Query 004011
Match_columns 779
No_of_seqs 130 out of 134
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 15:58:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004011hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0615 Serine/threonine prote 99.4 2.9E-13 6.4E-18 147.8 6.0 109 129-238 41-160 (475)
2 PF00498 FHA: FHA domain; Int 99.4 2.8E-12 6.1E-17 105.5 8.4 67 154-224 1-68 (68)
3 cd00060 FHA Forkhead associate 99.3 2.3E-11 5E-16 104.4 10.4 97 134-234 1-101 (102)
4 TIGR03354 VI_FHA type VI secre 98.8 5.2E-09 1.1E-13 114.9 7.9 81 146-231 18-102 (396)
5 COG1716 FOG: FHA domain [Signa 98.5 5.7E-07 1.2E-11 86.7 9.5 76 146-228 83-159 (191)
6 smart00240 FHA Forkhead associ 98.5 2.1E-07 4.6E-12 72.6 5.0 50 154-207 1-52 (52)
7 PLN02927 antheraxanthin epoxid 98.4 5.7E-07 1.2E-11 104.8 8.5 88 143-235 545-646 (668)
8 KOG0737 AAA+-type ATPase [Post 97.9 1.3E-05 2.8E-10 87.9 6.6 98 430-532 68-165 (386)
9 COG3456 Predicted component of 97.9 1.6E-05 3.5E-10 88.1 6.3 78 149-236 23-103 (430)
10 CHL00195 ycf46 Ycf46; Provisio 97.1 0.0025 5.5E-08 72.6 10.7 82 442-532 216-297 (489)
11 KOG1881 Anion exchanger adapto 97.0 0.0005 1.1E-08 80.5 3.5 87 151-239 176-270 (793)
12 KOG1882 Transcriptional regula 96.4 0.0082 1.8E-07 63.5 7.3 100 127-227 164-279 (293)
13 KOG0740 AAA+-type ATPase [Post 96.3 0.012 2.5E-07 66.5 8.3 67 450-523 149-215 (428)
14 KOG0245 Kinesin-like protein [ 96.0 0.017 3.6E-07 70.4 8.1 82 149-237 474-558 (1221)
15 COG0464 SpoVK ATPases of the A 94.9 0.044 9.6E-07 61.5 6.2 96 431-532 215-314 (494)
16 KOG0733 Nuclear AAA ATPase (VC 94.7 0.048 1E-06 64.2 5.8 85 446-537 182-266 (802)
17 PRK05342 clpX ATP-dependent pr 94.7 0.045 9.7E-07 61.4 5.5 86 443-531 59-145 (412)
18 TIGR00390 hslU ATP-dependent p 94.5 0.038 8.2E-07 62.7 4.5 70 458-531 14-84 (441)
19 PRK03992 proteasome-activating 94.2 0.045 9.8E-07 60.4 4.1 79 447-532 124-203 (389)
20 TIGR01241 FtsH_fam ATP-depende 93.9 0.044 9.6E-07 61.9 3.5 78 445-530 46-124 (495)
21 PRK05201 hslU ATP-dependent pr 93.5 0.078 1.7E-06 60.3 4.5 68 461-532 20-88 (443)
22 TIGR00382 clpX endopeptidase C 93.4 0.1 2.2E-06 58.8 5.2 83 446-531 68-153 (413)
23 TIGR01243 CDC48 AAA family ATP 93.2 0.085 1.8E-06 62.5 4.4 76 450-532 449-525 (733)
24 KOG0736 Peroxisome assembly fa 93.1 0.22 4.8E-06 60.1 7.4 96 428-530 646-741 (953)
25 KOG0730 AAA+-type ATPase [Post 93.1 0.11 2.3E-06 61.5 4.8 78 446-530 426-504 (693)
26 KOG0738 AAA+-type ATPase [Post 92.9 0.11 2.4E-06 58.6 4.5 78 447-531 205-282 (491)
27 CHL00176 ftsH cell division pr 92.7 0.11 2.5E-06 61.3 4.3 82 443-531 172-253 (638)
28 PRK12377 putative replication 92.6 0.19 4.2E-06 52.9 5.5 84 431-527 51-137 (248)
29 PF00004 AAA: ATPase family as 92.3 0.1 2.2E-06 46.4 2.7 36 495-532 1-36 (132)
30 COG1219 ClpX ATP-dependent pro 91.9 0.16 3.6E-06 56.3 4.1 69 461-531 66-134 (408)
31 KOG0744 AAA+-type ATPase [Post 91.9 0.084 1.8E-06 58.6 1.8 75 442-521 130-204 (423)
32 PRK07952 DNA replication prote 91.5 0.38 8.2E-06 50.6 6.1 88 430-531 48-139 (244)
33 KOG0739 AAA+-type ATPase [Post 91.0 0.26 5.7E-06 54.4 4.4 77 447-530 126-202 (439)
34 KOG0733 Nuclear AAA ATPase (VC 90.7 0.31 6.7E-06 57.8 5.0 92 450-557 507-600 (802)
35 PTZ00454 26S protease regulato 90.3 0.3 6.5E-06 54.7 4.3 77 447-530 138-215 (398)
36 PRK08116 hypothetical protein; 90.0 0.4 8.6E-06 50.7 4.7 88 432-530 63-153 (268)
37 TIGR01242 26Sp45 26S proteasom 89.8 0.28 6.1E-06 53.2 3.6 77 448-530 116-192 (364)
38 COG1223 Predicted ATPase (AAA+ 89.7 0.19 4E-06 54.7 2.1 40 491-532 150-189 (368)
39 KOG2293 Daxx-interacting prote 88.8 1 2.2E-05 52.3 7.1 92 133-234 432-530 (547)
40 PF00004 AAA: ATPase family as 88.6 0.95 2.1E-05 40.3 5.4 57 689-748 45-113 (132)
41 KOG0731 AAA+-type ATPase conta 88.2 0.48 1E-05 57.3 4.2 78 446-530 303-380 (774)
42 TIGR02500 type_III_yscD type I 87.9 0.79 1.7E-05 51.3 5.4 63 147-215 15-80 (410)
43 TIGR01663 PNK-3'Pase polynucle 87.1 1.8 4E-05 50.5 7.9 97 133-235 13-109 (526)
44 TIGR01243 CDC48 AAA family ATP 86.5 0.69 1.5E-05 55.1 4.2 78 449-532 173-250 (733)
45 CHL00206 ycf2 Ycf2; Provisiona 85.7 0.58 1.3E-05 61.3 3.2 42 490-533 1628-1669(2281)
46 PF07724 AAA_2: AAA domain (Cd 84.4 0.79 1.7E-05 45.5 2.9 37 494-532 5-45 (171)
47 PF13207 AAA_17: AAA domain; P 84.1 0.84 1.8E-05 40.8 2.7 32 494-527 1-32 (121)
48 TIGR02640 gas_vesic_GvpN gas v 83.8 1.2 2.5E-05 46.7 4.0 36 491-528 20-55 (262)
49 PTZ00361 26 proteosome regulat 83.5 1.4 3E-05 50.2 4.7 67 462-532 189-255 (438)
50 KOG0734 AAA+-type ATPase conta 83.4 1.3 2.9E-05 52.1 4.5 83 439-528 289-371 (752)
51 KOG2045 5'-3' exonuclease XRN1 83.3 1.6 3.6E-05 53.7 5.3 74 584-667 1115-1188(1493)
52 COG1222 RPT1 ATP-dependent 26S 82.6 0.98 2.1E-05 50.9 3.0 52 475-530 170-221 (406)
53 KOG1880 Nuclear inhibitor of p 82.4 2.3 5E-05 46.8 5.6 82 149-234 35-118 (337)
54 PLN00020 ribulose bisphosphate 81.8 1.1 2.4E-05 50.8 3.0 44 492-537 148-191 (413)
55 TIGR02988 YaaA_near_RecF S4 do 78.7 1.8 3.9E-05 35.8 2.6 27 196-223 32-58 (59)
56 PRK08939 primosomal protein Dn 76.2 3.2 7E-05 45.0 4.4 85 435-530 108-195 (306)
57 KOG0727 26S proteasome regulat 76.1 2.1 4.5E-05 46.8 2.9 65 462-530 161-225 (408)
58 smart00363 S4 S4 RNA-binding d 75.8 3.6 7.7E-05 31.5 3.4 28 197-225 25-52 (60)
59 cd00754 MoaD Ubiquitin domain 75.7 2.6 5.6E-05 35.8 2.8 26 199-226 51-76 (80)
60 PRK04195 replication factor C 75.7 2.6 5.6E-05 47.9 3.7 37 492-530 39-75 (482)
61 PRK10733 hflB ATP-dependent me 75.2 3 6.5E-05 49.5 4.1 78 446-531 144-222 (644)
62 PRK00131 aroK shikimate kinase 74.4 3.1 6.7E-05 39.1 3.3 34 492-527 4-37 (175)
63 PF02597 ThiS: ThiS family; I 74.3 2.1 4.5E-05 36.0 1.9 28 199-226 45-73 (77)
64 TIGR01650 PD_CobS cobaltochela 74.2 5.2 0.00011 44.4 5.4 33 492-526 64-96 (327)
65 TIGR01687 moaD_arch MoaD famil 74.1 2.8 6.2E-05 36.7 2.8 28 199-226 57-84 (88)
66 PRK08118 topology modulation p 73.2 2.8 6E-05 41.2 2.8 35 493-529 2-36 (167)
67 PRK06921 hypothetical protein; 72.9 3.3 7.2E-05 43.9 3.4 72 435-518 65-141 (266)
68 cd00464 SK Shikimate kinase (S 70.9 3.8 8.2E-05 38.0 2.9 31 494-526 1-31 (154)
69 smart00382 AAA ATPases associa 70.5 5.2 0.00011 34.3 3.5 35 492-528 2-39 (148)
70 PRK11034 clpA ATP-dependent Cl 70.0 3.4 7.5E-05 50.2 3.1 37 493-531 489-525 (758)
71 TIGR03689 pup_AAA proteasome A 69.2 5.1 0.00011 46.8 4.1 66 449-521 177-243 (512)
72 TIGR03420 DnaA_homol_Hda DnaA 69.1 7.9 0.00017 38.4 4.9 66 449-531 10-78 (226)
73 PF01479 S4: S4 domain; Inter 68.9 3.1 6.8E-05 32.6 1.7 24 197-221 25-48 (48)
74 TIGR02881 spore_V_K stage V sp 68.8 4.7 0.0001 41.9 3.4 47 484-532 34-87 (261)
75 PRK11130 moaD molybdopterin sy 67.7 5.4 0.00012 35.0 3.0 25 200-226 53-77 (81)
76 PF07728 AAA_5: AAA domain (dy 67.5 5.8 0.00013 36.6 3.4 33 495-529 2-34 (139)
77 PRK00080 ruvB Holliday junctio 67.2 5.9 0.00013 42.6 3.9 37 492-530 51-87 (328)
78 cd01428 ADK Adenylate kinase ( 66.6 5.2 0.00011 38.6 3.0 31 494-526 1-31 (194)
79 PF05496 RuvB_N: Holliday junc 65.9 6.2 0.00013 42.1 3.6 35 493-529 51-85 (233)
80 cd00565 ThiS ThiaminS ubiquiti 65.8 5.7 0.00012 33.4 2.7 27 199-225 32-60 (65)
81 TIGR00635 ruvB Holliday juncti 64.8 6.5 0.00014 41.2 3.5 35 492-528 30-64 (305)
82 PHA02544 44 clamp loader, smal 64.2 5.8 0.00013 41.7 3.0 35 493-529 44-78 (316)
83 COG0714 MoxR-like ATPases [Gen 63.9 8.6 0.00019 41.4 4.3 37 492-530 43-79 (329)
84 PRK00091 miaA tRNA delta(2)-is 63.2 6.1 0.00013 43.2 3.1 37 493-531 5-41 (307)
85 PRK00149 dnaA chromosomal repl 62.2 8.8 0.00019 43.2 4.2 68 449-530 117-189 (450)
86 COG0470 HolB ATPase involved i 62.0 12 0.00026 38.8 4.9 24 494-519 26-49 (325)
87 PRK08903 DnaA regulatory inact 61.7 18 0.00038 36.5 5.8 67 448-530 12-81 (227)
88 TIGR02639 ClpA ATP-dependent C 60.2 7.8 0.00017 46.6 3.5 36 494-531 486-521 (731)
89 smart00763 AAA_PrkA PrkA AAA d 59.8 25 0.00054 39.7 7.1 90 427-527 16-118 (361)
90 PRK06944 sulfur carrier protei 59.1 8.3 0.00018 32.0 2.5 27 199-225 32-60 (65)
91 cd01764 Urm1 Urm1-like ubuitin 58.9 7.5 0.00016 35.6 2.4 28 199-226 61-90 (94)
92 PRK13947 shikimate kinase; Pro 58.8 8.9 0.00019 36.6 3.0 32 494-527 3-34 (171)
93 PRK03839 putative kinase; Prov 58.6 8.5 0.00018 37.4 2.9 32 494-527 2-33 (180)
94 PRK06835 DNA replication prote 58.3 9.5 0.00021 42.0 3.5 45 484-530 175-222 (329)
95 cd00009 AAA The AAA+ (ATPases 57.9 13 0.00028 32.4 3.7 39 491-531 18-59 (151)
96 PRK07261 topology modulation p 57.9 9.2 0.0002 37.6 3.0 38 493-532 1-38 (171)
97 PLN02799 Molybdopterin synthas 57.1 10 0.00022 33.0 2.9 26 199-226 53-78 (82)
98 PRK06488 sulfur carrier protei 57.0 8.1 0.00017 32.5 2.1 26 200-225 33-60 (65)
99 PRK08181 transposase; Validate 57.0 23 0.00049 38.1 6.0 76 432-527 59-142 (269)
100 cd00165 S4 S4/Hsp/ tRNA synthe 57.0 11 0.00025 29.5 2.9 28 197-225 25-52 (70)
101 PRK14528 adenylate kinase; Pro 55.8 9.8 0.00021 37.8 2.9 32 493-526 2-33 (186)
102 TIGR01683 thiS thiamine biosyn 55.4 9.6 0.00021 32.0 2.3 28 198-225 30-59 (64)
103 TIGR00362 DnaA chromosomal rep 54.8 15 0.00032 40.7 4.3 36 493-530 137-177 (405)
104 KOG1892 Actin filament-binding 54.1 16 0.00035 45.8 4.7 84 148-239 374-459 (1629)
105 TIGR01682 moaD molybdopterin c 53.9 12 0.00026 32.5 2.8 26 199-226 51-76 (80)
106 PF14478 DUF4430: Domain of un 53.0 12 0.00025 32.0 2.5 24 200-223 43-67 (68)
107 TIGR01313 therm_gnt_kin carboh 52.9 12 0.00026 35.5 2.9 33 495-531 1-33 (163)
108 PRK13342 recombination factor 52.0 15 0.00032 41.1 3.7 34 493-528 37-70 (413)
109 PRK03731 aroL shikimate kinase 51.7 15 0.00033 35.1 3.4 33 493-527 3-35 (171)
110 cd02020 CMPK Cytidine monophos 51.7 13 0.00027 34.1 2.7 30 495-526 2-31 (147)
111 PHA02244 ATPase-like protein 51.4 15 0.00033 41.7 3.8 34 492-527 119-152 (383)
112 PRK14531 adenylate kinase; Pro 50.0 14 0.0003 36.4 2.8 29 493-523 3-31 (183)
113 PRK06217 hypothetical protein; 49.8 15 0.00032 36.1 3.0 33 493-527 2-34 (183)
114 PF13671 AAA_33: AAA domain; P 49.2 10 0.00022 34.7 1.7 30 495-526 2-31 (143)
115 cd02021 GntK Gluconate kinase 48.9 16 0.00035 34.1 3.0 30 495-526 2-31 (150)
116 PRK06893 DNA replication initi 48.3 18 0.0004 37.1 3.5 25 492-518 39-63 (229)
117 PRK14530 adenylate kinase; Pro 48.0 18 0.0004 36.4 3.4 32 492-525 3-34 (215)
118 CHL00095 clpC Clp protease ATP 47.6 16 0.00035 44.6 3.5 36 494-531 541-579 (821)
119 PRK06526 transposase; Provisio 47.6 36 0.00078 36.1 5.6 67 432-518 52-122 (254)
120 KOG0730 AAA+-type ATPase [Post 47.3 9.1 0.0002 46.1 1.3 40 490-531 216-255 (693)
121 KOG0745 Putative ATP-dependent 47.1 17 0.00036 42.6 3.2 35 494-530 228-262 (564)
122 TIGR01351 adk adenylate kinase 47.0 16 0.00034 36.7 2.8 31 494-526 1-31 (210)
123 PRK14532 adenylate kinase; Pro 46.9 18 0.00038 35.4 3.0 29 494-524 2-30 (188)
124 cd00227 CPT Chloramphenicol (C 46.3 14 0.0003 36.0 2.2 34 492-527 2-35 (175)
125 PRK05057 aroK shikimate kinase 45.7 20 0.00044 35.3 3.2 34 492-527 4-37 (172)
126 TIGR00763 lon ATP-dependent pr 45.3 33 0.00072 41.8 5.5 34 492-527 347-380 (775)
127 PLN03025 replication factor C 45.0 20 0.00043 38.6 3.3 24 493-518 35-58 (319)
128 PF01300 Sua5_yciO_yrdC: Telom 44.0 29 0.00062 34.6 4.0 58 686-744 25-84 (179)
129 TIGR03345 VI_ClpV1 type VI sec 43.5 17 0.00037 44.8 2.9 35 494-530 598-635 (852)
130 TIGR01359 UMP_CMP_kin_fam UMP- 43.3 21 0.00046 34.4 2.9 32 495-530 2-33 (183)
131 PRK13949 shikimate kinase; Pro 43.1 20 0.00043 35.4 2.8 33 493-527 2-34 (169)
132 TIGR00174 miaA tRNA isopenteny 42.6 21 0.00046 38.9 3.1 36 495-532 2-37 (287)
133 PRK13407 bchI magnesium chelat 42.4 32 0.00069 38.2 4.4 25 493-519 30-54 (334)
134 PRK08053 sulfur carrier protei 42.2 21 0.00047 30.2 2.5 27 199-225 33-61 (66)
135 PF03215 Rad17: Rad17 cell cyc 42.0 20 0.00043 42.1 2.9 31 493-525 45-76 (519)
136 PRK00279 adk adenylate kinase; 41.3 23 0.00049 35.7 2.9 33 494-530 2-34 (215)
137 PF05673 DUF815: Protein of un 41.3 35 0.00077 36.9 4.4 53 689-745 93-149 (249)
138 PRK14962 DNA polymerase III su 41.3 28 0.0006 40.3 3.9 27 492-520 36-62 (472)
139 PTZ00088 adenylate kinase 1; P 40.8 23 0.0005 37.1 2.9 33 493-527 7-39 (229)
140 PF14512 TM1586_NiRdase: Putat 40.6 21 0.00045 37.6 2.5 65 404-473 3-70 (206)
141 TIGR02880 cbbX_cfxQ probable R 40.2 22 0.00049 38.0 2.8 39 492-532 58-103 (284)
142 PRK06762 hypothetical protein; 40.1 29 0.00062 33.1 3.3 33 493-527 3-35 (166)
143 PRK08727 hypothetical protein; 39.9 48 0.001 34.3 5.0 21 493-515 42-62 (233)
144 PRK14527 adenylate kinase; Pro 39.8 23 0.00049 35.0 2.6 35 490-526 4-38 (191)
145 PLN02840 tRNA dimethylallyltra 39.8 23 0.0005 40.7 2.9 38 493-532 22-59 (421)
146 PRK00625 shikimate kinase; Pro 39.5 25 0.00054 35.2 2.8 32 494-527 2-33 (173)
147 PRK12402 replication factor C 39.4 26 0.00056 36.9 3.1 37 494-532 38-79 (337)
148 PRK06437 hypothetical protein; 39.2 33 0.00072 29.5 3.1 25 199-225 38-62 (67)
149 PRK15367 type III secretion sy 39.0 67 0.0015 36.9 6.3 69 144-221 16-84 (395)
150 PF01745 IPT: Isopentenyl tran 38.9 25 0.00054 37.7 2.8 36 495-532 4-39 (233)
151 PRK08233 hypothetical protein; 38.9 31 0.00066 32.9 3.2 36 493-530 4-40 (182)
152 KOG0241 Kinesin-like protein [ 38.7 55 0.0012 41.5 5.9 66 154-225 469-534 (1714)
153 PRK14088 dnaA chromosomal repl 38.7 35 0.00075 38.9 4.1 70 446-530 97-171 (440)
154 PRK08154 anaerobic benzoate ca 38.5 90 0.0019 33.8 7.0 41 483-526 125-165 (309)
155 COG0564 RluA Pseudouridylate s 38.2 42 0.0009 36.5 4.5 31 195-227 34-64 (289)
156 KOG0735 AAA+-type ATPase [Post 37.9 25 0.00054 43.3 2.9 42 489-532 428-473 (952)
157 PRK03992 proteasome-activating 37.9 66 0.0014 36.0 6.1 57 689-748 212-281 (389)
158 PF14451 Ub-Mut7C: Mut7-C ubiq 37.7 31 0.00068 31.2 2.9 26 198-225 50-75 (81)
159 PRK02496 adk adenylate kinase; 37.4 26 0.00057 34.1 2.6 31 494-526 3-33 (184)
160 COG2255 RuvB Holliday junction 37.0 25 0.00054 39.2 2.6 35 494-530 54-88 (332)
161 PF07726 AAA_3: ATPase family 36.9 32 0.00069 34.0 3.0 27 495-523 2-28 (131)
162 PF06068 TIP49: TIP49 C-termin 36.5 31 0.00067 39.6 3.2 41 490-532 48-90 (398)
163 PRK09183 transposase/IS protei 36.5 76 0.0017 33.6 6.0 74 434-527 58-138 (259)
164 PRK11860 bifunctional 3-phosph 36.4 22 0.00048 42.5 2.2 36 493-532 443-478 (661)
165 PRK14960 DNA polymerase III su 36.3 32 0.00069 42.0 3.5 27 492-520 37-63 (702)
166 PF13521 AAA_28: AAA domain; P 36.1 34 0.00073 32.7 3.1 39 703-741 108-155 (163)
167 CHL00181 cbbX CbbX; Provisiona 35.7 32 0.00069 37.1 3.1 25 492-518 59-83 (287)
168 PF13401 AAA_22: AAA domain; P 35.4 84 0.0018 28.2 5.3 55 687-746 73-127 (131)
169 PF01637 Arch_ATPase: Archaeal 34.9 91 0.002 30.2 5.8 57 686-744 102-165 (234)
170 KOG0728 26S proteasome regulat 34.8 26 0.00056 38.7 2.2 51 475-530 166-217 (404)
171 TIGR03689 pup_AAA proteasome A 34.2 64 0.0014 38.1 5.4 60 689-748 273-344 (512)
172 TIGR03574 selen_PSTK L-seryl-t 34.1 38 0.00082 34.9 3.2 31 495-527 2-35 (249)
173 smart00797 AHS2 Allophanate hy 33.8 90 0.0019 34.1 6.1 45 189-233 46-90 (280)
174 PF00005 ABC_tran: ABC transpo 33.4 82 0.0018 28.8 5.0 53 460-526 81-133 (137)
175 PRK04182 cytidylate kinase; Pr 32.8 39 0.00084 32.1 2.9 28 494-523 2-29 (180)
176 COG1188 Ribosome-associated he 32.6 47 0.001 31.6 3.3 31 196-228 32-62 (100)
177 PRK13946 shikimate kinase; Pro 32.4 36 0.00078 33.6 2.7 33 493-527 11-43 (184)
178 PRK04220 2-phosphoglycerate ki 32.3 36 0.00079 37.6 2.9 57 461-521 61-119 (301)
179 PRK10634 tRNA(ANN) t(6)A37 thr 32.0 78 0.0017 32.3 5.0 52 686-741 39-96 (190)
180 PF02626 AHS2: Allophanate hyd 31.9 96 0.0021 33.7 5.9 46 189-234 46-91 (271)
181 PRK14955 DNA polymerase III su 31.8 31 0.00068 38.5 2.4 51 453-521 15-65 (397)
182 TIGR02903 spore_lon_C ATP-depe 31.8 1.3E+02 0.0029 35.9 7.6 36 493-530 176-221 (615)
183 COG0324 MiaA tRNA delta(2)-iso 30.7 45 0.00098 37.0 3.3 38 493-532 4-41 (308)
184 PRK10348 ribosome-associated h 30.6 64 0.0014 31.9 4.0 36 197-235 33-68 (133)
185 TIGR01017 rpsD_bact ribosomal 30.5 41 0.00089 34.8 2.8 29 196-225 113-141 (200)
186 PRK01777 hypothetical protein; 30.5 46 0.001 31.0 2.8 27 197-225 49-75 (95)
187 PRK05659 sulfur carrier protei 30.3 41 0.00089 28.1 2.3 26 199-224 33-60 (66)
188 KOG1942 DNA helicase, TBP-inte 30.0 39 0.00085 38.1 2.6 54 691-747 278-336 (456)
189 COG1121 ZnuC ABC-type Mn/Zn tr 29.9 59 0.0013 35.2 3.9 52 462-532 118-169 (254)
190 PLN02674 adenylate kinase 29.9 38 0.00083 36.1 2.5 30 492-523 31-60 (244)
191 PF02367 UPF0079: Uncharacteri 29.9 34 0.00074 33.0 2.0 38 490-530 13-50 (123)
192 PRK11507 ribosome-associated p 29.8 44 0.00095 29.9 2.5 26 197-223 36-61 (70)
193 CHL00113 rps4 ribosomal protei 29.7 45 0.00098 34.8 2.9 29 196-225 112-140 (201)
194 KOG1969 DNA replication checkp 29.7 48 0.001 41.0 3.5 35 493-529 327-361 (877)
195 COG2501 S4-like RNA binding pr 29.7 52 0.0011 29.7 2.9 26 197-223 36-61 (73)
196 TIGR00057 Sua5/YciO/YrdC/YwlC 29.5 70 0.0015 32.8 4.2 56 686-743 40-96 (201)
197 TIGR03346 chaperone_ClpB ATP-d 29.2 47 0.001 41.0 3.5 38 493-532 596-636 (852)
198 TIGR02173 cyt_kin_arch cytidyl 29.2 48 0.001 31.3 2.8 30 494-525 2-31 (171)
199 TIGR01360 aden_kin_iso1 adenyl 29.1 50 0.0011 31.6 3.0 30 492-523 3-32 (188)
200 PRK14961 DNA polymerase III su 28.9 38 0.00083 37.3 2.4 26 493-520 39-64 (363)
201 TIGR00678 holB DNA polymerase 28.8 41 0.0009 33.0 2.4 29 491-521 13-41 (188)
202 KOG0743 AAA+-type ATPase [Post 28.7 64 0.0014 37.7 4.1 76 450-529 186-270 (457)
203 PHA02530 pseT polynucleotide k 28.6 51 0.0011 34.5 3.1 33 493-527 3-36 (300)
204 PRK10865 protein disaggregatio 28.5 42 0.00092 41.5 2.9 35 494-530 600-637 (857)
205 PRK06645 DNA polymerase III su 28.4 40 0.00086 39.5 2.5 29 492-522 43-71 (507)
206 PRK11630 hypothetical protein; 28.3 1.2E+02 0.0027 31.3 5.7 53 686-743 46-102 (206)
207 TIGR01817 nifA Nif-specific re 28.2 45 0.00099 38.5 2.9 43 486-530 213-258 (534)
208 PTZ00361 26 proteosome regulat 28.1 71 0.0015 36.9 4.4 58 688-748 263-333 (438)
209 PF00158 Sigma54_activat: Sigm 27.6 32 0.0007 34.2 1.4 47 483-531 13-62 (168)
210 PF13238 AAA_18: AAA domain; P 27.6 38 0.00083 29.9 1.8 22 495-518 1-22 (129)
211 TIGR02397 dnaX_nterm DNA polym 27.0 43 0.00094 35.7 2.3 27 493-521 37-63 (355)
212 PTZ00454 26S protease regulato 27.0 1.2E+02 0.0026 34.4 5.9 57 689-748 226-295 (398)
213 PRK05327 rpsD 30S ribosomal pr 26.9 52 0.0011 34.2 2.8 30 196-226 116-145 (203)
214 PRK05707 DNA polymerase III su 26.9 42 0.00091 37.0 2.2 30 489-520 19-48 (328)
215 PRK08084 DNA replication initi 26.9 58 0.0012 33.7 3.1 25 493-519 46-70 (235)
216 PRK13531 regulatory ATPase Rav 26.7 54 0.0012 38.7 3.2 27 492-520 39-65 (498)
217 TIGR01241 FtsH_fam ATP-depende 26.2 1.1E+02 0.0023 35.4 5.3 57 689-748 135-204 (495)
218 TIGR02639 ClpA ATP-dependent C 26.2 1E+02 0.0022 37.4 5.5 44 703-748 273-322 (731)
219 PRK13341 recombination factor 26.1 48 0.001 40.6 2.7 34 493-528 53-86 (725)
220 COG0522 RpsD Ribosomal protein 25.8 58 0.0013 34.2 2.9 38 196-234 117-154 (205)
221 CHL00206 ycf2 Ycf2; Provisiona 25.7 91 0.002 42.5 5.1 58 688-748 1719-1783(2281)
222 PF02875 Mur_ligase_C: Mur lig 25.6 1.3E+02 0.0028 26.3 4.7 58 687-744 24-81 (91)
223 KOG0736 Peroxisome assembly fa 25.2 48 0.001 41.3 2.4 43 487-531 426-468 (953)
224 PF13275 S4_2: S4 domain; PDB: 25.0 30 0.00066 30.3 0.6 26 197-223 32-57 (65)
225 PRK07471 DNA polymerase III su 24.9 50 0.0011 37.0 2.4 44 460-519 23-66 (365)
226 PRK07940 DNA polymerase III su 24.8 52 0.0011 37.3 2.6 28 491-520 35-62 (394)
227 PF05726 Pirin_C: Pirin C-term 24.7 68 0.0015 29.4 2.9 36 189-226 22-59 (104)
228 PRK07993 DNA polymerase III su 24.7 49 0.0011 36.6 2.3 27 491-519 23-49 (334)
229 PRK05896 DNA polymerase III su 24.6 51 0.0011 39.7 2.5 26 493-520 39-64 (605)
230 KOG0991 Replication factor C, 24.5 48 0.001 36.5 2.1 24 493-518 49-72 (333)
231 PRK08364 sulfur carrier protei 24.4 67 0.0014 27.7 2.6 26 198-225 40-65 (70)
232 PRK00889 adenylylsulfate kinas 24.4 77 0.0017 30.6 3.3 35 493-529 5-42 (175)
233 cd02019 NK Nucleoside/nucleoti 24.3 93 0.002 26.3 3.4 32 494-527 1-33 (69)
234 TIGR03069 PS_II_S4 photosystem 24.3 91 0.002 33.5 4.1 32 196-228 206-237 (257)
235 COG2104 ThiS Sulfur transfer p 24.3 67 0.0014 28.3 2.6 27 199-225 35-63 (68)
236 PRK14959 DNA polymerase III su 24.0 54 0.0012 39.6 2.6 46 460-521 20-65 (624)
237 PRK12338 hypothetical protein; 23.9 62 0.0013 36.1 2.8 34 493-530 5-38 (319)
238 PRK05954 precorrin-8X methylmu 23.7 95 0.0021 32.8 4.0 41 703-743 89-129 (203)
239 COG1428 Deoxynucleoside kinase 23.7 70 0.0015 34.1 3.0 31 491-523 3-33 (216)
240 PRK08769 DNA polymerase III su 23.5 54 0.0012 36.2 2.3 28 491-520 25-52 (319)
241 PRK14970 DNA polymerase III su 23.5 58 0.0013 35.5 2.6 27 492-520 39-65 (367)
242 cd02027 APSK Adenosine 5'-phos 23.2 83 0.0018 30.3 3.3 31 495-527 2-35 (149)
243 PF13509 S1_2: S1 domain; PDB: 23.0 1.1E+02 0.0025 25.7 3.7 43 186-240 14-56 (61)
244 COG0563 Adk Adenylate kinase a 22.9 63 0.0014 32.6 2.5 35 493-531 1-35 (178)
245 PRK14963 DNA polymerase III su 22.8 53 0.0012 38.4 2.2 26 493-520 37-62 (504)
246 PRK05563 DNA polymerase III su 22.7 56 0.0012 38.6 2.4 27 492-520 38-64 (559)
247 PF01337 Barstar: Barstar (bar 22.7 1.3E+02 0.0027 26.7 4.1 44 690-733 32-77 (90)
248 cd02034 CooC The accessory pro 22.6 99 0.0021 29.1 3.6 32 494-527 1-35 (116)
249 PRK14964 DNA polymerase III su 22.6 61 0.0013 38.0 2.6 27 492-520 35-61 (491)
250 TIGR03018 pepcterm_TyrKin exop 22.5 2.6E+02 0.0056 28.2 6.7 42 489-531 32-76 (207)
251 TIGR00150 HI0065_YjeE ATPase, 22.4 47 0.001 32.5 1.4 30 490-521 20-49 (133)
252 PF12774 AAA_6: Hydrolytic ATP 22.4 82 0.0018 33.2 3.3 34 495-530 35-68 (231)
253 PF13177 DNA_pol3_delta2: DNA 22.3 60 0.0013 31.8 2.2 26 491-518 18-43 (162)
254 PRK07399 DNA polymerase III su 22.3 64 0.0014 35.4 2.5 26 492-519 26-51 (314)
255 PRK10078 ribose 1,5-bisphospho 22.2 87 0.0019 30.9 3.3 34 493-528 3-36 (186)
256 PF11101 DUF2884: Protein of u 22.0 1E+02 0.0022 32.6 3.8 42 162-209 1-43 (229)
257 PRK05953 precorrin-8X methylmu 21.9 1E+02 0.0022 32.8 3.8 42 703-744 87-128 (208)
258 PRK14948 DNA polymerase III su 21.7 63 0.0014 38.8 2.6 27 492-520 38-64 (620)
259 PF13191 AAA_16: AAA ATPase do 21.7 87 0.0019 29.6 3.0 48 691-741 136-185 (185)
260 PF01583 APS_kinase: Adenylyls 21.7 90 0.002 31.4 3.2 41 494-536 4-47 (156)
261 COG0464 SpoVK ATPases of the A 21.7 1.8E+02 0.004 33.2 6.1 57 689-748 323-389 (494)
262 PF11012 DUF2850: Protein of u 21.6 1.6E+02 0.0034 27.1 4.4 42 193-239 20-61 (79)
263 PF13953 PapC_C: PapC C-termin 21.5 1.3E+02 0.0029 25.6 3.8 35 202-236 6-40 (68)
264 PRK07133 DNA polymerase III su 21.4 63 0.0014 39.7 2.5 28 492-521 40-67 (725)
265 cd05141 Barstar_evA4336-like B 21.4 1.6E+02 0.0035 26.1 4.4 44 690-733 32-77 (81)
266 PRK06305 DNA polymerase III su 21.3 62 0.0013 37.2 2.3 28 492-521 39-66 (451)
267 COG1484 DnaC DNA replication p 21.3 1.5E+02 0.0033 31.5 5.0 76 439-530 65-144 (254)
268 PRK07696 sulfur carrier protei 21.3 90 0.002 26.8 2.8 25 199-223 34-60 (67)
269 PLN02200 adenylate kinase fami 21.2 81 0.0018 33.0 3.0 34 493-530 44-77 (234)
270 PRK14087 dnaA chromosomal repl 21.2 1.1E+02 0.0023 35.3 4.2 68 450-531 111-183 (450)
271 PF07883 Cupin_2: Cupin domain 21.2 2.4E+02 0.0052 22.8 5.2 37 189-231 21-57 (71)
272 cd00489 Barstar_like Barstar i 21.1 1.4E+02 0.0031 27.0 4.1 44 690-734 32-75 (85)
273 PRK14958 DNA polymerase III su 21.1 67 0.0014 37.6 2.5 28 492-521 38-65 (509)
274 PRK05022 anaerobic nitric oxid 21.0 82 0.0018 36.4 3.2 45 485-531 203-250 (509)
275 TIGR00005 rluA_subfam pseudour 20.9 79 0.0017 33.7 2.8 27 196-223 29-55 (299)
276 TIGR01618 phage_P_loop phage n 20.9 77 0.0017 33.4 2.7 39 485-527 5-43 (220)
277 TIGR02902 spore_lonB ATP-depen 20.8 1E+02 0.0022 36.1 4.0 35 492-528 86-130 (531)
278 PRK14956 DNA polymerase III su 20.8 68 0.0015 37.7 2.5 27 493-521 41-67 (484)
279 PRK06090 DNA polymerase III su 20.6 68 0.0015 35.5 2.4 28 491-520 24-51 (319)
280 PF00625 Guanylate_kin: Guanyl 20.3 92 0.002 30.6 3.0 28 493-522 3-30 (183)
281 TIGR01242 26Sp45 26S proteasom 20.3 1.8E+02 0.0038 32.1 5.4 57 689-748 203-272 (364)
282 PRK06547 hypothetical protein; 20.3 82 0.0018 31.5 2.7 34 492-527 15-48 (172)
283 PRK06964 DNA polymerase III su 20.3 69 0.0015 35.8 2.4 29 490-520 19-47 (342)
284 PRK07440 hypothetical protein; 20.3 93 0.002 27.1 2.7 25 199-223 37-63 (70)
285 PRK06871 DNA polymerase III su 20.1 71 0.0015 35.5 2.4 28 491-520 23-50 (325)
No 1
>KOG0615 consensus Serine/threonine protein kinase Chk2 and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.39 E-value=2.9e-13 Score=147.80 Aligned_cols=109 Identities=22% Similarity=0.338 Sum_probs=97.1
Q ss_pred CCcccceeeeccCCCCCceeeecceEEEecccccceeecCCCcccceeEEEEE----------ec-CCCceEEEEEecCC
Q 004011 129 GSRIPWARLISQCSQNSHLSMTGAVFTVGHNRQCDLYLKDPSISKNLCRLRRI----------EN-GGPSGALLEITGGK 197 (779)
Q Consensus 129 ~~~~pWGRLlSq~sq~P~v~I~~~~fTvGR~~~CDl~L~d~~iS~~hCkI~r~----------e~-gg~~va~LEd~ssN 197 (779)
....||+||+-..-..+++++.+++||+||+..||+.++...+|..|++|... .+ +...++||+|.++|
T Consensus 41 ~~~~~r~r~~~v~~~~~~~d~~nd~f~fGR~~~~d~~ln~~~~s~~~~~i~~~~~~~~~~f~~dr~~~sn~~y~~DhS~n 120 (475)
T KOG0615|consen 41 ATVKPRARLVGVRRGIKSIDLANDEFTFGRGDSCDAPLNLNNVSNKHFKILLYNKISKIHFRIDRDKNSNRVYLHDHSRN 120 (475)
T ss_pred ccccchhhhcceeeccccceeccceEEecCCCcccccccCccccccchheeeeeeeeeeeecccCCCccceEEEEecccC
Confidence 34678999999999999999999999999999999999998888888877543 22 23468999999999
Q ss_pred ceEEECCeecCCCceEEeeCCCEEEEccCCCeeEEEeecCc
Q 004011 198 GEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSYIFQQLSD 238 (779)
Q Consensus 198 GtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIFq~l~~ 238 (779)
|| |||.+.++||.+.+|+|||||.++.+.+++|+|.+++-
T Consensus 121 GT-~VN~e~i~k~~~r~lkN~dei~is~p~~~~~v~~~~s~ 160 (475)
T KOG0615|consen 121 GT-FVNDEMIGKGLSRILKNGDEISISIPALKIFVFEDLSR 160 (475)
T ss_pred cc-cccHhHhhccccccccCCCEEEeccchhheeeeecccc
Confidence 96 99999999999999999999999999999999999743
No 2
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=99.35 E-value=2.8e-12 Score=105.48 Aligned_cols=67 Identities=33% Similarity=0.517 Sum_probs=58.7
Q ss_pred EEEecccccceeecCCCcccceeEEEEEecCCCceEEEEEec-CCceEEECCeecCCCceEEeeCCCEEEEc
Q 004011 154 FTVGHNRQCDLYLKDPSISKNLCRLRRIENGGPSGALLEITG-GKGEVEVNGNVHPKDSQVVLRGGDELVFS 224 (779)
Q Consensus 154 fTvGR~~~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~s-sNGtV~VNGkkVgKg~kviL~nGDEIvfs 224 (779)
|+|||+..||++|.++.||..||.|...+. ..++|+|++ .|| |||||+++.++..+.|.+||+|.|+
T Consensus 1 ~~iGR~~~~di~l~~~~iSr~Ha~i~~~~~---~~~~i~d~~s~ng-t~vng~~l~~~~~~~L~~gd~i~~G 68 (68)
T PF00498_consen 1 VTIGRSPDCDIVLPDPSISRRHARISFDDD---GQFYIEDLGSTNG-TFVNGQRLGPGEPVPLKDGDIIRFG 68 (68)
T ss_dssp EEEESSTTSSEEETSTTSSTTSEEEEEETT---EEEEEEESSSSS--EEETTEEESSTSEEEE-TTEEEEET
T ss_pred CEEcCCCCCCEEECCHheeeeeeEEEEece---eeEEEEeCCCCCc-EEECCEEcCCCCEEECCCCCEEEcC
Confidence 789999999999999999999999998644 349999985 688 5999999999999999999999884
No 3
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=99.28 E-value=2.3e-11 Score=104.44 Aligned_cols=97 Identities=24% Similarity=0.390 Sum_probs=81.2
Q ss_pred ceeeeccCC--CCCceeeec-ceEEEeccccc-ceeecCCCcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCC
Q 004011 134 WARLISQCS--QNSHLSMTG-AVFTVGHNRQC-DLYLKDPSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPK 209 (779)
Q Consensus 134 WGRLlSq~s--q~P~v~I~~-~~fTvGR~~~C-Dl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgK 209 (779)
|+.|.+++. ..+.+.|.. ..|+|||+..| |+.|.+..+|..||.|..... ....+++..+.||+ ||||+++.+
T Consensus 1 ~~~L~~~~~~~~~~~~~l~~~~~~~iGr~~~~~~i~l~~~~iS~~H~~i~~~~~--~~~~~~~~~s~~g~-~vn~~~~~~ 77 (102)
T cd00060 1 VPRLVVLSGDASGRRYYLDPGGTYTIGRDSDNCDIVLDDPSVSRRHAVIRYDGD--GGVVLIDLGSTNGT-FVNGQRVSP 77 (102)
T ss_pred CeEEEEecCCCceeEEEECCCCeEEECcCCCcCCEEcCCCCeeCcceEEEEcCC--CCEEEEECCCCCCe-EECCEECCC
Confidence 567777766 677889998 99999999999 999999999999999998542 23466777777985 999999999
Q ss_pred CceEEeeCCCEEEEccCCCeeEEEe
Q 004011 210 DSQVVLRGGDELVFSPSGKHSYIFQ 234 (779)
Q Consensus 210 g~kviL~nGDEIvfs~~~~~aYIFq 234 (779)
+..+.|..||+|.|+. +.+.|.|+
T Consensus 78 ~~~~~l~~gd~i~ig~-~~~~~~~~ 101 (102)
T cd00060 78 GEPVRLRDGDVIRLGN-TSISFRFE 101 (102)
T ss_pred CCcEECCCCCEEEECC-eEEEEEEe
Confidence 9999999999999976 45566654
No 4
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=98.84 E-value=5.2e-09 Score=114.89 Aligned_cols=81 Identities=26% Similarity=0.334 Sum_probs=69.8
Q ss_pred ceeeecceEEEecccccceeecCCC--cccceeEEEEEecCCCceEEEEEecCCceEEEC--CeecCCCceEEeeCCCEE
Q 004011 146 HLSMTGAVFTVGHNRQCDLYLKDPS--ISKNLCRLRRIENGGPSGALLEITGGKGEVEVN--GNVHPKDSQVVLRGGDEL 221 (779)
Q Consensus 146 ~v~I~~~~fTvGR~~~CDl~L~d~~--iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VN--GkkVgKg~kviL~nGDEI 221 (779)
.+.+....++|||+..||++|.|.. ||..||+|.+. ++ ..+|+|+|+||| ||| |..|++|..+.|+.||+|
T Consensus 18 ~~~f~~~~~~IGR~~~~d~~l~d~~~~VS~~Ha~I~~~--~g--~~~l~DlStNGT-~VN~sg~~l~~~~~~~L~~GD~I 92 (396)
T TIGR03354 18 QKTFGTNGGTIGRSEDCDWVLPDPERHVSGRHARIRYR--DG--AYLLTDLSTNGV-FLNGSGSPLGRGNPVRLEQGDRL 92 (396)
T ss_pred EEEECCCCEEEecCCCCCEEeCCCCCCcchhhcEEEEE--CC--EEEEEECCCCCe-EECCCCCCCCCCCceEcCCCCEE
Confidence 4577788899999999999999988 99999999975 23 378999988995 999 999999999999999999
Q ss_pred EEccCCCeeE
Q 004011 222 VFSPSGKHSY 231 (779)
Q Consensus 222 vfs~~~~~aY 231 (779)
.|+...-+++
T Consensus 93 ~iG~~~lrv~ 102 (396)
T TIGR03354 93 RLGDYEIRVS 102 (396)
T ss_pred EECCEEEEEE
Confidence 9977443333
No 5
>COG1716 FOG: FHA domain [Signal transduction mechanisms]
Probab=98.49 E-value=5.7e-07 Score=86.69 Aligned_cols=76 Identities=29% Similarity=0.428 Sum_probs=65.1
Q ss_pred ceeeecceEEEecccccceeecCCCcccceeEEEEEecCCCceEEEEEecC-CceEEECCeecCCCceEEeeCCCEEEEc
Q 004011 146 HLSMTGAVFTVGHNRQCDLYLKDPSISKNLCRLRRIENGGPSGALLEITGG-KGEVEVNGNVHPKDSQVVLRGGDELVFS 224 (779)
Q Consensus 146 ~v~I~~~~fTvGR~~~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ss-NGtV~VNGkkVgKg~kviL~nGDEIvfs 224 (779)
-+.+.+..+|+||...+|++|++..+|..||.|++.... .||||+++ ||| ||||.++.. .+.|+.||.|.|+
T Consensus 83 ~~~~~~~~~tigr~~~~~i~~~~~~vSR~Ha~l~~~~~~----~~~~d~~S~nGt-~vn~~~v~~--~~~l~~gd~i~i~ 155 (191)
T COG1716 83 VIVLGEPVTTIGRDPDNDIVLDDDVVSRRHAELRREGNE----VFLEDLGSTNGT-YVNGEKVRQ--RVLLQDGDVIRLG 155 (191)
T ss_pred ccccccceEEeccCCCCCEEcCCCccccceEEEEEeCCc----eEEEECCCCcce-EECCeEccC--cEEcCCCCEEEEC
Confidence 334555689999999999999999999999999986444 67899998 885 999999998 8999999999997
Q ss_pred cCCC
Q 004011 225 PSGK 228 (779)
Q Consensus 225 ~~~~ 228 (779)
....
T Consensus 156 ~~~~ 159 (191)
T COG1716 156 GTLA 159 (191)
T ss_pred ccce
Confidence 6443
No 6
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=98.48 E-value=2.1e-07 Score=72.59 Aligned_cols=50 Identities=32% Similarity=0.447 Sum_probs=43.4
Q ss_pred EEEeccc-ccceeecCCCcccceeEEEEEecCCCceEEEEEec-CCceEEECCeec
Q 004011 154 FTVGHNR-QCDLYLKDPSISKNLCRLRRIENGGPSGALLEITG-GKGEVEVNGNVH 207 (779)
Q Consensus 154 fTvGR~~-~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~s-sNGtV~VNGkkV 207 (779)
++|||.. .|++.|.++.+|..||+|+....+ .++|++.+ .||+ ||||++|
T Consensus 1 ~~iGr~~~~~~i~~~~~~vs~~H~~i~~~~~~---~~~i~d~~s~~gt-~vng~~v 52 (52)
T smart00240 1 VTIGRSSEDCDIQLPGPSISRRHAEIVYDGGG---RFYLIDLGSTNGT-FVNGKRI 52 (52)
T ss_pred CEeCCCCCCCCEEeCCCCcchhHcEEEECCCC---eEEEEECCCCCCe-eECCEEC
Confidence 5899999 999999999999999999974332 58999999 6885 9999875
No 7
>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase
Probab=98.40 E-value=5.7e-07 Score=104.80 Aligned_cols=88 Identities=18% Similarity=0.223 Sum_probs=72.7
Q ss_pred CCCceee---ecceEEEecccccce-----eecCCCcccceeEEEEEecCCCceEEEEEecC-CceEEECCee-----cC
Q 004011 143 QNSHLSM---TGAVFTVGHNRQCDL-----YLKDPSISKNLCRLRRIENGGPSGALLEITGG-KGEVEVNGNV-----HP 208 (779)
Q Consensus 143 q~P~v~I---~~~~fTvGR~~~CDl-----~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ss-NGtV~VNGkk-----Vg 208 (779)
+.+.|.| .+--|.|||..+||+ +|.++.||+.|.+|.+. ++ ..||||++| ||| ||||+. +.
T Consensus 545 ~~~~~~l~~~~~~p~~iG~~~~~~~~~~~i~i~~~~vS~~Ha~i~~~--~~--~~~~~Dl~S~nGT-~v~~~~~~r~~~~ 619 (668)
T PLN02927 545 VSETLCLTKDEDQPCIVGSEPDQDFPGMRIVIPSSQVSKMHARVIYK--DG--AFFLMDLRSEHGT-YVTDNEGRRYRAT 619 (668)
T ss_pred ccceeeeecCCCCCeEecCCCCcCCCCceEEecCCccChhHeEEEEE--CC--EEEEEECCCCCcc-EEeCCCCceEecC
Confidence 4466788 555599999999997 99999999999999985 22 379999999 996 998888 45
Q ss_pred CCceEEeeCCCEEEEccCCCeeEEEee
Q 004011 209 KDSQVVLRGGDELVFSPSGKHSYIFQQ 235 (779)
Q Consensus 209 Kg~kviL~nGDEIvfs~~~~~aYIFq~ 235 (779)
-|..+.|++||+|-|+..++-+|--..
T Consensus 620 p~~~~~l~~~d~I~~g~~~~~~fr~~~ 646 (668)
T PLN02927 620 PNFPARFRSSDIIEFGSDKKAAFRVKV 646 (668)
T ss_pred CCCceEeCCCCEEEeCCCcceeEEEEe
Confidence 677999999999999987765565443
No 8
>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=97.95 E-value=1.3e-05 Score=87.94 Aligned_cols=98 Identities=24% Similarity=0.326 Sum_probs=87.7
Q ss_pred HHHHHHHHHHHhcccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHH
Q 004011 430 ARRQAFKDSLQEGILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQET 509 (779)
Q Consensus 430 ~r~~~fk~~~~~~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~ 509 (779)
..-..|+..+...||.+.+|+|+|++--= -|.++..|-+..-.-|++.++.+ ...|...+.-|||-||+| .-..|
T Consensus 68 i~~ne~E~~i~s~~v~p~~I~v~f~DIgg--Le~v~~~L~e~VilPlr~pelF~-~g~Ll~p~kGiLL~GPpG--~GKTm 142 (386)
T KOG0737|consen 68 IQKNEYEKRIASDVVPPSEIGVSFDDIGG--LEEVKDALQELVILPLRRPELFA-KGKLLRPPKGILLYGPPG--TGKTM 142 (386)
T ss_pred hhhhHHHHHhhhcccchhhceeehhhccc--hHHHHHHHHHHHhhcccchhhhc-ccccccCCccceecCCCC--chHHH
Confidence 44567899999999999999999998766 79999999999999999999987 446677999999999999 68999
Q ss_pred HHHHHHhhccCeEEEEeccCCCC
Q 004011 510 LAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 510 LaKALA~~F~AkLLilDs~~l~G 532 (779)
||||+|++-||.+.-|+.+.+.+
T Consensus 143 lAKA~Akeaga~fInv~~s~lt~ 165 (386)
T KOG0737|consen 143 LAKAIAKEAGANFINVSVSNLTS 165 (386)
T ss_pred HHHHHHHHcCCCcceeeccccch
Confidence 99999999999999999988754
No 9
>COG3456 Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=97.90 E-value=1.6e-05 Score=88.10 Aligned_cols=78 Identities=28% Similarity=0.449 Sum_probs=65.6
Q ss_pred eecceEEEecccccceeecCC--CcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCCCce-EEeeCCCEEEEcc
Q 004011 149 MTGAVFTVGHNRQCDLYLKDP--SISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPKDSQ-VVLRGGDELVFSP 225 (779)
Q Consensus 149 I~~~~fTvGR~~~CDl~L~d~--~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgKg~k-viL~nGDEIvfs~ 225 (779)
+.....+|||+..||-.|.|+ .||+-||+|... +|. .||-|+|+|| ++|||-.+..|.- +-|..||||-++-
T Consensus 23 f~~~~g~IGrs~dcdW~i~D~~~~VS~~Hc~I~~~--dg~--f~L~DtS~g~-l~VNgs~~~~g~~~~RLqqGd~i~iG~ 97 (430)
T COG3456 23 FDRGGGVIGRSPDCDWQIDDPERFVSKQHCTISYR--DGG--FCLTDTSNGG-LLVNGSDLPLGEGSARLQQGDEILIGR 97 (430)
T ss_pred hhcCCcccccCCCCCccccCcccccchhheEEEec--CCe--EEEEecCCCc-eeecccccCCCCCccccccCCEEeecc
Confidence 345668999999999999996 699999999974 332 7899999666 5999999999988 9999999999954
Q ss_pred CCCeeEEEeec
Q 004011 226 SGKHSYIFQQL 236 (779)
Q Consensus 226 ~~~~aYIFq~l 236 (779)
|||.-.
T Consensus 98 -----y~i~V~ 103 (430)
T COG3456 98 -----YIIRVH 103 (430)
T ss_pred -----EEEEEE
Confidence 777754
No 10
>CHL00195 ycf46 Ycf46; Provisional
Probab=97.12 E-value=0.0025 Score=72.58 Aligned_cols=82 Identities=26% Similarity=0.212 Sum_probs=54.3
Q ss_pred cccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 442 GILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 442 ~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
++++-...+++|++.-- -++.|.-|....-.+.. ....|+ + +..+.|||.||+| .-..+||||+|++++++
T Consensus 216 ~~le~~~~~~~~~dvgG--l~~lK~~l~~~~~~~~~--~~~~~g--l-~~pkGILL~GPpG--TGKTllAkaiA~e~~~~ 286 (489)
T CHL00195 216 EILEFYSVNEKISDIGG--LDNLKDWLKKRSTSFSK--QASNYG--L-PTPRGLLLVGIQG--TGKSLTAKAIANDWQLP 286 (489)
T ss_pred ccccccCCCCCHHHhcC--HHHHHHHHHHHHHHhhH--HHHhcC--C-CCCceEEEECCCC--CcHHHHHHHHHHHhCCC
Confidence 45555566777776655 36667666543211111 111232 2 3457899999999 57889999999999999
Q ss_pred EEEEeccCCCC
Q 004011 522 LLIVDSLLLPG 532 (779)
Q Consensus 522 LLilDs~~l~G 532 (779)
|+.+|...|++
T Consensus 287 ~~~l~~~~l~~ 297 (489)
T CHL00195 287 LLRLDVGKLFG 297 (489)
T ss_pred EEEEEhHHhcc
Confidence 99999754443
No 11
>KOG1881 consensus Anion exchanger adaptor protein Kanadaptin, contains FHA domain [General function prediction only]
Probab=96.97 E-value=0.0005 Score=80.50 Aligned_cols=87 Identities=29% Similarity=0.363 Sum_probs=74.2
Q ss_pred cceEEEecccccceeecCCCcccceeEEEEEecC-------CCceEEEEEecC-CceEEECCeecCCCceEEeeCCCEEE
Q 004011 151 GAVFTVGHNRQCDLYLKDPSISKNLCRLRRIENG-------GPSGALLEITGG-KGEVEVNGNVHPKDSQVVLRGGDELV 222 (779)
Q Consensus 151 ~~~fTvGR~~~CDl~L~d~~iS~~hCkI~r~e~g-------g~~va~LEd~ss-NGtV~VNGkkVgKg~kviL~nGDEIv 222 (779)
...|+|||-..||+.+..++||..||.|-+-..+ +...-||.|+|+ -|| |+|-.+|.+..-+.++-|+.+-
T Consensus 176 ~~~~~fgr~~~cD~~~eHpsISr~h~vlQy~~~~~~~p~~s~~~g~~i~dlgsThgt-~~NK~rvppk~yir~~Vg~v~~ 254 (793)
T KOG1881|consen 176 AAACLFGRLGGCDVALEHPSISRFHAVLQYKASGPDDPCASNGEGWYIYDLGSTHGT-FLNKDRVPPKVYIRDRVGHVAR 254 (793)
T ss_pred ceeEEecccCCCccccccCcccccceeeeccCCCCCccccCCCCceEEeeccccccc-eeccccCCCcchhhhhHHHHHH
Confidence 3458999999999999999999999999874211 124589999999 686 9999999999999999999999
Q ss_pred EccCCCeeEEEeecCcc
Q 004011 223 FSPSGKHSYIFQQLSDD 239 (779)
Q Consensus 223 fs~~~~~aYIFq~l~~e 239 (779)
|.-+.+ +||||....+
T Consensus 255 fggsTr-l~i~Qgp~eD 270 (793)
T KOG1881|consen 255 FGGSTR-LYIFQGPEED 270 (793)
T ss_pred hcCceE-EEEeeCCCcC
Confidence 987765 9999987665
No 12
>KOG1882 consensus Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms]
Probab=96.41 E-value=0.0082 Score=63.52 Aligned_cols=100 Identities=22% Similarity=0.210 Sum_probs=74.4
Q ss_pred CCCCcccce--eeeccCCCCCc---eeeecceEEEeccc-ccceeecCCCcccceeEEEEE----e-cCC----CceEEE
Q 004011 127 KVGSRIPWA--RLISQCSQNSH---LSMTGAVFTVGHNR-QCDLYLKDPSISKNLCRLRRI----E-NGG----PSGALL 191 (779)
Q Consensus 127 k~~~~~pWG--RLlSq~sq~P~---v~I~~~~fTvGR~~-~CDl~L~d~~iS~~hCkI~r~----e-~gg----~~va~L 191 (779)
.++...||. ||++....-+- +-...+-|-+||.. --||-+..++-|+-||-|.-- + .+| -+--||
T Consensus 164 ppearkP~kRwrLy~fk~~e~l~~l~iHrqs~yL~gRerkIaDi~idhpScSKQHaviQyR~v~~~r~dGt~grrvkpYi 243 (293)
T KOG1882|consen 164 PPEARKPKKRWRLYPFKCYEVLPVLYIHRQSCYLDGRERKIADIPIDHPSCSKQHAVIQYRLVEFTRADGTVGRRVKPYI 243 (293)
T ss_pred CchhcCchhheecccccCCcccchheeeeeeeeecCceeeeeccCCCCccccccceeeeeeecccccCCCccceeeeeEE
Confidence 556677776 47766543333 24467779999955 567888889999999998642 1 222 234788
Q ss_pred EEecC-CceEEECCeecCCCceEEeeCCCEEEEccCC
Q 004011 192 EITGG-KGEVEVNGNVHPKDSQVVLRGGDELVFSPSG 227 (779)
Q Consensus 192 Ed~ss-NGtV~VNGkkVgKg~kviL~nGDEIvfs~~~ 227 (779)
=|+++ ||| |+|.++|.--.-..|..+|.|-|+.+.
T Consensus 244 iDLgS~NgT-fLNnk~IepqRYyEL~ekDvlkfgfs~ 279 (293)
T KOG1882|consen 244 IDLGSGNGT-FLNNKVIEPQRYYELREKDVLKFGFSS 279 (293)
T ss_pred EecCCCCcc-eecCcccCchheeeeecCceeeeccch
Confidence 88887 896 999999999999999999999997644
No 13
>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=96.31 E-value=0.012 Score=66.48 Aligned_cols=67 Identities=24% Similarity=0.282 Sum_probs=56.2
Q ss_pred ccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 450 EVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 450 ~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
+|-|+.||- -+..|.+|++++-.-+-..+. ...|.+.-+.|||.||+| --..||+||+|-+-+|.+.
T Consensus 149 ~v~~~di~g--l~~~k~~l~e~vi~p~lr~d~---F~glr~p~rglLLfGPpg--tGKtmL~~aiAsE~~atff 215 (428)
T KOG0740|consen 149 NVGWDDIAG--LEDAKQSLKEAVILPLLRPDL---FLGLREPVRGLLLFGPPG--TGKTMLAKAIATESGATFF 215 (428)
T ss_pred cccccCCcc--hhhHHHHhhhhhhhcccchHh---hhccccccchhheecCCC--CchHHHHHHHHhhhcceEe
Confidence 477999998 688899999988777766666 457888888999999999 5799999999999888753
No 14
>KOG0245 consensus Kinesin-like protein [Cytoskeleton]
Probab=96.03 E-value=0.017 Score=70.43 Aligned_cols=82 Identities=26% Similarity=0.449 Sum_probs=66.4
Q ss_pred eecceEEEecc---cccceeecCCCcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 149 MTGAVFTVGHN---RQCDLYLKDPSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 149 I~~~~fTvGR~---~~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
|-+-+-+|||. ..-||.|....|---||-|+.+ +|+-||.|+--..-- +|||||.|.- ...|..||.|+|+
T Consensus 474 ikeG~TrVG~~~a~~~~DI~LsG~~I~~qHC~i~~~--~g~~~vtl~p~e~ae-tyVNGk~v~e--p~qL~~GdRiilG- 547 (1221)
T KOG0245|consen 474 IKEGETRVGREDASSRQDIVLSGQLIREQHCSIRNE--GGNDVVTLEPCEDAE-TYVNGKLVTE--PTQLRSGDRIILG- 547 (1221)
T ss_pred eccCceecCCCCcccCCceEecchhhhhhceEEEec--CCCceEEeccCCccc-eeEccEEcCC--cceeccCCEEEEc-
Confidence 33445678974 4679999999999999999985 444578888777654 5999999987 7899999999995
Q ss_pred CCCeeEEEeecC
Q 004011 226 SGKHSYIFQQLS 237 (779)
Q Consensus 226 ~~~~aYIFq~l~ 237 (779)
++|+|.|.+..
T Consensus 548 -~~H~frfn~P~ 558 (1221)
T KOG0245|consen 548 -GNHVFRFNHPE 558 (1221)
T ss_pred -CceeEEecCHH
Confidence 58999999874
No 15
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=94.90 E-value=0.044 Score=61.51 Aligned_cols=96 Identities=22% Similarity=0.225 Sum_probs=68.2
Q ss_pred HHHHHHHHHHhcc----cCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHH
Q 004011 431 RRQAFKDSLQEGI----LGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIY 506 (779)
Q Consensus 431 r~~~fk~~~~~~V----vdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiY 506 (779)
..+-|++.|++.. +.-..-.|+|+..-= -+..|..|..+.=.-|++++. |..-.-.....|||.||+| .-
T Consensus 215 ~~~~~~~~l~~~~~~~~~~~~~~~v~~~digg--l~~~k~~l~e~v~~~~~~~e~--~~~~~~~~~~giLl~GpPG--tG 288 (494)
T COG0464 215 TEDDFEEALKKVLPSRGVLFEDEDVTLDDIGG--LEEAKEELKEAIETPLKRPEL--FRKLGLRPPKGVLLYGPPG--TG 288 (494)
T ss_pred cHHHHHHHHHhcCcccccccCCCCcceehhhc--HHHHHHHHHHHHHhHhhChHH--HHhcCCCCCCeeEEECCCC--CC
Confidence 3455666666643 223344455544332 377888998888888888876 3332223334999999998 57
Q ss_pred HHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 507 QETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 507 QE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
..|||||+|++.+++++.+|..++.+
T Consensus 289 KT~lAkava~~~~~~fi~v~~~~l~s 314 (494)
T COG0464 289 KTLLAKAVALESRSRFISVKGSELLS 314 (494)
T ss_pred HHHHHHHHHhhCCCeEEEeeCHHHhc
Confidence 99999999999999999999987765
No 16
>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=94.68 E-value=0.048 Score=64.18 Aligned_cols=85 Identities=24% Similarity=0.300 Sum_probs=66.2
Q ss_pred CCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEE
Q 004011 446 PENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIV 525 (779)
Q Consensus 446 g~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLil 525 (779)
..+.+|+|..+-- ++..-+.+. .- ..|++|+++..|+--.+| +.+||-||+| --..|||.|+|.++++++|-+
T Consensus 182 ~~~snv~f~diGG-~d~~~~el~-~l-i~~i~~Pe~~~~lGv~Pp--rGvLlHGPPG--CGKT~lA~AiAgel~vPf~~i 254 (802)
T KOG0733|consen 182 FPESNVSFSDIGG-LDKTLAELC-EL-IIHIKHPEVFSSLGVRPP--RGVLLHGPPG--CGKTSLANAIAGELGVPFLSI 254 (802)
T ss_pred CCCCCcchhhccC-hHHHHHHHH-HH-HHHhcCchhHhhcCCCCC--CceeeeCCCC--ccHHHHHHHHhhhcCCceEee
Confidence 5566888988765 233333332 22 357999999888776665 6799999999 578999999999999999999
Q ss_pred eccCCCCCCCCc
Q 004011 526 DSLLLPGGSSKE 537 (779)
Q Consensus 526 Ds~~l~G~~ske 537 (779)
-...+.+|.+-|
T Consensus 255 sApeivSGvSGE 266 (802)
T KOG0733|consen 255 SAPEIVSGVSGE 266 (802)
T ss_pred cchhhhcccCcc
Confidence 999998888865
No 17
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=94.67 E-value=0.045 Score=61.38 Aligned_cols=86 Identities=26% Similarity=0.371 Sum_probs=61.3
Q ss_pred ccCCCccccccccccccchhhHHHHHHhhhhccccCccccccc-CCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 443 ILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYA-SDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 443 Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt-~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
+..+++|.-.+++| .+=-|+.|.+|.-|+|-|++.-...... .+.....+.|||.||+| .-..+|||+||+.++.+
T Consensus 59 ~~~p~~i~~~L~~~-ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~G--tGKT~lAr~lA~~l~~p 135 (412)
T PRK05342 59 LPTPKEIKAHLDQY-VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTG--SGKTLLAQTLARILDVP 135 (412)
T ss_pred CCCHHHHHHHHhhH-eeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCC--CCHHHHHHHHHHHhCCC
Confidence 33444444444442 1225889999999999887764332111 13444567899999999 57899999999999999
Q ss_pred EEEEeccCCC
Q 004011 522 LLIVDSLLLP 531 (779)
Q Consensus 522 LLilDs~~l~ 531 (779)
+..+|.+.|.
T Consensus 136 f~~id~~~l~ 145 (412)
T PRK05342 136 FAIADATTLT 145 (412)
T ss_pred ceecchhhcc
Confidence 9999998875
No 18
>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=94.54 E-value=0.038 Score=62.68 Aligned_cols=70 Identities=19% Similarity=0.271 Sum_probs=56.1
Q ss_pred ccchhhHHHHHHhhhhccccCcccccccC-CCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 458 YYLSDITKNVLIASTYVHLKCNNFAKYAS-DLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 458 YYLSE~TK~vL~saayvHLk~~~~sKyt~-~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
.+--++.|.+|.-|.|.|.+...+.+-.+ .+.+ +.|||.||+| .-.-+|||+||+.++++++-+|.+.|.
T Consensus 14 IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p--~~ILLiGppG--~GKT~lAraLA~~l~~~fi~vdat~~~ 84 (441)
T TIGR00390 14 IIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTP--KNILMIGPTG--VGKTEIARRLAKLANAPFIKVEATKFT 84 (441)
T ss_pred ccCHHHHHHHHHHHHHhhhhhhccccccccccCC--ceEEEECCCC--CCHHHHHHHHHHHhCCeEEEeecceee
Confidence 33468999999999999977655543222 3333 7899999999 578889999999999999999998885
No 19
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=94.18 E-value=0.045 Score=60.37 Aligned_cols=79 Identities=23% Similarity=0.206 Sum_probs=59.0
Q ss_pred CccccccccccccchhhHHHHHHhhhhccccCcccc-cccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEE
Q 004011 447 ENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFA-KYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIV 525 (779)
Q Consensus 447 ~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~s-Kyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLil 525 (779)
+..+++|+++.. -|..+.-|..+....|++.++. +++ +. ..+.|||.||+| .-..+||||+|++++++++.+
T Consensus 124 ~~p~~~~~di~G--l~~~~~~l~~~i~~pl~~~~~~~~~g--~~-~p~gvLL~GppG--tGKT~lAkaia~~~~~~~i~v 196 (389)
T PRK03992 124 ESPNVTYEDIGG--LEEQIREVREAVELPLKKPELFEEVG--IE-PPKGVLLYGPPG--TGKTLLAKAVAHETNATFIRV 196 (389)
T ss_pred CCCCCCHHHhCC--cHHHHHHHHHHHHHHhhCHHHHHhcC--CC-CCCceEEECCCC--CChHHHHHHHHHHhCCCEEEe
Confidence 445788888765 4666666777766677776543 332 22 235799999999 579999999999999999999
Q ss_pred eccCCCC
Q 004011 526 DSLLLPG 532 (779)
Q Consensus 526 Ds~~l~G 532 (779)
+...|..
T Consensus 197 ~~~~l~~ 203 (389)
T PRK03992 197 VGSELVQ 203 (389)
T ss_pred ehHHHhH
Confidence 9888753
No 20
>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=93.94 E-value=0.044 Score=61.93 Aligned_cols=78 Identities=26% Similarity=0.322 Sum_probs=58.8
Q ss_pred CCCccccccccccccchhhHHHHHHhhhhccccCcc-cccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 445 GPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNN-FAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 445 dg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~-~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
..+..+++|+++.= -++.|.-|..... .|++.+ +.++.. ...+.|||.||+| .-..+||||||++++++++
T Consensus 46 ~~~~~~~~~~di~g--~~~~k~~l~~~~~-~l~~~~~~~~~g~---~~~~giLL~GppG--tGKT~la~alA~~~~~~~~ 117 (495)
T TIGR01241 46 NEEKPKVTFKDVAG--IDEAKEELMEIVD-FLKNPSKFTKLGA---KIPKGVLLVGPPG--TGKTLLAKAVAGEAGVPFF 117 (495)
T ss_pred cCCCCCCCHHHhCC--HHHHHHHHHHHHH-HHHCHHHHHhcCC---CCCCcEEEECCCC--CCHHHHHHHHHHHcCCCee
Confidence 34567899999974 5777777776555 366654 333332 3346799999999 5799999999999999999
Q ss_pred EEeccCC
Q 004011 524 IVDSLLL 530 (779)
Q Consensus 524 ilDs~~l 530 (779)
.++...|
T Consensus 118 ~i~~~~~ 124 (495)
T TIGR01241 118 SISGSDF 124 (495)
T ss_pred eccHHHH
Confidence 9887766
No 21
>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional
Probab=93.51 E-value=0.078 Score=60.27 Aligned_cols=68 Identities=19% Similarity=0.288 Sum_probs=54.5
Q ss_pred hhhHHHHHHhhhhccccCccccccc-CCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 461 SDITKNVLIASTYVHLKCNNFAKYA-SDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 461 SE~TK~vL~saayvHLk~~~~sKyt-~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
-++.|.+|..|.|-|.+...+..-. ..+.+ +.|||.||+| .-.-+|||+||+.++++++.+|.+.|..
T Consensus 20 Qe~AkkalavAl~~~~~r~~l~~~~~~e~~~--~~ILliGp~G--~GKT~LAr~LAk~l~~~fi~vD~t~f~e 88 (443)
T PRK05201 20 QDDAKRAVAIALRNRWRRMQLPEELRDEVTP--KNILMIGPTG--VGKTEIARRLAKLANAPFIKVEATKFTE 88 (443)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCcccccccCC--ceEEEECCCC--CCHHHHHHHHHHHhCChheeecchhhcc
Confidence 5889999999999998766554221 12333 7899999999 5678899999999999999999998863
No 22
>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=93.40 E-value=0.1 Score=58.77 Aligned_cols=83 Identities=29% Similarity=0.428 Sum_probs=58.7
Q ss_pred CCccccccccccccchhhHHHHHHhhhhccccCccc--cccc-CCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeE
Q 004011 446 PENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNF--AKYA-SDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARL 522 (779)
Q Consensus 446 g~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~--sKyt-~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkL 522 (779)
+++|.-.++++ -+--|+.|.+|.-|.|-|.+.-.. .+.. .+..-....|||.||+| .-..+|||+||+.+++++
T Consensus 68 p~~i~~~L~~~-ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~G--sGKT~lAraLA~~l~~pf 144 (413)
T TIGR00382 68 PKEIKAHLDEY-VIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTG--SGKTLLAQTLARILNVPF 144 (413)
T ss_pred HHHHHHHhcce-ecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCC--cCHHHHHHHHHHhcCCCe
Confidence 33333334433 233689999999999999887432 1111 11223456899999999 578899999999999999
Q ss_pred EEEeccCCC
Q 004011 523 LIVDSLLLP 531 (779)
Q Consensus 523 LilDs~~l~ 531 (779)
.++|.+.|.
T Consensus 145 ~~~da~~L~ 153 (413)
T TIGR00382 145 AIADATTLT 153 (413)
T ss_pred EEechhhcc
Confidence 999988874
No 23
>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=93.21 E-value=0.085 Score=62.54 Aligned_cols=76 Identities=24% Similarity=0.213 Sum_probs=59.7
Q ss_pred ccccccccccchhhHHHHHHhhhhccccCcccc-cccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 450 EVSFESFPYYLSDITKNVLIASTYVHLKCNNFA-KYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 450 ~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~s-Kyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
+++|++... -+..|..|....-..+++.++- ++. +. ..+.|||.||+| .-..+||||||+..++.++.++..
T Consensus 449 ~~~~~di~g--~~~~k~~l~~~v~~~~~~~~~~~~~g--~~-~~~giLL~GppG--tGKT~lakalA~e~~~~fi~v~~~ 521 (733)
T TIGR01243 449 NVRWSDIGG--LEEVKQELREAVEWPLKHPEIFEKMG--IR-PPKGVLLFGPPG--TGKTLLAKAVATESGANFIAVRGP 521 (733)
T ss_pred ccchhhccc--HHHHHHHHHHHHHhhhhCHHHHHhcC--CC-CCceEEEECCCC--CCHHHHHHHHHHhcCCCEEEEehH
Confidence 567777554 7899999998887778876654 332 22 235699999999 578999999999999999999988
Q ss_pred CCCC
Q 004011 529 LLPG 532 (779)
Q Consensus 529 ~l~G 532 (779)
.|..
T Consensus 522 ~l~~ 525 (733)
T TIGR01243 522 EILS 525 (733)
T ss_pred HHhh
Confidence 7754
No 24
>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]
Probab=93.11 E-value=0.22 Score=60.09 Aligned_cols=96 Identities=25% Similarity=0.295 Sum_probs=78.9
Q ss_pred hhHHHHHHHHHHHhcccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHH
Q 004011 428 ISARRQAFKDSLQEGILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQ 507 (779)
Q Consensus 428 ~~~r~~~fk~~~~~~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQ 507 (779)
+..+-.+.+++|-..|=-++==+|+||+--= -|.+|..+.+.--..|+|+++- +++|-.-| .|||-||+| .-.
T Consensus 646 f~kals~~~~~fs~aiGAPKIPnV~WdDVGG--LeevK~eIldTIqlPL~hpeLf--ssglrkRS-GILLYGPPG--TGK 718 (953)
T KOG0736|consen 646 FDKALSRLQKEFSDAIGAPKIPNVSWDDVGG--LEEVKTEILDTIQLPLKHPELF--SSGLRKRS-GILLYGPPG--TGK 718 (953)
T ss_pred HHHHHHHHHHhhhhhcCCCCCCccchhcccC--HHHHHHHHHHHhcCcccChhhh--hccccccc-eeEEECCCC--Cch
Confidence 4455566677777788888888999998776 6999999999999999999984 66776544 499999999 478
Q ss_pred HHHHHHHHhhccCeEEEEeccCC
Q 004011 508 ETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 508 E~LaKALA~~F~AkLLilDs~~l 530 (779)
..||||.|.+|...+|-+-.-.|
T Consensus 719 TLlAKAVATEcsL~FlSVKGPEL 741 (953)
T KOG0736|consen 719 TLLAKAVATECSLNFLSVKGPEL 741 (953)
T ss_pred HHHHHHHHhhceeeEEeecCHHH
Confidence 99999999999999887766555
No 25
>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=93.05 E-value=0.11 Score=61.53 Aligned_cols=78 Identities=29% Similarity=0.283 Sum_probs=64.4
Q ss_pred CCccccccccccccchhhHHHHHHhhhhccccCcc-cccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEE
Q 004011 446 PENIEVSFESFPYYLSDITKNVLIASTYVHLKCNN-FAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLI 524 (779)
Q Consensus 446 g~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~-~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLi 524 (779)
++--+|+|++.-= -|+-|.-|-.+.-.-|+|.+ |.+|+ -+..++|||.||+| --..+||||||++-++.+|-
T Consensus 426 ve~p~v~W~dIGG--lE~lK~elq~~V~~p~~~pe~F~r~G---i~ppkGVLlyGPPG--C~KT~lAkalAne~~~nFls 498 (693)
T KOG0730|consen 426 VEMPNVSWDDIGG--LEELKRELQQAVEWPLKHPEKFARFG---ISPPKGVLLYGPPG--CGKTLLAKALANEAGMNFLS 498 (693)
T ss_pred ccCCCCChhhccC--HHHHHHHHHHHHhhhhhchHHHHHhc---CCCCceEEEECCCC--cchHHHHHHHhhhhcCCeee
Confidence 7788999999884 38899999888888999975 44776 45678999999999 56889999999999999998
Q ss_pred EeccCC
Q 004011 525 VDSLLL 530 (779)
Q Consensus 525 lDs~~l 530 (779)
+=.-.|
T Consensus 499 vkgpEL 504 (693)
T KOG0730|consen 499 VKGPEL 504 (693)
T ss_pred ccCHHH
Confidence 754433
No 26
>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=92.92 E-value=0.11 Score=58.64 Aligned_cols=78 Identities=21% Similarity=0.278 Sum_probs=64.7
Q ss_pred CccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 447 ENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 447 ~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
++.+|.||+.== -++.|.+|-+|....+.-.+| ...|-..=+.|||.||+| .-..|||||+|.+.|.-+.-+-
T Consensus 205 ~np~ikW~DIag--l~~AK~lL~EAVvlPi~mPe~---F~GirrPWkgvLm~GPPG--TGKTlLAKAvATEc~tTFFNVS 277 (491)
T KOG0738|consen 205 RNPNIKWDDIAG--LHEAKKLLKEAVVLPIWMPEF---FKGIRRPWKGVLMVGPPG--TGKTLLAKAVATECGTTFFNVS 277 (491)
T ss_pred cCCCcChHhhcc--hHHHHHHHHHHHhhhhhhHHH---HhhcccccceeeeeCCCC--CcHHHHHHHHHHhhcCeEEEec
Confidence 356688877544 688999999999999875554 556667889999999999 4799999999999999988888
Q ss_pred ccCCC
Q 004011 527 SLLLP 531 (779)
Q Consensus 527 s~~l~ 531 (779)
++.|.
T Consensus 278 sstlt 282 (491)
T KOG0738|consen 278 SSTLT 282 (491)
T ss_pred hhhhh
Confidence 88874
No 27
>CHL00176 ftsH cell division protein; Validated
Probab=92.65 E-value=0.11 Score=61.25 Aligned_cols=82 Identities=17% Similarity=0.185 Sum_probs=60.2
Q ss_pred ccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeE
Q 004011 443 ILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARL 522 (779)
Q Consensus 443 Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkL 522 (779)
+....+.+++|+++.=+ +..|.-|-.... .|++.+. |..-=....+.|||.||+| .-..+||||||++.++++
T Consensus 172 ~~~~~~~~~~f~dv~G~--~~~k~~l~eiv~-~lk~~~~--~~~~g~~~p~gVLL~GPpG--TGKT~LAralA~e~~~p~ 244 (638)
T CHL00176 172 FQMEADTGITFRDIAGI--EEAKEEFEEVVS-FLKKPER--FTAVGAKIPKGVLLVGPPG--TGKTLLAKAIAGEAEVPF 244 (638)
T ss_pred hhcccCCCCCHHhccCh--HHHHHHHHHHHH-HHhCHHH--HhhccCCCCceEEEECCCC--CCHHHHHHHHHHHhCCCe
Confidence 34456788999997753 677777766654 3666443 2222234456799999999 579999999999999999
Q ss_pred EEEeccCCC
Q 004011 523 LIVDSLLLP 531 (779)
Q Consensus 523 LilDs~~l~ 531 (779)
+.++.+.|.
T Consensus 245 i~is~s~f~ 253 (638)
T CHL00176 245 FSISGSEFV 253 (638)
T ss_pred eeccHHHHH
Confidence 999887763
No 28
>PRK12377 putative replication protein; Provisional
Probab=92.57 E-value=0.19 Score=52.86 Aligned_cols=84 Identities=20% Similarity=0.325 Sum_probs=53.3
Q ss_pred HHHHHHHHHHhcccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHH
Q 004011 431 RRQAFKDSLQEGILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETL 510 (779)
Q Consensus 431 r~~~fk~~~~~~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~L 510 (779)
++.+.++-+.+.-++.+--+.|||||-.. .+..+.++ ..+... ..++..-..-|+|+||+| .-.-.|
T Consensus 51 ~~~~~~~~~~~s~i~~~~~~~tFdnf~~~-~~~~~~a~-~~a~~~---------a~~~~~~~~~l~l~G~~G--tGKThL 117 (248)
T PRK12377 51 QQLRVEKILNRSGIQPLHRKCSFANYQVQ-NDGQRYAL-SQAKSI---------ADELMTGCTNFVFSGKPG--TGKNHL 117 (248)
T ss_pred HHHHHHHHHHHcCCCcccccCCcCCcccC-ChhHHHHH-HHHHHH---------HHHHHhcCCeEEEECCCC--CCHHHH
Confidence 34556666778888999999999999432 23333333 333222 222222235799999999 578899
Q ss_pred HHHHHhhcc---CeEEEEec
Q 004011 511 AKALAKHFS---ARLLIVDS 527 (779)
Q Consensus 511 aKALA~~F~---AkLLilDs 527 (779)
|.|+|+++. ...+.+..
T Consensus 118 a~AIa~~l~~~g~~v~~i~~ 137 (248)
T PRK12377 118 AAAIGNRLLAKGRSVIVVTV 137 (248)
T ss_pred HHHHHHHHHHcCCCeEEEEH
Confidence 999999884 33444443
No 29
>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=92.33 E-value=0.1 Score=46.41 Aligned_cols=36 Identities=39% Similarity=0.517 Sum_probs=32.2
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
|||.||+| .-.-.|||+||++++++++.+|...+.+
T Consensus 1 ill~G~~G--~GKT~l~~~la~~l~~~~~~i~~~~~~~ 36 (132)
T PF00004_consen 1 ILLHGPPG--TGKTTLARALAQYLGFPFIEIDGSELIS 36 (132)
T ss_dssp EEEESSTT--SSHHHHHHHHHHHTTSEEEEEETTHHHT
T ss_pred CEEECcCC--CCeeHHHHHHHhhccccccccccccccc
Confidence 79999998 6799999999999999999999866653
No 30
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=91.86 E-value=0.16 Score=56.26 Aligned_cols=69 Identities=33% Similarity=0.398 Sum_probs=54.3
Q ss_pred hhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 461 SDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 461 SE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
-|+.|.+|-=|.|-|-|.-.+...-.+..=.---|||-||.|| -...||+-||+.+++++-|-|.+.|.
T Consensus 66 Qe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGs--GKTlLAqTLAk~LnVPFaiADATtLT 134 (408)
T COG1219 66 QEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGS--GKTLLAQTLAKILNVPFAIADATTLT 134 (408)
T ss_pred chhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCC--cHHHHHHHHHHHhCCCeeeccccchh
Confidence 5899999999999997764332222223333346999999995 68899999999999999999999993
No 31
>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=91.85 E-value=0.084 Score=58.57 Aligned_cols=75 Identities=31% Similarity=0.341 Sum_probs=59.4
Q ss_pred cccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 442 GILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 442 ~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
-++++.+..=-||+-=| --+-|+-|++-|.+-|+-.++ +-..+|-+-+|=|||-|||| .-...|.||||+++-+|
T Consensus 130 w~LPa~eF~glWEsLiy--ds~lK~~ll~Ya~s~l~fsek-~vntnlIt~NRliLlhGPPG--TGKTSLCKaLaQkLSIR 204 (423)
T KOG0744|consen 130 WYLPAAEFDGLWESLIY--DSNLKERLLSYAASALLFSEK-KVNTNLITWNRLILLHGPPG--TGKTSLCKALAQKLSIR 204 (423)
T ss_pred eeccchhhhhhHHHHhh--cccHHHHHHHHHHHHHHHHhc-CCCCceeeeeeEEEEeCCCC--CChhHHHHHHHHhheee
Confidence 35566666666887655 556788888877777875555 55679999999999999999 47899999999999888
No 32
>PRK07952 DNA replication protein DnaC; Validated
Probab=91.46 E-value=0.38 Score=50.62 Aligned_cols=88 Identities=19% Similarity=0.310 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHhcccCCCccccccccccccchhhHHHHHHhhh-hccccCcccccccCCCCCCCCceeecCCCCchHHHH
Q 004011 430 ARRQAFKDSLQEGILGPENIEVSFESFPYYLSDITKNVLIAST-YVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQE 508 (779)
Q Consensus 430 ~r~~~fk~~~~~~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saa-yvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE 508 (779)
.|+...+..+.+..+++..-.-|||||-.. .+..+.++..|- |+ .+.....+-++|+||+| .-..
T Consensus 48 ~~q~~~~~~~~~s~i~~~~~~~tFdnf~~~-~~~q~~al~~a~~~~-----------~~~~~~~~~~~l~G~~G--tGKT 113 (244)
T PRK07952 48 NRAMKMQRTFNRSGIRPLHQNCSFENYRVE-CEGQMNALSKARQYV-----------EEFDGNIASFIFSGKPG--TGKN 113 (244)
T ss_pred HHHHHHHHHHHHcCCCccccCCccccccCC-CchHHHHHHHHHHHH-----------HhhccCCceEEEECCCC--CCHH
Confidence 344455666788888988889999999654 333333433322 32 22222235799999999 5788
Q ss_pred HHHHHHHhhc---cCeEEEEeccCCC
Q 004011 509 TLAKALAKHF---SARLLIVDSLLLP 531 (779)
Q Consensus 509 ~LaKALA~~F---~AkLLilDs~~l~ 531 (779)
.|+.|||+++ +.+.++++..+|.
T Consensus 114 hLa~aia~~l~~~g~~v~~it~~~l~ 139 (244)
T PRK07952 114 HLAAAICNELLLRGKSVLIITVADIM 139 (244)
T ss_pred HHHHHHHHHHHhcCCeEEEEEHHHHH
Confidence 8999999998 6778888765543
No 33
>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=90.95 E-value=0.26 Score=54.44 Aligned_cols=77 Identities=25% Similarity=0.247 Sum_probs=59.5
Q ss_pred CccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 447 ENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 447 ~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
++=+|-|+.--- -|..|.+|-+|.-..+|...+....| ..=+.|||.||+|| -.-.||||.|.+-+.-+.-+-
T Consensus 126 EKPNVkWsDVAG--LE~AKeALKEAVILPIKFPqlFtGkR---~PwrgiLLyGPPGT--GKSYLAKAVATEAnSTFFSvS 198 (439)
T KOG0739|consen 126 EKPNVKWSDVAG--LEGAKEALKEAVILPIKFPQLFTGKR---KPWRGILLYGPPGT--GKSYLAKAVATEANSTFFSVS 198 (439)
T ss_pred cCCCCchhhhcc--chhHHHHHHhheeecccchhhhcCCC---CcceeEEEeCCCCC--cHHHHHHHHHhhcCCceEEee
Confidence 344566655443 68999999999988888665542222 23478999999994 678899999999999999999
Q ss_pred ccCC
Q 004011 527 SLLL 530 (779)
Q Consensus 527 s~~l 530 (779)
|++|
T Consensus 199 SSDL 202 (439)
T KOG0739|consen 199 SSDL 202 (439)
T ss_pred hHHH
Confidence 9998
No 34
>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=90.68 E-value=0.31 Score=57.76 Aligned_cols=92 Identities=24% Similarity=0.271 Sum_probs=67.4
Q ss_pred ccccccccccchhhHHHHHHhhhhccccCccccc-ccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 450 EVSFESFPYYLSDITKNVLIASTYVHLKCNNFAK-YASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 450 ~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sK-yt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
+||||+--- -++-|+-|.-|.-...|+.+..| .+-+. -..|||+||+| --...||||.|++-|+.++-+-.-
T Consensus 507 dVtW~dIGa--L~~vR~eL~~aI~~PiK~pd~~k~lGi~~---PsGvLL~GPPG--CGKTLlAKAVANEag~NFisVKGP 579 (802)
T KOG0733|consen 507 DVTWDDIGA--LEEVRLELNMAILAPIKRPDLFKALGIDA---PSGVLLCGPPG--CGKTLLAKAVANEAGANFISVKGP 579 (802)
T ss_pred CCChhhccc--HHHHHHHHHHHHhhhccCHHHHHHhCCCC---CCceEEeCCCC--ccHHHHHHHHhhhccCceEeecCH
Confidence 588888766 68889999999888999988763 32222 45799999999 578899999999999999877654
Q ss_pred CCCCCCCCccccccccchhhh-hhHHHHHH
Q 004011 529 LLPGGSSKEADSVKESSRTEK-ASMFAKRA 557 (779)
Q Consensus 529 ~l~G~~ske~es~k~~sesek-~S~~~KrS 557 (779)
.|+ .+...|+|| +-.++.|.
T Consensus 580 ELl---------NkYVGESErAVR~vFqRA 600 (802)
T KOG0733|consen 580 ELL---------NKYVGESERAVRQVFQRA 600 (802)
T ss_pred HHH---------HHHhhhHHHHHHHHHHHh
Confidence 442 344445555 44455544
No 35
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=90.28 E-value=0.3 Score=54.67 Aligned_cols=77 Identities=26% Similarity=0.356 Sum_probs=59.7
Q ss_pred CccccccccccccchhhHHHHHHhhhhccccCcccc-cccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEE
Q 004011 447 ENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFA-KYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIV 525 (779)
Q Consensus 447 ~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~s-Kyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLil 525 (779)
+.-+|+|++.-= -|..|..|..+.-..|++.++. +++ + ...+.|||.||+| .-..+||||||++.++.++-+
T Consensus 138 ~~p~v~~~digG--l~~~k~~l~~~v~~pl~~~~~~~~~G--l-~~pkgvLL~GppG--TGKT~LAkalA~~l~~~fi~i 210 (398)
T PTZ00454 138 EKPDVTYSDIGG--LDIQKQEIREAVELPLTCPELYEQIG--I-DPPRGVLLYGPPG--TGKTMLAKAVAHHTTATFIRV 210 (398)
T ss_pred CCCCCCHHHcCC--HHHHHHHHHHHHHHHhcCHHHHHhcC--C-CCCceEEEECCCC--CCHHHHHHHHHHhcCCCEEEE
Confidence 456788887544 6788888888887778877654 332 3 2457899999999 589999999999999999988
Q ss_pred eccCC
Q 004011 526 DSLLL 530 (779)
Q Consensus 526 Ds~~l 530 (779)
..+.|
T Consensus 211 ~~s~l 215 (398)
T PTZ00454 211 VGSEF 215 (398)
T ss_pred ehHHH
Confidence 77665
No 36
>PRK08116 hypothetical protein; Validated
Probab=89.96 E-value=0.4 Score=50.68 Aligned_cols=88 Identities=17% Similarity=0.251 Sum_probs=57.1
Q ss_pred HHHHHHHHHhcccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHH
Q 004011 432 RQAFKDSLQEGILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLA 511 (779)
Q Consensus 432 ~~~fk~~~~~~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~La 511 (779)
+.+.+.-+...+++.+-.+.|||||.. .+..+.++ .+|.-+++. +. .....+.-+||.||+| .-.-.||
T Consensus 63 ~~~~~~l~~~s~i~~~~~~~tFdnf~~--~~~~~~a~-~~a~~y~~~--~~----~~~~~~~gl~l~G~~G--tGKThLa 131 (268)
T PRK08116 63 QRRIERLKSNSLLDEKFRNSTFENFLF--DKGSEKAY-KIARKYVKK--FE----EMKKENVGLLLWGSVG--TGKTYLA 131 (268)
T ss_pred HHHHHHHHHhcCCCHHHHhcchhcccC--ChHHHHHH-HHHHHHHHH--HH----hhccCCceEEEECCCC--CCHHHHH
Confidence 335556666778888889999999983 44443322 222222221 11 1112345699999999 5788999
Q ss_pred HHHHhhc---cCeEEEEeccCC
Q 004011 512 KALAKHF---SARLLIVDSLLL 530 (779)
Q Consensus 512 KALA~~F---~AkLLilDs~~l 530 (779)
.|+|+++ +.+.+.++...|
T Consensus 132 ~aia~~l~~~~~~v~~~~~~~l 153 (268)
T PRK08116 132 ACIANELIEKGVPVIFVNFPQL 153 (268)
T ss_pred HHHHHHHHHcCCeEEEEEHHHH
Confidence 9999986 678888776554
No 37
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=89.82 E-value=0.28 Score=53.24 Aligned_cols=77 Identities=23% Similarity=0.200 Sum_probs=54.4
Q ss_pred ccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 448 NIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 448 ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.-+++|++. +--+..+..|..+....+++.++.+... +. ..+.|||.||+| .-..+||||+|+++++.++-+..
T Consensus 116 ~p~~~~~di--~Gl~~~~~~l~~~i~~~~~~~~~~~~~g-~~-~p~gvLL~GppG--tGKT~lakaia~~l~~~~~~v~~ 189 (364)
T TIGR01242 116 RPNVSYEDI--GGLEEQIREIREAVELPLKHPELFEEVG-IE-PPKGVLLYGPPG--TGKTLLAKAVAHETNATFIRVVG 189 (364)
T ss_pred CCCCCHHHh--CChHHHHHHHHHHHHHHhcCHHHHHhcC-CC-CCceEEEECCCC--CCHHHHHHHHHHhCCCCEEecch
Confidence 345677765 3356677777777766777766543211 22 245699999999 57899999999999999887765
Q ss_pred cCC
Q 004011 528 LLL 530 (779)
Q Consensus 528 ~~l 530 (779)
..+
T Consensus 190 ~~l 192 (364)
T TIGR01242 190 SEL 192 (364)
T ss_pred HHH
Confidence 544
No 38
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=89.75 E-value=0.19 Score=54.74 Aligned_cols=40 Identities=35% Similarity=0.463 Sum_probs=36.9
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
+-+.||.-||+| .-..|||||||+...++||.+-++.|.|
T Consensus 150 APknVLFyGppG--TGKTm~Akalane~kvp~l~vkat~liG 189 (368)
T COG1223 150 APKNVLFYGPPG--TGKTMMAKALANEAKVPLLLVKATELIG 189 (368)
T ss_pred CcceeEEECCCC--ccHHHHHHHHhcccCCceEEechHHHHH
Confidence 457899999999 5799999999999999999999999987
No 39
>KOG2293 consensus Daxx-interacting protein MSP58/p78, contains FHA domain [Transcription; Signal transduction mechanisms]
Probab=88.77 E-value=1 Score=52.33 Aligned_cols=92 Identities=18% Similarity=0.267 Sum_probs=66.0
Q ss_pred cceeeeccCCCCCceeeecceEEEeccc-ccceeecC------CCcccceeEEEEEecCCCceEEEEEecCCceEEECCe
Q 004011 133 PWARLISQCSQNSHLSMTGAVFTVGHNR-QCDLYLKD------PSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGN 205 (779)
Q Consensus 133 pWGRLlSq~sq~P~v~I~~~~fTvGR~~-~CDl~L~d------~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGk 205 (779)
+.+.|+ -+|--.-|.+.+.|+||.. .|.+-++- ..||.-.--|+....| . .+|--+|.- .++|||+
T Consensus 432 AiAvL~---Gr~skh~mrk~EVtlGRat~d~~VDIDLgkegpatKISRRQa~IkL~n~G-s--F~IkNlGK~-~I~vng~ 504 (547)
T KOG2293|consen 432 AIAVLY---GRFSKHYMRKKEVTLGRATGDLKVDIDLGKEGPATKISRRQALIKLKNDG-S--FFIKNLGKR-SILVNGG 504 (547)
T ss_pred eeEEEe---chhhHhhhcCcceEeeccCCCcceeeeccccCccceeeccceeEEeccCC-c--EEeccCcce-eEEeCCc
Confidence 556666 4444456899999999976 56555532 2466655555543333 3 566667776 5899999
Q ss_pred ecCCCceEEeeCCCEEEEccCCCeeEEEe
Q 004011 206 VHPKDSQVVLRGGDELVFSPSGKHSYIFQ 234 (779)
Q Consensus 206 kVgKg~kviL~nGDEIvfs~~~~~aYIFq 234 (779)
.|..|.+++|+|+--|-+. ..-|||.
T Consensus 505 ~l~~gq~~~L~~nclveIr---g~~FiF~ 530 (547)
T KOG2293|consen 505 ELDRGQKVILKNNCLVEIR---GLRFIFE 530 (547)
T ss_pred cccCCceEEeccCcEEEEc---cceEEEe
Confidence 9999999999999999884 3578887
No 40
>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=88.58 E-value=0.95 Score=40.29 Aligned_cols=57 Identities=30% Similarity=0.490 Sum_probs=42.0
Q ss_pred HHHHHHHHhhcccCc-CCEEEEEcchhhhccCC--------hhhHHHHHHHhccCCC---CEEEEeeccccC
Q 004011 689 AINELFEVALNESKS-SPLIVFVKDIEKSLTGN--------NDAYGALKSKLENLPS---NVVVIGSHTQLD 748 (779)
Q Consensus 689 lIqsLyEVL~S~S~t-~PlILYiKDVEK~L~gs--------~e~y~~fq~mLeKLsG---~VLIIGSq~~~D 748 (779)
.|..+|+-+.. . .|.||||.|+|+++... .+.++.|.+.|++... +|+|||.-+..+
T Consensus 45 ~i~~~~~~~~~---~~~~~vl~iDe~d~l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~ 113 (132)
T PF00004_consen 45 KIRDFFKKAKK---SAKPCVLFIDEIDKLFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPD 113 (132)
T ss_dssp HHHHHHHHHHH---TSTSEEEEEETGGGTSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGG
T ss_pred ccccccccccc---cccceeeeeccchhcccccccccccccccccceeeecccccccccccceeEEeeCChh
Confidence 34444444433 4 49999999999988877 6777788888888887 599999877644
No 41
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=88.20 E-value=0.48 Score=57.26 Aligned_cols=78 Identities=26% Similarity=0.256 Sum_probs=63.9
Q ss_pred CCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEE
Q 004011 446 PENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIV 525 (779)
Q Consensus 446 g~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLil 525 (779)
-.+++|+|+++== =|..|.-|.+-.- .||+.+. |.+-=.-.-+-+||+||+| .-...||||+|-+-|++++-+
T Consensus 303 ~~~t~V~FkDVAG--~deAK~El~E~V~-fLKNP~~--Y~~lGAKiPkGvLL~GPPG--TGKTLLAKAiAGEAgVPF~sv 375 (774)
T KOG0731|consen 303 EGNTGVKFKDVAG--VDEAKEELMEFVK-FLKNPEQ--YQELGAKIPKGVLLVGPPG--TGKTLLAKAIAGEAGVPFFSV 375 (774)
T ss_pred CCCCCCccccccC--cHHHHHHHHHHHH-HhcCHHH--HHHcCCcCcCceEEECCCC--CcHHHHHHHHhcccCCceeee
Confidence 6778899999875 7889999998775 7887653 3333334567899999999 478999999999999999999
Q ss_pred eccCC
Q 004011 526 DSLLL 530 (779)
Q Consensus 526 Ds~~l 530 (779)
-.+.|
T Consensus 376 SGSEF 380 (774)
T KOG0731|consen 376 SGSEF 380 (774)
T ss_pred chHHH
Confidence 88888
No 42
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=87.85 E-value=0.79 Score=51.31 Aligned_cols=63 Identities=17% Similarity=0.206 Sum_probs=47.0
Q ss_pred eeeecceEEEe-cccccceeecCCCcccceeEEEEEecCCCceEEEEEecCCceEEECC--eecCCCceEEe
Q 004011 147 LSMTGAVFTVG-HNRQCDLYLKDPSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNG--NVHPKDSQVVL 215 (779)
Q Consensus 147 v~I~~~~fTvG-R~~~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNG--kkVgKg~kviL 215 (779)
+.|....|+|| ++..||+.|.|..++..||.|.-...+ +.|.+. ..+ |.+|| .....|..+.+
T Consensus 15 ~~L~~g~~~iG~~~~~~di~L~d~~~~~~h~~l~v~~~~----~~l~~~-~~~-~~~~g~~~~~~~g~~l~~ 80 (410)
T TIGR02500 15 LPLPEGNLVLGTDAADCDIVLSDGGIAAVHVSLHVRLEG----VTLAGA-VEP-AWEEGGVLPDEEGTPLPS 80 (410)
T ss_pred EECCCCceEeccCCCCcEEEeCCCCccchheEEEEcCce----EEEecC-Ccc-eeECCcccccCCCCccCC
Confidence 46777889999 999999999999999999999964323 445432 233 68999 77777665443
No 43
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=87.11 E-value=1.8 Score=50.47 Aligned_cols=97 Identities=16% Similarity=0.160 Sum_probs=72.7
Q ss_pred cceeeeccCCCCCceeeecceEEEecccccceeecCCCcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCCCce
Q 004011 133 PWARLISQCSQNSHLSMTGAVFTVGHNRQCDLYLKDPSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPKDSQ 212 (779)
Q Consensus 133 pWGRLlSq~sq~P~v~I~~~~fTvGR~~~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgKg~k 212 (779)
.=|-|.|..+.+|-|.|....-.+||++-- .++|..-|+..-.+. .+.... .|.+-.+|.|=+ -|||..++||..
T Consensus 13 ~~c~l~~~~~~~~~~~~~~~~~~~gr~pet--~i~d~~cs~~qv~l~-a~~~~~-~v~~k~lg~np~-~~~~~~~~~~~~ 87 (526)
T TIGR01663 13 RICTLKPGEAEHHFIHLDAGALFLGRGPET--GIRDRKCSKRQIELQ-ADLEKA-TVALKQLGVNPC-GTGGLELKPGGE 87 (526)
T ss_pred eeeEecCCCCCCCeeccCCCceEEccCccc--ccchhhhchhhheee-ecccCc-eEEEEEccCCCc-ccCceEecCCCe
Confidence 358889999999999888777889998743 445666665555544 333333 377888999954 899999999999
Q ss_pred EEeeCCCEEEEccCCCeeEEEee
Q 004011 213 VVLRGGDELVFSPSGKHSYIFQQ 235 (779)
Q Consensus 213 viL~nGDEIvfs~~~~~aYIFq~ 235 (779)
+.|+.||.+-+. .+.|-|.++.
T Consensus 88 ~~l~~g~~l~~v-~~~~~~~~~f 109 (526)
T TIGR01663 88 GELGHGDLLEIV-NGLHPLTLQF 109 (526)
T ss_pred eeecCCCEEEEe-ccccceeEEe
Confidence 999999998874 4677775543
No 44
>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=86.50 E-value=0.69 Score=55.09 Aligned_cols=78 Identities=19% Similarity=0.206 Sum_probs=57.1
Q ss_pred cccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 449 IEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 449 i~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
-+++|+++- --+..+..|.......|+|.++.+... + ...+.|||.||+| .-..+||||||++++++++.++..
T Consensus 173 ~~~~~~di~--G~~~~~~~l~~~i~~~~~~~~~~~~~g-i-~~~~giLL~GppG--tGKT~laraia~~~~~~~i~i~~~ 246 (733)
T TIGR01243 173 PKVTYEDIG--GLKEAKEKIREMVELPMKHPELFEHLG-I-EPPKGVLLYGPPG--TGKTLLAKAVANEAGAYFISINGP 246 (733)
T ss_pred CCCCHHHhc--CHHHHHHHHHHHHHHHhhCHHHHHhcC-C-CCCceEEEECCCC--CChHHHHHHHHHHhCCeEEEEecH
Confidence 457888754 356667777776666677776543221 2 2346799999999 578999999999999999999987
Q ss_pred CCCC
Q 004011 529 LLPG 532 (779)
Q Consensus 529 ~l~G 532 (779)
.+.+
T Consensus 247 ~i~~ 250 (733)
T TIGR01243 247 EIMS 250 (733)
T ss_pred HHhc
Confidence 7643
No 45
>CHL00206 ycf2 Ycf2; Provisional
Probab=85.66 E-value=0.58 Score=61.33 Aligned_cols=42 Identities=21% Similarity=0.135 Sum_probs=38.1
Q ss_pred CCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCCC
Q 004011 490 TMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPGG 533 (779)
Q Consensus 490 s~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G~ 533 (779)
..++.|||-||+| .-+-+||||||.+.+|+++-+..+.|...
T Consensus 1628 ~pPKGILLiGPPG--TGKTlLAKALA~es~VPFIsISgs~fl~~ 1669 (2281)
T CHL00206 1628 SPSRGILVIGSIG--TGRSYLVKYLATNSYVPFITVFLNKFLDN 1669 (2281)
T ss_pred CCCCceEEECCCC--CCHHHHHHHHHHhcCCceEEEEHHHHhhc
Confidence 4678999999997 58999999999999999999999999743
No 46
>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=84.36 E-value=0.79 Score=45.50 Aligned_cols=37 Identities=35% Similarity=0.490 Sum_probs=31.5
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccC----eEEEEeccCCCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSA----RLLIVDSLLLPG 532 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~A----kLLilDs~~l~G 532 (779)
-|||.||.| .-...|||+||.++.. +|+.+|.+.+..
T Consensus 5 ~~ll~GpsG--vGKT~la~~la~~l~~~~~~~~~~~d~s~~~~ 45 (171)
T PF07724_consen 5 NFLLAGPSG--VGKTELAKALAELLFVGSERPLIRIDMSEYSE 45 (171)
T ss_dssp EEEEESSTT--SSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCS
T ss_pred EEEEECCCC--CCHHHHHHHHHHHhccCCccchHHHhhhcccc
Confidence 489999999 3555699999999998 999999988865
No 47
>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=84.09 E-value=0.84 Score=40.81 Aligned_cols=32 Identities=38% Similarity=0.583 Sum_probs=29.2
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.|+++||+| --.-+|||.||+.|+.+.+-+|.
T Consensus 1 vI~I~G~~g--sGKST~a~~La~~~~~~~i~~d~ 32 (121)
T PF13207_consen 1 VIIISGPPG--SGKSTLAKELAERLGFPVISMDD 32 (121)
T ss_dssp EEEEEESTT--SSHHHHHHHHHHHHTCEEEEEHH
T ss_pred CEEEECCCC--CCHHHHHHHHHHHHCCeEEEecc
Confidence 489999999 47889999999999999999998
No 48
>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=83.77 E-value=1.2 Score=46.65 Aligned_cols=36 Identities=25% Similarity=0.341 Sum_probs=31.7
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
.++.|||.||+| .-..+||++||+.+|.+++.+..+
T Consensus 20 ~g~~vLL~G~~G--tGKT~lA~~la~~lg~~~~~i~~~ 55 (262)
T TIGR02640 20 SGYPVHLRGPAG--TGKTTLAMHVARKRDRPVMLINGD 55 (262)
T ss_pred cCCeEEEEcCCC--CCHHHHHHHHHHHhCCCEEEEeCC
Confidence 457899999999 579999999999999999998543
No 49
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=83.49 E-value=1.4 Score=50.23 Aligned_cols=67 Identities=22% Similarity=0.183 Sum_probs=48.1
Q ss_pred hhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 462 DITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 462 E~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
+..+..|-.+.-..|.|.++.+... +. ..+.|||.||+| .-..+||||+|+.+++.++-++.+.|.+
T Consensus 189 ~~qi~~l~e~v~lpl~~p~~~~~~g-i~-~p~gVLL~GPPG--TGKT~LAraIA~el~~~fi~V~~seL~~ 255 (438)
T PTZ00361 189 EQQIQEIKEAVELPLTHPELYDDIG-IK-PPKGVILYGPPG--TGKTLLAKAVANETSATFLRVVGSELIQ 255 (438)
T ss_pred HHHHHHHHHHHHhhhhCHHHHHhcC-CC-CCcEEEEECCCC--CCHHHHHHHHHHhhCCCEEEEecchhhh
Confidence 4555555555555677765442211 22 335699999999 5789999999999999999888877754
No 50
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=83.39 E-value=1.3 Score=52.11 Aligned_cols=83 Identities=23% Similarity=0.215 Sum_probs=62.3
Q ss_pred HHhcccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhc
Q 004011 439 LQEGILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHF 518 (779)
Q Consensus 439 ~~~~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F 518 (779)
+...|.+-+.++|+|++-=- =++.|.=|-+-.- +||-+ .||++==--.-+.|||.||+| .-..+||||.|-+-
T Consensus 289 l~~ev~p~~~~nv~F~dVkG--~DEAK~ELeEiVe-fLkdP--~kftrLGGKLPKGVLLvGPPG--TGKTlLARAvAGEA 361 (752)
T KOG0734|consen 289 LDSEVDPEQMKNVTFEDVKG--VDEAKQELEEIVE-FLKDP--TKFTRLGGKLPKGVLLVGPPG--TGKTLLARAVAGEA 361 (752)
T ss_pred cccccChhhhcccccccccC--hHHHHHHHHHHHH-HhcCc--HHhhhccCcCCCceEEeCCCC--CchhHHHHHhhccc
Confidence 45778888889999987544 5788888877765 67653 355554444668899999999 57899999999999
Q ss_pred cCeEEEEecc
Q 004011 519 SARLLIVDSL 528 (779)
Q Consensus 519 ~AkLLilDs~ 528 (779)
++++.---.+
T Consensus 362 ~VPFF~~sGS 371 (752)
T KOG0734|consen 362 GVPFFYASGS 371 (752)
T ss_pred CCCeEecccc
Confidence 9987544333
No 51
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=83.33 E-value=1.6 Score=53.70 Aligned_cols=74 Identities=30% Similarity=0.451 Sum_probs=57.1
Q ss_pred CCCCccCccccCCcccCCCCeeeEeecCCCCCccCCCCCCCCCCcCCceeeecccCCCCceeeeccCCCCCCCCCCCCCC
Q 004011 584 LPKPEISTASSKNYTFKKGDRVKFVGNVTSGTTVQPTLRGPGIGFRGRVILPFEDNDFSKIGVRFDRSIPEGNNLGGFCE 663 (779)
Q Consensus 584 ~~k~e~s~~ts~~~t~kkGdrVkyvGs~~~~s~~~~~~R~ps~G~rG~V~l~fE~N~ssKVgVrFDk~i~dg~Dlg~~ce 663 (779)
.++...+.+-.+++.|+-||||-|+--+.. -+.|..|-|+.-.-.-.+--++|.||-+++.||+++|.|+
T Consensus 1115 ~lnp~~~~v~l~sq~f~lgdrVvyvqdsgk----------vPv~~kGTVvG~m~~~~~~~~~vlFd~~~~ngnn~~Gr~~ 1184 (1493)
T KOG2045|consen 1115 KLNPTLPDVYLSSQPFRLGDRVVYVQDSGK----------VPVGTKGTVVGIMPVTDDTFCKVLFDSPVPNGNNIHGRAE 1184 (1493)
T ss_pred hcCCCCcceeeccccccccceEEEeeccCc----------cccccccceEEEEecccccccceeecccccCCCccCceec
Confidence 334344555567888999999999875432 2357788887766665566789999999999999999999
Q ss_pred CCCc
Q 004011 664 DDHG 667 (779)
Q Consensus 664 ~~~g 667 (779)
..+|
T Consensus 1185 ~~~g 1188 (1493)
T KOG2045|consen 1185 DRVG 1188 (1493)
T ss_pred cccc
Confidence 8887
No 52
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=82.56 E-value=0.98 Score=50.87 Aligned_cols=52 Identities=29% Similarity=0.279 Sum_probs=39.3
Q ss_pred cccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 475 HLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 475 HLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
.|+|.++..-. .+. .-+.+||-||+| .-..+||||.||+-+|.++=+=.+.|
T Consensus 170 PL~~PElF~~~-GI~-PPKGVLLYGPPG--TGKTLLAkAVA~~T~AtFIrvvgSEl 221 (406)
T COG1222 170 PLKNPELFEEL-GID-PPKGVLLYGPPG--TGKTLLAKAVANQTDATFIRVVGSEL 221 (406)
T ss_pred cccCHHHHHHc-CCC-CCCceEeeCCCC--CcHHHHHHHHHhccCceEEEeccHHH
Confidence 56666653211 122 235799999999 57999999999999999998887777
No 53
>KOG1880 consensus Nuclear inhibitor of phosphatase-1 [General function prediction only]
Probab=82.37 E-value=2.3 Score=46.80 Aligned_cols=82 Identities=21% Similarity=0.276 Sum_probs=66.1
Q ss_pred eecceEEEeccc-ccceeecCCCcccceeEEEEEecCCCceEEEEEecCC-ceEEECCeecCCCceEEeeCCCEEEEccC
Q 004011 149 MTGAVFTVGHNR-QCDLYLKDPSISKNLCRLRRIENGGPSGALLEITGGK-GEVEVNGNVHPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 149 I~~~~fTvGR~~-~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssN-GtV~VNGkkVgKg~kviL~nGDEIvfs~~ 226 (779)
+..-.|.|||++ +|||+|+..+.|.+|--+...... ..+||=|++++ || |+-...+.+-+-+.|.-|--.-|+.+
T Consensus 35 ddkr~y~Fgrn~q~~df~idh~scSrvhaa~vyhkhl--~~~~lidl~s~hgt-f~g~~rL~~~~p~~l~i~~~~~fgas 111 (337)
T KOG1880|consen 35 DDKRRYLFGRNHQTCDFVIDHASCSRVHAALVYHKHL--SRIFLIDLGSTHGT-FLGNERLEPHKPVQLEIGSTFHFGAS 111 (337)
T ss_pred hhhhhhhhccCCCccceEeecchhhhhHhhhhhhhcc--ceEEEEEccCCcce-eeeeeeeccCCCccccCCceEEEecc
Confidence 345569999988 899999999999999877665333 34667777775 65 99999999999999999999999887
Q ss_pred CCeeEEEe
Q 004011 227 GKHSYIFQ 234 (779)
Q Consensus 227 ~~~aYIFq 234 (779)
.+ .|++.
T Consensus 112 Tr-~y~lr 118 (337)
T KOG1880|consen 112 TR-IYLLR 118 (337)
T ss_pred ce-eeeee
Confidence 76 56665
No 54
>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional
Probab=81.77 E-value=1.1 Score=50.81 Aligned_cols=44 Identities=11% Similarity=0.047 Sum_probs=37.0
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCCCCCCc
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPGGSSKE 537 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G~~ske 537 (779)
-+-+||.||+| --.-+||||+|+.+|+.++.++...|.+..--|
T Consensus 148 PlgllL~GPPG--cGKTllAraiA~elg~~~i~vsa~eL~sk~vGE 191 (413)
T PLN00020 148 PLILGIWGGKG--QGKSFQCELVFKKMGIEPIVMSAGELESENAGE 191 (413)
T ss_pred CeEEEeeCCCC--CCHHHHHHHHHHHcCCCeEEEEHHHhhcCcCCc
Confidence 35567899999 578999999999999999999999997655434
No 55
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=78.74 E-value=1.8 Score=35.80 Aligned_cols=27 Identities=30% Similarity=0.382 Sum_probs=22.0
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEE
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVF 223 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvf 223 (779)
..|.|+|||+.+.+ ....|+.||+|.|
T Consensus 32 ~~G~V~VNg~~~~~-~~~~l~~Gd~v~i 58 (59)
T TIGR02988 32 QENEVLVNGELENR-RGKKLYPGDVIEI 58 (59)
T ss_pred HcCCEEECCEEccC-CCCCCCCCCEEEe
Confidence 45779999999863 4679999999976
No 56
>PRK08939 primosomal protein DnaI; Reviewed
Probab=76.23 E-value=3.2 Score=45.01 Aligned_cols=85 Identities=14% Similarity=0.168 Sum_probs=52.0
Q ss_pred HHHHHHhcccCCCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHH
Q 004011 435 FKDSLQEGILGPENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKAL 514 (779)
Q Consensus 435 fk~~~~~~Vvdg~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKAL 514 (779)
.+..++..-++.+-.+.||++|.|- .+..+.++ ..+.-.++ .|.. ..-.+-|+|.||.| .-...|+.||
T Consensus 108 ~~~~i~~a~~p~~~~~atf~~~~~~-~~~~~~~~-~~~~~fi~-----~~~~--~~~~~gl~L~G~~G--~GKThLa~Ai 176 (306)
T PRK08939 108 IKKRIQSIYMPKDLLQASLADIDLD-DRDRLDAL-MAALDFLE-----AYPP--GEKVKGLYLYGDFG--VGKSYLLAAI 176 (306)
T ss_pred HHHHHHHcCCCHhHhcCcHHHhcCC-ChHHHHHH-HHHHHHHH-----Hhhc--cCCCCeEEEECCCC--CCHHHHHHHH
Confidence 4455556666666567899999874 22333332 22221221 1211 12346899999999 6888999999
Q ss_pred Hhhc---cCeEEEEeccCC
Q 004011 515 AKHF---SARLLIVDSLLL 530 (779)
Q Consensus 515 A~~F---~AkLLilDs~~l 530 (779)
|+++ |.+.+.+....|
T Consensus 177 a~~l~~~g~~v~~~~~~~l 195 (306)
T PRK08939 177 ANELAKKGVSSTLLHFPEF 195 (306)
T ss_pred HHHHHHcCCCEEEEEHHHH
Confidence 9998 566666655444
No 57
>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]
Probab=76.10 E-value=2.1 Score=46.81 Aligned_cols=65 Identities=26% Similarity=0.312 Sum_probs=52.7
Q ss_pred hhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 462 DITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 462 E~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
+-.|+-.-+|.-..|-|.++-+.+- +. .-|.+||-||+| .-..|||||.|||-.|.++=+-.+.|
T Consensus 161 d~qkqeireavelplt~~~ly~qig-id-pprgvllygppg--~gktml~kava~~t~a~firvvgsef 225 (408)
T KOG0727|consen 161 DVQKQEIREAVELPLTHADLYKQIG-ID-PPRGVLLYGPPG--TGKTMLAKAVANHTTAAFIRVVGSEF 225 (408)
T ss_pred hhhHHHHHHHHhccchHHHHHHHhC-CC-CCcceEEeCCCC--CcHHHHHHHHhhccchheeeeccHHH
Confidence 4567777788888888888876544 22 347799999999 57899999999999999998888888
No 58
>smart00363 S4 S4 RNA-binding domain.
Probab=75.81 E-value=3.6 Score=31.51 Aligned_cols=28 Identities=29% Similarity=0.504 Sum_probs=21.9
Q ss_pred CceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
+|.|+|||+.+.. ....|+.||.|.+..
T Consensus 25 ~g~i~vng~~~~~-~~~~l~~gd~i~~~~ 52 (60)
T smart00363 25 QGRVKVNGKKVTK-PSYIVKPGDVISVRG 52 (60)
T ss_pred cCCEEECCEEecC-CCeEeCCCCEEEEcc
Confidence 5679999999944 366789999998743
No 59
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=75.71 E-value=2.6 Score=35.85 Aligned_cols=26 Identities=31% Similarity=0.539 Sum_probs=22.0
Q ss_pred eEEECCeecCCCceEEeeCCCEEEEccC
Q 004011 199 EVEVNGNVHPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 199 tV~VNGkkVgKg~kviL~nGDEIvfs~~ 226 (779)
.|+|||+.+. ....|+.||||.|-.+
T Consensus 51 ~v~vNg~~v~--~~~~l~~gD~v~i~pp 76 (80)
T cd00754 51 RIAVNGEYVR--LDTPLKDGDEVAIIPP 76 (80)
T ss_pred EEEECCeEcC--CCcccCCCCEEEEeCC
Confidence 4899999998 4678999999998554
No 60
>PRK04195 replication factor C large subunit; Provisional
Probab=75.70 E-value=2.6 Score=47.92 Aligned_cols=37 Identities=27% Similarity=0.421 Sum_probs=33.0
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
.+.+||+||+| .-..+||+|||++++..++.++.+++
T Consensus 39 ~~~lLL~GppG--~GKTtla~ala~el~~~~ielnasd~ 75 (482)
T PRK04195 39 KKALLLYGPPG--VGKTSLAHALANDYGWEVIELNASDQ 75 (482)
T ss_pred CCeEEEECCCC--CCHHHHHHHHHHHcCCCEEEEccccc
Confidence 57899999999 68999999999999999999887664
No 61
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=75.22 E-value=3 Score=49.49 Aligned_cols=78 Identities=21% Similarity=0.286 Sum_probs=49.4
Q ss_pred CCccccccccccccchhhHHHHHHhhhhccccCcc-cccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEE
Q 004011 446 PENIEVSFESFPYYLSDITKNVLIASTYVHLKCNN-FAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLI 524 (779)
Q Consensus 446 g~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~-~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLi 524 (779)
...+..+|+++-- -+..+.-|...... ++..+ +..... ...+.|||.||+| .-..+|||+||++.+++++.
T Consensus 144 ~~~~~~~~~di~g--~~~~~~~l~~i~~~-~~~~~~~~~~~~---~~~~gill~G~~G--~GKt~~~~~~a~~~~~~f~~ 215 (644)
T PRK10733 144 EDQIKTTFADVAG--CDEAKEEVAELVEY-LREPSRFQKLGG---KIPKGVLMVGPPG--TGKTLLAKAIAGEAKVPFFT 215 (644)
T ss_pred chhhhCcHHHHcC--HHHHHHHHHHHHHH-hhCHHHHHhcCC---CCCCcEEEECCCC--CCHHHHHHHHHHHcCCCEEE
Confidence 3455666666533 34444444443332 33321 111111 2234599999999 57899999999999999999
Q ss_pred EeccCCC
Q 004011 525 VDSLLLP 531 (779)
Q Consensus 525 lDs~~l~ 531 (779)
++..+|.
T Consensus 216 is~~~~~ 222 (644)
T PRK10733 216 ISGSDFV 222 (644)
T ss_pred EehHHhH
Confidence 9987764
No 62
>PRK00131 aroK shikimate kinase; Reviewed
Probab=74.40 E-value=3.1 Score=39.07 Aligned_cols=34 Identities=29% Similarity=0.435 Sum_probs=28.6
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
...|+|.||+|| -.-+|||+||+.++.+++-.|.
T Consensus 4 ~~~i~l~G~~Gs--GKstla~~La~~l~~~~~d~d~ 37 (175)
T PRK00131 4 GPNIVLIGFMGA--GKSTIGRLLAKRLGYDFIDTDH 37 (175)
T ss_pred CCeEEEEcCCCC--CHHHHHHHHHHHhCCCEEEChH
Confidence 468999999994 6889999999999988775553
No 63
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=74.29 E-value=2.1 Score=36.03 Aligned_cols=28 Identities=36% Similarity=0.654 Sum_probs=24.0
Q ss_pred eEEECCeecCC-CceEEeeCCCEEEEccC
Q 004011 199 EVEVNGNVHPK-DSQVVLRGGDELVFSPS 226 (779)
Q Consensus 199 tV~VNGkkVgK-g~kviL~nGDEIvfs~~ 226 (779)
.|.|||+.+.+ +....|+.||||.|-.+
T Consensus 45 ~v~vN~~~v~~~~~~~~l~~gD~V~i~pp 73 (77)
T PF02597_consen 45 AVAVNGEIVPDDGLDTPLKDGDEVAILPP 73 (77)
T ss_dssp EEEETTEEEGGGTTTSBEETTEEEEEEES
T ss_pred EEEECCEEcCCccCCcCcCCCCEEEEECC
Confidence 58999999999 66789999999998543
No 64
>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=74.18 E-value=5.2 Score=44.36 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=29.5
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
.+.|||.||+| .-.-+||++||+.++.+++-+.
T Consensus 64 ~~~ilL~G~pG--tGKTtla~~lA~~l~~~~~rV~ 96 (327)
T TIGR01650 64 DRRVMVQGYHG--TGKSTHIEQIAARLNWPCVRVN 96 (327)
T ss_pred CCcEEEEeCCC--ChHHHHHHHHHHHHCCCeEEEE
Confidence 36799999999 6889999999999999998774
No 65
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=74.14 E-value=2.8 Score=36.73 Aligned_cols=28 Identities=25% Similarity=0.272 Sum_probs=22.9
Q ss_pred eEEECCeecCCCceEEeeCCCEEEEccC
Q 004011 199 EVEVNGNVHPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 199 tV~VNGkkVgKg~kviL~nGDEIvfs~~ 226 (779)
.|.|||+.+.......|+.||||+|-.|
T Consensus 57 ~v~vN~~~v~~~~~~~l~dgdev~i~Pp 84 (88)
T TIGR01687 57 IILVNGRNVDWGLGTELKDGDVVAIFPP 84 (88)
T ss_pred EEEECCEecCccCCCCCCCCCEEEEeCC
Confidence 4899999998765468999999998543
No 66
>PRK08118 topology modulation protein; Reviewed
Probab=73.24 E-value=2.8 Score=41.20 Aligned_cols=35 Identities=31% Similarity=0.527 Sum_probs=30.9
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLL 529 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~ 529 (779)
+||++.||+|+ -.-+|||.||+.++.+++-+|...
T Consensus 2 ~rI~I~G~~Gs--GKSTlak~L~~~l~~~~~~lD~l~ 36 (167)
T PRK08118 2 KKIILIGSGGS--GKSTLARQLGEKLNIPVHHLDALF 36 (167)
T ss_pred cEEEEECCCCC--CHHHHHHHHHHHhCCCceecchhh
Confidence 58999999994 567899999999999999999644
No 67
>PRK06921 hypothetical protein; Provisional
Probab=72.86 E-value=3.3 Score=43.88 Aligned_cols=72 Identities=18% Similarity=0.220 Sum_probs=43.9
Q ss_pred HHHHHHhcccCCCccccccccccccc-hhhHHHHHHhhhhccccCcccccccCCCC----CCCCceeecCCCCchHHHHH
Q 004011 435 FKDSLQEGILGPENIEVSFESFPYYL-SDITKNVLIASTYVHLKCNNFAKYASDLP----TMCPRILLSGPAGSEIYQET 509 (779)
Q Consensus 435 fk~~~~~~Vvdg~ei~VSFd~FPYYL-SE~TK~vL~saayvHLk~~~~sKyt~~Ls----s~s~rILLSGPaGsEiYQE~ 509 (779)
.+..+++.-++..-..-+|++|-+.- .++.+.++..| . +|..++. ....-|+|.||+| .-.-.
T Consensus 65 ~~~~~~~s~i~~~~~~~~F~nf~~~~~~~~~~~~~~~~-~---------~~~~~f~~~~~~~~~~l~l~G~~G--~GKTh 132 (266)
T PRK06921 65 IERLLKASEITEAFRKLTFKNFKTEGKPQAIKDAYECA-V---------EYVKDFEKIQESRKNSIALLGQPG--SGKTH 132 (266)
T ss_pred HHHHHHHcCCCHHHHhhhhhcCccCCccHHHHHHHHHH-H---------HHHHHHHHhcccCCCeEEEECCCC--CcHHH
Confidence 44556666666666678899998742 12222232211 1 2222222 2346799999999 57888
Q ss_pred HHHHHHhhc
Q 004011 510 LAKALAKHF 518 (779)
Q Consensus 510 LaKALA~~F 518 (779)
|+.|+|+++
T Consensus 133 La~aia~~l 141 (266)
T PRK06921 133 LLTAAANEL 141 (266)
T ss_pred HHHHHHHHH
Confidence 999999876
No 68
>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=70.91 E-value=3.8 Score=38.00 Aligned_cols=31 Identities=29% Similarity=0.418 Sum_probs=27.0
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
+|+|.||+|+ -.-+|||+||++++.+++-.|
T Consensus 1 ~i~l~G~~Gs--GKstla~~la~~l~~~~~~~d 31 (154)
T cd00464 1 NIVLIGMMGA--GKTTVGRLLAKALGLPFVDLD 31 (154)
T ss_pred CEEEEcCCCC--CHHHHHHHHHHHhCCCEEEch
Confidence 5999999994 578899999999999987666
No 69
>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=70.54 E-value=5.2 Score=34.29 Aligned_cols=35 Identities=34% Similarity=0.540 Sum_probs=29.4
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCe---EEEEecc
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSAR---LLIVDSL 528 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~Ak---LLilDs~ 528 (779)
.+.|+|.||+| .-..+|+++||+.+... .+.++..
T Consensus 2 ~~~~~l~G~~G--~GKTtl~~~l~~~~~~~~~~~~~~~~~ 39 (148)
T smart00382 2 GEVILIVGPPG--SGKTTLARALARELGPPGGGVIYIDGE 39 (148)
T ss_pred CCEEEEECCCC--CcHHHHHHHHHhccCCCCCCEEEECCE
Confidence 46899999999 57899999999999986 6666653
No 70
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=70.01 E-value=3.4 Score=50.17 Aligned_cols=37 Identities=24% Similarity=0.360 Sum_probs=32.9
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
..+||.||+| .-...|||+||+.++.+++.+|.+.+.
T Consensus 489 ~~~Lf~GP~G--vGKT~lAk~LA~~l~~~~i~id~se~~ 525 (758)
T PRK11034 489 GSFLFAGPTG--VGKTEVTVQLSKALGIELLRFDMSEYM 525 (758)
T ss_pred ceEEEECCCC--CCHHHHHHHHHHHhCCCcEEeechhhc
Confidence 3699999999 578889999999999999999988763
No 71
>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=69.22 E-value=5.1 Score=46.80 Aligned_cols=66 Identities=21% Similarity=0.332 Sum_probs=41.2
Q ss_pred cccccccccccchhhHHHHHHhhhhccccCcc-cccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 449 IEVSFESFPYYLSDITKNVLIASTYVHLKCNN-FAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 449 i~VSFd~FPYYLSE~TK~vL~saayvHLk~~~-~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
-+++|++.- =|. ..+..|..+.-.-+.|++ |.+|. +.+ -+.|||.||+|+ -..+||||+|++++.+
T Consensus 177 p~v~~~dIg-Gl~-~~i~~i~~~v~lp~~~~~l~~~~g--l~~-p~GILLyGPPGT--GKT~LAKAlA~eL~~~ 243 (512)
T TIGR03689 177 PDVTYADIG-GLD-SQIEQIRDAVELPFLHPELYREYD--LKP-PKGVLLYGPPGC--GKTLIAKAVANSLAQR 243 (512)
T ss_pred CCCCHHHcC-ChH-HHHHHHHHHHHHHhhCHHHHHhcc--CCC-CcceEEECCCCC--cHHHHHHHHHHhhccc
Confidence 356676632 133 444444444333344443 44554 333 357999999994 7899999999999765
No 72
>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=69.11 E-value=7.9 Score=38.40 Aligned_cols=66 Identities=14% Similarity=-0.011 Sum_probs=45.9
Q ss_pred cccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhcc---CeEEEE
Q 004011 449 IEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFS---ARLLIV 525 (779)
Q Consensus 449 i~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~---AkLLil 525 (779)
..-|||+|=+.-.+++...|-..+. ....+-|||.||+| .-...||++++++.. .+++.+
T Consensus 10 ~~~~~~~~~~~~~~~~~~~l~~~~~---------------~~~~~~lll~G~~G--~GKT~la~~~~~~~~~~~~~~~~i 72 (226)
T TIGR03420 10 DDPTFDNFYAGGNAELLAALRQLAA---------------GKGDRFLYLWGESG--SGKSHLLQAACAAAEERGKSAIYL 72 (226)
T ss_pred CchhhcCcCcCCcHHHHHHHHHHHh---------------cCCCCeEEEECCCC--CCHHHHHHHHHHHHHhcCCcEEEE
Confidence 4478888853345555555554432 12356799999999 578999999999874 678888
Q ss_pred eccCCC
Q 004011 526 DSLLLP 531 (779)
Q Consensus 526 Ds~~l~ 531 (779)
|...+.
T Consensus 73 ~~~~~~ 78 (226)
T TIGR03420 73 PLAELA 78 (226)
T ss_pred eHHHHH
Confidence 876654
No 73
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=68.87 E-value=3.1 Score=32.61 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=19.1
Q ss_pred CceEEECCeecCCCceEEeeCCCEE
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDEL 221 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEI 221 (779)
+|-|+|||+.+.+. ...+..||+|
T Consensus 25 ~g~V~VNg~~v~~~-~~~v~~~d~I 48 (48)
T PF01479_consen 25 QGRVKVNGKVVKDP-SYIVKPGDVI 48 (48)
T ss_dssp TTTEEETTEEESST-TSBESTTEEE
T ss_pred CCEEEECCEEEcCC-CCCCCCcCCC
Confidence 45699999999964 5667788886
No 74
>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=68.82 E-value=4.7 Score=41.90 Aligned_cols=47 Identities=23% Similarity=0.326 Sum_probs=33.6
Q ss_pred ccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhcc-------CeEEEEeccCCCC
Q 004011 484 YASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFS-------ARLLIVDSLLLPG 532 (779)
Q Consensus 484 yt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~-------AkLLilDs~~l~G 532 (779)
.+....+..+.|||.||+| .-..+|||++|+++. ..++.++..+|.|
T Consensus 34 ~g~~~~~~~~~vll~GppG--tGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~~l~~ 87 (261)
T TIGR02881 34 EGLKTSKQVLHMIFKGNPG--TGKTTVARILGKLFKEMNVLSKGHLIEVERADLVG 87 (261)
T ss_pred cCCCCCCCcceEEEEcCCC--CCHHHHHHHHHHHHHhcCcccCCceEEecHHHhhh
Confidence 4445556667899999999 589999999999862 2444555555544
No 75
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=67.68 E-value=5.4 Score=35.01 Aligned_cols=25 Identities=36% Similarity=0.501 Sum_probs=20.6
Q ss_pred EEECCeecCCCceEEeeCCCEEEEccC
Q 004011 200 VEVNGNVHPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 200 V~VNGkkVgKg~kviL~nGDEIvfs~~ 226 (779)
++||+..++.. .+|+.||||+|-.|
T Consensus 53 ~aVN~~~~~~~--~~l~dgDeVai~PP 77 (81)
T PRK11130 53 AAVNQTLVSFD--HPLTDGDEVAFFPP 77 (81)
T ss_pred EEECCEEcCCC--CCCCCCCEEEEeCC
Confidence 79999988754 47999999999554
No 76
>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=67.47 E-value=5.8 Score=36.62 Aligned_cols=33 Identities=30% Similarity=0.486 Sum_probs=28.6
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEeccC
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLL 529 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~ 529 (779)
|||.||+| .-.-+||++||+.++.+++.+-.+.
T Consensus 2 vlL~G~~G--~GKt~l~~~la~~~~~~~~~i~~~~ 34 (139)
T PF07728_consen 2 VLLVGPPG--TGKTTLARELAALLGRPVIRINCSS 34 (139)
T ss_dssp EEEEESSS--SSHHHHHHHHHHHHTCEEEEEE-TT
T ss_pred EEEECCCC--CCHHHHHHHHHHHhhcceEEEEecc
Confidence 79999999 6888999999999999999886543
No 77
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=67.20 E-value=5.9 Score=42.55 Aligned_cols=37 Identities=30% Similarity=0.475 Sum_probs=31.0
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
-+.+||+||+| .-...||+++|++++.++.......+
T Consensus 51 ~~~~ll~GppG--~GKT~la~~ia~~l~~~~~~~~~~~~ 87 (328)
T PRK00080 51 LDHVLLYGPPG--LGKTTLANIIANEMGVNIRITSGPAL 87 (328)
T ss_pred CCcEEEECCCC--ccHHHHHHHHHHHhCCCeEEEecccc
Confidence 45799999999 68999999999999999877665433
No 78
>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
Probab=66.55 E-value=5.2 Score=38.61 Aligned_cols=31 Identities=42% Similarity=0.552 Sum_probs=26.4
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
||+|.||+|| -.-++++.||+.++...|-+|
T Consensus 1 ~I~i~G~pGs--GKst~a~~La~~~~~~~i~~~ 31 (194)
T cd01428 1 RILLLGPPGS--GKGTQAERLAKKYGLPHISTG 31 (194)
T ss_pred CEEEECCCCC--CHHHHHHHHHHHcCCeEEECc
Confidence 6999999995 478999999999998776554
No 79
>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=65.89 E-value=6.2 Score=42.08 Aligned_cols=35 Identities=26% Similarity=0.469 Sum_probs=27.7
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLL 529 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~ 529 (779)
+-+||.||+| .-..+||+.+|+++++.+-++-...
T Consensus 51 ~h~lf~GPPG--~GKTTLA~IIA~e~~~~~~~~sg~~ 85 (233)
T PF05496_consen 51 DHMLFYGPPG--LGKTTLARIIANELGVNFKITSGPA 85 (233)
T ss_dssp -EEEEESSTT--SSHHHHHHHHHHHCT--EEEEECCC
T ss_pred ceEEEECCCc--cchhHHHHHHHhccCCCeEeccchh
Confidence 3489999999 6789999999999999998776543
No 80
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=65.75 E-value=5.7 Score=33.39 Aligned_cols=27 Identities=26% Similarity=0.571 Sum_probs=22.3
Q ss_pred eEEECCeecCCC--ceEEeeCCCEEEEcc
Q 004011 199 EVEVNGNVHPKD--SQVVLRGGDELVFSP 225 (779)
Q Consensus 199 tV~VNGkkVgKg--~kviL~nGDEIvfs~ 225 (779)
.|.|||+.|.+. ....|+.||+|.|-+
T Consensus 32 ~V~vNg~~v~~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 32 AVALNGEIVPRSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred EEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 368999999986 458999999998844
No 81
>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=64.82 E-value=6.5 Score=41.17 Aligned_cols=35 Identities=31% Similarity=0.483 Sum_probs=30.0
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
.+-+||.||+| .-..+||+++|++++.++.+++..
T Consensus 30 ~~~~ll~Gp~G--~GKT~la~~ia~~~~~~~~~~~~~ 64 (305)
T TIGR00635 30 LDHLLLYGPPG--LGKTTLAHIIANEMGVNLKITSGP 64 (305)
T ss_pred CCeEEEECCCC--CCHHHHHHHHHHHhCCCEEEeccc
Confidence 35589999999 688899999999999998877654
No 82
>PHA02544 44 clamp loader, small subunit; Provisional
Probab=64.17 E-value=5.8 Score=41.75 Aligned_cols=35 Identities=31% Similarity=0.335 Sum_probs=29.7
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLL 529 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~ 529 (779)
.-+||.||+| ....+||+|||++++..++.++...
T Consensus 44 ~~lll~G~~G--~GKT~la~~l~~~~~~~~~~i~~~~ 78 (316)
T PHA02544 44 NMLLHSPSPG--TGKTTVAKALCNEVGAEVLFVNGSD 78 (316)
T ss_pred eEEEeeCcCC--CCHHHHHHHHHHHhCccceEeccCc
Confidence 3556699999 7899999999999999988887655
No 83
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=63.89 E-value=8.6 Score=41.42 Aligned_cols=37 Identities=27% Similarity=0.421 Sum_probs=33.4
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
.+.+||-||+| .-..+|||+||..++.++..+-.+..
T Consensus 43 ~~~vll~G~PG--~gKT~la~~lA~~l~~~~~~i~~t~~ 79 (329)
T COG0714 43 GGHVLLEGPPG--VGKTLLARALARALGLPFVRIQCTPD 79 (329)
T ss_pred CCCEEEECCCC--ccHHHHHHHHHHHhCCCeEEEecCCC
Confidence 56799999998 78999999999999999999888755
No 84
>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
Probab=63.18 E-value=6.1 Score=43.15 Aligned_cols=37 Identities=27% Similarity=0.411 Sum_probs=33.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
+-|+++||+| --.-.||.+||++|++.++-.|+..+|
T Consensus 5 ~~i~i~Gptg--sGKt~la~~la~~~~~~iis~Ds~Qvy 41 (307)
T PRK00091 5 KVIVIVGPTA--SGKTALAIELAKRLNGEIISADSMQVY 41 (307)
T ss_pred eEEEEECCCC--cCHHHHHHHHHHhCCCcEEecccccee
Confidence 4699999999 468889999999999999999999886
No 85
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=62.19 E-value=8.8 Score=43.24 Aligned_cols=68 Identities=18% Similarity=0.258 Sum_probs=44.1
Q ss_pred cccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhc-----cCeEE
Q 004011 449 IEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHF-----SARLL 523 (779)
Q Consensus 449 i~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F-----~AkLL 523 (779)
-..|||+|- ..+..+.++..|-.+ + .+-....+.++|.||+| .-.-.|++|+|+++ +++.+
T Consensus 117 ~~~tfd~fv--~g~~n~~a~~~~~~~-------~---~~~~~~~~~l~l~G~~G--~GKThL~~ai~~~~~~~~~~~~v~ 182 (450)
T PRK00149 117 PKYTFDNFV--VGKSNRLAHAAALAV-------A---ENPGKAYNPLFIYGGVG--LGKTHLLHAIGNYILEKNPNAKVV 182 (450)
T ss_pred CCCcccccc--cCCCcHHHHHHHHHH-------H---hCcCccCCeEEEECCCC--CCHHHHHHHHHHHHHHhCCCCeEE
Confidence 345899984 355555444433221 1 11112335599999999 68889999999987 66777
Q ss_pred EEeccCC
Q 004011 524 IVDSLLL 530 (779)
Q Consensus 524 ilDs~~l 530 (779)
-+.+..|
T Consensus 183 yi~~~~~ 189 (450)
T PRK00149 183 YVTSEKF 189 (450)
T ss_pred EEEHHHH
Confidence 7777665
No 86
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=61.98 E-value=12 Score=38.81 Aligned_cols=24 Identities=42% Similarity=0.581 Sum_probs=22.9
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhcc
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFS 519 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~ 519 (779)
++||+||+| +....+|.|||+++.
T Consensus 26 alL~~Gp~G--~Gktt~a~~lA~~l~ 49 (325)
T COG0470 26 ALLFYGPPG--VGKTTAALALAKELL 49 (325)
T ss_pred eeeeeCCCC--CCHHHHHHHHHHHHh
Confidence 899999999 799999999999998
No 87
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=61.73 E-value=18 Score=36.51 Aligned_cols=67 Identities=18% Similarity=0.060 Sum_probs=43.4
Q ss_pred ccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhc---cCeEEE
Q 004011 448 NIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHF---SARLLI 524 (779)
Q Consensus 448 ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F---~AkLLi 524 (779)
+-..|||+|.=--++.....|..+.. . ....+-++|.||+| .-...||+|++++. +.+...
T Consensus 12 ~~~~~~d~f~~~~~~~~~~~l~~~~~-------------~-~~~~~~~~l~G~~G--~GKT~La~ai~~~~~~~~~~~~~ 75 (227)
T PRK08903 12 PPPPTFDNFVAGENAELVARLRELAA-------------G-PVADRFFYLWGEAG--SGRSHLLQALVADASYGGRNARY 75 (227)
T ss_pred CChhhhcccccCCcHHHHHHHHHHHh-------------c-cCCCCeEEEECCCC--CCHHHHHHHHHHHHHhCCCcEEE
Confidence 34478999963233333333333221 0 12345799999999 48999999999975 567777
Q ss_pred EeccCC
Q 004011 525 VDSLLL 530 (779)
Q Consensus 525 lDs~~l 530 (779)
+|...+
T Consensus 76 i~~~~~ 81 (227)
T PRK08903 76 LDAASP 81 (227)
T ss_pred EehHHh
Confidence 777655
No 88
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=60.19 E-value=7.8 Score=46.60 Aligned_cols=36 Identities=31% Similarity=0.411 Sum_probs=32.3
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
.+||.||+| .-...|||+||+.++.++..+|.+.+.
T Consensus 486 ~~lf~Gp~G--vGKT~lA~~la~~l~~~~~~~d~se~~ 521 (731)
T TIGR02639 486 SFLFTGPTG--VGKTELAKQLAEALGVHLERFDMSEYM 521 (731)
T ss_pred eEEEECCCC--ccHHHHHHHHHHHhcCCeEEEeCchhh
Confidence 489999999 578899999999999999999987763
No 89
>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=59.77 E-value=25 Score=39.70 Aligned_cols=90 Identities=13% Similarity=0.153 Sum_probs=57.5
Q ss_pred hhhHHHHHHHHHHHhcccCC-Cccccccccccccc-----hhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCC
Q 004011 427 LISARRQAFKDSLQEGILGP-ENIEVSFESFPYYL-----SDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGP 500 (779)
Q Consensus 427 ~~~~r~~~fk~~~~~~Vvdg-~ei~VSFd~FPYYL-----SE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGP 500 (779)
.+-+-.|++-+.+....+.- .+-+-+-..||+|= .+.++.-|++..... ...+....+-+||.||
T Consensus 16 ~~~~a~qr~~dmI~~~g~~~~~~~~~~~~~y~~F~~~~~G~~~~i~~lv~~l~~~---------a~g~~~~r~il~L~GP 86 (361)
T smart00763 16 VAANAHQRLLDMIGEAGVEDVVENNRGIKRYRFFDHDFFGMEEAIERFVNYFKSA---------AQGLEERKQILYLLGP 86 (361)
T ss_pred HHHHHHHHHHHHHhccCcEEeccCCcceeeccccchhccCcHHHHHHHHHHHHHH---------HhcCCCCCcEEEEECC
Confidence 46666777777766544330 00011235688775 677777777533211 1234444455699999
Q ss_pred CCchHHHHHHHHHHHhhccC-------eEEEEec
Q 004011 501 AGSEIYQETLAKALAKHFSA-------RLLIVDS 527 (779)
Q Consensus 501 aGsEiYQE~LaKALA~~F~A-------kLLilDs 527 (779)
+| --.-+||++||+.++. ++..+--
T Consensus 87 PG--sGKStla~~La~~l~~ys~t~eG~~Y~~~~ 118 (361)
T smart00763 87 VG--GGKSSLVECLKRGLEEYSKTPEGRRYTFKW 118 (361)
T ss_pred CC--CCHHHHHHHHHHHHhhhcccccCceEEEEe
Confidence 99 4788899999999988 8887755
No 90
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=59.13 E-value=8.3 Score=32.04 Aligned_cols=27 Identities=30% Similarity=0.458 Sum_probs=22.6
Q ss_pred eEEECCeecCCC--ceEEeeCCCEEEEcc
Q 004011 199 EVEVNGNVHPKD--SQVVLRGGDELVFSP 225 (779)
Q Consensus 199 tV~VNGkkVgKg--~kviL~nGDEIvfs~ 225 (779)
.|.|||+.+.|. ....|+.||+|.|-+
T Consensus 32 ~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 32 AVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred EEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 478999999875 478899999998844
No 91
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=58.91 E-value=7.5 Score=35.61 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=23.6
Q ss_pred eEEECCeecC--CCceEEeeCCCEEEEccC
Q 004011 199 EVEVNGNVHP--KDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 199 tV~VNGkkVg--Kg~kviL~nGDEIvfs~~ 226 (779)
-|+|||+-+. .|-...|+.||||+|-.+
T Consensus 61 ~VlvN~~di~~l~g~~t~L~dgD~v~i~P~ 90 (94)
T cd01764 61 IVLINDTDWELLGEEDYILEDGDHVVFIST 90 (94)
T ss_pred EEEECCccccccCCcccCCCCcCEEEEECC
Confidence 4899999986 678899999999998543
No 92
>PRK13947 shikimate kinase; Provisional
Probab=58.82 E-value=8.9 Score=36.55 Aligned_cols=32 Identities=28% Similarity=0.355 Sum_probs=27.7
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.|+|.||+|+ -.-+++|+||+.++.+++-.|.
T Consensus 3 ~I~l~G~~Gs--GKst~a~~La~~lg~~~id~d~ 34 (171)
T PRK13947 3 NIVLIGFMGT--GKTTVGKRVATTLSFGFIDTDK 34 (171)
T ss_pred eEEEEcCCCC--CHHHHHHHHHHHhCCCEEECch
Confidence 5999999994 5789999999999999876664
No 93
>PRK03839 putative kinase; Provisional
Probab=58.56 E-value=8.5 Score=37.36 Aligned_cols=32 Identities=22% Similarity=0.323 Sum_probs=27.7
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
+|+|.|++|+ -.-+++|+||+.++.+++-+|-
T Consensus 2 ~I~l~G~pGs--GKsT~~~~La~~~~~~~id~d~ 33 (180)
T PRK03839 2 IIAITGTPGV--GKTTVSKLLAEKLGYEYVDLTE 33 (180)
T ss_pred EEEEECCCCC--CHHHHHHHHHHHhCCcEEehhh
Confidence 6999999994 6788999999999998876663
No 94
>PRK06835 DNA replication protein DnaC; Validated
Probab=58.27 E-value=9.5 Score=42.02 Aligned_cols=45 Identities=16% Similarity=0.265 Sum_probs=32.0
Q ss_pred ccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCC
Q 004011 484 YASDLPTMCPRILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLL 530 (779)
Q Consensus 484 yt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l 530 (779)
|+.++.....-+||.||+| .-.-.||.|+|+++ |...+.++..+|
T Consensus 175 f~~~f~~~~~~Lll~G~~G--tGKThLa~aIa~~l~~~g~~V~y~t~~~l 222 (329)
T PRK06835 175 FIENFDKNNENLLFYGNTG--TGKTFLSNCIAKELLDRGKSVIYRTADEL 222 (329)
T ss_pred HHHHHhccCCcEEEECCCC--CcHHHHHHHHHHHHHHCCCeEEEEEHHHH
Confidence 4455555557899999999 57888999999987 445555554433
No 95
>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=57.92 E-value=13 Score=32.43 Aligned_cols=39 Identities=33% Similarity=0.439 Sum_probs=32.5
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCCC
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLLP 531 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l~ 531 (779)
..+-|++.||+| .-.-+|++++++++ +.+.+.+|...+.
T Consensus 18 ~~~~v~i~G~~G--~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~ 59 (151)
T cd00009 18 PPKNLLLYGPPG--TGKTTLARAIANELFRPGAPFLYLNASDLL 59 (151)
T ss_pred CCCeEEEECCCC--CCHHHHHHHHHHHhhcCCCCeEEEehhhhh
Confidence 446799999999 57889999999998 8888888876554
No 96
>PRK07261 topology modulation protein; Provisional
Probab=57.91 E-value=9.2 Score=37.62 Aligned_cols=38 Identities=29% Similarity=0.479 Sum_probs=32.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
.||++.||+| .-.-+||+.||..++.+.+-+|...+..
T Consensus 1 ~ri~i~G~~G--sGKSTla~~l~~~~~~~~i~~D~~~~~~ 38 (171)
T PRK07261 1 MKIAIIGYSG--SGKSTLARKLSQHYNCPVLHLDTLHFQP 38 (171)
T ss_pred CEEEEEcCCC--CCHHHHHHHHHHHhCCCeEecCCEEecc
Confidence 4899999999 5788999999999999999999765543
No 97
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=57.07 E-value=10 Score=32.96 Aligned_cols=26 Identities=27% Similarity=0.487 Sum_probs=21.2
Q ss_pred eEEECCeecCCCceEEeeCCCEEEEccC
Q 004011 199 EVEVNGNVHPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 199 tV~VNGkkVgKg~kviL~nGDEIvfs~~ 226 (779)
.|.|||+.++ ...+|+.||||.|-.|
T Consensus 53 ~vavN~~~v~--~~~~l~dgDeVai~Pp 78 (82)
T PLN02799 53 VLALNEEYTT--ESAALKDGDELAIIPP 78 (82)
T ss_pred EEEECCEEcC--CCcCcCCCCEEEEeCC
Confidence 3789999986 4678999999999654
No 98
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=56.98 E-value=8.1 Score=32.48 Aligned_cols=26 Identities=35% Similarity=0.543 Sum_probs=22.8
Q ss_pred EEECCeecCCCc--eEEeeCCCEEEEcc
Q 004011 200 VEVNGNVHPKDS--QVVLRGGDELVFSP 225 (779)
Q Consensus 200 V~VNGkkVgKg~--kviL~nGDEIvfs~ 225 (779)
|-|||+.|.|.. ...|+.||+|.|-+
T Consensus 33 vavN~~iv~~~~~~~~~L~dgD~Ieiv~ 60 (65)
T PRK06488 33 TAVNGELVHKEARAQFVLHEGDRIEILS 60 (65)
T ss_pred EEECCEEcCHHHcCccccCCCCEEEEEE
Confidence 799999999975 78999999998744
No 99
>PRK08181 transposase; Validated
Probab=56.96 E-value=23 Score=38.09 Aligned_cols=76 Identities=25% Similarity=0.370 Sum_probs=49.6
Q ss_pred HHHHHHHHHhcccCCCccccccccccccc----hhhHHHHHHhh-hhccccCcccccccCCCCCCCCceeecCCCCchHH
Q 004011 432 RQAFKDSLQEGILGPENIEVSFESFPYYL----SDITKNVLIAS-TYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIY 506 (779)
Q Consensus 432 ~~~fk~~~~~~Vvdg~ei~VSFd~FPYYL----SE~TK~vL~sa-ayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiY 506 (779)
....+..+++.=++. .-|||+|-|.- +......|-.| .|++ + ..-|+|.||+| .-
T Consensus 59 ~~~~~r~lk~A~~p~---~~tle~fd~~~~~~~~~~~~~~L~~~~~~~~--~-------------~~nlll~Gp~G--tG 118 (269)
T PRK08181 59 RRRIERHLAEAHLPP---GKTLDSFDFEAVPMVSKAQVMAIAAGDSWLA--K-------------GANLLLFGPPG--GG 118 (269)
T ss_pred HHHHHHHHHHCCCCC---CCCHhhCCccCCCCCCHHHHHHHHHHHHHHh--c-------------CceEEEEecCC--Cc
Confidence 445666677766665 36999998863 45555555555 4543 1 13499999999 47
Q ss_pred HHHHHHHHHhhc---cCeEEEEec
Q 004011 507 QETLAKALAKHF---SARLLIVDS 527 (779)
Q Consensus 507 QE~LaKALA~~F---~AkLLilDs 527 (779)
.-.||.|+|++. |.+.+.+..
T Consensus 119 KTHLa~Aia~~a~~~g~~v~f~~~ 142 (269)
T PRK08181 119 KSHLAAAIGLALIENGWRVLFTRT 142 (269)
T ss_pred HHHHHHHHHHHHHHcCCceeeeeH
Confidence 888999998754 444554444
No 100
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=56.95 E-value=11 Score=29.52 Aligned_cols=28 Identities=32% Similarity=0.447 Sum_probs=21.3
Q ss_pred CceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
.|.|+|||+.+.+ ....++.||.|.+..
T Consensus 25 ~g~V~vn~~~~~~-~~~~v~~~d~i~i~~ 52 (70)
T cd00165 25 HGHVLVNGKVVTK-PSYKVKPGDVIEVDG 52 (70)
T ss_pred cCCEEECCEEccC-CccCcCCCCEEEEcC
Confidence 4569999999854 356778899988743
No 101
>PRK14528 adenylate kinase; Provisional
Probab=55.77 E-value=9.8 Score=37.85 Aligned_cols=32 Identities=28% Similarity=0.418 Sum_probs=27.1
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
++|++.||+|+ -.-++++.||++++.+.+..|
T Consensus 2 ~~i~i~G~pGs--GKtt~a~~la~~~~~~~is~~ 33 (186)
T PRK14528 2 KNIIFMGPPGA--GKGTQAKILCERLSIPQISTG 33 (186)
T ss_pred cEEEEECCCCC--CHHHHHHHHHHHhCCCeeeCC
Confidence 68999999995 468899999999998876554
No 102
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=55.35 E-value=9.6 Score=31.99 Aligned_cols=28 Identities=29% Similarity=0.590 Sum_probs=22.7
Q ss_pred ceEEECCeecCCCc--eEEeeCCCEEEEcc
Q 004011 198 GEVEVNGNVHPKDS--QVVLRGGDELVFSP 225 (779)
Q Consensus 198 GtV~VNGkkVgKg~--kviL~nGDEIvfs~ 225 (779)
-.|-|||+.|.|.. ...|+.||+|.+-+
T Consensus 30 v~v~vN~~iv~~~~~~~~~L~~gD~veii~ 59 (64)
T TIGR01683 30 VAVAVNGEIVPRSEWDDTILKEGDRIEIVT 59 (64)
T ss_pred EEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 35689999998874 57899999998744
No 103
>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=54.83 E-value=15 Score=40.72 Aligned_cols=36 Identities=19% Similarity=0.361 Sum_probs=29.2
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhc-----cCeEEEEeccCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHF-----SARLLIVDSLLL 530 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F-----~AkLLilDs~~l 530 (779)
..+||.||+| .-.-.|++|+|+++ +++.+.+....|
T Consensus 137 n~l~l~G~~G--~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~ 177 (405)
T TIGR00362 137 NPLFIYGGVG--LGKTHLLHAIGNEILENNPNAKVVYVSSEKF 177 (405)
T ss_pred CeEEEECCCC--CcHHHHHHHHHHHHHHhCCCCcEEEEEHHHH
Confidence 4589999999 58899999999987 677777776555
No 104
>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]
Probab=54.14 E-value=16 Score=45.84 Aligned_cols=84 Identities=24% Similarity=0.378 Sum_probs=62.9
Q ss_pred eeecceEEEeccccc--ceeecCCCcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 148 SMTGAVFTVGHNRQC--DLYLKDPSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 148 ~I~~~~fTvGR~~~C--Dl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
.|..+.--||....- .|.|-.+.|-.-||-|.-. +| |+-+.-.+..-.+||||-.|-. .-||.+|+.|-|+-
T Consensus 374 ~L~~~vtEVGs~~~~~~~iqLfGP~IqprHc~it~m--eG--VvTvTP~~~DA~t~VnGh~isq--ttiL~~G~~v~fGa 447 (1629)
T KOG1892|consen 374 RLQLSVTEVGSEKLDDNSIQLFGPGIQPRHCDITNM--EG--VVTVTPRSMDAETYVNGHRISQ--TTILQSGMKVQFGA 447 (1629)
T ss_pred EeccCceeccccccCCcceeeeCCCCCccccchhhc--cc--eEEecccccchhhhccceecch--hhhhccCCEEEecc
Confidence 455556667776644 7888889999999999864 33 3445555556667999999876 78999999999966
Q ss_pred CCCeeEEEeecCcc
Q 004011 226 SGKHSYIFQQLSDD 239 (779)
Q Consensus 226 ~~~~aYIFq~l~~e 239 (779)
.|.|-|.+.+.+
T Consensus 448 --~hsfkF~dss~d 459 (1629)
T KOG1892|consen 448 --SHSFKFVDSSQD 459 (1629)
T ss_pred --ceeEEecCCchh
Confidence 578999876543
No 105
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=53.88 E-value=12 Score=32.48 Aligned_cols=26 Identities=35% Similarity=0.546 Sum_probs=21.8
Q ss_pred eEEECCeecCCCceEEeeCCCEEEEccC
Q 004011 199 EVEVNGNVHPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 199 tV~VNGkkVgKg~kviL~nGDEIvfs~~ 226 (779)
.|.|||+.+.. ...|+.||||+|-.|
T Consensus 51 ~v~vn~~~v~~--~~~l~dgDevai~Pp 76 (80)
T TIGR01682 51 MVAVNEEYVTD--DALLNEGDEVAFIPP 76 (80)
T ss_pred EEEECCEEcCC--CcCcCCCCEEEEeCC
Confidence 37999999996 679999999998543
No 106
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=53.00 E-value=12 Score=32.02 Aligned_cols=24 Identities=25% Similarity=0.419 Sum_probs=17.0
Q ss_pred EEECCeecCCC-ceEEeeCCCEEEE
Q 004011 200 VEVNGNVHPKD-SQVVLRGGDELVF 223 (779)
Q Consensus 200 V~VNGkkVgKg-~kviL~nGDEIvf 223 (779)
.+|||+....| ..+.|++||.|.|
T Consensus 43 ~~vNG~~~~~ga~~~~l~~GD~i~~ 67 (68)
T PF14478_consen 43 YYVNGESANVGAGSYKLKDGDKITW 67 (68)
T ss_dssp EEETTEE-SS-CCC-B--TTEEEEE
T ss_pred EEECCEEhhcCcceeEeCCCCEEEe
Confidence 68999999998 5789999999988
No 107
>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family. This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.
Probab=52.87 E-value=12 Score=35.53 Aligned_cols=33 Identities=36% Similarity=0.478 Sum_probs=26.3
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
|+|.||+|+ -.-+||++||+.+++.++ |.-+|.
T Consensus 1 i~l~G~~Gs--GKSTla~~l~~~l~~~~v--~~D~~~ 33 (163)
T TIGR01313 1 FVLMGVAGS--GKSTIASALAHRLGAKFI--EGDDLH 33 (163)
T ss_pred CEEECCCCC--CHHHHHHHHHHhcCCeEE--eCcccc
Confidence 789999994 678999999999997664 555553
No 108
>PRK13342 recombination factor protein RarA; Reviewed
Probab=51.97 E-value=15 Score=41.14 Aligned_cols=34 Identities=26% Similarity=0.409 Sum_probs=30.2
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
+.|||.||+| .-..+||++||+.++.+++.++..
T Consensus 37 ~~ilL~GppG--tGKTtLA~~ia~~~~~~~~~l~a~ 70 (413)
T PRK13342 37 SSMILWGPPG--TGKTTLARIIAGATDAPFEALSAV 70 (413)
T ss_pred ceEEEECCCC--CCHHHHHHHHHHHhCCCEEEEecc
Confidence 3699999999 589999999999999999888764
No 109
>PRK03731 aroL shikimate kinase II; Reviewed
Probab=51.70 E-value=15 Score=35.11 Aligned_cols=33 Identities=27% Similarity=0.403 Sum_probs=27.8
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.+|+|.|++|+ -.-+++|.||+.++.+++=.|.
T Consensus 3 ~~i~~~G~~Gs--GKst~~~~la~~lg~~~~d~D~ 35 (171)
T PRK03731 3 QPLFLVGARGC--GKTTVGMALAQALGYRFVDTDQ 35 (171)
T ss_pred CeEEEECCCCC--CHHHHHHHHHHHhCCCEEEccH
Confidence 67999999994 6788999999999998775553
No 110
>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=51.65 E-value=13 Score=34.07 Aligned_cols=30 Identities=43% Similarity=0.542 Sum_probs=26.2
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
|.++||+|| ---++||.||+.++.+++-.|
T Consensus 2 I~i~G~~Gs--GKst~a~~la~~~~~~~~~~~ 31 (147)
T cd02020 2 IAIDGPAGS--GKSTVAKLLAKKLGLPYLDTG 31 (147)
T ss_pred EEEECCCCC--CHHHHHHHHHHHhCCceeccc
Confidence 789999995 477899999999999987776
No 111
>PHA02244 ATPase-like protein
Probab=51.45 E-value=15 Score=41.72 Aligned_cols=34 Identities=18% Similarity=0.344 Sum_probs=30.0
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
...|||.||+| .-..+||+|||+.++.+++.++.
T Consensus 119 ~~PVLL~GppG--tGKTtLA~aLA~~lg~pfv~In~ 152 (383)
T PHA02244 119 NIPVFLKGGAG--SGKNHIAEQIAEALDLDFYFMNA 152 (383)
T ss_pred CCCEEEECCCC--CCHHHHHHHHHHHhCCCEEEEec
Confidence 45699999999 68999999999999999988763
No 112
>PRK14531 adenylate kinase; Provisional
Probab=49.99 E-value=14 Score=36.40 Aligned_cols=29 Identities=34% Similarity=0.479 Sum_probs=25.1
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
+||++.||+|| -.-++++.||+++|+..+
T Consensus 3 ~~i~i~G~pGs--GKsT~~~~la~~~g~~~i 31 (183)
T PRK14531 3 QRLLFLGPPGA--GKGTQAARLCAAHGLRHL 31 (183)
T ss_pred cEEEEECCCCC--CHHHHHHHHHHHhCCCeE
Confidence 68999999994 678899999999997754
No 113
>PRK06217 hypothetical protein; Validated
Probab=49.78 E-value=15 Score=36.12 Aligned_cols=33 Identities=36% Similarity=0.434 Sum_probs=28.0
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.+|+|.|++|| -.-+|+|+||+.++.+.+=+|.
T Consensus 2 ~~I~i~G~~Gs--GKSTla~~L~~~l~~~~~~~D~ 34 (183)
T PRK06217 2 MRIHITGASGS--GTTTLGAALAERLDIPHLDTDD 34 (183)
T ss_pred eEEEEECCCCC--CHHHHHHHHHHHcCCcEEEcCc
Confidence 37999999994 6889999999999988766664
No 114
>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=49.21 E-value=10 Score=34.70 Aligned_cols=30 Identities=50% Similarity=0.693 Sum_probs=24.3
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
|+|+||+|| -.-+|||.|++.+++..+-.|
T Consensus 2 ii~~G~pgs--GKSt~a~~l~~~~~~~~i~~D 31 (143)
T PF13671_consen 2 IILCGPPGS--GKSTLAKRLAKRLGAVVISQD 31 (143)
T ss_dssp EEEEESTTS--SHHHHHHHHHHHSTEEEEEHH
T ss_pred EEEECCCCC--CHHHHHHHHHHHCCCEEEeHH
Confidence 799999995 578899999999995544444
No 115
>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
Probab=48.87 E-value=16 Score=34.13 Aligned_cols=30 Identities=37% Similarity=0.484 Sum_probs=24.9
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
|+|+||+|+ -.-++||.|++.+++.++=.|
T Consensus 2 i~l~G~~Gs--GKST~a~~l~~~~~~~~i~~D 31 (150)
T cd02021 2 IVVMGVSGS--GKSTVGKALAERLGAPFIDGD 31 (150)
T ss_pred EEEEcCCCC--CHHHHHHHHHhhcCCEEEeCc
Confidence 789999994 578999999999998765433
No 116
>PRK06893 DNA replication initiation factor; Validated
Probab=48.28 E-value=18 Score=37.10 Aligned_cols=25 Identities=24% Similarity=0.352 Sum_probs=21.4
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhc
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHF 518 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F 518 (779)
++-++|.||+| .-.-.|+.|+||++
T Consensus 39 ~~~l~l~G~~G--~GKThL~~ai~~~~ 63 (229)
T PRK06893 39 QPFFYIWGGKS--SGKSHLLKAVSNHY 63 (229)
T ss_pred CCeEEEECCCC--CCHHHHHHHHHHHH
Confidence 46689999999 57888999999886
No 117
>PRK14530 adenylate kinase; Provisional
Probab=48.01 E-value=18 Score=36.40 Aligned_cols=32 Identities=34% Similarity=0.505 Sum_probs=27.3
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEE
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIV 525 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLil 525 (779)
.++|+|.||+|| -.-++++.||+.++...+-.
T Consensus 3 ~~~I~i~G~pGs--GKsT~~~~La~~~~~~~i~~ 34 (215)
T PRK14530 3 QPRILLLGAPGA--GKGTQSSNLAEEFGVEHVTT 34 (215)
T ss_pred CCEEEEECCCCC--CHHHHHHHHHHHhCCeEEec
Confidence 468999999995 58899999999999876644
No 118
>CHL00095 clpC Clp protease ATP binding subunit
Probab=47.65 E-value=16 Score=44.61 Aligned_cols=36 Identities=33% Similarity=0.488 Sum_probs=31.3
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLLP 531 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l~ 531 (779)
.+||.||+| .-...|||+||+++ +..++-+|.+.|.
T Consensus 541 ~~lf~Gp~G--vGKt~lA~~LA~~l~~~~~~~~~~d~s~~~ 579 (821)
T CHL00095 541 SFLFSGPTG--VGKTELTKALASYFFGSEDAMIRLDMSEYM 579 (821)
T ss_pred EEEEECCCC--CcHHHHHHHHHHHhcCCccceEEEEchhcc
Confidence 489999999 67889999999986 5789999998874
No 119
>PRK06526 transposase; Provisional
Probab=47.62 E-value=36 Score=36.15 Aligned_cols=67 Identities=19% Similarity=0.208 Sum_probs=44.3
Q ss_pred HHHHHHHHHhcccCCCcccccccccccc----chhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHH
Q 004011 432 RQAFKDSLQEGILGPENIEVSFESFPYY----LSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQ 507 (779)
Q Consensus 432 ~~~fk~~~~~~Vvdg~ei~VSFd~FPYY----LSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQ 507 (779)
....+..+++.=++.. -||++|-|- +...+-..|-++.|++ ..+.|+|.||+| .-.
T Consensus 52 ~~~~~~~lk~a~~p~~---~~le~fd~~~~~~~~~~~~~~l~~~~fi~---------------~~~nlll~Gp~G--tGK 111 (254)
T PRK06526 52 SHGGEGRIRAARFPAR---KSLEEFDFDHQRSLKRDTIAHLGTLDFVT---------------GKENVVFLGPPG--TGK 111 (254)
T ss_pred HHHHHHHHHhCCCCCC---CChhhccCccCCCcchHHHHHHhcCchhh---------------cCceEEEEeCCC--Cch
Confidence 3456666777777774 577777663 3333444444555543 235789999999 578
Q ss_pred HHHHHHHHhhc
Q 004011 508 ETLAKALAKHF 518 (779)
Q Consensus 508 E~LaKALA~~F 518 (779)
-.||.|||++.
T Consensus 112 ThLa~al~~~a 122 (254)
T PRK06526 112 THLAIGLGIRA 122 (254)
T ss_pred HHHHHHHHHHH
Confidence 88999998875
No 120
>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=47.29 E-value=9.1 Score=46.12 Aligned_cols=40 Identities=28% Similarity=0.396 Sum_probs=35.7
Q ss_pred CCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 490 TMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 490 s~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
+..+.+||.||+| .-..+|++|.|++.+|.|+.+....+.
T Consensus 216 ~~prg~Ll~gppg--~Gkt~l~~aVa~e~~a~~~~i~~peli 255 (693)
T KOG0730|consen 216 KPPRGLLLYGPPG--TGKTFLVRAVANEYGAFLFLINGPELI 255 (693)
T ss_pred CCCCCccccCCCC--CChHHHHHHHHHHhCceeEecccHHHH
Confidence 3568999999998 678999999999999999999998773
No 121
>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=47.08 E-value=17 Score=42.59 Aligned_cols=35 Identities=37% Similarity=0.546 Sum_probs=32.7
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
-|||-||.|| -...||+-||+-+++++-|-|.+.|
T Consensus 228 NvLllGPtGs--GKTllaqTLAr~ldVPfaIcDcTtL 262 (564)
T KOG0745|consen 228 NVLLLGPTGS--GKTLLAQTLARVLDVPFAICDCTTL 262 (564)
T ss_pred cEEEECCCCC--chhHHHHHHHHHhCCCeEEecccch
Confidence 4899999995 6889999999999999999999999
No 122
>TIGR01351 adk adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
Probab=47.01 E-value=16 Score=36.73 Aligned_cols=31 Identities=32% Similarity=0.503 Sum_probs=26.0
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
||++.||+|| -.-++|+.||++||+..|-.+
T Consensus 1 rI~i~G~pGs--GKsT~a~~La~~~g~~~is~g 31 (210)
T TIGR01351 1 RLVLLGPPGS--GKGTQAKRIAEKYGLPHISTG 31 (210)
T ss_pred CEEEECCCCC--CHHHHHHHHHHHcCCCeeehh
Confidence 6999999996 478999999999998766543
No 123
>PRK14532 adenylate kinase; Provisional
Probab=46.92 E-value=18 Score=35.36 Aligned_cols=29 Identities=28% Similarity=0.307 Sum_probs=24.7
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEE
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLI 524 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLi 524 (779)
+|+|.||+|| -.-++++.||+++|...+-
T Consensus 2 ~i~~~G~pGs--GKsT~a~~la~~~g~~~is 30 (188)
T PRK14532 2 NLILFGPPAA--GKGTQAKRLVEERGMVQLS 30 (188)
T ss_pred EEEEECCCCC--CHHHHHHHHHHHcCCeEEe
Confidence 5999999994 6888999999999976653
No 124
>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=46.27 E-value=14 Score=35.98 Aligned_cols=34 Identities=21% Similarity=0.275 Sum_probs=27.8
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
++=|+|+||+|+ -.-+|||+|++.++...+.++.
T Consensus 2 ~~~i~l~G~~gs--GKst~a~~l~~~~~~~~~~~~~ 35 (175)
T cd00227 2 GRIIILNGGSSA--GKSSIARALQSVLAEPWLHFGV 35 (175)
T ss_pred CCEEEEECCCCC--CHHHHHHHHHHhhCCCccccCc
Confidence 456999999994 6789999999999887765554
No 125
>PRK05057 aroK shikimate kinase I; Reviewed
Probab=45.72 E-value=20 Score=35.28 Aligned_cols=34 Identities=26% Similarity=0.458 Sum_probs=29.4
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
..+|+|.||.|+ -.-+|+|+||+.++.+++-.|.
T Consensus 4 ~~~I~liG~~Ga--GKStl~~~La~~l~~~~vd~D~ 37 (172)
T PRK05057 4 KRNIFLVGPMGA--GKSTIGRQLAQQLNMEFYDSDQ 37 (172)
T ss_pred CCEEEEECCCCc--CHHHHHHHHHHHcCCcEEECCc
Confidence 457999999994 6789999999999999887775
No 126
>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=45.33 E-value=33 Score=41.78 Aligned_cols=34 Identities=26% Similarity=0.510 Sum_probs=29.7
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.+.+||.||+| .-..+|||+||+.++.++.-++.
T Consensus 347 ~~~lll~GppG--~GKT~lAk~iA~~l~~~~~~i~~ 380 (775)
T TIGR00763 347 GPILCLVGPPG--VGKTSLGKSIAKALNRKFVRFSL 380 (775)
T ss_pred CceEEEECCCC--CCHHHHHHHHHHHhcCCeEEEeC
Confidence 35799999999 57789999999999999988864
No 127
>PLN03025 replication factor C subunit; Provisional
Probab=45.03 E-value=20 Score=38.56 Aligned_cols=24 Identities=42% Similarity=0.652 Sum_probs=21.1
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhc
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHF 518 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F 518 (779)
+.+||+||+| .-..+||+|||+.+
T Consensus 35 ~~lll~Gp~G--~GKTtla~~la~~l 58 (319)
T PLN03025 35 PNLILSGPPG--TGKTTSILALAHEL 58 (319)
T ss_pred ceEEEECCCC--CCHHHHHHHHHHHH
Confidence 3489999999 68899999999986
No 128
>PF01300 Sua5_yciO_yrdC: Telomere recombination; InterPro: IPR006070 The YrdC family of hypothetical proteins are widely distributed in eukaryotes and prokaryotes and occur as: (i) independent proteins, (ii) with C-terminal extensions, and (iii) as domains in larger proteins, some of which are implicated in regulation []. The YrdC protein, which consists solely of this domain, forms an alpha/beta twisted open-sheet structure composed of seven alpha helices and seven beta strands []. YrdC from Escherichia coli preferentially binds to double-stranded RNA and DNA. YrdC is predicted to be an rRNA maturation factor, as deletions in its gene lead to immature ribosomal 30S subunits and, consequently, fewer translating ribosomes []. Therefore, YrdC may function by keeping an rRNA structure needed for proper processing of 16S rRNA, especially at lower temperatures. Sua5 is an example of a multi-domain protein that contains an N-terminal YrdC-like domain and a C-terminal Sua5 domain. Sua5 was identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a translation initiation defect in the cytochrome c gene and is required for normal growth in yeast; however its exact function remains unknown []. HypF is involved in the synthesis of the active site of [NiFe]-hydrogenases [].; PDB: 3L7V_A 1KK9_A 1K7J_A 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A 2EQA_A ....
Probab=44.02 E-value=29 Score=34.59 Aligned_cols=58 Identities=21% Similarity=0.314 Sum_probs=40.1
Q ss_pred hHHHHHHHHHHhhcccCcCCEEEEEcchhhhccCC-hhhHHHHHHHhcc-CCCCEEEEeec
Q 004011 686 DKLAINELFEVALNESKSSPLIVFVKDIEKSLTGN-NDAYGALKSKLEN-LPSNVVVIGSH 744 (779)
Q Consensus 686 eKLlIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs-~e~y~~fq~mLeK-LsG~VLIIGSq 744 (779)
.+-+++.||++=.-. ...|+||++.|++++-.=- .++...+.+.+++ +||++.+|--.
T Consensus 25 n~~av~ri~~iK~R~-~~Kpl~ll~~~~~~l~~~~~~~~~~~~~~l~~~~wPgp~t~I~~~ 84 (179)
T PF01300_consen 25 NPEAVERIYKIKQRP-KNKPLILLVSSIEQLEEYVDSPVSPKARRLLEKFWPGPLTLILPA 84 (179)
T ss_dssp SHHHHHHHHHHHTSS-TTS--EEEESSHHHHHHHEETT--HHHHHHHHHCHSSSEEEEEEE
T ss_pred CHHHHHHHHHhhccc-CCCCEEEEECCHHHHHHHhhccccHHHHHHHHhccccCeeEeecc
Confidence 567899999987663 6789999999988754311 2344556667777 89999999875
No 129
>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=43.47 E-value=17 Score=44.84 Aligned_cols=35 Identities=29% Similarity=0.429 Sum_probs=30.3
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLL 530 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l 530 (779)
-+||.||+| .-...||||||+.+ +..+..+|.+.+
T Consensus 598 ~~lf~Gp~G--vGKT~lA~~La~~l~~~~~~~~~~dmse~ 635 (852)
T TIGR03345 598 VFLLVGPSG--VGKTETALALAELLYGGEQNLITINMSEF 635 (852)
T ss_pred EEEEECCCC--CCHHHHHHHHHHHHhCCCcceEEEeHHHh
Confidence 389999999 57888999999998 668999997766
No 130
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=43.25 E-value=21 Score=34.38 Aligned_cols=32 Identities=19% Similarity=0.243 Sum_probs=25.8
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
|++.||+|| -.-++|++||+++++. .+++.++
T Consensus 2 i~i~G~pGs--GKst~a~~la~~~~~~--~is~~d~ 33 (183)
T TIGR01359 2 VFVLGGPGS--GKGTQCAKIVENFGFT--HLSAGDL 33 (183)
T ss_pred EEEECCCCC--CHHHHHHHHHHHcCCe--EEECChH
Confidence 899999994 6889999999999865 4555444
No 131
>PRK13949 shikimate kinase; Provisional
Probab=43.14 E-value=20 Score=35.36 Aligned_cols=33 Identities=36% Similarity=0.503 Sum_probs=28.3
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
++|+|.||+|+ -.-+|+|.||+.++.+.+=+|.
T Consensus 2 ~~I~liG~~Gs--GKstl~~~La~~l~~~~id~D~ 34 (169)
T PRK13949 2 ARIFLVGYMGA--GKTTLGKALARELGLSFIDLDF 34 (169)
T ss_pred cEEEEECCCCC--CHHHHHHHHHHHcCCCeecccH
Confidence 47999999995 5778999999999988777774
No 132
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=42.60 E-value=21 Score=38.89 Aligned_cols=36 Identities=33% Similarity=0.532 Sum_probs=32.8
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
|.+.||+| .-.-.||-+||+++++.++-+|+..+|=
T Consensus 2 i~i~G~t~--~GKs~la~~l~~~~~~~iis~Ds~qvY~ 37 (287)
T TIGR00174 2 IFIMGPTA--VGKSQLAIQLAKKLNAEIISVDSMQIYK 37 (287)
T ss_pred EEEECCCC--CCHHHHHHHHHHhCCCcEEEechhheee
Confidence 78999998 4788899999999999999999999973
No 133
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=42.36 E-value=32 Score=38.20 Aligned_cols=25 Identities=28% Similarity=0.341 Sum_probs=22.0
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhcc
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFS 519 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~ 519 (779)
+.+||.||+| .-..|||||||+-+-
T Consensus 30 ~~vLl~G~pG--~gKT~lar~la~llP 54 (334)
T PRK13407 30 GGVLVFGDRG--TGKSTAVRALAALLP 54 (334)
T ss_pred CcEEEEcCCC--CCHHHHHHHHHHHCC
Confidence 4599999999 689999999999864
No 134
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=42.25 E-value=21 Score=30.23 Aligned_cols=27 Identities=19% Similarity=0.583 Sum_probs=22.8
Q ss_pred eEEECCeecCCC--ceEEeeCCCEEEEcc
Q 004011 199 EVEVNGNVHPKD--SQVVLRGGDELVFSP 225 (779)
Q Consensus 199 tV~VNGkkVgKg--~kviL~nGDEIvfs~ 225 (779)
.|-|||+.|.|. ....|+.||+|.+-+
T Consensus 33 aVavN~~iv~r~~w~~~~L~~gD~Ieii~ 61 (66)
T PRK08053 33 ALAINQQIIPREQWAQHIVQDGDQILLFQ 61 (66)
T ss_pred EEEECCEEeChHHcCccccCCCCEEEEEE
Confidence 468999999988 777899999998743
No 135
>PF03215 Rad17: Rad17 cell cycle checkpoint protein
Probab=42.00 E-value=20 Score=42.07 Aligned_cols=31 Identities=39% Similarity=0.493 Sum_probs=25.1
Q ss_pred Cce-eecCCCCchHHHHHHHHHHHhhccCeEEEE
Q 004011 493 PRI-LLSGPAGSEIYQETLAKALAKHFSARLLIV 525 (779)
Q Consensus 493 ~rI-LLSGPaGsEiYQE~LaKALA~~F~AkLLil 525 (779)
++| ||+||+| --.-+++|.||+++|.++.--
T Consensus 45 ~~iLlLtGP~G--~GKtttv~~La~elg~~v~Ew 76 (519)
T PF03215_consen 45 KRILLLTGPSG--CGKTTTVKVLAKELGFEVQEW 76 (519)
T ss_pred cceEEEECCCC--CCHHHHHHHHHHHhCCeeEEe
Confidence 345 5699999 467889999999999987653
No 136
>PRK00279 adk adenylate kinase; Reviewed
Probab=41.33 E-value=23 Score=35.75 Aligned_cols=33 Identities=27% Similarity=0.439 Sum_probs=26.4
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
||++.||+|| -.-++++.||+++++..| ++.++
T Consensus 2 ~I~v~G~pGs--GKsT~a~~la~~~~~~~i--s~~dl 34 (215)
T PRK00279 2 RLILLGPPGA--GKGTQAKFIAEKYGIPHI--STGDM 34 (215)
T ss_pred EEEEECCCCC--CHHHHHHHHHHHhCCcEE--ECCcc
Confidence 7999999994 677999999999996555 44444
No 137
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=41.30 E-value=35 Score=36.86 Aligned_cols=53 Identities=28% Similarity=0.538 Sum_probs=41.9
Q ss_pred HHHHHHHHhhcccCcCCEEEEEcchhhhccCChhhHHHHHHHhc----cCCCCEEEEeecc
Q 004011 689 AINELFEVALNESKSSPLIVFVKDIEKSLTGNNDAYGALKSKLE----NLPSNVVVIGSHT 745 (779)
Q Consensus 689 lIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs~e~y~~fq~mLe----KLsG~VLIIGSq~ 745 (779)
-|..|+++|.. +...+|||+-|.. |-.+...|..||..|| .-|.||+|.-.-|
T Consensus 93 ~l~~l~~~l~~--~~~kFIlf~DDLs--Fe~~d~~yk~LKs~LeGgle~~P~NvliyATSN 149 (249)
T PF05673_consen 93 DLPELLDLLRD--RPYKFILFCDDLS--FEEGDTEYKALKSVLEGGLEARPDNVLIYATSN 149 (249)
T ss_pred cHHHHHHHHhc--CCCCEEEEecCCC--CCCCcHHHHHHHHHhcCccccCCCcEEEEEecc
Confidence 34556666653 5689999999954 7888999999999986 7899999987644
No 138
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=41.28 E-value=28 Score=40.29 Aligned_cols=27 Identities=30% Similarity=0.519 Sum_probs=23.5
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.+.+||+||+| ....+||++||+.+..
T Consensus 36 ~~~~Lf~GPpG--tGKTTlA~~lA~~l~~ 62 (472)
T PRK14962 36 SHAYIFAGPRG--TGKTTVARILAKSLNC 62 (472)
T ss_pred CeEEEEECCCC--CCHHHHHHHHHHHhcc
Confidence 34589999999 6899999999999875
No 139
>PTZ00088 adenylate kinase 1; Provisional
Probab=40.84 E-value=23 Score=37.07 Aligned_cols=33 Identities=24% Similarity=0.328 Sum_probs=27.8
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
-||+|.||+|| -.-++|+.||+.+++..+-+|-
T Consensus 7 mrIvl~G~PGs--GK~T~a~~La~~~g~~~is~gd 39 (229)
T PTZ00088 7 LKIVLFGAPGV--GKGTFAEILSKKENLKHINMGN 39 (229)
T ss_pred ceEEEECCCCC--CHHHHHHHHHHHhCCcEEECCh
Confidence 46999999994 6789999999999988776664
No 140
>PF14512 TM1586_NiRdase: Putative TM nitroreductase; PDB: 1VKW_A.
Probab=40.59 E-value=21 Score=37.56 Aligned_cols=65 Identities=14% Similarity=0.233 Sum_probs=28.7
Q ss_pred hhhhhhHHHHHHHhhhcCCCCCchhhHHHHHHHHHHHhcccCCCccccccccccccc---hhhHHHHHHhhhh
Q 004011 404 ISKILDEQREIRELLKDSDRPTVLISARRQAFKDSLQEGILGPENIEVSFESFPYYL---SDITKNVLIASTY 473 (779)
Q Consensus 404 ~~k~lee~~e~~~~~~~~~~~~s~~~~r~~~fk~~~~~~Vvdg~ei~VSFd~FPYYL---SE~TK~vL~saay 473 (779)
|-++++.|.-||..++..-. .-. ++..++-..+.|.+.-+.++.|..||||+ ++.....|..|.|
T Consensus 3 i~EaI~~RhSVRky~dk~l~----e~i-~~~I~~l~i~~I~~~~~~k~~~~~~~~yi~~~~~k~~~~l~n~GY 70 (206)
T PF14512_consen 3 IYEAIFKRHSVRKYLDKPLP----EEI-KEEIENLHIQLITDKLDWKIKLSKAPNYIAAYSEKKDDYLENAGY 70 (206)
T ss_dssp HHHHHHH--B---B--S-------HHH-HHHHHH-----SS-----EEE-SSSSEEEE----SSHHHHHHHHH
T ss_pred HHHHHHHhcchhccCCCCCC----HHH-HHHHHHHHHHHhhhhhcceecccCCCeEEEEEecCCcchHHhcCH
Confidence 56677888887777433221 222 23344444667777778888899999998 4555567888888
No 141
>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=40.16 E-value=22 Score=37.95 Aligned_cols=39 Identities=23% Similarity=0.271 Sum_probs=28.9
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC-------eEEEEeccCCCC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA-------RLLIVDSLLLPG 532 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A-------kLLilDs~~l~G 532 (779)
+..|||.||+|| -..+||+++|+.+.. .++.++..+|.+
T Consensus 58 ~~~vll~G~pGT--GKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l~~ 103 (284)
T TIGR02880 58 TLHMSFTGNPGT--GKTTVALRMAQILHRLGYVRKGHLVSVTRDDLVG 103 (284)
T ss_pred CceEEEEcCCCC--CHHHHHHHHHHHHHHcCCcccceEEEecHHHHhH
Confidence 346999999995 899999999987742 466666555543
No 142
>PRK06762 hypothetical protein; Provisional
Probab=40.06 E-value=29 Score=33.12 Aligned_cols=33 Identities=27% Similarity=0.435 Sum_probs=26.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.-|+|+|++| --.-++|++|+++++....++|.
T Consensus 3 ~li~i~G~~G--sGKST~A~~L~~~l~~~~~~i~~ 35 (166)
T PRK06762 3 TLIIIRGNSG--SGKTTIAKQLQERLGRGTLLVSQ 35 (166)
T ss_pred eEEEEECCCC--CCHHHHHHHHHHHhCCCeEEecH
Confidence 3589999999 46889999999999666666653
No 143
>PRK08727 hypothetical protein; Validated
Probab=39.92 E-value=48 Score=34.29 Aligned_cols=21 Identities=48% Similarity=0.597 Sum_probs=13.3
Q ss_pred CceeecCCCCchHHHHHHHHHHH
Q 004011 493 PRILLSGPAGSEIYQETLAKALA 515 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA 515 (779)
.-|+|.||+| .-.-.|+.|++
T Consensus 42 ~~l~l~G~~G--~GKThL~~a~~ 62 (233)
T PRK08727 42 DWLYLSGPAG--TGKTHLALALC 62 (233)
T ss_pred CeEEEECCCC--CCHHHHHHHHH
Confidence 3499999999 23444444443
No 144
>PRK14527 adenylate kinase; Provisional
Probab=39.81 E-value=23 Score=34.98 Aligned_cols=35 Identities=26% Similarity=0.360 Sum_probs=28.1
Q ss_pred CCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 490 TMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 490 s~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
+....|++.||+|| -.-++|+.||+++++..+-.|
T Consensus 4 ~~~~~i~i~G~pGs--GKsT~a~~La~~~~~~~is~g 38 (191)
T PRK14527 4 TKNKVVIFLGPPGA--GKGTQAERLAQELGLKKLSTG 38 (191)
T ss_pred CCCcEEEEECCCCC--CHHHHHHHHHHHhCCCCCCcc
Confidence 34578999999995 578999999999998665543
No 145
>PLN02840 tRNA dimethylallyltransferase
Probab=39.78 E-value=23 Score=40.72 Aligned_cols=38 Identities=32% Similarity=0.468 Sum_probs=33.8
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
+-|++.||+| --.-.||+.||++|++.++-+|+..+|-
T Consensus 22 ~vi~I~Gptg--sGKTtla~~La~~~~~~iis~Ds~qvYr 59 (421)
T PLN02840 22 KVIVISGPTG--AGKSRLALELAKRLNGEIISADSVQVYR 59 (421)
T ss_pred eEEEEECCCC--CCHHHHHHHHHHHCCCCeEeccccceec
Confidence 3599999999 4688899999999999999999988874
No 146
>PRK00625 shikimate kinase; Provisional
Probab=39.48 E-value=25 Score=35.22 Aligned_cols=32 Identities=31% Similarity=0.398 Sum_probs=27.8
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
.|+|.|++|+ -.-+++|+||++++.+.+=+|-
T Consensus 2 ~I~LiG~pGs--GKTT~~k~La~~l~~~~id~D~ 33 (173)
T PRK00625 2 QIFLCGLPTV--GKTSFGKALAKFLSLPFFDTDD 33 (173)
T ss_pred EEEEECCCCC--CHHHHHHHHHHHhCCCEEEhhH
Confidence 4999999994 6788999999999999877774
No 147
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=39.38 E-value=26 Score=36.90 Aligned_cols=37 Identities=19% Similarity=0.296 Sum_probs=29.8
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhcc-----CeEEEEeccCCCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFS-----ARLLIVDSLLLPG 532 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~-----AkLLilDs~~l~G 532 (779)
-+||.||+| .-..+||+|+|+++. .+.+.++..++..
T Consensus 38 ~lll~Gp~G--tGKT~la~~~~~~l~~~~~~~~~~~i~~~~~~~ 79 (337)
T PRK12402 38 HLLVQGPPG--SGKTAAVRALARELYGDPWENNFTEFNVADFFD 79 (337)
T ss_pred eEEEECCCC--CCHHHHHHHHHHHhcCcccccceEEechhhhhh
Confidence 599999999 578999999999874 4567778777653
No 148
>PRK06437 hypothetical protein; Provisional
Probab=39.16 E-value=33 Score=29.54 Aligned_cols=25 Identities=20% Similarity=0.219 Sum_probs=21.0
Q ss_pred eEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 199 EVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 199 tV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
.|.|||+.+. ...+|+.||+|.+-.
T Consensus 38 aV~vNg~iv~--~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 38 VVIVNGSPVL--EDHNVKKEDDVLILE 62 (67)
T ss_pred EEEECCEECC--CceEcCCCCEEEEEe
Confidence 4679999998 688999999998743
No 149
>PRK15367 type III secretion system protein SsaD; Provisional
Probab=39.00 E-value=67 Score=36.94 Aligned_cols=69 Identities=17% Similarity=0.314 Sum_probs=46.6
Q ss_pred CCceeeecceEEEecccccceeecCCCcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCCCceEEeeCCCEE
Q 004011 144 NSHLSMTGAVFTVGHNRQCDLYLKDPSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPKDSQVVLRGGDEL 221 (779)
Q Consensus 144 ~P~v~I~~~~fTvGR~~~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEI 221 (779)
-..+.+-.-+||+|- +.||++|.-..-..+ .-+++.++ ++|+ ...++|+|||....-+...+|+..=||
T Consensus 16 GrEl~Lp~G~~tlG~-~gcDi~lpL~~~~~~---~L~i~e~g---i~l~--~~~~~vwVnG~~~~~~~~LPl~q~Ie~ 84 (395)
T PRK15367 16 GREVWLNEGNLSLGE-KGCDICIPLTINEKI---ILREQADS---LFVD--AGKARVRVNGRRFNPNKPLPSSGVLQV 84 (395)
T ss_pred CcEEecCCCceeecC-CCceEEEECCCCCEE---EEEEcCCc---EEEe--cCCceEEECCEEcCCCCCCCCcchhhh
Confidence 445567778899999 569999976543322 22243333 3333 335789999999999988888776554
No 150
>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid [].; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.
Probab=38.93 E-value=25 Score=37.70 Aligned_cols=36 Identities=31% Similarity=0.398 Sum_probs=27.4
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
+|+-||.| .-.-.||=+||+.||++++++|.-..|.
T Consensus 4 ~~i~GpT~--tGKt~~ai~lA~~~g~pvI~~Driq~y~ 39 (233)
T PF01745_consen 4 YLIVGPTG--TGKTALAIALAQKTGAPVISLDRIQCYP 39 (233)
T ss_dssp EEEE-STT--SSHHHHHHHHHHHH--EEEEE-SGGG-G
T ss_pred EEEECCCC--CChhHHHHHHHHHhCCCEEEecceeccc
Confidence 68999998 4678899999999999999999988863
No 151
>PRK08233 hypothetical protein; Provisional
Probab=38.85 E-value=31 Score=32.93 Aligned_cols=36 Identities=19% Similarity=0.252 Sum_probs=29.8
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhcc-CeEEEEeccCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFS-ARLLIVDSLLL 530 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~-AkLLilDs~~l 530 (779)
.-|.+.||+| --.-+||++||++|+ ..++.+|...+
T Consensus 4 ~iI~I~G~~G--sGKtTla~~L~~~l~~~~~~~~d~~~~ 40 (182)
T PRK08233 4 KIITIAAVSG--GGKTTLTERLTHKLKNSKALYFDRYDF 40 (182)
T ss_pred eEEEEECCCC--CCHHHHHHHHHhhCCCCceEEECCEEc
Confidence 4588899999 478899999999995 77888887654
No 152
>KOG0241 consensus Kinesin-like protein [Cytoskeleton]
Probab=38.72 E-value=55 Score=41.54 Aligned_cols=66 Identities=23% Similarity=0.294 Sum_probs=50.7
Q ss_pred EEEecccccceeecCCCcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 154 FTVGHNRQCDLYLKDPSISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 154 fTvGR~~~CDl~L~d~~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
--+|-...-||+|-.-.|--.||.|. |+..|. ++++-+..- ..+|||..|-. +-.|.+||.|-.+-
T Consensus 469 tlig~~~~~~i~l~glgi~p~h~vid-I~~dg~--l~~~p~~~~-R~~VNGs~v~~--~t~L~~GdRiLwGn 534 (1714)
T KOG0241|consen 469 TLIGLFKSQDIQLSGLGIQPKHCVID-IESDGE--LRLTPLLNA-RSCVNGSLVCS--TTQLWHGDRILWGN 534 (1714)
T ss_pred eeeccccCcceeeecCcccCccceee-eccCCc--EEecccccc-eeeecCceecc--ccccccCceEEecc
Confidence 34677778888888878888999999 444443 666666655 46999999987 78899999998844
No 153
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=38.71 E-value=35 Score=38.92 Aligned_cols=70 Identities=19% Similarity=0.257 Sum_probs=44.1
Q ss_pred CCccccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhc-----cC
Q 004011 446 PENIEVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHF-----SA 520 (779)
Q Consensus 446 g~ei~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F-----~A 520 (779)
+-+-..|||||= ..+..+.++..|--+. . +-..-+ .++|.||+| .-.-.|+.|+|+++ +.
T Consensus 97 ~l~~~~tFdnFv--~g~~n~~a~~~~~~~~-~---------~~~~~n-~l~lyG~~G--~GKTHLl~ai~~~l~~~~~~~ 161 (440)
T PRK14088 97 PLNPDYTFENFV--VGPGNSFAYHAALEVA-K---------NPGRYN-PLFIYGGVG--LGKTHLLQSIGNYVVQNEPDL 161 (440)
T ss_pred CCCCCCcccccc--cCCchHHHHHHHHHHH-h---------CcCCCC-eEEEEcCCC--CcHHHHHHHHHHHHHHhCCCC
Confidence 345668999975 3454444433322211 1 111122 399999999 57889999999875 57
Q ss_pred eEEEEeccCC
Q 004011 521 RLLIVDSLLL 530 (779)
Q Consensus 521 kLLilDs~~l 530 (779)
+.+.+++.+|
T Consensus 162 ~v~yi~~~~f 171 (440)
T PRK14088 162 RVMYITSEKF 171 (440)
T ss_pred eEEEEEHHHH
Confidence 7888887665
No 154
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=38.51 E-value=90 Score=33.83 Aligned_cols=41 Identities=22% Similarity=0.279 Sum_probs=31.8
Q ss_pred cccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 483 KYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 483 Kyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
.|.+.+.+. ..|.|.|+.|+ -.-+++|+||+.+|.+++-+|
T Consensus 125 ~~~~~~~~~-~~I~l~G~~Gs--GKStvg~~La~~Lg~~~id~D 165 (309)
T PRK08154 125 GAGRRAARR-RRIALIGLRGA--GKSTLGRMLAARLGVPFVELN 165 (309)
T ss_pred hhhhhccCC-CEEEEECCCCC--CHHHHHHHHHHHcCCCEEeHH
Confidence 445555444 47999999994 578899999999999988555
No 155
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=38.24 E-value=42 Score=36.52 Aligned_cols=31 Identities=29% Similarity=0.320 Sum_probs=26.0
Q ss_pred cCCceEEECCeecCCCceEEeeCCCEEEEccCC
Q 004011 195 GGKGEVEVNGNVHPKDSQVVLRGGDELVFSPSG 227 (779)
Q Consensus 195 ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~ 227 (779)
-.+|-|.|||+.+. ....|..||.|.+..+.
T Consensus 34 i~~g~v~vNg~~v~--~~~~l~~gd~i~~~~~~ 64 (289)
T COG0564 34 IRKGRVRVNGKKVK--PSYKLKPGDVVRIPLPE 64 (289)
T ss_pred HHCCCEEECCEEcc--CCeeeCCCCEEEEeccc
Confidence 34668999999999 68999999999996643
No 156
>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=37.92 E-value=25 Score=43.32 Aligned_cols=42 Identities=38% Similarity=0.467 Sum_probs=33.0
Q ss_pred CCCCCceeecCCCCchHHHHHHHHHHHhhccCeEE----EEeccCCCC
Q 004011 489 PTMCPRILLSGPAGSEIYQETLAKALAKHFSARLL----IVDSLLLPG 532 (779)
Q Consensus 489 ss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLL----ilDs~~l~G 532 (779)
-...+.|||-||.| .-...|||||++||.-+++ ++|.+-+.|
T Consensus 428 v~~~~~Ill~G~~G--sGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~ 473 (952)
T KOG0735|consen 428 VFRHGNILLNGPKG--SGKTNLVKALFDYYSKDLIAHVEIVSCSTLDG 473 (952)
T ss_pred ccccccEEEeCCCC--CCHhHHHHHHHHHhccccceEEEEEechhccc
Confidence 34678999999999 6889999999999996654 455555544
No 157
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=37.87 E-value=66 Score=36.01 Aligned_cols=57 Identities=26% Similarity=0.515 Sum_probs=38.2
Q ss_pred HHHHHHHHhhcccCcCCEEEEEcchhhhccC--------ChhhHHHHHHHhccCC-----CCEEEEeeccccC
Q 004011 689 AINELFEVALNESKSSPLIVFVKDIEKSLTG--------NNDAYGALKSKLENLP-----SNVVVIGSHTQLD 748 (779)
Q Consensus 689 lIqsLyEVL~S~S~t~PlILYiKDVEK~L~g--------s~e~y~~fq~mLeKLs-----G~VLIIGSq~~~D 748 (779)
.+..+|+.... ..|-||||.|++.++.. ..+.-..|-..|..+. ++|+|||.-+..|
T Consensus 212 ~i~~~f~~a~~---~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~ 281 (389)
T PRK03992 212 LVRELFELARE---KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRID 281 (389)
T ss_pred HHHHHHHHHHh---cCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChh
Confidence 46678887765 78999999999997642 2233333444444333 4899999888765
No 158
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=37.69 E-value=31 Score=31.18 Aligned_cols=26 Identities=31% Similarity=0.442 Sum_probs=22.8
Q ss_pred ceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 198 GEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 198 GtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
|.|+|||+.++- .++|+.||.|.+..
T Consensus 50 ~~i~vNG~~v~~--~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 50 GLILVNGRPVDF--DYRLKDGDRVAVYP 75 (81)
T ss_pred EEEEECCEECCC--cccCCCCCEEEEEe
Confidence 578999999998 59999999998854
No 159
>PRK02496 adk adenylate kinase; Provisional
Probab=37.40 E-value=26 Score=34.12 Aligned_cols=31 Identities=29% Similarity=0.471 Sum_probs=26.5
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
||++.||+|+ -.-++++.||+.++...+-.|
T Consensus 3 ~i~i~G~pGs--GKst~a~~la~~~~~~~i~~~ 33 (184)
T PRK02496 3 RLIFLGPPGA--GKGTQAVVLAEHLHIPHISTG 33 (184)
T ss_pred EEEEECCCCC--CHHHHHHHHHHHhCCcEEEhH
Confidence 6999999994 578999999999998776654
No 160
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=36.96 E-value=25 Score=39.21 Aligned_cols=35 Identities=34% Similarity=0.528 Sum_probs=29.6
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
-|||.||+| +-..+||.=+|++.|++|=+--.-.|
T Consensus 54 HvLl~GPPG--lGKTTLA~IIA~Emgvn~k~tsGp~l 88 (332)
T COG2255 54 HVLLFGPPG--LGKTTLAHIIANELGVNLKITSGPAL 88 (332)
T ss_pred eEEeeCCCC--CcHHHHHHHHHHHhcCCeEecccccc
Confidence 489999998 89999999999999999876544333
No 161
>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=36.92 E-value=32 Score=34.00 Aligned_cols=27 Identities=41% Similarity=0.591 Sum_probs=20.0
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
|||-|++| .-..+||||||+..+...-
T Consensus 2 vLleg~PG--~GKT~la~~lA~~~~~~f~ 28 (131)
T PF07726_consen 2 VLLEGVPG--VGKTTLAKALARSLGLSFK 28 (131)
T ss_dssp EEEES-----HHHHHHHHHHHHHTT--EE
T ss_pred EeeECCCc--cHHHHHHHHHHHHcCCcee
Confidence 79999999 8899999999999997653
No 162
>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=36.52 E-value=31 Score=39.55 Aligned_cols=41 Identities=24% Similarity=0.381 Sum_probs=31.1
Q ss_pred CCCCceeecCCCCchHHHHHHHHHHHhhcc--CeEEEEeccCCCC
Q 004011 490 TMCPRILLSGPAGSEIYQETLAKALAKHFS--ARLLIVDSLLLPG 532 (779)
Q Consensus 490 s~s~rILLSGPaGsEiYQE~LaKALA~~F~--AkLLilDs~~l~G 532 (779)
-+++.|||.||+|| -..-||=|+|+.+| +++-.+..+.+|.
T Consensus 48 ~aGr~iLiaGppGt--GKTAlA~~ia~eLG~~~PF~~isgSEiyS 90 (398)
T PF06068_consen 48 IAGRAILIAGPPGT--GKTALAMAIAKELGEDVPFVSISGSEIYS 90 (398)
T ss_dssp -TT-EEEEEE-TTS--SHHHHHHHHHHHCTTTS-EEEEEGGGG-B
T ss_pred ccCcEEEEeCCCCC--CchHHHHHHHHHhCCCCCeeEcccceeee
Confidence 36899999999994 68889999999999 7777777777765
No 163
>PRK09183 transposase/IS protein; Provisional
Probab=36.45 E-value=76 Score=33.62 Aligned_cols=74 Identities=16% Similarity=0.230 Sum_probs=44.5
Q ss_pred HHHHHHHhcccCCCcccccccccccc----chhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHH
Q 004011 434 AFKDSLQEGILGPENIEVSFESFPYY----LSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQET 509 (779)
Q Consensus 434 ~fk~~~~~~Vvdg~ei~VSFd~FPYY----LSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~ 509 (779)
..+..+++.=++.. -||++|-|- +....-..|-.+.| +. ....|+|.||+| .-.-.
T Consensus 58 ~~~~~~k~a~~p~~---~~l~~fd~~~~~~~~~~~i~~L~~~~~--i~-------------~~~~v~l~Gp~G--tGKTh 117 (259)
T PRK09183 58 KQAMYTRMAAFPAV---KTFEEYDFTFATGAPQKQLQSLRSLSF--IE-------------RNENIVLLGPSG--VGKTH 117 (259)
T ss_pred HHHHHHHhCCCCCC---CcHhhcccccCCCCCHHHHHHHhcCCc--hh-------------cCCeEEEEeCCC--CCHHH
Confidence 34455666656654 667766662 33333333333333 21 135699999999 57889
Q ss_pred HHHHHHhhc---cCeEEEEec
Q 004011 510 LAKALAKHF---SARLLIVDS 527 (779)
Q Consensus 510 LaKALA~~F---~AkLLilDs 527 (779)
|+.|||+.. |.+.+.++.
T Consensus 118 La~al~~~a~~~G~~v~~~~~ 138 (259)
T PRK09183 118 LAIALGYEAVRAGIKVRFTTA 138 (259)
T ss_pred HHHHHHHHHHHcCCeEEEEeH
Confidence 999998763 556665553
No 164
>PRK11860 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional
Probab=36.43 E-value=22 Score=42.46 Aligned_cols=36 Identities=31% Similarity=0.369 Sum_probs=31.5
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
++|.+.||+|| -.-+++|+||++|+.+. +|+-.||-
T Consensus 443 ~~i~i~g~~~~--gks~~~~~l~~~~~~~~--~~~~~~~~ 478 (661)
T PRK11860 443 PVICIDGPTAS--GKGTVAARVAEALGYHY--LDSGALYR 478 (661)
T ss_pred ceEEeeCCCCC--CHHHHHHHHHHHhCCeE--ecHHHhhh
Confidence 58999999994 68899999999999987 78888874
No 165
>PRK14960 DNA polymerase III subunits gamma and tau; Provisional
Probab=36.31 E-value=32 Score=41.99 Aligned_cols=27 Identities=30% Similarity=0.474 Sum_probs=24.1
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
...+||+||+| .-..++||+||+.++.
T Consensus 37 ~HAyLF~GPpG--vGKTTlAriLAK~LnC 63 (702)
T PRK14960 37 HHAYLFTGTRG--VGKTTIARILAKCLNC 63 (702)
T ss_pred CeEEEEECCCC--CCHHHHHHHHHHHhCC
Confidence 36889999999 6899999999999875
No 166
>PF13521 AAA_28: AAA domain; PDB: 1LW7_A.
Probab=36.13 E-value=34 Score=32.72 Aligned_cols=39 Identities=13% Similarity=0.054 Sum_probs=22.1
Q ss_pred cCCEEEEEcchhhh---------ccCChhhHHHHHHHhccCCCCEEEE
Q 004011 703 SSPLIVFVKDIEKS---------LTGNNDAYGALKSKLENLPSNVVVI 741 (779)
Q Consensus 703 t~PlILYiKDVEK~---------L~gs~e~y~~fq~mLeKLsG~VLII 741 (779)
..-+|+|++-..-| +....+++..++.+|+.+.-++++|
T Consensus 108 ~yd~v~~l~~~~~~~~D~~R~~~~~~r~~~~~~~~~~l~~~~~~~~~v 155 (163)
T PF13521_consen 108 RYDLVFLLPPDPPWEQDGVRPEDPEERERIDELLKELLERHGIPYIIV 155 (163)
T ss_dssp --SEEEEEE----------------SHHHHHHHHHHHHHGGG---EEE
T ss_pred CCCEEEEeCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHCCCeEEEe
Confidence 35567776654443 1245678889999999999999999
No 167
>CHL00181 cbbX CbbX; Provisional
Probab=35.67 E-value=32 Score=37.05 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=21.6
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhc
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHF 518 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F 518 (779)
...|||.||+| .-..++||+||+.+
T Consensus 59 ~~~ill~G~pG--tGKT~lAr~la~~~ 83 (287)
T CHL00181 59 GLHMSFTGSPG--TGKTTVALKMADIL 83 (287)
T ss_pred CceEEEECCCC--CCHHHHHHHHHHHH
Confidence 44599999999 57999999999975
No 168
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=35.44 E-value=84 Score=28.22 Aligned_cols=55 Identities=13% Similarity=0.209 Sum_probs=43.9
Q ss_pred HHHHHHHHHHhhcccCcCCEEEEEcchhhhccCChhhHHHHHHHhccCCCCEEEEeeccc
Q 004011 687 KLAINELFEVALNESKSSPLIVFVKDIEKSLTGNNDAYGALKSKLENLPSNVVVIGSHTQ 746 (779)
Q Consensus 687 KLlIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs~e~y~~fq~mLeKLsG~VLIIGSq~~ 746 (779)
.-+++.+.+.+.. ....+|.|-|++.+. +.++++.++.+++.-.-+||++|-...
T Consensus 73 ~~l~~~~~~~l~~---~~~~~lviDe~~~l~--~~~~l~~l~~l~~~~~~~vvl~G~~~l 127 (131)
T PF13401_consen 73 DELRSLLIDALDR---RRVVLLVIDEADHLF--SDEFLEFLRSLLNESNIKVVLVGTPEL 127 (131)
T ss_dssp HHHHHHHHHHHHH---CTEEEEEEETTHHHH--THHHHHHHHHHTCSCBEEEEEEESSTT
T ss_pred HHHHHHHHHHHHh---cCCeEEEEeChHhcC--CHHHHHHHHHHHhCCCCeEEEEEChhh
Confidence 3344888888887 444899999999955 699999999999977778899987743
No 169
>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=34.93 E-value=91 Score=30.21 Aligned_cols=57 Identities=23% Similarity=0.367 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHhhcccCcCCEEEEEcchhhhc---cCChhhHHHHHHHhccCC----CCEEEEeec
Q 004011 686 DKLAINELFEVALNESKSSPLIVFVKDIEKSL---TGNNDAYGALKSKLENLP----SNVVVIGSH 744 (779)
Q Consensus 686 eKLlIqsLyEVL~S~S~t~PlILYiKDVEK~L---~gs~e~y~~fq~mLeKLs----G~VLIIGSq 744 (779)
....+..+++.+....+. +||.|-|++.+. .....+...|++.++.+. -.+|++||.
T Consensus 102 ~~~~l~~~~~~l~~~~~~--~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~ 165 (234)
T PF01637_consen 102 SFSALERLLEKLKKKGKK--VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS 165 (234)
T ss_dssp -G--HHHHHHHHHHCHCC--EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred HHHHHHHHHHHHHhcCCc--EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence 456678888888874444 999999999988 245677788888888732 246667765
No 170
>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]
Probab=34.77 E-value=26 Score=38.74 Aligned_cols=51 Identities=27% Similarity=0.354 Sum_probs=38.9
Q ss_pred cccCcccccccCCCCCCC-CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 475 HLKCNNFAKYASDLPTMC-PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 475 HLk~~~~sKyt~~Lss~s-~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
..||.++. ..|.-+- ..+||-||+|| -...||+|.|||-+.+++=+-.+.|
T Consensus 166 PvKHPELF---~aLGIaQPKGvlLygppgt--GktLlaraVahht~c~firvsgsel 217 (404)
T KOG0728|consen 166 PVKHPELF---EALGIAQPKGVLLYGPPGT--GKTLLARAVAHHTDCTFIRVSGSEL 217 (404)
T ss_pred cccCHHHH---HhcCCCCCcceEEecCCCC--chhHHHHHHHhhcceEEEEechHHH
Confidence 45666663 3444333 57999999994 6778999999999999998877666
No 171
>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=34.25 E-value=64 Score=38.07 Aligned_cols=60 Identities=28% Similarity=0.493 Sum_probs=39.4
Q ss_pred HHHHHHHHhhcc-cCcCCEEEEEcchhhhccCCh---------hhHHHHHHHhccCC--CCEEEEeeccccC
Q 004011 689 AINELFEVALNE-SKSSPLIVFVKDIEKSLTGNN---------DAYGALKSKLENLP--SNVVVIGSHTQLD 748 (779)
Q Consensus 689 lIqsLyEVL~S~-S~t~PlILYiKDVEK~L~gs~---------e~y~~fq~mLeKLs--G~VLIIGSq~~~D 748 (779)
.+..+|+.+... +...|.||||-+++.++..+. +..+.|-..|+.+. ++|+|||.-++.+
T Consensus 273 ~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d 344 (512)
T TIGR03689 273 QIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNRED 344 (512)
T ss_pred HHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChh
Confidence 455667666543 345799999999999775321 22334445555555 6899999877654
No 172
>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=34.07 E-value=38 Score=34.93 Aligned_cols=31 Identities=35% Similarity=0.584 Sum_probs=25.6
Q ss_pred eeecCCCCchHHHHHHHHHHHhhcc---CeEEEEec
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFS---ARLLIVDS 527 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~---AkLLilDs 527 (779)
|+|+|++|| -.-++|++||++|+ .+..++|.
T Consensus 2 Ivl~G~pGS--GKST~a~~La~~l~~~~~~v~~i~~ 35 (249)
T TIGR03574 2 IILTGLPGV--GKSTFSKELAKKLSEKNIDVIILGT 35 (249)
T ss_pred EEEEcCCCC--CHHHHHHHHHHHHHHcCCceEEEcc
Confidence 899999994 68899999999995 55667765
No 173
>smart00797 AHS2 Allophanate hydrolase subunit 2. This domain represents subunit 2 of allophanate hydrolase (AHS2).
Probab=33.78 E-value=90 Score=34.11 Aligned_cols=45 Identities=18% Similarity=0.333 Sum_probs=36.7
Q ss_pred EEEEEecCCceEEECCeecCCCceEEeeCCCEEEEccCCCeeEEE
Q 004011 189 ALLEITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSYIF 233 (779)
Q Consensus 189 a~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIF 233 (779)
+++=++|....+.|||+.+.-...+.++.||++.|..+..=++.|
T Consensus 46 ~~iAitGA~~~~~ln~~~~~~~~~~~v~~Gd~L~~g~~~~G~R~Y 90 (280)
T smart00797 46 AVIALTGADFPATLDGQPVPPWKPFLVRAGQVLSLGAPKAGARAY 90 (280)
T ss_pred cEEEEeCCCCeeeECCEEcCCCeEEEECCCCEEEeCCCCCccEEE
Confidence 446678888789999999999999999999999998876533444
No 174
>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=33.40 E-value=82 Score=28.75 Aligned_cols=53 Identities=30% Similarity=0.352 Sum_probs=36.4
Q ss_pred chhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEe
Q 004011 460 LSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVD 526 (779)
Q Consensus 460 LSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilD 526 (779)
..++.+.+|-.....++....+-+....|+ |.|..+=.||+||++ +.+|||||
T Consensus 81 ~~~~~~~~l~~l~~~~~~~~~~~~~~~~LS------------~Ge~~rl~la~al~~--~~~llllD 133 (137)
T PF00005_consen 81 SDERIEEVLKKLGLEDLLDRKIGQRASSLS------------GGEKQRLALARALLK--NPKLLLLD 133 (137)
T ss_dssp HHHHHHHHHHHTTHGGGTGSBGTSCGGGSC------------HHHHHHHHHHHHHHT--TSSEEEEE
T ss_pred ccccccccccccccccccccccccccchhh------------HHHHHHHHHHHHHHc--CCCEEEEe
Confidence 345666666666666655555544444444 558888889999987 58999999
No 175
>PRK04182 cytidylate kinase; Provisional
Probab=32.79 E-value=39 Score=32.08 Aligned_cols=28 Identities=36% Similarity=0.551 Sum_probs=24.1
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
.|.|+|++|| -.-+++|+||+.+|.+++
T Consensus 2 ~I~i~G~~Gs--GKstia~~la~~lg~~~i 29 (180)
T PRK04182 2 IITISGPPGS--GKTTVARLLAEKLGLKHV 29 (180)
T ss_pred EEEEECCCCC--CHHHHHHHHHHHcCCcEe
Confidence 5899999995 578899999999998754
No 176
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=32.63 E-value=47 Score=31.63 Aligned_cols=31 Identities=29% Similarity=0.341 Sum_probs=24.7
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEEccCCC
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGK 228 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~ 228 (779)
..|-|.|||..+.- ...++-||+|.+....+
T Consensus 32 ~~GrV~vNG~~aKp--S~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 32 EGGRVKVNGQRAKP--SKEVKVGDILTIRFGNK 62 (100)
T ss_pred HCCeEEECCEEccc--ccccCCCCEEEEEeCCc
Confidence 35789999999943 66789999999977543
No 177
>PRK13946 shikimate kinase; Provisional
Probab=32.40 E-value=36 Score=33.64 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=28.3
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
+.|+|.|++|+ -.-+++|.||+.+|.+++-.|.
T Consensus 11 ~~I~l~G~~Gs--GKsti~~~LA~~Lg~~~id~D~ 43 (184)
T PRK13946 11 RTVVLVGLMGA--GKSTVGRRLATMLGLPFLDADT 43 (184)
T ss_pred CeEEEECCCCC--CHHHHHHHHHHHcCCCeECcCH
Confidence 47999999994 5788999999999999776664
No 178
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=32.33 E-value=36 Score=37.55 Aligned_cols=57 Identities=21% Similarity=0.236 Sum_probs=36.5
Q ss_pred hhhHHHHHHhhhhccccCcccccccCCCCC--CCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 461 SDITKNVLIASTYVHLKCNNFAKYASDLPT--MCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 461 SE~TK~vL~saayvHLk~~~~sKyt~~Lss--~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
.+-+...|..+.|-++... |- ..+.+-. ..--||++||+| .-.-+||+.||++|+..
T Consensus 61 ~~~V~~~L~~~~~~~~~~~-y~-~~~~i~~~~~p~iIlI~G~sg--sGKStlA~~La~~l~~~ 119 (301)
T PRK04220 61 RRRVYYKLIEKDYEEVAEK-YL-LWRRIRKSKEPIIILIGGASG--VGTSTIAFELASRLGIR 119 (301)
T ss_pred HHHHHHHHHHhCcHhHHHH-HH-HHHHHhcCCCCEEEEEECCCC--CCHHHHHHHHHHHhCCC
Confidence 4556666666666665543 21 1111111 113599999999 46788999999999987
No 179
>PRK10634 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional
Probab=32.00 E-value=78 Score=32.30 Aligned_cols=52 Identities=15% Similarity=0.234 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHhhcccCcCCEEEEEcchhhhcc---C---ChhhHHHHHHHhccCCCCEEEE
Q 004011 686 DKLAINELFEVALNESKSSPLIVFVKDIEKSLT---G---NNDAYGALKSKLENLPSNVVVI 741 (779)
Q Consensus 686 eKLlIqsLyEVL~S~S~t~PlILYiKDVEK~L~---g---s~e~y~~fq~mLeKLsG~VLII 741 (779)
.+-+++.||+ |..-....||+|++.|.+++.. . +++. .+.+....||++.+|
T Consensus 39 n~~Av~ri~~-iK~R~~~Kpl~ll~~~~~~l~~~~~~~~~~~~~---~~l~~~~wPGPlTli 96 (190)
T PRK10634 39 SETAVMRLLE-LKQRPVDKGLILIAANYEQLKPYIDDSMLTDAQ---RETIFSCWPGPVTFV 96 (190)
T ss_pred CHHHHHHHHH-HhCCCCCCCcEEEECCHHHHHHHHHhcCCCHHH---HHHHHHhCCCCEEEE
Confidence 5678999999 4555778899999999877542 1 1222 244455679999988
No 180
>PF02626 AHS2: Allophanate hydrolase subunit 2; InterPro: IPR003778 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 2 of allophanate hydrolase (AHS2) which is found in urea carboxylase.; PDB: 3MML_G 3VA7_A 3OEP_A 3OPF_C 3ORE_B.
Probab=31.88 E-value=96 Score=33.69 Aligned_cols=46 Identities=24% Similarity=0.439 Sum_probs=35.4
Q ss_pred EEEEEecCCceEEECCeecCCCceEEeeCCCEEEEccCCCeeEEEe
Q 004011 189 ALLEITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSYIFQ 234 (779)
Q Consensus 189 a~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIFq 234 (779)
+.+=++|..-.+.|||+.+.-++.+.++-||+|.|..+.+=+|.|-
T Consensus 46 ~~ialtGa~~~~~lng~~~~~~~~~~v~~Gd~L~~~~~~~G~r~YL 91 (271)
T PF02626_consen 46 TVIALTGADFEATLNGKPVPMWQPFLVKAGDVLKFGPPRSGARAYL 91 (271)
T ss_dssp EEEEEEESCEEEEETTEEE-TTSEEEE-TT-EEEEEEESSECEEEE
T ss_pred eEEEEECCCCceEECCEEccCCEEEEECCCCEEEecCCCCccEEEE
Confidence 4466678877789999999999999999999999988766555554
No 181
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=31.82 E-value=31 Score=38.50 Aligned_cols=51 Identities=18% Similarity=0.229 Sum_probs=35.9
Q ss_pred cccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 453 FESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 453 Fd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
|+++-. .|+.+..|..+.- . ......+||+||+| .-..++|+++|+++...
T Consensus 15 ~~eiiG--q~~~~~~L~~~~~----~----------~~~~ha~lf~Gp~G--~GKtt~A~~~a~~l~c~ 65 (397)
T PRK14955 15 FADITA--QEHITRTIQNSLR----M----------GRVGHGYIFSGLRG--VGKTTAARVFAKAVNCQ 65 (397)
T ss_pred HhhccC--hHHHHHHHHHHHH----h----------CCcceeEEEECCCC--CCHHHHHHHHHHHhcCC
Confidence 555433 6777776655332 1 12345799999999 78999999999999764
No 182
>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=31.79 E-value=1.3e+02 Score=35.93 Aligned_cols=36 Identities=31% Similarity=0.427 Sum_probs=28.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhc----------cCeEEEEeccCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHF----------SARLLIVDSLLL 530 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F----------~AkLLilDs~~l 530 (779)
+.|||.||+| .-..+||+++++.. +.+++.+|...+
T Consensus 176 ~~vlL~Gp~G--tGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l 221 (615)
T TIGR02903 176 QHIILYGPPG--VGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL 221 (615)
T ss_pred CeEEEECCCC--CCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhc
Confidence 4599999999 57899999997654 456888887655
No 183
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=30.72 E-value=45 Score=37.01 Aligned_cols=38 Identities=29% Similarity=0.440 Sum_probs=34.1
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
+.|+|.||.+ --.--||=+||+.|++.++-+||-..|.
T Consensus 4 ~~i~I~GPTA--sGKT~lai~LAk~~~~eIIs~DSmQvYr 41 (308)
T COG0324 4 KLIVIAGPTA--SGKTALAIALAKRLGGEIISLDSMQVYR 41 (308)
T ss_pred cEEEEECCCC--cCHHHHHHHHHHHcCCcEEecchhhhcC
Confidence 5699999998 4677799999999999999999999985
No 184
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=30.62 E-value=64 Score=31.93 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=25.5
Q ss_pred CceEEECCeecCCCceEEeeCCCEEEEccCCCeeEEEee
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSYIFQQ 235 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIFq~ 235 (779)
.|.|+|||... |- ...+..||+|.|.. +...|++.-
T Consensus 33 ~G~V~vnG~~~-Kp-s~~V~~gd~l~v~~-~~~~~~v~V 68 (133)
T PRK10348 33 GGKVHYNGQRS-KP-SKIVELNATLTLRQ-GNDERTVIV 68 (133)
T ss_pred CCCEEECCEEC-CC-CCccCCCCEEEEEE-CCEEEEEEE
Confidence 47799999994 43 34457899999955 445666664
No 185
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=30.50 E-value=41 Score=34.79 Aligned_cols=29 Identities=24% Similarity=0.337 Sum_probs=23.0
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
..|.|+|||+.+.+. ...++.||+|.+.-
T Consensus 113 ~~G~V~VNgk~v~~p-s~~V~~GD~I~V~~ 141 (200)
T TIGR01017 113 SHGHILVNGKKVDIP-SYQVRPGDIISIKE 141 (200)
T ss_pred HCCCEEECCEEeCCC-CCCCCCCCEEEEee
Confidence 467899999999764 55778899998843
No 186
>PRK01777 hypothetical protein; Validated
Probab=30.50 E-value=46 Score=30.96 Aligned_cols=27 Identities=26% Similarity=0.293 Sum_probs=22.4
Q ss_pred CceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
.+.|.|||+.+.- ..+|+.||.|.+.-
T Consensus 49 ~~~vgI~Gk~v~~--d~~L~dGDRVeIyr 75 (95)
T PRK01777 49 KNKVGIYSRPAKL--TDVLRDGDRVEIYR 75 (95)
T ss_pred cceEEEeCeECCC--CCcCCCCCEEEEec
Confidence 3568999999976 67999999998743
No 187
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=30.31 E-value=41 Score=28.07 Aligned_cols=26 Identities=38% Similarity=0.670 Sum_probs=22.0
Q ss_pred eEEECCeecCCC--ceEEeeCCCEEEEc
Q 004011 199 EVEVNGNVHPKD--SQVVLRGGDELVFS 224 (779)
Q Consensus 199 tV~VNGkkVgKg--~kviL~nGDEIvfs 224 (779)
.|-|||+.|.|. ...+|+.||+|-+-
T Consensus 33 av~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 33 AVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred EEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 477999999987 67889999999774
No 188
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=29.96 E-value=39 Score=38.12 Aligned_cols=54 Identities=17% Similarity=0.291 Sum_probs=36.9
Q ss_pred HHHHHHhh-----cccCcCCEEEEEcchhhhccCChhhHHHHHHHhccCCCCEEEEeecccc
Q 004011 691 NELFEVAL-----NESKSSPLIVFVKDIEKSLTGNNDAYGALKSKLENLPSNVVVIGSHTQL 747 (779)
Q Consensus 691 qsLyEVL~-----S~S~t~PlILYiKDVEK~L~gs~e~y~~fq~mLeKLsG~VLIIGSq~~~ 747 (779)
+++-+|+. -+++.-|=+|||..|--+= -|-|.-+.+.|+.==.||||..|.--+
T Consensus 278 ~eiNkvVn~Yid~GvAElvPGVLFIDEVhMLD---iEcFTyL~kalES~iaPivifAsNrG~ 336 (456)
T KOG1942|consen 278 GEINKVVNKYIDQGVAELVPGVLFIDEVHMLD---IECFTYLHKALESPIAPIVIFASNRGM 336 (456)
T ss_pred HHHHHHHHHHHhcchhhhcCcceEeeehhhhh---hHHHHHHHHHhcCCCCceEEEecCCcc
Confidence 45556654 4567889999998765422 233445778888888899999886543
No 189
>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]
Probab=29.95 E-value=59 Score=35.23 Aligned_cols=52 Identities=27% Similarity=0.385 Sum_probs=37.1
Q ss_pred hhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCCC
Q 004011 462 DITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLPG 532 (779)
Q Consensus 462 E~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~G 532 (779)
+..+.+|-...-.|++++.+.+ || |-+.=+=.||||||. +.+||+||= .|.|
T Consensus 118 ~~v~~aL~~Vgm~~~~~r~i~~-------------LS---GGQ~QRV~lARAL~~--~p~lllLDE-P~~g 169 (254)
T COG1121 118 EKVDEALERVGMEDLRDRQIGE-------------LS---GGQKQRVLLARALAQ--NPDLLLLDE-PFTG 169 (254)
T ss_pred HHHHHHHHHcCchhhhCCcccc-------------cC---cHHHHHHHHHHHhcc--CCCEEEecC-Cccc
Confidence 4445566666667888766543 22 557888889999998 689999994 6665
No 190
>PLN02674 adenylate kinase
Probab=29.94 E-value=38 Score=36.10 Aligned_cols=30 Identities=27% Similarity=0.407 Sum_probs=25.3
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
..+|+|.||+|+ -.-++++.||++|+..-+
T Consensus 31 ~~~i~l~G~PGs--GKgT~a~~La~~~~~~hi 60 (244)
T PLN02674 31 DKRLILIGPPGS--GKGTQSPIIKDEYCLCHL 60 (244)
T ss_pred CceEEEECCCCC--CHHHHHHHHHHHcCCcEE
Confidence 478999999995 577899999999996544
No 191
>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.
Probab=29.87 E-value=34 Score=33.03 Aligned_cols=38 Identities=29% Similarity=0.274 Sum_probs=25.9
Q ss_pred CCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 490 TMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 490 s~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
+...-|||+|+-| --..+|+|+||+.||.+- .+-|-.|
T Consensus 13 ~~g~vi~L~GdLG--aGKTtf~r~l~~~lg~~~-~V~SPTF 50 (123)
T PF02367_consen 13 KPGDVILLSGDLG--AGKTTFVRGLARALGIDE-EVTSPTF 50 (123)
T ss_dssp SS-EEEEEEESTT--SSHHHHHHHHHHHTT--S-----TTT
T ss_pred CCCCEEEEECCCC--CCHHHHHHHHHHHcCCCC-CcCCCCe
Confidence 4456799999999 578899999999999875 4455444
No 192
>PRK11507 ribosome-associated protein; Provisional
Probab=29.81 E-value=44 Score=29.92 Aligned_cols=26 Identities=27% Similarity=0.629 Sum_probs=21.1
Q ss_pred CceEEECCeecCCCceEEeeCCCEEEE
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDELVF 223 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEIvf 223 (779)
.|.|.|||+.-.+ +..-|..||.|.|
T Consensus 36 eg~V~VNGeve~r-RgkKl~~GD~V~~ 61 (70)
T PRK11507 36 EGQVKVDGAVETR-KRCKIVAGQTVSF 61 (70)
T ss_pred cCceEECCEEecc-cCCCCCCCCEEEE
Confidence 4789999997655 4667899999998
No 193
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=29.74 E-value=45 Score=34.81 Aligned_cols=29 Identities=17% Similarity=0.231 Sum_probs=23.2
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
..|.|+|||+.+.+. ...++.||+|.+.-
T Consensus 112 ~~G~V~VNGk~v~~p-s~~Vk~GD~I~V~~ 140 (201)
T CHL00113 112 NHGHILVNGRIVDIP-SYRCKPKDIITVKD 140 (201)
T ss_pred HCCcEEECCEEecCc-cccCCCCCEEEEcc
Confidence 467899999999864 56778899998843
No 194
>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=29.72 E-value=48 Score=41.03 Aligned_cols=35 Identities=29% Similarity=0.432 Sum_probs=29.5
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLL 529 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~ 529 (779)
+=.||||||| +-..+||.-+||+-|-+.+=+-.+|
T Consensus 327 KilLL~GppG--lGKTTLAHViAkqaGYsVvEINASD 361 (877)
T KOG1969|consen 327 KILLLCGPPG--LGKTTLAHVIAKQAGYSVVEINASD 361 (877)
T ss_pred ceEEeecCCC--CChhHHHHHHHHhcCceEEEecccc
Confidence 3457899999 9999999999999999987766554
No 195
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=29.66 E-value=52 Score=29.74 Aligned_cols=26 Identities=42% Similarity=0.664 Sum_probs=21.5
Q ss_pred CceEEECCeecCCCceEEeeCCCEEEE
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDELVF 223 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEIvf 223 (779)
+|.|+|||+.-.+ +.+-|..||.|-|
T Consensus 36 eg~V~vNGe~EtR-RgkKlr~gd~V~i 61 (73)
T COG2501 36 EGEVKVNGEVETR-RGKKLRDGDVVEI 61 (73)
T ss_pred CCeEEECCeeeec-cCCEeecCCEEEE
Confidence 5689999998776 3567889999988
No 196
>TIGR00057 Sua5/YciO/YrdC/YwlC family protein. partial match to sua5, which is involved in regulation of translation initiation. 3' end of sua5 has matches to sua5, BS3690, and weakly to AF0781 and BB0734.
Probab=29.46 E-value=70 Score=32.76 Aligned_cols=56 Identities=18% Similarity=0.270 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHhhcccCcCCEEEEEcchhhhccCChhhHHHHHHHhcc-CCCCEEEEee
Q 004011 686 DKLAINELFEVALNESKSSPLIVFVKDIEKSLTGNNDAYGALKSKLEN-LPSNVVVIGS 743 (779)
Q Consensus 686 eKLlIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs~e~y~~fq~mLeK-LsG~VLIIGS 743 (779)
.+-+++.||+.=. -.+..|++|.+.|.+++..= -++-...++++++ .||++-+|--
T Consensus 40 ~~~av~ri~~iK~-R~~~Kpl~~l~~~~~~l~~~-~~~~~~~~~l~~~~~Pgp~T~Il~ 96 (201)
T TIGR00057 40 DEDAVRRLYRIKG-RPSNKPLTVLVSDLSEIEKY-AYVPDDAKRLMKKFWPGPLTLVLK 96 (201)
T ss_pred CHHHHHHHHHHhC-CCCCCCeEEEECCHHHHHHH-hcCCHHHHHHHHhcCCCCeEEEEE
Confidence 5678999999764 46789999999998874331 1111223345544 7898887753
No 197
>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=29.23 E-value=47 Score=40.97 Aligned_cols=38 Identities=29% Similarity=0.406 Sum_probs=31.8
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLLPG 532 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l~G 532 (779)
..+||.||+| .-...|||+||+.+ +.+++.+|.+.+..
T Consensus 596 ~~~Lf~Gp~G--vGKt~lA~~La~~l~~~~~~~i~~d~s~~~~ 636 (852)
T TIGR03346 596 GSFLFLGPTG--VGKTELAKALAEFLFDDEDAMVRIDMSEYME 636 (852)
T ss_pred eEEEEEcCCC--CCHHHHHHHHHHHhcCCCCcEEEEechhhcc
Confidence 3589999999 67889999999987 57899999887643
No 198
>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=29.22 E-value=48 Score=31.26 Aligned_cols=30 Identities=43% Similarity=0.602 Sum_probs=24.9
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhccCeEEEE
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHFSARLLIV 525 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F~AkLLil 525 (779)
-|.++|++|| -.-++|++||+.++.+++-.
T Consensus 2 iI~i~G~~GS--GKstia~~la~~lg~~~~~~ 31 (171)
T TIGR02173 2 IITISGPPGS--GKTTVAKILAEKLSLKLISA 31 (171)
T ss_pred EEEEECCCCC--CHHHHHHHHHHHcCCceecH
Confidence 4899999995 56799999999999885443
No 199
>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
Probab=29.13 E-value=50 Score=31.65 Aligned_cols=30 Identities=23% Similarity=0.435 Sum_probs=25.1
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
.+.|++.||+|| -.-+|++.||+++|...+
T Consensus 3 ~~ii~i~G~~Gs--GKsTl~~~l~~~~g~~~~ 32 (188)
T TIGR01360 3 CKIIFIVGGPGS--GKGTQCEKIVEKYGFTHL 32 (188)
T ss_pred CcEEEEECCCCC--CHHHHHHHHHHHhCCcEE
Confidence 468999999994 788999999999986543
No 200
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=28.88 E-value=38 Score=37.31 Aligned_cols=26 Identities=38% Similarity=0.538 Sum_probs=23.1
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
+.+||+||+| .-..+||++||+.+..
T Consensus 39 h~~L~~Gp~G--~GKTtla~~la~~l~c 64 (363)
T PRK14961 39 HAWLLSGTRG--VGKTTIARLLAKSLNC 64 (363)
T ss_pred eEEEEecCCC--CCHHHHHHHHHHHhcC
Confidence 4689999999 6899999999999874
No 201
>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=28.77 E-value=41 Score=32.95 Aligned_cols=29 Identities=38% Similarity=0.552 Sum_probs=24.1
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
.++.+||.||.| .....+|+++|+.+-.+
T Consensus 13 ~~~~~L~~G~~G--~gkt~~a~~~~~~l~~~ 41 (188)
T TIGR00678 13 LAHAYLFAGPEG--VGKELLALALAKALLCE 41 (188)
T ss_pred CCeEEEEECCCC--CCHHHHHHHHHHHHcCC
Confidence 457899999998 78889999999887543
No 202
>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=28.70 E-value=64 Score=37.73 Aligned_cols=76 Identities=16% Similarity=0.139 Sum_probs=57.3
Q ss_pred ccccccccc---------cchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 450 EVSFESFPY---------YLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 450 ~VSFd~FPY---------YLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.-.|..||+ =+....|.-++.=-.-.++.+++- .+.=-+=-|--||-|||| .-.-.|+=|+|+|++=
T Consensus 186 ~~~W~~v~f~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~Y--krvGkawKRGYLLYGPPG--TGKSS~IaAmAn~L~y 261 (457)
T KOG0743|consen 186 GGEWRSVGFPHPSTFETLAMDPDLKERIIDDLDDFIKGKDFY--KRVGKAWKRGYLLYGPPG--TGKSSFIAAMANYLNY 261 (457)
T ss_pred CCcceecCCCCCCCccccccChhHHHHHHHHHHHHHhcchHH--HhcCcchhccceeeCCCC--CCHHHHHHHHHhhcCC
Confidence 344666665 257788888888888888888874 444455668899999999 4688899999999998
Q ss_pred eEEEEeccC
Q 004011 521 RLLIVDSLL 529 (779)
Q Consensus 521 kLLilDs~~ 529 (779)
.+-.|.-+.
T Consensus 262 dIydLeLt~ 270 (457)
T KOG0743|consen 262 DIYDLELTE 270 (457)
T ss_pred ceEEeeecc
Confidence 776666543
No 203
>PHA02530 pseT polynucleotide kinase; Provisional
Probab=28.57 E-value=51 Score=34.55 Aligned_cols=33 Identities=30% Similarity=0.228 Sum_probs=25.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhc-cCeEEEEec
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHF-SARLLIVDS 527 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F-~AkLLilDs 527 (779)
.-|+|.||+|| -.-+|||.||++| +...|-.|.
T Consensus 3 ~liil~G~pGS--GKSTla~~L~~~~~~~~~l~~D~ 36 (300)
T PHA02530 3 KIILTVGVPGS--GKSTWAREFAAKNPKAVNVNRDD 36 (300)
T ss_pred EEEEEEcCCCC--CHHHHHHHHHHHCCCCEEEeccH
Confidence 35899999994 6889999999999 665554443
No 204
>PRK10865 protein disaggregation chaperone; Provisional
Probab=28.49 E-value=42 Score=41.54 Aligned_cols=35 Identities=29% Similarity=0.483 Sum_probs=29.4
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLL 530 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l 530 (779)
-+||.||+| .-...|||+||+++ +..++.+|.+.|
T Consensus 600 ~~Lf~Gp~G--~GKT~lA~aLa~~l~~~~~~~i~id~se~ 637 (857)
T PRK10865 600 SFLFLGPTG--VGKTELCKALANFMFDSDDAMVRIDMSEF 637 (857)
T ss_pred eEEEECCCC--CCHHHHHHHHHHHhhcCCCcEEEEEhHHh
Confidence 589999999 57888999999987 456888888766
No 205
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=28.44 E-value=40 Score=39.54 Aligned_cols=29 Identities=28% Similarity=0.342 Sum_probs=25.6
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeE
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARL 522 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkL 522 (779)
.+.+||+||+| .-..++|++||+.+....
T Consensus 43 ~~a~Lf~Gp~G--~GKTT~ArilAk~Lnc~~ 71 (507)
T PRK06645 43 AGGYLLTGIRG--VGKTTSARIIAKAVNCSA 71 (507)
T ss_pred CceEEEECCCC--CCHHHHHHHHHHHhcCcc
Confidence 56799999999 789999999999998754
No 206
>PRK11630 hypothetical protein; Provisional
Probab=28.31 E-value=1.2e+02 Score=31.30 Aligned_cols=53 Identities=21% Similarity=0.307 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHhhcccCcCCEEEEEcchhhhcc---CChhhHHHHHHHhc-cCCCCEEEEee
Q 004011 686 DKLAINELFEVALNESKSSPLIVFVKDIEKSLT---GNNDAYGALKSKLE-NLPSNVVVIGS 743 (779)
Q Consensus 686 eKLlIqsLyEVL~S~S~t~PlILYiKDVEK~L~---gs~e~y~~fq~mLe-KLsG~VLIIGS 743 (779)
..-+++.||++=. -.+..||||++.|.+++.. -+.+.+ +.++ -.||++-+|--
T Consensus 46 n~~Av~~l~~lK~-R~~~Kpl~ll~~~~~~~~~~~~~~~~~~----~l~~~~wPGplT~Il~ 102 (206)
T PRK11630 46 DKNAMERICRIRQ-LPDGHNFTLMCRDLSELSTYSFVDNVAF----RLMKNNTPGNYTFILK 102 (206)
T ss_pred CHHHHHHHHHHcC-CCCCCCeEEEECCHHHHHHHhcCCHHHH----HHHHhcCCCCeEEEEE
Confidence 5668999999664 4678899999999876433 223333 4443 35999988864
No 207
>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=28.21 E-value=45 Score=38.48 Aligned_cols=43 Identities=23% Similarity=0.276 Sum_probs=35.1
Q ss_pred CCCCCCCCceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCC
Q 004011 486 SDLPTMCPRILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLL 530 (779)
Q Consensus 486 ~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l 530 (779)
..+.....-|||.|++|| -.++||++|.++- +.+++.+|...+
T Consensus 213 ~~~a~~~~pvli~Ge~Gt--GK~~lA~~ih~~s~r~~~pfv~i~c~~~ 258 (534)
T TIGR01817 213 RVVARSNSTVLLRGESGT--GKELIAKAIHYLSPRAKRPFVKVNCAAL 258 (534)
T ss_pred HHHhCcCCCEEEECCCCc--cHHHHHHHHHHhCCCCCCCeEEeecCCC
Confidence 344456778999999995 6999999998873 579999999776
No 208
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=28.08 E-value=71 Score=36.88 Aligned_cols=58 Identities=28% Similarity=0.424 Sum_probs=39.1
Q ss_pred HHHHHHHHHhhcccCcCCEEEEEcchhhhccCC--------hhhHHHHHHHhccC-----CCCEEEEeeccccC
Q 004011 688 LAINELFEVALNESKSSPLIVFVKDIEKSLTGN--------NDAYGALKSKLENL-----PSNVVVIGSHTQLD 748 (779)
Q Consensus 688 LlIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs--------~e~y~~fq~mLeKL-----sG~VLIIGSq~~~D 748 (779)
-.+..+|+.+.. ..|.||||-+++.++..+ .+....+...|..| .++|.||+.-+..|
T Consensus 263 ~~vr~lF~~A~~---~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d 333 (438)
T PTZ00361 263 KLVRELFRVAEE---NAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIE 333 (438)
T ss_pred HHHHHHHHHHHh---CCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChH
Confidence 347778887765 789999999999976422 23333344455544 45889998876555
No 209
>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=27.65 E-value=32 Score=34.18 Aligned_cols=47 Identities=23% Similarity=0.367 Sum_probs=34.9
Q ss_pred cccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCCC
Q 004011 483 KYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLLP 531 (779)
Q Consensus 483 Kyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l~ 531 (779)
+..+.+......|||.|++|| -.++|||++-++- +.+++.+|...+.
T Consensus 13 ~~~~~~a~~~~pVlI~GE~Gt--GK~~lA~~IH~~s~r~~~pfi~vnc~~~~ 62 (168)
T PF00158_consen 13 EQAKRAASSDLPVLITGETGT--GKELLARAIHNNSPRKNGPFISVNCAALP 62 (168)
T ss_dssp HHHHHHTTSTS-EEEECSTTS--SHHHHHHHHHHCSTTTTS-EEEEETTTS-
T ss_pred HHHHHHhCCCCCEEEEcCCCC--cHHHHHHHHHHhhhcccCCeEEEehhhhh
Confidence 334455566689999999996 5899999997764 4789999998774
No 210
>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C ....
Probab=27.57 E-value=38 Score=29.94 Aligned_cols=22 Identities=41% Similarity=0.489 Sum_probs=19.9
Q ss_pred eeecCCCCchHHHHHHHHHHHhhc
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHF 518 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F 518 (779)
|+|+|++| --.-+|||.|++++
T Consensus 1 I~i~G~~G--sGKtTia~~L~~~~ 22 (129)
T PF13238_consen 1 IGISGIPG--SGKTTIAKELAERL 22 (129)
T ss_dssp EEEEESTT--SSHHHHHHHHHHHH
T ss_pred CEEECCCC--CCHHHHHHHHHHHH
Confidence 89999999 47889999999998
No 211
>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=27.04 E-value=43 Score=35.69 Aligned_cols=27 Identities=30% Similarity=0.533 Sum_probs=23.3
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
+.+||.||+| ....++|++||+.+...
T Consensus 37 ~~~Ll~G~~G--~GKt~~a~~la~~l~~~ 63 (355)
T TIGR02397 37 HAYLFSGPRG--TGKTSIARIFAKALNCQ 63 (355)
T ss_pred eEEEEECCCC--CCHHHHHHHHHHHhcCC
Confidence 5689999998 78999999999997644
No 212
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=26.96 E-value=1.2e+02 Score=34.42 Aligned_cols=57 Identities=23% Similarity=0.437 Sum_probs=36.7
Q ss_pred HHHHHHHHhhcccCcCCEEEEEcchhhhccCC--------hhhHHHHHHHhccCC-----CCEEEEeeccccC
Q 004011 689 AINELFEVALNESKSSPLIVFVKDIEKSLTGN--------NDAYGALKSKLENLP-----SNVVVIGSHTQLD 748 (779)
Q Consensus 689 lIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs--------~e~y~~fq~mLeKLs-----G~VLIIGSq~~~D 748 (779)
.+..+|+.+.. ..|.||||-|++.++..+ .+.-..+-..|..+. .+|+|||.-+..|
T Consensus 226 ~lr~lf~~A~~---~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d 295 (398)
T PTZ00454 226 MVRDVFRLARE---NAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRAD 295 (398)
T ss_pred HHHHHHHHHHh---cCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCch
Confidence 46777777665 889999999999876432 122223334444432 4788888766544
No 213
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=26.91 E-value=52 Score=34.15 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=23.4
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEEccC
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvfs~~ 226 (779)
..|.|+|||+.+.+- ...|+.||+|.+.-.
T Consensus 116 ~~G~V~VNgk~v~~p-s~~v~~GD~I~v~~~ 145 (203)
T PRK05327 116 SHGHILVNGKKVNIP-SYRVKPGDVIEVREK 145 (203)
T ss_pred HCCcEEECCEEECCC-CcCCCCCCEEEECCc
Confidence 466799999999753 557899999998543
No 214
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=26.90 E-value=42 Score=36.99 Aligned_cols=30 Identities=37% Similarity=0.418 Sum_probs=25.0
Q ss_pred CCCCCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 489 PTMCPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 489 ss~s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.-..+++|++||.| +-..+||++||+.+--
T Consensus 19 ~r~~ha~Lf~G~~G--~GK~~~A~~~A~~llC 48 (328)
T PRK05707 19 GRHPHAYLLHGPAG--IGKRALAERLAAALLC 48 (328)
T ss_pred CCcceeeeeECCCC--CCHHHHHHHHHHHHcC
Confidence 34567899999999 7899999999998653
No 215
>PRK08084 DNA replication initiation factor; Provisional
Probab=26.87 E-value=58 Score=33.73 Aligned_cols=25 Identities=24% Similarity=0.179 Sum_probs=20.8
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhcc
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFS 519 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~ 519 (779)
+-++|.||+| .-.-.|+.|+|++..
T Consensus 46 ~~l~l~Gp~G--~GKThLl~a~~~~~~ 70 (235)
T PRK08084 46 GYIYLWSREG--AGRSHLLHAACAELS 70 (235)
T ss_pred CeEEEECCCC--CCHHHHHHHHHHHHH
Confidence 4689999999 577889999888765
No 216
>PRK13531 regulatory ATPase RavA; Provisional
Probab=26.68 E-value=54 Score=38.67 Aligned_cols=27 Identities=30% Similarity=0.511 Sum_probs=23.4
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
..-|||.||+| .-..+||||||+.++.
T Consensus 39 g~hVLL~GpPG--TGKT~LAraLa~~~~~ 65 (498)
T PRK13531 39 GESVFLLGPPG--IAKSLIARRLKFAFQN 65 (498)
T ss_pred CCCEEEECCCC--hhHHHHHHHHHHHhcc
Confidence 46699999999 7899999999997753
No 217
>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=26.24 E-value=1.1e+02 Score=35.36 Aligned_cols=57 Identities=23% Similarity=0.480 Sum_probs=35.8
Q ss_pred HHHHHHHHhhcccCcCCEEEEEcchhhhccCC--------h---hhHHHHHHHhccCC--CCEEEEeeccccC
Q 004011 689 AINELFEVALNESKSSPLIVFVKDIEKSLTGN--------N---DAYGALKSKLENLP--SNVVVIGSHTQLD 748 (779)
Q Consensus 689 lIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs--------~---e~y~~fq~mLeKLs--G~VLIIGSq~~~D 748 (779)
.+..+|+.+.. ..|-||||.|++.+.... . +..+.|-..++.+. ++|+|||.-+..+
T Consensus 135 ~l~~~f~~a~~---~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~ 204 (495)
T TIGR01241 135 RVRDLFEQAKK---NAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPD 204 (495)
T ss_pred HHHHHHHHHHh---cCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChh
Confidence 45666766654 789999999999976422 1 12222222334333 3699999887765
No 218
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=26.21 E-value=1e+02 Score=37.42 Aligned_cols=44 Identities=30% Similarity=0.431 Sum_probs=35.9
Q ss_pred cCCEEEEEcchhhhcc------CChhhHHHHHHHhccCCCCEEEEeeccccC
Q 004011 703 SSPLIVFVKDIEKSLT------GNNDAYGALKSKLENLPSNVVVIGSHTQLD 748 (779)
Q Consensus 703 t~PlILYiKDVEK~L~------gs~e~y~~fq~mLeKLsG~VLIIGSq~~~D 748 (779)
..|.||||.++..++. ++.+.++.|+..|+ .|.|.+||--|..+
T Consensus 273 ~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~--~g~i~~IgaTt~~e 322 (731)
T TIGR02639 273 EPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALS--SGKLRCIGSTTYEE 322 (731)
T ss_pred cCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHh--CCCeEEEEecCHHH
Confidence 5799999999999764 23567888999887 49999999988744
No 219
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=26.08 E-value=48 Score=40.57 Aligned_cols=34 Identities=29% Similarity=0.549 Sum_probs=29.5
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
+-+||.||+| .-..+||+++|++++..++.++..
T Consensus 53 ~slLL~GPpG--tGKTTLA~aIA~~~~~~f~~lna~ 86 (725)
T PRK13341 53 GSLILYGPPG--VGKTTLARIIANHTRAHFSSLNAV 86 (725)
T ss_pred ceEEEECCCC--CCHHHHHHHHHHHhcCcceeehhh
Confidence 4689999999 689999999999999888777754
No 220
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=25.78 E-value=58 Score=34.23 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=29.4
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEEccCCCeeEEEe
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSYIFQ 234 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIFq 234 (779)
+-|.|.|||++|.-- ...++-||||.+....+.-+.++
T Consensus 117 ~HGHI~VnGk~V~iP-Sy~V~~gdei~V~~k~~s~~~~~ 154 (205)
T COG0522 117 SHGHILVNGKRVNIP-SYLVSPGDEISVREKSKSPIKIK 154 (205)
T ss_pred hcceEEECCEEeccC-cEEecCCCEEEeeecccchhhhh
Confidence 457899999999996 88999999999966554433333
No 221
>CHL00206 ycf2 Ycf2; Provisional
Probab=25.71 E-value=91 Score=42.54 Aligned_cols=58 Identities=26% Similarity=0.350 Sum_probs=37.9
Q ss_pred HHHHHHHHHhhcccCcCCEEEEEcchhhhccCChhh--HHHHHHHhccC-----CCCEEEEeeccccC
Q 004011 688 LAINELFEVALNESKSSPLIVFVKDIEKSLTGNNDA--YGALKSKLENL-----PSNVVVIGSHTQLD 748 (779)
Q Consensus 688 LlIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs~e~--y~~fq~mLeKL-----sG~VLIIGSq~~~D 748 (779)
.-|..+||.+.. .+|-||||.+++.+-....+. .+.|-..|+.. ..+|||||+-+..|
T Consensus 1719 ~rIr~lFelARk---~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD 1783 (2281)
T CHL00206 1719 FYITLQFELAKA---MSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIASTHIPQ 1783 (2281)
T ss_pred HHHHHHHHHHHH---CCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEEeCCCcc
Confidence 347778888877 899999999999954432221 22332233322 24799999977555
No 222
>PF02875 Mur_ligase_C: Mur ligase family, glutamate ligase domain This Prosite entry is a subset of the Pfam family.; InterPro: IPR004101 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) [], MurD (6.3.2.9 from EC) [], MurE (6.3.2.13 from EC) [] and MurF (6.3.2.10 from EC) []. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the C-terminal domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes the C-terminal domain of folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) []. The C-terminal domain is almost always associated with the cytoplasmic peptidoglycan synthetases, N-terminal domain (see IPR000713 from INTERPRO).; GO: 0005524 ATP binding, 0016874 ligase activity, 0009058 biosynthetic process; PDB: 2Y68_A 3UAG_A 4UAG_A 2UAG_A 1E0D_A 2XPC_A 2WJP_A 2VTE_A 2Y67_A 1EEH_A ....
Probab=25.58 E-value=1.3e+02 Score=26.33 Aligned_cols=58 Identities=14% Similarity=0.143 Sum_probs=44.4
Q ss_pred HHHHHHHHHHhhcccCcCCEEEEEcchhhhccCChhhHHHHHHHhccCCCCEEEEeec
Q 004011 687 KLAINELFEVALNESKSSPLIVFVKDIEKSLTGNNDAYGALKSKLENLPSNVVVIGSH 744 (779)
Q Consensus 687 KLlIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs~e~y~~fq~mLeKLsG~VLIIGSq 744 (779)
--.+.++++.|.......++|+-+-+...+-....+.+..+.+++.++..-|++.|-.
T Consensus 24 p~s~~a~l~~l~~~~~~~~~i~V~G~~~d~g~~~~~~~~~~~~~~~~~~d~vi~~~~~ 81 (91)
T PF02875_consen 24 PDSIRALLEALKELYPKGRIIAVFGAMGDLGSKDKDFHEEIGELAAQLADVVILTGDN 81 (91)
T ss_dssp HHHHHHHHHHHHHHCTTSEEEEEEEEBTT-HTSHHHCHHHHHHHHTTCSSEEEEETSB
T ss_pred HHHHHHHHHHHHHhccCCcEEEEEccccccccccHHHHHHHHHHHHhcCCEEEEcCCC
Confidence 4578888888888777899999988765544455677889999999998886666643
No 223
>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.17 E-value=48 Score=41.29 Aligned_cols=43 Identities=37% Similarity=0.534 Sum_probs=38.3
Q ss_pred CCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 487 DLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 487 ~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
.+...++-.||.|++| --..++++|.|.+||..|+=+|++.|.
T Consensus 426 ~~~~~~~~vLLhG~~g--~GK~t~V~~vas~lg~h~~evdc~el~ 468 (953)
T KOG0736|consen 426 ALLTLNPSVLLHGPPG--SGKTTVVRAVASELGLHLLEVDCYELV 468 (953)
T ss_pred hccccceEEEEeCCCC--CChHHHHHHHHHHhCCceEeccHHHHh
Confidence 3455778999999999 578999999999999999999999984
No 224
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=24.99 E-value=30 Score=30.34 Aligned_cols=26 Identities=42% Similarity=0.643 Sum_probs=15.3
Q ss_pred CceEEECCeecCCCceEEeeCCCEEEE
Q 004011 197 KGEVEVNGNVHPKDSQVVLRGGDELVF 223 (779)
Q Consensus 197 NGtV~VNGkkVgKg~kviL~nGDEIvf 223 (779)
.|.|+|||+..-+ +..-|..||.|.|
T Consensus 32 ~g~V~VNGe~e~r-rg~Kl~~GD~V~~ 57 (65)
T PF13275_consen 32 EGEVKVNGEVETR-RGKKLRPGDVVEI 57 (65)
T ss_dssp HHHHEETTB-----SS----SSEEEEE
T ss_pred cCceEECCEEccc-cCCcCCCCCEEEE
Confidence 4679999998876 4677899999998
No 225
>PRK07471 DNA polymerase III subunit delta'; Validated
Probab=24.87 E-value=50 Score=36.95 Aligned_cols=44 Identities=23% Similarity=0.291 Sum_probs=32.5
Q ss_pred chhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhcc
Q 004011 460 LSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFS 519 (779)
Q Consensus 460 LSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~ 519 (779)
=.|..+..|..+.-- .-...++|++||.| +-..+||.++|+++-
T Consensus 23 Gq~~~~~~L~~~~~~--------------~rl~HA~Lf~Gp~G--~GK~~lA~~~A~~Ll 66 (365)
T PRK07471 23 GHAAAEAALLDAYRS--------------GRLHHAWLIGGPQG--IGKATLAYRMARFLL 66 (365)
T ss_pred ChHHHHHHHHHHHHc--------------CCCCceEEEECCCC--CCHHHHHHHHHHHHh
Confidence 367777777655432 12344899999999 799999999999873
No 226
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=24.77 E-value=52 Score=37.26 Aligned_cols=28 Identities=29% Similarity=0.442 Sum_probs=24.3
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
..+.+||.||+| .-..+||++||+.+..
T Consensus 35 l~ha~Lf~Gp~G--~GKt~lA~~lA~~l~c 62 (394)
T PRK07940 35 MTHAWLFTGPPG--SGRSVAARAFAAALQC 62 (394)
T ss_pred CCeEEEEECCCC--CcHHHHHHHHHHHhCC
Confidence 578899999999 7899999999998654
No 227
>PF05726 Pirin_C: Pirin C-terminal cupin domain; InterPro: IPR008778 This entry represents C-terminal domain of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures []. Pirin is composed of two structurally similar domains arranged face to face. The N-terminal domain additionally features four beta-strands, and the C-terminal domain also includes four additional -strands and a short alpha-helix. Although the two domains are similar, the C-terminal domain of Pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues []. Pirin is confirmed to be a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal beta-barrel of Pirin, may be significant in its role in regulating NFI DNA replication and NF-kappaB transcription factor activity []. Pirin structure has been found to closely resemble members of the cupin superfamily. Pirin contains the two characteristic sequences of the cupin superfamily, namely PG-(X)5-HXH-(X)4-E-(X)6-G and G-(X)5-PXG-(X)2-H-(X)3-N separated by a variable stretch of 15-50 amino acids. These motifs are best conserved in the N-terminal where the conserved histidine and glutamic acid residues correspond to the metal-coordinating residues. The C-terminal domain motifs lack the metal binding residues normally associated with the cupin fold []. Pirin was identified to be a metal-binding protein [], and was found that the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms. Pirin acts as a cofactor for the transcription factor NFI, the regulatory mechanism of which is generally believed to require the assistance of a metal ion []. Structural data supports the hypothesis that the bound iron of Pirin may participate in this transcriptional regulation by enhancing and stabilising the formation of the p50,Bcl3,DNA complex []. Metals have been implicated directly or indirectly in the NF-kappaB family of transcription factors that control expression of a number of early response genes associated with inflammatory responses, cell growth, cell cycle progression, and neoplastic transformation []. However, most metal-dependent transcription factors are DNA-binding proteins that bind to specific sequences when the metal binds to the protein. Pirin, on the other hand, appears to function differently and bind to the transcription factor DNA complex [].; PDB: 1J1L_A 3ACL_A 2P17_A.
Probab=24.72 E-value=68 Score=29.39 Aligned_cols=36 Identities=33% Similarity=0.518 Sum_probs=29.8
Q ss_pred EEEEEecCCceEEECCee--cCCCceEEeeCCCEEEEccC
Q 004011 189 ALLEITGGKGEVEVNGNV--HPKDSQVVLRGGDELVFSPS 226 (779)
Q Consensus 189 a~LEd~ssNGtV~VNGkk--VgKg~kviL~nGDEIvfs~~ 226 (779)
++|..+.+. +.|||.. +.++.-++|..||+|.|...
T Consensus 22 ~~iyv~~G~--~~v~~~~~~~~~~~~~~l~~g~~i~~~a~ 59 (104)
T PF05726_consen 22 AFIYVLEGS--VEVGGEEDPLEAGQLVVLEDGDEIELTAG 59 (104)
T ss_dssp EEEEEEESE--EEETTTTEEEETTEEEEE-SECEEEEEES
T ss_pred EEEEEEECc--EEECCCcceECCCcEEEECCCceEEEEEC
Confidence 667777665 6899996 99999999999999999776
No 228
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=24.66 E-value=49 Score=36.56 Aligned_cols=27 Identities=19% Similarity=0.276 Sum_probs=23.6
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhcc
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFS 519 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~ 519 (779)
...++|+.||.| +-...||+++|+++-
T Consensus 23 l~HA~Lf~G~~G--~Gk~~lA~~~A~~Ll 49 (334)
T PRK07993 23 GHHALLIQALPG--MGDDALIYALSRWLM 49 (334)
T ss_pred cceEEeeECCCC--CCHHHHHHHHHHHHc
Confidence 456899999999 889999999999873
No 229
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=24.60 E-value=51 Score=39.69 Aligned_cols=26 Identities=35% Similarity=0.571 Sum_probs=23.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
+.+|++||+| +...++|++||+.+..
T Consensus 39 hA~Lf~GP~G--vGKTTlA~~lAk~L~C 64 (605)
T PRK05896 39 HAYIFSGPRG--IGKTSIAKIFAKAINC 64 (605)
T ss_pred ceEEEECCCC--CCHHHHHHHHHHHhcC
Confidence 6799999999 7999999999999854
No 230
>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]
Probab=24.45 E-value=48 Score=36.46 Aligned_cols=24 Identities=33% Similarity=0.638 Sum_probs=20.4
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhc
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHF 518 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F 518 (779)
|.|+++||+| +-..+-+++|||.+
T Consensus 49 P~liisGpPG--~GKTTsi~~LAr~L 72 (333)
T KOG0991|consen 49 PNLIISGPPG--TGKTTSILCLAREL 72 (333)
T ss_pred CceEeeCCCC--CchhhHHHHHHHHH
Confidence 6799999999 67888899999863
No 231
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=24.42 E-value=67 Score=27.70 Aligned_cols=26 Identities=27% Similarity=0.391 Sum_probs=21.0
Q ss_pred ceEEECCeecCCCceEEeeCCCEEEEcc
Q 004011 198 GEVEVNGNVHPKDSQVVLRGGDELVFSP 225 (779)
Q Consensus 198 GtV~VNGkkVgKg~kviL~nGDEIvfs~ 225 (779)
-.|.|||+.+.. ...|+.||+|.|-.
T Consensus 40 v~v~vNg~iv~~--~~~l~~gD~Veii~ 65 (70)
T PRK08364 40 AIAKVNGKVALE--DDPVKDGDYVEVIP 65 (70)
T ss_pred EEEEECCEECCC--CcCcCCCCEEEEEc
Confidence 457799999964 67799999998843
No 232
>PRK00889 adenylylsulfate kinase; Provisional
Probab=24.37 E-value=77 Score=30.64 Aligned_cols=35 Identities=23% Similarity=0.362 Sum_probs=27.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhcc---CeEEEEeccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFS---ARLLIVDSLL 529 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~---AkLLilDs~~ 529 (779)
.-|.|.|++|+ -..+++++||+.+. -+.+++|+-.
T Consensus 5 ~~i~~~G~~Gs--GKST~a~~la~~l~~~g~~v~~id~D~ 42 (175)
T PRK00889 5 VTVWFTGLSGA--GKTTIARALAEKLREAGYPVEVLDGDA 42 (175)
T ss_pred eEEEEECCCCC--CHHHHHHHHHHHHHHcCCeEEEEcCcc
Confidence 36899999994 67899999999884 3578888643
No 233
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=24.35 E-value=93 Score=26.26 Aligned_cols=32 Identities=31% Similarity=0.561 Sum_probs=24.3
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhc-cCeEEEEec
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHF-SARLLIVDS 527 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F-~AkLLilDs 527 (779)
.|.++|++|+- .-+++++|++.| +-+.-++|.
T Consensus 1 ~i~i~G~~gsG--Kst~~~~l~~~l~~~~~~~i~~ 33 (69)
T cd02019 1 IIAITGGSGSG--KSTVAKKLAEQLGGRSVVVLDE 33 (69)
T ss_pred CEEEECCCCCC--HHHHHHHHHHHhcCCCEEEEeE
Confidence 37899999964 789999999997 345555554
No 234
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=24.32 E-value=91 Score=33.51 Aligned_cols=32 Identities=22% Similarity=0.340 Sum_probs=25.8
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEEccCCC
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGK 228 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~ 228 (779)
.+|.|.|||+.+.+. ...++.||.|.+.-.|+
T Consensus 206 ~~G~V~VNg~~v~~~-s~~v~~gD~IsvrG~Gr 237 (257)
T TIGR03069 206 KAGRLRLNWKTVTQP-SRELKVGDRLQLRGKGR 237 (257)
T ss_pred HCCeEEECCEEcCCC-CCcCCCCCEEEEcCCce
Confidence 578899999998765 45679999999976665
No 235
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=24.31 E-value=67 Score=28.30 Aligned_cols=27 Identities=30% Similarity=0.640 Sum_probs=22.6
Q ss_pred eEEECCeecCCC--ceEEeeCCCEEEEcc
Q 004011 199 EVEVNGNVHPKD--SQVVLRGGDELVFSP 225 (779)
Q Consensus 199 tV~VNGkkVgKg--~kviL~nGDEIvfs~ 225 (779)
.|-|||..|.|. ...+|++||+|-+-+
T Consensus 35 av~vNg~iVpr~~~~~~~l~~gD~ievv~ 63 (68)
T COG2104 35 AVAVNGEIVPRSQWADTILKEGDRIEVVR 63 (68)
T ss_pred EEEECCEEccchhhhhccccCCCEEEEEE
Confidence 478999999987 578999999997643
No 236
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.05 E-value=54 Score=39.60 Aligned_cols=46 Identities=26% Similarity=0.416 Sum_probs=33.7
Q ss_pred chhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 460 LSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 460 LSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
-.++.+..|..+.-- . ...+.+||+||.| .+..++|++||+.+...
T Consensus 20 GQe~v~~~L~~ai~~----~----------ri~ha~Lf~GPpG--~GKTtiArilAk~L~C~ 65 (624)
T PRK14959 20 GQETVKAILSRAAQE----N----------RVAPAYLFSGTRG--VGKTTIARIFAKALNCE 65 (624)
T ss_pred CCHHHHHHHHHHHHc----C----------CCCceEEEECCCC--CCHHHHHHHHHHhcccc
Confidence 456666666655431 1 1246799999999 79999999999999753
No 237
>PRK12338 hypothetical protein; Provisional
Probab=23.87 E-value=62 Score=36.06 Aligned_cols=34 Identities=24% Similarity=0.301 Sum_probs=27.4
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
.-||++|++| .-.-++|++||+.++++. +.++++
T Consensus 5 ~ii~i~G~sG--sGKST~a~~la~~l~~~~--~~~tD~ 38 (319)
T PRK12338 5 YVILIGSASG--IGKSTIASELARTLNIKH--LIETDF 38 (319)
T ss_pred EEEEEECCCC--CCHHHHHHHHHHHCCCeE--EccChH
Confidence 4689999999 578899999999999875 333455
No 238
>PRK05954 precorrin-8X methylmutase; Provisional
Probab=23.70 E-value=95 Score=32.77 Aligned_cols=41 Identities=22% Similarity=0.433 Sum_probs=35.9
Q ss_pred cCCEEEEEcchhhhccCChhhHHHHHHHhccCCCCEEEEee
Q 004011 703 SSPLIVFVKDIEKSLTGNNDAYGALKSKLENLPSNVVVIGS 743 (779)
Q Consensus 703 t~PlILYiKDVEK~L~gs~e~y~~fq~mLeKLsG~VLIIGS 743 (779)
.++++-|+.|.+..-.|.+|....+++..+.|++.|++||.
T Consensus 89 g~~v~C~i~~~~~~~~g~TRs~aam~~a~~~~~~~IvvIGN 129 (203)
T PRK05954 89 QNPIITAIDQVSIPLPGKTRTETGLLKCAQQYPEAIYVIGN 129 (203)
T ss_pred CCcEEEECCCccccccCCcHHHHHHHHHHHHCCCCEEEEeC
Confidence 47888899888777789999999999999999999999993
No 239
>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]
Probab=23.66 E-value=70 Score=34.10 Aligned_cols=31 Identities=32% Similarity=0.500 Sum_probs=27.0
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccCeEE
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSARLL 523 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLL 523 (779)
....|-+.||-| .-.-+||++||++++++.+
T Consensus 3 ~~~~IvI~G~IG--~GKSTLa~~La~~l~~~~~ 33 (216)
T COG1428 3 VAMVIVIEGMIG--AGKSTLAQALAEHLGFKVF 33 (216)
T ss_pred cccEEEEecccc--cCHHHHHHHHHHHhCCcee
Confidence 457899999998 6788999999999998854
No 240
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=23.54 E-value=54 Score=36.23 Aligned_cols=28 Identities=36% Similarity=0.584 Sum_probs=23.3
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
...++|++||.| +-...||++||+.+-.
T Consensus 25 l~HA~Lf~Gp~G--~GK~~lA~~lA~~LlC 52 (319)
T PRK08769 25 LGHGLLICGPEG--LGKRAVALALAEHVLA 52 (319)
T ss_pred cceeEeeECCCC--CCHHHHHHHHHHHHhC
Confidence 345899999999 7889999999988644
No 241
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.49 E-value=58 Score=35.46 Aligned_cols=27 Identities=30% Similarity=0.568 Sum_probs=23.6
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.+.+||+||+| ....++|++||+++..
T Consensus 39 ~~~~L~~G~~G--~GKt~~a~~la~~l~~ 65 (367)
T PRK14970 39 AQALLFCGPRG--VGKTTCARILARKINQ 65 (367)
T ss_pred CeEEEEECCCC--CCHHHHHHHHHHHhcC
Confidence 46899999998 7888999999999865
No 242
>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=23.16 E-value=83 Score=30.26 Aligned_cols=31 Identities=32% Similarity=0.560 Sum_probs=25.8
Q ss_pred eeecCCCCchHHHHHHHHHHHhhc---cCeEEEEec
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHF---SARLLIVDS 527 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs 527 (779)
|+++|++|| -.-+||++|+.++ +.+.+++|.
T Consensus 2 i~i~G~~Gs--GKSTla~~L~~~l~~~g~~~~~i~~ 35 (149)
T cd02027 2 IWLTGLSGS--GKSTIARALEEKLFQRGRPVYVLDG 35 (149)
T ss_pred EEEEcCCCC--CHHHHHHHHHHHHHHcCCCEEEEcC
Confidence 789999995 5689999999998 667777764
No 243
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=22.96 E-value=1.1e+02 Score=25.69 Aligned_cols=43 Identities=23% Similarity=0.348 Sum_probs=24.8
Q ss_pred CceEEEEEecCCceEEECCeecCCCceEEeeCCCEEEEccCCCeeEEEeecCccc
Q 004011 186 PSGALLEITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSYIFQQLSDDT 240 (779)
Q Consensus 186 ~~va~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIFq~l~~e~ 240 (779)
...+||+ .+.++.|+++.+-+. -.++-||||- +|||.+-...-
T Consensus 14 ~~g~fL~-~~~~~~vlLp~~e~~----~~~~~Gd~v~-------VFvY~D~~~rl 56 (61)
T PF13509_consen 14 EFGYFLD-DGEGKEVLLPKSEVP----EPLKVGDEVE-------VFVYLDKEGRL 56 (61)
T ss_dssp SSEEEEE-ETT-EEEEEEGGG----------TTSEEE-------EEEEE-TTS-E
T ss_pred CCEEEEE-CCCCCEEEechHHcC----CCCCCCCEEE-------EEEEECCCCCE
Confidence 3448887 555567898877664 3499999984 48888776543
No 244
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=22.86 E-value=63 Score=32.65 Aligned_cols=35 Identities=40% Similarity=0.455 Sum_probs=26.6
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
.||++-||+| --.-++||.||+.|+. .=+|.-+++
T Consensus 1 ~riiilG~pG--aGK~T~A~~La~~~~i--~hlstgd~~ 35 (178)
T COG0563 1 MRILILGPPG--AGKSTLAKKLAKKLGL--PHLDTGDIL 35 (178)
T ss_pred CeEEEECCCC--CCHHHHHHHHHHHhCC--cEEcHhHHh
Confidence 3799999999 4678999999999654 445654554
No 245
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.78 E-value=53 Score=38.38 Aligned_cols=26 Identities=31% Similarity=0.464 Sum_probs=22.7
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
..+||+||+| ....++|++||+++..
T Consensus 37 ha~Lf~GppG--tGKTTlA~~lA~~l~c 62 (504)
T PRK14963 37 HAYLFSGPRG--VGKTTTARLIAMAVNC 62 (504)
T ss_pred eEEEEECCCC--CCHHHHHHHHHHHHhc
Confidence 4589999999 6899999999999753
No 246
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=22.75 E-value=56 Score=38.56 Aligned_cols=27 Identities=33% Similarity=0.449 Sum_probs=23.5
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.+.+||+||.| ....++||+||+.+..
T Consensus 38 ~hayLf~Gp~G--tGKTt~Ak~lAkal~c 64 (559)
T PRK05563 38 SHAYLFSGPRG--TGKTSAAKIFAKAVNC 64 (559)
T ss_pred CeEEEEECCCC--CCHHHHHHHHHHHhcC
Confidence 46799999999 7899999999999864
No 247
>PF01337 Barstar: Barstar (barnase inhibitor); InterPro: IPR000468 Barstar is a small single chain protein. Barnase is the extracellular ribonuclease IPR001887 from INTERPRO of Bacillus amyloliquefaciens, and barstar its specific intracellular inhibitor [, ]. Expression of barstar is necessary to counter the lethal effect of expressed active barnase. The structure of the barnase-barstar complex is known [].; PDB: 2CX6_A 1B2U_F 1A19_A 1X1U_F 1B27_E 1X1W_F 1BGS_E 1X1Y_D 1B3S_D 1B2S_D ....
Probab=22.69 E-value=1.3e+02 Score=26.69 Aligned_cols=44 Identities=14% Similarity=0.311 Sum_probs=35.3
Q ss_pred HHHHHHHhhcc--cCcCCEEEEEcchhhhccCChhhHHHHHHHhcc
Q 004011 690 INELFEVALNE--SKSSPLIVFVKDIEKSLTGNNDAYGALKSKLEN 733 (779)
Q Consensus 690 IqsLyEVL~S~--S~t~PlILYiKDVEK~L~gs~e~y~~fq~mLeK 733 (779)
+++|+.+|... -...|++|.+++.+++....++.|..+.+.|+.
T Consensus 32 lDAl~D~L~d~~~~~~~~~~i~~~~~~~~~~~~~~~~~~l~~vl~~ 77 (90)
T PF01337_consen 32 LDALWDCLTDLSWIPEEPIVIIWENADKLKKRLPEDFEILLEVLED 77 (90)
T ss_dssp HHHHHHHHHCT---S-SSEEEEEETHHHHHHTTTCHCHHHHHHHHH
T ss_pred HHHHHHHhcCcccCCCCCEEEEEcCcHHHHHHhHHHHHHHHHHHHH
Confidence 57888888875 467899999999999988888888888777753
No 248
>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
Probab=22.61 E-value=99 Score=29.05 Aligned_cols=32 Identities=28% Similarity=0.536 Sum_probs=23.0
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEec
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHF---SARLLIVDS 527 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs 527 (779)
+|+|+|..| .-.-+++..||++| +-+.+++|.
T Consensus 1 ~i~~~GkgG--~GKTt~a~~la~~l~~~g~~V~~id~ 35 (116)
T cd02034 1 KIAITGKGG--VGKTTIAALLARYLAEKGKPVLAIDA 35 (116)
T ss_pred CEEEECCCC--CCHHHHHHHHHHHHHHCCCcEEEEEC
Confidence 389999988 34555565555555 778999995
No 249
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.59 E-value=61 Score=38.02 Aligned_cols=27 Identities=26% Similarity=0.394 Sum_probs=23.2
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.+.+||+||.| .-..++|++||+.+..
T Consensus 35 ~ha~Lf~Gp~G--~GKTT~ArilAk~LnC 61 (491)
T PRK14964 35 PQSILLVGASG--VGKTTCARIISLCLNC 61 (491)
T ss_pred CceEEEECCCC--ccHHHHHHHHHHHHcC
Confidence 56899999999 6889999999997654
No 250
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=22.46 E-value=2.6e+02 Score=28.18 Aligned_cols=42 Identities=19% Similarity=0.262 Sum_probs=31.2
Q ss_pred CCCCCceeecCCCC---chHHHHHHHHHHHhhccCeEEEEeccCCC
Q 004011 489 PTMCPRILLSGPAG---SEIYQETLAKALAKHFSARLLIVDSLLLP 531 (779)
Q Consensus 489 ss~s~rILLSGPaG---sEiYQE~LaKALA~~F~AkLLilDs~~l~ 531 (779)
....+.|.+.|+-| .=..--.||.+||++.|-|.|++|. ++.
T Consensus 32 ~~~~~vi~v~s~kgG~GkSt~a~nLA~~la~~~g~~VLlvD~-D~~ 76 (207)
T TIGR03018 32 KKNNNLIMVTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDA-DLR 76 (207)
T ss_pred CCCCeEEEEECCCCCCCHHHHHHHHHHHHHHhcCCeEEEEEC-CCC
Confidence 34557899998776 2245667888888888999999996 443
No 251
>TIGR00150 HI0065_YjeE ATPase, YjeE family. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.
Probab=22.45 E-value=47 Score=32.46 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=25.4
Q ss_pred CCCCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 490 TMCPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 490 s~s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
....-|+|+|+.| --.-+|+|+|++.+|..
T Consensus 20 ~~~~~i~l~G~lG--aGKTtl~~~l~~~lg~~ 49 (133)
T TIGR00150 20 DFGTVVLLKGDLG--AGKTTLVQGLLQGLGIQ 49 (133)
T ss_pred CCCCEEEEEcCCC--CCHHHHHHHHHHHcCCC
Confidence 3456799999999 57899999999999964
No 252
>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=22.39 E-value=82 Score=33.19 Aligned_cols=34 Identities=26% Similarity=0.323 Sum_probs=26.9
Q ss_pred eeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 495 ILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 495 ILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
-.+.||+|| -..-.+|+||+.||-.++++..+.-
T Consensus 35 ~~~~Gpagt--GKtetik~La~~lG~~~~vfnc~~~ 68 (231)
T PF12774_consen 35 GALSGPAGT--GKTETIKDLARALGRFVVVFNCSEQ 68 (231)
T ss_dssp EEEESSTTS--SHHHHHHHHHHCTT--EEEEETTSS
T ss_pred CCCcCCCCC--CchhHHHHHHHHhCCeEEEeccccc
Confidence 357999984 5666899999999999999998766
No 253
>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=22.32 E-value=60 Score=31.83 Aligned_cols=26 Identities=35% Similarity=0.551 Sum_probs=0.0
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhc
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHF 518 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F 518 (779)
....+||.||.| .....+|+++|+.+
T Consensus 18 l~ha~L~~G~~g--~gk~~~a~~~a~~l 43 (162)
T PF13177_consen 18 LPHALLFHGPSG--SGKKTLALAFARAL 43 (162)
T ss_dssp --SEEEEECSTT--SSHHHHHHHHHHHH
T ss_pred cceeEEEECCCC--CCHHHHHHHHHHHH
No 254
>PRK07399 DNA polymerase III subunit delta'; Validated
Probab=22.25 E-value=64 Score=35.35 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=22.5
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhcc
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFS 519 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~ 519 (779)
.+.+|++||.| .....+|+++|+++-
T Consensus 26 ~ha~Lf~G~~G--~Gk~~~A~~~a~~ll 51 (314)
T PRK07399 26 APAYLFAGPEG--VGRKLAALCFIEGLL 51 (314)
T ss_pred CceEEEECCCC--CCHHHHHHHHHHHHc
Confidence 46899999998 788899999999863
No 255
>PRK10078 ribose 1,5-bisphosphokinase; Provisional
Probab=22.24 E-value=87 Score=30.89 Aligned_cols=34 Identities=32% Similarity=0.481 Sum_probs=28.2
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEecc
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSL 528 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~ 528 (779)
.-|.|.||.|+ -.-+|+|+||..++..+++.|..
T Consensus 3 ~~i~l~G~sGs--GKsTl~~~l~~~~~~~~~~~~~~ 36 (186)
T PRK10078 3 KLIWLMGPSGS--GKDSLLAALRQREQTQLLVAHRY 36 (186)
T ss_pred cEEEEECCCCC--CHHHHHHHHhccCCCeEEEcCEE
Confidence 46889999995 58999999999998887766653
No 256
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=21.95 E-value=1e+02 Score=32.58 Aligned_cols=42 Identities=17% Similarity=0.224 Sum_probs=24.8
Q ss_pred cceeecCC-CcccceeEEEEEecCCCceEEEEEecCCceEEECCeecCC
Q 004011 162 CDLYLKDP-SISKNLCRLRRIENGGPSGALLEITGGKGEVEVNGNVHPK 209 (779)
Q Consensus 162 CDl~L~d~-~iS~~hCkI~r~e~gg~~va~LEd~ssNGtV~VNGkkVgK 209 (779)
|++-|++. .|....-.|.+. ++. ...+..+|.+||||++|.=
T Consensus 1 C~V~~~~dv~i~~~~l~v~~~--~~~----~~~I~~~g~L~i~G~~v~L 43 (229)
T PF11101_consen 1 CNVDLNYDVRINPQSLEVVQA--SGE----KLRIDPDGNLFINGKKVSL 43 (229)
T ss_pred CCccCCCCeEEeCCEEEEEeC--CCc----eEEEcCCCcEEECCEEccC
Confidence 55555543 455555556653 222 3344577789999988754
No 257
>PRK05953 precorrin-8X methylmutase; Validated
Probab=21.94 E-value=1e+02 Score=32.76 Aligned_cols=42 Identities=14% Similarity=0.298 Sum_probs=35.2
Q ss_pred cCCEEEEEcchhhhccCChhhHHHHHHHhccCCCCEEEEeec
Q 004011 703 SSPLIVFVKDIEKSLTGNNDAYGALKSKLENLPSNVVVIGSH 744 (779)
Q Consensus 703 t~PlILYiKDVEK~L~gs~e~y~~fq~mLeKLsG~VLIIGSq 744 (779)
.++++.|+.|.+-.-.+.+|....+++..+.|.|.||+||.-
T Consensus 87 g~~v~C~i~~~~v~~~g~TRs~aam~~a~~~~~g~IvvIGNA 128 (208)
T PRK05953 87 ANPVYCSTETITRPQKEKTRTAWGIETLARRYPEAIFVIGQS 128 (208)
T ss_pred CCeEEEECCCCCccccccCHHHHHHHHHHHHCCCCEEEEeCc
Confidence 478888888876555688999999999999999999999964
No 258
>PRK14948 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.73 E-value=63 Score=38.77 Aligned_cols=27 Identities=33% Similarity=0.591 Sum_probs=24.0
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.+.+||.||+| ....++|++||+.+..
T Consensus 38 ~~a~Lf~Gp~G--~GKttlA~~lAk~L~c 64 (620)
T PRK14948 38 APAYLFTGPRG--TGKTSSARILAKSLNC 64 (620)
T ss_pred CceEEEECCCC--CChHHHHHHHHHHhcC
Confidence 46799999999 6899999999999875
No 259
>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A.
Probab=21.71 E-value=87 Score=29.61 Aligned_cols=48 Identities=17% Similarity=0.310 Sum_probs=22.7
Q ss_pred HHHHHHhhcccCc-CCEEEEEcchhhhccCChhhHHHHHHHhccCCC-CEEEE
Q 004011 691 NELFEVALNESKS-SPLIVFVKDIEKSLTGNNDAYGALKSKLENLPS-NVVVI 741 (779)
Q Consensus 691 qsLyEVL~S~S~t-~PlILYiKDVEK~L~gs~e~y~~fq~mLeKLsG-~VLII 741 (779)
+.|.++|...+.. .|++|.|-|++..-..+ ...++..++.+.. |++||
T Consensus 136 ~~l~~~l~~~~~~~~~~vlviDd~d~~~~~~---~~~l~~l~~~~~~~~~~vv 185 (185)
T PF13191_consen 136 ELLREILRELAARRKPLVLVIDDLDWADPAS---LDLLRALARRLQNDPLLVV 185 (185)
T ss_dssp HHHHHHHTTS-SE---EEEEEETTTHHHTTH---HHHHHH-------------
T ss_pred HHHHHHHHHHHhCCCeEEEEEeCCCCCCcHH---HHHHHhcccccccccccCC
Confidence 6677776555544 68999999999544333 5557777777776 88876
No 260
>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....
Probab=21.66 E-value=90 Score=31.36 Aligned_cols=41 Identities=32% Similarity=0.476 Sum_probs=32.6
Q ss_pred ceeecCCCCchHHHHHHHHHHHhhc---cCeEEEEeccCCCCCCCC
Q 004011 494 RILLSGPAGSEIYQETLAKALAKHF---SARLLIVDSLLLPGGSSK 536 (779)
Q Consensus 494 rILLSGPaGsEiYQE~LaKALA~~F---~AkLLilDs~~l~G~~sk 536 (779)
.|+|+|.+||- ..+||++|.+.+ +.+..+||.-.+--+.+.
T Consensus 4 vIwltGlsGsG--KtTlA~~L~~~L~~~g~~~~~LDgD~lR~~l~~ 47 (156)
T PF01583_consen 4 VIWLTGLSGSG--KTTLARALERRLFARGIKVYLLDGDNLRHGLNA 47 (156)
T ss_dssp EEEEESSTTSS--HHHHHHHHHHHHHHTTS-EEEEEHHHHCTTTTT
T ss_pred EEEEECCCCCC--HHHHHHHHHHHHHHcCCcEEEecCcchhhccCC
Confidence 58999999964 789999999988 567999999877654443
No 261
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=21.65 E-value=1.8e+02 Score=33.19 Aligned_cols=57 Identities=33% Similarity=0.580 Sum_probs=40.6
Q ss_pred HHHHHHHHhhcccCcCCEEEEEcchhhhccCCh--------hhHHHHHHHhccCC--CCEEEEeeccccC
Q 004011 689 AINELFEVALNESKSSPLIVFVKDIEKSLTGNN--------DAYGALKSKLENLP--SNVVVIGSHTQLD 748 (779)
Q Consensus 689 lIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs~--------e~y~~fq~mLeKLs--G~VLIIGSq~~~D 748 (779)
.|..+|+-.- +..|-||||-.+++++.... +..+.|-..++.+. .+|+|||.-+..|
T Consensus 323 ~ir~~F~~A~---~~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~ 389 (494)
T COG0464 323 NIRELFEKAR---KLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPD 389 (494)
T ss_pred HHHHHHHHHH---cCCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCcc
Confidence 4556666555 48999999999999998443 55555555554332 3799999988766
No 262
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=21.59 E-value=1.6e+02 Score=27.07 Aligned_cols=42 Identities=21% Similarity=0.355 Sum_probs=25.5
Q ss_pred EecCCceEEECCeecCCCceEEeeCCCEEEEccCCCeeEEEeecCcc
Q 004011 193 ITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSYIFQQLSDD 239 (779)
Q Consensus 193 d~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIFq~l~~e 239 (779)
.++..| |++||..|...-. =.|+.|.|.+ |...|+|+-...+
T Consensus 20 ~l~~~G-V~~ngrlV~T~F~---fDG~~l~~~~-G~~~~~y~~~~~~ 61 (79)
T PF11012_consen 20 TLNESG-VFRNGRLVATSFE---FDGKTLEYRT-GSGTYRYQISGEN 61 (79)
T ss_pred EECCCc-EEECCCEEeeEEE---ECCCEEEEEE-CCeEEEEEEcCCC
Confidence 356788 7999999975311 1345555533 3346778766554
No 263
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=21.51 E-value=1.3e+02 Score=25.65 Aligned_cols=35 Identities=14% Similarity=0.197 Sum_probs=24.9
Q ss_pred ECCeecCCCceEEeeCCCEEEEccCCCeeEEEeec
Q 004011 202 VNGNVHPKDSQVVLRGGDELVFSPSGKHSYIFQQL 236 (779)
Q Consensus 202 VNGkkVgKg~kviL~nGDEIvfs~~~~~aYIFq~l 236 (779)
=||+.+.-|+.+...+|..|.+.-.+..+|+=...
T Consensus 6 ~~G~~lPfGA~v~~~~g~~~g~Vg~~G~vyl~~~~ 40 (68)
T PF13953_consen 6 ADGKPLPFGASVSDEDGNNIGIVGQDGQVYLSGLP 40 (68)
T ss_dssp TTSEE--TT-EEEETTSSEEEEB-GCGEEEEEEE-
T ss_pred CCCCcCCCCcEEEcCCCCEEEEEcCCCEEEEECCC
Confidence 47888999999998889999888888888876644
No 264
>PRK07133 DNA polymerase III subunits gamma and tau; Validated
Probab=21.40 E-value=63 Score=39.71 Aligned_cols=28 Identities=29% Similarity=0.460 Sum_probs=24.0
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
.+.+||+||+| ....++||+||+.+...
T Consensus 40 ~HAYLF~GP~G--tGKTt~AriLAk~LnC~ 67 (725)
T PRK07133 40 SHAYLFSGPRG--TGKTSVAKIFANALNCS 67 (725)
T ss_pred CeEEEEECCCC--CcHHHHHHHHHHHhccc
Confidence 46799999999 68999999999987653
No 265
>cd05141 Barstar_evA4336-like Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=21.36 E-value=1.6e+02 Score=26.14 Aligned_cols=44 Identities=11% Similarity=0.216 Sum_probs=37.1
Q ss_pred HHHHHHHhhccc--CcCCEEEEEcchhhhccCChhhHHHHHHHhcc
Q 004011 690 INELFEVALNES--KSSPLIVFVKDIEKSLTGNNDAYGALKSKLEN 733 (779)
Q Consensus 690 IqsLyEVL~S~S--~t~PlILYiKDVEK~L~gs~e~y~~fq~mLeK 733 (779)
+++|+..|...+ ...+++|.|.+...+....++.|..+.+.|+.
T Consensus 32 lDAl~DcL~d~~~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~vl~d 77 (81)
T cd05141 32 WDALADCLTDLSWWPAEGYVLVLRDGDALRAADPEDFATLLEILRD 77 (81)
T ss_pred HHHHHHHHcCcccCCCCCeEEEEeCcHHhhhcCHHHHHHHHHHHHH
Confidence 578999999886 67789999999999877888888888877764
No 266
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=21.35 E-value=62 Score=37.17 Aligned_cols=28 Identities=32% Similarity=0.425 Sum_probs=24.1
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
.+.+||.||+| ....++|++||+++...
T Consensus 39 ~ha~Lf~Gp~G--~GKtt~A~~lAk~l~c~ 66 (451)
T PRK06305 39 AHAYLFSGIRG--TGKTTLARIFAKALNCQ 66 (451)
T ss_pred ceEEEEEcCCC--CCHHHHHHHHHHHhcCC
Confidence 36699999998 79999999999998643
No 267
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=21.33 E-value=1.5e+02 Score=31.52 Aligned_cols=76 Identities=20% Similarity=0.308 Sum_probs=45.1
Q ss_pred HHhcccCCCccccccccccccchhh-HHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhh
Q 004011 439 LQEGILGPENIEVSFESFPYYLSDI-TKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKH 517 (779)
Q Consensus 439 ~~~~Vvdg~ei~VSFd~FPYYLSE~-TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~ 517 (779)
++....+.. -+|++|=|..... .|.+|..++- +.+ ++. ...-|+|.||+| .-.--||=||||+
T Consensus 65 ~~~a~~p~~---k~~~~~d~~~~~~~~~~~l~~~~~-------~~~---~~~-~~~nl~l~G~~G--~GKThLa~Ai~~~ 128 (254)
T COG1484 65 LRSASFPAK---KTFEEFDFEFQPGIDKKALEDLAS-------LVE---FFE-RGENLVLLGPPG--VGKTHLAIAIGNE 128 (254)
T ss_pred HHHhcCCcc---CCcccccccCCcchhHHHHHHHHH-------HHH---Hhc-cCCcEEEECCCC--CcHHHHHHHHHHH
Confidence 333444444 8899999987553 3433333321 111 122 566799999999 4555666666665
Q ss_pred c---cCeEEEEeccCC
Q 004011 518 F---SARLLIVDSLLL 530 (779)
Q Consensus 518 F---~AkLLilDs~~l 530 (779)
. |.+.+.+-..+|
T Consensus 129 l~~~g~sv~f~~~~el 144 (254)
T COG1484 129 LLKAGISVLFITAPDL 144 (254)
T ss_pred HHHcCCeEEEEEHHHH
Confidence 4 666677766555
No 268
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=21.26 E-value=90 Score=26.84 Aligned_cols=25 Identities=28% Similarity=0.427 Sum_probs=22.1
Q ss_pred eEEECCeecCCC--ceEEeeCCCEEEE
Q 004011 199 EVEVNGNVHPKD--SQVVLRGGDELVF 223 (779)
Q Consensus 199 tV~VNGkkVgKg--~kviL~nGDEIvf 223 (779)
.|-|||+.|.|. ...+|+.||+|-+
T Consensus 34 av~vN~~iv~r~~w~~~~L~~gD~iEI 60 (67)
T PRK07696 34 VVERNKDILQKDDHTDTSVFDGDQIEI 60 (67)
T ss_pred EEEECCEEeCHHHcCceecCCCCEEEE
Confidence 478999999998 6689999999976
No 269
>PLN02200 adenylate kinase family protein
Probab=21.23 E-value=81 Score=32.99 Aligned_cols=34 Identities=18% Similarity=0.165 Sum_probs=26.9
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeEEEEeccCC
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARLLIVDSLLL 530 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs~~l 530 (779)
..|++.||+|| -.-++++.||+++|... +++.++
T Consensus 44 ~ii~I~G~PGS--GKsT~a~~La~~~g~~h--is~gdl 77 (234)
T PLN02200 44 FITFVLGGPGS--GKGTQCEKIVETFGFKH--LSAGDL 77 (234)
T ss_pred EEEEEECCCCC--CHHHHHHHHHHHhCCeE--EEccHH
Confidence 46899999994 68889999999999764 454444
No 270
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=21.18 E-value=1.1e+02 Score=35.28 Aligned_cols=68 Identities=19% Similarity=0.262 Sum_probs=40.4
Q ss_pred ccccccccccchhhHHHHHHhhhhccccCcccccccCCCCCCCCceeecCCCCchHHHHHHHHHHHhhc-----cCeEEE
Q 004011 450 EVSFESFPYYLSDITKNVLIASTYVHLKCNNFAKYASDLPTMCPRILLSGPAGSEIYQETLAKALAKHF-----SARLLI 524 (779)
Q Consensus 450 ~VSFd~FPYYLSE~TK~vL~saayvHLk~~~~sKyt~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F-----~AkLLi 524 (779)
.-||||| +..+.-+.++..|-.+ .+ +-...-..++|.||+| .-.-.|+.|+|+++ +.+.+.
T Consensus 111 ~~tFdnF--v~g~~n~~A~~aa~~~-a~---------~~~~~~npl~i~G~~G--~GKTHLl~Ai~~~l~~~~~~~~v~y 176 (450)
T PRK14087 111 ENTFENF--VIGSSNEQAFIAVQTV-SK---------NPGISYNPLFIYGESG--MGKTHLLKAAKNYIESNFSDLKVSY 176 (450)
T ss_pred ccchhcc--cCCCcHHHHHHHHHHH-Hh---------CcCcccCceEEECCCC--CcHHHHHHHHHHHHHHhCCCCeEEE
Confidence 3689996 3455444444333222 11 1111235699999999 56778888888854 466666
Q ss_pred EeccCCC
Q 004011 525 VDSLLLP 531 (779)
Q Consensus 525 lDs~~l~ 531 (779)
+.+..|.
T Consensus 177 v~~~~f~ 183 (450)
T PRK14087 177 MSGDEFA 183 (450)
T ss_pred EEHHHHH
Confidence 6665553
No 271
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=21.16 E-value=2.4e+02 Score=22.80 Aligned_cols=37 Identities=27% Similarity=0.580 Sum_probs=29.3
Q ss_pred EEEEEecCCceEEECCeecCCCceEEeeCCCEEEEccCCCeeE
Q 004011 189 ALLEITGGKGEVEVNGNVHPKDSQVVLRGGDELVFSPSGKHSY 231 (779)
Q Consensus 189 a~LEd~ssNGtV~VNGkkVgKg~kviL~nGDEIvfs~~~~~aY 231 (779)
.++-++++.+++.++|+ .+.|+.||-|.+-....|.|
T Consensus 21 e~~~vl~G~~~~~~~~~------~~~l~~Gd~~~i~~~~~H~~ 57 (71)
T PF07883_consen 21 EFFYVLSGEGTLTVDGE------RVELKPGDAIYIPPGVPHQV 57 (71)
T ss_dssp EEEEEEESEEEEEETTE------EEEEETTEEEEEETTSEEEE
T ss_pred EEEEEEECCEEEEEccE------EeEccCCEEEEECCCCeEEE
Confidence 67888888888888765 89999999988866555555
No 272
>cd00489 Barstar_like Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it, thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=21.14 E-value=1.4e+02 Score=26.96 Aligned_cols=44 Identities=9% Similarity=0.215 Sum_probs=36.4
Q ss_pred HHHHHHHhhcccCcCCEEEEEcchhhhccCChhhHHHHHHHhccC
Q 004011 690 INELFEVALNESKSSPLIVFVKDIEKSLTGNNDAYGALKSKLENL 734 (779)
Q Consensus 690 IqsLyEVL~S~S~t~PlILYiKDVEK~L~gs~e~y~~fq~mLeKL 734 (779)
+++|+.+|..... .|++|.+++++.+-...++.+..+...|+..
T Consensus 32 lDAl~D~L~~~~~-~p~~i~~~~~~~~~~~~~~~~~~l~~il~d~ 75 (85)
T cd00489 32 LDALWDCLTGLVE-EPLVLRWRNLEHLKRLTPEDAESVLQCFRDV 75 (85)
T ss_pred HHHHHHHHcCCCC-CCeEEEEeccHHHHhhChHHHHHHHHHHHHH
Confidence 6799999998764 8999999999998777788888887777643
No 273
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.05 E-value=67 Score=37.60 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=24.1
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
...+||+||+| .-..++|++||+.+...
T Consensus 38 ~ha~Lf~Gp~G--~GKTt~A~~lAk~l~c~ 65 (509)
T PRK14958 38 HHAYLFTGTRG--VGKTTISRILAKCLNCE 65 (509)
T ss_pred CeeEEEECCCC--CCHHHHHHHHHHHhcCC
Confidence 34799999999 68899999999998753
No 274
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=20.99 E-value=82 Score=36.43 Aligned_cols=45 Identities=20% Similarity=0.313 Sum_probs=36.6
Q ss_pred cCCCCCCCCceeecCCCCchHHHHHHHHHHHhh---ccCeEEEEeccCCC
Q 004011 485 ASDLPTMCPRILLSGPAGSEIYQETLAKALAKH---FSARLLIVDSLLLP 531 (779)
Q Consensus 485 t~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~---F~AkLLilDs~~l~ 531 (779)
.+.++.....|||.|++| .-.+++|+||.++ -+.+++.+|...+.
T Consensus 203 i~~~a~~~~pVlI~Ge~G--tGK~~~A~~ih~~s~r~~~p~v~v~c~~~~ 250 (509)
T PRK05022 203 IEVVAASDLNVLILGETG--VGKELVARAIHAASPRADKPLVYLNCAALP 250 (509)
T ss_pred HHHHhCCCCcEEEECCCC--ccHHHHHHHHHHhCCcCCCCeEEEEcccCC
Confidence 444566778999999999 4699999999887 45799999987764
No 275
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=20.92 E-value=79 Score=33.69 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=20.8
Q ss_pred CCceEEECCeecCCCceEEeeCCCEEEE
Q 004011 196 GKGEVEVNGNVHPKDSQVVLRGGDELVF 223 (779)
Q Consensus 196 sNGtV~VNGkkVgKg~kviL~nGDEIvf 223 (779)
.+|.|+|||+.+.+ ....|+.||+|.+
T Consensus 29 ~~G~V~VNg~~~~~-~~~~v~~gd~I~i 55 (299)
T TIGR00005 29 ENGQVKVNGKVTAN-PKLKVKDGDRITV 55 (299)
T ss_pred HCCcEEECCEeccC-cccCCCCCCEEEE
Confidence 46779999965543 4678899999977
No 276
>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=20.90 E-value=77 Score=33.36 Aligned_cols=39 Identities=21% Similarity=0.234 Sum_probs=28.8
Q ss_pred cCCCCCCCCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 485 ASDLPTMCPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 485 t~~Lss~s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
..++......||+.|++| ...-+|||.||+ .+-||-+|.
T Consensus 5 ~~~~~~~~~~~liyG~~G--~GKtt~a~~~~~--~~~~~~~d~ 43 (220)
T TIGR01618 5 AGNIKRIPNMYLIYGKPG--TGKTSTIKYLPG--KTLVLSFDM 43 (220)
T ss_pred ccccCCCCcEEEEECCCC--CCHHHHHHhcCC--CCEEEeccc
Confidence 456777778899999999 688999999972 244444554
No 277
>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=20.79 E-value=1e+02 Score=36.14 Aligned_cols=35 Identities=20% Similarity=0.468 Sum_probs=28.7
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhh--------c--cCeEEEEecc
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKH--------F--SARLLIVDSL 528 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~--------F--~AkLLilDs~ 528 (779)
.+-|||.||+| .-.+++||+++++ | +++++.+|.+
T Consensus 86 ~~~vLi~Ge~G--tGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~ 130 (531)
T TIGR02902 86 PQHVIIYGPPG--VGKTAAARLVLEEAKKNPASPFKEGAAFVEIDAT 130 (531)
T ss_pred CceEEEECCCC--CCHHHHHHHHHHHhhhccCCCcCCCCCEEEEccc
Confidence 46799999999 5799999999864 3 4788999975
No 278
>PRK14956 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.76 E-value=68 Score=37.69 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=23.5
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCe
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSAR 521 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~Ak 521 (779)
..+||+||+| ....++|++||+.+.-.
T Consensus 41 ha~Lf~GP~G--tGKTTlAriLAk~Lnce 67 (484)
T PRK14956 41 HAYIFFGPRG--VGKTTIARILAKRLNCE 67 (484)
T ss_pred eEEEEECCCC--CCHHHHHHHHHHhcCcc
Confidence 4689999999 68999999999998753
No 279
>PRK06090 DNA polymerase III subunit delta'; Validated
Probab=20.63 E-value=68 Score=35.52 Aligned_cols=28 Identities=18% Similarity=0.316 Sum_probs=23.5
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
...++|++||.| +-...||+++|+++--
T Consensus 24 l~hA~L~~G~~G--~Gk~~lA~~~a~~llC 51 (319)
T PRK06090 24 IPGALLLQSDEG--LGVESLVELFSRALLC 51 (319)
T ss_pred cceeEeeECCCC--CCHHHHHHHHHHHHcC
Confidence 456899999998 6888999999998744
No 280
>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2.7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....
Probab=20.34 E-value=92 Score=30.57 Aligned_cols=28 Identities=43% Similarity=0.681 Sum_probs=23.1
Q ss_pred CceeecCCCCchHHHHHHHHHHHhhccCeE
Q 004011 493 PRILLSGPAGSEIYQETLAKALAKHFSARL 522 (779)
Q Consensus 493 ~rILLSGPaGsEiYQE~LaKALA~~F~AkL 522 (779)
+=|.|.||+|+ -.-+|+++|...|.-++
T Consensus 3 r~ivl~Gpsg~--GK~~l~~~L~~~~~~~~ 30 (183)
T PF00625_consen 3 RPIVLVGPSGS--GKSTLAKRLIQEFPDKF 30 (183)
T ss_dssp SEEEEESSTTS--SHHHHHHHHHHHSTTTE
T ss_pred CEEEEECCCCC--CHHHHHHHHHHhccccc
Confidence 45889999985 48999999999887554
No 281
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=20.32 E-value=1.8e+02 Score=32.05 Aligned_cols=57 Identities=26% Similarity=0.476 Sum_probs=34.8
Q ss_pred HHHHHHHHhhcccCcCCEEEEEcchhhhccCC--------hhhHHHHHHHh---ccC--CCCEEEEeeccccC
Q 004011 689 AINELFEVALNESKSSPLIVFVKDIEKSLTGN--------NDAYGALKSKL---ENL--PSNVVVIGSHTQLD 748 (779)
Q Consensus 689 lIqsLyEVL~S~S~t~PlILYiKDVEK~L~gs--------~e~y~~fq~mL---eKL--sG~VLIIGSq~~~D 748 (779)
.+..+|+.... ..|.||||.|++.++... .+.-..|-..| +.+ .++|+||+.-+..+
T Consensus 203 ~i~~~f~~a~~---~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~ 272 (364)
T TIGR01242 203 LVREIFELAKE---KAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPD 272 (364)
T ss_pred HHHHHHHHHHh---cCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChh
Confidence 45667776554 789999999999976422 11112222222 322 35888888877654
No 282
>PRK06547 hypothetical protein; Provisional
Probab=20.31 E-value=82 Score=31.50 Aligned_cols=34 Identities=35% Similarity=0.437 Sum_probs=28.8
Q ss_pred CCceeecCCCCchHHHHHHHHHHHhhccCeEEEEec
Q 004011 492 CPRILLSGPAGSEIYQETLAKALAKHFSARLLIVDS 527 (779)
Q Consensus 492 s~rILLSGPaGsEiYQE~LaKALA~~F~AkLLilDs 527 (779)
...|++.||+|| -.-+||+.||+.+++.++-+|.
T Consensus 15 ~~~i~i~G~~Gs--GKTt~a~~l~~~~~~~~~~~d~ 48 (172)
T PRK06547 15 MITVLIDGRSGS--GKTTLAGALAARTGFQLVHLDD 48 (172)
T ss_pred CEEEEEECCCCC--CHHHHHHHHHHHhCCCeecccc
Confidence 457999999994 7889999999999988776664
No 283
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=20.31 E-value=69 Score=35.77 Aligned_cols=29 Identities=31% Similarity=0.398 Sum_probs=24.5
Q ss_pred CCCCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 490 TMCPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 490 s~s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
-..+++||.||.| +-..+||+++|+.+..
T Consensus 19 rl~ha~Lf~Gp~G--~GK~~lA~~~A~~LlC 47 (342)
T PRK06964 19 RLPHALLLHGQAG--IGKLDFAQHLAQGLLC 47 (342)
T ss_pred CcceEEEEECCCC--CCHHHHHHHHHHHHcC
Confidence 3557899999999 7889999999988755
No 284
>PRK07440 hypothetical protein; Provisional
Probab=20.29 E-value=93 Score=27.08 Aligned_cols=25 Identities=32% Similarity=0.518 Sum_probs=21.7
Q ss_pred eEEECCeecCCC--ceEEeeCCCEEEE
Q 004011 199 EVEVNGNVHPKD--SQVVLRGGDELVF 223 (779)
Q Consensus 199 tV~VNGkkVgKg--~kviL~nGDEIvf 223 (779)
.|-+||+.|.|. ....|+.||+|-+
T Consensus 37 av~~N~~iv~r~~w~~~~L~~gD~IEI 63 (70)
T PRK07440 37 AVEYNGEILHRQFWEQTQVQPGDRLEI 63 (70)
T ss_pred EEEECCEEeCHHHcCceecCCCCEEEE
Confidence 578999999988 5689999999976
No 285
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=20.08 E-value=71 Score=35.45 Aligned_cols=28 Identities=25% Similarity=0.344 Sum_probs=23.6
Q ss_pred CCCceeecCCCCchHHHHHHHHHHHhhccC
Q 004011 491 MCPRILLSGPAGSEIYQETLAKALAKHFSA 520 (779)
Q Consensus 491 ~s~rILLSGPaGsEiYQE~LaKALA~~F~A 520 (779)
.+.++|++||.| +-...||++||+.+--
T Consensus 23 l~HA~Lf~G~~G--~GK~~lA~~~A~~llC 50 (325)
T PRK06871 23 GHHALLFKADSG--LGTEQLIRALAQWLMC 50 (325)
T ss_pred cceeEEeECCCC--CCHHHHHHHHHHHHcC
Confidence 345899999998 7899999999998744
Done!