAD-like hel 47.2 15 0.00032 21.2 1.6 14 49-62 130-143 (201)
389 TIGR01587 cas3_core CRISPR-ass 47.1 23 0.00049 23.5 2.6 15 48-62 124-138 (358)
390 KOG3361|consensus 46.8 31 0.00066 21.0 2.9 33 7-46 117-149 (157)
391 PF07015 VirC1: VirC1 protein; 46.7 64 0.0014 21.1 4.6 25 32-56 67-91 (231)
392 cd03216 ABC_Carb_Monos_I This 46.7 39 0.00085 20.0 3.4 19 40-58 92-110 (163)
393 COG1102 Cmk Cytidylate kinase 46.6 22 0.00048 22.4 2.3 23 2-26 13-35 (179)
394 PRK04182 cytidylate kinase; Pr 46.5 21 0.00045 21.0 2.2 17 3-19 14-30 (180)
395 PRK09361 radB DNA repair and r 46.5 69 0.0015 19.8 5.7 17 47-63 106-122 (225)
396 PRK02277 orotate phosphoribosy 46.4 12 0.00027 23.4 1.2 20 3-22 97-116 (200)
397 cd04146 RERG_RasL11_like RERG/ 46.3 56 0.0012 18.7 4.0 31 6-44 129-159 (165)
398 PRK05449 aspartate alpha-decar 46.1 19 0.00042 21.4 1.9 19 44-62 98-116 (126)
399 PF04748 Polysacc_deac_2: Dive 46.1 33 0.00071 21.8 3.1 47 4-52 131-179 (213)
400 PF09547 Spore_IV_A: Stage IV 46.1 57 0.0012 23.7 4.5 34 4-44 199-232 (492)
401 cd03243 ABC_MutS_homologs The 45.6 61 0.0013 19.8 4.2 13 47-59 107-119 (202)
402 PF04198 Sugar-bind: Putative 45.5 24 0.00051 22.9 2.5 46 2-47 96-145 (255)
403 KOG2227|consensus 45.4 30 0.00065 25.3 3.1 18 48-65 256-273 (529)
404 cd04177 RSR1 RSR1 subgroup. R 45.4 21 0.00046 20.8 2.1 15 37-51 152-166 (168)
405 PRK04169 geranylgeranylglycery 45.2 66 0.0014 20.9 4.5 47 10-62 28-75 (232)
406 COG4555 NatA ABC-type Na+ tran 45.2 26 0.00057 23.1 2.6 10 47-56 150-159 (245)
407 PF05729 NACHT: NACHT domain 44.8 41 0.00089 19.1 3.2 19 45-63 78-96 (166)
408 COG3265 GntK Gluconate kinase 44.6 23 0.00049 22.0 2.1 17 3-19 9-25 (161)
409 PF08303 tRNA_lig_kinase: tRNA 44.4 78 0.0017 19.8 4.6 48 3-55 13-61 (168)
410 cd04173 Rnd2_Rho7 Rnd2/Rho7 su 44.2 34 0.00073 21.7 3.0 35 4-46 138-173 (222)
411 TIGR02782 TrbB_P P-type conjug 44.2 42 0.00091 22.3 3.5 23 36-58 192-214 (299)
412 TIGR01768 GGGP-family geranylg 44.1 73 0.0016 20.6 4.5 44 12-61 25-69 (223)
413 cd02812 PcrB_like PcrB_like pr 43.9 87 0.0019 20.2 4.9 50 8-61 19-68 (219)
414 KOG1359|consensus 43.9 28 0.0006 24.2 2.6 24 36-60 211-234 (417)
415 TIGR00416 sms DNA repair prote 43.7 84 0.0018 22.3 5.1 27 36-62 158-184 (454)
416 PRK00039 ruvC Holliday junctio 43.2 21 0.00046 21.8 1.9 27 7-33 90-116 (164)
417 TIGR01618 phage_P_loop phage n 43.1 41 0.00089 21.6 3.3 27 36-62 67-95 (220)
418 COG1058 CinA Predicted nucleot 42.6 1E+02 0.0022 20.5 5.4 42 4-54 25-66 (255)
419 PRK08699 DNA polymerase III su 42.4 77 0.0017 21.4 4.6 30 33-62 94-127 (325)
420 COG4671 Predicted glycosyl tra 42.4 1.2E+02 0.0027 21.5 5.6 29 3-31 29-58 (400)
421 cd03282 ABC_MSH4_euk MutS4 hom 42.3 25 0.00055 22.0 2.2 20 36-57 98-117 (204)
422 PRK05057 aroK shikimate kinase 42.3 28 0.00062 21.0 2.4 20 3-22 18-37 (172)
423 PLN02234 1-deoxy-D-xylulose-5- 42.3 66 0.0014 24.1 4.5 38 9-55 278-319 (641)
424 cd03295 ABC_OpuCA_Osmoprotecti 42.2 65 0.0014 20.2 4.1 18 41-58 146-163 (242)
425 cd08769 DAP_dppA_2 Peptidase M 42.1 78 0.0017 21.1 4.5 22 4-25 137-158 (270)
426 PF09848 DUF2075: Uncharacteri 42.1 70 0.0015 21.5 4.4 16 48-63 83-98 (352)
427 COG1129 MglA ABC-type sugar tr 42.1 38 0.00081 24.6 3.2 50 5-61 156-212 (500)
428 PF08433 KTI12: Chromatin asso 42.0 1E+02 0.0022 20.3 6.7 58 3-60 15-82 (270)
429 PF06048 DUF927: Domain of unk 41.9 57 0.0012 21.4 3.9 49 3-61 207-255 (286)
430 PRK09064 5-aminolevulinate syn 41.6 34 0.00073 23.1 2.8 24 36-60 196-219 (407)
431 KOG0451|consensus 41.6 37 0.0008 25.7 3.1 54 2-64 374-427 (913)
432 PF13671 AAA_33: AAA domain; P 41.5 65 0.0014 18.0 6.4 27 3-31 13-39 (143)
433 TIGR01360 aden_kin_iso1 adenyl 41.1 65 0.0014 19.0 3.8 22 3-26 17-38 (188)
434 COG0514 RecQ Superfamily II DN 41.0 37 0.00081 25.2 3.1 37 15-61 108-144 (590)
435 cd01122 GP4d_helicase GP4d_hel 41.0 45 0.00098 21.2 3.2 21 43-63 135-155 (271)
436 PF12780 AAA_8: P-loop contain 40.9 56 0.0012 21.5 3.7 51 3-57 45-98 (268)
437 PF11760 CbiG_N: Cobalamin syn 40.6 58 0.0013 17.9 3.2 28 31-58 19-48 (84)
438 cd03284 ABC_MutS1 MutS1 homolo 40.6 35 0.00077 21.4 2.7 11 47-57 108-118 (216)
439 COG3854 SpoIIIAA ncharacterize 40.6 29 0.00063 23.4 2.3 21 39-59 209-229 (308)
440 PRK09404 sucA 2-oxoglutarate d 40.5 85 0.0018 24.6 5.0 51 7-67 402-453 (924)
441 cd04133 Rop_like Rop subfamily 40.2 44 0.00096 20.1 3.0 35 3-46 135-170 (176)
442 cd04141 Rit_Rin_Ric Rit/Rin/Ri 40.2 40 0.00086 19.9 2.7 20 4-23 128-147 (172)
443 PF13521 AAA_28: AAA domain; P 40.2 77 0.0017 18.5 4.9 25 3-28 13-37 (163)
444 cd03230 ABC_DR_subfamily_A Thi 39.8 58 0.0013 19.3 3.5 19 41-59 106-124 (173)
445 PRK06871 DNA polymerase III su 39.8 43 0.00094 22.7 3.1 30 33-62 88-121 (325)
446 TIGR00604 rad3 DNA repair heli 39.8 62 0.0013 24.1 4.1 39 15-62 196-234 (705)
447 PRK09401 reverse gyrase; Revie 39.7 26 0.00057 27.9 2.3 29 34-62 187-215 (1176)
448 cd03769 SR_IS607_transposase_l 39.6 38 0.00083 19.7 2.6 30 34-63 48-77 (134)
449 PRK13809 orotate phosphoribosy 39.4 29 0.00063 22.0 2.1 19 4-22 80-98 (206)
450 PLN02955 8-amino-7-oxononanoat 39.4 37 0.00079 24.4 2.8 24 37-61 268-291 (476)
451 TIGR01166 cbiO cobalt transpor 39.3 59 0.0013 19.5 3.4 15 44-58 141-155 (190)
452 PRK09112 DNA polymerase III su 39.2 24 0.00052 24.1 1.8 28 35-62 124-155 (351)
453 TIGR00228 ruvC crossover junct 39.2 68 0.0015 19.7 3.6 55 6-61 85-142 (156)
454 KOG2680|consensus 39.0 18 0.0004 25.3 1.2 41 3-44 80-122 (454)
455 PF03372 Exo_endo_phos: Endonu 38.9 43 0.00094 19.8 2.8 25 34-58 15-39 (249)
456 TIGR01090 apt adenine phosphor 38.8 12 0.00027 22.6 0.4 19 3-21 58-76 (169)
457 TIGR02173 cyt_kin_arch cytidyl 38.7 32 0.0007 20.0 2.2 19 2-20 13-31 (171)
458 PRK13631 cbiO cobalt transport 38.7 75 0.0016 21.2 4.1 18 40-57 186-203 (320)
459 TIGR01821 5aminolev_synth 5-am 38.6 40 0.00086 22.7 2.8 23 37-60 196-218 (402)
460 PF00155 Aminotran_1_2: Aminot 38.6 52 0.0011 21.5 3.3 29 33-62 166-194 (363)
461 COG1117 PstB ABC-type phosphat 38.5 50 0.0011 21.9 3.1 22 37-58 156-177 (253)
462 cd00529 RuvC_resolvase Hollida 38.2 39 0.00084 20.2 2.5 29 5-33 86-114 (154)
463 KOG1360|consensus 38.2 30 0.00066 25.0 2.2 25 36-61 321-345 (570)
464 PF01195 Pept_tRNA_hydro: Pept 38.2 34 0.00073 21.3 2.2 59 3-61 21-96 (184)
465 KOG0393|consensus 38.0 50 0.0011 21.1 3.0 35 3-46 141-176 (198)
466 PF09370 TIM-br_sig_trns: TIM- 38.0 1.1E+02 0.0024 20.6 4.7 25 30-54 194-218 (268)
467 PRK06027 purU formyltetrahydro 37.9 1.1E+02 0.0024 20.3 4.7 49 6-60 129-177 (286)
468 PF06506 PrpR_N: Propionate ca 37.9 70 0.0015 19.3 3.6 34 3-46 132-165 (176)
469 COG1489 SfsA DNA-binding prote 37.8 56 0.0012 21.5 3.3 49 17-65 129-189 (235)
470 COG1428 Deoxynucleoside kinase 37.8 34 0.00074 22.2 2.3 31 3-33 18-50 (216)
471 PF00910 RNA_helicase: RNA hel 37.7 21 0.00045 19.7 1.2 13 49-61 50-62 (107)
472 TIGR02788 VirB11 P-type DNA tr 37.6 38 0.00082 22.5 2.6 25 35-59 205-229 (308)
473 cd03226 ABC_cobalt_CbiO_domain 37.5 62 0.0013 19.7 3.4 16 43-58 139-154 (205)
474 PF03054 tRNA_Me_trans: tRNA m 37.5 37 0.00081 23.4 2.5 22 5-26 53-74 (356)
475 PF03808 Glyco_tran_WecB: Glyc 37.4 45 0.00098 20.2 2.7 22 33-54 86-107 (172)
476 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 37.3 53 0.0011 21.0 3.1 34 3-44 149-183 (232)
477 PRK05647 purN phosphoribosylgl 37.3 1.1E+02 0.0023 19.3 4.7 51 6-61 43-93 (200)
478 COG0621 MiaB 2-methylthioadeni 37.2 36 0.00078 24.3 2.5 31 23-53 300-330 (437)
479 PF03796 DnaB_C: DnaB-like hel 37.2 1.1E+02 0.0024 19.4 5.9 44 14-64 101-146 (259)
480 COG4178 ABC-type uncharacteriz 37.1 42 0.00091 25.0 2.9 20 40-59 525-544 (604)
481 TIGR01134 purF amidophosphorib 37.0 41 0.0009 23.7 2.8 16 3-18 285-300 (442)
482 COG3426 Butyrate kinase [Energ 37.0 36 0.00078 23.5 2.3 24 1-24 109-132 (358)
483 cd03246 ABCC_Protease_Secretio 36.9 68 0.0015 19.1 3.4 19 40-58 106-124 (173)
484 cd03297 ABC_ModC_molybdenum_tr 36.9 66 0.0014 19.7 3.5 16 43-58 144-159 (214)
485 cd03247 ABCC_cytochrome_bd The 36.9 67 0.0015 19.1 3.4 19 41-59 109-127 (178)
486 PF04951 Peptidase_M55: D-amin 36.8 1E+02 0.0022 20.5 4.4 22 4-25 137-158 (265)
487 cd04130 Wrch_1 Wrch-1 subfamil 36.8 39 0.00083 19.8 2.3 31 5-44 138-169 (173)
488 cd03223 ABCD_peroxisomal_ALDP 36.7 70 0.0015 19.0 3.4 19 41-59 102-120 (166)
489 cd00281 DAP_dppA Peptidase M55 36.7 1.1E+02 0.0023 20.4 4.5 23 4-26 136-158 (265)
490 PRK05339 PEP synthetase regula 36.7 1.3E+02 0.0028 20.1 5.3 44 3-53 19-63 (269)
491 PRK13543 cytochrome c biogenes 36.6 65 0.0014 19.8 3.4 17 42-58 149-165 (214)
492 TIGR00960 3a0501s02 Type II (G 36.5 67 0.0014 19.7 3.4 15 44-58 152-166 (216)
493 cd03213 ABCG_EPDR ABCG transpo 36.5 68 0.0015 19.5 3.4 16 44-59 125-140 (194)
494 cd03255 ABC_MJ0796_Lo1CDE_FtsE 36.4 63 0.0014 19.8 3.3 15 44-58 154-168 (218)
495 PRK08525 amidophosphoribosyltr 36.3 36 0.00078 24.0 2.4 15 3-17 287-301 (445)
496 cd08770 DAP_dppA_3 Peptidase M 36.2 1.1E+02 0.0024 20.4 4.5 23 4-26 137-159 (263)
497 PF02775 TPP_enzyme_C: Thiamin 36.1 90 0.0019 18.1 4.4 37 7-52 114-151 (153)
498 PF00676 E1_dh: Dehydrogenase 36.1 1.1E+02 0.0023 20.5 4.5 38 10-52 182-220 (300)
499 cd00462 PTH Peptidyl-tRNA hydr 36.0 26 0.00056 21.7 1.5 34 29-62 62-96 (171)
500 PRK12315 1-deoxy-D-xylulose-5- 35.9 1.3E+02 0.0028 22.1 5.1 39 8-55 201-241 (581)
No 1
>KOG0733|consensus
Probab=99.89 E-value=1.7e-23 Score=147.48 Aligned_cols=66 Identities=36% Similarity=0.702 Sum_probs=64.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|+||||+|+|.|.+|+.|.+++|+++|+||+|+.||++|++|+.++||||||||+|+|+++|++..
T Consensus 559 TLlAKAVANEag~NFisVKGPELlNkYVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~ 624 (802)
T KOG0733|consen 559 TLLAKAVANEAGANFISVKGPELLNKYVGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEG 624 (802)
T ss_pred HHHHHHHhhhccCceEeecCHHHHHHHhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCC
Confidence 899999999999999999999999999999999999999999999999999999999999999764
No 2
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=1.7e-22 Score=135.60 Aligned_cols=66 Identities=38% Similarity=0.540 Sum_probs=64.0
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|+||||+|++++++|+.+.+|+|+.+|+||+.+.||++|+.|++++||||||||||+|+.+|.+.+
T Consensus 199 TLLAkAVA~~T~AtFIrvvgSElVqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~ 264 (406)
T COG1222 199 TLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSG 264 (406)
T ss_pred HHHHHHHHhccCceEEEeccHHHHHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCC
Confidence 899999999999999999999999999999999999999999999999999999999999998753
No 3
>KOG0739|consensus
Probab=99.87 E-value=2.9e-22 Score=133.14 Aligned_cols=66 Identities=36% Similarity=0.585 Sum_probs=63.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
++||+|+|.+.+.+||.|+.++|+++|.||+|+.|+++|+.|++++|+||||||||++|++|+.++
T Consensus 180 SYLAKAVATEAnSTFFSvSSSDLvSKWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enE 245 (439)
T KOG0739|consen 180 SYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENE 245 (439)
T ss_pred HHHHHHHHhhcCCceEEeehHHHHHHHhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCc
Confidence 579999999999999999999999999999999999999999999999999999999999998764
No 4
>KOG0738|consensus
Probab=99.86 E-value=3.6e-22 Score=135.42 Aligned_cols=65 Identities=35% Similarity=0.497 Sum_probs=63.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|+||||+|.|++.+||+|+.+.+.|+|-||+|+.||-+|+.|+-++|++|||||||+||.+|++.
T Consensus 259 TlLAKAvATEc~tTFFNVSsstltSKwRGeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s 323 (491)
T KOG0738|consen 259 TLLAKAVATECGTTFFNVSSSTLTSKWRGESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGS 323 (491)
T ss_pred HHHHHHHHHhhcCeEEEechhhhhhhhccchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCc
Confidence 89999999999999999999999999999999999999999999999999999999999999875
No 5
>KOG0736|consensus
Probab=99.86 E-value=4.5e-22 Score=142.56 Aligned_cols=65 Identities=35% Similarity=0.658 Sum_probs=63.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|++|||+|.|++..|+.|.+++++.+|+|++|+|||++|++||+.+|||||+||+|+++|+|+..
T Consensus 719 TLlAKAVATEcsL~FlSVKGPELLNMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~s 783 (953)
T KOG0736|consen 719 TLLAKAVATECSLNFLSVKGPELLNMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGRS 783 (953)
T ss_pred HHHHHHHHhhceeeEEeecCHHHHHHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999864
No 6
>KOG0733|consensus
Probab=99.85 E-value=1.3e-21 Score=138.04 Aligned_cols=65 Identities=46% Similarity=0.781 Sum_probs=63.5
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|+||+++|+++++||+.++++++++.+.||+|++||++|++|+.++|||+||||||+|.++|+..
T Consensus 237 T~lA~AiAgel~vPf~~isApeivSGvSGESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~a 301 (802)
T KOG0733|consen 237 TSLANAIAGELGVPFLSISAPEIVSGVSGESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEA 301 (802)
T ss_pred HHHHHHHhhhcCCceEeecchhhhcccCcccHHHHHHHHHHHhccCCeEEEeecccccccchhhH
Confidence 89999999999999999999999999999999999999999999999999999999999999864
No 7
>KOG0730|consensus
Probab=99.84 E-value=1.6e-21 Score=137.67 Aligned_cols=65 Identities=38% Similarity=0.633 Sum_probs=63.2
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|++||++|++.+.+|+.+++++++++|+||+|+.|+++|++|++.+|||||+||||+++..|+++
T Consensus 482 T~lAkalAne~~~nFlsvkgpEL~sk~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~ 546 (693)
T KOG0730|consen 482 TLLAKALANEAGMNFLSVKGPELFSKYVGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGS 546 (693)
T ss_pred HHHHHHHhhhhcCCeeeccCHHHHHHhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999754
No 8
>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional
Probab=99.81 E-value=8.5e-20 Score=123.54 Aligned_cols=65 Identities=26% Similarity=0.300 Sum_probs=61.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-----cCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-----NSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-----~~p~iifiDEid~i~~~r~~~ 67 (69)
|++|+++|+++|++++.+++++|.++|+||+|++||++|+.|++ .+||||||||||+++++|++.
T Consensus 162 TllAraiA~elg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~ 231 (413)
T PLN00020 162 SFQCELVFKKMGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTT 231 (413)
T ss_pred HHHHHHHHHHcCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCC
Confidence 88999999999999999999999999999999999999999975 479999999999999998754
No 9
>KOG0734|consensus
Probab=99.79 E-value=1.1e-19 Score=127.32 Aligned_cols=66 Identities=32% Similarity=0.524 Sum_probs=63.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|+||||+|.|.++|||+.+++++-..|+|.+.++||.+|+.|++++||||||||||+++++|...+
T Consensus 351 TlLARAvAGEA~VPFF~~sGSEFdEm~VGvGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~~ 416 (752)
T KOG0734|consen 351 TLLARAVAGEAGVPFFYASGSEFDEMFVGVGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPSD 416 (752)
T ss_pred hHHHHHhhcccCCCeEeccccchhhhhhcccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCccH
Confidence 899999999999999999999999999999999999999999999999999999999999997653
No 10
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=99.78 E-value=5.2e-19 Score=121.73 Aligned_cols=65 Identities=42% Similarity=0.598 Sum_probs=63.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|++|+++|++++.+|+.+++++++++|+||++++|+++|..|++.+||||||||+|++++.|+..
T Consensus 290 T~lAkava~~~~~~fi~v~~~~l~sk~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~ 354 (494)
T COG0464 290 TLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPS 354 (494)
T ss_pred HHHHHHHHhhCCCeEEEeeCHHHhccccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999864
No 11
>KOG0740|consensus
Probab=99.74 E-value=3.2e-18 Score=116.96 Aligned_cols=65 Identities=38% Similarity=0.550 Sum_probs=62.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|+|++++|.|++..||.+++++|.++|+|++|+.||.+|+.|+..+|+|+||||+|+++.+|.+.
T Consensus 200 tmL~~aiAsE~~atff~iSassLtsK~~Ge~eK~vralf~vAr~~qPsvifidEidslls~Rs~~ 264 (428)
T KOG0740|consen 200 TMLAKAIATESGATFFNISASSLTSKYVGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKRSDN 264 (428)
T ss_pred HHHHHHHHhhhcceEeeccHHHhhhhccChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhcCCc
Confidence 79999999999999999999999999999999999999999999999999999999999998653
No 12
>KOG0735|consensus
Probab=99.73 E-value=6.1e-18 Score=121.13 Aligned_cols=66 Identities=39% Similarity=0.651 Sum_probs=63.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|+||.++|..++..|+.|.+++++++|+|.+|+++|.+|.+|+..+|||+|+||+|+++|+|+..+
T Consensus 715 T~la~a~a~~~~~~fisvKGPElL~KyIGaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDs 780 (952)
T KOG0735|consen 715 TLLASAIASNSNLRFISVKGPELLSKYIGASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHDS 780 (952)
T ss_pred HHHHHHHHhhCCeeEEEecCHHHHHHHhcccHHHHHHHHHHhhccCCeEEEeccccccCcccCCCC
Confidence 889999999999999999999999999999999999999999999999999999999999998653
No 13
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=99.73 E-value=4.8e-18 Score=111.49 Aligned_cols=63 Identities=29% Similarity=0.517 Sum_probs=61.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
|++|+++|+++++|++.+++.++++.++|++.++++++|+.|++.+|||+||||+|+|+-+|.
T Consensus 165 Tm~Akalane~kvp~l~vkat~liGehVGdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRr 227 (368)
T COG1223 165 TMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRR 227 (368)
T ss_pred HHHHHHHhcccCCceEEechHHHHHHHhhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhh
Confidence 899999999999999999999999999999999999999999999999999999999998775
No 14
>KOG0727|consensus
Probab=99.72 E-value=4.6e-18 Score=111.67 Aligned_cols=66 Identities=39% Similarity=0.549 Sum_probs=63.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|+|++++|+++...|+.+.+++++.+|.||+.+.+|.+|..|++++|+||||||||+|+.+|-+.+
T Consensus 203 tml~kava~~t~a~firvvgsefvqkylgegprmvrdvfrlakenapsiifideidaiatkrfdaq 268 (408)
T KOG0727|consen 203 TMLAKAVANHTTAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQ 268 (408)
T ss_pred HHHHHHHhhccchheeeeccHHHHHHHhccCcHHHHHHHHHHhccCCcEEEeehhhhHhhhhcccc
Confidence 899999999999999999999999999999999999999999999999999999999999886654
No 15
>KOG0728|consensus
Probab=99.72 E-value=1.1e-17 Score=109.83 Aligned_cols=65 Identities=31% Similarity=0.513 Sum_probs=62.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|++|+++|.++.+.|+.+++++++.+|.||+.+.+|++|-.|++++|+|||.||||+|++.|..+
T Consensus 195 tLlaraVahht~c~firvsgselvqk~igegsrmvrelfvmarehapsiifmdeidsigs~r~e~ 259 (404)
T KOG0728|consen 195 TLLARAVAHHTDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVES 259 (404)
T ss_pred hHHHHHHHhhcceEEEEechHHHHHHHhhhhHHHHHHHHHHHHhcCCceEeeecccccccccccC
Confidence 78999999999999999999999999999999999999999999999999999999999988764
No 16
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=7.7e-18 Score=118.72 Aligned_cols=65 Identities=37% Similarity=0.617 Sum_probs=62.8
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
.|+|||++|.+.++|||.+++|+++..|+|-+.+.+|.+|++|++++||||||||||++++.|+.
T Consensus 196 KTLLAkAvAgEA~VPFf~iSGS~FVemfVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~ 260 (596)
T COG0465 196 KTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGA 260 (596)
T ss_pred cHHHHHHHhcccCCCceeccchhhhhhhcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCC
Confidence 38999999999999999999999999999999999999999999999999999999999999963
No 17
>KOG0726|consensus
Probab=99.70 E-value=1.3e-17 Score=111.01 Aligned_cols=66 Identities=33% Similarity=0.558 Sum_probs=63.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|+||+|+|++++.+|+.+-+++++.+|.|++.+.+|++|+.|..++|+|+||||||+++.+|=+++
T Consensus 233 TLLAKAVANqTSATFlRvvGseLiQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~ 298 (440)
T KOG0726|consen 233 TLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSN 298 (440)
T ss_pred hHHHHHHhcccchhhhhhhhHHHHHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhccccccCC
Confidence 799999999999999999999999999999999999999999999999999999999999986654
No 18
>KOG0737|consensus
Probab=99.69 E-value=1.3e-17 Score=112.13 Aligned_cols=64 Identities=33% Similarity=0.453 Sum_probs=61.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|++.|.+|+.|+.+.+.++|+||+++.++.+|..|.+.+||||||||+|++.+.|..
T Consensus 141 TmlAKA~Akeaga~fInv~~s~lt~KWfgE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R~s 204 (386)
T KOG0737|consen 141 TMLAKAIAKEAGANFINVSVSNLTSKWFGEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRRS 204 (386)
T ss_pred HHHHHHHHHHcCCCcceeeccccchhhHHHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhccc
Confidence 8999999999999999999999999999999999999999999999999999999999988744
No 19
>KOG0731|consensus
Probab=99.68 E-value=6e-17 Score=116.43 Aligned_cols=63 Identities=40% Similarity=0.603 Sum_probs=61.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
|+||||+|.|.|+||+.+++++++..++|....++|.+|..|+.++||||||||||+++.+|.
T Consensus 358 TLLAKAiAGEAgVPF~svSGSEFvE~~~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~ 420 (774)
T KOG0731|consen 358 TLLAKAIAGEAGVPFFSVSGSEFVEMFVGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRG 420 (774)
T ss_pred HHHHHHHhcccCCceeeechHHHHHHhcccchHHHHHHHHHhhccCCeEEEeccccccccccc
Confidence 899999999999999999999999999999999999999999999999999999999999995
No 20
>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=99.67 E-value=1.6e-16 Score=113.91 Aligned_cols=64 Identities=45% Similarity=0.725 Sum_probs=62.0
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|++++.+|+.+++++++++|+|+++++++++|+.|+..+||||||||+|+++++|+.
T Consensus 501 T~lakalA~e~~~~fi~v~~~~l~~~~vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~ 564 (733)
T TIGR01243 501 TLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGA 564 (733)
T ss_pred HHHHHHHHHhcCCCEEEEehHHHhhcccCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCC
Confidence 7899999999999999999999999999999999999999999999999999999999998864
No 21
>CHL00195 ycf46 Ycf46; Provisional
Probab=99.66 E-value=2.6e-16 Score=109.31 Aligned_cols=63 Identities=24% Similarity=0.353 Sum_probs=60.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
|++|+++|++++.|++.++++++.++|+|+++++++++|+.|+..+||||||||||.++++++
T Consensus 273 TllAkaiA~e~~~~~~~l~~~~l~~~~vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~ 335 (489)
T CHL00195 273 SLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSE 335 (489)
T ss_pred HHHHHHHHHHhCCCEEEEEhHHhcccccChHHHHHHHHHHHHHhcCCcEEEehhhhhhhcccc
Confidence 789999999999999999999999999999999999999999999999999999999987644
No 22
>KOG0729|consensus
Probab=99.63 E-value=3.9e-16 Score=103.23 Aligned_cols=64 Identities=31% Similarity=0.443 Sum_probs=61.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+|+|+.++.-|+.|=+|+++.+|+||+.+.+|++|+.|+..+.||||+||||++++.|-+
T Consensus 225 tl~aravanrtdacfirvigselvqkyvgegarmvrelf~martkkaciiffdeidaiggarfd 288 (435)
T KOG0729|consen 225 TLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFD 288 (435)
T ss_pred hHHHHHHhcccCceEEeehhHHHHHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCcccc
Confidence 7899999999999999999999999999999999999999999999999999999999998854
No 23
>KOG0652|consensus
Probab=99.62 E-value=3.3e-16 Score=103.35 Aligned_cols=66 Identities=36% Similarity=0.627 Sum_probs=63.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|++||+.|++++.+|+.+.++.++.+|+|++.+.+|..|..|++.+|+||||||+|+|+.+|-+++
T Consensus 219 TlmARAcAaqT~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSe 284 (424)
T KOG0652|consen 219 TLMARACAAQTNATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSE 284 (424)
T ss_pred HHHHHHHHHhccchHHHhcchHHHhhhhcchHHHHHHHHHHhhccCCeEEEEechhhhcccccccc
Confidence 789999999999999999999999999999999999999999999999999999999999997753
No 24
>KOG0651|consensus
Probab=99.62 E-value=8.3e-16 Score=102.46 Aligned_cols=64 Identities=31% Similarity=0.482 Sum_probs=62.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|+..+++|+.+.++.+.++|.||+.+.||+.|..|+...|||||+||||+++++|..
T Consensus 180 Tlla~~Vaa~mg~nfl~v~ss~lv~kyiGEsaRlIRemf~yA~~~~pciifmdeiDAigGRr~s 243 (388)
T KOG0651|consen 180 TLLARAVAATMGVNFLKVVSSALVDKYIGESARLIRDMFRYAREVIPCIIFMDEIDAIGGRRFS 243 (388)
T ss_pred hHHHHHHHHhcCCceEEeeHhhhhhhhcccHHHHHHHHHHHHhhhCceEEeehhhhhhccEEec
Confidence 7899999999999999999999999999999999999999999999999999999999999854
No 25
>KOG0730|consensus
Probab=99.61 E-value=9.6e-16 Score=108.71 Aligned_cols=67 Identities=61% Similarity=0.912 Sum_probs=63.9
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcC-CeEEEEccccccccccccCC
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS-PSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~-p~iifiDEid~i~~~r~~~~ 68 (69)
.|++++++|++.++.++.++++++++++.||+++++|++|+.+.+++ |++|||||+|++|++|.+.+
T Consensus 231 kt~l~~aVa~e~~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~ 298 (693)
T KOG0730|consen 231 KTFLVRAVANEYGAFLFLINGPELISKFPGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREGAD 298 (693)
T ss_pred hHHHHHHHHHHhCceeEecccHHHHHhcccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccccc
Confidence 48899999999999999999999999999999999999999999999 99999999999999998753
No 26
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=99.55 E-value=1.4e-14 Score=98.57 Aligned_cols=64 Identities=39% Similarity=0.536 Sum_probs=61.2
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|++++.+|+.+.++++.++|+|++++.++++|+.|+..+|+||||||+|+++++|.+
T Consensus 193 T~LAkalA~~l~~~fi~i~~s~l~~k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~ 256 (398)
T PTZ00454 193 TMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFD 256 (398)
T ss_pred HHHHHHHHHhcCCCEEEEehHHHHHHhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhcccccc
Confidence 7899999999999999999999999999999999999999999999999999999999988743
No 27
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=99.55 E-value=1.9e-14 Score=97.47 Aligned_cols=64 Identities=41% Similarity=0.594 Sum_probs=61.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|++++.+|+.++++++.++|.|++++.++.+|+.++..+|+||||||+|+++++|.+
T Consensus 179 T~lAkaia~~~~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~ 242 (389)
T PRK03992 179 TLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTD 242 (389)
T ss_pred HHHHHHHHHHhCCCEEEeehHHHhHhhccchHHHHHHHHHHHHhcCCeEEEEechhhhhccccc
Confidence 7899999999999999999999999999999999999999999999999999999999988764
No 28
>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=99.55 E-value=9.8e-15 Score=101.01 Aligned_cols=64 Identities=38% Similarity=0.626 Sum_probs=61.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++++++|++++.+|+.++++++.+.++|+++++++++|+.|+..+||||||||+|+++++|+.
T Consensus 102 T~la~alA~~~~~~~~~i~~~~~~~~~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~ 165 (495)
T TIGR01241 102 TLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGA 165 (495)
T ss_pred HHHHHHHHHHcCCCeeeccHHHHHHHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhcccc
Confidence 7899999999999999999999999999999999999999999999999999999999988764
No 29
>CHL00206 ycf2 Ycf2; Provisional
Probab=99.52 E-value=2.9e-14 Score=109.54 Aligned_cols=63 Identities=16% Similarity=0.139 Sum_probs=54.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcc-----------------------------------------cChHHH--HHHH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKL-----------------------------------------AGESES--NLRK 39 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~-----------------------------------------~ges~~--~l~~ 39 (69)
|+||||+|+++++||+.++++++++++ +|+++. .|+.
T Consensus 1644 TlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~~~e~~e~~n~~~~~m~~~e~~~rIr~ 1723 (2281)
T CHL00206 1644 SYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMMNALTMDMMPKIDRFYITL 1723 (2281)
T ss_pred HHHHHHHHHhcCCceEEEEHHHHhhcccccccccccccccccccccccccccccchhhhhhcchhhhhhhhhhhHHHHHH
Confidence 789999999999999999999999765 223333 4999
Q ss_pred HHHHHHhcCCeEEEEccccccccccc
Q psy3868 40 AFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 40 if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
+|+.|++.+||||||||||+++++.+
T Consensus 1724 lFelARk~SPCIIFIDEIDaL~~~ds 1749 (2281)
T CHL00206 1724 QFELAKAMSPCIIWIPNIHDLNVNES 1749 (2281)
T ss_pred HHHHHHHCCCeEEEEEchhhcCCCcc
Confidence 99999999999999999999998643
No 30
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=99.49 E-value=4.2e-14 Score=97.33 Aligned_cols=64 Identities=36% Similarity=0.585 Sum_probs=61.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|++++.+|+.++++++.++|+|++++.++++|+.|+.++|+||||||+|+++.+|..
T Consensus 231 T~LAraIA~el~~~fi~V~~seL~~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~ 294 (438)
T PTZ00361 231 TLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYD 294 (438)
T ss_pred HHHHHHHHHhhCCCEEEEecchhhhhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCC
Confidence 8899999999999999999999999999999999999999999999999999999999988753
No 31
>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=99.49 E-value=1.7e-13 Score=78.73 Aligned_cols=62 Identities=39% Similarity=0.672 Sum_probs=59.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcC-CeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS-PSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~-p~iifiDEid~i~~~r 64 (69)
|++++.+|+.++.+++.++++++.+.+.+++++.++++|+.++... |+||||||+|.++++.
T Consensus 12 T~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~ 74 (132)
T PF00004_consen 12 TTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKS 74 (132)
T ss_dssp HHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHC
T ss_pred eHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccc
Confidence 7899999999999999999999999999999999999999999887 9999999999999877
No 32
>CHL00176 ftsH cell division protein; Validated
Probab=99.47 E-value=1.1e-13 Score=98.63 Aligned_cols=64 Identities=33% Similarity=0.556 Sum_probs=60.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|++.+.||+.++++++.+.++|.+.+.++.+|+.|+..+||||||||+|+++++|+.
T Consensus 230 T~LAralA~e~~~p~i~is~s~f~~~~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~ 293 (638)
T CHL00176 230 TLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGA 293 (638)
T ss_pred HHHHHHHHHHhCCCeeeccHHHHHHHhhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccC
Confidence 7899999999999999999999999999999999999999999999999999999999987753
No 33
>KOG0741|consensus
Probab=99.43 E-value=1.5e-13 Score=96.72 Aligned_cols=65 Identities=38% Similarity=0.555 Sum_probs=57.9
Q ss_pred hHHHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHHHh--------cCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEADK--------NSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--------~~p~iifiDEid~i~~~r~~~ 67 (69)
|++||.|.+-++. +--.||+++++++|+||+|++||++|..|.+ ..-.||.+||||+||..|++.
T Consensus 270 TLiARqIGkMLNArePKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~ 343 (744)
T KOG0741|consen 270 TLIARQIGKMLNAREPKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSM 343 (744)
T ss_pred hHHHHHHHHHhcCCCCcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCC
Confidence 7899999999984 5667999999999999999999999999964 345899999999999999874
No 34
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.42 E-value=4.3e-13 Score=95.58 Aligned_cols=64 Identities=34% Similarity=0.566 Sum_probs=61.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|+++++++++++.||+.++++++.+.++|.+++.++++|+.++..+||||||||+|+++++|+.
T Consensus 199 t~~~~~~a~~~~~~f~~is~~~~~~~~~g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~ 262 (644)
T PRK10733 199 TLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGA 262 (644)
T ss_pred HHHHHHHHHHcCCCEEEEehHHhHHhhhcccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCC
Confidence 7899999999999999999999999999999999999999999999999999999999988864
No 35
>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=99.40 E-value=6e-13 Score=93.08 Aligned_cols=64 Identities=34% Similarity=0.617 Sum_probs=57.6
Q ss_pred hHHHHHHHHHhCCc----------EEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAF----------FFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~----------~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifiDEid~i~~~r~~ 66 (69)
|++++++|++++.+ |+.+++++++++|+|+++++++.+|+.++.. .|+||||||+|+++++|+.
T Consensus 230 T~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~ 307 (512)
T TIGR03689 230 TLIAKAVANSLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGS 307 (512)
T ss_pred HHHHHHHHHhhccccccccCCceeEEeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCC
Confidence 78999999998654 7788899999999999999999999999764 7999999999999998864
No 36
>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=99.39 E-value=1.1e-12 Score=94.33 Aligned_cols=64 Identities=61% Similarity=0.934 Sum_probs=61.5
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++++++|++++.+++.++++++.+++.|+++++++++|+.+..+.|+||||||+|+++++|+.
T Consensus 226 T~laraia~~~~~~~i~i~~~~i~~~~~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~ 289 (733)
T TIGR01243 226 TLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREE 289 (733)
T ss_pred HHHHHHHHHHhCCeEEEEecHHHhcccccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccC
Confidence 7899999999999999999999999999999999999999999999999999999999998764
No 37
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=99.37 E-value=1.6e-12 Score=87.09 Aligned_cols=64 Identities=41% Similarity=0.588 Sum_probs=60.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|++++.+|+.+.++++..+|.|++++.++.+|+.++...|+||||||+|.++.+|.+
T Consensus 170 T~lakaia~~l~~~~~~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~ 233 (364)
T TIGR01242 170 TLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTD 233 (364)
T ss_pred HHHHHHHHHhCCCCEEecchHHHHHHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhcccccc
Confidence 7899999999999999999999999999999999999999999999999999999999887754
No 38
>KOG0732|consensus
Probab=99.34 E-value=9.9e-13 Score=97.25 Aligned_cols=64 Identities=41% Similarity=0.644 Sum_probs=60.3
Q ss_pred hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|..+. ..|+.-++++..++|+||.|++++.+|+.|++.+|+|||+||||.+++.|+.
T Consensus 313 Tl~araLa~~~s~~~~kisffmrkgaD~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSs 381 (1080)
T KOG0732|consen 313 TLMARALAAACSRGNRKISFFMRKGADCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSS 381 (1080)
T ss_pred hHHHHhhhhhhcccccccchhhhcCchhhccccCcHHHHHHHHHHHHhccCceEEeccccccccccccc
Confidence 789999999984 6889999999999999999999999999999999999999999999999964
No 39
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=99.09 E-value=3.6e-10 Score=81.58 Aligned_cols=62 Identities=21% Similarity=0.349 Sum_probs=56.6
Q ss_pred hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|++++++|.++ +.+++.++.+.+. .+|.|+.+++++++|+.++...|+||||||+|.|++.+
T Consensus 217 T~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g 290 (731)
T TIGR02639 217 TAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAG 290 (731)
T ss_pred HHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccC
Confidence 78999999987 7889999999998 57999999999999999988889999999999998764
No 40
>KOG0744|consensus
Probab=99.05 E-value=1.8e-10 Score=77.73 Aligned_cols=64 Identities=23% Similarity=0.316 Sum_probs=55.1
Q ss_pred hHHHHHHHHHhCC---------cEEEEchhhhhhcccChHHHHHHHHHHHHHhc-----CCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGA---------FFFLINGPEIMSKLAGESESNLRKAFEEADKN-----SPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~---------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~-----~p~iifiDEid~i~~~r~~ 66 (69)
|+|+|++|.++.. .++++|+..+++||++|+.+.|.++|++..+. .-..++|||+++++..|..
T Consensus 191 TSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s 268 (423)
T KOG0744|consen 191 TSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTS 268 (423)
T ss_pred hHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHh
Confidence 7899999999963 67999999999999999999999999998762 2345668999999988843
No 41
>CHL00095 clpC Clp protease ATP binding subunit
Probab=98.93 E-value=3.9e-09 Score=77.11 Aligned_cols=63 Identities=19% Similarity=0.334 Sum_probs=56.1
Q ss_pred hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
|.+|+.+|.+. +.+++.++.+.++ .+|.|+.+++++++|+.++...|+||||||+|.|.+.+.
T Consensus 214 Tal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~ 288 (821)
T CHL00095 214 TAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGA 288 (821)
T ss_pred HHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCC
Confidence 78889998886 4789999999988 469999999999999999888899999999999987654
No 42
>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=98.90 E-value=4e-09 Score=67.94 Aligned_cols=57 Identities=14% Similarity=0.322 Sum_probs=50.3
Q ss_pred hHHHHHHHHHh-------CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL-------GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~-------~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|++|+++|+.+ ..++++++++++.++|+|+++..++++|+.+ .++||||||+|.|.+
T Consensus 56 TtlA~~ia~~l~~~~~~~~~~~v~~~~~~l~~~~~g~~~~~~~~~~~~a---~~~VL~IDE~~~L~~ 119 (261)
T TIGR02881 56 TTVARILGKLFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIKKA---LGGVLFIDEAYSLAR 119 (261)
T ss_pred HHHHHHHHHHHHhcCcccCCceEEecHHHhhhhhccchHHHHHHHHHhc---cCCEEEEechhhhcc
Confidence 78999999874 2488999999999999999999999999887 368999999999974
No 43
>CHL00181 cbbX CbbX; Provisional
Probab=98.88 E-value=4.4e-09 Score=69.14 Aligned_cols=59 Identities=14% Similarity=0.263 Sum_probs=50.8
Q ss_pred hHHHHHHHHHhC-------CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLG-------AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~-------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|++|+++|..+. .+++.++.+++.++|+|+++.+++++|+.+ .+.||||||+|.+++.+
T Consensus 73 T~lAr~la~~~~~~g~~~~~~~~~v~~~~l~~~~~g~~~~~~~~~l~~a---~ggVLfIDE~~~l~~~~ 138 (287)
T CHL00181 73 TTVALKMADILYKLGYIKKGHLLTVTRDDLVGQYIGHTAPKTKEVLKKA---MGGVLFIDEAYYLYKPD 138 (287)
T ss_pred HHHHHHHHHHHHHcCCCCCCceEEecHHHHHHHHhccchHHHHHHHHHc---cCCEEEEEccchhccCC
Confidence 789999988762 369999999999999999999899998886 45899999999997654
No 44
>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=98.84 E-value=7.4e-09 Score=67.86 Aligned_cols=59 Identities=12% Similarity=0.229 Sum_probs=50.7
Q ss_pred hHHHHHHHHHhC-------CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLG-------AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~-------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|++|+++|..+. -+++.++++++.++|+|+++.+++++|+.+ .+++|||||+|.+.+++
T Consensus 72 T~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~~~~~g~~~~~~~~~~~~a---~~gvL~iDEi~~L~~~~ 137 (284)
T TIGR02880 72 TTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEILKRA---MGGVLFIDEAYYLYRPD 137 (284)
T ss_pred HHHHHHHHHHHHHcCCcccceEEEecHHHHhHhhcccchHHHHHHHHHc---cCcEEEEechhhhccCC
Confidence 788988888763 279999999999999999999999999887 45899999999997544
No 45
>PRK10865 protein disaggregation chaperone; Provisional
Probab=98.75 E-value=3.3e-08 Score=72.77 Aligned_cols=63 Identities=21% Similarity=0.344 Sum_probs=54.9
Q ss_pred hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r~ 65 (69)
|++++++|... +.+++.++.+.++ .+|.|+.++.++++|+.+.+ ..|+||||||+|.|.+.++
T Consensus 213 T~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~ 288 (857)
T PRK10865 213 TAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGK 288 (857)
T ss_pred HHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCC
Confidence 78999999988 7899999998887 55899999999999998654 5799999999999987653
No 46
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=3.7e-08 Score=66.58 Aligned_cols=66 Identities=30% Similarity=0.413 Sum_probs=55.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhh-cccChHHHH-HHHHHHHHH----hcCCeEEEEccccccccccccCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGESESN-LRKAFEEAD----KNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges~~~-l~~if~~a~----~~~p~iifiDEid~i~~~r~~~~ 68 (69)
|+||+.+|+.+++||-.-++..|.. .|+||...+ +.++.+.|. +.+..||||||||.|+++.++.+
T Consensus 111 TlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~S 182 (408)
T COG1219 111 TLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPS 182 (408)
T ss_pred HHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCC
Confidence 8999999999999999999999984 599998554 677776652 34689999999999998876654
No 47
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=98.72 E-value=2.3e-08 Score=68.74 Aligned_cols=57 Identities=26% Similarity=0.389 Sum_probs=50.0
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifiDEid~i~~~r~~ 66 (69)
|++|+.||..++.+|..+|+..- +.+.+|++|+.|++. +..|||+||||.+...+.+
T Consensus 62 TTlA~liA~~~~~~f~~~sAv~~-------gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD 122 (436)
T COG2256 62 TTLARLIAGTTNAAFEALSAVTS-------GVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQD 122 (436)
T ss_pred HHHHHHHHHhhCCceEEeccccc-------cHHHHHHHHHHHHHHHhcCCceEEEEehhhhcChhhhh
Confidence 89999999999999999999654 789999999999663 3699999999999877654
No 48
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=98.69 E-value=5.5e-08 Score=70.96 Aligned_cols=63 Identities=16% Similarity=0.316 Sum_probs=54.6
Q ss_pred hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
|++|+++|... +..++.++.+.++ .+|.|+.+++++++|+.+++..++||||||+|.|++.+.
T Consensus 221 T~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~ 295 (758)
T PRK11034 221 TAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGA 295 (758)
T ss_pred HHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCC
Confidence 67888888764 6778888888887 468999999999999999888899999999999987764
No 49
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=98.66 E-value=8.3e-08 Score=65.99 Aligned_cols=63 Identities=29% Similarity=0.378 Sum_probs=50.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhh-cccChHHH-HHHHHHHHH----HhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGESES-NLRKAFEEA----DKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges~~-~l~~if~~a----~~~~p~iifiDEid~i~~~r~ 65 (69)
|++|+++|+.+++||+.++++.+.. .|+|+... .+..+++.+ ....++||||||||.+.+++.
T Consensus 122 T~lAr~lA~~l~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~ 190 (412)
T PRK05342 122 TLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSE 190 (412)
T ss_pred HHHHHHHHHHhCCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccC
Confidence 7899999999999999999998864 69998644 456666542 345789999999999987643
No 50
>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=98.64 E-value=1.1e-07 Score=69.99 Aligned_cols=62 Identities=21% Similarity=0.344 Sum_probs=53.5
Q ss_pred hHHHHHHHHHh----------CCcEEEEchhhhh--hcccChHHHHHHHHHHHHHh-cCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL----------GAFFFLINGPEIM--SKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~----------~~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r 64 (69)
|++++++|... +.+++.++.+.++ .+|.|+.+++++++|+.+.+ ..|+||||||+|.|++.+
T Consensus 208 T~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g 282 (852)
T TIGR03346 208 TAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAG 282 (852)
T ss_pred HHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCC
Confidence 77888888885 6789999988886 56999999999999999865 469999999999998644
No 51
>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=98.62 E-value=9.9e-08 Score=65.70 Aligned_cols=64 Identities=30% Similarity=0.410 Sum_probs=50.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhh-cccChH-HHHHHHHHHHH----HhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGES-ESNLRKAFEEA----DKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges-~~~l~~if~~a----~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|..++.||..++++.+.. +|+|+. +..+..+++.+ ....|+||||||+|.+.+++++
T Consensus 130 T~lAraLA~~l~~pf~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~ 199 (413)
T TIGR00382 130 TLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSEN 199 (413)
T ss_pred HHHHHHHHHhcCCCeEEechhhccccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhcc
Confidence 7899999999999999999998763 589986 45566665533 2457899999999999986543
No 52
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=98.61 E-value=7.6e-08 Score=66.66 Aligned_cols=64 Identities=58% Similarity=0.838 Sum_probs=60.0
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
-|+++++++++ +..++.++++.+.++|.|+++.+++.+|+.++..+|+++++||+|.+.++|..
T Consensus 31 ~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~d~~~~~~~~~~~ 94 (494)
T COG0464 31 KTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSS 94 (494)
T ss_pred hhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEeechhhhcccCccc
Confidence 37899999999 87779999999999999999999999999999999999999999999999876
No 53
>KOG0736|consensus
Probab=98.59 E-value=1.6e-07 Score=68.80 Aligned_cols=65 Identities=20% Similarity=0.422 Sum_probs=61.2
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
|++++++|.++|.+++.++|.++.+.-.+-+|.++...|..|+.+.|+|||+-..|.+..+++++
T Consensus 445 ~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~dgg 509 (953)
T KOG0736|consen 445 TTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQDGG 509 (953)
T ss_pred HHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCCCc
Confidence 67899999999999999999999999999999999999999999999999999999999777654
No 54
>KOG0742|consensus
Probab=98.55 E-value=8.4e-08 Score=66.88 Aligned_cols=66 Identities=23% Similarity=0.360 Sum_probs=57.5
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccccCCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKREKREL 69 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r~~~~~ 69 (69)
|++|+.+|.+.|..+-...+.++ .+.-.+....|+++|+++++ ++.-+|||||.|++...|....|
T Consensus 398 Tm~ArelAr~SGlDYA~mTGGDV-APlG~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnktym 464 (630)
T KOG0742|consen 398 TMFARELARHSGLDYAIMTGGDV-APLGAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKTYM 464 (630)
T ss_pred hHHHHHHHhhcCCceehhcCCCc-cccchHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchhhh
Confidence 89999999999999999999887 55566788899999999987 56789999999999998887644
No 55
>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=98.55 E-value=1.2e-07 Score=69.02 Aligned_cols=61 Identities=16% Similarity=0.280 Sum_probs=50.5
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhh---------hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIM---------SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~---------~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|++|+++|+.++.+++.++.+.+. ..|+|.....+.+.|..+....| ||||||||.+.++.
T Consensus 361 T~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~g~i~~~l~~~~~~~~-villDEidk~~~~~ 430 (775)
T TIGR00763 361 TSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNP-LFLLDEIDKIGSSF 430 (775)
T ss_pred HHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCCCCchHHHHHHHhCcCCC-EEEEechhhcCCcc
Confidence 889999999999999998764431 36888888889999998866666 78999999998753
No 56
>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=98.55 E-value=2.8e-07 Score=67.99 Aligned_cols=63 Identities=17% Similarity=0.250 Sum_probs=53.3
Q ss_pred hHHHHHHHHHh----------CCcEEEEchhhhhh--cccChHHHHHHHHHHHHHh-cCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSL----------GAFFFLINGPEIMS--KLAGESESNLRKAFEEADK-NSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~----------~~~~~~v~~~~l~~--~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~~r~ 65 (69)
|.+++.+|... +.+++.++.+.+.+ ++.|+.+++++++|+.++. ..++||||||+|.+.+.++
T Consensus 222 Tal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~ 297 (852)
T TIGR03345 222 TAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGG 297 (852)
T ss_pred HHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCC
Confidence 78889999876 35688888888774 6999999999999999965 4789999999999997654
No 57
>KOG0745|consensus
Probab=98.52 E-value=2.6e-07 Score=64.51 Aligned_cols=63 Identities=30% Similarity=0.440 Sum_probs=54.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhh-hcccChH-HHHHHHHHHHHH----hcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIM-SKLAGES-ESNLRKAFEEAD----KNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~-~~~~ges-~~~l~~if~~a~----~~~p~iifiDEid~i~~~r~ 65 (69)
|+||+.+|.-+++||...+|..+. ..|+||. |.-|.++...|. +.+..|+|+||+|.|..+-.
T Consensus 240 TllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~~~~ 308 (564)
T KOG0745|consen 240 TLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITKKAE 308 (564)
T ss_pred hHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcccCc
Confidence 889999999999999999999997 4599997 777899998873 45789999999999985433
No 58
>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=98.46 E-value=1.1e-07 Score=61.33 Aligned_cols=54 Identities=26% Similarity=0.495 Sum_probs=35.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+||+.+|++++.+|..++++.+ +....+..++... ....||||||||.+.+..
T Consensus 64 TTLA~IIA~e~~~~~~~~sg~~i------~k~~dl~~il~~l--~~~~ILFIDEIHRlnk~~ 117 (233)
T PF05496_consen 64 TTLARIIANELGVNFKITSGPAI------EKAGDLAAILTNL--KEGDILFIDEIHRLNKAQ 117 (233)
T ss_dssp HHHHHHHHHHCT--EEEEECCC--------SCHHHHHHHHT----TT-EEEECTCCC--HHH
T ss_pred hHHHHHHHhccCCCeEeccchhh------hhHHHHHHHHHhc--CCCcEEEEechhhccHHH
Confidence 89999999999999999998765 2234555565554 346899999999987653
No 59
>KOG2028|consensus
Probab=98.40 E-value=5.6e-07 Score=62.16 Aligned_cols=57 Identities=21% Similarity=0.419 Sum_probs=48.6
Q ss_pred hHHHHHHHHHhCCc---EEEEchhhhhhcccChHHHHHHHHHHHHHh-----cCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAF---FFLINGPEIMSKLAGESESNLRKAFEEADK-----NSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~---~~~v~~~~l~~~~~ges~~~l~~if~~a~~-----~~p~iifiDEid~i~~~r~~ 66 (69)
|+||+.+++....+ |+++++.+- +.+.+|.+|+++++ .+..||||||||.+...+.+
T Consensus 176 TtlArlia~tsk~~SyrfvelSAt~a-------~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNksQQD 240 (554)
T KOG2028|consen 176 TTLARLIASTSKKHSYRFVELSATNA-------KTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNKSQQD 240 (554)
T ss_pred HHHHHHHHhhcCCCceEEEEEecccc-------chHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhhhhhh
Confidence 78999999998876 888888654 67889999999976 46899999999999887665
No 60
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=98.20 E-value=1.7e-06 Score=57.70 Aligned_cols=53 Identities=23% Similarity=0.519 Sum_probs=44.0
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
|+||..+|+|+|+++-..+++.+ +....+-.++...+ ...|+||||||++.+.
T Consensus 66 TTLA~IIA~Emgvn~k~tsGp~l------eK~gDlaaiLt~Le--~~DVLFIDEIHrl~~~ 118 (332)
T COG2255 66 TTLAHIIANELGVNLKITSGPAL------EKPGDLAAILTNLE--EGDVLFIDEIHRLSPA 118 (332)
T ss_pred HHHHHHHHHHhcCCeEecccccc------cChhhHHHHHhcCC--cCCeEEEehhhhcChh
Confidence 88999999999999999999888 45666777776653 3599999999999764
No 61
>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=98.04 E-value=1.4e-05 Score=44.69 Aligned_cols=62 Identities=26% Similarity=0.435 Sum_probs=50.2
Q ss_pred hHHHHHHHHHhCCc---EEEEchhhhhhc--------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLGAF---FFLINGPEIMSK--------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~~~---~~~v~~~~l~~~--------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|++++.++..+... ++.++++..... ........++.+++.++...|.+|++||++.+....
T Consensus 16 Ttl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDei~~~~~~~ 94 (148)
T smart00382 16 TTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAE 94 (148)
T ss_pred HHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCEEEEECCcccCCHH
Confidence 78899999999875 888888765432 334567788899999988889999999999997654
No 62
>KOG0735|consensus
Probab=98.02 E-value=1.5e-05 Score=58.65 Aligned_cols=61 Identities=25% Similarity=0.279 Sum_probs=53.6
Q ss_pred hHHHHHHHHHhC----CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLG----AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
|.|+++++++.. +++..++|+.+-.+-+....+.++.+|..+..++|+||++|++|.|++.
T Consensus 445 T~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~ 509 (952)
T KOG0735|consen 445 TNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYAPSIIVLDDLDCLASA 509 (952)
T ss_pred hHHHHHHHHHhccccceEEEEEechhccchhHHHHHHHHHHHHHHHHhhCCcEEEEcchhhhhcc
Confidence 679999999886 5778899999977767777888999999999999999999999999983
No 63
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=2.8e-05 Score=57.24 Aligned_cols=52 Identities=23% Similarity=0.413 Sum_probs=46.5
Q ss_pred CCcEEEEchhhhhhc--ccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 14 GAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 14 ~~~~~~v~~~~l~~~--~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
+..++.++.+.++.. |-|+-|.+++.+.+..++..+.||||||+|.|.+.-.
T Consensus 226 ~~~i~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~ 279 (786)
T COG0542 226 DKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGA 279 (786)
T ss_pred CCEEEEecHHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCc
Confidence 568899999999854 9999999999999999988899999999999977554
No 64
>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=97.82 E-value=1.2e-05 Score=55.87 Aligned_cols=57 Identities=19% Similarity=0.239 Sum_probs=48.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhh-cccC-hHHHHHHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAG-ESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~-~~~g-es~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
|++|+++|..++.||+.++++.+.. .|+| +.+..++.+|+.|... +| +|.+++.|..
T Consensus 61 T~lAraLA~~l~~~fi~vdat~~~e~g~vG~dvE~i~r~l~e~A~~~------i~-~d~i~~~r~~ 119 (441)
T TIGR00390 61 TEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAAVKL------VK-EEAIEKVRDR 119 (441)
T ss_pred HHHHHHHHHHhCCeEEEeecceeecCCcccCCHHHHHHHHHHHHHHH------HH-HHHHhHHHHH
Confidence 7899999999999999999998874 7999 6899999999999663 34 6888887743
No 65
>PRK13342 recombination factor protein RarA; Reviewed
Probab=97.80 E-value=6.6e-05 Score=51.37 Aligned_cols=53 Identities=25% Similarity=0.357 Sum_probs=43.0
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
|++|+++++.++.+|+.+++... +.+.++++++.++. .++.+|||||+|.+..
T Consensus 50 TtLA~~ia~~~~~~~~~l~a~~~-------~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~ 106 (413)
T PRK13342 50 TTLARIIAGATDAPFEALSAVTS-------GVKDLREVIEEARQRRSAGRRTILFIDEIHRFNK 106 (413)
T ss_pred HHHHHHHHHHhCCCEEEEecccc-------cHHHHHHHHHHHHHhhhcCCceEEEEechhhhCH
Confidence 78999999999999999988642 45667788877753 3678999999998864
No 66
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=97.78 E-value=3.8e-05 Score=56.55 Aligned_cols=61 Identities=13% Similarity=0.248 Sum_probs=47.0
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhh---------hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIM---------SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~---------~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|++++.+|+.++.+++.++.+... ..|.|.....+.+.+..+....| ++|+||+|.+.++.
T Consensus 363 Ttl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~~~~~g~~~G~~~~~l~~~~~~~~-villDEidk~~~~~ 432 (784)
T PRK10787 363 TSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGVKNP-LFLLDEIDKMSSDM 432 (784)
T ss_pred HHHHHHHHHHhCCCEEEEEcCCCCCHHHhccchhccCCCCCcHHHHHHHhcCCCCC-EEEEEChhhccccc
Confidence 789999999999999988765532 24777777777777776654444 78999999998764
No 67
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=97.66 E-value=0.00018 Score=40.59 Aligned_cols=58 Identities=31% Similarity=0.543 Sum_probs=40.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHH---HHHHHHHHHhcCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESN---LRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~---l~~if~~a~~~~p~iifiDEid~i 60 (69)
|++++.+++.+ +.+++.+++......+....... ....+.......+.+|++||++.+
T Consensus 33 T~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~ 96 (151)
T cd00009 33 TTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL 96 (151)
T ss_pred HHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhh
Confidence 67899999998 89999999988765433332222 122233344567899999999976
No 68
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=97.56 E-value=0.00019 Score=47.65 Aligned_cols=52 Identities=19% Similarity=0.476 Sum_probs=38.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|++|+++|++++..+...+++.+. ....+..++... ..+++|||||+|.+..
T Consensus 65 T~la~~ia~~l~~~~~~~~~~~~~------~~~~l~~~l~~l--~~~~vl~IDEi~~l~~ 116 (328)
T PRK00080 65 TTLANIIANEMGVNIRITSGPALE------KPGDLAAILTNL--EEGDVLFIDEIHRLSP 116 (328)
T ss_pred HHHHHHHHHHhCCCeEEEeccccc------ChHHHHHHHHhc--ccCCEEEEecHhhcch
Confidence 789999999999998887766442 233455555543 3579999999999864
No 69
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=97.54 E-value=7.5e-05 Score=54.91 Aligned_cols=60 Identities=18% Similarity=0.295 Sum_probs=40.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhh-----cccChHH-----HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMS-----KLAGESE-----SNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~-----~~~ges~-----~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|.+|+++|..++.+++.++++++.. +++|... ..-..+.+..+.+..+||||||+|.+.+
T Consensus 502 T~lAk~LA~~l~~~~i~id~se~~~~~~~~~LiG~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~~ 571 (758)
T PRK11034 502 TEVTVQLSKALGIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHP 571 (758)
T ss_pred HHHHHHHHHHhCCCcEEeechhhcccccHHHHcCCCCCcccccccchHHHHHHhCCCcEEEeccHhhhhH
Confidence 7899999999999999999887632 2333210 1111233334455669999999998854
No 70
>PRK04195 replication factor C large subunit; Provisional
Probab=97.51 E-value=0.00034 Score=48.80 Aligned_cols=54 Identities=19% Similarity=0.257 Sum_probs=41.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh------cCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK------NSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~------~~p~iifiDEid~i~~ 62 (69)
|++|+++|++++.+++.+++++.. +...++.+...+.. ..+.+|+|||+|.+..
T Consensus 53 Ttla~ala~el~~~~ielnasd~r------~~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~ 112 (482)
T PRK04195 53 TSLAHALANDYGWEVIELNASDQR------TADVIERVAGEAATSGSLFGARRKLILLDEVDGIHG 112 (482)
T ss_pred HHHHHHHHHHcCCCEEEEcccccc------cHHHHHHHHHHhhccCcccCCCCeEEEEecCccccc
Confidence 789999999999999999998752 23345555544432 2578999999999976
No 71
>PRK04132 replication factor C small subunit; Provisional
Probab=97.50 E-value=0.00032 Score=52.25 Aligned_cols=54 Identities=22% Similarity=0.282 Sum_probs=42.0
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcC------CeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNS------PSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~------p~iifiDEid~i~~ 62 (69)
|++|+++|+++ +.+++++|+++-. +...||++.+.+.... ..|++|||+|.+-.
T Consensus 580 TT~A~ala~~l~g~~~~~~~lElNASd~r------gid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~ 644 (846)
T PRK04132 580 TTAALALARELFGENWRHNFLELNASDER------GINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ 644 (846)
T ss_pred HHHHHHHHHhhhcccccCeEEEEeCCCcc------cHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCCH
Confidence 88999999998 5689999999841 3457888777654433 36999999999964
No 72
>KOG0741|consensus
Probab=97.46 E-value=0.00034 Score=50.47 Aligned_cols=57 Identities=26% Similarity=0.367 Sum_probs=45.5
Q ss_pred hHHHHHHHHHhCCcEEEE-chhhhhhcccChHH--HHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLI-NGPEIMSKLAGESE--SNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v-~~~~l~~~~~ges~--~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|.||-.+|...+.||+.+ ++.++.+ ..|++ ..++++|+.|++..-+||++|+|+.|.
T Consensus 552 TaLAA~iA~~S~FPFvKiiSpe~miG--~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLi 611 (744)
T KOG0741|consen 552 TALAAKIALSSDFPFVKIISPEDMIG--LSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLL 611 (744)
T ss_pred HHHHHHHHhhcCCCeEEEeChHHccC--ccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhh
Confidence 788999999999999985 5555533 23333 349999999999999999999999874
No 73
>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional
Probab=97.44 E-value=0.00017 Score=50.31 Aligned_cols=47 Identities=19% Similarity=0.162 Sum_probs=41.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhh-cccC-hHHHHHHHHHHHHHhcCC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAG-ESESNLRKAFEEADKNSP 49 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~-~~~g-es~~~l~~if~~a~~~~p 49 (69)
|++|+++|+.++.||+.++++.+.. .|+| +.+..++++|+.|....|
T Consensus 64 T~LAr~LAk~l~~~fi~vD~t~f~e~GyvG~d~e~~ir~L~~~A~~~~~ 112 (443)
T PRK05201 64 TEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKMVR 112 (443)
T ss_pred HHHHHHHHHHhCChheeecchhhccCCcccCCHHHHHHHHHHHHHHHhH
Confidence 7899999999999999999999986 6999 668999999999954444
No 74
>KOG1969|consensus
Probab=97.40 E-value=0.00042 Score=51.24 Aligned_cols=52 Identities=21% Similarity=0.322 Sum_probs=42.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh--------cCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK--------NSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--------~~p~iifiDEid~i 60 (69)
|+||+.+|++.|..++++|+|+= .+...+++....|.. .+|..|++||||.-
T Consensus 340 TTLAHViAkqaGYsVvEINASDe------Rt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa 399 (877)
T KOG1969|consen 340 TTLAHVIAKQAGYSVVEINASDE------RTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGA 399 (877)
T ss_pred hHHHHHHHHhcCceEEEeccccc------ccHHHHHHHHHHHHhhccccccCCCcceEEEecccCC
Confidence 78999999999999999999984 456666666666543 47999999999963
No 75
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=97.40 E-value=0.00031 Score=48.56 Aligned_cols=60 Identities=15% Similarity=0.241 Sum_probs=41.6
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHH-HHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESN-LRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~-l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|++++++++ +..++++++.++...+.+.-... ..+..+.. ..+.+|+|||+|.+.+++
T Consensus 162 ThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~--~~~dlLiiDDi~~l~~~~ 227 (450)
T PRK00149 162 THLLHAIGNYILEKNPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKY--RSVDVLLIDDIQFLAGKE 227 (450)
T ss_pred HHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHH--hcCCEEEEehhhhhcCCH
Confidence 78999999987 56789999998876654443221 22222222 257899999999997754
No 76
>KOG2004|consensus
Probab=97.34 E-value=0.00035 Score=51.65 Aligned_cols=59 Identities=20% Similarity=0.383 Sum_probs=48.4
Q ss_pred hHHHHHHHHHhCCcEEEEchh------hhh---hcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGP------EIM---SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~------~l~---~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|++++.||..+|..||.++.. ++- ..|+|....++=+..+....+.| +++|||||.+++
T Consensus 452 TSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHRRTYVGAMPGkiIq~LK~v~t~NP-liLiDEvDKlG~ 519 (906)
T KOG2004|consen 452 TSIAKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKVKTENP-LILIDEVDKLGS 519 (906)
T ss_pred ccHHHHHHHHhCCceEEEeccccccHHhhcccceeeeccCChHHHHHHHhhCCCCc-eEEeehhhhhCC
Confidence 789999999999999998764 333 34999998888888888877666 555999999985
No 77
>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=97.33 E-value=0.00056 Score=42.03 Aligned_cols=59 Identities=19% Similarity=0.266 Sum_probs=39.9
Q ss_pred hHHHHHHHHHhCC----cEEEEchhhhhhcccChHHHHHHHHHHHHH----hcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLGA----FFFLINGPEIMSKLAGESESNLRKAFEEAD----KNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~~----~~~~v~~~~l~~~~~ges~~~l~~if~~a~----~~~p~iifiDEid~i~~~ 63 (69)
|.+|+++|..+.. +++.++++++.. -++.+..+.++...+. .....|||+||||.+.++
T Consensus 17 T~la~~la~~l~~~~~~~~~~~d~s~~~~--~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~~~ 83 (171)
T PF07724_consen 17 TELAKALAELLFVGSERPLIRIDMSEYSE--GDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAHPS 83 (171)
T ss_dssp HHHHHHHHHHHT-SSCCEEEEEEGGGHCS--HHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCSHT
T ss_pred HHHHHHHHHHhccCCccchHHHhhhcccc--cchHHhhhhhhhhcccceeeccchhhhhhHHHhhcccc
Confidence 6799999999996 999999999865 1122333334443321 112349999999999873
No 78
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=97.32 E-value=0.00059 Score=49.87 Aligned_cols=58 Identities=21% Similarity=0.298 Sum_probs=41.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhc------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSK------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|.+|+++|..++.+++.++++++..+ |+|..+ -..+.+..+.+..+||||||+|.+-+
T Consensus 498 T~lA~~la~~l~~~~~~~d~se~~~~~~~~~lig~~~gyvg~~~--~~~l~~~~~~~p~~VvllDEieka~~ 567 (731)
T TIGR02639 498 TELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQ--GGLLTEAVRKHPHCVLLLDEIEKAHP 567 (731)
T ss_pred HHHHHHHHHHhcCCeEEEeCchhhhcccHHHHhcCCCCCcccch--hhHHHHHHHhCCCeEEEEechhhcCH
Confidence 78999999999999999998876431 333221 22344444556678999999998754
No 79
>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=97.31 E-value=0.00043 Score=47.13 Aligned_cols=60 Identities=13% Similarity=0.237 Sum_probs=40.4
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHH-HHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESES-NLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~-~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|++++++++ +..++++++.++...+.+.-.. .+....+.. ..+.+|+|||+|.+.+++
T Consensus 150 ThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~--~~~dlLiiDDi~~l~~~~ 215 (405)
T TIGR00362 150 THLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKY--RSVDLLLIDDIQFLAGKE 215 (405)
T ss_pred HHHHHHHHHHHHHhCCCCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHH--HhCCEEEEehhhhhcCCH
Confidence 78999999887 6789999998886654433211 122222222 236899999999997753
No 80
>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=97.30 E-value=0.00052 Score=44.70 Aligned_cols=53 Identities=19% Similarity=0.465 Sum_probs=36.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
|++++++|++++.++..++++.+.. ...+...+... ..+.+|||||+|.+.+.
T Consensus 44 T~la~~ia~~~~~~~~~~~~~~~~~------~~~l~~~l~~~--~~~~vl~iDEi~~l~~~ 96 (305)
T TIGR00635 44 TTLAHIIANEMGVNLKITSGPALEK------PGDLAAILTNL--EEGDVLFIDEIHRLSPA 96 (305)
T ss_pred HHHHHHHHHHhCCCEEEeccchhcC------chhHHHHHHhc--ccCCEEEEehHhhhCHH
Confidence 7899999999999887776654321 22333333332 35789999999998654
No 81
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=97.21 E-value=0.00076 Score=49.67 Aligned_cols=60 Identities=22% Similarity=0.359 Sum_probs=49.4
Q ss_pred hHHHHHHHHHhCCcEEEEchh------hhh---hcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGP------EIM---SKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~------~l~---~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
|+|++.||..+|..|+.++-. ++- ..|+|.-..++-+-.+.|....| ++++||||.+..+
T Consensus 364 TSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHRRTYIGamPGrIiQ~mkka~~~NP-v~LLDEIDKm~ss 432 (782)
T COG0466 364 TSLGKSIAKALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKAGVKNP-VFLLDEIDKMGSS 432 (782)
T ss_pred hhHHHHHHHHhCCCEEEEecCccccHHHhccccccccccCChHHHHHHHHhCCcCC-eEEeechhhccCC
Confidence 899999999999999998763 333 34899988888888888877666 4559999999875
No 82
>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=97.21 E-value=0.0014 Score=42.41 Aligned_cols=58 Identities=19% Similarity=0.240 Sum_probs=38.2
Q ss_pred hHHHHHHHHHhCCcEEEEch------hhhhhcccChHHHHHHHHH--------------------HHHHhcCCeEEEEcc
Q psy3868 3 YRLTTLCRDSLGAFFFLING------PEIMSKLAGESESNLRKAF--------------------EEADKNSPSIIFIDE 56 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~------~~l~~~~~ges~~~l~~if--------------------~~a~~~~p~iifiDE 56 (69)
|++|+++|+.+|.+++.+++ +++++.|.|...+.+..-| -.|. ..+.+|++||
T Consensus 35 T~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~~A~-~~g~~lllDE 113 (262)
T TIGR02640 35 TTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLTLAV-REGFTLVYDE 113 (262)
T ss_pred HHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCchHHHHH-HcCCEEEEcc
Confidence 78999999999999998865 4566655543322221111 1121 2457999999
Q ss_pred ccccc
Q psy3868 57 LDAIA 61 (69)
Q Consensus 57 id~i~ 61 (69)
++.+-
T Consensus 114 i~r~~ 118 (262)
T TIGR02640 114 FTRSK 118 (262)
T ss_pred hhhCC
Confidence 99864
No 83
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=97.20 E-value=0.00097 Score=49.03 Aligned_cols=54 Identities=22% Similarity=0.335 Sum_probs=40.2
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-----cCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-----NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-----~~p~iifiDEid~i~~~ 63 (69)
|++|+++++..+.+|+.+++... +.+.++++++.+.. ..+.+|||||+|.+...
T Consensus 66 TTLA~aIA~~~~~~f~~lna~~~-------~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~ 124 (725)
T PRK13341 66 TTLARIIANHTRAHFSSLNAVLA-------GVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKA 124 (725)
T ss_pred HHHHHHHHHHhcCcceeehhhhh-------hhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHH
Confidence 78999999999999999988642 23445666665532 34679999999998653
No 84
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=97.17 E-value=0.00086 Score=46.55 Aligned_cols=61 Identities=16% Similarity=0.297 Sum_probs=40.3
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhhhhcccChH-HHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGES-ESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges-~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|++++++++ +..++++++.+++..+...- ...+.+ |.......+.+|+|||++.+.++.
T Consensus 144 THLl~ai~~~l~~~~~~~~v~yi~~~~f~~~~~~~~~~~~~~~-f~~~~~~~~dvLlIDDi~~l~~~~ 210 (440)
T PRK14088 144 THLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNE-FREKYRKKVDVLLIDDVQFLIGKT 210 (440)
T ss_pred HHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHhcccHHH-HHHHHHhcCCEEEEechhhhcCcH
Confidence 78999999986 46788999988766543221 112222 222222468999999999987643
No 85
>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=97.14 E-value=0.00031 Score=47.40 Aligned_cols=59 Identities=20% Similarity=0.112 Sum_probs=42.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhc--ccChHHHHHH----------HHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSK--LAGESESNLR----------KAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~--~~ges~~~l~----------~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|++++.+|++++++++.++++..++. ++|...-.++ ..+-.|. ..++++++||+|..-+
T Consensus 78 Ttla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~-~~g~illlDEin~a~p 148 (327)
T TIGR01650 78 STHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWAL-QHNVALCFDEYDAGRP 148 (327)
T ss_pred HHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHH-hCCeEEEechhhccCH
Confidence 78999999999999999988777666 6665422211 1223332 3578999999998743
No 86
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=97.12 E-value=0.0018 Score=43.52 Aligned_cols=59 Identities=17% Similarity=0.164 Sum_probs=38.4
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhh----------hhcccC-------h-HHHHHHHHHHHHHh-cCCeEEEEcccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEI----------MSKLAG-------E-SESNLRKAFEEADK-NSPSIIFIDELD 58 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l----------~~~~~g-------e-s~~~l~~if~~a~~-~~p~iifiDEid 58 (69)
|++++.+++++ +..++++++... .....+ . ....+..+++..++ ..+.||+|||+|
T Consensus 69 T~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d 148 (394)
T PRK00411 69 TTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDIN 148 (394)
T ss_pred HHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHh
Confidence 67888888776 577888988532 222222 1 23344555555443 457899999999
Q ss_pred ccc
Q psy3868 59 AIA 61 (69)
Q Consensus 59 ~i~ 61 (69)
.+.
T Consensus 149 ~l~ 151 (394)
T PRK00411 149 YLF 151 (394)
T ss_pred Hhh
Confidence 998
No 87
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=96.96 E-value=0.0018 Score=46.96 Aligned_cols=61 Identities=11% Similarity=0.194 Sum_probs=43.5
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|++++++++ +..++++++.+++..+...-......-|+.-. ..+.+|+||||+.+..+.
T Consensus 328 THLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y-~~~DLLlIDDIq~l~gke 393 (617)
T PRK14086 328 THLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRY-REMDILLVDDIQFLEDKE 393 (617)
T ss_pred HHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHh-hcCCEEEEehhccccCCH
Confidence 78999999987 56889999999887765543332223344322 247999999999997754
No 88
>PHA02544 44 clamp loader, small subunit; Provisional
Probab=96.92 E-value=0.0028 Score=41.46 Aligned_cols=56 Identities=18% Similarity=0.335 Sum_probs=36.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHH-hcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEAD-KNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~-~~~p~iifiDEid~i~ 61 (69)
|+++++++++.+.+++.+++++ .+ +..-...+........ ...+.+|+|||+|.+.
T Consensus 57 T~la~~l~~~~~~~~~~i~~~~--~~-~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~ 113 (316)
T PHA02544 57 TTVAKALCNEVGAEVLFVNGSD--CR-IDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLG 113 (316)
T ss_pred HHHHHHHHHHhCccceEeccCc--cc-HHHHHHHHHHHHHhhcccCCCeEEEEECccccc
Confidence 7899999999999999999876 21 1111122222111111 1357899999999884
No 89
>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=96.81 E-value=0.0028 Score=47.31 Aligned_cols=58 Identities=19% Similarity=0.249 Sum_probs=40.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc------------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK------------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|.+|+++|..+ +..++.++++++..+ |+|..+.- .+.+..+++..+||+|||||..-+
T Consensus 610 T~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~g~~~gyvg~~~~g--~L~~~v~~~p~svvllDEieka~~ 682 (852)
T TIGR03345 610 TETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGG--VLTEAVRRKPYSVVLLDEVEKAHP 682 (852)
T ss_pred HHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhccccCCCCCcccccccc--hHHHHHHhCCCcEEEEechhhcCH
Confidence 78999999998 468889998876432 44443221 233445567789999999997654
No 90
>PF13173 AAA_14: AAA domain
Probab=96.73 E-value=0.0042 Score=35.96 Aligned_cols=57 Identities=23% Similarity=0.218 Sum_probs=34.9
Q ss_pred hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|++++.++.++. -.++.++..+.......+.. +.+.|......++.+|||||++.+-
T Consensus 16 Ttll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~iDEiq~~~ 74 (128)
T PF13173_consen 16 TTLLKQLAKDLLPPENILYINFDDPRDRRLADPD--LLEYFLELIKPGKKYIFIDEIQYLP 74 (128)
T ss_pred HHHHHHHHHHhcccccceeeccCCHHHHHHhhhh--hHHHHHHhhccCCcEEEEehhhhhc
Confidence 678888888876 67778877765332111111 2233333222378999999998773
No 91
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=96.71 E-value=0.0059 Score=40.57 Aligned_cols=60 Identities=20% Similarity=0.344 Sum_probs=38.2
Q ss_pred hHHHHHHHHHhC---------CcEEEEchhhhh----------hccc--C--------hHHHHHHHHHHHHHh-cCCeEE
Q psy3868 3 YRLTTLCRDSLG---------AFFFLINGPEIM----------SKLA--G--------ESESNLRKAFEEADK-NSPSII 52 (69)
Q Consensus 3 T~la~aia~~~~---------~~~~~v~~~~l~----------~~~~--g--------es~~~l~~if~~a~~-~~p~ii 52 (69)
|++++.+++++. ++++++++.... ..+. | ...+.++.+++.... ..+.||
T Consensus 54 T~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vl 133 (365)
T TIGR02928 54 TAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLII 133 (365)
T ss_pred HHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEE
Confidence 677888877653 578888875432 1111 1 123445667766643 457899
Q ss_pred EEcccccccc
Q psy3868 53 FIDELDAIAP 62 (69)
Q Consensus 53 fiDEid~i~~ 62 (69)
+|||+|.+..
T Consensus 134 vIDE~d~L~~ 143 (365)
T TIGR02928 134 VLDEIDYLVG 143 (365)
T ss_pred EECchhhhcc
Confidence 9999999973
No 92
>PRK07952 DNA replication protein DnaC; Validated
Probab=96.51 E-value=0.0063 Score=39.49 Aligned_cols=57 Identities=21% Similarity=0.364 Sum_probs=39.5
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccCh---HHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE---SESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge---s~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|+|+.++|+++ +..++.++.+++++...+. +.....++++.. ....+|+|||++...
T Consensus 113 ThLa~aia~~l~~~g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l--~~~dlLvIDDig~~~ 175 (244)
T PRK07952 113 NHLAAAICNELLLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLNDL--SNVDLLVIDEIGVQT 175 (244)
T ss_pred HHHHHHHHHHHHhcCCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHh--ccCCEEEEeCCCCCC
Confidence 77899999888 6788999999987643321 112233444443 257899999998865
No 93
>PRK14956 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.48 E-value=0.0091 Score=42.33 Aligned_cols=54 Identities=13% Similarity=0.216 Sum_probs=36.4
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+.+|+.+++. +++++++. ..+...+|++.+.+.. .+..|++|
T Consensus 54 TTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas------~~gVd~IReL~e~l~~~p~~g~~KV~II 127 (484)
T PRK14956 54 TTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAAS------NRGIENIRELRDNVKFAPMGGKYKVYII 127 (484)
T ss_pred HHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhh------cccHHHHHHHHHHHHhhhhcCCCEEEEE
Confidence 78999999998863 44555432 1234566776666542 34679999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 128 DEah~Ls~ 135 (484)
T PRK14956 128 DEVHMLTD 135 (484)
T ss_pred echhhcCH
Confidence 99999854
No 94
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=96.48 E-value=0.0068 Score=42.32 Aligned_cols=60 Identities=15% Similarity=0.263 Sum_probs=38.9
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
|+|++++++++ +..++++++.++...+...-...-...|.... ..+.+|+|||++.+.++
T Consensus 155 THLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~-~~~dvLiIDDiq~l~~k 217 (445)
T PRK12422 155 THLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFY-RNVDALFIEDIEVFSGK 217 (445)
T ss_pred HHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHc-ccCCEEEEcchhhhcCC
Confidence 78999999876 68889999887754432211110112243332 35789999999998764
No 95
>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=96.41 E-value=0.01 Score=36.84 Aligned_cols=51 Identities=16% Similarity=0.235 Sum_probs=36.1
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
|+++++++++. +.++++++++++.... ..+++..+ .+.+|+|||+|.+...
T Consensus 52 T~la~~~~~~~~~~~~~~~~i~~~~~~~~~--------~~~~~~~~--~~~lLvIDdi~~l~~~ 105 (226)
T TIGR03420 52 SHLLQAACAAAEERGKSAIYLPLAELAQAD--------PEVLEGLE--QADLVCLDDVEAIAGQ 105 (226)
T ss_pred HHHHHHHHHHHHhcCCcEEEEeHHHHHHhH--------HHHHhhcc--cCCEEEEeChhhhcCC
Confidence 67899998876 4788999998885321 23443332 3469999999998654
No 96
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.41 E-value=0.0099 Score=41.84 Aligned_cols=54 Identities=13% Similarity=0.206 Sum_probs=37.9
Q ss_pred hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+.+++ .++.++++. ..+...+|++.+.++. ....++||
T Consensus 50 TTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~------~~gid~iR~i~~~~~~~p~~~~~kVvII 123 (472)
T PRK14962 50 TTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAAS------NRGIDEIRKIRDAVGYRPMEGKYKVYII 123 (472)
T ss_pred HHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcc------cCCHHHHHHHHHHHhhChhcCCeEEEEE
Confidence 7899999999875 456665532 1234567777776643 23579999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 124 DE~h~Lt~ 131 (472)
T PRK14962 124 DEVHMLTK 131 (472)
T ss_pred EChHHhHH
Confidence 99999853
No 97
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.39 E-value=0.011 Score=41.93 Aligned_cols=54 Identities=11% Similarity=0.241 Sum_probs=37.6
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+.+++. ++++++++ ..+...+|++.+.+.- .+..|++|
T Consensus 52 Tt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas------~~~v~~iR~l~~~~~~~p~~~~~kV~iI 125 (509)
T PRK14958 52 TTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAAS------RTKVEDTRELLDNIPYAPTKGRFKVYLI 125 (509)
T ss_pred HHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccc------cCCHHHHHHHHHHHhhccccCCcEEEEE
Confidence 78999999999763 56666542 1244557777766532 23469999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+.+
T Consensus 126 DE~~~ls~ 133 (509)
T PRK14958 126 DEVHMLSG 133 (509)
T ss_pred EChHhcCH
Confidence 99999864
No 98
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.37 E-value=0.0076 Score=44.33 Aligned_cols=54 Identities=13% Similarity=0.255 Sum_probs=36.4
Q ss_pred hHHHHHHHHHhCC-----------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHH----hcCC
Q psy3868 3 YRLTTLCRDSLGA-----------------------------FFFLINGPEIMSKLAGESESNLRKAFEEAD----KNSP 49 (69)
Q Consensus 3 T~la~aia~~~~~-----------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~----~~~p 49 (69)
|++|+.+|+.+++ .++++++++ ..+...+|++.+.+. ..+.
T Consensus 52 TTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas------~~gVDdIReLie~~~~~P~~gr~ 125 (700)
T PRK12323 52 TTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAAS------NRGVDEMAQLLDKAVYAPTAGRF 125 (700)
T ss_pred HHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccc------cCCHHHHHHHHHHHHhchhcCCc
Confidence 7899999999876 344444431 123456777766653 2346
Q ss_pred eEEEEcccccccc
Q psy3868 50 SIIFIDELDAIAP 62 (69)
Q Consensus 50 ~iifiDEid~i~~ 62 (69)
.|++|||+|.|..
T Consensus 126 KViIIDEah~Ls~ 138 (700)
T PRK12323 126 KVYMIDEVHMLTN 138 (700)
T ss_pred eEEEEEChHhcCH
Confidence 7999999999854
No 99
>PLN03025 replication factor C subunit; Provisional
Probab=96.29 E-value=0.015 Score=38.58 Aligned_cols=55 Identities=13% Similarity=0.123 Sum_probs=35.1
Q ss_pred hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHh-------cCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADK-------NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-------~~p~iifiDEid~i~~~ 63 (69)
|++|+++|+++. ..++++++++.. +...++...+.... ..+.+++|||+|.+...
T Consensus 48 Ttla~~la~~l~~~~~~~~~~eln~sd~~------~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~ 114 (319)
T PLN03025 48 TTSILALAHELLGPNYKEAVLELNASDDR------GIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSG 114 (319)
T ss_pred HHHHHHHHHHHhcccCccceeeecccccc------cHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCHH
Confidence 789999999973 347778876542 12234444332211 24679999999998653
No 100
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=96.08 E-value=0.013 Score=43.85 Aligned_cols=54 Identities=13% Similarity=0.221 Sum_probs=36.3
Q ss_pred hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++++++|+.+++ .++++++++ ..+...++++.+.+.. .+..|++|
T Consensus 52 TTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas------~rgVDdIReLIe~a~~~P~~gr~KVIII 125 (830)
T PRK07003 52 TTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAAS------NRGVDEMAALLERAVYAPVDARFKVYMI 125 (830)
T ss_pred HHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEEecccc------cccHHHHHHHHHHHHhccccCCceEEEE
Confidence 7889999998875 244444432 1234567777776542 34579999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.|-.
T Consensus 126 DEah~LT~ 133 (830)
T PRK07003 126 DEVHMLTN 133 (830)
T ss_pred eChhhCCH
Confidence 99999854
No 101
>PRK14960 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.07 E-value=0.021 Score=42.12 Aligned_cols=54 Identities=11% Similarity=0.207 Sum_probs=37.3
Q ss_pred hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+.+++ .++++++++- .+...+|++.+.+.. .+..|++|
T Consensus 51 TTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~------~~VddIReli~~~~y~P~~gk~KV~II 124 (702)
T PRK14960 51 TTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASR------TKVEDTRELLDNVPYAPTQGRFKVYLI 124 (702)
T ss_pred HHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEeccccc------CCHHHHHHHHHHHhhhhhcCCcEEEEE
Confidence 7899999999876 4555555421 234567777766532 34679999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+-.
T Consensus 125 DEVh~LS~ 132 (702)
T PRK14960 125 DEVHMLST 132 (702)
T ss_pred echHhcCH
Confidence 99998853
No 102
>CHL00095 clpC Clp protease ATP binding subunit
Probab=96.02 E-value=0.0096 Score=44.23 Aligned_cols=58 Identities=21% Similarity=0.277 Sum_probs=39.1
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhh-----c-------ccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMS-----K-------LAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~-----~-------~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|.+|+++|..+ +.+++.++.+++.. + |+|-.+ ...+.+..+....+||+|||+|.+-+
T Consensus 553 t~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l~g~~~gyvg~~~--~~~l~~~~~~~p~~VvllDeieka~~ 625 (821)
T CHL00095 553 TELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNE--GGQLTEAVRKKPYTVVLFDEIEKAHP 625 (821)
T ss_pred HHHHHHHHHHhcCCccceEEEEchhccccccHHHhcCCCCcccCcCc--cchHHHHHHhCCCeEEEECChhhCCH
Confidence 67999999987 36888888877632 2 333222 22355555555558999999998754
No 103
>PRK06893 DNA replication initiation factor; Validated
Probab=95.99 E-value=0.013 Score=37.18 Aligned_cols=52 Identities=12% Similarity=0.131 Sum_probs=31.1
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|++++|++. +....+++.... .....++++.. .+..+|+|||++.+.+++
T Consensus 53 ThL~~ai~~~~~~~~~~~~y~~~~~~--------~~~~~~~~~~~--~~~dlLilDDi~~~~~~~ 107 (229)
T PRK06893 53 SHLLKAVSNHYLLNQRTAIYIPLSKS--------QYFSPAVLENL--EQQDLVCLDDLQAVIGNE 107 (229)
T ss_pred HHHHHHHHHHHHHcCCCeEEeeHHHh--------hhhhHHHHhhc--ccCCEEEEeChhhhcCCh
Confidence 78999999886 234444444321 11112333333 246899999999987654
No 104
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=95.89 E-value=0.044 Score=35.90 Aligned_cols=60 Identities=15% Similarity=0.159 Sum_probs=37.1
Q ss_pred hHHHHHHHHHhC-----CcEEEEchhhhhhcc-------------cCh-------HHHHHHHHHHHHHhc-----CCeEE
Q psy3868 3 YRLTTLCRDSLG-----AFFFLINGPEIMSKL-------------AGE-------SESNLRKAFEEADKN-----SPSII 52 (69)
Q Consensus 3 T~la~aia~~~~-----~~~~~v~~~~l~~~~-------------~ge-------s~~~l~~if~~a~~~-----~p~ii 52 (69)
|++|+++++++. .+++.++++++...+ .+. ....++.+.+..... .+.+|
T Consensus 50 T~la~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl 129 (337)
T PRK12402 50 TAAVRALARELYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTI 129 (337)
T ss_pred HHHHHHHHHHhcCcccccceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEE
Confidence 788999999874 357888887764321 111 123344444343332 34699
Q ss_pred EEcccccccc
Q psy3868 53 FIDELDAIAP 62 (69)
Q Consensus 53 fiDEid~i~~ 62 (69)
+|||+|.+..
T Consensus 130 ilDe~~~l~~ 139 (337)
T PRK12402 130 LLDNAEALRE 139 (337)
T ss_pred EEeCcccCCH
Confidence 9999998853
No 105
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=95.83 E-value=0.028 Score=39.31 Aligned_cols=60 Identities=13% Similarity=0.205 Sum_probs=40.2
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHHH---HHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESES---NLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~~---~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|++++++++ +..++++++.++...+...-.. .+.+..+.. ..+.+|+|||++.+.+++
T Consensus 155 THLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~--~~~dvLiIDDiq~l~~k~ 222 (450)
T PRK14087 155 THLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEI--CQNDVLIIDDVQFLSYKE 222 (450)
T ss_pred HHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHh--ccCCEEEEeccccccCCH
Confidence 77889998854 4788899999987665543221 222222222 356799999999987654
No 106
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=95.65 E-value=0.014 Score=38.78 Aligned_cols=60 Identities=20% Similarity=0.213 Sum_probs=36.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhc--ccChHHHHHH----HHHHHHHh--cCC--eEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSK--LAGESESNLR----KAFEEADK--NSP--SIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~--~~ges~~~l~----~if~~a~~--~~p--~iifiDEid~i~~ 62 (69)
|++|+.+|..++.+|+.+.+..-+.. .+|...-.-+ ..|..... ... +++|+|||+...+
T Consensus 57 T~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEInra~p 126 (329)
T COG0714 57 TLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEINRAPP 126 (329)
T ss_pred HHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEeccccCCH
Confidence 78999999999999999988644322 3343221111 11111110 111 4999999998654
No 107
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=95.65 E-value=0.035 Score=38.30 Aligned_cols=30 Identities=17% Similarity=0.315 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEccccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~~ 63 (69)
...+|++++.+.. ....|+||||+|.+...
T Consensus 99 i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~ 132 (394)
T PRK07940 99 VDEVRELVTIAARRPSTGRWRIVVIEDADRLTER 132 (394)
T ss_pred HHHHHHHHHHHHhCcccCCcEEEEEechhhcCHH
Confidence 4568899988754 23469999999999653
No 108
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=95.65 E-value=0.028 Score=43.13 Aligned_cols=32 Identities=34% Similarity=0.479 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHh--cCCeEEEEcccccccccc
Q psy3868 33 SESNLRKAFEEADK--NSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 33 s~~~l~~if~~a~~--~~p~iifiDEid~i~~~r 64 (69)
+...+.++|..... ....||+|||||.|..+.
T Consensus 852 S~evLerLF~~L~k~~r~v~IIILDEID~L~kK~ 885 (1164)
T PTZ00112 852 SFKILDRLFNQNKKDNRNVSILIIDEIDYLITKT 885 (1164)
T ss_pred HHHHHHHHHhhhhcccccceEEEeehHhhhCccH
Confidence 34567788877632 346799999999998653
No 109
>PRK07994 DNA polymerase III subunits gamma and tau; Validated
Probab=95.64 E-value=0.027 Score=41.27 Aligned_cols=54 Identities=13% Similarity=0.233 Sum_probs=35.2
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+.+++. ++++++++ ..+...+|++.+.+.. ....|++|
T Consensus 52 TTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas------~~~VddiR~li~~~~~~p~~g~~KV~II 125 (647)
T PRK07994 52 TTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLIEIDAAS------RTKVEDTRELLDNVQYAPARGRFKVYLI 125 (647)
T ss_pred HHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccc------cCCHHHHHHHHHHHHhhhhcCCCEEEEE
Confidence 78999999998773 34444432 0123456666665532 34579999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 126 DEah~Ls~ 133 (647)
T PRK07994 126 DEVHMLSR 133 (647)
T ss_pred echHhCCH
Confidence 99998864
No 110
>PHA02244 ATPase-like protein
Probab=95.58 E-value=0.023 Score=39.26 Aligned_cols=59 Identities=25% Similarity=0.340 Sum_probs=34.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccC---hHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAG---ESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~g---es~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|++|+++|..++.||+.++...-.....| ....-...-|-.|. ..+.++++||++.+.+
T Consensus 133 TtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~-~~GgvLiLDEId~a~p 194 (383)
T PHA02244 133 NHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAF-KKGGLFFIDEIDASIP 194 (383)
T ss_pred HHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHh-hcCCEEEEeCcCcCCH
Confidence 78999999999999999885311111111 11100001122222 3578999999997643
No 111
>PRK08181 transposase; Validated
Probab=95.55 E-value=0.026 Score=37.12 Aligned_cols=60 Identities=17% Similarity=0.268 Sum_probs=40.0
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccC-hHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAG-ESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~g-es~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|+.++++++ |..++.++.++++..... .......+.++.. .++.+|+|||++.+..++
T Consensus 120 THLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l--~~~dLLIIDDlg~~~~~~ 183 (269)
T PRK08181 120 SHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKL--DKFDLLILDDLAYVTKDQ 183 (269)
T ss_pred HHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHH--hcCCEEEEeccccccCCH
Confidence 67888888654 678888999888765421 1112334445443 357899999999876543
No 112
>PRK08116 hypothetical protein; Validated
Probab=95.47 E-value=0.042 Score=35.93 Aligned_cols=55 Identities=15% Similarity=0.359 Sum_probs=35.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhccc----ChHHHHHHHHHHHHHhcCCeEEEEccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLA----GESESNLRKAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~----ges~~~l~~if~~a~~~~p~iifiDEid~ 59 (69)
|+|+.++++++ +.+++.++.++++..+. +.+.....++++.. ....+|+|||+..
T Consensus 128 ThLa~aia~~l~~~~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l--~~~dlLviDDlg~ 189 (268)
T PRK08116 128 TYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSL--VNADLLILDDLGA 189 (268)
T ss_pred HHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHh--cCCCEEEEecccC
Confidence 78999999986 78999999988766432 11111222333333 2346999999954
No 113
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=95.33 E-value=0.067 Score=38.14 Aligned_cols=30 Identities=27% Similarity=0.477 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 33 SESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 33 s~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
+...++.+.+.+.. ....|++|||+|.+..
T Consensus 109 ~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~ 142 (507)
T PRK06645 109 SVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSK 142 (507)
T ss_pred CHHHHHHHHHHHHhccccCCcEEEEEEChhhcCH
Confidence 46678888888754 2457999999998853
No 114
>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []. The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=95.31 E-value=0.0025 Score=36.97 Aligned_cols=56 Identities=18% Similarity=0.195 Sum_probs=32.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhh------hhcccChHHHHHHHHHHHH---H-hcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEI------MSKLAGESESNLRKAFEEA---D-KNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l------~~~~~ges~~~l~~if~~a---~-~~~p~iifiDEid~i~ 61 (69)
|.+++.+|+.++.+++.++++.. .+.|.-. .-..-|... + -..++++||||++..-
T Consensus 13 t~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~---~~~~~~~~~~l~~a~~~~~il~lDEin~a~ 78 (139)
T PF07728_consen 13 TTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPS---NGQFEFKDGPLVRAMRKGGILVLDEINRAP 78 (139)
T ss_dssp HHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET----TTTTCEEE-CCCTTHHEEEEEEESSCGG--
T ss_pred HHHHHHHHHHhhcceEEEEeccccccccceeeeeec---ccccccccccccccccceeEEEECCcccCC
Confidence 78999999999999988877653 2222211 000000000 0 0158999999999653
No 115
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=95.22 E-value=0.07 Score=36.11 Aligned_cols=54 Identities=15% Similarity=0.246 Sum_probs=34.7
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+++++. ++.+++++ ..+...++++.+.+.. ....|++|
T Consensus 52 Ttla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~------~~~v~~ir~i~~~~~~~p~~~~~kviII 125 (363)
T PRK14961 52 TTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAAS------RTKVEEMREILDNIYYSPSKSRFKVYLI 125 (363)
T ss_pred HHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhcCcccCCceEEEE
Confidence 78999999998742 23333321 1234557777776542 23469999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+-.
T Consensus 126 DEa~~l~~ 133 (363)
T PRK14961 126 DEVHMLSR 133 (363)
T ss_pred EChhhcCH
Confidence 99998853
No 116
>PRK14951 DNA polymerase III subunits gamma and tau; Provisional
Probab=95.22 E-value=0.051 Score=39.60 Aligned_cols=54 Identities=13% Similarity=0.239 Sum_probs=35.5
Q ss_pred hHHHHHHHHHhCC-----------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCC
Q psy3868 3 YRLTTLCRDSLGA-----------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSP 49 (69)
Q Consensus 3 T~la~aia~~~~~-----------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p 49 (69)
|++|+++|+.+++ .++++++++ ..+...+|++.+.+.. .+-
T Consensus 52 TtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas------~~~Vd~iReli~~~~~~p~~g~~ 125 (618)
T PRK14951 52 TTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAAS------NRGVDEVQQLLEQAVYKPVQGRF 125 (618)
T ss_pred HHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCccc------ccCHHHHHHHHHHHHhCcccCCc
Confidence 7899999999875 244444432 1234567777776532 224
Q ss_pred eEEEEcccccccc
Q psy3868 50 SIIFIDELDAIAP 62 (69)
Q Consensus 50 ~iifiDEid~i~~ 62 (69)
.|++|||+|.+..
T Consensus 126 KV~IIDEvh~Ls~ 138 (618)
T PRK14951 126 KVFMIDEVHMLTN 138 (618)
T ss_pred eEEEEEChhhCCH
Confidence 6999999999864
No 117
>PRK09183 transposase/IS protein; Provisional
Probab=95.22 E-value=0.041 Score=35.76 Aligned_cols=62 Identities=13% Similarity=0.268 Sum_probs=40.4
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccC-hHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAG-ESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~g-es~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
|+++.+++.+. |..+..++..++...+.. .....+..+|+.. ...+.+++|||++.....+.
T Consensus 116 ThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~-~~~~dlLiiDdlg~~~~~~~ 181 (259)
T PRK09183 116 THLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRG-VMAPRLLIIDEIGYLPFSQE 181 (259)
T ss_pred HHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHH-hcCCCEEEEcccccCCCChH
Confidence 67888886653 677888888887644321 1122355566554 34678999999988755543
No 118
>PRK05642 DNA replication initiation factor; Validated
Probab=95.16 E-value=0.087 Score=33.62 Aligned_cols=52 Identities=17% Similarity=0.252 Sum_probs=35.0
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|+++++++. +..+++++..++... ...+.+..+. ..+|+|||++.+.+++
T Consensus 59 THLl~a~~~~~~~~~~~v~y~~~~~~~~~--------~~~~~~~~~~--~d~LiiDDi~~~~~~~ 113 (234)
T PRK05642 59 SHLLQAACLRFEQRGEPAVYLPLAELLDR--------GPELLDNLEQ--YELVCLDDLDVIAGKA 113 (234)
T ss_pred HHHHHHHHHHHHhCCCcEEEeeHHHHHhh--------hHHHHHhhhh--CCEEEEechhhhcCCh
Confidence 77889988754 578888988887642 1223333322 2588999999887654
No 119
>PRK14969 DNA polymerase III subunits gamma and tau; Provisional
Probab=95.12 E-value=0.076 Score=37.89 Aligned_cols=54 Identities=15% Similarity=0.269 Sum_probs=35.8
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+.+|+.+++. +++++++. ..+...+|++.+.+.. ....|++|
T Consensus 52 Tt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~------~~~vd~ir~l~~~~~~~p~~~~~kVvII 125 (527)
T PRK14969 52 TTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAAS------NTQVDAMRELLDNAQYAPTRGRFKVYII 125 (527)
T ss_pred HHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeeccc------cCCHHHHHHHHHHHhhCcccCCceEEEE
Confidence 78999999998763 23333221 1235568888877643 23569999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 126 DEad~ls~ 133 (527)
T PRK14969 126 DEVHMLSK 133 (527)
T ss_pred cCcccCCH
Confidence 99998854
No 120
>PRK14957 DNA polymerase III subunits gamma and tau; Provisional
Probab=95.09 E-value=0.088 Score=37.90 Aligned_cols=54 Identities=13% Similarity=0.204 Sum_probs=34.4
Q ss_pred hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+.+|+.+++ .++++++..- . +...++++.+.+.. ....|++|
T Consensus 52 TTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas~----~--gvd~ir~ii~~~~~~p~~g~~kViII 125 (546)
T PRK14957 52 TTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASR----T--GVEETKEILDNIQYMPSQGRYKVYLI 125 (546)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeecccc----c--CHHHHHHHHHHHHhhhhcCCcEEEEE
Confidence 7899999998865 3333433211 1 23456666666542 34679999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 126 DEa~~ls~ 133 (546)
T PRK14957 126 DEVHMLSK 133 (546)
T ss_pred echhhccH
Confidence 99998854
No 121
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=95.09 E-value=0.052 Score=34.00 Aligned_cols=46 Identities=9% Similarity=0.139 Sum_probs=31.9
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|+++++++++. +.++..+++.++... +.. ...+.+|+|||+|.+.+
T Consensus 56 T~La~ai~~~~~~~~~~~~~i~~~~~~~~------------~~~--~~~~~~liiDdi~~l~~ 104 (227)
T PRK08903 56 SHLLQALVADASYGGRNARYLDAASPLLA------------FDF--DPEAELYAVDDVERLDD 104 (227)
T ss_pred HHHHHHHHHHHHhCCCcEEEEehHHhHHH------------Hhh--cccCCEEEEeChhhcCc
Confidence 78899998875 568888888776321 111 23467899999998754
No 122
>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=94.99 E-value=0.038 Score=41.36 Aligned_cols=58 Identities=24% Similarity=0.301 Sum_probs=37.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc-----c-------cChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----L-------AGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~-------~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|.+|+++|..+ +.+++.++++.+... + +|-.+ -..+.+..+....+|||+||||.+-+
T Consensus 609 t~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l~g~~~g~~g~~~--~g~l~~~v~~~p~~vlllDeieka~~ 681 (852)
T TIGR03346 609 TELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEE--GGQLTEAVRRKPYSVVLFDEVEKAHP 681 (852)
T ss_pred HHHHHHHHHHhcCCCCcEEEEechhhcccchHHHhcCCCCCccCccc--ccHHHHHHHcCCCcEEEEeccccCCH
Confidence 67999999887 468898988776332 1 22111 12344444455567999999997643
No 123
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=94.96 E-value=0.06 Score=30.47 Aligned_cols=28 Identities=18% Similarity=0.271 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
....+.+.+...+....+|+|||+|.+.
T Consensus 73 ~~l~~~~~~~l~~~~~~~lviDe~~~l~ 100 (131)
T PF13401_consen 73 DELRSLLIDALDRRRVVLLVIDEADHLF 100 (131)
T ss_dssp HHHHHHHHHHHHHCTEEEEEEETTHHHH
T ss_pred HHHHHHHHHHHHhcCCeEEEEeChHhcC
Confidence 3334444455555555699999999974
No 124
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=94.86 E-value=0.065 Score=37.48 Aligned_cols=63 Identities=16% Similarity=0.270 Sum_probs=38.5
Q ss_pred hHHHHHHHHHhCC-----c-EEEEchhh---------------hhhcccChHHHHHH---HHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGA-----F-FFLINGPE---------------IMSKLAGESESNLR---KAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~-----~-~~~v~~~~---------------l~~~~~ges~~~l~---~if~~a~~----~~p~iifi 54 (69)
|+|++.+++.... . ++.+.... +.+.+-...+..++ .+.+.|+. .+..+||+
T Consensus 183 TTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~~e~G~dVlL~i 262 (416)
T PRK09376 183 TVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRLVEHGKDVVILL 262 (416)
T ss_pred hHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEE
Confidence 6788888887743 2 22222221 33444455566655 55555543 36889999
Q ss_pred ccccccccccc
Q psy3868 55 DELDAIAPKRE 65 (69)
Q Consensus 55 DEid~i~~~r~ 65 (69)
||+++++....
T Consensus 263 DsItR~arAqr 273 (416)
T PRK09376 263 DSITRLARAYN 273 (416)
T ss_pred EChHHHHHHHH
Confidence 99999986543
No 125
>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=94.81 E-value=0.18 Score=30.85 Aligned_cols=54 Identities=17% Similarity=0.295 Sum_probs=33.5
Q ss_pred hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~ 62 (69)
+++|++|-+... .||+.++|+.+-. +..-.++|-.. .......|||||||.+-+
T Consensus 36 ~~lA~~IH~~s~r~~~pfi~vnc~~~~~------~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~ 107 (168)
T PF00158_consen 36 ELLARAIHNNSPRKNGPFISVNCAALPE------ELLESELFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDLPP 107 (168)
T ss_dssp HHHHHHHHHCSTTTTS-EEEEETTTS-H------HHHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS-H
T ss_pred HHHHHHHHHhhhcccCCeEEEehhhhhc------chhhhhhhccccccccccccccCCceeeccceEEeecchhhhHH
Confidence 467888877653 6999999988721 22223444321 122567999999999864
No 126
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=94.79 E-value=0.085 Score=38.59 Aligned_cols=53 Identities=13% Similarity=0.216 Sum_probs=32.2
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHH----hcCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEAD----KNSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~----~~~p~iifi 54 (69)
|++|+.+|+.+.+. ++++++..- .+-..+|++-+.+. .....||+|
T Consensus 52 TtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpDv~eId~a~~------~~Id~iR~L~~~~~~~p~~g~~kVIII 125 (624)
T PRK14959 52 TTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVDVVEIDGASN------RGIDDAKRLKEAIGYAPMEGRYKVFII 125 (624)
T ss_pred HHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCceEEEecccc------cCHHHHHHHHHHHHhhhhcCCceEEEE
Confidence 67899999998763 445544211 12233444333322 235679999
Q ss_pred ccccccc
Q psy3868 55 DELDAIA 61 (69)
Q Consensus 55 DEid~i~ 61 (69)
||+|.+-
T Consensus 126 DEad~Lt 132 (624)
T PRK14959 126 DEAHMLT 132 (624)
T ss_pred EChHhCC
Confidence 9999985
No 127
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=94.75 E-value=0.12 Score=38.30 Aligned_cols=54 Identities=19% Similarity=0.320 Sum_probs=35.6
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+.++++ +++++++ .+.+...+|++.+.++. ....|++|
T Consensus 52 TTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaA------s~~gVd~IRelle~a~~~P~~gk~KVIII 125 (709)
T PRK08691 52 TTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAA------SNTGIDNIREVLENAQYAPTAGKYKVYII 125 (709)
T ss_pred HHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEEecc------ccCCHHHHHHHHHHHHhhhhhCCcEEEEE
Confidence 78999999987653 2233321 12345678888876632 24579999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 126 DEad~Ls~ 133 (709)
T PRK08691 126 DEVHMLSK 133 (709)
T ss_pred ECccccCH
Confidence 99998753
No 128
>PRK14949 DNA polymerase III subunits gamma and tau; Provisional
Probab=94.71 E-value=0.086 Score=40.18 Aligned_cols=54 Identities=13% Similarity=0.212 Sum_probs=34.4
Q ss_pred hHHHHHHHHHhCCcE------------------------EEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAFF------------------------FLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~~------------------------~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+.+++.- +++++++ -.+...+|++.+.+.. .+..|++|
T Consensus 52 TTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas------~~kVDdIReLie~v~~~P~~gk~KViII 125 (944)
T PRK14949 52 TSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAAS------RTKVDDTRELLDNVQYRPSRGRFKVYLI 125 (944)
T ss_pred HHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEecccc------ccCHHHHHHHHHHHHhhhhcCCcEEEEE
Confidence 789999999998741 2222211 0124456776665532 34579999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.|-.
T Consensus 126 DEAh~LT~ 133 (944)
T PRK14949 126 DEVHMLSR 133 (944)
T ss_pred echHhcCH
Confidence 99999853
No 129
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=94.71 E-value=0.12 Score=36.76 Aligned_cols=54 Identities=13% Similarity=0.145 Sum_probs=37.2
Q ss_pred hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+.+|+.+++ .++++++++- .+...+|++.+.+.. ....|++|
T Consensus 49 TT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~------~~vddIR~Iie~~~~~P~~~~~KVvII 122 (491)
T PRK14964 49 TTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASN------TSVDDIKVILENSCYLPISSKFKVYII 122 (491)
T ss_pred HHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccC------CCHHHHHHHHHHHHhccccCCceEEEE
Confidence 6788888886543 4566666431 245678888877743 34579999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 123 DEah~Ls~ 130 (491)
T PRK14964 123 DEVHMLSN 130 (491)
T ss_pred eChHhCCH
Confidence 99998853
No 130
>PRK08727 hypothetical protein; Validated
Probab=94.63 E-value=0.16 Score=32.34 Aligned_cols=53 Identities=25% Similarity=0.270 Sum_probs=33.9
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~ 65 (69)
|++++++++++ +....+++..++. ..+.++++.. .+..+|+|||+|.+..++.
T Consensus 55 ThL~~a~~~~~~~~~~~~~y~~~~~~~--------~~~~~~~~~l--~~~dlLiIDDi~~l~~~~~ 110 (233)
T PRK08727 55 THLALALCAAAEQAGRSSAYLPLQAAA--------GRLRDALEAL--EGRSLVALDGLESIAGQRE 110 (233)
T ss_pred HHHHHHHHHHHHHcCCcEEEEeHHHhh--------hhHHHHHHHH--hcCCEEEEeCcccccCChH
Confidence 67888886654 4566666655542 2344455544 3457999999999876543
No 131
>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=94.60 E-value=0.081 Score=34.07 Aligned_cols=52 Identities=19% Similarity=0.292 Sum_probs=40.5
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|..++.+|+-+|.+++.++|++-+ ..+.+.++|.-+-. ..+-+.+||++.+-
T Consensus 46 tetik~La~~lG~~~~vfnc~~~~------~~~~l~ril~G~~~-~GaW~cfdefnrl~ 97 (231)
T PF12774_consen 46 TETIKDLARALGRFVVVFNCSEQM------DYQSLSRILKGLAQ-SGAWLCFDEFNRLS 97 (231)
T ss_dssp HHHHHHHHHCTT--EEEEETTSSS-------HHHHHHHHHHHHH-HT-EEEEETCCCSS
T ss_pred hhHHHHHHHHhCCeEEEecccccc------cHHHHHHHHHHHhh-cCchhhhhhhhhhh
Confidence 567999999999999999998864 57889999988755 47888899999874
No 132
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=94.55 E-value=0.046 Score=37.95 Aligned_cols=18 Identities=44% Similarity=0.739 Sum_probs=15.3
Q ss_pred CCeEEEEccccccccccc
Q psy3868 48 SPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 48 ~p~iifiDEid~i~~~r~ 65 (69)
+-.|+||||||.++.+.+
T Consensus 250 ~~GIvFIDEIDKIa~~~~ 267 (444)
T COG1220 250 QNGIVFIDEIDKIAKRGG 267 (444)
T ss_pred hcCeEEEehhhHHHhcCC
Confidence 458999999999998764
No 133
>KOG0743|consensus
Probab=94.52 E-value=0.093 Score=37.09 Aligned_cols=54 Identities=19% Similarity=0.241 Sum_probs=42.5
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+++-|+|+.++..++.++-++.. ..++ ++++.-.+ ...+||+|.+||+=+..|
T Consensus 249 SS~IaAmAn~L~ydIydLeLt~v~----~n~d--Lr~LL~~t--~~kSIivIEDIDcs~~l~ 302 (457)
T KOG0743|consen 249 SSFIAAMANYLNYDIYDLELTEVK----LDSD--LRHLLLAT--PNKSILLIEDIDCSFDLR 302 (457)
T ss_pred HHHHHHHHhhcCCceEEeeecccc----CcHH--HHHHHHhC--CCCcEEEEeecccccccc
Confidence 578889999999999999887762 2233 88988665 456999999999886533
No 134
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=94.49 E-value=0.054 Score=40.53 Aligned_cols=55 Identities=25% Similarity=0.344 Sum_probs=38.9
Q ss_pred hHHHHHHHHHhC---CcEEEEchhhhhhc------------ccChHHHHHHHHHHHH-HhcCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSLG---AFFFLINGPEIMSK------------LAGESESNLRKAFEEA-DKNSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~~---~~~~~v~~~~l~~~------------~~ges~~~l~~if~~a-~~~~p~iifiDEid~i 60 (69)
|-+|+++|..+. ..++.++.|+.+.+ |+|-.+. -.+..+ +++..|||++|||+.-
T Consensus 535 TELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLIGaPPGYVGyeeG---G~LTEaVRr~PySViLlDEIEKA 605 (786)
T COG0542 535 TELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEG---GQLTEAVRRKPYSVILLDEIEKA 605 (786)
T ss_pred HHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHhCCCCCCceeccc---cchhHhhhcCCCeEEEechhhhc
Confidence 779999999997 89999999888542 4443331 133334 3444589999999864
No 135
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=94.45 E-value=0.14 Score=33.21 Aligned_cols=59 Identities=15% Similarity=0.120 Sum_probs=40.4
Q ss_pred hHHHHHHHHHhC------------------------CcEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLG------------------------AFFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~------------------------~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|.+|.++|+++. ..++++++++....- -....++++-+.... ...-|++|
T Consensus 38 tt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~--i~~~~vr~~~~~~~~~~~~~~~kviii 115 (325)
T COG0470 38 TTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKID--IIVEQVRELAEFLSESPLEGGYKVVII 115 (325)
T ss_pred HHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCc--chHHHHHHHHHHhccCCCCCCceEEEe
Confidence 677888888887 588999998863321 234455555554432 34689999
Q ss_pred ccccccccc
Q psy3868 55 DELDAIAPK 63 (69)
Q Consensus 55 DEid~i~~~ 63 (69)
||+|.+-..
T Consensus 116 dead~mt~~ 124 (325)
T COG0470 116 DEADKLTED 124 (325)
T ss_pred CcHHHHhHH
Confidence 999998653
No 136
>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=94.41 E-value=0.082 Score=33.50 Aligned_cols=60 Identities=15% Similarity=0.282 Sum_probs=37.1
Q ss_pred hHHHHHHHHHh-----CCcEEEEchhhhhhcccChHH-HHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL-----GAFFFLINGPEIMSKLAGESE-SNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~-----~~~~~~v~~~~l~~~~~ges~-~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|.++++++. +..++++++.++...+...-. ..+.++.+.. ....+|+||++|.+..+.
T Consensus 48 THLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~--~~~DlL~iDDi~~l~~~~ 113 (219)
T PF00308_consen 48 THLLQAIANEAQKQHPGKRVVYLSAEEFIREFADALRDGEIEEFKDRL--RSADLLIIDDIQFLAGKQ 113 (219)
T ss_dssp HHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHH--CTSSEEEEETGGGGTTHH
T ss_pred HHHHHHHHHHHHhccccccceeecHHHHHHHHHHHHHcccchhhhhhh--hcCCEEEEecchhhcCch
Confidence 67888888764 567888988887554332211 1122222222 256889999999997653
No 137
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=94.41 E-value=0.1 Score=39.27 Aligned_cols=29 Identities=28% Similarity=0.394 Sum_probs=18.6
Q ss_pred HHHHHHHHHHH----HhcCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEA----DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a----~~~~p~iifiDEid~i~~ 62 (69)
...+|++-+.+ ......|++|||+|.|..
T Consensus 102 Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~ 134 (824)
T PRK07764 102 VDDARELRERAFFAPAESRYKIFIIDEAHMVTP 134 (824)
T ss_pred HHHHHHHHHHHHhchhcCCceEEEEechhhcCH
Confidence 34455544333 234567999999999854
No 138
>PRK14948 DNA polymerase III subunits gamma and tau; Provisional
Probab=94.37 E-value=0.17 Score=36.84 Aligned_cols=53 Identities=19% Similarity=0.244 Sum_probs=36.6
Q ss_pred hHHHHHHHHHhCCc--------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEE
Q psy3868 3 YRLTTLCRDSLGAF--------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSII 52 (69)
Q Consensus 3 T~la~aia~~~~~~--------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~ii 52 (69)
|++|+++|+.+++. ++++++ ..+.+...+|++.+.+.. ....|+
T Consensus 52 ttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~------~~~~~vd~IReii~~a~~~p~~~~~KVi 125 (620)
T PRK14948 52 TSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDA------ASNTGVDNIRELIERAQFAPVQARWKVY 125 (620)
T ss_pred HHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEec------cccCCHHHHHHHHHHHhhChhcCCceEE
Confidence 67899999998763 223322 123456788999888753 234799
Q ss_pred EEccccccc
Q psy3868 53 FIDELDAIA 61 (69)
Q Consensus 53 fiDEid~i~ 61 (69)
+|||+|.+-
T Consensus 126 IIDEad~Lt 134 (620)
T PRK14948 126 VIDECHMLS 134 (620)
T ss_pred EEECccccC
Confidence 999999884
No 139
>PRK12377 putative replication protein; Provisional
Probab=94.34 E-value=0.11 Score=33.83 Aligned_cols=57 Identities=19% Similarity=0.314 Sum_probs=36.0
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChH--HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGES--ESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges--~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|+|+.++++++ |..++.++.++++......- .....++++.. ....+|+|||+....
T Consensus 115 ThLa~AIa~~l~~~g~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l--~~~dLLiIDDlg~~~ 176 (248)
T PRK12377 115 NHLAAAIGNRLLAKGRSVIVVTVPDVMSRLHESYDNGQSGEKFLQEL--CKVDLLVLDEIGIQR 176 (248)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEHHHHHHHHHHHHhccchHHHHHHHh--cCCCEEEEcCCCCCC
Confidence 67888888887 57788888888866432100 00111233332 467999999997654
No 140
>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=94.28 E-value=0.15 Score=31.12 Aligned_cols=29 Identities=10% Similarity=0.312 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
...++++.+.+.. ....|++|||+|.+..
T Consensus 78 ~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~ 110 (188)
T TIGR00678 78 VDQVRELVEFLSRTPQESGRRVVIIEDAERMNE 110 (188)
T ss_pred HHHHHHHHHHHccCcccCCeEEEEEechhhhCH
Confidence 4567777777654 4567999999999864
No 141
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=94.26 E-value=0.098 Score=35.14 Aligned_cols=54 Identities=13% Similarity=0.229 Sum_probs=35.2
Q ss_pred hHHHHHHHHHhCCcE------------EEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFF------------FLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~------------~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
|++++++++.++.+. +.+++. ...+...++++++.+.. ..+.+++|||+|.+..
T Consensus 53 t~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~------~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~ 122 (367)
T PRK14970 53 TTCARILARKINQPGYDDPNEDFSFNIFELDAA------SNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSS 122 (367)
T ss_pred HHHHHHHHHHhcCCCCCCCCCCCCcceEEeccc------cCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCH
Confidence 678888988876521 222211 12345678888887753 2457999999998754
No 142
>PRK10865 protein disaggregation chaperone; Provisional
Probab=94.19 E-value=0.12 Score=38.79 Aligned_cols=57 Identities=23% Similarity=0.281 Sum_probs=35.3
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc-----cc-------ChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LA-------GESESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~-------ges~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|.+|++++..+ +.+++.++++++... .+ |..+. ..+-+..+....++|||||+|.+-
T Consensus 612 T~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~~--g~l~~~v~~~p~~vLllDEieka~ 683 (857)
T PRK10865 612 TELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEG--GYLTEAVRRRPYSVILLDEVEKAH 683 (857)
T ss_pred HHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHHHhCCCCcccccchh--HHHHHHHHhCCCCeEEEeehhhCC
Confidence 67999999887 457888988876432 11 22111 112222333344899999999764
No 143
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=94.15 E-value=0.18 Score=35.87 Aligned_cols=53 Identities=13% Similarity=0.154 Sum_probs=35.1
Q ss_pred hHHHHHHHHHhCC-----------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEc
Q psy3868 3 YRLTTLCRDSLGA-----------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFID 55 (69)
Q Consensus 3 T~la~aia~~~~~-----------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiD 55 (69)
|++|+++|+.+.+ .++.++++. ..+...+|++-+.+.. ..+.+++||
T Consensus 50 TTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~------~~~vd~iR~l~~~~~~~p~~~~~kVVIID 123 (504)
T PRK14963 50 TTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAAS------NNSVEDVRDLREKVLLAPLRGGRKVYILD 123 (504)
T ss_pred HHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhhccccCCCeEEEEE
Confidence 7889999998864 155566532 1234556776555532 357799999
Q ss_pred cccccc
Q psy3868 56 ELDAIA 61 (69)
Q Consensus 56 Eid~i~ 61 (69)
|+|.+.
T Consensus 124 Ead~ls 129 (504)
T PRK14963 124 EAHMMS 129 (504)
T ss_pred CccccC
Confidence 999774
No 144
>PRK08939 primosomal protein DnaI; Reviewed
Probab=94.09 E-value=0.1 Score=34.82 Aligned_cols=56 Identities=18% Similarity=0.370 Sum_probs=36.1
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i 60 (69)
|+|+.++|+++ |.++..+..++++...... ....+.+.++.. ....+|+|||+.+-
T Consensus 170 ThLa~Aia~~l~~~g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l--~~~dlLiIDDiG~e 229 (306)
T PRK08939 170 SYLLAAIANELAKKGVSSTLLHFPEFIRELKNSISDGSVKEKIDAV--KEAPVLMLDDIGAE 229 (306)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHh--cCCCEEEEecCCCc
Confidence 78889999888 6788888888875543211 011123333333 35789999999754
No 145
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=93.96 E-value=0.14 Score=33.27 Aligned_cols=51 Identities=25% Similarity=0.481 Sum_probs=33.7
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHH-------HH-hcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEE-------AD-KNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~-------a~-~~~p~iifiDEid~i~ 61 (69)
|+|+-|+++++ |.+++.++.+++++. |+..|.. .+ -....+|+|||+-+.-
T Consensus 119 ThLa~Ai~~~l~~~g~sv~f~~~~el~~~--------Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~ 180 (254)
T COG1484 119 THLAIAIGNELLKAGISVLFITAPDLLSK--------LKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEP 180 (254)
T ss_pred HHHHHHHHHHHHHcCCeEEEEEHHHHHHH--------HHHHHhcCchHHHHHHHhhcCCEEEEecccCcc
Confidence 56666666666 788999999998654 3333321 11 1356899999987653
No 146
>PRK14965 DNA polymerase III subunits gamma and tau; Provisional
Probab=93.95 E-value=0.18 Score=36.37 Aligned_cols=54 Identities=19% Similarity=0.299 Sum_probs=35.2
Q ss_pred hHHHHHHHHHhCCc------------------------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGAF------------------------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~~------------------------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+++|+.++++ ++++++.. ..+...++++.+.++. ....|++|
T Consensus 52 tt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~~eid~~s------~~~v~~ir~l~~~~~~~p~~~~~KVvII 125 (576)
T PRK14965 52 TSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVFEIDGAS------NTGVDDIRELRENVKYLPSRSRYKIFII 125 (576)
T ss_pred HHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCeeeeeccC------ccCHHHHHHHHHHHHhccccCCceEEEE
Confidence 67889999888653 34444322 1235567888777642 23369999
Q ss_pred cccccccc
Q psy3868 55 DELDAIAP 62 (69)
Q Consensus 55 DEid~i~~ 62 (69)
||+|.+..
T Consensus 126 dev~~Lt~ 133 (576)
T PRK14965 126 DEVHMLST 133 (576)
T ss_pred EChhhCCH
Confidence 99998854
No 147
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=93.95 E-value=0.21 Score=35.87 Aligned_cols=53 Identities=9% Similarity=0.194 Sum_probs=36.6
Q ss_pred hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEE
Q psy3868 3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifi 54 (69)
|++|+.+|+.+++ .+++++++ .+.+...+|++.+.+.. ....|++|
T Consensus 52 Tt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv~eidaa------s~~~vd~ir~i~~~v~~~p~~~~~kViII 125 (559)
T PRK05563 52 TSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAA------SNNGVDEIRDIRDKVKYAPSEAKYKVYII 125 (559)
T ss_pred HHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCeEEeecc------ccCCHHHHHHHHHHHhhCcccCCeEEEEE
Confidence 6788888888764 34445442 23456778888887753 34579999
Q ss_pred ccccccc
Q psy3868 55 DELDAIA 61 (69)
Q Consensus 55 DEid~i~ 61 (69)
||+|.+.
T Consensus 126 DE~~~Lt 132 (559)
T PRK05563 126 DEVHMLS 132 (559)
T ss_pred ECcccCC
Confidence 9999884
No 148
>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=93.66 E-value=0.1 Score=36.81 Aligned_cols=17 Identities=59% Similarity=0.851 Sum_probs=15.1
Q ss_pred CCeEEEEcccccccccc
Q psy3868 48 SPSIIFIDELDAIAPKR 64 (69)
Q Consensus 48 ~p~iifiDEid~i~~~r 64 (69)
+..||||||||.|+.+.
T Consensus 247 ~~GIVfiDEiDKIa~~~ 263 (441)
T TIGR00390 247 QSGIIFIDEIDKIAKKG 263 (441)
T ss_pred cCCEEEEEchhhhcccC
Confidence 57899999999999765
No 149
>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional
Probab=93.60 E-value=0.095 Score=36.97 Aligned_cols=18 Identities=44% Similarity=0.756 Sum_probs=15.5
Q ss_pred CCeEEEEccccccccccc
Q psy3868 48 SPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 48 ~p~iifiDEid~i~~~r~ 65 (69)
+-.||||||||.|+.+.+
T Consensus 249 ~~GIVfiDEiDKIa~~~~ 266 (443)
T PRK05201 249 QNGIVFIDEIDKIAARGG 266 (443)
T ss_pred cCCEEEEEcchhhcccCC
Confidence 568999999999998753
No 150
>PRK08084 DNA replication initiation factor; Provisional
Probab=93.60 E-value=0.13 Score=32.83 Aligned_cols=52 Identities=15% Similarity=0.131 Sum_probs=30.0
Q ss_pred hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+++++++++.. ..+.+++...... ...++.+...+ ..+|+|||++.+.++.
T Consensus 59 ThLl~a~~~~~~~~~~~v~y~~~~~~~~--------~~~~~~~~~~~--~dlliiDdi~~~~~~~ 113 (235)
T PRK08084 59 SHLLHAACAELSQRGRAVGYVPLDKRAW--------FVPEVLEGMEQ--LSLVCIDNIECIAGDE 113 (235)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEHHHHhh--------hhHHHHHHhhh--CCEEEEeChhhhcCCH
Confidence 678888887754 3455555544321 11122222222 3689999999987643
No 151
>PRK06526 transposase; Provisional
Probab=93.50 E-value=0.1 Score=33.99 Aligned_cols=60 Identities=13% Similarity=0.178 Sum_probs=36.4
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+++.+++.++ |..+...+.++++...... ....+.+.++.. ..+.+|+|||++.+...+
T Consensus 112 ThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l--~~~dlLIIDD~g~~~~~~ 175 (254)
T PRK06526 112 THLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKL--GRYPLLIVDEVGYIPFEP 175 (254)
T ss_pred HHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHh--ccCCEEEEcccccCCCCH
Confidence 67888887765 6677778887776543211 111222233222 357899999999876543
No 152
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=93.26 E-value=0.35 Score=31.81 Aligned_cols=47 Identities=15% Similarity=0.248 Sum_probs=35.9
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEcccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDELD 58 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEid 58 (69)
|+++|++.++. |+.+++|...++ ..+.++++..+. ..+-|||+|++.
T Consensus 66 SSlVkall~~y~~~GLRlIev~k~~L---------~~l~~l~~~l~~~~~kFIlf~DDLs 116 (249)
T PF05673_consen 66 SSLVKALLNEYADQGLRLIEVSKEDL---------GDLPELLDLLRDRPYKFILFCDDLS 116 (249)
T ss_pred HHHHHHHHHHHhhcCceEEEECHHHh---------ccHHHHHHHHhcCCCCEEEEecCCC
Confidence 67899998866 689999988777 346667777653 468999999853
No 153
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=93.19 E-value=0.19 Score=33.77 Aligned_cols=53 Identities=13% Similarity=0.169 Sum_probs=32.2
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHH-HHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNL-RKAFEEA---------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l-~~if~~a---------------~~~~p~iifiDEid~i~~ 62 (69)
+++|+++-... +.||+.++|+.+-. ..+ ..+|... .......|||||||.+-.
T Consensus 36 ~~lAr~iH~~s~r~~~pfv~vnc~~~~~-------~~l~~~lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L~~ 107 (329)
T TIGR02974 36 ELIAARLHYLSKRWQGPLVKLNCAALSE-------NLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATASL 107 (329)
T ss_pred HHHHHHHHHhcCccCCCeEEEeCCCCCh-------HHHHHHHhccccccccCcccccCCchhhCCCCEEEeCChHhCCH
Confidence 45777775544 46999999987622 111 1222211 112468899999998754
No 154
>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=93.19 E-value=0.23 Score=34.58 Aligned_cols=41 Identities=34% Similarity=0.431 Sum_probs=31.6
Q ss_pred hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
|.+|-++|.++| +||..++++++.|.-+..+| .|.+.|.++
T Consensus 64 TAlA~~ia~eLG~~~PF~~isgSEiyS~e~kKTE-~L~qa~Rra 106 (398)
T PF06068_consen 64 TALAMAIAKELGEDVPFVSISGSEIYSSEVKKTE-ALTQAFRRA 106 (398)
T ss_dssp HHHHHHHHHHCTTTS-EEEEEGGGG-BTTC-HHH-HHHHHHHCS
T ss_pred hHHHHHHHHHhCCCCCeeEcccceeeecccCchH-HHHHHHHHh
Confidence 789999999998 89999999999998887776 455566554
No 155
>PRK06921 hypothetical protein; Provisional
Probab=93.17 E-value=0.31 Score=31.90 Aligned_cols=54 Identities=20% Similarity=0.220 Sum_probs=32.5
Q ss_pred hHHHHHHHHHh----CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccc
Q psy3868 3 YRLTTLCRDSL----GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 3 T~la~aia~~~----~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~ 59 (69)
|+|+.++|+++ |..++.++..+++..... .-....+..+.. ....+|+|||++.
T Consensus 131 ThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~-~~~~~~~~~~~~--~~~dlLiIDDl~~ 188 (266)
T PRK06921 131 THLLTAAANELMRKKGVPVLYFPFVEGFGDLKD-DFDLLEAKLNRM--KKVEVLFIDDLFK 188 (266)
T ss_pred HHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHH-HHHHHHHHHHHh--cCCCEEEEecccc
Confidence 67888888876 567788888776543211 111112222222 3578999999944
No 156
>PF14516 AAA_35: AAA-like domain
Probab=92.97 E-value=0.28 Score=32.88 Aligned_cols=17 Identities=35% Similarity=0.741 Sum_probs=14.9
Q ss_pred cCCeEEEEccccccccc
Q psy3868 47 NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~ 63 (69)
.+|-||+|||+|++...
T Consensus 126 ~~~lVL~iDEiD~l~~~ 142 (331)
T PF14516_consen 126 DKPLVLFIDEIDRLFEY 142 (331)
T ss_pred CCCEEEEEechhhhccC
Confidence 57999999999999863
No 157
>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=92.94 E-value=0.49 Score=31.27 Aligned_cols=30 Identities=13% Similarity=0.340 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHhc----CCeEEEEcccccccc
Q psy3868 33 SESNLRKAFEEADKN----SPSIIFIDELDAIAP 62 (69)
Q Consensus 33 s~~~l~~if~~a~~~----~p~iifiDEid~i~~ 62 (69)
+...++++++.+... ...+++|||+|.+..
T Consensus 98 ~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~ 131 (355)
T TIGR02397 98 GVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSK 131 (355)
T ss_pred CHHHHHHHHHHHhcCcccCCceEEEEeChhhcCH
Confidence 455688888877542 346999999998843
No 158
>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=92.90 E-value=0.69 Score=26.47 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=18.7
Q ss_pred HHHHHHHhcCCeEEEEccccccccc
Q psy3868 39 KAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 39 ~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
.....+....|.+++|||+..+...
T Consensus 76 ~~~~~~~~~~~~~lviDe~~~~~~~ 100 (165)
T cd01120 76 KAERLRERGGDDLIILDELTRLVRA 100 (165)
T ss_pred HHHHHHhCCCCEEEEEEcHHHHHHH
Confidence 3445556678999999999988643
No 159
>KOG1051|consensus
Probab=92.72 E-value=0.39 Score=36.61 Aligned_cols=56 Identities=14% Similarity=0.307 Sum_probs=40.2
Q ss_pred hHHHHHHHHHh---CCcEEEEchhh------hhhc---ccChHHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPE------IMSK---LAGESESNLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~------l~~~---~~ges~~~l~~if~~a~~~~p~iifiDEid~i 60 (69)
|-||+++|..+ .-.++.++.++ +.+. |+|..+- -++.+..++..-+||||||||.-
T Consensus 605 t~lAkaLA~~~Fgse~~~IriDmse~~evskligsp~gyvG~e~g--g~LteavrrrP~sVVLfdeIEkA 672 (898)
T KOG1051|consen 605 TELAKALAEYVFGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEEG--GQLTEAVKRRPYSVVLFEEIEKA 672 (898)
T ss_pred HHHHHHHHHHHcCCccceEEechhhhhhhhhccCCCcccccchhH--HHHHHHHhcCCceEEEEechhhc
Confidence 56888998887 35788888885 2222 5666543 36777777777799999999964
No 160
>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=92.70 E-value=0.15 Score=31.38 Aligned_cols=56 Identities=13% Similarity=0.298 Sum_probs=33.4
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccCh-HHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE-SESNLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~~~~p~iifiDEid~i 60 (69)
|++|.++++++ |.++..++.++++...-.. ......+.++.. ..+.+|+|||+-..
T Consensus 61 ThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l--~~~dlLilDDlG~~ 120 (178)
T PF01695_consen 61 THLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRL--KRVDLLILDDLGYE 120 (178)
T ss_dssp HHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHH--HTSSCEEEETCTSS
T ss_pred HHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCcc--ccccEeccccccee
Confidence 56777776654 7888999999987653221 111233344443 24688889998654
No 161
>PRK06835 DNA replication protein DnaC; Validated
Probab=92.66 E-value=0.36 Score=32.63 Aligned_cols=57 Identities=16% Similarity=0.241 Sum_probs=36.7
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccCh---HHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGE---SESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ge---s~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|+|+.++|+++ |..++.++.++++...... ........++.. ....+|+|||+....
T Consensus 197 ThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l--~~~DLLIIDDlG~e~ 259 (329)
T PRK06835 197 TFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLL--INCDLLIIDDLGTEK 259 (329)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHh--ccCCEEEEeccCCCC
Confidence 78999999887 6788999999886653211 111112223332 245899999997654
No 162
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=92.63 E-value=0.3 Score=34.66 Aligned_cols=62 Identities=8% Similarity=0.083 Sum_probs=35.9
Q ss_pred hHHHHHHHHHhCCc-------EEEEc----hhhhhhcccCh--H----HHHHHHHHHHHHh--cCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLGAF-------FFLIN----GPEIMSKLAGE--S----ESNLRKAFEEADK--NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~~~-------~~~v~----~~~l~~~~~ge--s----~~~l~~if~~a~~--~~p~iifiDEid~i~~~ 63 (69)
|++|+.+|..++.. .+.+. ..+++.++.-. + ...+.++.+.|+. ..|++|+||||+.--.+
T Consensus 208 T~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani~ 287 (459)
T PRK11331 208 TFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLS 287 (459)
T ss_pred HHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCHH
Confidence 78899999887531 22222 23444333111 1 1134455566655 36899999999976544
Q ss_pred c
Q psy3868 64 R 64 (69)
Q Consensus 64 r 64 (69)
+
T Consensus 288 k 288 (459)
T PRK11331 288 K 288 (459)
T ss_pred H
Confidence 3
No 163
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=92.51 E-value=0.6 Score=32.03 Aligned_cols=63 Identities=24% Similarity=0.403 Sum_probs=37.6
Q ss_pred hHHHHHHHHHhCCc-----EEEEchhhh----------hh-----cccChHHH-HHHHHHHHHHh-cCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSLGAF-----FFLINGPEI----------MS-----KLAGESES-NLRKAFEEADK-NSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~~~~-----~~~v~~~~l----------~~-----~~~ges~~-~l~~if~~a~~-~~p~iifiDEid~i 60 (69)
|..++-+..++.-+ ++++||-.. .. +..|.+.. ..+.+++.... ....||.+||+|.|
T Consensus 56 T~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L 135 (366)
T COG1474 56 TATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDAL 135 (366)
T ss_pred hHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhh
Confidence 45566666666433 788888433 23 22333322 24444444433 46789999999999
Q ss_pred ccccc
Q psy3868 61 APKRE 65 (69)
Q Consensus 61 ~~~r~ 65 (69)
..+.+
T Consensus 136 ~~~~~ 140 (366)
T COG1474 136 VDKDG 140 (366)
T ss_pred ccccc
Confidence 88753
No 164
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=92.30 E-value=0.19 Score=35.15 Aligned_cols=41 Identities=29% Similarity=0.302 Sum_probs=34.0
Q ss_pred hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
|.||-++|.++| .||..++++++.|.-+..+|.. .+.|..+
T Consensus 79 TAlA~gIa~eLG~dvPF~~isgsEiYS~E~kKTE~L-~qa~Rra 121 (450)
T COG1224 79 TALAMGIARELGEDVPFVAISGSEIYSLEVKKTEAL-TQALRRA 121 (450)
T ss_pred HHHHHHHHHHhCCCCCceeeccceeeeecccHHHHH-HHHHHHh
Confidence 779999999998 8999999999999888877765 4455555
No 165
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=92.28 E-value=0.24 Score=35.07 Aligned_cols=53 Identities=17% Similarity=0.257 Sum_probs=33.9
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHH-HHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNL-RKAFEEA---------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l-~~if~~a---------------~~~~p~iifiDEid~i~~ 62 (69)
+++|++|.... +.||+.++|+.+-. ..+ ..+|... .......|||||||.+-.
T Consensus 233 ~~lA~~ih~~s~r~~~pfv~i~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~ 304 (534)
T TIGR01817 233 ELIAKAIHYLSPRAKRPFVKVNCAALSE-------TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISP 304 (534)
T ss_pred HHHHHHHHHhCCCCCCCeEEeecCCCCH-------HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCH
Confidence 57888888775 46999999987622 111 1222211 112467899999998754
No 166
>TIGR00602 rad24 checkpoint protein rad24. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.21 E-value=0.18 Score=37.01 Aligned_cols=60 Identities=13% Similarity=-0.004 Sum_probs=37.1
Q ss_pred hHHHHHHHHHhCCcEEE-Echhhhh-------------hc--ccChHHHHHHHHHHHHHh----------cCCeEEEEcc
Q psy3868 3 YRLTTLCRDSLGAFFFL-INGPEIM-------------SK--LAGESESNLRKAFEEADK----------NSPSIIFIDE 56 (69)
Q Consensus 3 T~la~aia~~~~~~~~~-v~~~~l~-------------~~--~~ges~~~l~~if~~a~~----------~~p~iifiDE 56 (69)
|++++.+|++++..+.+ .++.... .. .+....+.++++...+.. ....||||||
T Consensus 124 TTl~~~la~~l~~~~~Ew~npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDE 203 (637)
T TIGR00602 124 STTIKILSKELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVED 203 (637)
T ss_pred HHHHHHHHHHhhhHHHHHhhhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeec
Confidence 67899999998876644 3332111 00 011234556666766642 3567999999
Q ss_pred cccccc
Q psy3868 57 LDAIAP 62 (69)
Q Consensus 57 id~i~~ 62 (69)
+|.+..
T Consensus 204 iPn~~~ 209 (637)
T TIGR00602 204 LPNQFY 209 (637)
T ss_pred chhhch
Confidence 988764
No 167
>KOG0732|consensus
Probab=92.19 E-value=0.14 Score=39.58 Aligned_cols=61 Identities=26% Similarity=0.309 Sum_probs=46.2
Q ss_pred HHHHHHHHHh-CCcEEEEchhhhhhcc-cChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 4 RLTTLCRDSL-GAFFFLINGPEIMSKL-AGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 4 ~la~aia~~~-~~~~~~v~~~~l~~~~-~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
.+..+|-+.+ +.++....-+.+++.. .++.+..|..+|-.|++.+|||+||-.+|--....
T Consensus 607 ~lg~aIlh~~~~~~v~s~~issll~d~~~~~~~~~iv~i~~eaR~~~psi~~ip~~d~w~~~~ 669 (1080)
T KOG0732|consen 607 YLGPAILHRLEGLPVQSLDISSLLSDEGTEDLEEEIVHIFMEARKTTPSIVFIPNVDEWARVI 669 (1080)
T ss_pred cccHHHHHHHhccchHHHHHHHHHhccccccHHHHHHHHHHHHhccCCceeeccchhhhhhcC
Confidence 3445555555 4677777777777765 77788999999999999999999999888665443
No 168
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=92.16 E-value=0.38 Score=33.65 Aligned_cols=60 Identities=17% Similarity=0.216 Sum_probs=41.4
Q ss_pred hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
|+|.+|++++.. ..+++++..+++..++-.--.+=-+-|+.-. .-.+++||+++.+.++.
T Consensus 127 THLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y--~~dlllIDDiq~l~gk~ 191 (408)
T COG0593 127 THLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY--SLDLLLIDDIQFLAGKE 191 (408)
T ss_pred HHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh--ccCeeeechHhHhcCCh
Confidence 788898888873 4688888888866655443332223344433 45789999999998874
No 169
>PRK14953 DNA polymerase III subunits gamma and tau; Provisional
Probab=92.09 E-value=0.6 Score=33.15 Aligned_cols=28 Identities=14% Similarity=0.228 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIA 61 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~ 61 (69)
...+|.+-+.+.. ..+.|++|||+|.+.
T Consensus 101 vd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt 132 (486)
T PRK14953 101 IDDIRALRDAVSYTPIKGKYKVYIIDEAHMLT 132 (486)
T ss_pred HHHHHHHHHHHHhCcccCCeeEEEEEChhhcC
Confidence 4456666665543 345799999999884
No 170
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=91.82 E-value=0.67 Score=33.98 Aligned_cols=53 Identities=8% Similarity=0.208 Sum_probs=34.1
Q ss_pred hHHHHHHHHHhCC------------------------cEEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEE
Q psy3868 3 YRLTTLCRDSLGA------------------------FFFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFI 54 (69)
Q Consensus 3 T~la~aia~~~~~------------------------~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifi 54 (69)
|++|+++|+.+.+ .+++++++. ..+...+|++.+.+... ...|++|
T Consensus 52 TTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~DiieIdaas------~igVd~IReIi~~~~~~P~~~~~KVIII 125 (605)
T PRK05896 52 TSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIVELDAAS------NNGVDEIRNIIDNINYLPTTFKYKVYII 125 (605)
T ss_pred HHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCceEEecccc------ccCHHHHHHHHHHHHhchhhCCcEEEEE
Confidence 6788888888753 334444322 12345678877766432 3469999
Q ss_pred ccccccc
Q psy3868 55 DELDAIA 61 (69)
Q Consensus 55 DEid~i~ 61 (69)
||+|.+-
T Consensus 126 DEad~Lt 132 (605)
T PRK05896 126 DEAHMLS 132 (605)
T ss_pred echHhCC
Confidence 9999874
No 171
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=91.61 E-value=0.75 Score=31.57 Aligned_cols=29 Identities=17% Similarity=0.225 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
...++++-+.+.. ....+++|||+|.+..
T Consensus 109 id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~ 141 (397)
T PRK14955 109 VDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSI 141 (397)
T ss_pred HHHHHHHHHHHhhchhcCCeEEEEEeChhhCCH
Confidence 4567776655532 2346999999998853
No 172
>PRK14952 DNA polymerase III subunits gamma and tau; Provisional
Probab=91.61 E-value=0.62 Score=33.91 Aligned_cols=29 Identities=17% Similarity=0.197 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
...+|++-+.+.. ....|++|||+|.+-.
T Consensus 100 vd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~ 132 (584)
T PRK14952 100 VDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTT 132 (584)
T ss_pred HHHHHHHHHHHHhhhhcCCceEEEEECCCcCCH
Confidence 4556666555432 3456999999998853
No 173
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=91.55 E-value=0.32 Score=35.01 Aligned_cols=57 Identities=21% Similarity=0.218 Sum_probs=32.9
Q ss_pred hHHHHHHHHH-----------hCCcEEEEchhhhhhc-----ccChHHH--------HHHHHHHHHHhcCCeEEEEcccc
Q psy3868 3 YRLTTLCRDS-----------LGAFFFLINGPEIMSK-----LAGESES--------NLRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 3 T~la~aia~~-----------~~~~~~~v~~~~l~~~-----~~ges~~--------~l~~if~~a~~~~p~iifiDEid 58 (69)
+++|+++-+. .+.||+.+||+.+-.. .+|..+. .-.-+|+.| ....||+|||+
T Consensus 256 e~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e~lleseLFG~~~gaftga~~~~~~Gl~e~A---~gGTLfLdeI~ 332 (538)
T PRK15424 256 ELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGSRRGGRAGLFEIA---HGGTLFLDEIG 332 (538)
T ss_pred HHHHHHHHHhhcccccccCccCCCCeEEeecccCChhhHHHHhcCCccccccCccccccCCchhcc---CCCEEEEcChH
Confidence 4678887665 4579999999876321 1111000 000123332 35689999999
Q ss_pred cccc
Q psy3868 59 AIAP 62 (69)
Q Consensus 59 ~i~~ 62 (69)
.+-.
T Consensus 333 ~Lp~ 336 (538)
T PRK15424 333 EMPL 336 (538)
T ss_pred hCCH
Confidence 8754
No 174
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=91.35 E-value=0.77 Score=33.21 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
...++++.+.+.. ....|++|||+|.+-.
T Consensus 101 vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~ 133 (563)
T PRK06647 101 VQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSN 133 (563)
T ss_pred HHHHHHHHHHHHhchhcCCCEEEEEEChhhcCH
Confidence 4566776655432 3567999999998853
No 175
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=91.33 E-value=0.4 Score=33.89 Aligned_cols=57 Identities=19% Similarity=0.250 Sum_probs=33.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccChHH-------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGESE-------SNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ges~-------~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
+++|+++-... +.||+.++|+.+-.. .+|... ..-.-.|+.| ....|||||||.+..
T Consensus 224 ~~~A~~ih~~s~r~~~p~v~v~c~~~~~~~~e~~lfG~~~g~~~ga~~~~~g~~~~a---~gGtL~ldeI~~L~~ 295 (509)
T PRK05022 224 ELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAFTGAISNRSGKFELA---DGGTLFLDEIGELPL 295 (509)
T ss_pred HHHHHHHHHhCCcCCCCeEEEEcccCChHHHHHHhcCccccccCCCcccCCcchhhc---CCCEEEecChhhCCH
Confidence 56888887764 479999999877321 111100 0000123222 356799999999864
No 176
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=91.22 E-value=0.81 Score=33.37 Aligned_cols=29 Identities=17% Similarity=0.334 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
...||++.+.++. ....|++|||+|.+..
T Consensus 114 vd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~ 146 (598)
T PRK09111 114 VDDIREIIESVRYRPVSARYKVYIIDEVHMLST 146 (598)
T ss_pred HHHHHHHHHHHHhchhcCCcEEEEEEChHhCCH
Confidence 4568888887753 2457999999999853
No 177
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=91.14 E-value=1 Score=29.22 Aligned_cols=54 Identities=20% Similarity=0.266 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhC-----CcEEEEchhhhhhcccChHHHHHHHHHHHHHh------cCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLG-----AFFFLINGPEIMSKLAGESESNLRKAFEEADK------NSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~-----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~------~~p~iifiDEid~i~~ 62 (69)
|++++++++++. .+++.+++++- .....+++.+..... ..+.+|+|||+|.+..
T Consensus 52 t~~~~~l~~~l~~~~~~~~~i~~~~~~~------~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~ 116 (319)
T PRK00440 52 TTAALALARELYGEDWRENFLELNASDE------RGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS 116 (319)
T ss_pred HHHHHHHHHHHcCCccccceEEeccccc------cchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH
Confidence 678889988873 34566655432 111223333222211 2356999999998854
No 178
>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=91.03 E-value=0.87 Score=33.19 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=17.3
Q ss_pred hHHHHHHHHHh----------CCcEEEEchhhh
Q psy3868 3 YRLTTLCRDSL----------GAFFFLINGPEI 25 (69)
Q Consensus 3 T~la~aia~~~----------~~~~~~v~~~~l 25 (69)
|++|+++.+.. +.+|+.+++..+
T Consensus 189 TTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l 221 (615)
T TIGR02903 189 TTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL 221 (615)
T ss_pred HHHHHHHHHhhhhccCCcccCCCCeEEEechhc
Confidence 67888887655 357899988765
No 179
>PRK08118 topology modulation protein; Reviewed
Probab=90.73 E-value=1 Score=27.34 Aligned_cols=42 Identities=10% Similarity=0.001 Sum_probs=28.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
|++|+.+++.++.+++.++.--....|...+...+.++.+..
T Consensus 15 STlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~~~~~~~~~~ 56 (167)
T PRK08118 15 STLARQLGEKLNIPVHHLDALFWKPNWEGVPKEEQITVQNEL 56 (167)
T ss_pred HHHHHHHHHHhCCCceecchhhcccCCcCCCHHHHHHHHHHH
Confidence 789999999999999888764433345555554555554443
No 180
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=90.66 E-value=0.35 Score=34.94 Aligned_cols=53 Identities=8% Similarity=0.183 Sum_probs=33.7
Q ss_pred hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHH-HHHHHHHH------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESN-LRKAFEEA------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~-l~~if~~a------------~~~~p~iifiDEid~i~~ 62 (69)
+++|+++-+... .||+.+||..+- +.. -.++|... .......|||||||.+-.
T Consensus 362 ~~~A~~ih~~s~r~~~pfv~vnc~~~~-------~~~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l~~ 430 (638)
T PRK11388 362 ALLAQAIHNESERAAGPYIAVNCQLYP-------DEALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYLSP 430 (638)
T ss_pred HHHHHHHHHhCCccCCCeEEEECCCCC-------hHHHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhCCH
Confidence 468898877654 699999997762 111 12333211 112467899999998754
No 181
>KOG1051|consensus
Probab=90.45 E-value=1.3 Score=33.95 Aligned_cols=51 Identities=20% Similarity=0.322 Sum_probs=39.8
Q ss_pred CcEEEEchhhhh--hcccChHHHHHHHHHHHHH-hcCCeEEEEccccccccccc
Q psy3868 15 AFFFLINGPEIM--SKLAGESESNLRKAFEEAD-KNSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 15 ~~~~~v~~~~l~--~~~~ges~~~l~~if~~a~-~~~p~iifiDEid~i~~~r~ 65 (69)
..++.++-..+. .++-|+-+.+++.+-+.+. .....|||+||++-+.+...
T Consensus 244 ~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg~g~ 297 (898)
T KOG1051|consen 244 KKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGELHWLVGSGS 297 (898)
T ss_pred cceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecceeeeecCCC
Confidence 455666665444 4588999999999999988 45788999999999977654
No 182
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=90.06 E-value=1.7 Score=29.03 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=35.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDEL 57 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEi 57 (69)
++++||+-++. +..+++|+..++. .+-.+++..+. ..+-|||+|+.
T Consensus 99 SSLVKA~~~e~~~~glrLVEV~k~dl~---------~Lp~l~~~Lr~~~~kFIlFcDDL 148 (287)
T COG2607 99 SSLVKALLNEYADEGLRLVEVDKEDLA---------TLPDLVELLRARPEKFILFCDDL 148 (287)
T ss_pred HHHHHHHHHHHHhcCCeEEEEcHHHHh---------hHHHHHHHHhcCCceEEEEecCC
Confidence 57889888877 4789999998873 45667777765 46789999985
No 183
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=89.93 E-value=0.27 Score=33.47 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=32.4
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHH-HHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLR-KAFEEA---------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~-~if~~a---------------~~~~p~iifiDEid~i~~ 62 (69)
+.+|+++-... +.||+.++|+.+.. ..+. .+|... ....+..|||||||.+.+
T Consensus 176 ~~~a~~ih~~s~~~~~~~i~~~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~ 247 (441)
T PRK10365 176 ELVARAIHASSARSEKPLVTLNCAALNE-------SLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISP 247 (441)
T ss_pred HHHHHHHHHcCCCCCCCeeeeeCCCCCH-------HHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccCCH
Confidence 35677775443 47999999987632 2222 223211 122467899999999865
No 184
>KOG0989|consensus
Probab=89.75 E-value=0.36 Score=33.04 Aligned_cols=60 Identities=17% Similarity=0.141 Sum_probs=33.8
Q ss_pred hHHHHHHHHHhCC------cEEEEchhhhhhcccCh-HHHHHHHHHHHHH-----hcCC-eEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGA------FFFLINGPEIMSKLAGE-SESNLRKAFEEAD-----KNSP-SIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~------~~~~v~~~~l~~~~~ge-s~~~l~~if~~a~-----~~~p-~iifiDEid~i~~ 62 (69)
|+.++++|.++.. .+...++++-.+.-++. .-++-.++-..-. .+.| -|+.+||+|++..
T Consensus 71 TStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmts 143 (346)
T KOG0989|consen 71 TSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTS 143 (346)
T ss_pred hHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhH
Confidence 7789999999876 34455666654433222 2222222211111 1223 7999999999865
No 185
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=89.56 E-value=0.71 Score=33.14 Aligned_cols=57 Identities=21% Similarity=0.211 Sum_probs=32.8
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccChHH--------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGESE--------SNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ges~--------~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
+++|+++-+.. +.||+.+||..+-.. ..|..+ ..-.-+|+.| ....||+||||.+-.
T Consensus 249 e~lA~~IH~~S~r~~~pfv~inC~~l~e~lleseLFG~~~gaftga~~~~~~Gl~e~A---~gGTLfLdeI~~Lp~ 321 (526)
T TIGR02329 249 ELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGYEEGAFTGARRGGRTGLIEAA---HRGTLFLDEIGEMPL 321 (526)
T ss_pred HHHHHHHHHhcCcCCCCEEEeccccCChhHHHHHhcCCcccccccccccccccchhhc---CCceEEecChHhCCH
Confidence 46788876554 469999999876221 111000 0001122222 356799999998854
No 186
>PRK07133 DNA polymerase III subunits gamma and tau; Validated
Probab=89.10 E-value=1.6 Score=32.76 Aligned_cols=59 Identities=14% Similarity=0.213 Sum_probs=35.0
Q ss_pred hHHHHHHHHHhCCcEEE---Echhhhh------------hcccChHHHHHHHHHHHHHh----cCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFL---INGPEIM------------SKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~~~~~~---v~~~~l~------------~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~ 61 (69)
|++|+++|+.+.++-.. -.|..+. ......+...+|++.+.+.. ....|++|||+|.+-
T Consensus 54 Tt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT 131 (725)
T PRK07133 54 TSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLS 131 (725)
T ss_pred HHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCC
Confidence 67899999988763210 0111110 00001235668888887754 345799999999875
No 187
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=88.76 E-value=0.47 Score=33.72 Aligned_cols=51 Identities=18% Similarity=0.318 Sum_probs=33.4
Q ss_pred HHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHH-HHHHHH---------------hcCCeEEEEccccccc
Q psy3868 4 RLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRK-AFEEAD---------------KNSPSIIFIDELDAIA 61 (69)
Q Consensus 4 ~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~-if~~a~---------------~~~p~iifiDEid~i~ 61 (69)
++|++|=.... .||+.+||..+ .+..+.. +|-..+ ......||+|||..+.
T Consensus 179 lvAr~IH~~S~R~~~PFVavNcaAi-------p~~l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mp 248 (464)
T COG2204 179 LVARAIHQASPRAKGPFIAVNCAAI-------PENLLESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMP 248 (464)
T ss_pred HHHHHHHhhCcccCCCceeeecccC-------CHHHHHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccCC
Confidence 45666655543 59999999877 4444444 554322 1246789999998764
No 188
>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
Probab=88.54 E-value=2.1 Score=27.87 Aligned_cols=18 Identities=17% Similarity=0.370 Sum_probs=14.7
Q ss_pred cCCeEEEEcccccccccc
Q psy3868 47 NSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~r 64 (69)
.++.++|+||+.++...-
T Consensus 102 G~~vll~iDei~r~a~a~ 119 (249)
T cd01128 102 GKDVVILLDSITRLARAY 119 (249)
T ss_pred CCCEEEEEECHHHhhhhh
Confidence 468999999999987543
No 189
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=88.32 E-value=1.7 Score=24.71 Aligned_cols=58 Identities=9% Similarity=0.062 Sum_probs=35.8
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
+..|...|+.+..+-...-.+.+....-..+.++.+.++.....+|++.++|.|++.-
T Consensus 24 ~~~a~~~g~~i~~~~~d~~~s~~~~~~R~~~~~ll~~~~~~~~d~ivv~~~~Rl~R~~ 81 (137)
T cd00338 24 REYAARNGLEVVGEYEDAGSSATSLVDRPGLQRLLADVKAGKIDVVLVEKLDRLSRNL 81 (137)
T ss_pred HHHHHHCCCEEEEEEEeCCCCcccccCCHHHHHHHHHHHcCCCCEEEEEecchhhCCH
Confidence 3445555665433222111122212335568888888887788999999999998754
No 190
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=88.31 E-value=1.2 Score=31.75 Aligned_cols=57 Identities=23% Similarity=0.367 Sum_probs=32.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccChHH-------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGESE-------SNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ges~-------~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
+++|+++-... +.||+.++|+.+-.. .+|... ..-..+|+.| ....|||||||.+.+
T Consensus 241 ~~lA~aiH~~s~r~~~pfv~inca~~~~~~~e~elFG~~~~~~~~~~~~~~g~~e~a---~~GtL~LdeI~~L~~ 312 (520)
T PRK10820 241 DLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAPGAYPNALEGKKGFFEQA---NGGSVLLDEIGEMSP 312 (520)
T ss_pred HHHHHHHHHhCCCCCCCeEEeccccCCHHHHHHHhcCCCCCCcCCcccCCCChhhhc---CCCEEEEeChhhCCH
Confidence 46788875443 369999999876321 111100 0001123332 357789999998864
No 191
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=88.31 E-value=0.85 Score=33.38 Aligned_cols=56 Identities=20% Similarity=0.249 Sum_probs=34.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc-----ccCh--------HHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK-----LAGE--------SESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~-----~~ge--------s~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
|++|+++-... +.||+.++|..+-.. ++|. ..+.. ..|+.+ ....|||||||.+-.
T Consensus 413 ~~lA~~ih~~s~r~~~~~v~i~c~~~~~~~~~~~lfg~~~~~~~g~~~~~~-g~le~a---~~GtL~Ldei~~L~~ 484 (686)
T PRK15429 413 ELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAFTGASAQRI-GRFELA---DKSSLFLDEVGDMPL 484 (686)
T ss_pred HHHHHHHHHhcCCCCCCeEEEecccCChhHhhhhhcCcccccccccccchh-hHHHhc---CCCeEEEechhhCCH
Confidence 57889887754 469999999875321 2221 11111 123333 467899999998754
No 192
>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=88.21 E-value=0.64 Score=28.29 Aligned_cols=29 Identities=38% Similarity=0.472 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHhc-CCeEEEEccccccc
Q psy3868 33 SESNLRKAFEEADKN-SPSIIFIDELDAIA 61 (69)
Q Consensus 33 s~~~l~~if~~a~~~-~p~iifiDEid~i~ 61 (69)
....+.++++...+. .+.+|+|||++.+.
T Consensus 102 ~~~~l~~~~~~l~~~~~~~iiviDe~~~~~ 131 (234)
T PF01637_consen 102 SFSALERLLEKLKKKGKKVIIVIDEFQYLA 131 (234)
T ss_dssp -G--HHHHHHHHHHCHCCEEEEEETGGGGG
T ss_pred HHHHHHHHHHHHHhcCCcEEEEEecHHHHh
Confidence 456678888887664 35999999999998
No 193
>PRK14950 DNA polymerase III subunits gamma and tau; Provisional
Probab=87.98 E-value=1.9 Score=31.19 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
...+|++-+.+.. ....|++|||+|.+..
T Consensus 102 vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~ 134 (585)
T PRK14950 102 VDDAREIIERVQFRPALARYKVYIIDEVHMLST 134 (585)
T ss_pred HHHHHHHHHHHhhCcccCCeEEEEEeChHhCCH
Confidence 4456666555432 2457999999998853
No 194
>PRK11823 DNA repair protein RadA; Provisional
Probab=87.71 E-value=1.8 Score=30.41 Aligned_cols=28 Identities=18% Similarity=0.482 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 36 NLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 36 ~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
.+.++++..++.+|.+|+||++..+...
T Consensus 144 ~l~~i~~~i~~~~~~lVVIDSIq~l~~~ 171 (446)
T PRK11823 144 NLEAILATIEEEKPDLVVIDSIQTMYSP 171 (446)
T ss_pred CHHHHHHHHHhhCCCEEEEechhhhccc
Confidence 4667777777789999999999988753
No 195
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=87.63 E-value=1.2 Score=29.83 Aligned_cols=57 Identities=18% Similarity=0.206 Sum_probs=32.2
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhh-----cccChHH-------HHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMS-----KLAGESE-------SNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~-----~~~ges~-------~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
+++|+++-... +.||+.++|..+-. .++|... ..-...|+. .....|||||||.+..
T Consensus 43 ~~lA~~iH~~s~r~~~pfv~v~c~~~~~~~~~~~lfg~~~~~~~g~~~~~~g~l~~---a~gGtL~l~~i~~L~~ 114 (326)
T PRK11608 43 ELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFER---ADGGTLFLDELATAPM 114 (326)
T ss_pred HHHHHHHHHhCCccCCCeEEEeCCCCCHHHHHHHHccccccccCCcccccCCchhc---cCCCeEEeCChhhCCH
Confidence 46777775544 36999999987621 1112110 000112222 2457899999999864
No 196
>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=87.19 E-value=0.68 Score=33.12 Aligned_cols=15 Identities=33% Similarity=0.806 Sum_probs=12.5
Q ss_pred CCeEEEEcccccccc
Q psy3868 48 SPSIIFIDELDAIAP 62 (69)
Q Consensus 48 ~p~iifiDEid~i~~ 62 (69)
...+|||||||.+-+
T Consensus 175 ~gG~L~IdEI~~L~~ 189 (531)
T TIGR02902 175 HGGVLFIDEIGELHP 189 (531)
T ss_pred CCcEEEEechhhCCH
Confidence 457999999998864
No 197
>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.
Probab=86.91 E-value=0.53 Score=29.05 Aligned_cols=19 Identities=37% Similarity=0.477 Sum_probs=13.9
Q ss_pred CCeEEEEcccccccccccc
Q psy3868 48 SPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 48 ~p~iifiDEid~i~~~r~~ 66 (69)
..++|+|||+..+++.|..
T Consensus 79 ~~~liviDEa~~~~~~r~~ 97 (193)
T PF05707_consen 79 KGSLIVIDEAQNFFPSRSW 97 (193)
T ss_dssp TT-EEEETTGGGTSB---T
T ss_pred CCcEEEEECChhhcCCCcc
Confidence 6899999999999998876
No 198
>PRK14954 DNA polymerase III subunits gamma and tau; Provisional
Probab=86.69 E-value=2.7 Score=30.89 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
...|+.+-+.+.. ....|++|||+|.+..
T Consensus 109 vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~ 141 (620)
T PRK14954 109 VDDIRQLRENVRYGPQKGRYRVYIIDEVHMLST 141 (620)
T ss_pred HHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCH
Confidence 4566666555522 3456999999998853
No 199
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=86.07 E-value=2 Score=30.53 Aligned_cols=63 Identities=19% Similarity=0.380 Sum_probs=42.7
Q ss_pred hhHHHHHHHHHh-CCcEEEEchhhhhhcc------cC--------hHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 2 SYRLTTLCRDSL-GAFFFLINGPEIMSKL------AG--------ESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 2 ~T~la~aia~~~-~~~~~~v~~~~l~~~~------~g--------es~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
||+|-+..++-. ..++++|++.+-...+ .| -.|.++..+.+...+.+|.+++||-|-.+....
T Consensus 107 STLLLQva~~lA~~~~vLYVsGEES~~QiklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~p~lvVIDSIQT~~s~~ 184 (456)
T COG1066 107 STLLLQVAARLAKRGKVLYVSGEESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAELEQEKPDLVVIDSIQTLYSEE 184 (456)
T ss_pred HHHHHHHHHHHHhcCcEEEEeCCcCHHHHHHHHHHhCCCccceEEehhcCHHHHHHHHHhcCCCEEEEeccceeeccc
Confidence 566655444433 1278888775433222 12 156778999999999999999999998887654
No 200
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=85.96 E-value=2.6 Score=29.64 Aligned_cols=16 Identities=25% Similarity=0.389 Sum_probs=13.1
Q ss_pred cCCeEEEEcccccccc
Q psy3868 47 NSPSIIFIDELDAIAP 62 (69)
Q Consensus 47 ~~p~iifiDEid~i~~ 62 (69)
....|++|||+|.+..
T Consensus 120 ~~~kvvIIdead~lt~ 135 (451)
T PRK06305 120 SRYKIYIIDEVHMLTK 135 (451)
T ss_pred CCCEEEEEecHHhhCH
Confidence 4578999999998853
No 201
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=85.76 E-value=1.1 Score=30.79 Aligned_cols=54 Identities=15% Similarity=0.207 Sum_probs=32.4
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHH---------------HHhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEE---------------ADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~---------------a~~~~p~iifiDEid~i~~ 62 (69)
+++|+++.... +.||+.++|..+-..+. -..+|.. .....+..|||||||.+-.
T Consensus 171 ~~~A~~ih~~~~~~~~~~~~~~c~~~~~~~~------~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~ 242 (463)
T TIGR01818 171 ELVARALHRHSPRANGPFIALNMAAIPKDLI------ESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPL 242 (463)
T ss_pred HHHHHHHHHhCCCCCCCeEEEeCCCCCHHHH------HHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCH
Confidence 46777776654 46999999977622111 1112221 1122467899999998764
No 202
>PF13304 AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T_B 3QKT_A 1II8_B 3QKR_B 3QKU_A.
Probab=85.64 E-value=1.5 Score=26.14 Aligned_cols=31 Identities=23% Similarity=0.208 Sum_probs=20.7
Q ss_pred cChHHHHHHHHHHHHHhcCC--eEEEEcccccc
Q psy3868 30 AGESESNLRKAFEEADKNSP--SIIFIDELDAI 60 (69)
Q Consensus 30 ~ges~~~l~~if~~a~~~~p--~iifiDEid~i 60 (69)
.|.+++++-.++.......+ .+++|||.|.-
T Consensus 237 ~S~G~~~~l~l~~~l~~~~~~~~illiDEpE~~ 269 (303)
T PF13304_consen 237 LSSGEKRLLSLLSLLLSAKKNGSILLIDEPENH 269 (303)
T ss_dssp --HHHHHHHHHHHHHHTTTTT-SEEEEESSSTT
T ss_pred CCHHHHHHHHHHHHHhCcCCCCeEEEecCCcCC
Confidence 37778887566666554433 99999999864
No 203
>KOG1942|consensus
Probab=85.54 E-value=0.58 Score=32.31 Aligned_cols=38 Identities=32% Similarity=0.546 Sum_probs=22.3
Q ss_pred hhhhhcccChHHHHHHHHHHHHH-hcCCeEEEEcccccc
Q psy3868 23 PEIMSKLAGESESNLRKAFEEAD-KNSPSIIFIDELDAI 60 (69)
Q Consensus 23 ~~l~~~~~ges~~~l~~if~~a~-~~~p~iifiDEid~i 60 (69)
.++..+..||-.+.+.+-.++-. +.-|.++||||++-+
T Consensus 270 TEITdkLR~eiNkvVn~Yid~GvAElvPGVLFIDEVhML 308 (456)
T KOG1942|consen 270 TEITDKLRGEINKVVNKYIDQGVAELVPGVLFIDEVHML 308 (456)
T ss_pred chhHHHHHHHHHHHHHHHHhcchhhhcCcceEeeehhhh
Confidence 33444444444444444444322 356999999999865
No 204
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=85.48 E-value=2.8 Score=29.00 Aligned_cols=56 Identities=23% Similarity=0.248 Sum_probs=28.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i 60 (69)
|++.+.+..+..-+++.++-.++..... .-......+..+.......||+|||+..
T Consensus 51 Ttll~~l~~~~~~~~iy~~~~d~~~~~~--~l~d~~~~~~~~~~~~~~yifLDEIq~v 106 (398)
T COG1373 51 TTLLKLLIKGLLEEIIYINFDDLRLDRI--ELLDLLRAYIELKEREKSYIFLDEIQNV 106 (398)
T ss_pred HHHHHHHHhhCCcceEEEEecchhcchh--hHHHHHHHHHHhhccCCceEEEecccCc
Confidence 4444777766654455555555432211 1122222222222224589999999875
No 205
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]
Probab=85.25 E-value=0.81 Score=32.96 Aligned_cols=59 Identities=14% Similarity=0.249 Sum_probs=36.1
Q ss_pred hHHHHHHHHHhCCcE--E-----------EEchh---hh--hhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDSLGAFF--F-----------LINGP---EI--MSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~~~~~~--~-----------~v~~~---~l--~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i 60 (69)
|++||.+|+.+++.= . .++.. ++ ++.-...+...+|++-+.++- .+.-|++|||+|-+
T Consensus 52 Tt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHML 131 (515)
T COG2812 52 TTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHML 131 (515)
T ss_pred hhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhh
Confidence 778999999887641 0 01111 11 011222356678888888742 45679999999987
Q ss_pred c
Q psy3868 61 A 61 (69)
Q Consensus 61 ~ 61 (69)
-
T Consensus 132 S 132 (515)
T COG2812 132 S 132 (515)
T ss_pred h
Confidence 4
No 206
>PRK15115 response regulator GlrR; Provisional
Probab=84.96 E-value=1.3 Score=30.27 Aligned_cols=55 Identities=18% Similarity=0.244 Sum_probs=33.8
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~~ 63 (69)
+++|+++.... +.+|+.++|..+-..+ .-..+|..+ .......|||||||.+.+.
T Consensus 171 ~~lA~~ih~~s~r~~~~f~~i~c~~~~~~~------~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~ 243 (444)
T PRK15115 171 EILAQAIHNASPRASKPFIAINCGALPEQL------LESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAP 243 (444)
T ss_pred HHHHHHHHHhcCCCCCCeEEEeCCCCCHHH------HHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEccccCCHH
Confidence 56788776664 4799999998762211 111233221 1123578999999988653
No 207
>PRK07261 topology modulation protein; Provisional
Probab=84.65 E-value=3.4 Score=25.03 Aligned_cols=31 Identities=3% Similarity=-0.009 Sum_probs=22.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGES 33 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges 33 (69)
|++|+.++..++.+++.++.-.....|....
T Consensus 14 STla~~l~~~~~~~~i~~D~~~~~~~~~~~~ 44 (171)
T PRK07261 14 STLARKLSQHYNCPVLHLDTLHFQPNWQERD 44 (171)
T ss_pred HHHHHHHHHHhCCCeEecCCEEeccccccCC
Confidence 6799999999999988877654444454444
No 208
>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].
Probab=84.41 E-value=2.6 Score=28.52 Aligned_cols=25 Identities=12% Similarity=0.294 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCCeEEEEcccccccc
Q psy3868 38 RKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 38 ~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
.++....+..++-+|+|||+|.+..
T Consensus 135 ~~~~~llr~~~vrmLIIDE~H~lLa 159 (302)
T PF05621_consen 135 QQVLRLLRRLGVRMLIIDEFHNLLA 159 (302)
T ss_pred HHHHHHHHHcCCcEEEeechHHHhc
Confidence 3344555667999999999999743
No 209
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=84.07 E-value=0.97 Score=32.99 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=11.7
Q ss_pred CeEEEEcccccccc
Q psy3868 49 PSIIFIDELDAIAP 62 (69)
Q Consensus 49 p~iifiDEid~i~~ 62 (69)
..+|||||++.+-+
T Consensus 127 ~GiL~lDEi~~l~~ 140 (633)
T TIGR02442 127 RGILYIDEVNLLDD 140 (633)
T ss_pred CCeEEeChhhhCCH
Confidence 46999999998865
No 210
>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]
Probab=83.62 E-value=1.3 Score=27.61 Aligned_cols=36 Identities=19% Similarity=0.264 Sum_probs=23.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEE 43 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~ 43 (69)
|++.+++|+.++.+|+-.+ .++.+-.|. .+.++|+.
T Consensus 16 STIGr~LAk~L~~~F~D~D--~~Ie~~~g~---sI~eIF~~ 51 (172)
T COG0703 16 STIGRALAKALNLPFIDTD--QEIEKRTGM---SIAEIFEE 51 (172)
T ss_pred hHHHHHHHHHcCCCcccch--HHHHHHHCc---CHHHHHHH
Confidence 7899999999999997654 344444443 24444444
No 211
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=83.42 E-value=0.92 Score=29.57 Aligned_cols=17 Identities=35% Similarity=0.679 Sum_probs=14.3
Q ss_pred cCCeEEEEccccccccc
Q psy3868 47 NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~ 63 (69)
..+-||+|||+|++-+.
T Consensus 171 ~~~iViiIDdLDR~~~~ 187 (325)
T PF07693_consen 171 KKRIVIIIDDLDRCSPE 187 (325)
T ss_pred CceEEEEEcchhcCCcH
Confidence 57899999999998654
No 212
>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=83.41 E-value=1.8 Score=31.56 Aligned_cols=48 Identities=23% Similarity=0.127 Sum_probs=35.9
Q ss_pred hHHHHHHHHHhCCcE-----EEEch-----hhhhhcccChHHHHHHHHHHHHHhcCCe
Q psy3868 3 YRLTTLCRDSLGAFF-----FLING-----PEIMSKLAGESESNLRKAFEEADKNSPS 50 (69)
Q Consensus 3 T~la~aia~~~~~~~-----~~v~~-----~~l~~~~~ges~~~l~~if~~a~~~~p~ 50 (69)
|++++++++.++.+. +..|+ +-+..-+.|.+++.++..|+.|++..|+
T Consensus 51 T~la~~la~~l~~~~~~~~~~~~n~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~ 108 (608)
T TIGR00764 51 SMLAKAMAELLPDEELEDILVYPNPEDPNMPRIVEVPAGEGREIVEDYKKKAFKQPSS 108 (608)
T ss_pred HHHHHHHHHHcCchhheeEEEEeCCCCCchHHHHHHHHhhchHHHHHHHHHhhcccch
Confidence 789999999997652 23333 3344558899999999999999886654
No 213
>PRK13531 regulatory ATPase RavA; Provisional
Probab=83.38 E-value=0.91 Score=32.60 Aligned_cols=56 Identities=16% Similarity=0.239 Sum_probs=29.0
Q ss_pred hHHHHHHHHHhCC--cEEEEc-----hhhhhhcccChH-HHHH--HHHHHHHHhc---CCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGA--FFFLIN-----GPEIMSKLAGES-ESNL--RKAFEEADKN---SPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~--~~~~v~-----~~~l~~~~~ges-~~~l--~~if~~a~~~---~p~iifiDEid~i~~ 62 (69)
|++|++++...+. +|..++ ++++ +|.. -... ..-|...... ...++|+|||..+.+
T Consensus 53 T~LAraLa~~~~~~~~F~~~~~~fttp~DL----fG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~rasp 121 (498)
T PRK13531 53 SLIARRLKFAFQNARAFEYLMTRFSTPEEV----FGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWKAGP 121 (498)
T ss_pred HHHHHHHHHHhcccCcceeeeeeecCcHHh----cCcHHHhhhhhcCchhhhcCCccccccEEeecccccCCH
Confidence 7899999987653 333332 3344 3321 1111 1123221111 234999999986654
No 214
>PF07931 CPT: Chloramphenicol phosphotransferase-like protein; InterPro: IPR012853 The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Q56148 from SWISSPROT) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite [, ]. ; GO: 0005524 ATP binding, 0016740 transferase activity; PDB: 1QHX_A 1QHN_A 1GRR_A 1QHY_A 1QHS_A 1GRQ_A.
Probab=83.36 E-value=8 Score=23.93 Aligned_cols=26 Identities=4% Similarity=0.079 Sum_probs=22.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSK 28 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~ 28 (69)
|++|+++.+.+.-|++.++...+...
T Consensus 15 Ssia~~Lq~~~~~p~~~l~~D~f~~~ 40 (174)
T PF07931_consen 15 SSIARALQERLPEPWLHLSVDTFVDM 40 (174)
T ss_dssp HHHHHHHHHHSSS-EEEEEHHHHHHH
T ss_pred HHHHHHHHHhCcCCeEEEecChHHhh
Confidence 78999999999999999999888773
No 215
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=82.06 E-value=2 Score=29.38 Aligned_cols=54 Identities=11% Similarity=0.182 Sum_probs=32.3
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~ 62 (69)
+++|+++.... +.+|+.++|..+-..+ .-..+|-.. .......|||||||.+.+
T Consensus 180 ~~lA~~ih~~s~~~~~~~~~i~c~~~~~~~------~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~ 251 (457)
T PRK11361 180 ELIARAIHYNSRRAKGPFIKVNCAALPESL------LESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPL 251 (457)
T ss_pred HHHHHHHHHhCCCCCCCeEEEECCCCCHHH------HHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhCCH
Confidence 45777776554 4699999998762211 111222211 112356899999999865
No 216
>PRK06620 hypothetical protein; Validated
Probab=81.98 E-value=2.2 Score=26.98 Aligned_cols=12 Identities=8% Similarity=0.329 Sum_probs=9.7
Q ss_pred CeEEEEcccccc
Q psy3868 49 PSIIFIDELDAI 60 (69)
Q Consensus 49 p~iifiDEid~i 60 (69)
..+++|||||.+
T Consensus 86 ~d~lliDdi~~~ 97 (214)
T PRK06620 86 YNAFIIEDIENW 97 (214)
T ss_pred CCEEEEeccccc
Confidence 478999999954
No 217
>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]
Probab=81.88 E-value=6.3 Score=25.99 Aligned_cols=46 Identities=13% Similarity=0.034 Sum_probs=41.0
Q ss_pred HHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCe
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPS 50 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~ 50 (69)
-+|++|.+.|+.++.+|+-.=+..|.++-.+.-+.+-++|+.+...
T Consensus 53 ~vka~Aek~Gl~IvSINAlypFn~wt~~~~a~a~~la~yA~acGA~ 98 (272)
T COG4130 53 EVKALAEKAGLTIVSINALYPFNEWTEERVAEARGLADYAAACGAK 98 (272)
T ss_pred HHHHHHHHcCcEEEEeeccccccccChHHHHHHHHHHHHHHhcCCc
Confidence 3689999999999999998888999999999999999999886543
No 218
>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2.7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....
Probab=81.60 E-value=2.6 Score=25.04 Aligned_cols=29 Identities=21% Similarity=0.261 Sum_probs=22.2
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGES 33 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges 33 (69)
|++++.+|..++++|+.++- ++....|.+
T Consensus 6 Stvg~~lA~~L~~~fiD~D~--~i~~~~g~s 34 (158)
T PF01202_consen 6 STVGKLLAKRLGRPFIDLDD--EIEERTGMS 34 (158)
T ss_dssp HHHHHHHHHHHTSEEEEHHH--HHHHHHTSH
T ss_pred HHHHHHHHHHhCCCccccCH--HHHHHhCCc
Confidence 78999999999999977644 455556643
No 219
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=81.38 E-value=2 Score=29.67 Aligned_cols=54 Identities=15% Similarity=0.183 Sum_probs=32.9
Q ss_pred hHHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEA---------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a---------------~~~~p~iifiDEid~i~~ 62 (69)
+++|+++..... .||+.++|+.+-. +..-..+|... ....+..|||||||.+..
T Consensus 175 ~~lA~~ih~~s~~~~~~~i~i~c~~~~~------~~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~ 246 (469)
T PRK10923 175 ELVAHALHRHSPRAKAPFIALNMAAIPK------DLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPL 246 (469)
T ss_pred HHHHHHHHhcCCCCCCCeEeeeCCCCCH------HHHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCH
Confidence 567888777653 6999999987722 11122233211 012356789999997754
No 220
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=80.87 E-value=2.1 Score=29.26 Aligned_cols=53 Identities=19% Similarity=0.209 Sum_probs=32.5
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcccChHHHHHH-HHHHHH---------------HhcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKLAGESESNLR-KAFEEA---------------DKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~~ges~~~l~-~if~~a---------------~~~~p~iifiDEid~i~~ 62 (69)
+.+|+++-... +.||+.++|..+-. ..+. .+|... ....+..|||||||.+.+
T Consensus 176 ~~lA~~ih~~s~~~~~~~v~v~c~~~~~-------~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~ 247 (445)
T TIGR02915 176 EVLARALHQLSDRKDKRFVAINCAAIPE-------NLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPL 247 (445)
T ss_pred HHHHHHHHHhCCcCCCCeEEEECCCCCh-------HHHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhCCH
Confidence 45777776554 36899999987622 2221 223211 112467899999998864
No 221
>PRK13947 shikimate kinase; Provisional
Probab=80.84 E-value=8.6 Score=22.66 Aligned_cols=28 Identities=14% Similarity=0.148 Sum_probs=20.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccCh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE 32 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge 32 (69)
|++++.+|+.+|++|+..+ .+.....|.
T Consensus 15 st~a~~La~~lg~~~id~d--~~~~~~~g~ 42 (171)
T PRK13947 15 TTVGKRVATTLSFGFIDTD--KEIEKMTGM 42 (171)
T ss_pred HHHHHHHHHHhCCCEEECc--hhhhhhcCC
Confidence 7899999999999997654 344443443
No 222
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=80.73 E-value=7 Score=28.69 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHhc----CCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADKN----SPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~~----~p~iifiDEid~i~~ 62 (69)
...++.+.+.+... ..-|++|||+|.+..
T Consensus 103 vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~ 135 (614)
T PRK14971 103 VDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQ 135 (614)
T ss_pred HHHHHHHHHHHhhCcccCCcEEEEEECcccCCH
Confidence 45677777776432 345999999998853
No 223
>PRK07631 amidophosphoribosyltransferase; Provisional
Probab=80.69 E-value=2.8 Score=29.89 Aligned_cols=53 Identities=13% Similarity=0.214 Sum_probs=33.0
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccC---------hHHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAG---------ESESNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~g---------es~~~l~~if~~a~~--~~p~iifiDEi 57 (69)
|..+|+.+|+++|.|+.. .-+..++.| +-.++++..|...+. ....|+++||+
T Consensus 294 ~~~~A~gla~~~gip~~~---~lik~~~~~Rt~i~~~~~~R~~nv~~~f~~~~~~v~gk~VlLVDDs 357 (475)
T PRK07631 294 SISAAIGYAEATGIPYEL---GLIKNRYVGRTFIQPSQALREQGVKMKLSPVRGVVEGKRVVMVDDS 357 (475)
T ss_pred HHHHHHHHHHHHCCCccc---ceEEEecCCCCCcCCCHHHHHHHHhhhhhhcccccCCceEEEEeee
Confidence 456899999999998843 001111222 244567778864322 34679999986
No 224
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=80.27 E-value=4.1 Score=28.63 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=34.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhh-cccChH-HHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMS-KLAGES-ESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~-~~~ges-~~~l~~if~~a 44 (69)
|-+||-+|+-.+.||+.|.++.+.. +|+|.. +..+|.+-+.+
T Consensus 64 TEIARRLAkl~~aPFiKVEATKfTEVGYVGrDVesivRDLve~a 107 (444)
T COG1220 64 TEIARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVEIA 107 (444)
T ss_pred HHHHHHHHHHhCCCeEEEEeeeeeecccccccHHHHHHHHHHHH
Confidence 6799999999999999999998864 488875 66677777665
No 225
>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family.
Probab=80.25 E-value=11 Score=22.98 Aligned_cols=13 Identities=31% Similarity=0.629 Sum_probs=10.6
Q ss_pred cCCeEEEEccccc
Q psy3868 47 NSPSIIFIDELDA 59 (69)
Q Consensus 47 ~~p~iifiDEid~ 59 (69)
..|.++++||.-+
T Consensus 77 ~~~~llllDEp~~ 89 (185)
T smart00534 77 TENSLVLLDELGR 89 (185)
T ss_pred CCCeEEEEecCCC
Confidence 4799999999743
No 226
>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H.
Probab=80.21 E-value=1.1 Score=25.94 Aligned_cols=45 Identities=18% Similarity=0.386 Sum_probs=28.0
Q ss_pred HHHHHHHHHhC---CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 4 RLTTLCRDSLG---AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 4 ~la~aia~~~~---~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
++|+.+....+ .+|+.+++..+- .++++.+ .+..|||+|+|.+-+
T Consensus 36 ~~A~~lh~~~~~~~~~~~~~~~~~~~-----------~~~l~~a---~~gtL~l~~i~~L~~ 83 (138)
T PF14532_consen 36 LLARALHRYSGRANGPFIVIDCASLP-----------AELLEQA---KGGTLYLKNIDRLSP 83 (138)
T ss_dssp HHHHCCHHTTTTCCS-CCCCCHHCTC-----------HHHHHHC---TTSEEEEECGCCS-H
T ss_pred HHHHHHHhhcCccCCCeEEechhhCc-----------HHHHHHc---CCCEEEECChHHCCH
Confidence 46666666554 366666666542 3345444 778999999999865
No 227
>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=80.18 E-value=4.5 Score=27.86 Aligned_cols=29 Identities=17% Similarity=0.477 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 35 SNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 35 ~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
..+.++++.....+|.+|+||++..+...
T Consensus 145 ~~le~I~~~i~~~~~~lVVIDSIq~l~~~ 173 (372)
T cd01121 145 TNLEDILASIEELKPDLVIIDSIQTVYSS 173 (372)
T ss_pred CcHHHHHHHHHhcCCcEEEEcchHHhhcc
Confidence 34667777777789999999999988643
No 228
>KOG3406|consensus
Probab=79.88 E-value=2.1 Score=25.66 Aligned_cols=29 Identities=10% Similarity=0.086 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCcEEEEchhhhhhcccCh
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEIMSKLAGE 32 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l~~~~~ge 32 (69)
-|+.+++++-+.|++.+...-.++.|.|=
T Consensus 67 KLVeALcaeh~iplikV~d~k~LGew~Gl 95 (134)
T KOG3406|consen 67 KLVEALCAEHQIPLIKVGDAKELGEWAGL 95 (134)
T ss_pred HHHHHHHhhcCCCeEEeccchhhhhhhce
Confidence 47899999999999999988888888773
No 229
>PRK13946 shikimate kinase; Provisional
Probab=79.77 E-value=8.4 Score=23.42 Aligned_cols=21 Identities=14% Similarity=0.061 Sum_probs=17.9
Q ss_pred hhHHHHHHHHHhCCcEEEEch
Q psy3868 2 SYRLTTLCRDSLGAFFFLING 22 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~ 22 (69)
.|++++.+|+.+|.+|+..+.
T Consensus 23 Ksti~~~LA~~Lg~~~id~D~ 43 (184)
T PRK13946 23 KSTVGRRLATMLGLPFLDADT 43 (184)
T ss_pred HHHHHHHHHHHcCCCeECcCH
Confidence 378999999999999987664
No 230
>PHA00729 NTP-binding motif containing protein
Probab=79.77 E-value=7.9 Score=25.09 Aligned_cols=12 Identities=0% Similarity=-0.238 Sum_probs=9.9
Q ss_pred hHHHHHHHHHhC
Q psy3868 3 YRLTTLCRDSLG 14 (69)
Q Consensus 3 T~la~aia~~~~ 14 (69)
|++|.+++.+++
T Consensus 31 T~LA~aLa~~l~ 42 (226)
T PHA00729 31 TTYALKVARDVF 42 (226)
T ss_pred HHHHHHHHHHHH
Confidence 678999998875
No 231
>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=79.68 E-value=6.3 Score=24.94 Aligned_cols=17 Identities=12% Similarity=0.392 Sum_probs=13.8
Q ss_pred HhcCCeEEEEccccccc
Q psy3868 45 DKNSPSIIFIDELDAIA 61 (69)
Q Consensus 45 ~~~~p~iifiDEid~i~ 61 (69)
...++.+|+|||+|.+-
T Consensus 120 ~~~~~~vliiDe~~~l~ 136 (269)
T TIGR03015 120 AAGKRALLVVDEAQNLT 136 (269)
T ss_pred hCCCCeEEEEECcccCC
Confidence 34678999999999874
No 232
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=79.58 E-value=8.3 Score=28.00 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
-..+|++.+.... ....|++|||+|.+..
T Consensus 99 Id~IRelie~~~~~P~~~~~KVvIIDEad~Lt~ 131 (535)
T PRK08451 99 IDDIRELIEQTKYKPSMARFKIFIIDEVHMLTK 131 (535)
T ss_pred HHHHHHHHHHHhhCcccCCeEEEEEECcccCCH
Confidence 4567777765432 2246999999998854
No 233
>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]
Probab=79.18 E-value=0.68 Score=32.38 Aligned_cols=48 Identities=17% Similarity=0.253 Sum_probs=29.6
Q ss_pred HHHH-hCCcEEEEchhhhhhcccChHHHHHHHHHHHHH-------h--------cCCeEEEEcccccccc
Q psy3868 9 CRDS-LGAFFFLINGPEIMSKLAGESESNLRKAFEEAD-------K--------NSPSIIFIDELDAIAP 62 (69)
Q Consensus 9 ia~~-~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~-------~--------~~p~iifiDEid~i~~ 62 (69)
.+.. .+.||+.+||+.+... .. ..++|-..+ . .....||+|||+.+-+
T Consensus 124 ~s~r~~~~PFI~~NCa~~~en-----~~-~~eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~ 187 (403)
T COG1221 124 LSARRAEAPFIAFNCAAYSEN-----LQ-EAELFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPP 187 (403)
T ss_pred hhhcccCCCEEEEEHHHhCcC-----HH-HHHHhccccceeecccCCcCchheecCCCEEehhhhhhCCH
Confidence 3444 5789999999987322 11 112554332 1 1357999999998743
No 234
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. 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. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=78.19 E-value=2.3 Score=30.92 Aligned_cols=58 Identities=10% Similarity=0.186 Sum_probs=34.1
Q ss_pred hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHHH---------hcCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEAD---------KNSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a~---------~~~p~iifiDEid~i~~ 62 (69)
|++|+++++.++ .||+.+.....-...+|.- .+.+.+...+ +....+||+||++.+-+
T Consensus 30 s~lar~l~~~~~~~~pfv~i~~~~t~d~L~G~i--dl~~~~~~g~~~~~~G~L~~A~~GvL~lDEi~rl~~ 98 (589)
T TIGR02031 30 TALARALAEILPPIMPFVELPLGVTEDRLIGGI--DVEESLAGGQRVTQPGLLDEAPRGVLYVDMANLLDD 98 (589)
T ss_pred HHHHHHHHHhCCcCCCeEecCcccchhhcccch--hhhhhhhcCcccCCCCCeeeCCCCcEeccchhhCCH
Confidence 679999999875 3688887544434445542 1111111110 11235999999998864
No 235
>PRK06781 amidophosphoribosyltransferase; Provisional
Probab=77.89 E-value=1.9 Score=30.62 Aligned_cols=53 Identities=15% Similarity=0.205 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccC---------hHHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAG---------ESESNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~g---------es~~~l~~if~~a~~--~~p~iifiDEi 57 (69)
|..+|..+|+++|.|+... -+..++.| +-.++++..|...+. ....|+++||+
T Consensus 294 ~~~~A~~~a~~~gip~~~~---lik~~~~~rt~~~~~~~~R~~~v~~~f~~~~~~i~gk~VlLVDDv 357 (471)
T PRK06781 294 SISAAIGYAEATGIPYELG---LIKNRYVGRTFIQPSQELREQGVKMKLSAVRGVVEGKRVVMIDDS 357 (471)
T ss_pred HHHHHHHHHHHhCCCcccc---eEEEccCCCCCcCCCHHHHHHHHhcceeccccccCCceEEEEece
Confidence 4568999999999987531 01112222 234457777753222 34679999986
No 236
>KOG1514|consensus
Probab=77.70 E-value=1.1 Score=33.64 Aligned_cols=52 Identities=27% Similarity=0.437 Sum_probs=31.6
Q ss_pred CcEEEEchhhhh----------hcccChH------HHHHHHHHHHHHh-cCCeEEEEcccccccccccc
Q psy3868 15 AFFFLINGPEIM----------SKLAGES------ESNLRKAFEEADK-NSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 15 ~~~~~v~~~~l~----------~~~~ges------~~~l~~if~~a~~-~~p~iifiDEid~i~~~r~~ 66 (69)
..++++|+-.+. ..+.|+. -..+..=|..... ..++||+|||.|.|+.++.+
T Consensus 458 f~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~Qd 526 (767)
T KOG1514|consen 458 FDYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQD 526 (767)
T ss_pred ccEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHH
Confidence 577888875443 2334442 2224444442222 46899999999999987653
No 237
>PRK00131 aroK shikimate kinase; Reviewed
Probab=77.58 E-value=12 Score=21.85 Aligned_cols=27 Identities=22% Similarity=0.255 Sum_probs=19.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAG 31 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~g 31 (69)
|++++.+|..++.+++.. ..+.....|
T Consensus 18 stla~~La~~l~~~~~d~--d~~~~~~~g 44 (175)
T PRK00131 18 STIGRLLAKRLGYDFIDT--DHLIEARAG 44 (175)
T ss_pred HHHHHHHHHHhCCCEEEC--hHHHHHHcC
Confidence 789999999999988754 444444434
No 238
>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=77.29 E-value=1.2 Score=31.12 Aligned_cols=13 Identities=38% Similarity=0.935 Sum_probs=10.4
Q ss_pred CCeEEEEcccccc
Q psy3868 48 SPSIIFIDELDAI 60 (69)
Q Consensus 48 ~p~iifiDEid~i 60 (69)
-|.||||||+|-|
T Consensus 278 vpGVLFIDEvHmL 290 (398)
T PF06068_consen 278 VPGVLFIDEVHML 290 (398)
T ss_dssp EE-EEEEESGGGS
T ss_pred ecceEEecchhhc
Confidence 3999999999876
No 239
>KOG2680|consensus
Probab=77.10 E-value=3 Score=29.02 Aligned_cols=23 Identities=30% Similarity=0.539 Sum_probs=16.1
Q ss_pred HHHHHHHHh----cCCeEEEEcccccc
Q psy3868 38 RKAFEEADK----NSPSIIFIDELDAI 60 (69)
Q Consensus 38 ~~if~~a~~----~~p~iifiDEid~i 60 (69)
.+++++-.+ .-|.+|||||+|-|
T Consensus 274 ~KV~eWreEGKAeivpGVLFIDEvHML 300 (454)
T KOG2680|consen 274 TKVAEWREEGKAEIVPGVLFIDEVHML 300 (454)
T ss_pred HHHHHHHhcCCeeeccceEEEeeehhh
Confidence 345555443 34999999999865
No 240
>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=76.66 E-value=3.7 Score=22.72 Aligned_cols=20 Identities=15% Similarity=0.144 Sum_probs=17.4
Q ss_pred hHHHHHHHHHhCCcEEEEch
Q psy3868 3 YRLTTLCRDSLGAFFFLING 22 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~ 22 (69)
|++|+.+|..+|.+++..+-
T Consensus 13 ST~a~~La~~~~~~~i~~d~ 32 (121)
T PF13207_consen 13 STLAKELAERLGFPVISMDD 32 (121)
T ss_dssp HHHHHHHHHHHTCEEEEEHH
T ss_pred HHHHHHHHHHHCCeEEEecc
Confidence 78999999999998877665
No 241
>PF09820 AAA-ATPase_like: Predicted AAA-ATPase; InterPro: IPR018631 This entry is predicted to be an AAA-ATPase domain []. It is usually found together with IPR012547 from INTERPRO.
Probab=76.57 E-value=5 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHh--cCCeEEEEcccccccc
Q psy3868 35 SNLRKAFEEADK--NSPSIIFIDELDAIAP 62 (69)
Q Consensus 35 ~~l~~if~~a~~--~~p~iifiDEid~i~~ 62 (69)
..+..+.+.+.+ .+|.||+|||-|....
T Consensus 128 ~~l~~li~~l~~~~~~kvvlLIDEYD~p~~ 157 (284)
T PF09820_consen 128 DSLKDLIEYLYEKYGKKVVLLIDEYDKPIN 157 (284)
T ss_pred HHHHHHHHHHHHHhCCceEEEecCccHHHH
Confidence 334444444322 5799999999998654
No 242
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=76.39 E-value=6.4 Score=23.97 Aligned_cols=45 Identities=18% Similarity=0.286 Sum_probs=30.3
Q ss_pred HHHHhCCcEEEEchhhhhhcccChHHHH-HHHHHHHHHhcCCeEEEEccccc
Q psy3868 9 CRDSLGAFFFLINGPEIMSKLAGESESN-LRKAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 9 ia~~~~~~~~~v~~~~l~~~~~ges~~~-l~~if~~a~~~~p~iifiDEid~ 59 (69)
+|...|...+.+ ++-.|...+. +-++++.|-+....++|++|+|-
T Consensus 22 iaygfg~k~lV~------tka~g~AAQsGIp~~~kla~k~G~~vlvf~dL~D 67 (147)
T COG4080 22 IAYGFGAKRLVL------TKAKGSAAQSGIPEVLKLAFKLGKPVLVFPDLDD 67 (147)
T ss_pred HHcccCccEEEE------EecccHhhhhccHHHHHHHHHhCCcEEEehhHHH
Confidence 344455555444 3445555555 88899999888888888888763
No 243
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=75.90 E-value=7.7 Score=26.19 Aligned_cols=30 Identities=10% Similarity=0.231 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 33 SESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 33 s~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
+...+|++-+.+.. ...-|++|||+|.+-.
T Consensus 87 ~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~ 120 (328)
T PRK05707 87 KVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNR 120 (328)
T ss_pred CHHHHHHHHHHHhhccccCCCeEEEECChhhCCH
Confidence 34667777666543 4567889999999854
No 244
>PF12846 AAA_10: AAA-like domain
Probab=75.70 E-value=3.1 Score=26.33 Aligned_cols=17 Identities=35% Similarity=0.554 Sum_probs=15.0
Q ss_pred cCCeEEEEccccccccc
Q psy3868 47 NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~ 63 (69)
..|.++++||++.+...
T Consensus 219 ~~~~~i~iDEa~~~~~~ 235 (304)
T PF12846_consen 219 GRPKIIVIDEAHNFLSN 235 (304)
T ss_pred CceEEEEeCCccccccc
Confidence 57899999999998876
No 245
>PRK09087 hypothetical protein; Validated
Probab=75.37 E-value=6.3 Score=25.08 Aligned_cols=14 Identities=21% Similarity=0.394 Sum_probs=9.2
Q ss_pred hHHHHHHHHHhCCc
Q psy3868 3 YRLTTLCRDSLGAF 16 (69)
Q Consensus 3 T~la~aia~~~~~~ 16 (69)
|+|++++++..+..
T Consensus 58 ThLl~~~~~~~~~~ 71 (226)
T PRK09087 58 THLASIWREKSDAL 71 (226)
T ss_pred HHHHHHHHHhcCCE
Confidence 56777777765554
No 246
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=75.25 E-value=7.3 Score=27.53 Aligned_cols=18 Identities=17% Similarity=0.377 Sum_probs=14.8
Q ss_pred cCCeEEEEcccccccccc
Q psy3868 47 NSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~r 64 (69)
.+..+||+||++.++...
T Consensus 254 GkdVVLlIDEitR~arAq 271 (415)
T TIGR00767 254 KKDVVILLDSITRLARAY 271 (415)
T ss_pred CCCeEEEEEChhHHHHHH
Confidence 468899999999987644
No 247
>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]
Probab=75.07 E-value=5.8 Score=25.04 Aligned_cols=54 Identities=17% Similarity=0.089 Sum_probs=35.0
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHH--------HHH---HHHHHHhcCCeEEEEcc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESN--------LRK---AFEEADKNSPSIIFIDE 56 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~--------l~~---if~~a~~~~p~iifiDE 56 (69)
|.||+.+|+..|.++...-+-+.+-...|..+.. ++- --+.+.+.++.|+|||-
T Consensus 22 StLv~kLA~~fnt~~~wEY~Re~v~~~l~gdeal~y~Dy~~ia~Gq~~~~d~av~~a~~v~fiDT 86 (187)
T COG3172 22 STLVNKLANIFNTTSAWEYGREYVFEHLGGDEALQYSDYAKIALGQAAYEDAAVRYANKVAFIDT 86 (187)
T ss_pred HHHHHHHHHHhCCCchhHHHHHHHHHHhCCchhhhhccHHHHHhhhHHHHHHHHhCCCceEEEec
Confidence 6799999999999887766666655545544321 111 11224457889999985
No 248
>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.
Probab=75.07 E-value=6.3 Score=23.71 Aligned_cols=40 Identities=18% Similarity=0.209 Sum_probs=24.1
Q ss_pred CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 15 AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 15 ~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
..++.++-.-++++ .+++.+. .......+|+|||.|.|-.
T Consensus 120 adivi~~y~yl~~~-------~~~~~~~-~~~~~~~ivI~DEAHNL~~ 159 (174)
T PF06733_consen 120 ADIVICNYNYLFDP-------SIRKSLF-GIDLKDNIVIFDEAHNLED 159 (174)
T ss_dssp -SEEEEETHHHHSH-------HHHHHHC-T--CCCEEEEETTGGGCGG
T ss_pred CCEEEeCHHHHhhH-------HHHhhhc-cccccCcEEEEecccchHH
Confidence 56677777777643 1222222 2235678999999999865
No 249
>KOG1968|consensus
Probab=75.02 E-value=2.5 Score=32.39 Aligned_cols=60 Identities=20% Similarity=0.219 Sum_probs=39.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccCh-------HHHHHHHHHHH---HHh-cCCe-EEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE-------SESNLRKAFEE---ADK-NSPS-IIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge-------s~~~l~~if~~---a~~-~~p~-iifiDEid~i~~ 62 (69)
|..+.++|.++|..+++.|+++.-++.... +...|..-|.. .+. +.+. +|++||+|.++.
T Consensus 371 T~~~h~~~k~~g~~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~ 442 (871)
T KOG1968|consen 371 TTAAHKAAKELGFKVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG 442 (871)
T ss_pred hhhHhhhhhhcccceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc
Confidence 788899999999999999999775443222 11223333311 111 2333 899999999987
No 250
>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid
Probab=74.58 E-value=3.7 Score=25.60 Aligned_cols=23 Identities=30% Similarity=0.654 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHhcCCeEEEEccc
Q psy3868 35 SNLRKAFEEADKNSPSIIFIDEL 57 (69)
Q Consensus 35 ~~l~~if~~a~~~~p~iifiDEi 57 (69)
++++++++.+....|.++++||.
T Consensus 92 ~~~~~iL~~~~~~~p~llllDEp 114 (199)
T cd03283 92 RRLKEIVEKAKKGEPVLFLLDEI 114 (199)
T ss_pred HHHHHHHHhccCCCCeEEEEecc
Confidence 55777777775568999999995
No 251
>PRK07272 amidophosphoribosyltransferase; Provisional
Probab=74.30 E-value=3.6 Score=29.43 Aligned_cols=56 Identities=9% Similarity=0.224 Sum_probs=31.7
Q ss_pred hhHHHHHHHHHhCCcEEE--Echhhhhhcc--cCh--HHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 2 SYRLTTLCRDSLGAFFFL--INGPEIMSKL--AGE--SESNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~--v~~~~l~~~~--~ge--s~~~l~~if~~a~~--~~p~iifiDEi 57 (69)
|..+|+.+|.++|.|+.. +........+ .+. -.++++..|...+. ....|+++||+
T Consensus 296 a~~lA~~la~~lgip~~~~lvk~~~~~rt~~~~~q~~R~~~vr~~f~~~~~~~~gk~vllVDDv 359 (484)
T PRK07272 296 SLSAASGYAEESGLPYEMGLVKNQYVARTFIQPTQELREQGVRMKLSAVSGVVKGKRVVMVDDS 359 (484)
T ss_pred HHHHHHHHHHHHCCCcccCeEEEccCCccccCCCHHHHHHHHhhCccccccccCCCEEEEEccc
Confidence 467899999999998732 1111111111 122 23456766753222 24579999986
No 252
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=74.26 E-value=16 Score=21.70 Aligned_cols=51 Identities=14% Similarity=0.092 Sum_probs=36.8
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEccc
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDEL 57 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEi 57 (69)
..+.++.+...+.+--+--.+...|+..+.+++.-+..++ ..-.|.|+||-
T Consensus 47 ~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~L~~~~~~~v~~~DEr 98 (138)
T PRK00109 47 EKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFANRLEGRFGLPVVLVDER 98 (138)
T ss_pred HHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHHHHHHHHHHhCCCEEEEcCC
Confidence 3566677777777766655677778888888888777754 35679999994
No 253
>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=73.96 E-value=19 Score=22.59 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHH-hcCCeEEEEccccc
Q psy3868 34 ESNLRKAFEEAD-KNSPSIIFIDELDA 59 (69)
Q Consensus 34 ~~~l~~if~~a~-~~~p~iifiDEid~ 59 (69)
...++++-.... ...|.++++||..+
T Consensus 93 ~~el~~l~~~l~~~~~~slvllDE~~~ 119 (213)
T cd03281 93 MIDLYQVSKALRLATRRSLVLIDEFGK 119 (213)
T ss_pred HHHHHHHHHHHHhCCCCcEEEeccccC
Confidence 344444443322 35799999999754
No 254
>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1
Probab=73.49 E-value=3.6 Score=27.84 Aligned_cols=31 Identities=16% Similarity=0.166 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 33 SESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 33 s~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
...+++++.++..+....+|++||+|.....
T Consensus 157 ~~sRl~ql~~W~g~dfdgvivfDEcH~akn~ 187 (303)
T PF13872_consen 157 YRSRLDQLVDWCGEDFDGVIVFDECHKAKNL 187 (303)
T ss_pred ccchHHHHHHHHhcCCCceEEeccchhcCCC
Confidence 3567999999988777889999999988654
No 255
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=72.83 E-value=3.6 Score=25.39 Aligned_cols=53 Identities=17% Similarity=0.196 Sum_probs=28.6
Q ss_pred hHHHHHHHHHhCC---cEEEEchhhhhhcccChHH--HHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 3 YRLTTLCRDSLGA---FFFLINGPEIMSKLAGESE--SNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 3 T~la~aia~~~~~---~~~~v~~~~l~~~~~ges~--~~l~~if~~a~~--~~p~iifiDEi 57 (69)
..+++.++..++. .+..... -..+..+..+ ++++..|..... ....||++|||
T Consensus 102 ~~la~~l~~~~~~~~~~l~r~~~--~~Q~~l~~~~R~~n~~~~f~~~~~~~~~~~vllvDDV 161 (190)
T TIGR00201 102 DLLAQCLSRWLFNYHNIVIRLNN--ETQSKLKATLRFLNLENAFDLKNNSFQGRNIVLVDDV 161 (190)
T ss_pred HHHHHHHHHHhCCCcceEEEecc--cccccCCHHHHHHHHhCcEEccCCCCCCCEEEEEeee
Confidence 4677888777653 2222222 1122233333 457777764322 24579999997
No 256
>PF04465 DUF499: Protein of unknown function (DUF499); InterPro: IPR007555 This is a family of uncharacterised hypothetical prokaryotic proteins.
Probab=72.62 E-value=2.3 Score=33.14 Aligned_cols=25 Identities=40% Similarity=0.539 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
...++++|+. .||+|+|||+=..+.
T Consensus 89 ~~~L~eLl~~----~P~LILiDEl~~Y~~ 113 (1035)
T PF04465_consen 89 KDVLRELLGG----RPVLILIDELVAYAR 113 (1035)
T ss_pred HHHHHHHhCC----CCEEEEeecHHHHHH
Confidence 5678888853 699999999876665
No 257
>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]
Probab=72.54 E-value=5.2 Score=27.88 Aligned_cols=49 Identities=16% Similarity=0.445 Sum_probs=32.7
Q ss_pred HHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH-------Hh--------cCCeEEEEcccccccccc
Q psy3868 10 RDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA-------DK--------NSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 10 a~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a-------~~--------~~p~iifiDEid~i~~~r 64 (69)
-.++.-+|++|||..+- |++ .+..+|-.. +. .....+|+|||..++.+.
T Consensus 235 rhq~sg~fvevncatlr----gd~--amsalfghvkgaftga~~~r~gllrsadggmlfldeigelgade 298 (531)
T COG4650 235 RHQFSGAFVEVNCATLR----GDT--AMSALFGHVKGAFTGARESREGLLRSADGGMLFLDEIGELGADE 298 (531)
T ss_pred HHhcCCceEEEeeeeec----Cch--HHHHHHhhhccccccchhhhhhhhccCCCceEehHhhhhcCccH
Confidence 45567799999998883 332 344555443 22 236799999999887543
No 258
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=72.18 E-value=2.3 Score=29.98 Aligned_cols=14 Identities=36% Similarity=0.797 Sum_probs=11.8
Q ss_pred cCCeEEEEcccccc
Q psy3868 47 NSPSIIFIDELDAI 60 (69)
Q Consensus 47 ~~p~iifiDEid~i 60 (69)
.-|.||||||+|-|
T Consensus 290 lVpGVLFIDEvHmL 303 (450)
T COG1224 290 LVPGVLFIDEVHML 303 (450)
T ss_pred eecceEEEechhhh
Confidence 34999999999865
No 259
>PRK06217 hypothetical protein; Validated
Probab=71.93 E-value=18 Score=21.87 Aligned_cols=20 Identities=10% Similarity=-0.003 Sum_probs=17.1
Q ss_pred hHHHHHHHHHhCCcEEEEch
Q psy3868 3 YRLTTLCRDSLGAFFFLING 22 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~ 22 (69)
|++++++++.+|.+++.++.
T Consensus 15 STla~~L~~~l~~~~~~~D~ 34 (183)
T PRK06217 15 TTLGAALAERLDIPHLDTDD 34 (183)
T ss_pred HHHHHHHHHHcCCcEEEcCc
Confidence 78999999999999877653
No 260
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=71.29 E-value=5.4 Score=23.92 Aligned_cols=56 Identities=16% Similarity=0.086 Sum_probs=28.5
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChH--HH-HHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGES--ES-NLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges--~~-~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
+...+...+.++++.+|..+-....|.+ .| +|....+..-...+..-.-|+.|+++
T Consensus 86 i~l~~~~~~i~v~~y~P~~vKk~vtG~G~A~KeqV~~mv~~ll~l~~~~~~~d~aDAlA 144 (149)
T PF02075_consen 86 ILLAAAQRGIPVFEYTPSEVKKAVTGNGRASKEQVAFMVRKLLGLDEKPKPDDAADALA 144 (149)
T ss_dssp HHHHHHTTT--EEEEEHHHHHHHHTSSTT--HHHHHHHHHHHTT----SS-S-THHHHH
T ss_pred HHHHHHHcCCeEEEECHHHHHHHhhCCCccCHHHHHHHHHHHhCCCCCCCccchHhhHh
Confidence 4455667899999999999876544543 22 24333333222222222368888875
No 261
>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=71.21 E-value=29 Score=23.69 Aligned_cols=31 Identities=26% Similarity=0.368 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 33 SESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 33 s~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
.++.+..+-...++..+.+|+||-+-++.++
T Consensus 118 ~eq~l~i~~~li~s~~~~lIVIDSvaal~~~ 148 (325)
T cd00983 118 GEQALEIADSLVRSGAVDLIVVDSVAALVPK 148 (325)
T ss_pred HHHHHHHHHHHHhccCCCEEEEcchHhhccc
Confidence 4444555544456678999999999999864
No 262
>KOG2170|consensus
Probab=71.20 E-value=5.9 Score=27.24 Aligned_cols=29 Identities=21% Similarity=0.334 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
++.-+.+-..++.++.++.++||+|.+-+
T Consensus 164 ~eL~~~v~~~v~~C~rslFIFDE~DKmp~ 192 (344)
T KOG2170|consen 164 EELKNRVRGTVQACQRSLFIFDEVDKLPP 192 (344)
T ss_pred HHHHHHHHHHHHhcCCceEEechhhhcCH
Confidence 33445555666778999999999998743
No 263
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=70.43 E-value=2.3 Score=30.45 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=12.2
Q ss_pred CCeEEEEcccccccc
Q psy3868 48 SPSIIFIDELDAIAP 62 (69)
Q Consensus 48 ~p~iifiDEid~i~~ 62 (69)
...+|||||++.+.+
T Consensus 295 ~~GvLfLDEi~e~~~ 309 (499)
T TIGR00368 295 HNGVLFLDELPEFKR 309 (499)
T ss_pred CCCeEecCChhhCCH
Confidence 457999999998754
No 264
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=69.93 E-value=13 Score=21.89 Aligned_cols=51 Identities=22% Similarity=0.178 Sum_probs=35.7
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc--CCeEEEEccc
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN--SPSIIFIDEL 57 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~--~p~iifiDEi 57 (69)
..+..+.+..-+.+--+--.+...|+..+.+++.-+..... .-.|.|+||-
T Consensus 44 ~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~f~~~L~~~~~~ipV~~~DEr 96 (135)
T PF03652_consen 44 KKLIEEYQIDGIVVGLPLNMDGSESEQARRVRKFAEELKKRFPGIPVILVDER 96 (135)
T ss_dssp HHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHHHHHHHHHHH-TSEEEEEECS
T ss_pred HHHHHHhCCCEEEEeCCcccCCCccHHHHHHHHHHHHHHHhcCCCcEEEECCC
Confidence 34566667666666666666677788888888877776653 5679999994
No 265
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=69.39 E-value=18 Score=20.78 Aligned_cols=58 Identities=12% Similarity=0.111 Sum_probs=36.1
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
.+..|.+.|+++..+-...=.+.... .-..+.++++.++.....+|++.++|.|++..
T Consensus 24 ~~~~a~~~g~~i~~~~~d~~~Sg~~~-~Rp~l~~ll~~~~~g~~~~ivv~~~~Rl~R~~ 81 (148)
T smart00857 24 LRAYAKANGWEVVRIYEDEGVSGKKA-DRPGLQRLLADLRAGDIDVLVVYKLDRLGRSL 81 (148)
T ss_pred HHHHHHHCCCEEEEEEEeCCCcCCCC-CCHHHHHHHHHHHcCCCCEEEEeccchhhCcH
Confidence 34456666877644311110121111 24568889988888777899999999998753
No 266
>cd01873 RhoBTB RhoBTB subfamily. Members of the RhoBTB subfamily of Rho GTPases are present in vertebrates, Drosophila, and Dictyostelium. RhoBTB proteins are characterized by a modular organization, consisting of a GTPase domain, a proline rich region, a tandem of two BTB (Broad-Complex, Tramtrack, and Bric a brac) domains, and a C-terminal region of unknown function. RhoBTB proteins may act as docking points for multiple components participating in signal transduction cascades. RhoBTB genes appeared upregulated in some cancer cell lines, suggesting a participation of RhoBTB proteins in the pathogenesis of particular tumors. Note that the Dictyostelium RacA GTPase domain is more closely related to Rac proteins than to RhoBTB proteins, where RacA actually belongs. Thus, the Dictyostelium RacA is not included here. Most Rho proteins contain a lipid modification site at the C-terminus; however, RhoBTB is one of few Rho subfamilies that lack this feature.
Probab=69.10 E-value=7.4 Score=24.00 Aligned_cols=35 Identities=11% Similarity=0.177 Sum_probs=26.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK 46 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~ 46 (69)
+.-++.+|.+.+++|+++|+-+ ..+|.++|+.+.+
T Consensus 159 ~~e~~~~a~~~~~~~~E~SAkt---------~~~V~e~F~~~~~ 193 (195)
T cd01873 159 PETGRAVAKELGIPYYETSVVT---------QFGVKDVFDNAIR 193 (195)
T ss_pred HHHHHHHHHHhCCEEEEcCCCC---------CCCHHHHHHHHHH
Confidence 4467889999999999987742 2458888988743
No 267
>PRK11595 DNA utilization protein GntX; Provisional
Probab=68.70 E-value=6.6 Score=24.97 Aligned_cols=54 Identities=15% Similarity=0.170 Sum_probs=29.3
Q ss_pred hHHHHHHHHHhCCcEEE-----EchhhhhhcccChH--HHHHHHHHHHHHh-cCCeEEEEccc
Q psy3868 3 YRLTTLCRDSLGAFFFL-----INGPEIMSKLAGES--ESNLRKAFEEADK-NSPSIIFIDEL 57 (69)
Q Consensus 3 T~la~aia~~~~~~~~~-----v~~~~l~~~~~ges--~~~l~~if~~a~~-~~p~iifiDEi 57 (69)
..+|+.++..++.++.. +.... -....+.. .++++..|..... ....||++|||
T Consensus 135 ~~la~~la~~~~~~~~~~~l~r~~~~~-~q~~l~~~~R~~n~~~~f~~~~~~~~~~vllvDDv 196 (227)
T PRK11595 135 DLLCRPLARWLGCDYDSEALTRTRATA-TQHFLSARLRKRNLKNAFRLELPVQGQHMAIVDDV 196 (227)
T ss_pred HHHHHHHHHHHCCCCcccceEEecCCC-CcccCCHHHHhhhhhhhhccCCCCCCCEEEEEeee
Confidence 46889999999986521 11111 01122222 3335666764322 23479999987
No 268
>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=68.41 E-value=6.2 Score=25.13 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHhcCCeEEEEccccc
Q psy3868 35 SNLRKAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 35 ~~l~~if~~a~~~~p~iifiDEid~ 59 (69)
+.++.+++.+ ..|+++++||+-+
T Consensus 98 ~~~~~il~~~--~~~sLvLlDE~~~ 120 (218)
T cd03286 98 SETANILRHA--TPDSLVILDELGR 120 (218)
T ss_pred HHHHHHHHhC--CCCeEEEEecccC
Confidence 4455666654 5789999999743
No 269
>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.
Probab=68.22 E-value=24 Score=23.77 Aligned_cols=53 Identities=17% Similarity=0.130 Sum_probs=32.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccC-hH-----------HHHHHHHHHHHHhcCCeEEEEcc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAG-ES-----------ESNLRKAFEEADKNSPSIIFIDE 56 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~g-es-----------~~~l~~if~~a~~~~p~iifiDE 56 (69)
|+|++.++...+.+++.--+.+......+ +. ..+.... ..+.+.++.+||+|-
T Consensus 176 stl~~~l~~~~~~~~v~E~~R~~~~~~~~~~~~l~~~d~~~i~~g~~~~~-~~~~~~a~~iif~D~ 240 (325)
T TIGR01526 176 STLVNKLAAVFNTTSAWEYAREYVEEKLGGDEALQYSDYAQIALGQQRYI-DYAVRHAHKIAFIDT 240 (325)
T ss_pred HHHHHHHHHhhCCCEEeehhHHHHHHhcCCCcccCHHHHHHHHHHHHHHH-HHHHhhcCCeEEEcC
Confidence 78999999999999887777655543321 11 1111121 223345678999984
No 270
>PRK13948 shikimate kinase; Provisional
Probab=67.06 E-value=9.7 Score=23.57 Aligned_cols=28 Identities=14% Similarity=0.209 Sum_probs=20.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccCh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE 32 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge 32 (69)
|++++.+|..++.+|+..+ .+.....|.
T Consensus 24 STvg~~La~~lg~~~iD~D--~~ie~~~g~ 51 (182)
T PRK13948 24 SRIGWELSRALMLHFIDTD--RYIERVTGK 51 (182)
T ss_pred HHHHHHHHHHcCCCEEECC--HHHHHHHhC
Confidence 7899999999999998655 444444443
No 271
>KOG2228|consensus
Probab=66.99 E-value=12 Score=26.24 Aligned_cols=35 Identities=43% Similarity=0.592 Sum_probs=21.5
Q ss_pred ccChHHHHHHHHHHHHHh----cCCeEEEE-ccccccccc
Q psy3868 29 LAGESESNLRKAFEEADK----NSPSIIFI-DELDAIAPK 63 (69)
Q Consensus 29 ~~ges~~~l~~if~~a~~----~~p~iifi-DEid~i~~~ 63 (69)
-.|....++.++....+. .+..|||| ||+|.+++-
T Consensus 113 ~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h 152 (408)
T KOG2228|consen 113 SFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPH 152 (408)
T ss_pred eecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccc
Confidence 345556666667766644 22335554 899999874
No 272
>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=66.78 E-value=24 Score=20.75 Aligned_cols=55 Identities=18% Similarity=0.328 Sum_probs=32.1
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhcc---c----ChHHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSKL---A----GESESNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~~---~----ges~~~l~~if~~a~~--~~p~iifiDEi 57 (69)
|++++.++..+ +.+.+.++...+.... . .+....++.+...++. .+..++++|-.
T Consensus 13 STla~~L~~~l~~~g~~~~~i~~d~~r~~l~~~~~~~~~~~~~~~~~~~~~a~~l~~~G~~VIid~~ 79 (149)
T cd02027 13 STIARALEEKLFQRGRPVYVLDGDNVRHGLNKDLGFSREDREENIRRIAEVAKLLADAGLIVIAAFI 79 (149)
T ss_pred HHHHHHHHHHHHHcCCCEEEEcCHHHHHhhhhccCCCcchHHHHHHHHHHHHHHHHhCCCEEEEccC
Confidence 67899999988 6667777765553211 1 1223445555554443 24567777743
No 273
>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=66.60 E-value=8 Score=25.57 Aligned_cols=28 Identities=32% Similarity=0.457 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
.-..|-.|..+....|.|+++||+=+.+
T Consensus 151 GM~aRLaFsia~~~~pdILllDEvlavG 178 (249)
T COG1134 151 GMYARLAFSVATHVEPDILLLDEVLAVG 178 (249)
T ss_pred HHHHHHHHhhhhhcCCCEEEEehhhhcC
Confidence 3346667888878889999999985543
No 274
>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=66.37 E-value=16 Score=20.90 Aligned_cols=28 Identities=25% Similarity=0.370 Sum_probs=20.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccCh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE 32 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge 32 (69)
|++++.+|..++.+++..+ .+.....|.
T Consensus 13 stla~~la~~l~~~~~~~d--~~~~~~~~~ 40 (154)
T cd00464 13 TTVGRLLAKALGLPFVDLD--ELIEQRAGM 40 (154)
T ss_pred HHHHHHHHHHhCCCEEEch--HHHHHHcCC
Confidence 7899999999999987554 454444443
No 275
>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=66.25 E-value=9 Score=22.73 Aligned_cols=25 Identities=8% Similarity=0.198 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCCeEEEEcccccccc
Q psy3868 38 RKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 38 ~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
..+...+....|.+++|||+-.+..
T Consensus 85 ~~i~~~~~~~~~~~lviD~~~~~~~ 109 (187)
T cd01124 85 QRLKDAIEEFKAKRVVIDSVSGLLL 109 (187)
T ss_pred HHHHHHHHHhCCCEEEEeCcHHHhh
Confidence 4455555667899999999988754
No 276
>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=66.22 E-value=13 Score=25.00 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=20.1
Q ss_pred cChHHHHHHHHHHHHHhcCCeEEEEcccc
Q psy3868 30 AGESESNLRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 30 ~ges~~~l~~if~~a~~~~p~iifiDEid 58 (69)
+|.......+..+.+-...|.+|++||+-
T Consensus 177 vg~~~~~~~~~l~~~lr~~pd~i~vgEir 205 (343)
T TIGR01420 177 VGLDTLSFANALRAALREDPDVILIGEMR 205 (343)
T ss_pred cCCCCcCHHHHHHHhhccCCCEEEEeCCC
Confidence 34333345566666667899999999983
No 277
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=65.91 E-value=4.4 Score=31.91 Aligned_cols=28 Identities=43% Similarity=0.595 Sum_probs=20.9
Q ss_pred HHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
+.+=|+...+.++..||+|++|++...-
T Consensus 192 L~k~~e~L~~~kFdfifVDDVDA~Lkas 219 (1187)
T COG1110 192 LSKRFEELSKLKFDFIFVDDVDAILKAS 219 (1187)
T ss_pred HHhhHHHhcccCCCEEEEccHHHHHhcc
Confidence 4444555555689999999999998654
No 278
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=65.90 E-value=27 Score=22.00 Aligned_cols=53 Identities=15% Similarity=0.271 Sum_probs=36.0
Q ss_pred HHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
.+..+|+++|..++..|..+= +++ +...+-++.++| .+-|.++++|+--....
T Consensus 15 avE~aa~~iGgRCIS~S~GNP-T~l---sG~elV~lIk~a-~~DPV~VMfDD~G~~g~ 67 (180)
T PF14097_consen 15 AVEIAAKNIGGRCISQSAGNP-TPL---SGEELVELIKQA-PHDPVLVMFDDKGFIGE 67 (180)
T ss_pred HHHHHHHHhCcEEEeccCCCC-CcC---CHHHHHHHHHhC-CCCCEEEEEeCCCCCCC
Confidence 456788999999998876542 112 334555566665 57799999999665543
No 279
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=65.66 E-value=3.3 Score=29.09 Aligned_cols=15 Identities=33% Similarity=0.514 Sum_probs=12.3
Q ss_pred CCeEEEEcccccccc
Q psy3868 48 SPSIIFIDELDAIAP 62 (69)
Q Consensus 48 ~p~iifiDEid~i~~ 62 (69)
+-.+++|||+|++--
T Consensus 202 aFD~liIDEVDAFP~ 216 (441)
T COG4098 202 AFDLLIIDEVDAFPF 216 (441)
T ss_pred hccEEEEeccccccc
Confidence 457999999999853
No 280
>PHA00012 I assembly protein
Probab=65.30 E-value=5.5 Score=27.64 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=18.0
Q ss_pred cCCeEEEEccccccccccccC
Q psy3868 47 NSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~r~~~ 67 (69)
...+++++||+...++.|..+
T Consensus 80 p~gsLlVlDEaq~~fp~R~~~ 100 (361)
T PHA00012 80 SKNGLLVLDECGTWFNSRSWN 100 (361)
T ss_pred CCCcEEEEECcccccCCCCcC
Confidence 456899999999999998854
No 281
>KOG0991|consensus
Probab=65.29 E-value=11 Score=25.35 Aligned_cols=56 Identities=20% Similarity=0.204 Sum_probs=29.3
Q ss_pred hHHHHHHHHHh-C----CcEEEEchhhhhhcccChHHHHHHHHHHHHHhc----CCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSL-G----AFFFLINGPEIMSKLAGESESNLRKAFEEADKN----SPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~-~----~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~----~p~iifiDEid~i~ 61 (69)
|+-+.++|.++ | =-++++|+|+=- .. +..++==+.|.+-+-. +-.||.+||.|++-
T Consensus 62 TTsi~~LAr~LLG~~~ke~vLELNASdeR--GI-DvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT 126 (333)
T KOG0991|consen 62 TTSILCLARELLGDSYKEAVLELNASDER--GI-DVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMT 126 (333)
T ss_pred hhHHHHHHHHHhChhhhhHhhhccCcccc--cc-HHHHHHHHHHHHhhccCCCCceeEEEeeccchhh
Confidence 34445555554 1 245667766531 11 1233333455544322 33699999999984
No 282
>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=64.83 E-value=3.6 Score=22.35 Aligned_cols=16 Identities=13% Similarity=0.351 Sum_probs=13.3
Q ss_pred CCeEEEEccccccccc
Q psy3868 48 SPSIIFIDELDAIAPK 63 (69)
Q Consensus 48 ~p~iifiDEid~i~~~ 63 (69)
...++++||+|.+...
T Consensus 103 ~~~~iiiDE~h~~~~~ 118 (144)
T cd00046 103 KLDLLILDEAHRLLNQ 118 (144)
T ss_pred cCCEEEEeCHHHHhhc
Confidence 5789999999998654
No 283
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=64.79 E-value=26 Score=20.44 Aligned_cols=56 Identities=7% Similarity=0.063 Sum_probs=34.3
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
+..|.+.|+++..+=-..-.+.. ...-..+.++.+.+++....+|++-++|.|+++
T Consensus 28 ~~~a~~~g~~i~~~~~D~~~SG~-~~~Rp~l~~ll~~~~~g~vd~vvv~~ldRl~R~ 83 (140)
T cd03770 28 EEYAKENGLENIRHYIDDGFSGT-TFDRPGFNRMIEDIEAGKIDIVIVKDMSRLGRN 83 (140)
T ss_pred HHHHHHCCCEEEEEEEcCCCcCC-cCCCHHHHHHHHHHHcCCCCEEEEeccchhccC
Confidence 44566667765432111101111 112456888888888777789999999999875
No 284
>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=64.61 E-value=40 Score=22.96 Aligned_cols=31 Identities=29% Similarity=0.384 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 33 SESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 33 s~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
.++.+..+-...++..+.+|+||-+-++.++
T Consensus 118 ~eq~l~~~~~li~~~~~~lIVIDSv~al~~~ 148 (321)
T TIGR02012 118 GEQALEIAETLVRSGAVDIIVVDSVAALVPK 148 (321)
T ss_pred HHHHHHHHHHHhhccCCcEEEEcchhhhccc
Confidence 3445555555556678999999999999864
No 285
>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a
Probab=64.15 E-value=23 Score=21.70 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=10.9
Q ss_pred cCCeEEEEccccc
Q psy3868 47 NSPSIIFIDELDA 59 (69)
Q Consensus 47 ~~p~iifiDEid~ 59 (69)
..|.++++||.-+
T Consensus 107 ~~p~llllDEp~~ 119 (200)
T cd03280 107 DPDSLVLLDELGS 119 (200)
T ss_pred CCCcEEEEcCCCC
Confidence 5799999999764
No 286
>PRK03731 aroL shikimate kinase II; Reviewed
Probab=64.14 E-value=8.4 Score=22.79 Aligned_cols=20 Identities=15% Similarity=0.114 Sum_probs=17.0
Q ss_pred hhHHHHHHHHHhCCcEEEEc
Q psy3868 2 SYRLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~ 21 (69)
.|++++.+|..+|.+++..+
T Consensus 15 Kst~~~~la~~lg~~~~d~D 34 (171)
T PRK03731 15 KTTVGMALAQALGYRFVDTD 34 (171)
T ss_pred HHHHHHHHHHHhCCCEEEcc
Confidence 37899999999999997654
No 287
>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.
Probab=64.07 E-value=7.4 Score=23.17 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=10.9
Q ss_pred CCeEEEEcccccc
Q psy3868 48 SPSIIFIDELDAI 60 (69)
Q Consensus 48 ~p~iifiDEid~i 60 (69)
.|.++++||..+=
T Consensus 99 ~~~llllDEp~~g 111 (162)
T cd03227 99 PRPLYILDEIDRG 111 (162)
T ss_pred CCCEEEEeCCCCC
Confidence 7899999998653
No 288
>PRK00625 shikimate kinase; Provisional
Probab=63.53 E-value=8.1 Score=23.66 Aligned_cols=19 Identities=16% Similarity=0.078 Sum_probs=16.9
Q ss_pred hHHHHHHHHHhCCcEEEEc
Q psy3868 3 YRLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~ 21 (69)
|++++.+|+.++.+++.++
T Consensus 14 TT~~k~La~~l~~~~id~D 32 (173)
T PRK00625 14 TSFGKALAKFLSLPFFDTD 32 (173)
T ss_pred HHHHHHHHHHhCCCEEEhh
Confidence 7899999999999997765
No 289
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=63.43 E-value=19 Score=24.74 Aligned_cols=29 Identities=10% Similarity=0.218 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHH----hcCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEAD----KNSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~----~~~p~iifiDEid~i~~ 62 (69)
...||++-+.+. ...|.|++|||+|.+-.
T Consensus 123 VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~ 155 (365)
T PRK07471 123 VDEVRELISFFGLTAAEGGWRVVIVDTADEMNA 155 (365)
T ss_pred HHHHHHHHHHhCcCcccCCCEEEEEechHhcCH
Confidence 344666665543 35688999999998853
No 290
>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=63.27 E-value=18 Score=23.02 Aligned_cols=26 Identities=15% Similarity=0.128 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i 60 (69)
+...+.+.+.. ..++++|++|+++..
T Consensus 88 ~~~~~~l~~~L-~~~~~LlVlDdv~~~ 113 (287)
T PF00931_consen 88 EELQDQLRELL-KDKRCLLVLDDVWDE 113 (287)
T ss_dssp HHHHHHHHHHH-CCTSEEEEEEEE-SH
T ss_pred ccccccchhhh-ccccceeeeeeeccc
Confidence 33444454444 345999999998764
No 291
>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=63.07 E-value=10 Score=22.68 Aligned_cols=55 Identities=24% Similarity=0.362 Sum_probs=29.2
Q ss_pred hHHHHHHHHHhCCcEEEEchh-hhh-hcccChHHHHHHHHHHHHHh--------cCCeEEEEccccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGP-EIM-SKLAGESESNLRKAFEEADK--------NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~-~l~-~~~~ges~~~l~~if~~a~~--------~~p~iifiDEid~i~~~ 63 (69)
|++|+++|+.++..|..+.+. +++ +...|.. +|+.... .-..|+|+|||.+.-++
T Consensus 13 T~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~------v~~~~~~~f~~~~GPif~~ill~DEiNrappk 77 (131)
T PF07726_consen 13 TTLAKALARSLGLSFKRIQFTPDLLPSDILGFP------VYDQETGEFEFRPGPIFTNILLADEINRAPPK 77 (131)
T ss_dssp HHHHHHHHHHTT--EEEEE--TT--HHHHHEEE------EEETTTTEEEEEE-TT-SSEEEEETGGGS-HH
T ss_pred HHHHHHHHHHcCCceeEEEecCCCCcccceeee------eeccCCCeeEeecChhhhceeeecccccCCHH
Confidence 789999999999999877653 222 2222221 1111100 12369999999876553
No 292
>PHA00350 putative assembly protein
Probab=62.69 E-value=5.3 Score=28.00 Aligned_cols=19 Identities=37% Similarity=0.459 Sum_probs=16.5
Q ss_pred CCeEEEEcccccccccccc
Q psy3868 48 SPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 48 ~p~iifiDEid~i~~~r~~ 66 (69)
..++|+|||+..+++.|.+
T Consensus 81 ~gaLIViDEaq~~~p~r~~ 99 (399)
T PHA00350 81 RGALYVIDEAQMIFPKRLG 99 (399)
T ss_pred CCCEEEEECchhhcCCCcc
Confidence 5689999999999998754
No 293
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=62.43 E-value=11 Score=26.39 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=13.7
Q ss_pred cCCeEEEEcccccccc
Q psy3868 47 NSPSIIFIDELDAIAP 62 (69)
Q Consensus 47 ~~p~iifiDEid~i~~ 62 (69)
+.+..|++||+|.+..
T Consensus 145 ~~~~liI~DE~Hh~~a 160 (442)
T COG1061 145 NEFGLIIFDEVHHLPA 160 (442)
T ss_pred cccCEEEEEccccCCc
Confidence 4789999999999875
No 294
>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A.
Probab=62.26 E-value=3.6 Score=24.24 Aligned_cols=16 Identities=38% Similarity=0.727 Sum_probs=11.1
Q ss_pred cCCeEEEEcccccccc
Q psy3868 47 NSPSIIFIDELDAIAP 62 (69)
Q Consensus 47 ~~p~iifiDEid~i~~ 62 (69)
.+|.+|+||++|.+.+
T Consensus 149 ~~~~vlviDd~d~~~~ 164 (185)
T PF13191_consen 149 RKPLVLVIDDLDWADP 164 (185)
T ss_dssp ---EEEEEETTTHHHT
T ss_pred CCeEEEEEeCCCCCCc
Confidence 3579999999997653
No 295
>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional
Probab=61.86 E-value=28 Score=25.10 Aligned_cols=28 Identities=11% Similarity=-0.009 Sum_probs=20.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccCh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGE 32 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ge 32 (69)
|++++.+|+.+|++|+.++- .+....|.
T Consensus 20 ttvg~~LA~~L~~~fiD~D~--~ie~~~g~ 47 (542)
T PRK14021 20 TRVGKEVAQMMRLPFADADV--EIEREIGM 47 (542)
T ss_pred HHHHHHHHHHhCCCEEEchH--HHHHHHCc
Confidence 78999999999999987764 33443343
No 296
>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=61.58 E-value=39 Score=21.42 Aligned_cols=56 Identities=9% Similarity=0.081 Sum_probs=29.6
Q ss_pred hHHHHHHHHHh---CCcEEEEchhhhhhc---ccChHHHHHHHHHHHH-Hh--cCCeEEEEcccc
Q psy3868 3 YRLTTLCRDSL---GAFFFLINGPEIMSK---LAGESESNLRKAFEEA-DK--NSPSIIFIDELD 58 (69)
Q Consensus 3 T~la~aia~~~---~~~~~~v~~~~l~~~---~~ges~~~l~~if~~a-~~--~~p~iifiDEid 58 (69)
|++|+.++..+ +.++..++...+... |....++.++.....+ +. .+...+++|...
T Consensus 13 ST~a~~La~~l~~~~~~v~~i~~D~lr~~~~~~~~~~e~~~~~~~~~~i~~~l~~~~~VI~D~~~ 77 (249)
T TIGR03574 13 STFSKELAKKLSEKNIDVIILGTDLIRESFPVWKEKYEEFIRDSTLYLIKTALKNKYSVIVDDTN 77 (249)
T ss_pred HHHHHHHHHHHHHcCCceEEEccHHHHHHhHHhhHHhHHHHHHHHHHHHHHHHhCCCeEEEeccc
Confidence 67899998877 466777766544222 2222333344333221 11 234456777654
No 297
>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=61.11 E-value=7 Score=24.16 Aligned_cols=27 Identities=22% Similarity=0.506 Sum_probs=18.6
Q ss_pred ChHHHHHHHHHHHHHhcCCeEEEEccc
Q psy3868 31 GESESNLRKAFEEADKNSPSIIFIDEL 57 (69)
Q Consensus 31 ges~~~l~~if~~a~~~~p~iifiDEi 57 (69)
|.......+..+.+-...|.+|++||+
T Consensus 57 g~~~~~~~~~i~~aLr~~pd~ii~gEi 83 (198)
T cd01131 57 GLDTLSFENALKAALRQDPDVILVGEM 83 (198)
T ss_pred CCCccCHHHHHHHHhcCCcCEEEEcCC
Confidence 333334555566666678999999998
No 298
>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=60.98 E-value=8.8 Score=23.67 Aligned_cols=15 Identities=27% Similarity=0.552 Sum_probs=10.4
Q ss_pred cCCeEEEEccccccc
Q psy3868 47 NSPSIIFIDELDAIA 61 (69)
Q Consensus 47 ~~p~iifiDEid~i~ 61 (69)
....++++||+|+=.
T Consensus 157 ~~~p~~ilDEvd~~L 171 (220)
T PF02463_consen 157 KPSPFLILDEVDAAL 171 (220)
T ss_dssp S--SEEEEESTTTTS
T ss_pred ccccccccccccccc
Confidence 456788999999754
No 299
>cd00006 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.
Probab=60.54 E-value=19 Score=20.49 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=18.6
Q ss_pred cChHHHHHHHHHHHHHhcCCeEEEEcc
Q psy3868 30 AGESESNLRKAFEEADKNSPSIIFIDE 56 (69)
Q Consensus 30 ~ges~~~l~~if~~a~~~~p~iifiDE 56 (69)
+++..++++++++......+.+||.|=
T Consensus 40 ~~~~~~~i~~~i~~~~~~~~viil~Dl 66 (122)
T cd00006 40 PDDLLEKIKAALAELDSGEGVLILTDL 66 (122)
T ss_pred HHHHHHHHHHHHHHhCCCCcEEEEEeC
Confidence 445677788888777555677777763
No 300
>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=60.54 E-value=29 Score=19.56 Aligned_cols=20 Identities=15% Similarity=0.193 Sum_probs=17.5
Q ss_pred hhHHHHHHHHHhCCcEEEEc
Q psy3868 2 SYRLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~ 21 (69)
.|++|+.+|.+++.|++..+
T Consensus 12 Kst~a~~la~~~~~~~~~~~ 31 (147)
T cd02020 12 KSTVAKLLAKKLGLPYLDTG 31 (147)
T ss_pred HHHHHHHHHHHhCCceeccc
Confidence 47899999999999998765
No 301
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=60.44 E-value=20 Score=23.62 Aligned_cols=56 Identities=14% Similarity=0.116 Sum_probs=32.2
Q ss_pred hHHHHHHHHHhCCc--------EEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 3 YRLTTLCRDSLGAF--------FFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 3 T~la~aia~~~~~~--------~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
|.+|+++|..+.+. ++.+.+. -++ .-+...+|++-+.+.. ....|++||++|.+-.
T Consensus 40 ~~la~~~a~~l~c~~~~~~h~D~~~~~~~--~~~--~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~ 107 (313)
T PRK05564 40 SLLAKEIALKILGKSQQREYVDIIEFKPI--NKK--SIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTE 107 (313)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCeEEeccc--cCC--CCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCH
Confidence 56888888876432 2233221 011 1133457777665432 3457999999998743
No 302
>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=60.17 E-value=28 Score=20.82 Aligned_cols=23 Identities=4% Similarity=0.037 Sum_probs=18.2
Q ss_pred hHHHHHHHHHhCCcEEEEchhhh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEI 25 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l 25 (69)
|++++.++.+++.+++.++...+
T Consensus 16 st~a~~l~~~~~~~~~~~~~D~~ 38 (175)
T cd00227 16 SSIARALQSVLAEPWLHFGVDSF 38 (175)
T ss_pred HHHHHHHHHhhCCCccccCccHH
Confidence 78999999999888776665544
No 303
>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=59.88 E-value=13 Score=25.74 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=34.4
Q ss_pred hHHHHHHHHHhCC-------cEEEEch----hhhhhcccChHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLGA-------FFFLING----PEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~~-------~~~~v~~----~~l~~~~~ges~~~l~~if~~a 44 (69)
|++|+++++.++. +++.+.. +.+....++=-.+.+|..|...
T Consensus 92 Stla~~La~~l~~ys~t~eG~~Y~~~~~~~~sp~~e~Pl~l~p~~~r~~~~~~ 144 (361)
T smart00763 92 SSLVECLKRGLEEYSKTPEGRRYTFKWNGEESPMHEDPLHLFPDELREDLEDE 144 (361)
T ss_pred HHHHHHHHHHHhhhcccccCceEEEEecCCCCCCccCCcccCCHHHHHHHHHH
Confidence 7899999999987 9999988 6666666676788888888554
No 304
>TIGR02858 spore_III_AA stage III sporulation protein AA. Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.
Probab=59.84 E-value=12 Score=24.62 Aligned_cols=22 Identities=23% Similarity=0.347 Sum_probs=16.7
Q ss_pred HHHHHHHHHhcCCeEEEEcccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid 58 (69)
...++..++...|.+|++||+-
T Consensus 183 ~~~~~~~i~~~~P~villDE~~ 204 (270)
T TIGR02858 183 AEGMMMLIRSMSPDVIVVDEIG 204 (270)
T ss_pred HHHHHHHHHhCCCCEEEEeCCC
Confidence 3346666777899999999963
No 305
>PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional
Probab=59.65 E-value=34 Score=20.13 Aligned_cols=46 Identities=22% Similarity=0.309 Sum_probs=31.7
Q ss_pred HHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEc
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFID 55 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiD 55 (69)
+++.++ -+.++..+.+.+ ..-+|....++++..+.+.. ...++|.|
T Consensus 20 ~~~~i~--~~~~i~~~gg~~--d~~~gt~~~~i~~ai~~~~~-dGVlVltD 65 (124)
T PRK14484 20 LIKQMA--PDVPIIYAGGTE--DGRIGTSFDQIQEAIEKNES-DGVLIFFD 65 (124)
T ss_pred HHHHhh--CCCCEEEecCCC--CCCccchHHHHHHHHHhcCc-CCeEEEEe
Confidence 345555 356776666654 45688889999999999866 56666665
No 306
>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=59.41 E-value=14 Score=22.51 Aligned_cols=26 Identities=23% Similarity=0.440 Sum_probs=19.4
Q ss_pred HHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
+.++.+.+.+..|.+|+||-+.++..
T Consensus 86 ~~~l~~~~~~~~~~lvVIDSis~l~~ 111 (209)
T TIGR02237 86 IQKTSKFIDRDSASLVVVDSFTALYR 111 (209)
T ss_pred HHHHHHHHhhcCccEEEEeCcHHHhH
Confidence 55555555556899999999999864
No 307
>PF00456 Transketolase_N: Transketolase, thiamine diphosphate binding domain; InterPro: IPR005474 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; PDB: 3M49_B 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 3HYL_A 3RIM_A ....
Probab=59.19 E-value=30 Score=23.57 Aligned_cols=38 Identities=21% Similarity=0.447 Sum_probs=26.3
Q ss_pred HhCCcEEEE-chhhhhhcccChHHHHHHHHHHHHHhc--CCeEEEEcccc
Q psy3868 12 SLGAFFFLI-NGPEIMSKLAGESESNLRKAFEEADKN--SPSIIFIDELD 58 (69)
Q Consensus 12 ~~~~~~~~v-~~~~l~~~~~ges~~~l~~if~~a~~~--~p~iifiDEid 58 (69)
..|+.++.+ ++.++ ..|.+.|+.|+.. +|.+|+.+=+-
T Consensus 204 a~Gw~v~~v~dGhd~---------~~i~~A~~~a~~~~~kP~~Ii~~Tvk 244 (332)
T PF00456_consen 204 AFGWNVIEVCDGHDV---------EAIYAAIEEAKASKGKPTVIIARTVK 244 (332)
T ss_dssp HTT-EEEEEEETTBH---------HHHHHHHHHHHHSTSS-EEEEEEE-T
T ss_pred HhhhhhcccccCcHH---------HHHHHHHHHHHhcCCCCceeecceEE
Confidence 347888887 66654 6788899998764 89999887553
No 308
>PRK06762 hypothetical protein; Provisional
Probab=58.83 E-value=35 Score=19.98 Aligned_cols=27 Identities=11% Similarity=0.197 Sum_probs=20.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKL 29 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~ 29 (69)
|++|+.++..++..+..++...+....
T Consensus 16 ST~A~~L~~~l~~~~~~i~~D~~r~~l 42 (166)
T PRK06762 16 TTIAKQLQERLGRGTLLVSQDVVRRDM 42 (166)
T ss_pred HHHHHHHHHHhCCCeEEecHHHHHHHh
Confidence 789999999987667777777765433
No 309
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=58.76 E-value=13 Score=19.56 Aligned_cols=54 Identities=20% Similarity=0.225 Sum_probs=32.3
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh----cCCeEEEEccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK----NSPSIIFIDELDA 59 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~----~~p~iifiDEid~ 59 (69)
.--++.+|..+|.+-+.=++...+ ..+.+-.|+++.+.|.+ .+..-|-.++||.
T Consensus 6 ~esvk~iAes~Gi~~l~de~a~~L---a~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ 63 (66)
T PF02969_consen 6 QESVKDIAESLGISNLSDEAAKAL---AEDVEYRLREIIQEALKFMRHSKRTKLTTDDINS 63 (66)
T ss_dssp HHHHHHHHHHTT---B-HHHHHHH---HHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHH---HHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHH
Confidence 446789999999866555444443 34678889999998854 4455555555553
No 310
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=58.48 E-value=8.7 Score=23.39 Aligned_cols=18 Identities=11% Similarity=0.217 Sum_probs=13.5
Q ss_pred hhHHHHHHHHHhCCcEEE
Q psy3868 2 SYRLTTLCRDSLGAFFFL 19 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~ 19 (69)
++.+++.+|..+|.+++.
T Consensus 12 g~~Ia~~LA~~Lg~~~~d 29 (179)
T PF13189_consen 12 GREIAERLAEKLGYPYYD 29 (179)
T ss_dssp HHHHHHHHHHHCT--EE-
T ss_pred hHHHHHHHHHHcCCccCC
Confidence 678999999999998864
No 311
>COG3412 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.14 E-value=34 Score=20.47 Aligned_cols=47 Identities=19% Similarity=0.266 Sum_probs=34.5
Q ss_pred HHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEc
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFID 55 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiD 55 (69)
+++.++. .+|+....+.+ +..+|-+...+.+....++......+|.|
T Consensus 21 li~em~~--dv~i~~~gGtd--dg~iGTs~~~I~~aI~~~~~ad~~lif~D 67 (129)
T COG3412 21 LIREMAG--DVPITYAGGTD--DGQIGTSFEKIMEAIEKANEADHVLVFYD 67 (129)
T ss_pred HHHHHhC--CCceEEecCCC--CCCcCcCHHHHHHHHHhccccCceEEEEe
Confidence 4555555 57777776654 56789999999998887766667788877
No 312
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=58.04 E-value=39 Score=22.35 Aligned_cols=46 Identities=20% Similarity=0.267 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHh-CCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEE
Q psy3868 2 SYRLTTLCRDSL-GAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFI 54 (69)
Q Consensus 2 ~T~la~aia~~~-~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifi 54 (69)
+..++++...+. +..+-...-+.+ .++.++.++++.+++ .+.+||-
T Consensus 12 Ae~v~~A~l~QF~~~~~~~~~~p~I------~~~~~~~~il~~i~~-~~~iV~~ 58 (255)
T PF03618_consen 12 AETVARAALAQFPDVEFEIHRFPFI------RTEEQLDEILEEIKE-ENAIVFY 58 (255)
T ss_pred HHHHHHHHHHhCCCCceEEEECCCc------CCHHHHHHHHHHHhc-cCCEEEE
Confidence 456888888887 455444333333 478899999999977 5556654
No 313
>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=57.94 E-value=4.8 Score=23.34 Aligned_cols=16 Identities=31% Similarity=0.453 Sum_probs=13.1
Q ss_pred CCeEEEEccccccccc
Q psy3868 48 SPSIIFIDELDAIAPK 63 (69)
Q Consensus 48 ~p~iifiDEid~i~~~ 63 (69)
....|++||+|.+...
T Consensus 119 ~~~~iViDE~h~l~~~ 134 (169)
T PF00270_consen 119 RLSLIVIDEAHHLSDE 134 (169)
T ss_dssp TESEEEEETHHHHHHT
T ss_pred cceeeccCcccccccc
Confidence 3688999999998763
No 314
>PRK14532 adenylate kinase; Provisional
Probab=57.89 E-value=22 Score=21.38 Aligned_cols=24 Identities=4% Similarity=0.026 Sum_probs=17.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSK 28 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~ 28 (69)
|++++.+|+++|+++ ++..+++.+
T Consensus 14 sT~a~~la~~~g~~~--is~~d~lr~ 37 (188)
T PRK14532 14 GTQAKRLVEERGMVQ--LSTGDMLRA 37 (188)
T ss_pred HHHHHHHHHHcCCeE--EeCcHHHHH
Confidence 678999999998766 555555554
No 315
>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=57.69 E-value=23 Score=19.88 Aligned_cols=18 Identities=28% Similarity=0.499 Sum_probs=13.0
Q ss_pred HHHHHHhcCCeEEEEccc
Q psy3868 40 AFEEADKNSPSIIFIDEL 57 (69)
Q Consensus 40 if~~a~~~~p~iifiDEi 57 (69)
.+..+-...|.++++||-
T Consensus 118 ~la~al~~~~~llllDEP 135 (137)
T PF00005_consen 118 ALARALLKNPKLLLLDEP 135 (137)
T ss_dssp HHHHHHHTTSSEEEEEST
T ss_pred HHHHHHHcCCCEEEEeCC
Confidence 344444578999999994
No 316
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=57.61 E-value=3 Score=26.78 Aligned_cols=55 Identities=20% Similarity=0.225 Sum_probs=27.6
Q ss_pred hHHHHHHHHHhCCcEEE--Ech-hhhhhcccChHHHHHHHHHHHHHhc-C-CeEEEEccc
Q psy3868 3 YRLTTLCRDSLGAFFFL--ING-PEIMSKLAGESESNLRKAFEEADKN-S-PSIIFIDEL 57 (69)
Q Consensus 3 T~la~aia~~~~~~~~~--v~~-~~l~~~~~ges~~~l~~if~~a~~~-~-p~iifiDEi 57 (69)
..+++.++..+|.+++. +.. +.-.+.--.+-.++++..|...... . ..|++||||
T Consensus 134 ~~la~~l~~~~~~~~~~~r~k~~~~q~~l~~~~rr~nl~~aF~~~~~~~~~~~vlLvDDV 193 (225)
T COG1040 134 ELLARALARRLGKPIALRRVKDTSPQQGLKALERRRNLKGAFRLKKGIEEPKNVLLVDDV 193 (225)
T ss_pred HHHHHHHHHHhCchHHHHHHhccccccccchHHHHHhccCCeecCCCCCCCCeEEEEecc
Confidence 45677777777765411 011 1111112223345566666655332 2 369999987
No 317
>COG0156 BioF 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]
Probab=57.17 E-value=13 Score=25.98 Aligned_cols=27 Identities=26% Similarity=0.460 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
-..|+++-+.++++. +.+++||.|+++
T Consensus 187 iApL~~l~~L~~ky~-a~L~VDEAHa~G 213 (388)
T COG0156 187 IAPLPELVELAEKYG-ALLYVDEAHAVG 213 (388)
T ss_pred cCCHHHHHHHHHHhC-cEEEEEcccccc
Confidence 467888888887765 999999999986
No 318
>PHA02552 4 head completion protein; Provisional
Probab=56.93 E-value=17 Score=22.28 Aligned_cols=16 Identities=19% Similarity=0.110 Sum_probs=12.8
Q ss_pred HHHHHHHHhCCcEEEE
Q psy3868 5 LTTLCRDSLGAFFFLI 20 (69)
Q Consensus 5 la~aia~~~~~~~~~v 20 (69)
.|+++|.+-|+.|..+
T Consensus 122 Aa~~~a~~~Gw~F~ii 137 (151)
T PHA02552 122 AARALCEKKGWKFKII 137 (151)
T ss_pred HHHHHHHHcCCEEEEE
Confidence 4677888888888887
No 319
>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.
Probab=56.84 E-value=17 Score=22.50 Aligned_cols=25 Identities=24% Similarity=0.509 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHh----cCCeEEEEccccc
Q psy3868 35 SNLRKAFEEADK----NSPSIIFIDELDA 59 (69)
Q Consensus 35 ~~l~~if~~a~~----~~p~iifiDEid~ 59 (69)
+..++.|+.|++ ....+|++|||-.
T Consensus 79 ~~~~~~~~~a~~~i~~~~~dlvILDEi~~ 107 (172)
T PF02572_consen 79 AAAREGLEEAKEAISSGEYDLVILDEINY 107 (172)
T ss_dssp HHHHHHHHHHHHHTT-TT-SEEEEETHHH
T ss_pred HHHHHHHHHHHHHHhCCCCCEEEEcchHH
Confidence 568888888865 3578999999843
No 320
>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription
Probab=56.75 E-value=8.5 Score=26.67 Aligned_cols=47 Identities=23% Similarity=0.337 Sum_probs=30.6
Q ss_pred cEEEEchhhhhhc--ccChHHHHHHHHHHHHHhcCCeEEEEccc-cccccccc
Q psy3868 16 FFFLINGPEIMSK--LAGESESNLRKAFEEADKNSPSIIFIDEL-DAIAPKRE 65 (69)
Q Consensus 16 ~~~~v~~~~l~~~--~~ges~~~l~~if~~a~~~~p~iifiDEi-d~i~~~r~ 65 (69)
.|++.+-.++.+. +-=+.+ +.+|.+|.+.+|.-|++||+ |.|++.++
T Consensus 165 ~Fv~msy~e~t~~~NldI~~p---~NiF~~Aa~~GPiaIImDECMe~Lg~~~~ 214 (369)
T PF02456_consen 165 KFVEMSYDEATSPENLDITNP---NNIFAQAAKKGPIAIIMDECMEKLGSHKS 214 (369)
T ss_pred cceeecHhhhCCccccCCCCc---hHHHHHHHhcCCEEEEhHHHHHHhcCCCC
Confidence 5566666665433 111223 45999999999999999996 55555543
No 321
>PRK13810 orotate phosphoribosyltransferase; Provisional
Probab=56.66 E-value=9 Score=23.93 Aligned_cols=46 Identities=17% Similarity=0.239 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccc
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 57 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEi 57 (69)
-+|-++|.++|.|++.+.... +-.|+.. .++........|+++||+
T Consensus 86 plA~~vA~~l~~p~v~vRK~~---k~~g~~~-----~~~g~~~~g~rVlIVDDV 131 (187)
T PRK13810 86 PLATAVSLETGLPLLIVRKSV---KDYGTGS-----RFVGDLKPEDRIVMLEDV 131 (187)
T ss_pred HHHHHHHHHhCCCEEEEecCC---CccCCCc-----eEEccCCCcCEEEEEEec
Confidence 477888889999999887752 2233321 122222234567777775
No 322
>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=56.50 E-value=22 Score=23.60 Aligned_cols=35 Identities=20% Similarity=0.362 Sum_probs=25.0
Q ss_pred hhhhcccCh----HHHHHHHHHHHHHhcCCeEEEEccccc
Q psy3868 24 EIMSKLAGE----SESNLRKAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 24 ~l~~~~~ge----s~~~l~~if~~a~~~~p~iifiDEid~ 59 (69)
.+..+++++ +|++=.++++.+ -..|.+.++||.|+
T Consensus 135 ~~l~R~vN~GFSGGEkKR~EilQ~~-~lePkl~ILDE~DS 173 (251)
T COG0396 135 EFLERYVNEGFSGGEKKRNEILQLL-LLEPKLAILDEPDS 173 (251)
T ss_pred HHhhcccCCCcCcchHHHHHHHHHH-hcCCCEEEecCCCc
Confidence 445555554 466666777666 67899999999986
No 323
>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=56.36 E-value=11 Score=24.01 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHhcCCeEEEEcccc
Q psy3868 35 SNLRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 35 ~~l~~if~~a~~~~p~iifiDEid 58 (69)
++++.+++.+ ..|.++++||+.
T Consensus 99 ~~~~~il~~~--~~~sLvllDE~~ 120 (222)
T cd03287 99 SETSHILSNC--TSRSLVILDELG 120 (222)
T ss_pred HHHHHHHHhC--CCCeEEEEccCC
Confidence 4455566554 468999999963
No 324
>PRK03839 putative kinase; Provisional
Probab=56.32 E-value=13 Score=22.31 Aligned_cols=19 Identities=16% Similarity=0.265 Sum_probs=16.5
Q ss_pred hHHHHHHHHHhCCcEEEEc
Q psy3868 3 YRLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~ 21 (69)
|++++.+|+.++.+++.++
T Consensus 14 sT~~~~La~~~~~~~id~d 32 (180)
T PRK03839 14 TTVSKLLAEKLGYEYVDLT 32 (180)
T ss_pred HHHHHHHHHHhCCcEEehh
Confidence 6799999999999997755
No 325
>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated
Probab=56.26 E-value=22 Score=22.29 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHh----cCCeEEEEccccc
Q psy3868 33 SESNLRKAFEEADK----NSPSIIFIDELDA 59 (69)
Q Consensus 33 s~~~l~~if~~a~~----~~p~iifiDEid~ 59 (69)
..+..++.|+.+++ ....+|++||+-.
T Consensus 96 ~~~~~~~~~~~a~~~l~~~~~dlvVLDEi~~ 126 (178)
T PRK07414 96 EKKALQELWQYTQAVVDEGRYSLVVLDELSL 126 (178)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCEEEEehhHH
Confidence 45668888988865 3568999999854
No 326
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=56.08 E-value=5.9 Score=29.01 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=16.2
Q ss_pred HHHHHHHHHh---CCcEEEEchhhh
Q psy3868 4 RLTTLCRDSL---GAFFFLINGPEI 25 (69)
Q Consensus 4 ~la~aia~~~---~~~~~~v~~~~l 25 (69)
++|++|=+.. +-||+.+||+-+
T Consensus 283 lfA~~IH~~S~R~~~PFIaiNCaAi 307 (560)
T COG3829 283 LFARAIHNLSPRANGPFIAINCAAI 307 (560)
T ss_pred HHHHHHHhcCcccCCCeEEEecccC
Confidence 4677665555 469999999766
No 327
>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=55.85 E-value=14 Score=24.65 Aligned_cols=18 Identities=33% Similarity=0.562 Sum_probs=14.8
Q ss_pred HHHHHHHhcCCeEEEEcc
Q psy3868 39 KAFEEADKNSPSIIFIDE 56 (69)
Q Consensus 39 ~if~~a~~~~p~iifiDE 56 (69)
..+.+|-...|.+||+||
T Consensus 154 vaLARAialdPell~~DE 171 (263)
T COG1127 154 VALARAIALDPELLFLDE 171 (263)
T ss_pred HHHHHHHhcCCCEEEecC
Confidence 356667778999999999
No 328
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=55.80 E-value=11 Score=22.47 Aligned_cols=19 Identities=16% Similarity=0.403 Sum_probs=14.4
Q ss_pred HHhcCCeEEEEcccccccc
Q psy3868 44 ADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 44 a~~~~p~iifiDEid~i~~ 62 (69)
++..+|.++|+||=-.+..
T Consensus 98 ~~~~~P~vv~vd~~N~i~~ 116 (126)
T TIGR00223 98 ARTHRPNVAYFEGDNEIKR 116 (126)
T ss_pred HhcCCCEEEEECCCCCEEE
Confidence 4568999999998655543
No 329
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=55.55 E-value=13 Score=28.43 Aligned_cols=44 Identities=14% Similarity=0.342 Sum_probs=25.5
Q ss_pred EEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccCC
Q psy3868 17 FFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKRE 68 (69)
Q Consensus 17 ~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~~ 68 (69)
++...|.++.-...+. +.++.|... -.+++||||.+..+..+.+
T Consensus 126 ILiTTPEsL~lll~~~---~~r~~l~~v-----r~VIVDEiHel~~sKRG~~ 169 (814)
T COG1201 126 ILITTPESLAILLNSP---KFRELLRDV-----RYVIVDEIHALAESKRGVQ 169 (814)
T ss_pred EEEeChhHHHHHhcCH---HHHHHhcCC-----cEEEeehhhhhhccccchh
Confidence 3444444443333332 555666554 3566999999997655544
No 330
>PRK13949 shikimate kinase; Provisional
Probab=55.54 E-value=21 Score=21.58 Aligned_cols=19 Identities=21% Similarity=0.232 Sum_probs=16.9
Q ss_pred hHHHHHHHHHhCCcEEEEc
Q psy3868 3 YRLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~ 21 (69)
|++++.+|+.++.+++..+
T Consensus 15 stl~~~La~~l~~~~id~D 33 (169)
T PRK13949 15 TTLGKALARELGLSFIDLD 33 (169)
T ss_pred HHHHHHHHHHcCCCeeccc
Confidence 6799999999999988766
No 331
>PF09895 DUF2122: RecB-family nuclease (DUF2122); InterPro: IPR018665 This family of archaeal proteins include RecB nuclease-like proteins as well as proteins of no known function.
Probab=55.41 E-value=17 Score=20.95 Aligned_cols=22 Identities=32% Similarity=0.421 Sum_probs=16.2
Q ss_pred HHHHHHHHHhcCCeEEEEcccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid 58 (69)
|-++|+.|-+....+|++.|++
T Consensus 8 IPe~~KlA~K~gk~livlpdl~ 29 (106)
T PF09895_consen 8 IPEAFKLALKLGKSLIVLPDLK 29 (106)
T ss_pred CHHHHHHHHHcCCcEEEeCCHH
Confidence 5567888877777777777764
No 332
>KOG1942|consensus
Probab=55.36 E-value=17 Score=25.41 Aligned_cols=41 Identities=24% Similarity=0.285 Sum_probs=32.1
Q ss_pred hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
|.+|-+++.++| +||-...+|+..|.-+-.+|-. .+-|.++
T Consensus 78 TAlAlaisqELG~kvPFcpmvgSEvyS~EvKKTEvL-menfRRa 120 (456)
T KOG1942|consen 78 TALALAISQELGPKVPFCPMVGSEVYSNEVKKTEVL-MENFRRA 120 (456)
T ss_pred hHHHHHHHHHhCCCCCcccccchhhhhhhhhHHHHH-HHHHHHH
Confidence 678999999997 7999999999988777666544 4456665
No 333
>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=55.07 E-value=40 Score=20.17 Aligned_cols=30 Identities=23% Similarity=0.316 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 33 SESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 33 s~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
....+|++.+.... ...-|++|||+|.+-.
T Consensus 83 ~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~ 116 (162)
T PF13177_consen 83 KIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTE 116 (162)
T ss_dssp SHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-H
T ss_pred hHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhH
Confidence 34667777777643 3578999999998853
No 334
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=55.02 E-value=11 Score=21.93 Aligned_cols=14 Identities=36% Similarity=0.862 Sum_probs=11.6
Q ss_pred HHHhcCCeEEEEcc
Q psy3868 43 EADKNSPSIIFIDE 56 (69)
Q Consensus 43 ~a~~~~p~iifiDE 56 (69)
.++..+|.++|+||
T Consensus 96 e~~~~~P~vv~vd~ 109 (111)
T cd06919 96 EAEGHKPKVVLVDE 109 (111)
T ss_pred HHhcCCCEEEEeCC
Confidence 35568999999997
No 335
>cd04102 RabL3 RabL3 (Rab-like3) subfamily. RabL3s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown.
Probab=54.97 E-value=25 Score=21.94 Aligned_cols=41 Identities=17% Similarity=0.079 Sum_probs=30.7
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChH-HHHHHHHHHHHHh
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGES-ESNLRKAFEEADK 46 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges-~~~l~~if~~a~~ 46 (69)
+.-+|.++|.+.+.++|.+.-+-..|.+ ..+|++.|+.+.+
T Consensus 156 ~~~ia~~~~~~~i~~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 197 (202)
T cd04102 156 RGFVAEQGNAEEINLNCTNGRLLAAGSSDAVKLSRFFDKVIE 197 (202)
T ss_pred hhhHHHhcCCceEEEecCCcccccCCCccHHHHHHHHHHHHH
Confidence 3468999999999999987655545543 5568899988754
No 336
>PRK09246 amidophosphoribosyltransferase; Provisional
Probab=54.96 E-value=15 Score=26.38 Aligned_cols=52 Identities=10% Similarity=0.191 Sum_probs=29.7
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccC---------hHHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAG---------ESESNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~g---------es~~~l~~if~~a~~--~~p~iifiDEi 57 (69)
..+|+.+|..++.|+..- -+..++.| +-.++++..|..... ....|+++||+
T Consensus 305 ~~~A~~la~~lgip~~~~---l~k~~~~~rt~i~~~q~~R~~~vr~~f~~~~~~v~gK~VlLVDDv 367 (501)
T PRK09246 305 RDAALEIARILGVPYREG---FVKNRYVGRTFIMPGQAQRKKSVRQKLNAIRAEFKGKNVLLVDDS 367 (501)
T ss_pred HHHHHHHHHHHCCCccce---EEEEecccccccCcCHHHHHHHHHhhcCCccccccCCeEEEEecc
Confidence 468899999999887421 01111211 234456666643221 24579999986
No 337
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=54.74 E-value=19 Score=21.53 Aligned_cols=30 Identities=17% Similarity=0.375 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHh-cCCeEEEEccccccccc
Q psy3868 34 ESNLRKAFEEADK-NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 34 ~~~l~~if~~a~~-~~p~iifiDEid~i~~~ 63 (69)
...++++.+.+++ ..|.+|+||-+..+...
T Consensus 126 ~~~~~~l~~~~~~~~~~~lvviD~l~~~~~~ 156 (193)
T PF13481_consen 126 DEDLEELEAALKELYGPDLVVIDPLQSLHDG 156 (193)
T ss_dssp HHHHHHHHHHHTT----SEEEEE-GGGG--S
T ss_pred hHHHHHHHHHHhhcCCCcEEEEcCHHHHhcC
Confidence 4456777777777 67999999999988875
No 338
>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=54.67 E-value=8.1 Score=22.47 Aligned_cols=15 Identities=20% Similarity=0.321 Sum_probs=12.1
Q ss_pred CCeEEEEcccccccc
Q psy3868 48 SPSIIFIDELDAIAP 62 (69)
Q Consensus 48 ~p~iifiDEid~i~~ 62 (69)
.-.+|++||+|....
T Consensus 146 ~~~~vI~DEaH~~~~ 160 (184)
T PF04851_consen 146 KFDLVIIDEAHHYPS 160 (184)
T ss_dssp SESEEEEETGGCTHH
T ss_pred cCCEEEEehhhhcCC
Confidence 457999999998754
No 339
>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria. Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.
Probab=54.39 E-value=14 Score=26.12 Aligned_cols=29 Identities=24% Similarity=0.409 Sum_probs=20.1
Q ss_pred HHHHHHHHHhcCCeEEEEcccccccccccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid~i~~~r~~ 66 (69)
+.+++..+ .++.-+|+|||++.+..-+.+
T Consensus 229 L~~~lr~a-Gy~GLlI~lDE~e~l~kl~~~ 257 (416)
T PF10923_consen 229 LARFLRDA-GYKGLLILLDELENLYKLRND 257 (416)
T ss_pred HHHHHHHc-CCCceEEEEechHHHHhcCCh
Confidence 33344333 478899999999999765543
No 340
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=54.31 E-value=19 Score=23.09 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHhcCCeEEEEcccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid 58 (69)
-+.++.+++.+ ...++++|||+-
T Consensus 110 ~~~~~~il~~~--~~~sLvliDE~g 132 (235)
T PF00488_consen 110 MKRLSSILRNA--TEKSLVLIDELG 132 (235)
T ss_dssp HHHHHHHHHH----TTEEEEEESTT
T ss_pred HHHHHhhhhhc--ccceeeeccccc
Confidence 45577777665 357899999974
No 341
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=54.13 E-value=38 Score=22.70 Aligned_cols=29 Identities=21% Similarity=0.348 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
-..+|++-+.+.. ...-|++|||+|.+-.
T Consensus 92 id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~ 124 (329)
T PRK08058 92 KDQIRYLKEEFSKSGVESNKKVYIIEHADKMTA 124 (329)
T ss_pred HHHHHHHHHHHhhCCcccCceEEEeehHhhhCH
Confidence 3456666655432 3457999999998854
No 342
>TIGR00708 cobA cob(I)alamin adenosyltransferase. Alternate name: corrinoid adenosyltransferase.
Probab=54.04 E-value=24 Score=21.93 Aligned_cols=26 Identities=19% Similarity=0.383 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHh----cCCeEEEEccccc
Q psy3868 34 ESNLRKAFEEADK----NSPSIIFIDELDA 59 (69)
Q Consensus 34 ~~~l~~if~~a~~----~~p~iifiDEid~ 59 (69)
.+..++.|+.|++ ..-.+|++||+-.
T Consensus 79 ~~~~~~~~~~a~~~l~~~~~DlvVLDEi~~ 108 (173)
T TIGR00708 79 TAIAKAAWQHAKEMLADPELDLVLLDELTY 108 (173)
T ss_pred HHHHHHHHHHHHHHHhcCCCCEEEehhhHH
Confidence 4557788888876 4578999999853
No 343
>COG1922 WecG Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]
Probab=53.99 E-value=16 Score=24.20 Aligned_cols=26 Identities=15% Similarity=0.307 Sum_probs=19.9
Q ss_pred hcccChHHHHHHHHHHHHHhcCCeEEEE
Q psy3868 27 SKLAGESESNLRKAFEEADKNSPSIIFI 54 (69)
Q Consensus 27 ~~~~ges~~~l~~if~~a~~~~p~iifi 54 (69)
++|....+. ..+++.....+|+|||+
T Consensus 142 ~GYf~~~e~--~~i~~~I~~s~pdil~V 167 (253)
T COG1922 142 DGYFDPEEE--EAIVERIAASGPDILLV 167 (253)
T ss_pred CCCCChhhH--HHHHHHHHhcCCCEEEE
Confidence 356666666 58888988999999975
No 344
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=53.84 E-value=21 Score=22.02 Aligned_cols=25 Identities=8% Similarity=-0.012 Sum_probs=17.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKL 29 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~ 29 (69)
|++|+.+|+. .++..++-.+++...
T Consensus 14 ~T~A~~La~~--~~i~hlstgd~~r~~ 38 (178)
T COG0563 14 STLAKKLAKK--LGLPHLDTGDILRAA 38 (178)
T ss_pred HHHHHHHHHH--hCCcEEcHhHHhHhh
Confidence 6789999999 555667766665443
No 345
>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....
Probab=53.64 E-value=9.6 Score=25.21 Aligned_cols=19 Identities=21% Similarity=0.330 Sum_probs=14.8
Q ss_pred cCCeEEEEccccccccccc
Q psy3868 47 NSPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~r~ 65 (69)
..+.++++||+|++.-+..
T Consensus 196 r~~~~~ivDEvDs~LiDea 214 (266)
T PF07517_consen 196 RGFDFAIVDEVDSILIDEA 214 (266)
T ss_dssp SSSSEEEECTHHHHTTTGC
T ss_pred CCCCEEEEeccceEEEecC
Confidence 3578999999999975543
No 346
>COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism]
Probab=53.39 E-value=12 Score=22.23 Aligned_cols=17 Identities=29% Similarity=0.663 Sum_probs=13.6
Q ss_pred HHhcCCeEEEEcccccc
Q psy3868 44 ADKNSPSIIFIDELDAI 60 (69)
Q Consensus 44 a~~~~p~iifiDEid~i 60 (69)
++.++|.++|+||=-.+
T Consensus 97 ~~~~~Pkvv~~d~~N~i 113 (126)
T COG0853 97 AKTHKPKVVVVDEKNEI 113 (126)
T ss_pred HhccCCeEEEECCCCch
Confidence 56789999999985544
No 347
>PF05763 DUF835: Protein of unknown function (DUF835); InterPro: IPR008553 The members of this archaebacterial protein entry are around 250-300 amino acid residues in length. The function of these proteins is not known.
Probab=53.39 E-value=25 Score=20.89 Aligned_cols=29 Identities=28% Similarity=0.511 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHH----HhcCCeEEEEccccccc
Q psy3868 33 SESNLRKAFEEA----DKNSPSIIFIDELDAIA 61 (69)
Q Consensus 33 s~~~l~~if~~a----~~~~p~iifiDEid~i~ 61 (69)
++.++..+.+.+ ++....+|+||-+|.|.
T Consensus 56 ~Pt~L~~l~~~i~~fl~~~~~~vViiD~lEYL~ 88 (136)
T PF05763_consen 56 SPTNLHKLLDTIVRFLKENGNGVVIIDGLEYLI 88 (136)
T ss_pred CchhhHHHHHHHHHHHHhCCCcEEEEecHHHHH
Confidence 344555444444 44467799999888764
No 348
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=53.33 E-value=28 Score=23.14 Aligned_cols=20 Identities=25% Similarity=0.313 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHhCCcEEEEc
Q psy3868 2 SYRLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~ 21 (69)
.|++++.+|..+|++|+.++
T Consensus 146 KStvg~~La~~Lg~~~id~D 165 (309)
T PRK08154 146 KSTLGRMLAARLGVPFVELN 165 (309)
T ss_pred HHHHHHHHHHHcCCCEEeHH
Confidence 37899999999999998544
No 349
>cd04131 Rnd Rnd subfamily. The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. Most Rho 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 most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=53.04 E-value=21 Score=21.49 Aligned_cols=36 Identities=22% Similarity=0.327 Sum_probs=25.2
Q ss_pred hHHHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHHHh
Q psy3868 3 YRLTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEADK 46 (69)
Q Consensus 3 T~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a~~ 46 (69)
+.-++.+|.+.+. +|+++|+.+ | +..|+++|..+.+
T Consensus 137 ~~e~~~~a~~~~~~~~~E~SA~~------~--~~~v~~~F~~~~~ 173 (178)
T cd04131 137 YEQGCAIAKQLGAEIYLECSAFT------S--EKSVRDIFHVATM 173 (178)
T ss_pred HHHHHHHHHHhCCCEEEECccCc------C--CcCHHHHHHHHHH
Confidence 3457788999996 798887743 1 2238889988754
No 350
>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=52.68 E-value=49 Score=20.57 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=23.3
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccc
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 57 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEi 57 (69)
+..|..+|+|++..... .+....+++..+..+...-.+||||-.
T Consensus 49 ~~~a~~l~vp~~~~~~~-------~~~~~~~~~~l~~~~~~~~D~vlIDT~ 92 (196)
T PF00448_consen 49 KTYAEILGVPFYVARTE-------SDPAEIAREALEKFRKKGYDLVLIDTA 92 (196)
T ss_dssp HHHHHHHTEEEEESSTT-------SCHHHHHHHHHHHHHHTTSSEEEEEE-
T ss_pred HHHHHHhccccchhhcc-------hhhHHHHHHHHHHHhhcCCCEEEEecC
Confidence 45566666666553211 012334555666665555567777753
No 351
>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]
Probab=52.19 E-value=27 Score=23.13 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=12.4
Q ss_pred HHHHHHhcCCeEEEEcc
Q psy3868 40 AFEEADKNSPSIIFIDE 56 (69)
Q Consensus 40 if~~a~~~~p~iifiDE 56 (69)
++.+|-...|.++++||
T Consensus 149 ~lARAL~~~p~lllLDE 165 (254)
T COG1121 149 LLARALAQNPDLLLLDE 165 (254)
T ss_pred HHHHHhccCCCEEEecC
Confidence 44555567888888888
No 352
>PTZ00132 GTP-binding nuclear protein Ran; Provisional
Probab=52.18 E-value=52 Score=20.10 Aligned_cols=13 Identities=23% Similarity=0.677 Sum_probs=10.2
Q ss_pred hcCCeEEEEcccc
Q psy3868 46 KNSPSIIFIDELD 58 (69)
Q Consensus 46 ~~~p~iifiDEid 58 (69)
...|.++++||--
T Consensus 168 ~~~p~~~~ldEp~ 180 (215)
T PTZ00132 168 TNDPNLVFVGAPA 180 (215)
T ss_pred hhcccceecCCcc
Confidence 3579999999843
No 353
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=51.97 E-value=7 Score=25.30 Aligned_cols=18 Identities=17% Similarity=0.150 Sum_probs=15.1
Q ss_pred HHHHHHHHHhCCcEEEEc
Q psy3868 4 RLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~ 21 (69)
.+|.++|..+|.|++.+.
T Consensus 124 ~lA~~lA~~L~~p~vi~R 141 (238)
T PRK08558 124 PLAVAIASYFGADLVYAK 141 (238)
T ss_pred HHHHHHHHHHCcCEEEEE
Confidence 478889999999998763
No 354
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=51.65 E-value=32 Score=19.63 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=23.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEAD 45 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~ 45 (69)
+.-++.+|.+.+.+++++++.+ ..++.++|..+.
T Consensus 124 ~~~~~~~~~~~~~~~~e~Sa~~---------~~~v~~~f~~~i 157 (162)
T PF00071_consen 124 VEEAQEFAKELGVPYFEVSAKN---------GENVKEIFQELI 157 (162)
T ss_dssp HHHHHHHHHHTTSEEEEEBTTT---------TTTHHHHHHHHH
T ss_pred hhHHHHHHHHhCCEEEEEECCC---------CCCHHHHHHHHH
Confidence 3457788899999999988754 245666666653
No 355
>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=51.59 E-value=30 Score=21.11 Aligned_cols=26 Identities=12% Similarity=0.290 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHh----cCCeEEEEcccccc
Q psy3868 35 SNLRKAFEEADK----NSPSIIFIDELDAI 60 (69)
Q Consensus 35 ~~l~~if~~a~~----~~p~iifiDEid~i 60 (69)
+..++.|+.+++ ....+|++||+-..
T Consensus 78 ~~a~~~~~~a~~~~~~~~~dLlVLDEi~~a 107 (159)
T cd00561 78 AAAAEGWAFAKEAIASGEYDLVILDEINYA 107 (159)
T ss_pred HHHHHHHHHHHHHHhcCCCCEEEEechHhH
Confidence 346667777654 45789999998654
No 356
>cd02016 TPP_E1_OGDC_like Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of the tricarboxylic acid cycle.
Probab=51.45 E-value=46 Score=22.11 Aligned_cols=49 Identities=24% Similarity=0.277 Sum_probs=32.9
Q ss_pred HHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc-CCeEEEEcccccccccccc
Q psy3868 8 LCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN-SPSIIFIDELDAIAPKREK 66 (69)
Q Consensus 8 aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~-~p~iifiDEid~i~~~r~~ 66 (69)
..|...+.|.+.||+.+... .-+..+...+.+++. +|.+| |..+-++.+
T Consensus 201 ~~a~~~gip~~~VdG~D~~a-----V~~a~~~A~~~~r~g~gp~lI-----e~~tYR~~G 250 (265)
T cd02016 201 DVAKMIGAPIFHVNGDDPEA-----VVRATRLALEYRQKFKKDVVI-----DLVCYRRHG 250 (265)
T ss_pred HHHeecCCCEEEEcCCCHHH-----HHHHHHHHHHHHHhcCCCEEE-----EEEEecCCC
Confidence 35566689999999988742 345566677777774 56665 666655544
No 357
>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function.
Probab=51.43 E-value=15 Score=23.94 Aligned_cols=28 Identities=29% Similarity=0.540 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHh-------cCCeEEEEcccccccc
Q psy3868 35 SNLRKAFEEADK-------NSPSIIFIDELDAIAP 62 (69)
Q Consensus 35 ~~l~~if~~a~~-------~~p~iifiDEid~i~~ 62 (69)
..++.+|+..++ .++.+|+||+++.|..
T Consensus 115 ~~L~~L~~~I~~~l~~~~~~~~~~liIDdls~Ll~ 149 (249)
T PF09807_consen 115 SSLRSLYEFIQEALSPADSNGSVVLIIDDLSVLLS 149 (249)
T ss_pred chHHHHHHHHHHHHhhccCCCCeEEEEeCHHHHHH
Confidence 347888877643 4578999999998764
No 358
>COG4517 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.43 E-value=15 Score=21.04 Aligned_cols=35 Identities=26% Similarity=0.389 Sum_probs=27.2
Q ss_pred cChHHHHHHHHHHHHHhc-C--CeEEEEcccccccccc
Q psy3868 30 AGESESNLRKAFEEADKN-S--PSIIFIDELDAIAPKR 64 (69)
Q Consensus 30 ~ges~~~l~~if~~a~~~-~--p~iifiDEid~i~~~r 64 (69)
+.-++.+++.-|.-.++. - -+|+=|||+|..+..+
T Consensus 50 VDPseEkLk~eF~gv~rs~~PmhaivRIdeV~~kG~~~ 87 (109)
T COG4517 50 VDPSEEKLKHEFAGVKRSHLPMHAIVRIDEVDKKGQSV 87 (109)
T ss_pred ECccHHHHHHHhhccccccCcceeEEeeeehhhcCCee
Confidence 444788999999887653 2 3899999999988755
No 359
>COG3959 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism]
Probab=51.15 E-value=35 Score=22.50 Aligned_cols=36 Identities=22% Similarity=0.462 Sum_probs=27.1
Q ss_pred hCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 13 LGAFFFLINGPEIMSKLAGESESNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 13 ~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--~~p~iifiDEi 57 (69)
.|+.++++++.++ ..|.+.|+.++. .+|.+|+.|-+
T Consensus 204 FGw~V~evdG~d~---------~~i~~a~~~~~~~~~rP~~IIa~Tv 241 (243)
T COG3959 204 FGWEVIEVDGHDI---------EEIVEALEKAKGSKGRPTVIIAKTV 241 (243)
T ss_pred cCceEEEEcCcCH---------HHHHHHHHhhhccCCCCeEEEEecc
Confidence 4788899988776 456677777765 38999987754
No 360
>PRK12270 kgd alpha-ketoglutarate decarboxylase; Reviewed
Probab=51.12 E-value=49 Score=26.58 Aligned_cols=54 Identities=20% Similarity=0.263 Sum_probs=36.5
Q ss_pred HHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccccccccC
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r~~~ 67 (69)
-+.-+|+..++|.|.||+.+-.. .....+-.|+..++....|+ ||.+|-+|.+.
T Consensus 705 y~td~ak~~~~PifhVNGdDpeA-----v~~va~lA~~yr~~f~~dVv----IdlvcYRrrGH 758 (1228)
T PRK12270 705 YATDVAKMIQAPIFHVNGDDPEA-----VVRVARLAFEYRQRFHKDVV----IDLVCYRRRGH 758 (1228)
T ss_pred hhHHHHhhcCCCEEeECCCCHHH-----HHHHHHHHHHHHHHcCCCeE----EEEEEEeecCC
Confidence 34456667889999999987632 23445666777666455555 58888877765
No 361
>PRK05788 cobalamin biosynthesis protein CbiG; Validated
Probab=50.80 E-value=45 Score=22.54 Aligned_cols=51 Identities=16% Similarity=0.189 Sum_probs=29.6
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH----------------------HhcCCeEEEEcccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA----------------------DKNSPSIIFIDELD 58 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a----------------------~~~~p~iifiDEid 58 (69)
--+++.++..++..+|... .+ +.+.-...+++.|... +..-|.||.+||--
T Consensus 16 ~~la~~l~~~l~~~~~~~~--~~---~~~~~~~~~~~~f~~~d~iIfI~A~GIaVR~IAP~l~dK~~DPaVvvvDe~G 88 (315)
T PRK05788 16 RDLAERLKAKLKADCYTSE--KL---EYEGFADAFEEAFGCYDALIFIMATGIAVRVIAPLLKDKWSDPAVVVVDEKG 88 (315)
T ss_pred HHHHHHHHHhcccceecch--hh---ccCCHHHHHHHHHhcCCeEEEEEChHHHHHHhchhhhccCcCCCEEEEeCCC
Confidence 3467778887776654332 11 1233344566666652 12458999999943
No 362
>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold. This family is restricted to bacterial proteins, none of which have currently been characterised.
Probab=50.63 E-value=16 Score=26.54 Aligned_cols=30 Identities=23% Similarity=0.409 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHh----cCCeE-EEEcccccccccc
Q psy3868 35 SNLRKAFEEADK----NSPSI-IFIDELDAIAPKR 64 (69)
Q Consensus 35 ~~l~~if~~a~~----~~p~i-ifiDEid~i~~~r 64 (69)
..+.++|+..=+ .+|.+ +||||.|-++..-
T Consensus 237 wLLsELfe~LPEvGD~dkPklVfFfDEAHLLF~da 271 (502)
T PF05872_consen 237 WLLSELFEQLPEVGDLDKPKLVFFFDEAHLLFNDA 271 (502)
T ss_pred HHHHHHHHhCccCCCCCCceEEEEEechhhhhcCC
Confidence 357778877633 35665 5689999998643
No 363
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=50.58 E-value=51 Score=19.42 Aligned_cols=22 Identities=32% Similarity=0.335 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHhcCCeEEEEcc
Q psy3868 35 SNLRKAFEEADKNSPSIIFIDE 56 (69)
Q Consensus 35 ~~l~~if~~a~~~~p~iifiDE 56 (69)
..++++++...+..-.+|+||=
T Consensus 81 ~~l~~~l~~l~~~~yD~iiiD~ 102 (195)
T PF01656_consen 81 ELLREILESLIKSDYDYIIIDT 102 (195)
T ss_dssp HHHHHHHHHHHHTTSSEEEEEE
T ss_pred HHHHHHHHHhhhccccceeecc
Confidence 4577888886665578888884
No 364
>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=50.50 E-value=24 Score=22.72 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 33 SESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 33 s~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
+|++.-.+.... ...|.|+++||+-+-.
T Consensus 137 GE~QriAliR~L-q~~P~ILLLDE~TsAL 164 (223)
T COG4619 137 GEKQRIALIRNL-QFMPKILLLDEITSAL 164 (223)
T ss_pred hHHHHHHHHHHh-hcCCceEEecCchhhc
Confidence 455544444444 4679999999987654
No 365
>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional
Probab=50.41 E-value=58 Score=22.68 Aligned_cols=18 Identities=6% Similarity=-0.166 Sum_probs=14.7
Q ss_pred hHHHHHHHHHhCCcEEEE
Q psy3868 3 YRLTTLCRDSLGAFFFLI 20 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v 20 (69)
|+|++++|...|.+.+.-
T Consensus 233 TTL~~~La~~~g~~~v~E 250 (399)
T PRK08099 233 STLVNKLANIFNTTSAWE 250 (399)
T ss_pred HHHHHHHHHHhCCCeeee
Confidence 789999999999876543
No 366
>PRK07349 amidophosphoribosyltransferase; Provisional
Probab=50.40 E-value=14 Score=26.61 Aligned_cols=17 Identities=6% Similarity=-0.058 Sum_probs=13.9
Q ss_pred hhHHHHHHHHHhCCcEE
Q psy3868 2 SYRLTTLCRDSLGAFFF 18 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~ 18 (69)
+..+|..+|.++|.|+.
T Consensus 323 g~~~A~g~A~~lgip~~ 339 (500)
T PRK07349 323 GIPAAIGFSQASGIPYA 339 (500)
T ss_pred cHHHHHHHHHHHCCCch
Confidence 34579999999999985
No 367
>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated
Probab=50.40 E-value=30 Score=21.84 Aligned_cols=28 Identities=29% Similarity=0.463 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHh----cCCeEEEEcccccc
Q psy3868 33 SESNLRKAFEEADK----NSPSIIFIDELDAI 60 (69)
Q Consensus 33 s~~~l~~if~~a~~----~~p~iifiDEid~i 60 (69)
..+..++.|+.|++ ..-.+|++|||-..
T Consensus 96 ~~~~~~~~~~~a~~~l~~~~ydlvVLDEi~~A 127 (191)
T PRK05986 96 DIAAAREGWEEAKRMLADESYDLVVLDELTYA 127 (191)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCEEEEehhhHH
Confidence 34567788888876 35689999998543
No 368
>PRK12571 1-deoxy-D-xylulose-5-phosphate synthase; Provisional
Probab=50.35 E-value=34 Score=25.30 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=30.1
Q ss_pred HHHHhCCcEE-EEchhhhhhcccChHHHHHHHHHHHHHh--cCCeEEEEccc
Q psy3868 9 CRDSLGAFFF-LINGPEIMSKLAGESESNLRKAFEEADK--NSPSIIFIDEL 57 (69)
Q Consensus 9 ia~~~~~~~~-~v~~~~l~~~~~ges~~~l~~if~~a~~--~~p~iifiDEi 57 (69)
.=...|+.++ .+++.++ ..|.+.|+.++. .+|.+|...=+
T Consensus 241 ~f~a~G~~~~~~vdGhd~---------~~l~~al~~ak~~~~~P~~I~~~T~ 283 (641)
T PRK12571 241 LFEELGFTYVGPIDGHDM---------EALLSVLRAARARADGPVLVHVVTE 283 (641)
T ss_pred HHHHcCCEEECccCCCCH---------HHHHHHHHHHHhCCCCCEEEEEEec
Confidence 4456788888 6888765 678889999886 57999876543
No 369
>TIGR01769 GGGP geranylgeranylglyceryl phosphate synthase. This model represents geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The active enzyme is reported to be a homopentamer in Methanobacterium thermoautotrophicum but is reported to be a homodimer in Thermoplasma acidophilum.
Probab=50.02 E-value=65 Score=20.50 Aligned_cols=45 Identities=27% Similarity=0.489 Sum_probs=33.5
Q ss_pred HHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh--cCCeEEEEccccccc
Q psy3868 11 DSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK--NSPSIIFIDELDAIA 61 (69)
Q Consensus 11 ~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--~~p~iifiDEid~i~ 61 (69)
.+.|...+.+.++ .|-++.++.++.+..++ .-|.++|.=..+.+.
T Consensus 21 ~~~gtDaI~VGGS------~gvt~~~~~~~v~~ik~~~~lPvilfp~~~~~i~ 67 (205)
T TIGR01769 21 KDAGTDAIMVGGS------LGIVESNLDQTVKKIKKITNLPVILFPGNVNGLS 67 (205)
T ss_pred HhcCCCEEEEcCc------CCCCHHHHHHHHHHHHhhcCCCEEEECCCccccC
Confidence 3457888888776 35578889989998887 369999976655544
No 370
>PRK09694 helicase Cas3; Provisional
Probab=49.86 E-value=20 Score=27.61 Aligned_cols=16 Identities=25% Similarity=0.407 Sum_probs=13.0
Q ss_pred hcCCeEEEEccccccc
Q psy3868 46 KNSPSIIFIDELDAIA 61 (69)
Q Consensus 46 ~~~p~iifiDEid~i~ 61 (69)
....++|+|||||++-
T Consensus 437 ~La~svvIiDEVHAyD 452 (878)
T PRK09694 437 GLGRSVLIVDEVHAYD 452 (878)
T ss_pred hhccCeEEEechhhCC
Confidence 3567899999999873
No 371
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=49.81 E-value=53 Score=20.01 Aligned_cols=24 Identities=13% Similarity=0.272 Sum_probs=19.1
Q ss_pred HHHHHHhCCcEEEEchhhhhhccc
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLA 30 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ 30 (69)
..+|.+.|..++.+.++++..+++
T Consensus 79 ~~lae~~g~~v~i~~Ggt~ar~~i 102 (158)
T PF01976_consen 79 KKLAEKYGYKVYIATGGTLARKII 102 (158)
T ss_pred HHHHHHcCCEEEEEcChHHHHHHH
Confidence 467899999999999988855443
No 372
>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=49.80 E-value=46 Score=23.08 Aligned_cols=29 Identities=21% Similarity=0.344 Sum_probs=20.1
Q ss_pred cChHHHHHHHHHHHHHhcCCeEEEEcccc
Q psy3868 30 AGESESNLRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 30 ~ges~~~l~~if~~a~~~~p~iifiDEid 58 (69)
+|..........+.+-+..|.+|++.|+.
T Consensus 207 vg~~~~~~~~~l~~aLR~~PD~I~vGEiR 235 (372)
T TIGR02525 207 IGRDVDSFANGIRLALRRAPKIIGVGEIR 235 (372)
T ss_pred cCCCccCHHHHHHHhhccCCCEEeeCCCC
Confidence 34333345566666667899999999985
No 373
>KOG0922|consensus
Probab=49.77 E-value=21 Score=26.81 Aligned_cols=57 Identities=18% Similarity=0.237 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHhCCcE-----EEEchhhh-----hhcccChHHHHHHHHHHHHHhcCCeEEEEccccc
Q psy3868 2 SYRLTTLCRDSLGAFF-----FLINGPEI-----MSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 2 ~T~la~aia~~~~~~~-----~~v~~~~l-----~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~ 59 (69)
+.++|+-+|.|.++.+ +.+.-.+. .=+|.-+ .=.+|+++..---.+=++|.+||+|.
T Consensus 108 avslA~RVAeE~~~~lG~~VGY~IRFed~ts~~TrikymTD-G~LLRE~l~Dp~LskYsvIIlDEAHE 174 (674)
T KOG0922|consen 108 AVSLAKRVAEEMGCQLGEEVGYTIRFEDSTSKDTRIKYMTD-GMLLREILKDPLLSKYSVIILDEAHE 174 (674)
T ss_pred HHHHHHHHHHHhCCCcCceeeeEEEecccCCCceeEEEecc-hHHHHHHhcCCccccccEEEEechhh
Confidence 4679999999998733 22222222 1223333 23567777665445668999999973
No 374
>PRK04296 thymidine kinase; Provisional
Probab=49.64 E-value=22 Score=21.78 Aligned_cols=23 Identities=22% Similarity=0.342 Sum_probs=15.1
Q ss_pred HHHHHHHH--hcCCeEEEEcccccc
Q psy3868 38 RKAFEEAD--KNSPSIIFIDELDAI 60 (69)
Q Consensus 38 ~~if~~a~--~~~p~iifiDEid~i 60 (69)
.++++.++ ...+.+|+|||+..+
T Consensus 66 ~~~~~~~~~~~~~~dvviIDEaq~l 90 (190)
T PRK04296 66 TDIFELIEEEGEKIDCVLIDEAQFL 90 (190)
T ss_pred HHHHHHHHhhCCCCCEEEEEccccC
Confidence 34444443 346789999999765
No 375
>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=49.31 E-value=31 Score=20.46 Aligned_cols=41 Identities=20% Similarity=0.152 Sum_probs=22.9
Q ss_pred CcEEEEchhhhhhcccChHHHHHHHHHHHH--HhcCCeEEEEc
Q psy3868 15 AFFFLINGPEIMSKLAGESESNLRKAFEEA--DKNSPSIIFID 55 (69)
Q Consensus 15 ~~~~~v~~~~l~~~~~ges~~~l~~if~~a--~~~~p~iifiD 55 (69)
.+++.++...+.....++-...++++.+.. +..+|..||||
T Consensus 51 ~~v~~l~~GCiCC~~~~~l~~~l~~l~~~~~~~~~~~d~I~IE 93 (158)
T cd03112 51 EEIIEMNNGCICCTVRGDLIRALLDLLERLDAGKIAFDRIVIE 93 (158)
T ss_pred ceEEEeCCCEeEeeCchhHHHHHHHHHHHHHhccCCCCEEEEE
Confidence 345555554444444445555565555542 34578888875
No 376
>cd04121 Rab40 Rab40 subfamily. This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide d
Probab=49.21 E-value=25 Score=21.51 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=23.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEAD 45 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~ 45 (69)
.--++.+|.+.+++++++|+.+ ..+|.++|+.+.
T Consensus 130 ~~~~~~~a~~~~~~~~e~SAk~---------g~~V~~~F~~l~ 163 (189)
T cd04121 130 TEQAQAYAERNGMTFFEVSPLC---------NFNITESFTELA 163 (189)
T ss_pred HHHHHHHHHHcCCEEEEecCCC---------CCCHHHHHHHHH
Confidence 3457788888899999987743 244666777653
No 377
>KOG0058|consensus
Probab=49.08 E-value=18 Score=27.35 Aligned_cols=55 Identities=22% Similarity=0.294 Sum_probs=31.5
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChH------HHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGES------ESNLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges------~~~l~~if~~a~~~~p~iifiDEid~i 60 (69)
+...|+..+++=|.-+-++=.+.-+||. .++=|-...+|--..|+|+++||.-+-
T Consensus 574 i~~AAk~ANah~FI~~~p~gY~T~VGEkG~qLSGGQKQRIAIARALlr~P~VLILDEATSA 634 (716)
T KOG0058|consen 574 IEAAAKMANAHEFITNFPDGYNTVVGEKGSQLSGGQKQRIAIARALLRNPRVLILDEATSA 634 (716)
T ss_pred HHHHHHHhChHHHHHhCccccccccCCccccccchHHHHHHHHHHHhcCCCEEEEechhhh
Confidence 3455666666544444444345556663 233344444444478999999997554
No 378
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=48.91 E-value=27 Score=21.84 Aligned_cols=27 Identities=26% Similarity=0.289 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 35 SNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 35 ~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
..+..+-+...+..|.+++|||+..+.
T Consensus 107 ~ll~~l~~~i~~~~~~~iviDs~t~~~ 133 (234)
T PRK06067 107 KLLELIIEFIKSKREDVIIIDSLTIFA 133 (234)
T ss_pred HHHHHHHHHHHhcCCCEEEEecHHHHH
Confidence 334444444455689999999998763
No 379
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=48.89 E-value=30 Score=21.96 Aligned_cols=28 Identities=21% Similarity=0.330 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
+..+.++.+......|.++++||+-++.
T Consensus 103 ~~~l~~il~~~~~~~~~~lVIDe~t~~l 130 (230)
T PRK08533 103 RKFLKKLMNTRRFYEKDVIIIDSLSSLI 130 (230)
T ss_pred HHHHHHHHHHHHhcCCCEEEEECccHHh
Confidence 4456666666666789999999998875
No 380
>cd02012 TPP_TK Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the pentose phosphate pathway and provides precursors for nucleotide, aromatic amino acid and vitamin biosynthesis. In addition, the enzyme plays a central role in the Calvin cycle in plants. Typically, TKs are homodimers. They require TPP and divalent cations, such as magnesium ions, for activity.
Probab=48.89 E-value=70 Score=20.52 Aligned_cols=39 Identities=23% Similarity=0.368 Sum_probs=26.3
Q ss_pred HHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh--cCCeEEEEc
Q psy3868 8 LCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK--NSPSIIFID 55 (69)
Q Consensus 8 aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--~~p~iifiD 55 (69)
.++...|++++.+++ .....+.+.|+.+++ .+|++|.+.
T Consensus 185 ~~~~a~G~~~~~v~G---------~d~~~l~~al~~a~~~~~~P~~I~~~ 225 (255)
T cd02012 185 KKFEAFGWNVIEVDG---------HDVEEILAALEEAKKSKGKPTLIIAK 225 (255)
T ss_pred HHHHHcCCeEEEECC---------CCHHHHHHHHHHHHHcCCCCEEEEEE
Confidence 345556777776653 345677888888865 579888765
No 381
>PF12694 MoCo_carrier: Putative molybdenum carrier; InterPro: IPR024755 The structure of proteins in this family contain central beta strands with flanking alpha helices. The structure is similar to that of a molybdenum cofactor carrier protein.; PDB: 3IMK_A.
Probab=48.36 E-value=62 Score=19.75 Aligned_cols=42 Identities=12% Similarity=-0.002 Sum_probs=29.5
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEE
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSII 52 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~ii 52 (69)
+|.+-..+|.+.+.|++.++.. .......+++....+...+|
T Consensus 78 Gt~lT~~~a~~~~KP~l~i~~~---------~~~~~~~v~~wl~~~~i~vL 119 (145)
T PF12694_consen 78 GTALTVEFARKHGKPCLHIDLS---------IPEAAAAVAEWLREHNIRVL 119 (145)
T ss_dssp HHHHHHHHHHHTT--EEEETS----------HHHHHHHHHHHHHHTT--EE
T ss_pred HHHHHHHHHHHhCCCEEEEecC---------cccHHHHHHHHHHHCCceEE
Confidence 5788899999999999998443 24457888998888877776
No 382
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=48.21 E-value=17 Score=21.35 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=9.1
Q ss_pred HHhcCCeEEEEcccc
Q psy3868 44 ADKNSPSIIFIDELD 58 (69)
Q Consensus 44 a~~~~p~iifiDEid 58 (69)
++..+|.++|+||=-
T Consensus 98 ~~~~~P~vv~vd~~N 112 (116)
T PF02261_consen 98 AKNHKPKVVFVDEKN 112 (116)
T ss_dssp HHH---EEEEEETTS
T ss_pred HhhCCCEEEEECCCC
Confidence 456899999999843
No 383
>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=48.11 E-value=56 Score=20.66 Aligned_cols=11 Identities=55% Similarity=0.791 Sum_probs=9.8
Q ss_pred cCCeEEEEccc
Q psy3868 47 NSPSIIFIDEL 57 (69)
Q Consensus 47 ~~p~iifiDEi 57 (69)
..|.++++||.
T Consensus 108 ~~~sLvLLDEp 118 (222)
T cd03285 108 TENSLIIIDEL 118 (222)
T ss_pred CCCeEEEEecC
Confidence 57999999998
No 384
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=47.86 E-value=20 Score=25.68 Aligned_cols=44 Identities=20% Similarity=0.499 Sum_probs=27.5
Q ss_pred CCcEEEEchhhh---------hhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 14 GAFFFLINGPEI---------MSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 14 ~~~~~~v~~~~l---------~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
..||+-+||..+ ++.-+|..++ .-+|++| ...-+|+|||-.+.+
T Consensus 255 ~~pFlalNCA~lPe~~aEsElFG~apg~~gk--~GffE~A---ngGTVlLDeIgEmSp 307 (511)
T COG3283 255 SKPFLALNCASLPEDAAESELFGHAPGDEGK--KGFFEQA---NGGTVLLDEIGEMSP 307 (511)
T ss_pred CCCeeEeecCCCchhHhHHHHhcCCCCCCCc--cchhhhc---cCCeEEeehhhhcCH
Confidence 479999999554 4434443222 2466665 235677999987654
No 385
>PF13558 SbcCD_C: Putative exonuclease SbcCD, C subunit; PDB: 3QG5_B 3QF7_A 3THO_A 3EUK_H 3EUJ_A 3AV0_B 3AUY_B 3AUX_A.
Probab=47.70 E-value=13 Score=20.19 Aligned_cols=11 Identities=45% Similarity=1.038 Sum_probs=9.4
Q ss_pred cCCeEEEEccc
Q psy3868 47 NSPSIIFIDEL 57 (69)
Q Consensus 47 ~~p~iifiDEi 57 (69)
..|.+||+||.
T Consensus 62 ~~~~~l~lDEa 72 (90)
T PF13558_consen 62 DSPRLLFLDEA 72 (90)
T ss_dssp TTBSEEEEEST
T ss_pred CCcCEEEEeCC
Confidence 35899999997
No 386
>cd04172 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight
Probab=47.51 E-value=26 Score=21.25 Aligned_cols=34 Identities=18% Similarity=0.223 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCC-cEEEEchhhhhhcccChHHHH-HHHHHHHHHh
Q psy3868 4 RLTTLCRDSLGA-FFFLINGPEIMSKLAGESESN-LRKAFEEADK 46 (69)
Q Consensus 4 ~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~-l~~if~~a~~ 46 (69)
--++.+|.+.+. +|+++|+-+ ..+ |.++|..+..
T Consensus 142 ~~~~~~a~~~~~~~~~E~SAk~---------~~n~v~~~F~~~~~ 177 (182)
T cd04172 142 DQGANMAKQIGAATYIECSALQ---------SENSVRDIFHVATL 177 (182)
T ss_pred HHHHHHHHHcCCCEEEECCcCC---------CCCCHHHHHHHHHH
Confidence 346788899995 899887742 334 8889988754
No 387
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=47.26 E-value=57 Score=19.05 Aligned_cols=50 Identities=12% Similarity=0.033 Sum_probs=32.6
Q ss_pred HHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEccc
Q psy3868 8 LCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFIDEL 57 (69)
Q Consensus 8 aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiDEi 57 (69)
.+.++.+..-+.+--+--++...++..+.+++.-+..+. ..-.|.|+||-
T Consensus 42 ~~i~~~~~~~iVvGlP~~~dG~~~~~a~~v~~f~~~L~~~~~~~v~~~DEr 92 (130)
T TIGR00250 42 ELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEGRFGVPVVLWDER 92 (130)
T ss_pred HHHHHcCCCEEEEeccCCCCcCcCHHHHHHHHHHHHHHHHhCCCEEEEcCC
Confidence 455556666666655544566667777777777776644 35678999984
No 388
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=47.25 E-value=15 Score=21.21 Aligned_cols=14 Identities=14% Similarity=0.387 Sum_probs=11.6
Q ss_pred CeEEEEcccccccc
Q psy3868 49 PSIIFIDELDAIAP 62 (69)
Q Consensus 49 p~iifiDEid~i~~ 62 (69)
..+|++||+|.+..
T Consensus 130 ~~~iIiDE~h~~~~ 143 (201)
T smart00487 130 VDLVILDEAHRLLD 143 (201)
T ss_pred CCEEEEECHHHHhc
Confidence 45899999999875
No 389
>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=47.15 E-value=23 Score=23.49 Aligned_cols=15 Identities=20% Similarity=0.372 Sum_probs=12.4
Q ss_pred CCeEEEEcccccccc
Q psy3868 48 SPSIIFIDELDAIAP 62 (69)
Q Consensus 48 ~p~iifiDEid~i~~ 62 (69)
..++++|||+|.+..
T Consensus 124 ~~~~iViDE~h~~~~ 138 (358)
T TIGR01587 124 ANSLLIFDEVHFYDE 138 (358)
T ss_pred cCCEEEEeCCCCCCH
Confidence 347899999999875
No 390
>KOG3361|consensus
Probab=46.83 E-value=31 Score=21.04 Aligned_cols=33 Identities=12% Similarity=0.126 Sum_probs=27.3
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK 46 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~ 46 (69)
..||+++..|-+.+.|+.| .|..|+...+..+.
T Consensus 117 teIAKeL~LPPVKLHCSML-------AEDAIKaAikdyk~ 149 (157)
T KOG3361|consen 117 TEIAKELSLPPVKLHCSML-------AEDAIKAAIKDYKE 149 (157)
T ss_pred HHHHHhccCCchhhhhHHH-------HHHHHHHHHHHHHH
Confidence 3689999999999999999 67788887777654
No 391
>PF07015 VirC1: VirC1 protein; InterPro: IPR009744 This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon, which enhances T-DNA processing probably, does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA [].
Probab=46.72 E-value=64 Score=21.08 Aligned_cols=25 Identities=20% Similarity=0.383 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHHHHhcCCeEEEEcc
Q psy3868 32 ESESNLRKAFEEADKNSPSIIFIDE 56 (69)
Q Consensus 32 es~~~l~~if~~a~~~~p~iifiDE 56 (69)
.....++++.+.+...+...+|+|=
T Consensus 67 ~e~~~l~~~~e~a~~~~~d~VlvDl 91 (231)
T PF07015_consen 67 DELTILEDAYEAAEASGFDFVLVDL 91 (231)
T ss_pred cchhhHHHHHHHHHhcCCCEEEEeC
Confidence 3455788888887766667788873
No 392
>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=46.67 E-value=39 Score=20.00 Aligned_cols=19 Identities=16% Similarity=0.284 Sum_probs=13.6
Q ss_pred HHHHHHhcCCeEEEEcccc
Q psy3868 40 AFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 40 if~~a~~~~p~iifiDEid 58 (69)
.+..+-...|.++++||--
T Consensus 92 ~laral~~~p~illlDEP~ 110 (163)
T cd03216 92 EIARALARNARLLILDEPT 110 (163)
T ss_pred HHHHHHhcCCCEEEEECCC
Confidence 3444445789999999954
No 393
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=46.62 E-value=22 Score=22.42 Aligned_cols=23 Identities=13% Similarity=0.166 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhh
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIM 26 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~ 26 (69)
.|++++.+|.++|.+++ ++..++
T Consensus 13 ~TTva~~lAe~~gl~~v--saG~iF 35 (179)
T COG1102 13 KTTVARELAEHLGLKLV--SAGTIF 35 (179)
T ss_pred hhHHHHHHHHHhCCcee--eccHHH
Confidence 47899999999999985 444443
No 394
>PRK04182 cytidylate kinase; Provisional
Probab=46.53 E-value=21 Score=20.96 Aligned_cols=17 Identities=18% Similarity=0.174 Sum_probs=15.3
Q ss_pred hHHHHHHHHHhCCcEEE
Q psy3868 3 YRLTTLCRDSLGAFFFL 19 (69)
Q Consensus 3 T~la~aia~~~~~~~~~ 19 (69)
|++++.+|..+|.+++.
T Consensus 14 stia~~la~~lg~~~id 30 (180)
T PRK04182 14 TTVARLLAEKLGLKHVS 30 (180)
T ss_pred HHHHHHHHHHcCCcEec
Confidence 78999999999998875
No 395
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=46.51 E-value=69 Score=19.78 Aligned_cols=17 Identities=12% Similarity=0.247 Sum_probs=14.4
Q ss_pred cCCeEEEEccccccccc
Q psy3868 47 NSPSIIFIDELDAIAPK 63 (69)
Q Consensus 47 ~~p~iifiDEid~i~~~ 63 (69)
.++.+++||-+.++.+.
T Consensus 106 ~~~~lvVIDsi~al~~~ 122 (225)
T PRK09361 106 ENVGLIVLDSATSLYRL 122 (225)
T ss_pred hcccEEEEeCcHHHhHH
Confidence 58999999999988753
No 396
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=46.45 E-value=12 Score=23.37 Aligned_cols=20 Identities=30% Similarity=0.343 Sum_probs=14.7
Q ss_pred hHHHHHHHHHhCCcEEEEch
Q psy3868 3 YRLTTLCRDSLGAFFFLING 22 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~ 22 (69)
-.+|..+|.+++.++.....
T Consensus 97 ~~~A~~lA~~L~~~~~~~~~ 116 (200)
T PRK02277 97 VPLATLVADELGKDLAIYHP 116 (200)
T ss_pred HHHHHHHHHHhCCCcEEEec
Confidence 35788888899988765544
No 397
>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily. RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tu
Probab=46.32 E-value=56 Score=18.75 Aligned_cols=31 Identities=23% Similarity=0.422 Sum_probs=16.7
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
++.++...+.+++++++-+ +..++.++|+.+
T Consensus 129 ~~~~~~~~~~~~~e~Sa~~--------~~~~v~~~f~~l 159 (165)
T cd04146 129 GEKLASELGCLFFEVSAAE--------DYDGVHSVFHEL 159 (165)
T ss_pred HHHHHHHcCCEEEEeCCCC--------CchhHHHHHHHH
Confidence 4455666666666665421 123566666655
No 398
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=46.10 E-value=19 Score=21.44 Aligned_cols=19 Identities=32% Similarity=0.655 Sum_probs=14.8
Q ss_pred HHhcCCeEEEEcccccccc
Q psy3868 44 ADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 44 a~~~~p~iifiDEid~i~~ 62 (69)
++..+|.++|+||=..+-.
T Consensus 98 ~~~~~P~vv~vd~~N~i~~ 116 (126)
T PRK05449 98 AKTHKPKVVFVDEDNRIKE 116 (126)
T ss_pred HhcCCCEEEEECCCCCEEE
Confidence 4568999999998766654
No 399
>PF04748 Polysacc_deac_2: Divergent polysaccharide deacetylase; InterPro: IPR006837 This is a family of uncharacterised proteins that includes YibQ.; PDB: 2QV5_A 2NLY_A.
Probab=46.07 E-value=33 Score=21.83 Aligned_cols=47 Identities=15% Similarity=0.089 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCcEEEEchhhhhhcc--cChHHHHHHHHHHHHHhcCCeEE
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEIMSKL--AGESESNLRKAFEEADKNSPSII 52 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l~~~~--~ges~~~l~~if~~a~~~~p~ii 52 (69)
+.+..+|.+.|.|+...+- +++.- .+.-.++++++-..|+++..+|.
T Consensus 131 s~a~~~A~~~gvp~~~rdv--fLD~~~~~~~I~~ql~~~~~~A~~~G~aI~ 179 (213)
T PF04748_consen 131 SVAPQVAKELGVPAARRDV--FLDNDQDEAAIRRQLDQAARIARKQGSAIA 179 (213)
T ss_dssp -SHHHHHHHCT--EEE-SE--ETTST-SHHHHHHHHHHHHHHHHCCSEEEE
T ss_pred cHHHHHHHHcCCCEEeece--ecCCCCCHHHHHHHHHHHHHhhhhcCcEEE
Confidence 5688899999998876432 33321 22234455555556666655555
No 400
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=46.06 E-value=57 Score=23.71 Aligned_cols=34 Identities=15% Similarity=0.281 Sum_probs=28.6
Q ss_pred HHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
.|+..+....++|++.+||.++ ++..+..+++.+
T Consensus 199 ~L~~eL~ekY~vpVlpvnc~~l-------~~~DI~~Il~~v 232 (492)
T PF09547_consen 199 ELAEELEEKYDVPVLPVNCEQL-------REEDITRILEEV 232 (492)
T ss_pred HHHHHHHHHhCCcEEEeehHHc-------CHHHHHHHHHHH
Confidence 4778888888999999999998 677888888776
No 401
>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru
Probab=45.57 E-value=61 Score=19.83 Aligned_cols=13 Identities=38% Similarity=0.664 Sum_probs=10.6
Q ss_pred cCCeEEEEccccc
Q psy3868 47 NSPSIIFIDELDA 59 (69)
Q Consensus 47 ~~p~iifiDEid~ 59 (69)
..|.++++||.-+
T Consensus 107 ~~~~llllDEp~~ 119 (202)
T cd03243 107 TPRSLVLIDELGR 119 (202)
T ss_pred cCCeEEEEecCCC
Confidence 5799999999743
No 402
>PF04198 Sugar-bind: Putative sugar-binding domain; InterPro: IPR007324 This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. One of these proteins, Q8U7I7 from SWISSPROT, has an N-terminal helix-turn-helix IPR000792 from INTERPRO that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.; GO: 0030246 carbohydrate binding; PDB: 3KV1_A 3EFB_C 2W48_A 3BXH_A 3BXE_A 2OKG_A 3BXF_A 3BXG_A 2R5F_A 2O0M_A ....
Probab=45.50 E-value=24 Score=22.91 Aligned_cols=46 Identities=15% Similarity=0.343 Sum_probs=29.0
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccC----hHHHHHHHHHHHHHhc
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAG----ESESNLRKAFEEADKN 47 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~g----es~~~l~~if~~a~~~ 47 (69)
+..+++.+|..+|...+.+..+-+++.--- ..+..++++++.+++.
T Consensus 96 ~~~i~~~lA~~~g~~~~~l~aP~~~~s~~~~~~l~~~~~i~~~l~~~~~~ 145 (255)
T PF04198_consen 96 ANEIARRLAEKLGGKYYFLPAPAFVDSPELRDALLAEPSIREVLDLARKA 145 (255)
T ss_dssp HHHHHHHHHHHHTSEEE---SBSB-SSHHHHHHHHTSHHHHHHHHHHCT-
T ss_pred HHHHHHHHHHHhCCcEEEEeCCccCCCHHHHHHHHhChHHHHHHHHHHhC
Confidence 356899999999998888888777543111 1345688888887654
No 403
>KOG2227|consensus
Probab=45.44 E-value=30 Score=25.28 Aligned_cols=18 Identities=17% Similarity=0.418 Sum_probs=14.6
Q ss_pred CCeEEEEccccccccccc
Q psy3868 48 SPSIIFIDELDAIAPKRE 65 (69)
Q Consensus 48 ~p~iifiDEid~i~~~r~ 65 (69)
.+-++++||+|.|+.++.
T Consensus 256 ~~~llVlDEmD~L~tr~~ 273 (529)
T KOG2227|consen 256 FMLLLVLDEMDHLITRSQ 273 (529)
T ss_pred ceEEEEechhhHHhhccc
Confidence 488999999999995543
No 404
>cd04177 RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. 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 featu
Probab=45.37 E-value=21 Score=20.75 Aligned_cols=15 Identities=7% Similarity=0.177 Sum_probs=6.9
Q ss_pred HHHHHHHHHhcCCeE
Q psy3868 37 LRKAFEEADKNSPSI 51 (69)
Q Consensus 37 l~~if~~a~~~~p~i 51 (69)
+.++|+..-+.-.|+
T Consensus 152 i~~~f~~i~~~~~~~ 166 (168)
T cd04177 152 VDEVFIDLVRQIICV 166 (168)
T ss_pred HHHHHHHHHHHHhhh
Confidence 444555554433443
No 405
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=45.23 E-value=66 Score=20.89 Aligned_cols=47 Identities=21% Similarity=0.437 Sum_probs=33.5
Q ss_pred HHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc-CCeEEEEcccccccc
Q psy3868 10 RDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN-SPSIIFIDELDAIAP 62 (69)
Q Consensus 10 a~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~-~p~iifiDEid~i~~ 62 (69)
..+.|...+.|.+|+ |-++.++.++.+..++. -|+|+|.=..+.+.+
T Consensus 28 ~~~~gtdai~vGGS~------~vt~~~~~~~v~~ik~~~lPvilfp~~~~~i~~ 75 (232)
T PRK04169 28 ICESGTDAIIVGGSD------GVTEENVDELVKAIKEYDLPVILFPGNIEGISP 75 (232)
T ss_pred HHhcCCCEEEEcCCC------ccchHHHHHHHHHHhcCCCCEEEeCCCccccCc
Confidence 344577888787665 44678888888888874 499999866665543
No 406
>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]
Probab=45.15 E-value=26 Score=23.05 Aligned_cols=10 Identities=50% Similarity=0.982 Sum_probs=8.1
Q ss_pred cCCeEEEEcc
Q psy3868 47 NSPSIIFIDE 56 (69)
Q Consensus 47 ~~p~iifiDE 56 (69)
+.|+++++||
T Consensus 150 h~P~i~vlDE 159 (245)
T COG4555 150 HDPSILVLDE 159 (245)
T ss_pred cCCCeEEEcC
Confidence 5788888887
No 407
>PF05729 NACHT: NACHT domain
Probab=44.82 E-value=41 Score=19.09 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=15.2
Q ss_pred HhcCCeEEEEccccccccc
Q psy3868 45 DKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 45 ~~~~p~iifiDEid~i~~~ 63 (69)
....+.+|+||.+|.+...
T Consensus 78 ~~~~~~llilDglDE~~~~ 96 (166)
T PF05729_consen 78 EKNKRVLLILDGLDELEEQ 96 (166)
T ss_pred HcCCceEEEEechHhcccc
Confidence 3467889999999999874
No 408
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=44.55 E-value=23 Score=22.00 Aligned_cols=17 Identities=24% Similarity=0.256 Sum_probs=15.3
Q ss_pred hHHHHHHHHHhCCcEEE
Q psy3868 3 YRLTTLCRDSLGAFFFL 19 (69)
Q Consensus 3 T~la~aia~~~~~~~~~ 19 (69)
|++++++|.++|++|+.
T Consensus 9 Stvg~~lA~~lg~~fid 25 (161)
T COG3265 9 STVGSALAERLGAKFID 25 (161)
T ss_pred HHHHHHHHHHcCCceec
Confidence 67999999999999976
No 409
>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=44.44 E-value=78 Score=19.77 Aligned_cols=48 Identities=13% Similarity=0.197 Sum_probs=28.8
Q ss_pred hHHHHHHHHHhC-CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEc
Q psy3868 3 YRLTTLCRDSLG-AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFID 55 (69)
Q Consensus 3 T~la~aia~~~~-~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiD 55 (69)
|+++.++++=.| +.- +...++.++ ...+-++++.+...+....++|.|
T Consensus 13 TTva~aL~~LFg~wgH--vQnDnI~~k---~~~~f~~~~l~~L~~~~~~vViaD 61 (168)
T PF08303_consen 13 TTVALALSNLFGEWGH--VQNDNITGK---RKPKFIKAVLELLAKDTHPVVIAD 61 (168)
T ss_pred HHHHHHHHHHcCCCCc--cccCCCCCC---CHHHHHHHHHHHHhhCCCCEEEEe
Confidence 678888888877 433 455555443 345556666666644444555565
No 410
>cd04173 Rnd2_Rho7 Rnd2/Rho7 subfamily. Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/Rho7 failed to migrate to upper layers of the brain, suggesting that Rnd2/Rho7 plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/Rho7 degradation is necessary for proper cellular migration. The Rnd2/Rho7 GEF Rapostlin is found primarily in the brain and together with Rnd2/Rho7 induces dendrite branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction. Rnd2/Rho7 is also found to be expressed in sperma
Probab=44.22 E-value=34 Score=21.72 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHHHh
Q psy3868 4 RLTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEADK 46 (69)
Q Consensus 4 ~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a~~ 46 (69)
.-+..+|.+.|. +|++.++.+ ++..|+++|..|..
T Consensus 138 e~g~~~ak~~~~~~y~E~SAk~--------~~~~V~~~F~~~~~ 173 (222)
T cd04173 138 EQGTVLAKQVGAVSYVECSSRS--------SERSVRDVFHVATV 173 (222)
T ss_pred HHHHHHHHHcCCCEEEEcCCCc--------CCcCHHHHHHHHHH
Confidence 356778888885 899887743 12348889998854
No 411
>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=44.17 E-value=42 Score=22.33 Aligned_cols=23 Identities=13% Similarity=0.339 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhcCCeEEEEcccc
Q psy3868 36 NLRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 36 ~l~~if~~a~~~~p~iifiDEid 58 (69)
.+.++.+.+-+..|..|++.|+-
T Consensus 192 ~~~~~l~~aLR~~pD~iivGEiR 214 (299)
T TIGR02782 192 SMTRLLKATLRLRPDRIIVGEVR 214 (299)
T ss_pred CHHHHHHHHhcCCCCEEEEeccC
Confidence 56778888888899999999984
No 412
>TIGR01768 GGGP-family geranylgeranylglyceryl phosphate synthase family protein. This model represents a family of sequences including geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The clade of bacterial sequences may have the same function or a closely related function. This model supercedes TIGR00265, which has been retired.
Probab=44.06 E-value=73 Score=20.63 Aligned_cols=44 Identities=20% Similarity=0.310 Sum_probs=31.6
Q ss_pred HhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc-CCeEEEEccccccc
Q psy3868 12 SLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN-SPSIIFIDELDAIA 61 (69)
Q Consensus 12 ~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~-~p~iifiDEid~i~ 61 (69)
+.|...+.+.+++ |.+..++.++.+..++. -|++||.=..+.+.
T Consensus 25 ~~gtdai~vGGS~------~vt~~~~~~~v~~ik~~~lPvilfp~~~~~i~ 69 (223)
T TIGR01768 25 ESGTDAILIGGSQ------GVTYEKTDTLIEALRRYGLPIILFPSNPTNVS 69 (223)
T ss_pred hcCCCEEEEcCCC------cccHHHHHHHHHHHhccCCCEEEeCCCccccC
Confidence 4477888887665 45777888888888764 59999886655544
No 413
>cd02812 PcrB_like PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.
Probab=43.88 E-value=87 Score=20.19 Aligned_cols=50 Identities=16% Similarity=0.310 Sum_probs=32.3
Q ss_pred HHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 8 LCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 8 aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
.++.+.|...+.+.+++=.. ++..++-++.++.++.-|+++|.=..+.+.
T Consensus 19 ~~~~~~gtdai~vGGS~~v~----~~~~~~~~~ik~~~~~~Pvilfp~~~~~i~ 68 (219)
T cd02812 19 KLAEESGTDAIMVGGSDGVS----STLDNVVRLIKRIRRPVPVILFPSNPEAVS 68 (219)
T ss_pred HHHHhcCCCEEEECCccchh----hhHHHHHHHHHHhcCCCCEEEeCCCccccC
Confidence 45666789999998876221 344555555555544469999987766553
No 414
>KOG1359|consensus
Probab=43.85 E-value=28 Score=24.24 Aligned_cols=24 Identities=33% Similarity=0.408 Sum_probs=17.5
Q ss_pred HHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 36 NLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 36 ~l~~if~~a~~~~p~iifiDEid~i 60 (69)
-+.++-+.+++ ...++||||+|+=
T Consensus 211 Pl~ei~~La~k-YgaLlfiDecHaT 234 (417)
T KOG1359|consen 211 PLEEISQLAKK-YGALLFIDECHAT 234 (417)
T ss_pred cHHHHHHHHHh-cCcEEEEeecccc
Confidence 45566666655 4789999999974
No 415
>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=43.70 E-value=84 Score=22.28 Aligned_cols=27 Identities=15% Similarity=0.364 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 36 NLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 36 ~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
.+.++.+.+.+.+|.+++||.+-.+..
T Consensus 158 ~~~~I~~~i~~~~~~~vVIDSIq~l~~ 184 (454)
T TIGR00416 158 NWEQICANIEEENPQACVIDSIQTLYS 184 (454)
T ss_pred CHHHHHHHHHhcCCcEEEEecchhhcc
Confidence 355666666778899999999988764
No 416
>PRK00039 ruvC Holliday junction resolvase; Reviewed
Probab=43.16 E-value=21 Score=21.79 Aligned_cols=27 Identities=11% Similarity=0.037 Sum_probs=20.4
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChH
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGES 33 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges 33 (69)
...+...+.|+++.++..+-.-..|.+
T Consensus 90 ~la~~~~~ipv~ey~P~~VKk~vtG~G 116 (164)
T PRK00039 90 ILAAAQRGLPVAEYTPLQVKKAVVGYG 116 (164)
T ss_pred HHHHHHcCCCEEEECHHHhhhhhcCCC
Confidence 345667799999999999876655553
No 417
>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=43.06 E-value=41 Score=21.58 Aligned_cols=27 Identities=15% Similarity=0.176 Sum_probs=17.2
Q ss_pred HHHHHHHHHHh--cCCeEEEEcccccccc
Q psy3868 36 NLRKAFEEADK--NSPSIIFIDELDAIAP 62 (69)
Q Consensus 36 ~l~~if~~a~~--~~p~iifiDEid~i~~ 62 (69)
.+.+.+..+.. .....|+||.|+.+..
T Consensus 67 ~~~d~l~~~~~~~~~ydtVVIDsI~~l~~ 95 (220)
T TIGR01618 67 AMVEFYVMQNIQAVKYDNIVIDNISALQN 95 (220)
T ss_pred HHHHHHHHHHhccccCCEEEEecHHHHHH
Confidence 33444444332 4568999999998754
No 418
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=42.58 E-value=1e+02 Score=20.49 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEE
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFI 54 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifi 54 (69)
.|++-+.. .|.++..+. .+|+.+..|.+.+..+.+. +.+|++
T Consensus 25 ~la~~L~~-~G~~v~~~~-------~VgD~~~~I~~~l~~a~~r-~D~vI~ 66 (255)
T COG1058 25 FLADELTE-LGVDLARIT-------TVGDNPDRIVEALREASER-ADVVIT 66 (255)
T ss_pred HHHHHHHh-cCceEEEEE-------ecCCCHHHHHHHHHHHHhC-CCEEEE
Confidence 34444433 377766553 4899999999999999887 777765
No 419
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=42.40 E-value=77 Score=21.41 Aligned_cols=30 Identities=10% Similarity=0.203 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHh----cCCeEEEEcccccccc
Q psy3868 33 SESNLRKAFEEADK----NSPSIIFIDELDAIAP 62 (69)
Q Consensus 33 s~~~l~~if~~a~~----~~p~iifiDEid~i~~ 62 (69)
+...||++-+.+.. ....|++||++|.+-+
T Consensus 94 ~id~iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~ 127 (325)
T PRK08699 94 KIDAVREIIDNVYLTSVRGGLRVILIHPAESMNL 127 (325)
T ss_pred CHHHHHHHHHHHhhCcccCCceEEEEechhhCCH
Confidence 45678887777743 3457889999998854
No 420
>COG4671 Predicted glycosyl transferase [General function prediction only]
Probab=42.40 E-value=1.2e+02 Score=21.48 Aligned_cols=29 Identities=21% Similarity=0.348 Sum_probs=17.7
Q ss_pred hHHHHHHHHH-hCCcEEEEchhhhhhcccC
Q psy3868 3 YRLTTLCRDS-LGAFFFLINGPEIMSKLAG 31 (69)
Q Consensus 3 T~la~aia~~-~~~~~~~v~~~~l~~~~~g 31 (69)
+.+|+++..+ ++..++.++++.....+.+
T Consensus 29 ~~Ia~aLv~d~~~~~Il~IsG~~~~~~F~~ 58 (400)
T COG4671 29 LRIAHALVEDYLGFDILIISGGPPAGGFPG 58 (400)
T ss_pred HHHHHHHhhcccCceEEEEeCCCccCCCCC
Confidence 4566666666 3566677777666555444
No 421
>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=42.31 E-value=25 Score=21.99 Aligned_cols=20 Identities=25% Similarity=0.434 Sum_probs=13.7
Q ss_pred HHHHHHHHHHhcCCeEEEEccc
Q psy3868 36 NLRKAFEEADKNSPSIIFIDEL 57 (69)
Q Consensus 36 ~l~~if~~a~~~~p~iifiDEi 57 (69)
++..++.. ...|.++++||.
T Consensus 98 ~~~~il~~--~~~~~lvllDE~ 117 (204)
T cd03282 98 ETAYILDY--ADGDSLVLIDEL 117 (204)
T ss_pred HHHHHHHh--cCCCcEEEeccc
Confidence 34455443 356899999996
No 422
>PRK05057 aroK shikimate kinase I; Reviewed
Probab=42.29 E-value=28 Score=20.95 Aligned_cols=20 Identities=10% Similarity=0.071 Sum_probs=17.2
Q ss_pred hHHHHHHHHHhCCcEEEEch
Q psy3868 3 YRLTTLCRDSLGAFFFLING 22 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~ 22 (69)
|++++.+|+.++.+++..+.
T Consensus 18 Stl~~~La~~l~~~~vd~D~ 37 (172)
T PRK05057 18 STIGRQLAQQLNMEFYDSDQ 37 (172)
T ss_pred HHHHHHHHHHcCCcEEECCc
Confidence 68999999999999887764
No 423
>PLN02234 1-deoxy-D-xylulose-5-phosphate synthase
Probab=42.25 E-value=66 Score=24.08 Aligned_cols=38 Identities=21% Similarity=0.425 Sum_probs=28.5
Q ss_pred HHHHhCCcEE-EEchhhhhhcccChHHHHHHHHHHHHHhc---CCeEEEEc
Q psy3868 9 CRDSLGAFFF-LINGPEIMSKLAGESESNLRKAFEEADKN---SPSIIFID 55 (69)
Q Consensus 9 ia~~~~~~~~-~v~~~~l~~~~~ges~~~l~~if~~a~~~---~p~iifiD 55 (69)
.-.++|+.++ .+++.++ ..|.++|+.++.. +|.+|...
T Consensus 278 ~fe~fG~~~~g~vDGHd~---------~~l~~al~~~k~~~~~~P~vI~~~ 319 (641)
T PLN02234 278 LFEELGFHYVGPVDGHNI---------DDLVSILETLKSTKTIGPVLIHVV 319 (641)
T ss_pred HHHHcCCEEEeeECCCCH---------HHHHHHHHHHHhcCCCCCEEEEEE
Confidence 3456788888 8888776 5788888888753 68888765
No 424
>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=42.24 E-value=65 Score=20.18 Aligned_cols=18 Identities=22% Similarity=0.340 Sum_probs=11.0
Q ss_pred HHHHHhcCCeEEEEcccc
Q psy3868 41 FEEADKNSPSIIFIDELD 58 (69)
Q Consensus 41 f~~a~~~~p~iifiDEid 58 (69)
+..+--..|.++++||--
T Consensus 146 laral~~~p~llllDEPt 163 (242)
T cd03295 146 VARALAADPPLLLMDEPF 163 (242)
T ss_pred HHHHHhcCCCEEEecCCc
Confidence 333334677888888753
No 425
>cd08769 DAP_dppA_2 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacteriz
Probab=42.15 E-value=78 Score=21.12 Aligned_cols=22 Identities=14% Similarity=0.229 Sum_probs=18.5
Q ss_pred HHHHHHHHHhCCcEEEEchhhh
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEI 25 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l 25 (69)
.|--++|.+.|+|+..|++.+.
T Consensus 137 ~lNa~~Ag~~gVPV~lVsGDd~ 158 (270)
T cd08769 137 LINAAYAGEFGVPVVLVAGDSE 158 (270)
T ss_pred HHHHHHHhhcCCCEEEEecCHH
Confidence 4566899999999999998765
No 426
>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=42.10 E-value=70 Score=21.49 Aligned_cols=16 Identities=25% Similarity=0.451 Sum_probs=13.4
Q ss_pred CCeEEEEccccccccc
Q psy3868 48 SPSIIFIDELDAIAPK 63 (69)
Q Consensus 48 ~p~iifiDEid~i~~~ 63 (69)
.-.+|++||.+.+..+
T Consensus 83 ~~DviivDEAqrl~~~ 98 (352)
T PF09848_consen 83 KYDVIIVDEAQRLRTK 98 (352)
T ss_pred cCCEEEEehhHhhhhc
Confidence 3589999999999874
No 427
>COG1129 MglA ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]
Probab=42.06 E-value=38 Score=24.64 Aligned_cols=50 Identities=20% Similarity=0.305 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHH---HhcCCeEEEE----ccccccc
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEA---DKNSPSIIFI----DELDAIA 61 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a---~~~~p~iifi----DEid~i~ 61 (69)
+|||++. +..++.++-++- .=+++..+.+|+.. ++..-+|||| ||+-.+|
T Consensus 156 IArAl~~--~arllIlDEPTa-----aLt~~E~~~Lf~~ir~Lk~~Gv~ii~ISHrl~Ei~~i~ 212 (500)
T COG1129 156 IARALSF--DARVLILDEPTA-----ALTVKETERLFDLIRRLKAQGVAIIYISHRLDEVFEIA 212 (500)
T ss_pred HHHHHhc--CCCEEEEcCCcc-----cCCHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHHHhc
Confidence 5566655 344555554331 11344555555554 4466788887 6665554
No 428
>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []. The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.
Probab=41.99 E-value=1e+02 Score=20.34 Aligned_cols=58 Identities=14% Similarity=0.222 Sum_probs=31.4
Q ss_pred hHHHHHHHHH---hCCcEEEEchhhhh-hc--c-cChHHHHHHHHHHHHHh---cCCeEEEEcccccc
Q psy3868 3 YRLTTLCRDS---LGAFFFLINGPEIM-SK--L-AGESESNLRKAFEEADK---NSPSIIFIDELDAI 60 (69)
Q Consensus 3 T~la~aia~~---~~~~~~~v~~~~l~-~~--~-~ges~~~l~~if~~a~~---~~p~iifiDEid~i 60 (69)
|++|+.++.. .+..+..++-..+. .. | -...|+.+|..+..+.. .+..|+++|+.-.+
T Consensus 15 Tt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls~~~iVI~Dd~nYi 82 (270)
T PF08433_consen 15 TTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALSKDTIVILDDNNYI 82 (270)
T ss_dssp HHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHTT-SEEEE-S---S
T ss_pred HHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhccCeEEEEeCCchH
Confidence 5677777765 45777778766654 11 2 23458887777766643 45688889986544
No 429
>PF06048 DUF927: Domain of unknown function (DUF927); InterPro: IPR009270 This entry is represented by Bacteriophage PT1028, Orf1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=41.92 E-value=57 Score=21.42 Aligned_cols=49 Identities=12% Similarity=0.112 Sum_probs=26.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
|++.+..+.-+|.|- .+...|-+ |..- +=..|..+....+++||+...-
T Consensus 207 Tt~~~~a~Sv~G~p~------~l~~sw~~-T~n~---le~~a~~~nd~~l~lDE~~~~~ 255 (286)
T PF06048_consen 207 TTALQLAASVWGNPD------GLIRSWNS-TDNG---LERTAAAHNDLPLVLDELSQAD 255 (286)
T ss_pred HHHHHHhhhhCcCch------hhhhcchh-hHHH---HHHHHHHcCCcceEehhccccc
Confidence 344555555555544 33344433 2222 2223445678899999987643
No 430
>PRK09064 5-aminolevulinate synthase; Validated
Probab=41.61 E-value=34 Score=23.10 Aligned_cols=24 Identities=25% Similarity=0.501 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 36 NLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 36 ~l~~if~~a~~~~p~iifiDEid~i 60 (69)
.++++.+.++++ ..+|++||++.+
T Consensus 196 ~l~~i~~l~~~~-~~~livDEa~~~ 219 (407)
T PRK09064 196 PIAEICDLADKY-NALTYLDEVHAV 219 (407)
T ss_pred CHHHHHHHHHHc-CCEEEEECCCcc
Confidence 367777777665 689999999983
No 431
>KOG0451|consensus
Probab=41.59 E-value=37 Score=25.67 Aligned_cols=54 Identities=20% Similarity=0.186 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccccc
Q psy3868 2 SYRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~~r 64 (69)
||.-+.-||+..++|++.||+.+ +.|-.+.-|-.|+.-++.+..|+ ||-.|-+|
T Consensus 374 Ss~ycsDiaK~~~~pviHVNGD~-----PEevvraTrLAf~Yqr~FRKDvf----IdL~CfRr 427 (913)
T KOG0451|consen 374 SSAYCSDIAKSIQAPVIHVNGDD-----PEEVVRATRLAFRYQREFRKDVF----IDLNCFRR 427 (913)
T ss_pred cchhhhHHHHHhCCCEEEeCCCC-----HHHHHHHHHHHHHHHHHhhhhhe----eehHHHHH
Confidence 45556778889999999999865 23445556667777777666665 55666555
No 432
>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=41.47 E-value=65 Score=18.03 Aligned_cols=27 Identities=33% Similarity=0.413 Sum_probs=19.8
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccC
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAG 31 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~g 31 (69)
|++++.+++.++ ...++...+.....+
T Consensus 13 St~a~~l~~~~~--~~~i~~D~~~~~~~~ 39 (143)
T PF13671_consen 13 STLAKRLAKRLG--AVVISQDEIRRRLAG 39 (143)
T ss_dssp HHHHHHHHHHST--EEEEEHHHHHHHHCC
T ss_pred HHHHHHHHHHCC--CEEEeHHHHHHHHcc
Confidence 789999999988 555777776655444
No 433
>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=41.13 E-value=65 Score=18.96 Aligned_cols=22 Identities=5% Similarity=0.040 Sum_probs=15.9
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIM 26 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~ 26 (69)
|++++.++.++|.+. ++.++++
T Consensus 17 sTl~~~l~~~~g~~~--~~~g~~~ 38 (188)
T TIGR01360 17 GTQCEKIVEKYGFTH--LSTGDLL 38 (188)
T ss_pred HHHHHHHHHHhCCcE--EeHHHHH
Confidence 688999999988665 4554444
No 434
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=41.04 E-value=37 Score=25.18 Aligned_cols=37 Identities=24% Similarity=0.310 Sum_probs=28.2
Q ss_pred CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 15 AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 15 ~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
..+++++|..+.+. .+++..+...-+.+.|||.|.+.
T Consensus 108 ~klLyisPErl~~~----------~f~~~L~~~~i~l~vIDEAHCiS 144 (590)
T COG0514 108 LKLLYISPERLMSP----------RFLELLKRLPISLVAIDEAHCIS 144 (590)
T ss_pred eeEEEECchhhcCh----------HHHHHHHhCCCceEEechHHHHh
Confidence 58889999888543 35555556788999999999874
No 435
>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=40.99 E-value=45 Score=21.17 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=16.2
Q ss_pred HHHhcCCeEEEEccccccccc
Q psy3868 43 EADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 43 ~a~~~~p~iifiDEid~i~~~ 63 (69)
.++...|.+|+||.+..+...
T Consensus 135 ~~~~~~~~~vvID~l~~l~~~ 155 (271)
T cd01122 135 MAVSHGIQHIIIDNLSIMVSD 155 (271)
T ss_pred HHhcCCceEEEECCHHHHhcc
Confidence 344568999999999988654
No 436
>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=40.90 E-value=56 Score=21.52 Aligned_cols=51 Identities=22% Similarity=0.283 Sum_probs=32.2
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChH--HHHHHHHHHHHH-hcCCeEEEEccc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGES--ESNLRKAFEEAD-KNSPSIIFIDEL 57 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges--~~~l~~if~~a~-~~~p~iifiDEi 57 (69)
.++++..|.-.+..++.+..+. ..|.. ...+++++..|- +.+|.+++++|-
T Consensus 45 ~sl~rLaa~i~~~~~~~i~~~~----~y~~~~f~~dLk~~~~~ag~~~~~~vfll~d~ 98 (268)
T PF12780_consen 45 QSLARLAAFICGYEVFQIEITK----GYSIKDFKEDLKKALQKAGIKGKPTVFLLTDS 98 (268)
T ss_dssp HHHHHHHHHHTTEEEE-TTTST----TTHHHHHHHHHHHHHHHHHCS-S-EEEEEECC
T ss_pred HHHHHHHHHHhccceEEEEeeC----CcCHHHHHHHHHHHHHHHhccCCCeEEEecCc
Confidence 4578877888888888886542 22222 345778877764 467899988774
No 437
>PF11760 CbiG_N: Cobalamin synthesis G N-terminal; InterPro: IPR021744 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process []. Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B. The N-terminal of the enzyme is conserved in this family, and the C-terminal and the mid-sections are conserved independently in other families, CbiG_C and CbiG_mid, although the distinct function of each region is unclear. ; PDB: 3EEQ_B.
Probab=40.60 E-value=58 Score=17.94 Aligned_cols=28 Identities=14% Similarity=0.190 Sum_probs=14.4
Q ss_pred ChHHHHHHHHHHHHH--hcCCeEEEEcccc
Q psy3868 31 GESESNLRKAFEEAD--KNSPSIIFIDELD 58 (69)
Q Consensus 31 ges~~~l~~if~~a~--~~~p~iifiDEid 58 (69)
+...-.+|.+-...+ ..-|.||.+||--
T Consensus 19 ~A~GivvR~iap~l~dK~~DPaVvvvde~g 48 (84)
T PF11760_consen 19 MAAGIVVRAIAPLLKDKDTDPAVVVVDEDG 48 (84)
T ss_dssp S-HHHHHHHHHHH---TTT--EEEEE-TT-
T ss_pred eCcHHHHHHhChhhcccCCCCCEEEEeCCC
Confidence 344556666666553 3579999999953
No 438
>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam
Probab=40.58 E-value=35 Score=21.43 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=9.9
Q ss_pred cCCeEEEEccc
Q psy3868 47 NSPSIIFIDEL 57 (69)
Q Consensus 47 ~~p~iifiDEi 57 (69)
..|.++++||.
T Consensus 108 ~~~~llllDEp 118 (216)
T cd03284 108 TERSLVLLDEI 118 (216)
T ss_pred CCCeEEEEecC
Confidence 57999999996
No 439
>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]
Probab=40.55 E-value=29 Score=23.40 Aligned_cols=21 Identities=24% Similarity=0.439 Sum_probs=16.0
Q ss_pred HHHHHHHhcCCeEEEEccccc
Q psy3868 39 KAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 39 ~if~~a~~~~p~iifiDEid~ 59 (69)
-+....++..|-++++|||-.
T Consensus 209 gmmmaIrsm~PEViIvDEIGt 229 (308)
T COG3854 209 GMMMAIRSMSPEVIIVDEIGT 229 (308)
T ss_pred HHHHHHHhcCCcEEEEecccc
Confidence 344455778999999999854
No 440
>PRK09404 sucA 2-oxoglutarate dehydrogenase E1 component; Reviewed
Probab=40.53 E-value=85 Score=24.62 Aligned_cols=51 Identities=24% Similarity=0.213 Sum_probs=34.8
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhc-CCeEEEEccccccccccccC
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN-SPSIIFIDELDAIAPKREKR 67 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~-~p~iifiDEid~i~~~r~~~ 67 (69)
-.+|...+.|.+.||+.+... .-..++...+.+++. +|.+| |.++-++.+.
T Consensus 402 sd~Ak~~giP~~~VDG~D~~A-----V~~a~~~A~e~~r~g~gPvlI-----E~~tYR~~GH 453 (924)
T PRK09404 402 TDVAKMVQAPIFHVNGDDPEA-----VVFATRLALEYRQKFKKDVVI-----DLVCYRRHGH 453 (924)
T ss_pred HHHHeecCCcEEEEcCCCHHH-----HHHHHHHHHHHHHhcCcCEEE-----EEEEecCCCC
Confidence 346677789999999988742 345566677777764 56655 7777666553
No 441
>cd04133 Rop_like Rop subfamily. The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example,
Probab=40.22 E-value=44 Score=20.15 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=25.2
Q ss_pred hHHHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHHHh
Q psy3868 3 YRLTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEADK 46 (69)
Q Consensus 3 T~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a~~ 46 (69)
+.-++.+|.+.+. +|+++++.+ ..+|+++|+.+.+
T Consensus 135 ~~~~~~~a~~~~~~~~~E~SAk~---------~~nV~~~F~~~~~ 170 (176)
T cd04133 135 TAQGEELRKQIGAAAYIECSSKT---------QQNVKAVFDAAIK 170 (176)
T ss_pred HHHHHHHHHHcCCCEEEECCCCc---------ccCHHHHHHHHHH
Confidence 3356778888887 688887753 3468888988754
No 442
>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign
Probab=40.20 E-value=40 Score=19.94 Aligned_cols=20 Identities=10% Similarity=0.044 Sum_probs=13.0
Q ss_pred HHHHHHHHHhCCcEEEEchh
Q psy3868 4 RLTTLCRDSLGAFFFLINGP 23 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~ 23 (69)
.-++.+|++.+++++++++.
T Consensus 128 ~~~~~~a~~~~~~~~e~Sa~ 147 (172)
T cd04141 128 EEGRNLAREFNCPFFETSAA 147 (172)
T ss_pred HHHHHHHHHhCCEEEEEecC
Confidence 34556666777777777664
No 443
>PF13521 AAA_28: AAA domain; PDB: 1LW7_A.
Probab=40.20 E-value=77 Score=18.50 Aligned_cols=25 Identities=16% Similarity=0.041 Sum_probs=16.4
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhc
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSK 28 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~ 28 (69)
|+|++.+++. |.+++.=.+..+...
T Consensus 13 TTL~~~L~~~-g~~~v~E~ar~~~~~ 37 (163)
T PF13521_consen 13 TTLIEALAAR-GYPVVPEYAREIIEE 37 (163)
T ss_dssp HHHHHHHHHH-T-EEE--TTHHHHHH
T ss_pred HHHHHHHHHc-CCeEEeecHHHHHHH
Confidence 7889999988 988886555555533
No 444
>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=39.78 E-value=58 Score=19.34 Aligned_cols=19 Identities=21% Similarity=0.457 Sum_probs=13.6
Q ss_pred HHHHHhcCCeEEEEccccc
Q psy3868 41 FEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 41 f~~a~~~~p~iifiDEid~ 59 (69)
+..+-...|.++++||--+
T Consensus 106 laral~~~p~illlDEPt~ 124 (173)
T cd03230 106 LAQALLHDPELLILDEPTS 124 (173)
T ss_pred HHHHHHcCCCEEEEeCCcc
Confidence 4444457899999999643
No 445
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=39.77 E-value=43 Score=22.75 Aligned_cols=30 Identities=10% Similarity=0.330 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHH----hcCCeEEEEcccccccc
Q psy3868 33 SESNLRKAFEEAD----KNSPSIIFIDELDAIAP 62 (69)
Q Consensus 33 s~~~l~~if~~a~----~~~p~iifiDEid~i~~ 62 (69)
+...+|++-+.+. ..+--|++||++|.+-.
T Consensus 88 ~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~ 121 (325)
T PRK06871 88 GVDQVREINEKVSQHAQQGGNKVVYIQGAERLTE 121 (325)
T ss_pred CHHHHHHHHHHHhhccccCCceEEEEechhhhCH
Confidence 4556777655553 23457999999999864
No 446
>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=39.75 E-value=62 Score=24.05 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=23.8
Q ss_pred CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 15 AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 15 ~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
+.++..+-.-++++ .+|+.+. .....+||+|||.|.|-.
T Consensus 196 advIi~pYnyl~dp-------~~r~~~~--~~l~~~ivI~DEAHNL~d 234 (705)
T TIGR00604 196 ANIVLLPYQYLLDP-------KIRSAVS--IELKDSIVIFDEAHNLDN 234 (705)
T ss_pred CCEEEechHHhcCH-------HHHHHhh--cccccCEEEEECccchHH
Confidence 44555555556543 3333343 235679999999998853
No 447
>PRK09401 reverse gyrase; Reviewed
Probab=39.71 E-value=26 Score=27.88 Aligned_cols=29 Identities=31% Similarity=0.552 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
...+.+.++......-..+++||+|.+..
T Consensus 187 p~rL~~~~~~l~~~~~~~lVvDEaD~~L~ 215 (1176)
T PRK09401 187 SQFLSKNFDELPKKKFDFVFVDDVDAVLK 215 (1176)
T ss_pred HHHHHHHHHhccccccCEEEEEChHHhhh
Confidence 33444444433334478899999999875
No 448
>cd03769 SR_IS607_transposase_like Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.
Probab=39.63 E-value=38 Score=19.67 Aligned_cols=30 Identities=20% Similarity=0.143 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhcCCeEEEEccccccccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELDAIAPK 63 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid~i~~~ 63 (69)
-..+.++.+.++.....+|++.++|.|++.
T Consensus 48 Rp~l~~ll~~i~~g~~d~lvV~~ldRl~R~ 77 (134)
T cd03769 48 RKGLLKLLEDVLAGKVERVVITYKDRLARF 77 (134)
T ss_pred CHHHHHHHHHHHcCCCCEEEEEeccHHHHh
Confidence 355788888887776679999999999864
No 449
>PRK13809 orotate phosphoribosyltransferase; Provisional
Probab=39.45 E-value=29 Score=22.00 Aligned_cols=19 Identities=16% Similarity=-0.034 Sum_probs=15.8
Q ss_pred HHHHHHHHHhCCcEEEEch
Q psy3868 4 RLTTLCRDSLGAFFFLING 22 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~ 22 (69)
-+|.++|.+++.|+..+..
T Consensus 80 ~~A~~vA~~l~~p~~~~RK 98 (206)
T PRK13809 80 TLATSISLKYNIPMVLRRK 98 (206)
T ss_pred HHHHHHHHHhCCCEEEEeC
Confidence 4788889999999988765
No 450
>PLN02955 8-amino-7-oxononanoate synthase
Probab=39.38 E-value=37 Score=24.45 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=18.0
Q ss_pred HHHHHHHHHhcCCeEEEEccccccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
+.++-+.++++ .+.|++||.+.++
T Consensus 268 L~eL~~L~~~~-ga~LiVDEAH~~G 291 (476)
T PLN02955 268 MEELSQLRKKY-GFLLVIDDAHGTF 291 (476)
T ss_pred HHHHHHHHHHc-CcEEEEcccccCc
Confidence 55666666554 6999999999965
No 451
>TIGR01166 cbiO cobalt transport protein ATP-binding subunit. This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.
Probab=39.32 E-value=59 Score=19.53 Aligned_cols=15 Identities=27% Similarity=0.479 Sum_probs=11.3
Q ss_pred HHhcCCeEEEEcccc
Q psy3868 44 ADKNSPSIIFIDELD 58 (69)
Q Consensus 44 a~~~~p~iifiDEid 58 (69)
|-...|.++++||--
T Consensus 141 al~~~p~llllDEPt 155 (190)
T TIGR01166 141 AVAMRPDVLLLDEPT 155 (190)
T ss_pred HHhcCCCEEEEcCCc
Confidence 334679999999953
No 452
>PRK09112 DNA polymerase III subunit delta'; Validated
Probab=39.23 E-value=24 Score=24.12 Aligned_cols=28 Identities=18% Similarity=0.236 Sum_probs=18.4
Q ss_pred HHHHHHHHHHH----hcCCeEEEEcccccccc
Q psy3868 35 SNLRKAFEEAD----KNSPSIIFIDELDAIAP 62 (69)
Q Consensus 35 ~~l~~if~~a~----~~~p~iifiDEid~i~~ 62 (69)
..+|++-+... ..+..|++|||+|.+-.
T Consensus 124 d~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~ 155 (351)
T PRK09112 124 DEIRRVGHFLSQTSGDGNWRIVIIDPADDMNR 155 (351)
T ss_pred HHHHHHHHHhhhccccCCceEEEEEchhhcCH
Confidence 44555544432 24567999999999854
No 453
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=39.21 E-value=68 Score=19.66 Aligned_cols=55 Identities=15% Similarity=0.126 Sum_probs=33.2
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChH---HHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGES---ESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges---~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
+-..+.+.+.|+++.++..+-....|.+ ..+|...-+..-......- -|+.|+|+
T Consensus 85 illa~~~~~ipv~Ey~P~~vKkavtG~G~A~KeQV~~mV~~lL~l~~~p~-~DaaDALA 142 (156)
T TIGR00228 85 AIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRRLLKLPANPQ-ADAADALA 142 (156)
T ss_pred HHHHHHHcCCCEEEECHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCCCCC-CCHHHHHH
Confidence 3455667799999999998866655553 2234444443322222112 58999875
No 454
>KOG2680|consensus
Probab=39.02 E-value=18 Score=25.29 Aligned_cols=41 Identities=29% Similarity=0.340 Sum_probs=30.6
Q ss_pred hHHHHHHHHHhC--CcEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLG--AFFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~--~~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
|.+|-.+++.+| .||..++++++++--...+|+. .+.|..+
T Consensus 80 tAiAmg~sksLG~~tpF~~i~gSEI~SlEmsKTEAl-tQAfRks 122 (454)
T KOG2680|consen 80 TAIAMGMSKSLGDDTPFTSISGSEIYSLEMSKTEAL-TQAFRKS 122 (454)
T ss_pred eeeeeehhhhhCCCCceeeeecceeeeecccHHHHH-HHHHHHh
Confidence 446667788887 6999999999998877777665 4455554
No 455
>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling []. Proteins this domain is found in include: AP endonuclease proteins (4.2.99.18 from EC), DNase I proteins (3.1.21.1 from EC), Synaptojanin an inositol-1,4,5-trisphosphate phosphatase (3.1.3.56 from EC) and Sphingomyelinase (3.1.4.12 from EC).; PDB: 2J63_A 2JC4_A 3TEB_B 3MTC_A 3N9V_B 1ZWX_A 2F1N_A 1Y21_A 1NTF_A 2IMQ_X ....
Probab=38.90 E-value=43 Score=19.78 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhcCCeEEEEcccc
Q psy3868 34 ESNLRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 34 ~~~l~~if~~a~~~~p~iifiDEid 58 (69)
.++.+++.+...+..|.||.+-|+.
T Consensus 15 ~~~~~~i~~~i~~~~~Dii~LQEv~ 39 (249)
T PF03372_consen 15 DRKRREIAQWIAELDPDIIALQEVR 39 (249)
T ss_dssp HHHHHHHHHHHHHHT-SEEEEEEEE
T ss_pred hhHHHHHHHHHHhcCCCEEEEecch
Confidence 4566778888888889999999997
No 456
>TIGR01090 apt adenine phosphoribosyltransferase. A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for this model and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage.
Probab=38.81 E-value=12 Score=22.56 Aligned_cols=19 Identities=16% Similarity=0.210 Sum_probs=14.6
Q ss_pred hHHHHHHHHHhCCcEEEEc
Q psy3868 3 YRLTTLCRDSLGAFFFLIN 21 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~ 21 (69)
-.+|..+|..++.|+..+.
T Consensus 58 ~~~A~~la~~L~~~~~~i~ 76 (169)
T TIGR01090 58 FIFGAALAYKLGVGFVPVR 76 (169)
T ss_pred HHHHHHHHHHHCCCEEEEE
Confidence 3578889999999876543
No 457
>TIGR02173 cyt_kin_arch cytidylate kinase, putative. Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.
Probab=38.73 E-value=32 Score=19.98 Aligned_cols=19 Identities=5% Similarity=0.072 Sum_probs=15.8
Q ss_pred hhHHHHHHHHHhCCcEEEE
Q psy3868 2 SYRLTTLCRDSLGAFFFLI 20 (69)
Q Consensus 2 ~T~la~aia~~~~~~~~~v 20 (69)
.|++++.+++.+|.+++..
T Consensus 13 Kstia~~la~~lg~~~~~~ 31 (171)
T TIGR02173 13 KTTVAKILAEKLSLKLISA 31 (171)
T ss_pred HHHHHHHHHHHcCCceecH
Confidence 3789999999999887654
No 458
>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=38.70 E-value=75 Score=21.23 Aligned_cols=18 Identities=28% Similarity=0.324 Sum_probs=11.1
Q ss_pred HHHHHHhcCCeEEEEccc
Q psy3868 40 AFEEADKNSPSIIFIDEL 57 (69)
Q Consensus 40 if~~a~~~~p~iifiDEi 57 (69)
.+..|-...|.+|++||-
T Consensus 186 aiAraL~~~p~iLLLDEP 203 (320)
T PRK13631 186 AIAGILAIQPEILIFDEP 203 (320)
T ss_pred HHHHHHHcCCCEEEEECC
Confidence 344444467777777774
No 459
>TIGR01821 5aminolev_synth 5-aminolevulinic acid synthase. This model represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives.
Probab=38.57 E-value=40 Score=22.75 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=18.1
Q ss_pred HHHHHHHHHhcCCeEEEEcccccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid~i 60 (69)
++++.+.++++ .+++++||++++
T Consensus 196 l~~i~~l~~~~-~~~livDea~~~ 218 (402)
T TIGR01821 196 IEEICDLADKY-GALTYLDEVHAV 218 (402)
T ss_pred HHHHHHHHHHc-CCEEEEeCcccc
Confidence 67777777665 689999999984
No 460
>PF00155 Aminotran_1_2: Aminotransferase class I and II 1-aminocyclopropane-1-carboxylate synthase signature aspartate aminotransferase signature; InterPro: IPR004839 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into class I and class II. This entry includes proteins from both subfamilies.; GO: 0016769 transferase activity, transferring nitrogenous groups, 0030170 pyridoxal phosphate binding, 0009058 biosynthetic process; PDB: 3NRA_B 3P6K_B 3OP7_A 3ASB_A 3ASA_A 1W7M_A 3FVX_A 1W7N_A 3FVU_B 3FVS_A ....
Probab=38.56 E-value=52 Score=21.54 Aligned_cols=29 Identities=31% Similarity=0.195 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEcccccccc
Q psy3868 33 SESNLRKAFEEADKNSPSIIFIDELDAIAP 62 (69)
Q Consensus 33 s~~~l~~if~~a~~~~p~iifiDEid~i~~ 62 (69)
+...++++.+.++++ ...|++||+.....
T Consensus 166 ~~~~l~~l~~~~~~~-~~~ii~De~y~~~~ 194 (363)
T PF00155_consen 166 SLEELRELAELAREY-NIIIIVDEAYSDLI 194 (363)
T ss_dssp -HHHHHHHHHHHHHT-TSEEEEEETTTTGB
T ss_pred ccccccchhhhhccc-ccceeeeeceeccc
Confidence 678899999998776 78888999987654
No 461
>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=38.45 E-value=50 Score=21.92 Aligned_cols=22 Identities=23% Similarity=0.350 Sum_probs=15.9
Q ss_pred HHHHHHHHHhcCCeEEEEcccc
Q psy3868 37 LRKAFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 37 l~~if~~a~~~~p~iifiDEid 58 (69)
=|-...+|-+..|.||++||--
T Consensus 156 QRLcIARalAv~PeVlLmDEPt 177 (253)
T COG1117 156 QRLCIARALAVKPEVLLMDEPT 177 (253)
T ss_pred HHHHHHHHHhcCCcEEEecCcc
Confidence 3445555666789999999953
No 462
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=38.23 E-value=39 Score=20.18 Aligned_cols=29 Identities=10% Similarity=0.053 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCcEEEEchhhhhhcccChH
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIMSKLAGES 33 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~~~~~ges 33 (69)
.+...+...+.|+++++|..+..-+.|.+
T Consensus 86 vi~~~~~~~~i~v~e~~P~~vKk~~tG~G 114 (154)
T cd00529 86 ALILALANRNLPVFEYTPNQVKKAVTGYG 114 (154)
T ss_pred HHHHHHHHcCCCEEEEccCeeEEEEECCC
Confidence 34456667799999999999877776764
No 463
>KOG1360|consensus
Probab=38.21 E-value=30 Score=25.03 Aligned_cols=25 Identities=32% Similarity=0.498 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 36 NLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 36 ~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
-|+++-+.|.++ .+|-|+||+++.+
T Consensus 321 pleelcDvah~y-GAiTFlDEVHAVG 345 (570)
T KOG1360|consen 321 PLEELCDVAHKY-GAITFLDEVHAVG 345 (570)
T ss_pred CHHHHHHHHHHh-Cceeeeehhhhhc
Confidence 356666666554 6899999999875
No 464
>PF01195 Pept_tRNA_hydro: Peptidyl-tRNA hydrolase; InterPro: IPR001328 Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis [, ]. Bacterial PTH has been found to be evolutionary related to a yeast protein [].; GO: 0004045 aminoacyl-tRNA hydrolase activity; PDB: 3KJZ_A 3KK0_A 3P2J_A 3V2I_A 3TCN_A 3TD6_A 2Z2K_A 3TD2_A 2Z2J_B 2JRC_A ....
Probab=38.18 E-value=34 Score=21.27 Aligned_cols=59 Identities=14% Similarity=0.112 Sum_probs=33.4
Q ss_pred hHHHHHHHHHhCCcEEEEch--hhh------------h--hcccChHHHHHHHHHHHHHh-cCCeEEEEccccccc
Q psy3868 3 YRLTTLCRDSLGAFFFLING--PEI------------M--SKLAGESESNLRKAFEEADK-NSPSIIFIDELDAIA 61 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~--~~l------------~--~~~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~ 61 (69)
-++...+|...+.++..-.. +.+ + ..|...|...|+++.+..+- ..-.+|+-||+|.=.
T Consensus 21 ~~~ld~la~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~KP~TyMN~SG~~V~~~~~~~~i~~~~ilVihDdldl~~ 96 (184)
T PF01195_consen 21 FMVLDRLASRLGLSWKQKKKFKSLISEGSIKGEKVILLKPQTYMNLSGKAVKKILSFYKIPPENILVIHDDLDLPL 96 (184)
T ss_dssp HHHHHHHHHHTT---EEEGGGTEEEEEEEETTEEEEEEEESSTGGGHHHHHHHHHHHTT--GGGEEEEEEETTSST
T ss_pred HHHHHHHHHHhCCCccccccceeEEEEEEEeeeeEEEEcCCCeEeCccHhHHHHHHHhCCCcceEEEEEeccCCCC
Confidence 45667777777654433321 000 0 13667788888888777643 234677779998644
No 465
>KOG0393|consensus
Probab=38.00 E-value=50 Score=21.08 Aligned_cols=35 Identities=17% Similarity=0.373 Sum_probs=23.8
Q ss_pred hHHHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHHHh
Q psy3868 3 YRLTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEADK 46 (69)
Q Consensus 3 T~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a~~ 46 (69)
+.=.+.+|+++|. .+++. +-+ +.+.++++|+.|..
T Consensus 141 ~~~g~~lA~~iga~~y~Ec--Sa~-------tq~~v~~vF~~a~~ 176 (198)
T KOG0393|consen 141 YEQGLELAKEIGAVKYLEC--SAL-------TQKGVKEVFDEAIR 176 (198)
T ss_pred HHHHHHHHHHhCcceeeee--hhh-------hhCCcHHHHHHHHH
Confidence 3456789999994 45544 444 34459999999865
No 466
>PF09370 TIM-br_sig_trns: TIM-barrel signal transduction protein; InterPro: IPR009215 Members of this family are predicted to have a TIM barrel fold, based on PSI-BLAST analysis (iteration 4) and on SCOP prediction (using SMART). Interestingly, this novel domain also exists as an N-terminal domain of sigma54-dependent transcriptional activators (enhancer-binding proteins). Because sigma54 dependent activators typically have a three-domain structure: the variable N-terminal regulatory (activation) domain involved in signal recognition/receiving, the central AAA-type ATPase domain, and the DNA-binding domain (see PIRSF003187 from PIRSF, PIRSF005263 from PIRSF, PIRSF003184 from PIRSF, PIRSF005263 from PIRSF, IPR014443 from INTERPRO for details), the proteins of the current entry may be predicted to play a role in signal recognition/receiving and signal transduction.; PDB: 2P10_C.
Probab=37.99 E-value=1.1e+02 Score=20.57 Aligned_cols=25 Identities=24% Similarity=0.494 Sum_probs=18.9
Q ss_pred cChHHHHHHHHHHHHHhcCCeEEEE
Q psy3868 30 AGESESNLRKAFEEADKNSPSIIFI 54 (69)
Q Consensus 30 ~ges~~~l~~if~~a~~~~p~iifi 54 (69)
+.+..+.++++++.+++..|.+|.+
T Consensus 194 l~~a~~~~~~i~~aa~~v~~dii~l 218 (268)
T PF09370_consen 194 LEEAAERIQEIFDAARAVNPDIIVL 218 (268)
T ss_dssp HHHHHHHHHHHHHHHHCC-TT-EEE
T ss_pred HHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 4457788999999999988888776
No 467
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=37.93 E-value=1.1e+02 Score=20.34 Aligned_cols=49 Identities=16% Similarity=0.231 Sum_probs=29.4
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEcccccc
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAI 60 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i 60 (69)
++++|.+.|.|++.++.... ...+.+.. +.+..++.+|.++++=-.-.+
T Consensus 129 ~~~lA~~~gIp~~~~~~~~~---~~~~~~~~---~~~~l~~~~~Dlivlagy~~i 177 (286)
T PRK06027 129 LRSLVERFGIPFHHVPVTKE---TKAEAEAR---LLELIDEYQPDLVVLARYMQI 177 (286)
T ss_pred HHHHHHHhCCCEEEeccCcc---ccchhHHH---HHHHHHHhCCCEEEEecchhh
Confidence 56779999999998866421 11122333 444455677888876544433
No 468
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=37.92 E-value=70 Score=19.33 Aligned_cols=34 Identities=29% Similarity=0.292 Sum_probs=23.1
Q ss_pred hHHHHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh
Q psy3868 3 YRLTTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK 46 (69)
Q Consensus 3 T~la~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~ 46 (69)
...+..+|.+.|.+.+.+.. +...++..++.|.+
T Consensus 132 g~~~~~~A~~~gl~~v~i~s----------g~esi~~Al~eA~~ 165 (176)
T PF06506_consen 132 GGVVCRLARKLGLPGVLIES----------GEESIRRALEEALR 165 (176)
T ss_dssp SHHHHHHHHHTTSEEEESS------------HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHcCCcEEEEEe----------cHHHHHHHHHHHHH
Confidence 34567788999999888755 34567777777653
No 469
>COG1489 SfsA DNA-binding protein, stimulates sugar fermentation [General function prediction only]
Probab=37.84 E-value=56 Score=21.48 Aligned_cols=49 Identities=14% Similarity=0.371 Sum_probs=33.1
Q ss_pred EEEEchhhhhhcccC--------hHHHHHHHHHHHHHh-cCCeEEEE---ccccccccccc
Q psy3868 17 FFLINGPEIMSKLAG--------ESESNLRKAFEEADK-NSPSIIFI---DELDAIAPKRE 65 (69)
Q Consensus 17 ~~~v~~~~l~~~~~g--------es~~~l~~if~~a~~-~~p~iifi---DEid~i~~~r~ 65 (69)
+++|.+-.+....+| .+.+-|+.+-+.+++ +++.++|+ ++++.+.+.+.
T Consensus 129 ~vEVK~vtL~~~~~a~FPDApT~RG~KHLreL~~~~~~G~ra~vlf~v~r~d~~~F~P~~e 189 (235)
T COG1489 129 YVEVKSVTLVENGVAMFPDAPTARGQKHLRELERLAKEGYRAVVLFLVLRSDITRFSPNRE 189 (235)
T ss_pred EEEEeeEEEeeCCEEECCCCcchhhHHHHHHHHHHHHcCCceEEEEEEecCCCcEECcccc
Confidence 355555444443333 367889999999988 56666666 78888887664
No 470
>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]
Probab=37.80 E-value=34 Score=22.20 Aligned_cols=31 Identities=13% Similarity=0.225 Sum_probs=20.4
Q ss_pred hHHHHHHHHHhCCcEEE--EchhhhhhcccChH
Q psy3868 3 YRLTTLCRDSLGAFFFL--INGPEIMSKLAGES 33 (69)
Q Consensus 3 T~la~aia~~~~~~~~~--v~~~~l~~~~~ges 33 (69)
|+||+++|++++.+.+. +.-..++.++..+.
T Consensus 18 STLa~~La~~l~~~~~~E~vednp~L~~FY~d~ 50 (216)
T COG1428 18 STLAQALAEHLGFKVFYELVEDNPFLDLFYEDP 50 (216)
T ss_pred HHHHHHHHHHhCCceeeecccCChHHHHHHHhH
Confidence 78999999999965543 33334455555443
No 471
>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=37.74 E-value=21 Score=19.75 Aligned_cols=13 Identities=15% Similarity=0.427 Sum_probs=8.5
Q ss_pred CeEEEEccccccc
Q psy3868 49 PSIIFIDELDAIA 61 (69)
Q Consensus 49 p~iifiDEid~i~ 61 (69)
..++++||+...-
T Consensus 50 q~vvi~DD~~~~~ 62 (107)
T PF00910_consen 50 QPVVIIDDFGQDN 62 (107)
T ss_pred CcEEEEeecCccc
Confidence 3556688877654
No 472
>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=37.59 E-value=38 Score=22.45 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHhcCCeEEEEccccc
Q psy3868 35 SNLRKAFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 35 ~~l~~if~~a~~~~p~iifiDEid~ 59 (69)
-.+.+++..+-+..|.+|++||+-.
T Consensus 205 ~~~~~~l~~~Lr~~pd~ii~gE~r~ 229 (308)
T TIGR02788 205 VTPKDLLQSCLRMRPDRIILGELRG 229 (308)
T ss_pred cCHHHHHHHHhcCCCCeEEEeccCC
Confidence 3467788878788999999999853
No 473
>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
Probab=37.51 E-value=62 Score=19.70 Aligned_cols=16 Identities=19% Similarity=0.233 Sum_probs=11.7
Q ss_pred HHHhcCCeEEEEcccc
Q psy3868 43 EADKNSPSIIFIDELD 58 (69)
Q Consensus 43 ~a~~~~p~iifiDEid 58 (69)
.+-...|.++++||--
T Consensus 139 ral~~~p~llllDEPt 154 (205)
T cd03226 139 AALLSGKDLLIFDEPT 154 (205)
T ss_pred HHHHhCCCEEEEeCCC
Confidence 3334689999999953
No 474
>PF03054 tRNA_Me_trans: tRNA methyl transferase; InterPro: IPR004506 tRNA-specific 2-thiouridylase catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34.; GO: 0016740 transferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 2DET_A 2DER_A 2DEU_A 2HMA_A.
Probab=37.46 E-value=37 Score=23.44 Aligned_cols=22 Identities=14% Similarity=0.179 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCcEEEEchhhhh
Q psy3868 5 LTTLCRDSLGAFFFLINGPEIM 26 (69)
Q Consensus 5 la~aia~~~~~~~~~v~~~~l~ 26 (69)
-|+.+|+.+|.|++.++..+.+
T Consensus 53 ~a~~va~~LgIp~~v~d~~~~f 74 (356)
T PF03054_consen 53 DARRVAEKLGIPHYVVDLREEF 74 (356)
T ss_dssp HHHHHHHHHT--EEEEETHHHH
T ss_pred HHHHHHHhcCCCEEEEChHHHH
Confidence 4889999999999999997764
No 475
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=37.42 E-value=45 Score=20.20 Aligned_cols=22 Identities=18% Similarity=0.478 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHhcCCeEEEE
Q psy3868 33 SESNLRKAFEEADKNSPSIIFI 54 (69)
Q Consensus 33 s~~~l~~if~~a~~~~p~iifi 54 (69)
.+...+++.+..++..|.+||+
T Consensus 86 ~~~~~~~i~~~I~~~~pdiv~v 107 (172)
T PF03808_consen 86 DEEEEEAIINRINASGPDIVFV 107 (172)
T ss_pred ChhhHHHHHHHHHHcCCCEEEE
Confidence 3445556666666667777664
No 476
>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily. Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho 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 most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=37.31 E-value=53 Score=21.04 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=23.2
Q ss_pred hHHHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 3 YRLTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 3 T~la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
+--++.+|.+.+. +|+++|+-+ | +.+|.++|..+
T Consensus 149 ~~e~~~~a~~~~~~~~~EtSAkt------g--~~~V~e~F~~~ 183 (232)
T cd04174 149 YEQGCALAKQLGAEVYLECSAFT------S--EKSIHSIFRSA 183 (232)
T ss_pred HHHHHHHHHHcCCCEEEEccCCc------C--CcCHHHHHHHH
Confidence 3457889999998 688887742 1 22577777765
No 477
>PRK05647 purN phosphoribosylglycinamide formyltransferase; Reviewed
Probab=37.27 E-value=1.1e+02 Score=19.25 Aligned_cols=51 Identities=16% Similarity=0.200 Sum_probs=29.7
Q ss_pred HHHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEEEccccccc
Q psy3868 6 TTLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 61 (69)
Q Consensus 6 a~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iifiDEid~i~ 61 (69)
++..|.+.|+|++.++..++-++ +..=.++.+..+..+|.++++=-...+.
T Consensus 43 ~~~~a~~~gIp~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~D~iv~~~~~~ii 93 (200)
T PRK05647 43 GLERAEAAGIPTFVLDHKDFPSR-----EAFDAALVEALDAYQPDLVVLAGFMRIL 93 (200)
T ss_pred HHHHHHHcCCCEEEECccccCch-----hHhHHHHHHHHHHhCcCEEEhHHhhhhC
Confidence 46778899999988876554211 1111134444556678888765444333
No 478
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.24 E-value=36 Score=24.26 Aligned_cols=31 Identities=13% Similarity=0.344 Sum_probs=25.0
Q ss_pred hhhhhcccChHHHHHHHHHHHHHhcCCeEEE
Q psy3868 23 PEIMSKLAGESESNLRKAFEEADKNSPSIIF 53 (69)
Q Consensus 23 ~~l~~~~~ges~~~l~~if~~a~~~~p~iif 53 (69)
++++-+|+|||+....+..+..++.++.-++
T Consensus 300 tDiIVGFPgETeedFe~tl~lv~e~~fd~~~ 330 (437)
T COG0621 300 TDIIVGFPGETEEDFEETLDLVEEVRFDRLH 330 (437)
T ss_pred ccEEEECCCCCHHHHHHHHHHHHHhCCCEEe
Confidence 4566789999999999999999887766554
No 479
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=37.21 E-value=1.1e+02 Score=19.43 Aligned_cols=44 Identities=11% Similarity=0.368 Sum_probs=26.1
Q ss_pred CCcEEEEchhhhhhcccChHHHHHHHHHHHHHh--cCCeEEEEcccccccccc
Q psy3868 14 GAFFFLINGPEIMSKLAGESESNLRKAFEEADK--NSPSIIFIDELDAIAPKR 64 (69)
Q Consensus 14 ~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~--~~p~iifiDEid~i~~~r 64 (69)
..+++..+.+.+ +...|+......+. ....+||||-++.+-..+
T Consensus 101 ~~~l~i~~~~~~-------~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~ 146 (259)
T PF03796_consen 101 DLPLYIEDTPSL-------TIDDIESKIRRLKREGKKVDVVFIDYLQLLKSED 146 (259)
T ss_dssp TSEEEEEESSS--------BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSC
T ss_pred hCcEEEECCCCC-------CHHHHHHHHHHHHhhccCCCEEEechHHHhcCCC
Confidence 455555444332 44455555544433 466799999999887743
No 480
>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]
Probab=37.12 E-value=42 Score=25.00 Aligned_cols=20 Identities=30% Similarity=0.514 Sum_probs=15.4
Q ss_pred HHHHHHhcCCeEEEEccccc
Q psy3868 40 AFEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 40 if~~a~~~~p~iifiDEid~ 59 (69)
.|.+.-=++|.++|+||.=+
T Consensus 525 afARilL~kP~~v~LDEATs 544 (604)
T COG4178 525 AFARLLLHKPKWVFLDEATS 544 (604)
T ss_pred HHHHHHHcCCCEEEEecchh
Confidence 56555568999999999743
No 481
>TIGR01134 purF amidophosphoribosyltransferase. Alternate name: glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase.
Probab=37.04 E-value=41 Score=23.72 Aligned_cols=16 Identities=6% Similarity=-0.120 Sum_probs=13.1
Q ss_pred hHHHHHHHHHhCCcEE
Q psy3868 3 YRLTTLCRDSLGAFFF 18 (69)
Q Consensus 3 T~la~aia~~~~~~~~ 18 (69)
...|+.+|..++.|+.
T Consensus 285 ~~~A~~la~~lgip~~ 300 (442)
T TIGR01134 285 RSAALGFAQASGIPYR 300 (442)
T ss_pred HHHHHHHHHHhCCCch
Confidence 4578899999998875
No 482
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=36.96 E-value=36 Score=23.48 Aligned_cols=24 Identities=8% Similarity=0.178 Sum_probs=20.4
Q ss_pred ChhHHHHHHHHHhCCcEEEEchhh
Q psy3868 1 MSYRLTTLCRDSLGAFFFLINGPE 24 (69)
Q Consensus 1 ~~T~la~aia~~~~~~~~~v~~~~ 24 (69)
|+-.+|+-+|..+|+|-|.|+|-.
T Consensus 109 LGaiiA~~ia~~~gvPayIVDPvv 132 (358)
T COG3426 109 LGAIIANRIAKALGVPAYIVDPVV 132 (358)
T ss_pred hhHHHHHHHhhhcCCCeeeeCcee
Confidence 456789999999999999999844
No 483
>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra
Probab=36.93 E-value=68 Score=19.06 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=13.5
Q ss_pred HHHHHHhcCCeEEEEcccc
Q psy3868 40 AFEEADKNSPSIIFIDELD 58 (69)
Q Consensus 40 if~~a~~~~p~iifiDEid 58 (69)
.+..+-...|.++++||--
T Consensus 106 ~la~al~~~p~~lllDEPt 124 (173)
T cd03246 106 GLARALYGNPRILVLDEPN 124 (173)
T ss_pred HHHHHHhcCCCEEEEECCc
Confidence 3444445789999999954
No 484
>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=36.93 E-value=66 Score=19.70 Aligned_cols=16 Identities=25% Similarity=0.376 Sum_probs=11.7
Q ss_pred HHHhcCCeEEEEcccc
Q psy3868 43 EADKNSPSIIFIDELD 58 (69)
Q Consensus 43 ~a~~~~p~iifiDEid 58 (69)
.+-...|.++++||--
T Consensus 144 ~al~~~p~llllDEPt 159 (214)
T cd03297 144 RALAAQPELLLLDEPF 159 (214)
T ss_pred HHHhcCCCEEEEcCCc
Confidence 3334689999999953
No 485
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=36.89 E-value=67 Score=19.13 Aligned_cols=19 Identities=16% Similarity=0.272 Sum_probs=13.5
Q ss_pred HHHHHhcCCeEEEEccccc
Q psy3868 41 FEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 41 f~~a~~~~p~iifiDEid~ 59 (69)
+..+-...|.++++||--+
T Consensus 109 laral~~~p~~lllDEP~~ 127 (178)
T cd03247 109 LARILLQDAPIVLLDEPTV 127 (178)
T ss_pred HHHHHhcCCCEEEEECCcc
Confidence 4444457899999999643
No 486
>PF04951 Peptidase_M55: D-aminopeptidase; InterPro: IPR007035 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M55 (DppA aminopeptidase family, clan MN). The type example is Bacillus subtilis DppA, which is a binuclear zinc-dependent, D-specific aminopeptidase. The structure reveals that DppA is a new example of a self-compartmentalising protease, a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organised in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterised by the SXDXEG key sequence []. The only known substrates are D-ala-D-ala and D-ala-gly-gly.; PDB: 1HI9_A.
Probab=36.79 E-value=1e+02 Score=20.53 Aligned_cols=22 Identities=18% Similarity=0.273 Sum_probs=16.6
Q ss_pred HHHHHHHHHhCCcEEEEchhhh
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEI 25 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l 25 (69)
.|--++|.+.|+|+..|++.+.
T Consensus 137 ~lna~~Ag~~GVPV~lVsGD~~ 158 (265)
T PF04951_consen 137 GLNAALAGYYGVPVVLVSGDDA 158 (265)
T ss_dssp HHHHHHHHHTT--EEEEEEEHH
T ss_pred HHHHHHHhhcCCcEEEEeCcHH
Confidence 3556889999999999999876
No 487
>cd04130 Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus,
Probab=36.77 E-value=39 Score=19.76 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=21.0
Q ss_pred HHHHHHHHhCC-cEEEEchhhhhhcccChHHHHHHHHHHHH
Q psy3868 5 LTTLCRDSLGA-FFFLINGPEIMSKLAGESESNLRKAFEEA 44 (69)
Q Consensus 5 la~aia~~~~~-~~~~v~~~~l~~~~~ges~~~l~~if~~a 44 (69)
-++.++.+.+. +++++|+- +..+++++|+.+
T Consensus 138 ~~~~~a~~~~~~~~~e~Sa~---------~~~~v~~lf~~~ 169 (173)
T cd04130 138 RAKALAEKIGACEYIECSAL---------TQKNLKEVFDTA 169 (173)
T ss_pred HHHHHHHHhCCCeEEEEeCC---------CCCCHHHHHHHH
Confidence 35667777776 88888762 345677788765
No 488
>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt
Probab=36.74 E-value=70 Score=18.97 Aligned_cols=19 Identities=26% Similarity=0.548 Sum_probs=13.3
Q ss_pred HHHHHhcCCeEEEEccccc
Q psy3868 41 FEEADKNSPSIIFIDELDA 59 (69)
Q Consensus 41 f~~a~~~~p~iifiDEid~ 59 (69)
+..+-...|.++++||--+
T Consensus 102 laral~~~p~~lllDEPt~ 120 (166)
T cd03223 102 FARLLLHKPKFVFLDEATS 120 (166)
T ss_pred HHHHHHcCCCEEEEECCcc
Confidence 3344457899999999543
No 489
>cd00281 DAP_dppA Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacterized
Probab=36.70 E-value=1.1e+02 Score=20.45 Aligned_cols=23 Identities=17% Similarity=0.296 Sum_probs=19.2
Q ss_pred HHHHHHHHHhCCcEEEEchhhhh
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEIM 26 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l~ 26 (69)
.|--++|.+.|+|+..+++.+-+
T Consensus 136 ~lna~~Ag~~gVPV~lvsGDd~~ 158 (265)
T cd00281 136 HLNALTAGYYGVPVVMVAGDAEV 158 (265)
T ss_pred HHHHHHHhhcCCCEEEEecCHHH
Confidence 35668999999999999998763
No 490
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=36.66 E-value=1.3e+02 Score=20.12 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=27.6
Q ss_pred hHHHHHHHHHhC-CcEEEEchhhhhhcccChHHHHHHHHHHHHHhcCCeEEE
Q psy3868 3 YRLTTLCRDSLG-AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIF 53 (69)
Q Consensus 3 T~la~aia~~~~-~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~~~p~iif 53 (69)
..+++++..+.. .++....-+-+ .+..++.++.+.++... .+||
T Consensus 19 e~v~~A~l~QF~~~~~~~~~~p~v------~~~~~~~~i~~~~~~~~-~iV~ 63 (269)
T PRK05339 19 ETVGRAALSQFPNVEFEEHRYPFV------RTEEKADEVLEEINAER-PIVF 63 (269)
T ss_pred HHHHHHHHHhCCCCCeeEEEeCCc------CCHHHHHHHHHHHHhcC-CEEE
Confidence 357777777763 55433322222 47888999999997744 4554
No 491
>PRK13543 cytochrome c biogenesis protein CcmA; Provisional
Probab=36.59 E-value=65 Score=19.84 Aligned_cols=17 Identities=12% Similarity=0.059 Sum_probs=12.2
Q ss_pred HHHHhcCCeEEEEcccc
Q psy3868 42 EEADKNSPSIIFIDELD 58 (69)
Q Consensus 42 ~~a~~~~p~iifiDEid 58 (69)
..+-...|.++++||--
T Consensus 149 aral~~~p~llllDEPt 165 (214)
T PRK13543 149 ARLWLSPAPLWLLDEPY 165 (214)
T ss_pred HHHHhcCCCEEEEeCCc
Confidence 33334689999999954
No 492
>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein.
Probab=36.53 E-value=67 Score=19.67 Aligned_cols=15 Identities=27% Similarity=0.423 Sum_probs=11.2
Q ss_pred HHhcCCeEEEEcccc
Q psy3868 44 ADKNSPSIIFIDELD 58 (69)
Q Consensus 44 a~~~~p~iifiDEid 58 (69)
|-...|.++++||--
T Consensus 152 al~~~p~llllDEPt 166 (216)
T TIGR00960 152 AIVHKPPLLLADEPT 166 (216)
T ss_pred HHhcCCCEEEEeCCC
Confidence 334679999999953
No 493
>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.
Probab=36.51 E-value=68 Score=19.49 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=11.8
Q ss_pred HHhcCCeEEEEccccc
Q psy3868 44 ADKNSPSIIFIDELDA 59 (69)
Q Consensus 44 a~~~~p~iifiDEid~ 59 (69)
+-...|.++++||-.+
T Consensus 125 al~~~p~illlDEP~~ 140 (194)
T cd03213 125 ELVSNPSLLFLDEPTS 140 (194)
T ss_pred HHHcCCCEEEEeCCCc
Confidence 3346899999999643
No 494
>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=36.40 E-value=63 Score=19.77 Aligned_cols=15 Identities=47% Similarity=0.561 Sum_probs=11.3
Q ss_pred HHhcCCeEEEEcccc
Q psy3868 44 ADKNSPSIIFIDELD 58 (69)
Q Consensus 44 a~~~~p~iifiDEid 58 (69)
|-...|.++++||--
T Consensus 154 al~~~p~lllLDEP~ 168 (218)
T cd03255 154 ALANDPKIILADEPT 168 (218)
T ss_pred HHccCCCEEEEcCCc
Confidence 334679999999954
No 495
>PRK08525 amidophosphoribosyltransferase; Provisional
Probab=36.27 E-value=36 Score=24.05 Aligned_cols=15 Identities=13% Similarity=-0.013 Sum_probs=12.7
Q ss_pred hHHHHHHHHHhCCcE
Q psy3868 3 YRLTTLCRDSLGAFF 17 (69)
Q Consensus 3 T~la~aia~~~~~~~ 17 (69)
...|+.+|+.++.|+
T Consensus 287 ~~~A~~~A~~lgip~ 301 (445)
T PRK08525 287 VPAAIGYAQESGIPF 301 (445)
T ss_pred HHHHHHHHHHhCCCc
Confidence 457899999999987
No 496
>cd08770 DAP_dppA_3 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacteriz
Probab=36.24 E-value=1.1e+02 Score=20.40 Aligned_cols=23 Identities=13% Similarity=0.229 Sum_probs=19.1
Q ss_pred HHHHHHHHHhCCcEEEEchhhhh
Q psy3868 4 RLTTLCRDSLGAFFFLINGPEIM 26 (69)
Q Consensus 4 ~la~aia~~~~~~~~~v~~~~l~ 26 (69)
.|--++|.+.|+|+..+++.+-+
T Consensus 137 ~lna~~Ag~~gVPV~lvsGD~~~ 159 (263)
T cd08770 137 LINAYTAAYLGVPVVFVSGDAGL 159 (263)
T ss_pred HHHHHHHhhcCCCEEEEecCHHH
Confidence 45668999999999999997764
No 497
>PF02775 TPP_enzyme_C: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain; InterPro: IPR011766 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This represents the C-terminal TPP binding domain of TPP enzymes.; GO: 0003824 catalytic activity, 0030976 thiamine pyrophosphate binding; PDB: 2WVA_V 1ZPD_F 2WVG_B 2WVH_B 3OE1_D 2NXW_A 2Q5L_B 2Q5Q_B 2Q5J_A 2Q5O_A ....
Probab=36.13 E-value=90 Score=18.10 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=23.0
Q ss_pred HHHHHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEE
Q psy3868 7 TLCRDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSII 52 (69)
Q Consensus 7 ~aia~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~ii 52 (69)
..+|+..|.+.+.++..+ ...+++.++++.+ ..|++|
T Consensus 114 ~~~a~a~G~~~~~v~~~~---------~~el~~al~~a~~~~gp~vI 151 (153)
T PF02775_consen 114 AALAEAFGIKGARVTTPD---------PEELEEALREALESGGPAVI 151 (153)
T ss_dssp HHHHHHTTSEEEEESCHS---------HHHHHHHHHHHHHSSSEEEE
T ss_pred HHHHHHcCCcEEEEccCC---------HHHHHHHHHHHHhCCCcEEE
Confidence 356777788777665542 2556666766654 466665
No 498
>PF00676 E1_dh: Dehydrogenase E1 component; InterPro: IPR001017 This entry includes a number of dehydrogenases all of which use thiamine pyrophosphate as a cofactor and are members of a multienzyme complex. Pyruvate dehydrogenase (1.2.4.1 from EC), a component of the multienzyme pyruvate dehydrogenase complex; 2-oxoglutarate dehydrogenase (1.2.4.2 from EC), a component of the multienzyme 2-oxoglutarate dehydrogenase which contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3); and 2-oxoisovalerate dehydrogenase (1.2.4.4 from EC), a component of the multienzyme branched-chain alpha-keto dehydrogenase complex all belong to this family.; GO: 0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 0008152 metabolic process; PDB: 1X7Y_A 1V1M_A 1X7W_A 1OLU_A 2J9F_A 2BEW_A 1V11_A 2BFE_A 1U5B_A 2BEU_A ....
Probab=36.06 E-value=1.1e+02 Score=20.45 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=27.1
Q ss_pred HHHhCCcEEEEchhhhhhcccChHHHHHHHHHHHHHh-cCCeEE
Q psy3868 10 RDSLGAFFFLINGPEIMSKLAGESESNLRKAFEEADK-NSPSII 52 (69)
Q Consensus 10 a~~~~~~~~~v~~~~l~~~~~ges~~~l~~if~~a~~-~~p~ii 52 (69)
|...|.|.+.|++.++.. .-..++...+.+++ .+|++|
T Consensus 182 a~~~gip~~~VDG~D~~a-----v~~a~~~A~~~~R~g~gP~li 220 (300)
T PF00676_consen 182 AKGYGIPGIRVDGNDVEA-----VYEAAKEAVEYARAGKGPVLI 220 (300)
T ss_dssp GGGTTSEEEEEETTSHHH-----HHHHHHHHHHHHHTTT--EEE
T ss_pred hhccCCcEEEECCEeHHH-----HHHHHHHHHHHHhcCCCCEEE
Confidence 445688999999988853 45567788888887 567777
No 499
>cd00462 PTH Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts.
Probab=36.01 E-value=26 Score=21.69 Aligned_cols=34 Identities=12% Similarity=-0.000 Sum_probs=21.4
Q ss_pred ccChHHHHHHHHHHHHHh-cCCeEEEEcccccccc
Q psy3868 29 LAGESESNLRKAFEEADK-NSPSIIFIDELDAIAP 62 (69)
Q Consensus 29 ~~ges~~~l~~if~~a~~-~~p~iifiDEid~i~~ 62 (69)
|...|.+.|+++++.-+- ....+++-||+|-=++
T Consensus 62 yMN~SG~~V~~~~~~~~i~~~~ilVihDdldl~~G 96 (171)
T cd00462 62 YMNLSGEAVAALANFYKIPPEDILVIHDDLDLPLG 96 (171)
T ss_pred ccccccHHHHHHHHhcCCChhHEEEEEecCCCCCc
Confidence 555677777777765432 2236667799996543
No 500
>PRK12315 1-deoxy-D-xylulose-5-phosphate synthase; Provisional
Probab=35.93 E-value=1.3e+02 Score=22.08 Aligned_cols=39 Identities=23% Similarity=0.466 Sum_probs=29.0
Q ss_pred HHHHHhCCcEEEE-chhhhhhcccChHHHHHHHHHHHHHh-cCCeEEEEc
Q psy3868 8 LCRDSLGAFFFLI-NGPEIMSKLAGESESNLRKAFEEADK-NSPSIIFID 55 (69)
Q Consensus 8 aia~~~~~~~~~v-~~~~l~~~~~ges~~~l~~if~~a~~-~~p~iifiD 55 (69)
.+....|++.+.+ ++.++ ..+.++|+.+++ .+|.+|.+.
T Consensus 201 ~~~~a~G~~~~~v~DG~D~---------~~l~~a~~~a~~~~gP~~i~~~ 241 (581)
T PRK12315 201 NLFKAMGLDYRYVEDGNDI---------ESLIEAFKEVKDIDHPIVLHIH 241 (581)
T ss_pred HHHHhcCCeEEEeeCCCCH---------HHHHHHHHHHHhCCCCEEEEEE
Confidence 4567789999888 88776 466777877776 568888654
Done!