Query psy11421
Match_columns 687
No_of_seqs 287 out of 2011
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 17:59:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11421hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0272 Lig NAD-dependent DNA 100.0 3E-202 6E-207 1670.0 71.6 665 10-679 3-667 (667)
2 PRK07956 ligA NAD-dependent DN 100.0 7E-187 1E-191 1595.9 77.9 662 11-680 2-664 (665)
3 PRK14350 ligA NAD-dependent DN 100.0 9E-186 2E-190 1579.0 76.8 651 14-680 5-667 (669)
4 TIGR00575 dnlj DNA ligase, NAD 100.0 1E-184 2E-189 1576.6 75.5 649 21-674 1-652 (652)
5 PRK14351 ligA NAD-dependent DN 100.0 2E-183 4E-188 1566.3 78.5 659 7-680 25-684 (689)
6 PRK08097 ligB NAD-dependent DN 100.0 4E-153 8E-158 1280.9 62.0 532 9-593 25-558 (562)
7 smart00532 LIGANc Ligase N fam 100.0 9E-138 2E-142 1137.3 52.0 440 15-459 2-441 (441)
8 cd00114 LIGANc NAD+ dependent 100.0 9.5E-95 2.1E-99 765.1 35.2 306 17-327 2-307 (307)
9 PF01653 DNA_ligase_aden: NAD- 100.0 3.1E-94 6.6E-99 764.3 31.6 313 13-328 2-315 (315)
10 PF03120 DNA_ligase_OB: NAD-de 100.0 1.6E-31 3.5E-36 227.7 9.9 82 330-411 1-82 (82)
11 PRK06195 DNA polymerase III su 99.6 2.7E-16 5.9E-21 168.2 8.9 77 604-680 218-308 (309)
12 PRK06063 DNA polymerase III su 99.6 4E-16 8.6E-21 167.0 9.1 74 607-681 233-308 (313)
13 PF12826 HHH_2: Helix-hairpin- 99.6 2.6E-15 5.7E-20 123.6 6.9 64 521-584 1-64 (64)
14 COG5275 BRCT domain type II [G 99.5 4.2E-14 9.1E-19 138.4 8.1 81 603-683 153-234 (276)
15 cd07894 Adenylation_RNA_ligase 99.2 3.9E-10 8.4E-15 122.0 15.1 144 119-303 49-194 (342)
16 PLN03122 Poly [ADP-ribose] pol 99.1 1.1E-10 2.3E-15 137.4 8.7 78 603-681 186-267 (815)
17 PF00533 BRCT: BRCA1 C Terminu 98.8 3.6E-08 7.8E-13 82.9 8.8 74 604-678 3-78 (78)
18 PF14520 HHH_5: Helix-hairpin- 98.7 8.6E-09 1.9E-13 83.7 4.2 57 456-513 4-60 (60)
19 PF12738 PTCB-BRCT: twin BRCT 98.7 1.6E-08 3.4E-13 82.7 5.5 62 611-673 2-63 (63)
20 cd07896 Adenylation_kDNA_ligas 98.7 8.2E-08 1.8E-12 94.4 11.4 139 119-307 17-162 (174)
21 PRK09125 DNA ligase; Provision 98.6 3.3E-06 7.2E-11 89.6 20.6 198 119-375 44-248 (282)
22 cd00027 BRCT Breast Cancer Sup 98.6 2.7E-07 5.9E-12 74.8 9.2 70 609-678 1-71 (72)
23 cd07898 Adenylation_DNA_ligase 98.5 3.1E-06 6.7E-11 85.3 16.3 165 118-319 21-195 (201)
24 smart00292 BRCT breast cancer 98.5 6.5E-07 1.4E-11 74.2 8.9 75 606-680 2-79 (80)
25 cd07901 Adenylation_DNA_ligase 98.4 3.9E-06 8.4E-11 85.1 13.7 155 118-306 25-192 (207)
26 PF03119 DNA_ligase_ZBD: NAD-d 98.4 1.5E-07 3.3E-12 64.6 2.0 28 417-445 1-28 (28)
27 PRK03180 ligB ATP-dependent DN 98.4 1.7E-05 3.8E-10 90.7 19.5 216 119-376 205-435 (508)
28 TIGR02779 NHEJ_ligase_lig DNA 98.3 3E-05 6.5E-10 83.0 18.7 209 118-376 12-234 (298)
29 cd07906 Adenylation_DNA_ligase 98.3 1.3E-05 2.8E-10 80.1 13.3 162 119-319 17-184 (190)
30 PRK07636 ligB ATP-dependent DN 98.2 0.00018 4E-09 76.1 21.6 205 118-377 18-228 (275)
31 cd07900 Adenylation_DNA_ligase 98.2 3.7E-05 8E-10 78.7 15.8 179 87-307 11-204 (219)
32 PF14520 HHH_5: Helix-hairpin- 98.2 3.2E-06 6.9E-11 68.7 6.2 55 522-576 4-59 (60)
33 PRK05601 DNA polymerase III su 98.2 2.8E-06 6.2E-11 92.0 7.3 74 606-680 294-369 (377)
34 PF01068 DNA_ligase_A_M: ATP d 98.2 3.5E-05 7.6E-10 77.1 14.5 157 118-306 19-189 (202)
35 TIGR00574 dnl1 DNA ligase I, A 98.2 9.2E-05 2E-09 85.1 19.2 220 119-378 188-433 (514)
36 PRK08224 ligC ATP-dependent DN 98.1 8.8E-05 1.9E-09 81.1 17.9 214 119-376 25-249 (350)
37 cd06846 Adenylation_DNA_ligase 98.1 3E-05 6.5E-10 76.8 12.2 150 118-319 19-177 (182)
38 cd07897 Adenylation_DNA_ligase 98.1 6E-05 1.3E-09 76.5 14.4 157 118-307 24-191 (207)
39 cd07903 Adenylation_DNA_ligase 98.0 0.00023 5.1E-09 72.9 17.7 167 118-319 33-216 (225)
40 COG1793 CDC9 ATP-dependent DNA 98.0 0.00044 9.5E-09 77.9 20.9 215 119-376 134-366 (444)
41 PRK01109 ATP-dependent DNA lig 97.9 0.00028 6E-09 82.4 18.0 216 119-377 249-492 (590)
42 cd07905 Adenylation_DNA_ligase 97.9 0.00012 2.6E-09 73.5 12.9 158 118-306 16-180 (194)
43 PHA00454 ATP-dependent DNA lig 97.9 0.0027 5.8E-08 68.6 23.6 217 119-376 28-269 (315)
44 PLN03123 poly [ADP-ribose] pol 97.9 2.1E-05 4.6E-10 95.2 7.8 76 604-680 391-469 (981)
45 cd07902 Adenylation_DNA_ligase 97.9 0.00027 5.9E-09 72.0 14.5 152 119-307 35-200 (213)
46 PF12826 HHH_2: Helix-hairpin- 97.9 1.6E-05 3.4E-10 65.6 4.3 58 459-518 5-62 (64)
47 cd08039 Adenylation_DNA_ligase 97.9 0.00031 6.7E-09 72.7 14.9 170 117-307 21-215 (235)
48 PRK09633 ligD ATP-dependent DN 97.9 0.00054 1.2E-08 79.9 18.5 187 118-339 16-221 (610)
49 PHA02587 30 DNA ligase; Provis 97.8 0.0017 3.6E-08 74.3 21.1 222 119-378 153-412 (488)
50 PRK09247 ATP-dependent DNA lig 97.8 0.00064 1.4E-08 78.6 17.6 219 118-377 225-465 (539)
51 PRK09632 ATP-dependent DNA lig 97.8 0.0014 2.9E-08 78.1 19.7 209 118-377 477-695 (764)
52 PRK00116 ruvA Holliday junctio 97.7 0.00012 2.6E-09 73.4 8.4 53 526-578 76-131 (192)
53 COG1796 POL4 DNA polymerase IV 97.7 2.5E-05 5.4E-10 82.5 3.1 59 458-516 94-153 (326)
54 PRK14670 uvrC excinuclease ABC 97.6 6.8E-05 1.5E-09 86.5 6.3 53 526-578 517-569 (574)
55 KOG2841|consensus 97.6 4.9E-05 1.1E-09 76.7 4.0 60 520-579 191-251 (254)
56 PRK08609 hypothetical protein; 97.6 2.4E-05 5.2E-10 90.8 1.7 58 459-516 90-148 (570)
57 PRK12766 50S ribosomal protein 97.6 0.00011 2.3E-09 74.9 6.1 52 526-577 6-58 (232)
58 PRK05972 ligD ATP-dependent DN 97.5 0.0031 6.8E-08 75.8 18.4 179 119-343 250-435 (860)
59 PLN03113 DNA ligase 1; Provisi 97.5 0.0028 6E-08 75.4 17.4 221 118-376 391-637 (744)
60 PRK14667 uvrC excinuclease ABC 97.4 0.00018 3.9E-09 83.0 6.2 50 526-576 517-566 (567)
61 TIGR01448 recD_rel helicase, p 97.4 0.00048 1E-08 82.3 9.6 122 449-576 78-202 (720)
62 cd07895 Adenylation_mRNA_cappi 97.4 0.0016 3.5E-08 66.3 12.2 156 118-324 41-214 (215)
63 PRK00558 uvrC excinuclease ABC 97.3 0.0003 6.6E-09 82.0 6.2 52 526-577 546-597 (598)
64 PRK14973 DNA topoisomerase I; 97.3 0.0012 2.6E-08 80.5 11.3 127 449-576 790-931 (936)
65 PRK12766 50S ribosomal protein 97.2 0.00051 1.1E-08 70.0 5.8 54 458-512 4-57 (232)
66 PRK00116 ruvA Holliday junctio 97.1 0.0011 2.5E-08 66.5 7.5 57 458-514 74-131 (192)
67 COG1948 MUS81 ERCC4-type nucle 97.1 0.0011 2.3E-08 68.8 6.7 53 526-578 185-237 (254)
68 PRK13482 DNA integrity scannin 97.0 0.0015 3.2E-08 70.8 6.7 52 526-577 290-341 (352)
69 TIGR01209 RNA ligase, Pab1020 97.0 0.015 3.2E-07 63.8 14.4 165 84-304 60-228 (374)
70 PRK14669 uvrC excinuclease ABC 96.9 0.0014 3.1E-08 76.5 6.7 50 527-578 556-605 (624)
71 PF00633 HHH: Helix-hairpin-he 96.9 0.0014 3E-08 45.9 4.0 30 545-574 1-30 (30)
72 PRK14671 uvrC excinuclease ABC 96.9 0.0015 3.2E-08 76.6 6.6 49 526-576 572-620 (621)
73 PRK14672 uvrC excinuclease ABC 96.9 0.0013 2.9E-08 76.5 5.9 51 527-577 612-662 (691)
74 PRK14666 uvrC excinuclease ABC 96.8 0.0015 3.3E-08 76.4 6.0 51 526-576 640-690 (694)
75 COG0322 UvrC Nuclease subunit 96.7 0.002 4.3E-08 74.5 5.4 49 526-575 533-581 (581)
76 TIGR00575 dnlj DNA ligase, NAD 96.6 0.0032 7E-08 74.2 6.2 80 458-545 467-552 (652)
77 PRK14973 DNA topoisomerase I; 96.5 0.023 5E-07 69.6 13.1 149 415-575 635-796 (936)
78 PF03118 RNA_pol_A_CTD: Bacter 96.5 0.0052 1.1E-07 51.0 5.1 52 461-513 15-66 (66)
79 PRK08609 hypothetical protein; 96.4 0.0059 1.3E-07 71.2 7.3 85 491-575 48-143 (570)
80 PRK14668 uvrC excinuclease ABC 96.4 0.0044 9.6E-08 72.0 6.0 49 527-575 529-577 (577)
81 TIGR00084 ruvA Holliday juncti 96.3 0.0038 8.3E-08 62.7 4.3 52 458-512 73-128 (191)
82 COG1423 ATP-dependent DNA liga 96.3 0.078 1.7E-06 57.0 14.1 168 83-306 68-238 (382)
83 PRK07956 ligA NAD-dependent DN 96.3 0.0053 1.2E-07 72.6 5.8 80 458-545 480-565 (665)
84 KOG1968|consensus 96.3 0.0032 7E-08 75.9 4.0 70 603-672 170-240 (871)
85 PRK14351 ligA NAD-dependent DN 96.2 0.0056 1.2E-07 72.5 5.8 17 16-32 61-77 (689)
86 PRK14605 ruvA Holliday junctio 96.0 0.025 5.3E-07 57.0 8.2 72 490-576 54-129 (194)
87 PRK13766 Hef nuclease; Provisi 95.9 0.011 2.4E-07 71.4 6.3 53 526-578 718-770 (773)
88 PRK07758 hypothetical protein; 95.9 0.019 4.1E-07 50.7 5.8 51 462-513 39-89 (95)
89 PRK00254 ski2-like helicase; P 95.8 0.028 6E-07 67.5 8.9 52 526-577 648-700 (720)
90 COG2003 RadC DNA repair protei 95.8 0.081 1.8E-06 54.0 10.7 115 517-633 27-165 (224)
91 PRK13901 ruvA Holliday junctio 95.7 0.037 7.9E-07 55.7 8.1 71 490-575 53-127 (196)
92 PRK14606 ruvA Holliday junctio 95.7 0.039 8.4E-07 55.3 8.0 73 490-577 54-130 (188)
93 PRK00254 ski2-like helicase; P 95.7 0.014 3.1E-07 70.0 5.7 54 459-513 647-700 (720)
94 PRK14605 ruvA Holliday junctio 95.6 0.033 7.2E-07 56.1 7.4 53 458-513 74-130 (194)
95 PRK08097 ligB NAD-dependent DN 95.5 0.012 2.6E-07 68.0 4.4 19 458-476 460-478 (562)
96 TIGR00084 ruvA Holliday juncti 95.5 0.024 5.1E-07 57.0 6.0 69 490-573 53-125 (191)
97 TIGR01259 comE comEA protein. 95.4 0.014 3E-07 54.3 3.6 61 481-575 58-118 (120)
98 TIGR00426 competence protein C 95.4 0.037 8E-07 46.1 5.8 23 553-575 45-67 (69)
99 TIGR00596 rad1 DNA repair prot 95.4 0.022 4.9E-07 68.6 6.2 51 526-578 760-811 (814)
100 PRK14601 ruvA Holliday junctio 95.4 0.058 1.3E-06 53.8 8.1 72 490-576 54-129 (183)
101 PRK14604 ruvA Holliday junctio 95.4 0.058 1.2E-06 54.4 8.0 73 490-577 54-130 (195)
102 smart00483 POLXc DNA polymeras 95.3 0.042 9E-07 60.0 7.2 64 491-554 48-121 (334)
103 TIGR01448 recD_rel helicase, p 95.3 0.047 1E-06 65.5 8.3 75 496-576 89-168 (720)
104 TIGR01259 comE comEA protein. 95.2 0.029 6.3E-07 52.2 4.8 47 457-511 68-118 (120)
105 PRK02362 ski2-like helicase; P 95.1 0.021 4.5E-07 68.7 4.9 63 447-512 639-704 (737)
106 PRK14602 ruvA Holliday junctio 95.1 0.049 1.1E-06 55.3 6.5 73 490-577 55-131 (203)
107 PRK14600 ruvA Holliday junctio 95.0 0.069 1.5E-06 53.4 7.4 48 526-575 76-127 (186)
108 PRK14350 ligA NAD-dependent DN 95.0 0.027 5.8E-07 66.6 5.0 81 458-546 471-564 (669)
109 PRK14670 uvrC excinuclease ABC 94.8 0.039 8.6E-07 64.1 5.8 57 454-513 512-568 (574)
110 PF14229 DUF4332: Domain of un 94.8 0.2 4.3E-06 46.7 9.4 83 463-558 1-89 (122)
111 PRK14603 ruvA Holliday junctio 94.6 0.066 1.4E-06 54.1 6.1 73 490-577 53-129 (197)
112 PRK02515 psbU photosystem II c 94.6 0.039 8.5E-07 51.5 4.0 26 483-508 53-78 (132)
113 PRK04301 radA DNA repair and r 94.5 0.06 1.3E-06 58.1 6.1 55 458-513 7-61 (317)
114 PRK01172 ski2-like helicase; P 94.5 0.067 1.5E-06 63.7 6.7 63 449-512 601-666 (674)
115 PRK14601 ruvA Holliday junctio 94.4 0.12 2.5E-06 51.7 7.2 53 458-513 74-130 (183)
116 PF00633 HHH: Helix-hairpin-he 94.2 0.058 1.3E-06 37.8 3.2 28 482-509 2-29 (30)
117 COG0272 Lig NAD-dependent DNA 94.2 0.044 9.6E-07 63.8 4.2 81 456-544 478-564 (667)
118 PRK13901 ruvA Holliday junctio 94.1 0.12 2.7E-06 52.0 6.6 53 458-513 73-129 (196)
119 PRK14666 uvrC excinuclease ABC 94.1 0.078 1.7E-06 62.5 6.0 54 458-513 638-691 (694)
120 TIGR02307 RNA_lig_RNL2 RNA lig 94.1 0.25 5.4E-06 53.4 9.4 128 117-279 24-165 (325)
121 PRK14604 ruvA Holliday junctio 94.0 0.053 1.1E-06 54.7 3.8 53 458-513 74-130 (195)
122 PRK14602 ruvA Holliday junctio 93.9 0.062 1.3E-06 54.5 4.2 52 459-513 76-131 (203)
123 PRK14606 ruvA Holliday junctio 93.9 0.058 1.3E-06 54.1 4.0 53 458-513 74-130 (188)
124 PRK13913 3-methyladenine DNA g 93.9 0.25 5.4E-06 50.7 8.5 83 468-575 50-141 (218)
125 PHA02142 putative RNA ligase 93.9 0.57 1.2E-05 51.5 11.7 147 117-302 168-343 (366)
126 TIGR01954 nusA_Cterm_rpt trans 93.8 0.2 4.3E-06 38.6 6.0 47 465-512 1-47 (50)
127 PRK14603 ruvA Holliday junctio 93.8 0.061 1.3E-06 54.3 3.8 53 458-513 73-129 (197)
128 TIGR03252 uncharacterized HhH- 93.7 0.31 6.7E-06 48.3 8.6 84 469-577 39-137 (177)
129 PRK14600 ruvA Holliday junctio 93.6 0.064 1.4E-06 53.7 3.7 52 458-513 74-129 (186)
130 TIGR02236 recomb_radA DNA repa 93.6 0.12 2.7E-06 55.4 6.2 51 461-512 3-53 (310)
131 COG0632 RuvA Holliday junction 93.5 0.14 3E-06 51.9 5.8 50 526-576 76-129 (201)
132 COG1796 POL4 DNA polymerase IV 93.3 0.24 5.2E-06 53.0 7.4 114 459-575 18-148 (326)
133 PRK14672 uvrC excinuclease ABC 93.1 0.19 4.1E-06 59.2 6.8 60 459-520 610-669 (691)
134 cd00141 NT_POLXc Nucleotidyltr 92.9 0.22 4.7E-06 53.8 6.7 62 491-552 45-115 (307)
135 TIGR00426 competence protein C 92.9 0.19 4.1E-06 41.8 4.8 58 483-542 8-66 (69)
136 KOG2534|consensus 92.7 0.78 1.7E-05 49.0 10.1 136 490-655 55-200 (353)
137 COG1623 Predicted nucleic-acid 92.6 0.14 3.1E-06 53.7 4.6 50 527-576 297-346 (349)
138 PRK14667 uvrC excinuclease ABC 92.6 0.18 3.9E-06 58.7 5.9 50 459-511 516-565 (567)
139 COG1555 ComEA DNA uptake prote 92.4 0.18 3.9E-06 48.7 4.7 58 484-575 90-147 (149)
140 PF12836 HHH_3: Helix-hairpin- 92.2 0.073 1.6E-06 43.9 1.5 30 484-513 7-36 (65)
141 PRK02515 psbU photosystem II c 92.0 0.27 5.9E-06 46.1 5.2 41 527-575 65-107 (132)
142 COG0632 RuvA Holliday junction 92.0 0.14 3E-06 51.9 3.5 20 492-511 109-128 (201)
143 cd00141 NT_POLXc Nucleotidyltr 92.0 0.12 2.5E-06 55.8 3.2 47 458-515 86-132 (307)
144 PRK00558 uvrC excinuclease ABC 91.7 0.22 4.9E-06 58.4 5.2 52 459-512 545-596 (598)
145 PRK00024 hypothetical protein; 91.3 0.56 1.2E-05 48.4 7.2 57 519-575 29-86 (224)
146 TIGR00608 radc DNA repair prot 91.3 0.4 8.6E-06 49.2 6.0 57 519-575 19-80 (218)
147 PF10391 DNA_pol_lambd_f: Fing 91.2 0.19 4.1E-06 39.8 2.7 27 460-487 5-31 (52)
148 PF09414 RNA_ligase: RNA ligas 90.7 0.3 6.4E-06 48.3 4.4 155 119-304 2-174 (186)
149 PRK14668 uvrC excinuclease ABC 90.4 0.33 7.2E-06 56.7 5.0 50 459-510 527-576 (577)
150 COG0177 Nth Predicted EndoIII- 90.4 1.1 2.4E-05 45.7 8.1 42 467-510 48-92 (211)
151 PRK10702 endonuclease III; Pro 90.3 1.1 2.5E-05 45.7 8.2 78 467-575 48-129 (211)
152 KOG1929|consensus 89.6 0.53 1.2E-05 56.6 5.9 75 605-680 102-177 (811)
153 PRK13482 DNA integrity scannin 89.1 0.68 1.5E-05 50.6 5.8 55 461-517 291-345 (352)
154 COG1645 Uncharacterized Zn-fin 88.7 0.26 5.6E-06 46.3 2.0 23 414-438 27-49 (131)
155 TIGR02236 recomb_radA DNA repa 88.7 0.76 1.7E-05 49.3 5.9 50 527-576 3-53 (310)
156 KOG0967|consensus 87.9 6.1 0.00013 46.1 12.5 179 87-303 345-532 (714)
157 PRK14669 uvrC excinuclease ABC 87.7 0.7 1.5E-05 54.5 5.1 59 454-517 550-608 (624)
158 TIGR02238 recomb_DMC1 meiotic 87.5 1 2.2E-05 48.8 6.0 54 460-514 4-57 (313)
159 COG1948 MUS81 ERCC4-type nucle 87.4 0.82 1.8E-05 47.8 4.9 52 460-513 185-236 (254)
160 PTZ00035 Rad51 protein; Provis 86.8 1.1 2.4E-05 49.0 5.9 55 459-514 25-79 (337)
161 PRK01172 ski2-like helicase; P 86.8 2.6 5.6E-05 50.3 9.4 55 521-575 610-665 (674)
162 PF01396 zf-C4_Topoisom: Topoi 86.7 0.65 1.4E-05 34.5 2.7 28 416-444 2-31 (39)
163 PRK00420 hypothetical protein; 86.1 0.5 1.1E-05 43.4 2.2 24 414-438 22-45 (112)
164 PRK05182 DNA-directed RNA poly 86.0 1.3 2.7E-05 48.0 5.6 52 461-513 252-303 (310)
165 cd00080 HhH2_motif Helix-hairp 85.5 0.77 1.7E-05 39.0 3.0 26 527-552 26-51 (75)
166 COG0322 UvrC Nuclease subunit 85.3 1.1 2.5E-05 52.2 5.2 119 372-510 462-580 (581)
167 PRK10736 hypothetical protein; 85.3 5.8 0.00013 44.1 10.4 113 522-639 7-142 (374)
168 KOG3226|consensus 85.1 2.4 5.1E-05 46.2 6.9 71 606-677 317-387 (508)
169 TIGR02027 rpoA DNA-directed RN 84.8 1.5 3.3E-05 47.1 5.5 53 460-513 237-289 (297)
170 PRK04301 radA DNA repair and r 84.7 1.5 3.3E-05 47.3 5.6 50 527-576 10-60 (317)
171 COG2231 Uncharacterized protei 84.4 5.2 0.00011 40.5 8.6 107 467-576 49-170 (215)
172 TIGR00194 uvrC excinuclease AB 84.3 0.66 1.4E-05 54.3 2.7 30 527-556 545-574 (574)
173 PLN03187 meiotic recombination 84.1 1.6 3.5E-05 47.9 5.5 56 458-514 32-87 (344)
174 cd00056 ENDO3c endonuclease II 84.1 3.4 7.3E-05 39.7 7.1 23 553-575 81-103 (158)
175 smart00278 HhH1 Helix-hairpin- 83.9 0.8 1.7E-05 30.7 1.9 18 492-509 2-19 (26)
176 PRK13766 Hef nuclease; Provisi 83.3 1.7 3.7E-05 52.6 5.8 51 461-513 719-769 (773)
177 smart00478 ENDO3c endonuclease 83.2 5.2 0.00011 38.0 8.0 66 481-575 23-92 (149)
178 PRK14671 uvrC excinuclease ABC 83.2 1.3 2.9E-05 52.3 4.6 49 459-511 571-619 (621)
179 TIGR01954 nusA_Cterm_rpt trans 83.1 3.4 7.5E-05 31.6 5.5 41 533-573 3-44 (50)
180 PF06677 Auto_anti-p27: Sjogre 82.6 1 2.2E-05 34.0 2.1 24 414-438 16-39 (41)
181 KOG2841|consensus 82.4 1.8 3.8E-05 44.6 4.5 59 449-513 191-249 (254)
182 smart00483 POLXc DNA polymeras 82.1 0.62 1.3E-05 50.9 1.2 29 459-488 91-119 (334)
183 TIGR01084 mutY A/G-specific ad 81.9 5.2 0.00011 42.6 8.1 69 469-540 47-122 (275)
184 PF12836 HHH_3: Helix-hairpin- 81.9 1 2.3E-05 37.0 2.3 30 548-577 7-36 (65)
185 COG1555 ComEA DNA uptake prote 81.7 0.9 1.9E-05 43.9 2.1 43 547-589 89-131 (149)
186 PRK09482 flap endonuclease-lik 81.6 1.7 3.6E-05 45.8 4.2 26 527-552 186-211 (256)
187 PF01331 mRNA_cap_enzyme: mRNA 81.0 4.5 9.8E-05 40.3 6.9 139 119-304 17-178 (192)
188 PRK00423 tfb transcription ini 80.8 2.4 5.3E-05 45.8 5.2 34 415-452 11-45 (310)
189 TIGR01083 nth endonuclease III 80.5 7.8 0.00017 38.8 8.4 76 469-575 47-126 (191)
190 TIGR03491 RecB family nuclease 80.4 3.4 7.4E-05 47.1 6.5 65 443-514 199-263 (457)
191 COG1623 Predicted nucleic-acid 80.4 3 6.4E-05 44.2 5.4 99 435-544 241-346 (349)
192 PF01367 5_3_exonuc: 5'-3' exo 80.0 0.16 3.5E-06 45.8 -3.4 25 527-551 22-46 (101)
193 cd00008 53EXOc 5'-3' exonuclea 79.9 2.2 4.9E-05 44.3 4.5 26 527-552 187-212 (240)
194 smart00611 SEC63 Domain of unk 79.8 4.4 9.4E-05 43.4 6.8 63 449-513 144-206 (312)
195 PF14229 DUF4332: Domain of un 79.6 2.3 4.9E-05 39.7 3.9 49 443-494 41-89 (122)
196 PRK02362 ski2-like helicase; P 79.1 4.7 0.0001 48.7 7.5 54 521-576 650-704 (737)
197 PRK13910 DNA glycosylase MutY; 79.0 4.9 0.00011 43.1 6.7 65 480-545 23-95 (289)
198 TIGR02776 NHEJ_ligase_prk DNA 78.2 33 0.00073 40.2 13.7 180 151-376 3-192 (552)
199 PF11731 Cdd1: Pathogenicity l 78.2 2.2 4.9E-05 37.9 3.2 31 459-490 14-44 (93)
200 PF09151 DUF1936: Domain of un 78.0 2.5 5.4E-05 29.6 2.7 26 417-444 3-33 (36)
201 smart00475 53EXOc 5'-3' exonuc 77.8 2.4 5.1E-05 44.7 3.9 26 527-552 190-215 (259)
202 TIGR02239 recomb_RAD51 DNA rep 77.5 4.3 9.3E-05 44.0 5.9 53 461-514 5-57 (316)
203 PRK07758 hypothetical protein; 77.1 5.7 0.00012 35.4 5.4 39 535-573 46-85 (95)
204 PRK09202 nusA transcription el 77.1 8.4 0.00018 44.1 8.3 102 460-562 359-466 (470)
205 PF09297 zf-NADH-PPase: NADH p 76.5 2 4.3E-05 30.3 2.0 23 416-438 4-26 (32)
206 smart00278 HhH1 Helix-hairpin- 76.4 2.3 4.9E-05 28.5 2.2 20 556-575 2-21 (26)
207 PF01927 Mut7-C: Mut7-C RNAse 75.9 2.7 5.8E-05 40.4 3.4 55 371-428 50-104 (147)
208 KOG0966|consensus 75.6 86 0.0019 38.0 15.8 163 118-307 250-424 (881)
209 PLN03186 DNA repair protein RA 75.4 6.4 0.00014 43.2 6.6 55 459-514 30-84 (342)
210 PF14803 Nudix_N_2: Nudix N-te 74.4 2.9 6.2E-05 30.2 2.3 23 416-438 1-27 (34)
211 KOG1929|consensus 73.9 5 0.00011 48.5 5.6 74 604-678 7-80 (811)
212 cd01703 PolY_Pol_iota DNA Poly 73.5 4.8 0.0001 44.8 5.1 50 458-510 173-237 (379)
213 PF13248 zf-ribbon_3: zinc-rib 73.3 1.7 3.7E-05 29.2 0.9 20 415-438 2-21 (26)
214 KOG0966|consensus 73.3 9 0.0002 45.8 7.3 77 603-679 630-709 (881)
215 PRK07220 DNA topoisomerase I; 73.0 5.1 0.00011 48.5 5.5 47 459-506 688-734 (740)
216 CHL00013 rpoA RNA polymerase a 72.9 4.8 0.0001 43.9 4.8 49 464-513 269-317 (327)
217 PRK03352 DNA polymerase IV; Va 72.6 4.4 9.6E-05 44.2 4.5 50 458-510 178-227 (346)
218 PRK14976 5'-3' exonuclease; Pr 72.4 3.1 6.7E-05 44.4 3.1 25 527-551 195-219 (281)
219 cd01701 PolY_Rev1 DNA polymera 70.6 5.3 0.00012 44.7 4.7 50 459-511 224-275 (404)
220 COG0122 AlkA 3-methyladenine D 70.3 20 0.00044 38.4 8.7 70 479-574 144-217 (285)
221 cd08689 C2_fungal_Pkc1p C2 dom 70.3 5.6 0.00012 36.3 3.8 53 297-353 27-79 (109)
222 COG5241 RAD10 Nucleotide excis 69.9 2.7 5.9E-05 41.6 1.9 53 526-578 170-222 (224)
223 COG2231 Uncharacterized protei 68.6 3.9 8.5E-05 41.4 2.7 39 537-575 96-135 (215)
224 TIGR00596 rad1 DNA repair prot 68.6 5.7 0.00012 48.5 4.6 48 461-512 761-809 (814)
225 PRK01216 DNA polymerase IV; Va 68.4 6.9 0.00015 43.1 4.9 48 459-509 180-227 (351)
226 COG1096 Predicted RNA-binding 68.0 4.3 9.3E-05 40.5 2.8 61 377-451 117-179 (188)
227 KOG1921|consensus 67.6 18 0.00038 37.7 7.1 34 534-571 141-175 (286)
228 PF03118 RNA_pol_A_CTD: Bacter 66.7 12 0.00025 31.1 4.7 34 542-575 31-64 (66)
229 PF09862 DUF2089: Protein of u 65.5 4.5 9.8E-05 37.3 2.3 25 418-450 1-25 (113)
230 PRK10880 adenine DNA glycosyla 65.5 16 0.00034 40.4 6.8 74 469-545 51-132 (350)
231 PRK03858 DNA polymerase IV; Va 65.4 7.3 0.00016 43.3 4.4 48 459-509 175-222 (396)
232 TIGR00588 ogg 8-oxoguanine DNA 65.1 15 0.00032 39.8 6.5 21 554-574 219-239 (310)
233 smart00279 HhH2 Helix-hairpin- 64.3 5.6 0.00012 29.0 2.1 16 494-509 19-34 (36)
234 PF09889 DUF2116: Uncharacteri 64.3 2.8 6.1E-05 34.1 0.6 29 415-450 3-31 (59)
235 KOG3084|consensus 64.2 3.4 7.3E-05 44.3 1.3 29 415-445 150-178 (345)
236 PRK03348 DNA polymerase IV; Pr 63.6 8.8 0.00019 43.8 4.7 49 459-510 182-230 (454)
237 cd01702 PolY_Pol_eta DNA Polym 63.3 8.7 0.00019 42.4 4.4 50 459-510 184-235 (359)
238 COG1997 RPL43A Ribosomal prote 62.1 6.6 0.00014 34.3 2.5 24 415-438 35-58 (89)
239 PF14716 HHH_8: Helix-hairpin- 61.8 8.6 0.00019 31.9 3.1 20 556-575 48-67 (68)
240 TIGR00608 radc DNA repair prot 61.3 12 0.00026 38.5 4.7 67 445-514 17-83 (218)
241 PF07754 DUF1610: Domain of un 60.4 6.3 0.00014 26.3 1.6 21 418-438 1-21 (24)
242 PF14952 zf-tcix: Putative tre 59.7 5.6 0.00012 30.3 1.4 26 416-447 12-37 (44)
243 smart00661 RPOL9 RNA polymeras 59.6 6.3 0.00014 30.5 1.8 22 417-438 2-25 (52)
244 PRK10308 3-methyl-adenine DNA 59.6 48 0.001 35.4 9.1 70 479-549 155-234 (283)
245 PRK00398 rpoP DNA-directed RNA 59.4 6.1 0.00013 30.2 1.6 22 417-438 5-26 (46)
246 COG2251 Predicted nuclease (Re 59.3 13 0.00028 41.9 4.7 76 416-514 206-281 (474)
247 cd01700 PolY_Pol_V_umuC umuC s 59.3 13 0.00027 40.6 4.8 49 458-510 177-225 (344)
248 PF08271 TF_Zn_Ribbon: TFIIB z 59.0 8.9 0.00019 28.9 2.5 22 417-438 2-24 (43)
249 COG3877 Uncharacterized protei 58.9 7.5 0.00016 35.2 2.3 29 413-449 4-32 (122)
250 PRK13844 recombination protein 58.8 7.3 0.00016 39.5 2.6 24 491-514 15-38 (200)
251 PF04994 TfoX_C: TfoX C-termin 58.1 7.3 0.00016 33.7 2.1 30 457-487 3-32 (81)
252 TIGR00615 recR recombination p 57.3 8.1 0.00018 39.0 2.6 23 491-513 11-33 (195)
253 cd00729 rubredoxin_SM Rubredox 56.9 5.9 0.00013 28.5 1.1 11 414-424 17-27 (34)
254 PRK00076 recR recombination pr 56.9 8.3 0.00018 39.0 2.6 23 491-513 11-33 (196)
255 PRK14133 DNA polymerase IV; Pr 56.1 15 0.00034 40.0 4.8 49 459-511 175-223 (347)
256 PF11731 Cdd1: Pathogenicity l 54.7 16 0.00034 32.6 3.7 32 526-557 15-47 (93)
257 COG2888 Predicted Zn-ribbon RN 54.3 4.9 0.00011 32.6 0.4 32 414-449 8-39 (61)
258 PF13240 zinc_ribbon_2: zinc-r 54.0 5.4 0.00012 26.2 0.5 18 417-438 1-18 (23)
259 PRK02406 DNA polymerase IV; Va 53.9 17 0.00037 39.6 4.7 48 458-509 169-216 (343)
260 PF06044 DRP: Dam-replacing fa 53.0 6.4 0.00014 40.8 1.1 28 416-447 32-63 (254)
261 PRK03980 flap endonuclease-1; 53.0 12 0.00026 40.3 3.2 25 527-551 193-217 (292)
262 PRK10445 endonuclease VIII; Pr 52.8 9.2 0.0002 40.4 2.3 22 417-438 237-260 (263)
263 COG0353 RecR Recombinational D 52.6 11 0.00023 38.0 2.5 23 491-513 12-34 (198)
264 PF04606 Ogr_Delta: Ogr/Delta- 52.5 15 0.00033 28.3 2.8 30 417-448 1-38 (47)
265 TIGR00593 pola DNA polymerase 52.2 11 0.00024 46.5 3.2 21 491-511 185-205 (887)
266 PRK00241 nudC NADH pyrophospha 50.7 10 0.00022 39.9 2.2 24 415-438 99-122 (256)
267 PRK01103 formamidopyrimidine/5 50.7 8.6 0.00019 40.8 1.7 25 417-445 247-273 (274)
268 PRK01810 DNA polymerase IV; Va 50.2 20 0.00044 40.0 4.6 49 459-511 181-229 (407)
269 cd03468 PolY_like DNA Polymera 50.2 22 0.00047 38.3 4.8 52 454-509 167-218 (335)
270 cd00424 PolY Y-family of DNA p 49.8 23 0.00051 38.6 4.9 49 459-511 175-224 (343)
271 COG1779 C4-type Zn-finger prot 49.6 11 0.00024 38.0 2.1 30 458-487 87-116 (201)
272 PRK03103 DNA polymerase IV; Re 49.6 22 0.00047 39.8 4.8 50 459-512 183-232 (409)
273 COG1592 Rubrerythrin [Energy p 49.1 8.6 0.00019 37.8 1.3 12 413-424 147-158 (166)
274 PRK03760 hypothetical protein; 49.0 20 0.00044 33.2 3.7 53 336-389 62-116 (117)
275 PRK11088 rrmA 23S rRNA methylt 48.6 6.7 0.00014 41.3 0.4 35 417-455 4-38 (272)
276 PRK02794 DNA polymerase IV; Pr 48.5 20 0.00044 40.3 4.3 48 459-510 211-258 (419)
277 COG4277 Predicted DNA-binding 48.2 21 0.00045 38.3 3.9 65 529-595 304-368 (404)
278 COG0258 Exo 5'-3' exonuclease 48.1 15 0.00033 39.6 3.1 25 527-551 202-226 (310)
279 KOG0442|consensus 47.8 20 0.00044 43.3 4.2 52 526-578 824-875 (892)
280 TIGR03674 fen_arch flap struct 47.7 16 0.00034 40.1 3.2 27 526-552 239-265 (338)
281 COG1656 Uncharacterized conser 47.1 9.9 0.00022 37.2 1.3 52 372-428 57-110 (165)
282 PRK05755 DNA polymerase I; Pro 46.9 15 0.00032 45.5 3.1 28 491-523 187-214 (880)
283 PTZ00035 Rad51 protein; Provis 46.7 37 0.0008 37.2 5.8 52 524-575 24-76 (337)
284 PF11798 IMS_HHH: IMS family H 46.6 15 0.00032 26.0 1.8 19 459-477 13-31 (32)
285 PRK14173 bifunctional 5,10-met 46.3 38 0.00081 36.4 5.6 58 622-685 15-86 (287)
286 cd00128 XPG Xeroderma pigmento 46.1 18 0.0004 39.0 3.4 24 527-550 227-250 (316)
287 KOG2906|consensus 46.1 15 0.00032 32.9 2.1 26 416-445 2-29 (105)
288 cd00080 HhH2_motif Helix-hairp 46.1 29 0.00064 29.4 3.9 28 458-487 23-50 (75)
289 PF12482 DUF3701: Phage integr 46.1 31 0.00067 31.0 4.2 47 466-513 22-72 (96)
290 PF10391 DNA_pol_lambd_f: Fing 45.8 21 0.00045 28.3 2.7 26 526-551 5-31 (52)
291 PF13549 ATP-grasp_5: ATP-gras 45.7 44 0.00095 34.5 5.9 48 247-305 10-57 (222)
292 PRK09482 flap endonuclease-lik 45.7 38 0.00082 35.8 5.5 48 457-513 182-229 (256)
293 COG3743 Uncharacterized conser 45.6 19 0.00041 34.0 2.8 40 458-498 68-107 (133)
294 PRK11827 hypothetical protein; 45.4 16 0.00035 29.9 2.1 22 417-438 10-31 (60)
295 PRK07945 hypothetical protein; 45.3 26 0.00056 38.3 4.4 49 492-541 50-98 (335)
296 PF02371 Transposase_20: Trans 45.0 34 0.00074 29.6 4.3 23 556-578 3-25 (87)
297 PTZ00205 DNA polymerase kappa; 44.8 24 0.00053 41.3 4.2 47 459-509 311-357 (571)
298 COG0258 Exo 5'-3' exonuclease 44.4 37 0.00081 36.6 5.4 50 456-515 197-247 (310)
299 PTZ00217 flap endonuclease-1; 43.8 20 0.00043 40.2 3.2 25 527-551 239-263 (393)
300 PRK14890 putative Zn-ribbon RN 43.8 8.1 0.00018 31.4 0.1 24 415-438 7-30 (59)
301 smart00611 SEC63 Domain of unk 43.7 35 0.00076 36.4 5.0 52 526-577 154-206 (312)
302 PTZ00446 vacuolar sorting prot 43.3 49 0.0011 33.4 5.6 52 7-58 125-176 (191)
303 PRK03609 umuC DNA polymerase V 42.9 33 0.00072 38.6 4.9 41 458-501 180-220 (422)
304 PF04919 DUF655: Protein of un 42.6 43 0.00094 33.4 5.0 53 488-540 113-166 (181)
305 cd00166 SAM Sterile alpha moti 42.4 61 0.0013 25.3 5.1 44 467-513 17-61 (63)
306 PF08792 A2L_zn_ribbon: A2L zi 42.2 22 0.00049 25.5 2.2 24 415-438 3-26 (33)
307 KOG2534|consensus 42.1 29 0.00064 37.5 4.0 52 520-571 53-113 (353)
308 PRK14810 formamidopyrimidine-D 41.6 17 0.00037 38.6 2.2 22 417-438 246-269 (272)
309 KOG3524|consensus 41.2 20 0.00044 42.3 2.8 69 606-677 118-186 (850)
310 PLN03187 meiotic recombination 40.9 50 0.0011 36.4 5.8 48 526-573 34-82 (344)
311 KOG2875|consensus 40.6 32 0.0007 36.5 3.9 39 535-573 191-236 (323)
312 PRK14811 formamidopyrimidine-D 40.3 19 0.0004 38.3 2.2 22 417-438 237-260 (269)
313 TIGR02238 recomb_DMC1 meiotic 40.3 49 0.0011 35.9 5.5 47 529-575 7-54 (313)
314 PRK13945 formamidopyrimidine-D 40.3 18 0.0004 38.5 2.2 23 416-438 255-279 (282)
315 PF02150 RNA_POL_M_15KD: RNA p 39.8 17 0.00037 26.3 1.3 26 416-445 2-28 (35)
316 PRK00432 30S ribosomal protein 39.8 17 0.00038 28.5 1.4 22 416-438 21-42 (50)
317 TIGR00577 fpg formamidopyrimid 39.7 18 0.0004 38.3 2.1 22 417-438 247-270 (272)
318 PF14579 HHH_6: Helix-hairpin- 39.6 59 0.0013 28.3 5.0 27 461-487 31-60 (90)
319 PRK12495 hypothetical protein; 39.5 15 0.00033 37.5 1.4 23 414-438 41-63 (226)
320 PRK14906 DNA-directed RNA poly 39.5 36 0.00078 43.7 4.8 53 460-513 1316-1368(1460)
321 TIGR00612 ispG_gcpE 1-hydroxy- 39.0 20 0.00043 39.1 2.2 14 380-393 223-236 (346)
322 PF14716 HHH_8: Helix-hairpin- 38.6 29 0.00062 28.7 2.7 21 492-512 48-68 (68)
323 PRK14976 5'-3' exonuclease; Pr 38.3 58 0.0013 34.8 5.6 46 459-513 193-238 (281)
324 PRK14182 bifunctional 5,10-met 38.1 49 0.0011 35.4 5.0 61 622-685 13-87 (282)
325 PTZ00111 DNA replication licen 38.0 24 0.00053 43.5 3.0 38 386-423 235-291 (915)
326 PRK01229 N-glycosylase/DNA lya 37.9 30 0.00065 35.4 3.2 20 554-573 117-137 (208)
327 PF01071 GARS_A: Phosphoribosy 37.7 63 0.0014 32.7 5.4 44 253-306 7-50 (194)
328 cd03586 PolY_Pol_IV_kappa DNA 37.5 46 0.00099 35.9 4.8 48 459-510 173-220 (334)
329 PRK00024 hypothetical protein; 37.5 52 0.0011 34.0 4.9 35 480-514 55-89 (224)
330 PF13005 zf-IS66: zinc-finger 37.0 18 0.00039 27.5 1.1 14 415-428 2-15 (47)
331 PF02371 Transposase_20: Trans 36.9 22 0.00048 30.8 1.8 40 526-567 5-44 (87)
332 PRK14185 bifunctional 5,10-met 36.7 44 0.00096 35.9 4.4 60 623-684 14-87 (293)
333 PF10772 DUF2597: Protein of u 36.7 1.1E+02 0.0025 28.8 6.4 54 153-223 19-74 (134)
334 PF13453 zf-TFIIB: Transcripti 36.6 32 0.00068 25.6 2.4 22 417-438 1-24 (41)
335 KOG2043|consensus 36.5 45 0.00097 41.3 4.9 67 610-679 660-726 (896)
336 PHA00626 hypothetical protein 36.5 27 0.00059 28.1 2.0 36 417-464 2-42 (59)
337 PF02889 Sec63: Sec63 Brl doma 36.5 67 0.0015 34.2 5.9 53 458-511 149-201 (314)
338 PF02643 DUF192: Uncharacteriz 36.2 60 0.0013 29.4 4.6 72 316-388 24-107 (108)
339 PF13719 zinc_ribbon_5: zinc-r 36.1 21 0.00044 26.1 1.2 23 416-438 3-30 (37)
340 PF11672 DUF3268: Protein of u 36.1 26 0.00055 31.8 2.1 14 415-428 2-15 (102)
341 COG1458 Predicted DNA-binding 36.0 62 0.0013 32.7 4.9 53 616-681 157-209 (221)
342 COG1491 Predicted RNA-binding 35.6 1.2E+02 0.0026 30.5 6.7 37 490-526 129-165 (202)
343 COG2835 Uncharacterized conser 35.4 30 0.00064 28.3 2.1 22 417-438 10-31 (60)
344 COG4068 Uncharacterized protei 35.4 13 0.00029 30.0 0.2 25 414-445 7-31 (64)
345 COG2093 DNA-directed RNA polym 35.1 23 0.00051 29.1 1.5 15 417-431 20-35 (64)
346 PRK09678 DNA-binding transcrip 34.5 36 0.00077 28.9 2.6 41 417-459 3-53 (72)
347 PRK14188 bifunctional 5,10-met 34.2 71 0.0015 34.5 5.5 61 623-685 15-89 (296)
348 PF11858 DUF3378: Domain of un 34.1 64 0.0014 28.0 4.2 57 97-162 8-64 (81)
349 PF14354 Lar_restr_allev: Rest 34.1 36 0.00077 27.3 2.5 25 417-445 5-37 (61)
350 COG0821 gcpE 1-hydroxy-2-methy 33.9 28 0.00061 37.9 2.3 73 380-473 225-312 (361)
351 PRK14166 bifunctional 5,10-met 33.9 63 0.0014 34.6 5.0 60 622-684 13-86 (282)
352 PF07282 OrfB_Zn_ribbon: Putat 33.9 28 0.00061 28.6 1.9 24 415-438 28-51 (69)
353 COG0266 Nei Formamidopyrimidin 33.8 27 0.00058 37.2 2.1 23 416-438 246-270 (273)
354 PF07191 zinc-ribbons_6: zinc- 33.8 34 0.00074 28.9 2.3 27 412-438 27-55 (70)
355 PRK14178 bifunctional 5,10-met 33.8 70 0.0015 34.2 5.3 58 622-685 12-83 (279)
356 TIGR02306 RNA_lig_DRB0094 RNA 33.7 70 0.0015 35.2 5.4 68 117-186 158-235 (341)
357 smart00475 53EXOc 5'-3' exonuc 33.5 58 0.0013 34.3 4.7 27 459-487 188-214 (259)
358 COG1439 Predicted nucleic acid 33.3 21 0.00046 35.5 1.2 12 416-427 154-165 (177)
359 PRK14189 bifunctional 5,10-met 33.2 74 0.0016 34.1 5.4 61 622-685 15-89 (285)
360 cd00350 rubredoxin_like Rubred 33.1 23 0.00049 25.2 1.0 11 414-424 16-26 (33)
361 PRK14193 bifunctional 5,10-met 33.1 65 0.0014 34.6 4.9 60 623-685 16-89 (284)
362 PF03811 Zn_Tnp_IS1: InsA N-te 33.0 38 0.00083 24.8 2.2 24 415-438 5-34 (36)
363 PF00763 THF_DHG_CYH: Tetrahyd 32.8 27 0.00058 32.2 1.8 58 623-683 13-84 (117)
364 smart00834 CxxC_CXXC_SSSS Puta 32.6 27 0.00058 25.5 1.4 14 414-427 25-38 (41)
365 TIGR01057 topA_arch DNA topois 32.6 29 0.00062 41.3 2.4 27 416-443 590-618 (618)
366 PF08394 Arc_trans_TRASH: Arch 32.5 33 0.00072 25.4 1.8 31 418-451 1-37 (37)
367 PRK14181 bifunctional 5,10-met 32.1 84 0.0018 33.8 5.6 58 622-685 12-83 (287)
368 PF11948 DUF3465: Protein of u 32.1 87 0.0019 29.7 5.0 65 283-388 30-95 (131)
369 PRK07945 hypothetical protein; 32.1 70 0.0015 35.0 5.1 46 527-575 53-100 (335)
370 PF09511 RNA_lig_T4_1: RNA lig 32.0 31 0.00066 35.3 2.2 61 82-147 13-74 (221)
371 smart00746 TRASH metallochaper 31.9 42 0.0009 22.4 2.3 27 418-447 1-35 (39)
372 PF07647 SAM_2: SAM domain (St 31.6 66 0.0014 25.8 3.7 48 464-514 17-65 (66)
373 PRK14171 bifunctional 5,10-met 31.5 82 0.0018 33.9 5.4 61 623-685 15-89 (288)
374 TIGR02098 MJ0042_CXXC MJ0042 f 31.3 29 0.00062 25.1 1.4 22 417-438 4-30 (38)
375 PRK14190 bifunctional 5,10-met 30.7 75 0.0016 34.1 4.9 61 622-685 15-89 (284)
376 PRK08402 replication factor A; 30.5 27 0.00058 38.7 1.5 24 414-438 212-235 (355)
377 PRK00421 murC UDP-N-acetylmura 30.5 1.8E+02 0.004 32.9 8.4 48 630-678 48-103 (461)
378 cd00008 53EXOc 5'-3' exonuclea 30.3 96 0.0021 32.2 5.6 27 459-487 185-211 (240)
379 COG1571 Predicted DNA-binding 30.1 25 0.00054 39.5 1.2 73 377-457 314-387 (421)
380 PRK01438 murD UDP-N-acetylmura 30.1 1.9E+02 0.0042 32.8 8.5 55 624-678 54-115 (480)
381 PLN02616 tetrahydrofolate dehy 30.1 69 0.0015 35.5 4.6 70 613-684 75-159 (364)
382 PF04014 Antitoxin-MazE: Antid 30.0 58 0.0012 24.8 2.9 22 371-392 13-34 (47)
383 PF00536 SAM_1: SAM domain (St 29.9 74 0.0016 25.4 3.8 45 467-514 18-63 (64)
384 COG0389 DinP Nucleotidyltransf 29.8 55 0.0012 36.0 3.9 49 457-509 176-224 (354)
385 PRK09521 exosome complex RNA-b 29.8 1.7E+02 0.0036 29.2 7.0 64 376-452 116-181 (189)
386 TIGR00375 conserved hypothetic 29.8 49 0.0011 36.9 3.5 71 417-510 261-356 (374)
387 PF03564 DUF1759: Protein of u 29.6 2E+02 0.0043 26.8 7.2 73 519-593 42-115 (145)
388 PF09851 SHOCT: Short C-termin 29.5 94 0.002 21.8 3.6 28 23-53 3-30 (31)
389 TIGR03037 anthran_nbaC 3-hydro 29.5 94 0.002 30.5 4.9 67 378-456 73-147 (159)
390 PRK14194 bifunctional 5,10-met 29.4 87 0.0019 33.9 5.2 60 622-684 16-89 (301)
391 PRK14184 bifunctional 5,10-met 29.2 83 0.0018 33.8 4.9 60 623-684 14-87 (286)
392 PF09723 Zn-ribbon_8: Zinc rib 29.1 38 0.00083 25.4 1.7 14 414-427 25-39 (42)
393 PRK12496 hypothetical protein; 28.8 23 0.0005 34.8 0.7 16 181-196 19-34 (164)
394 PRK01229 N-glycosylase/DNA lya 28.7 2E+02 0.0044 29.4 7.5 55 487-543 68-139 (208)
395 PF14690 zf-ISL3: zinc-finger 28.7 48 0.001 24.9 2.3 14 415-428 2-15 (47)
396 cd04482 RPA2_OBF_like RPA2_OBF 28.7 73 0.0016 28.0 3.7 12 377-388 46-57 (91)
397 PRK10308 3-methyl-adenine DNA 28.6 63 0.0014 34.6 4.0 21 554-574 206-226 (283)
398 PRK14168 bifunctional 5,10-met 28.6 81 0.0018 34.1 4.8 61 623-685 16-90 (297)
399 PF04423 Rad50_zn_hook: Rad50 28.5 21 0.00047 28.1 0.3 10 417-426 22-31 (54)
400 PF00122 E1-E2_ATPase: E1-E2 A 28.3 32 0.00068 34.8 1.6 28 374-402 47-74 (230)
401 COG2075 RPL24A Ribosomal prote 28.3 26 0.00055 29.2 0.7 23 416-438 4-34 (66)
402 COG0551 TopA Zn-finger domain 28.3 49 0.0011 31.3 2.8 30 415-445 17-48 (140)
403 COG2104 ThiS Sulfur transfer p 27.9 1.1E+02 0.0024 25.7 4.4 25 371-396 21-45 (68)
404 PLN02897 tetrahydrofolate dehy 27.8 87 0.0019 34.5 4.9 73 611-685 56-143 (345)
405 PF08605 Rad9_Rad53_bind: Fung 27.4 22 0.00047 33.8 0.2 27 371-402 52-78 (131)
406 PRK14169 bifunctional 5,10-met 27.4 98 0.0021 33.2 5.1 60 623-685 14-87 (282)
407 TIGR01206 lysW lysine biosynth 27.3 45 0.00098 26.7 1.9 11 417-427 4-14 (54)
408 TIGR00615 recR recombination p 27.2 91 0.002 31.6 4.5 19 603-621 95-113 (195)
409 COG2816 NPY1 NTP pyrophosphohy 27.0 38 0.00083 36.1 1.9 23 416-438 112-134 (279)
410 PRK00076 recR recombination pr 27.0 87 0.0019 31.8 4.3 18 603-620 95-112 (196)
411 PRK14175 bifunctional 5,10-met 26.8 93 0.002 33.4 4.8 61 622-685 15-89 (286)
412 PRK14191 bifunctional 5,10-met 26.4 1E+02 0.0022 33.2 4.9 61 623-685 14-88 (285)
413 PRK00366 ispG 4-hydroxy-3-meth 26.0 38 0.00083 37.3 1.7 14 380-393 232-245 (360)
414 COG1885 Uncharacterized protei 26.0 32 0.0007 31.1 1.0 11 416-426 50-60 (115)
415 PRK14177 bifunctional 5,10-met 25.9 1.1E+02 0.0025 32.8 5.2 62 622-685 15-90 (284)
416 PRK13844 recombination protein 25.7 1E+02 0.0022 31.5 4.5 18 603-620 99-116 (200)
417 PF07191 zinc-ribbons_6: zinc- 25.7 60 0.0013 27.5 2.4 20 417-438 3-22 (70)
418 PF14579 HHH_6: Helix-hairpin- 25.6 77 0.0017 27.6 3.3 54 493-549 29-82 (90)
419 PF05191 ADK_lid: Adenylate ki 25.6 42 0.00092 24.5 1.4 17 413-429 19-35 (36)
420 PF08734 GYD: GYD domain; Int 25.5 1.3E+02 0.0028 26.5 4.7 56 623-678 22-90 (91)
421 COG0353 RecR Recombinational D 25.5 92 0.002 31.6 4.2 20 603-622 96-115 (198)
422 PRK14186 bifunctional 5,10-met 25.4 1E+02 0.0022 33.4 4.8 61 623-685 15-89 (297)
423 PF14490 HHH_4: Helix-hairpin- 25.3 47 0.001 29.3 1.9 52 521-576 13-67 (94)
424 COG1241 MCM2 Predicted ATPase 25.3 81 0.0017 37.9 4.4 40 363-402 86-130 (682)
425 PF14490 HHH_4: Helix-hairpin- 25.2 51 0.0011 29.0 2.1 49 462-511 17-66 (94)
426 COG4469 CoiA Competence protei 25.1 35 0.00076 37.1 1.3 16 415-430 25-40 (342)
427 PF01780 Ribosomal_L37ae: Ribo 24.9 41 0.00089 29.8 1.4 24 415-438 35-58 (90)
428 PF10571 UPF0547: Uncharacteri 24.8 36 0.00078 23.1 0.8 9 417-425 2-10 (26)
429 PF13717 zinc_ribbon_4: zinc-r 24.8 43 0.00094 24.3 1.3 22 417-438 4-30 (36)
430 TIGR00686 phnA alkylphosphonat 24.7 55 0.0012 30.0 2.2 21 417-438 4-24 (109)
431 PRK07726 DNA topoisomerase III 24.6 44 0.00095 40.1 2.1 27 416-444 611-639 (658)
432 PLN03186 DNA repair protein RA 24.5 1.3E+02 0.0028 33.1 5.5 51 525-575 30-81 (342)
433 KOG2875|consensus 24.4 1.2E+02 0.0025 32.5 4.8 88 443-540 131-235 (323)
434 COG1326 Uncharacterized archae 24.1 38 0.00082 34.1 1.1 22 417-438 8-35 (201)
435 PRK00564 hypA hydrogenase nick 24.0 52 0.0011 30.4 2.0 45 330-389 22-67 (117)
436 PLN02516 methylenetetrahydrofo 24.0 2.7E+02 0.0058 30.2 7.6 127 497-651 78-217 (299)
437 PRK14172 bifunctional 5,10-met 24.0 1.2E+02 0.0026 32.5 4.9 61 622-684 14-88 (278)
438 PF14205 Cys_rich_KTR: Cystein 23.5 49 0.0011 26.6 1.4 9 417-425 6-14 (55)
439 PRK09612 rpl2p 50S ribosomal p 23.4 68 0.0015 33.5 2.9 94 329-450 38-132 (238)
440 PF01194 RNA_pol_N: RNA polyme 23.3 43 0.00093 27.5 1.1 13 414-426 3-15 (60)
441 TIGR00595 priA primosomal prot 23.1 83 0.0018 36.5 3.9 57 415-477 222-281 (505)
442 PRK14167 bifunctional 5,10-met 23.0 1.3E+02 0.0027 32.6 5.0 61 622-685 14-88 (297)
443 PF07820 TraC: TraC-like prote 22.7 2.6E+02 0.0057 24.9 5.9 49 10-58 3-61 (92)
444 TIGR00373 conserved hypothetic 22.7 39 0.00086 32.9 1.0 13 417-429 130-142 (158)
445 PRK03352 DNA polymerase IV; Va 22.6 1.3E+02 0.0028 32.8 5.1 63 498-560 142-215 (346)
446 TIGR02239 recomb_RAD51 DNA rep 22.4 1.2E+02 0.0026 33.0 4.7 47 529-575 7-54 (316)
447 PRK14724 DNA topoisomerase III 22.3 84 0.0018 39.5 4.0 52 417-480 757-816 (987)
448 TIGR03252 uncharacterized HhH- 22.3 83 0.0018 31.4 3.1 23 491-513 115-137 (177)
449 TIGR01384 TFS_arch transcripti 22.1 53 0.0011 29.3 1.6 25 417-447 2-26 (104)
450 PRK04690 murD UDP-N-acetylmura 22.1 3.2E+02 0.0069 31.2 8.3 34 644-677 69-106 (468)
451 PRK10220 hypothetical protein; 22.0 66 0.0014 29.5 2.2 21 417-438 5-25 (111)
452 PRK14176 bifunctional 5,10-met 22.0 1.4E+02 0.0031 32.1 5.1 70 614-685 11-95 (287)
453 COG2824 PhnA Uncharacterized Z 21.8 66 0.0014 29.4 2.1 21 417-438 5-25 (112)
454 PF12760 Zn_Tnp_IS1595: Transp 21.8 62 0.0013 24.6 1.7 22 417-438 20-42 (46)
455 TIGR03595 Obg_CgtA_exten Obg f 21.7 78 0.0017 26.5 2.5 17 372-388 47-63 (69)
456 PRK14714 DNA polymerase II lar 21.7 3.4E+02 0.0073 35.0 8.7 38 247-284 474-514 (1337)
457 PRK03858 DNA polymerase IV; Va 21.6 1.3E+02 0.0027 33.5 4.9 28 354-385 29-56 (396)
458 TIGR00100 hypA hydrogenase nic 21.6 58 0.0013 30.0 1.8 44 331-389 23-66 (115)
459 PF04551 GcpE: GcpE protein; 21.5 42 0.00091 37.0 1.0 38 247-284 160-197 (359)
460 PF04216 FdhE: Protein involve 21.5 54 0.0012 35.0 1.9 23 415-437 172-201 (290)
461 PF11372 DUF3173: Domain of un 21.4 81 0.0018 25.8 2.4 23 488-511 4-26 (59)
462 PRK06266 transcription initiat 21.2 46 0.00099 33.2 1.1 12 417-428 138-149 (178)
463 PRK14180 bifunctional 5,10-met 21.2 1.5E+02 0.0032 31.8 5.0 61 623-685 14-88 (282)
464 KOG2041|consensus 21.1 1.5E+02 0.0034 35.5 5.4 53 103-157 104-156 (1189)
465 COG0773 MurC UDP-N-acetylmuram 21.0 2.1E+02 0.0046 32.8 6.4 57 622-678 40-103 (459)
466 PF14164 YqzH: YqzH-like prote 21.0 2.7E+02 0.0059 23.2 5.3 38 23-60 8-46 (64)
467 PRK14183 bifunctional 5,10-met 20.9 1.4E+02 0.0031 31.9 4.8 61 623-685 14-88 (281)
468 PF04475 DUF555: Protein of un 20.9 45 0.00097 30.0 0.8 11 416-426 48-58 (102)
469 COG2003 RadC DNA repair protei 20.8 1E+02 0.0022 31.9 3.6 62 447-515 29-90 (224)
470 TIGR03826 YvyF flagellar opero 20.7 62 0.0013 31.0 1.8 92 416-514 4-111 (137)
471 COG0190 FolD 5,10-methylene-te 20.6 1.7E+02 0.0037 31.4 5.3 62 622-685 12-87 (283)
472 PF09237 GAGA: GAGA factor; I 20.6 38 0.00081 26.9 0.3 29 414-456 23-51 (54)
473 PTZ00255 60S ribosomal protein 20.5 79 0.0017 28.1 2.3 24 415-438 36-59 (90)
474 COG3024 Uncharacterized protei 20.5 48 0.001 27.5 0.9 23 416-438 8-31 (65)
475 KOG2093|consensus 20.3 88 0.0019 38.3 3.3 63 453-518 545-607 (1016)
476 PRK05776 DNA topoisomerase I; 20.3 67 0.0015 38.6 2.5 29 415-444 596-632 (670)
477 TIGR02605 CxxC_CxxC_SSSS putat 20.2 65 0.0014 24.9 1.6 9 415-423 26-34 (52)
478 PHA02325 hypothetical protein 20.2 91 0.002 25.8 2.4 30 415-447 3-32 (72)
479 PF09538 FYDLN_acid: Protein o 20.2 49 0.0011 30.3 1.0 12 415-426 26-37 (108)
480 COG3357 Predicted transcriptio 20.1 49 0.0011 29.3 0.9 16 411-426 72-87 (97)
481 PRK07219 DNA topoisomerase I; 20.0 62 0.0013 39.9 2.1 76 416-495 734-813 (822)
No 1
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.7e-202 Score=1669.97 Aligned_cols=665 Identities=45% Similarity=0.724 Sum_probs=643.3
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccc
Q psy11421 10 NFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKM 89 (687)
Q Consensus 10 ~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pM 89 (687)
++.+++++|.+|+++|++|+++||++|+|.|||++||+|+++|++||.+||++.++|||||+||+.+..+|.||+|.+||
T Consensus 3 ~~~~~~~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~~lE~~~Pel~~~dSPtqrVG~~~~~~F~kv~H~~pM 82 (667)
T COG0272 3 SMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELITPDSPTQRVGAAPLNAFKKVRHPVPM 82 (667)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhccCCCCCChHHHHHHHHHHHHHHHhCCCcCCCCCCccccCccchhccccccCCCcc
Confidence 46777899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCccc
Q psy11421 90 MSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVL 169 (687)
Q Consensus 90 lSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l 169 (687)
|||+|+||.+||.+|++|+.+.++. +..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|
T Consensus 83 lSL~naf~~~el~~f~~ri~~~~~~--~~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~~IP~~l 160 (667)
T COG0272 83 LSLDNAFDEEELRAFDRRIRKFLGD--SVEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRSIPLKL 160 (667)
T ss_pred cchhhcCCHHHHHHHHHHHHHhcCC--CcceEEEeecceEEEEEEEECCEEEEeeccCCCccccchhhhhhhHhhhhhhc
Confidence 9999999999999999999998873 67899999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCH
Q psy11421 170 NIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSH 249 (687)
Q Consensus 170 ~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~ 249 (687)
++ +|..+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|.||+|+|+...+...+.||
T Consensus 161 ~~--~p~~lEVRGEvfm~k~~F~~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~ita~R~L~~f~y~~~~~~~~~~~~t~ 238 (667)
T COG0272 161 PG--APAVLEVRGEVFMPKEDFEALNEEREEEGEKPFANPRNAAAGSLRQLDPKITAKRKLGFFIYAVGDGEEGLLADTQ 238 (667)
T ss_pred cC--CCceEEEEeEEEEeHHHHHHHHHHHHHhCCCCcCChhhhhhhhhhccCHHHHhcCCceEEEEeCCccCCCCCccCH
Confidence 85 6899999999999999999999999999999999999999999999999999999999999999876542336899
Q ss_pred HHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCce
Q psy11421 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE 329 (687)
Q Consensus 250 ~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~ 329 (687)
++.|++|++|||+|+++.+.|.|.+|+.+||++|.+.|+.|||+|||+||||||+++|+.||+|+|+||||||||||+++
T Consensus 239 ~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyKFpa~e 318 (667)
T COG0272 239 SERLAFLKAWGFPVNPYTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYKFPAEE 318 (667)
T ss_pred HHHHHHHHHcCCCCCcHhhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEeccHHHHHHhCCccCCCceeeeecCCchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11421 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (687)
Q Consensus 330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (687)
+.|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+|+||+|||+|.|.|||||||+|++|+.+.|+++.
T Consensus 319 ~~T~l~dI~~qVGRTG~iTPvA~L~PV~laG~~VsrATLHN~d~I~rkdIrIGDtV~V~kAGdVIP~V~~Vv~e~R~~~~ 398 (667)
T COG0272 319 AVTKLLDIEVQVGRTGAITPVARLEPVELAGVTVSRATLHNVDEIKRKDIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNE 398 (667)
T ss_pred eeeEEEEEEEecCCceeeeeeEEEEeEEECCEEEEEeecCCHHHHHhcCCCCCCEEEEEecCCCCcceeeeecccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC
Q psy11421 410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489 (687)
Q Consensus 410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~ 489 (687)
.+|.+|++||+|||+|++.++++.+||+|+.. ||+|.+++|.||+||+||||+|||+|+|++|+++++|++++|||+|+
T Consensus 399 ~~~~~P~~CP~C~s~l~r~~~e~~~rC~n~~~-C~aq~~e~l~hfvSr~AmdI~GLG~k~i~~L~e~~lI~~~~Dly~Lt 477 (667)
T COG0272 399 KPIPFPTHCPVCGSELVREEGEVVIRCTNGLN-CPAQLKERLIHFVSRNALDIDGLGEKIIEQLFEKGLIKDIADLYTLT 477 (667)
T ss_pred CCCCCCCCCCCCCCeeEeccCceeEecCCCCC-ChHHHhhheeeEecCCccCCCCcCHHHHHHHHHcCccCCHHHHHhCC
Confidence 99999999999999999988999999999767 99999999999999999999999999999999999999999999999
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK 569 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~ 569 (687)
.++|+.++|||+|+++||+++|++||+.+|+|||+||||||||+++|+.|+.+|+|+++|..|+.++|..++|||+++|.
T Consensus 478 ~~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~ 557 (667)
T COG0272 478 EEDLLSLEGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVAR 557 (667)
T ss_pred HHHHhhccchhhhHHHHHHHHHHHhccCCHHHHHHHcCCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEE
Q psy11421 570 AFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLV 649 (687)
Q Consensus 570 sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV 649 (687)
+|.+||+++.|++++++|.+.|+.+..........++|.||+|||||+|+.|+|++++++++++||+|++||||||||||
T Consensus 558 si~~ff~~~~~~~li~~L~~~g~~~~~~~~~~~~~~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vv 637 (667)
T COG0272 558 SIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVV 637 (667)
T ss_pred HHHHHHcCHHHHHHHHHHHHcCCCccccccccccccccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEeceecccccEEE
Confidence 99999999999999999999998876543222222789999999999999999999999999999999999999999999
Q ss_pred EcCCCCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11421 650 KGQKPGKKLEKAIKLNIKILDEKNFVKIVK 679 (687)
Q Consensus 650 ~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~ 679 (687)
+|+++|||++||++|||+||+|++|+++|+
T Consensus 638 aG~~aGSKl~kA~eLgv~i~~E~~~~~ll~ 667 (667)
T COG0272 638 AGENAGSKLAKAQELGVKIIDEEEFLALLG 667 (667)
T ss_pred EcCCCChHHHHHHHcCCeEecHHHHHHhhC
Confidence 999999999999999999999999999874
No 2
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=100.00 E-value=6.7e-187 Score=1595.94 Aligned_cols=662 Identities=45% Similarity=0.721 Sum_probs=633.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecccccc
Q psy11421 11 FSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMM 90 (687)
Q Consensus 11 ~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMl 90 (687)
++.++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+.+...|.||+|++|||
T Consensus 2 ~~~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~~~~~~Spt~~VG~~~~~~f~kv~H~~pMl 81 (665)
T PRK07956 2 MEEAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRVGGAPLDGFEKVRHLVPML 81 (665)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCccccCccccccCcceeCCCcCc
Confidence 45667899999999999999999999999999999999999999999999999999999999999888999999999999
Q ss_pred CCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccc
Q psy11421 91 SLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLN 170 (687)
Q Consensus 91 SL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~ 170 (687)
||+|+|+.+||.+|++|+.+.++. .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+
T Consensus 82 SL~k~~~~~el~~w~~r~~~~~~~-~~~~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~IP~~l~ 160 (665)
T PRK07956 82 SLDNAFSEEELRAFDKRVRKRLPD-PPLTYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLH 160 (665)
T ss_pred CccccCCHHHHHHHHHHHHHhcCC-CCcceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccCChhhc
Confidence 999999999999999999887752 2357999999999999999999999999999999999999999999999999996
Q ss_pred cCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEeccccc-CCCCCCCH
Q psy11421 171 IKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELR-GMNMPSSH 249 (687)
Q Consensus 171 ~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~-~~~~~~~~ 249 (687)
. ..|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|+..+ +.. +.+|
T Consensus 161 ~-~~p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~~~~~~-~~t~ 238 (665)
T PRK07956 161 G-NEPERLEVRGEVFMPKADFEALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEGGEL-PDSQ 238 (665)
T ss_pred c-cCCCeEEEEEEEEEEHHHHHHHHHHHHhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccccCCCC-CCCH
Confidence 3 258899999999999999999999999999999999999999999999999999999999999997433 222 4799
Q ss_pred HHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCce
Q psy11421 250 SELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE 329 (687)
Q Consensus 250 ~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~ 329 (687)
++.|++|++|||+++++.+.+.+.+++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++
T Consensus 239 ~e~l~~L~~~GF~v~~~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrWaiA~Kf~~~~ 318 (665)
T PRK07956 239 SEALEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKAPRWAIAYKFPAEE 318 (665)
T ss_pred HHHHHHHHHCCCCcCCceEeeCCHHHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHHhcCccCCCCCceeEecCCCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11421 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (687)
Q Consensus 330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (687)
++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++.
T Consensus 319 ~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrAtLhN~~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~ 398 (665)
T PRK07956 319 ATTKLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDE 398 (665)
T ss_pred eEEEEEEEEEecCCCceeeeEEEEEeEEECCEEEEEeecCCHHHHHHcCCCCCCEEEEEECCCccceeeeeecccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred ccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC
Q psy11421 410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489 (687)
Q Consensus 410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~ 489 (687)
.+|.+|++||+||++|++.++++.+||+|... ||+|++++|.||+||+||||+||||++|++||++|+|++++|||+|+
T Consensus 399 ~~~~~P~~CP~Cgs~l~~~~~~~~~~C~n~~~-C~aq~~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~ 477 (665)
T PRK07956 399 REIVMPTHCPVCGSELVRVEGEAVLRCTNGLS-CPAQLKERLIHFVSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLT 477 (665)
T ss_pred ccCcCCCCCCCCCCEeEecCCCeEEECCCCCC-CHHHHHHHHHHhhcccccCCCCcCHHHHHHHHHcCCCCCHHHHHhcC
Confidence 89999999999999999888899999999756 99999999999999999999999999999999999999999999999
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVK 569 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~ 569 (687)
.++|..++|||+|+++||+++|+.+|+.+|+|||+|||||+||+++|++|+++|++++++..|+.++|.+++|||+++|+
T Consensus 478 ~~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~ 557 (665)
T PRK07956 478 AEDLLGLEGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQ 557 (665)
T ss_pred HHHHhcCcCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEE
Q psy11421 570 AFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLV 649 (687)
Q Consensus 570 sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV 649 (687)
+|++||+++.|++++++|.+.|+++.... .+.+|+|++|||||+|+.|+|++++++|+++||+|++|||++|||||
T Consensus 558 sI~~ff~~~~~~~~i~~L~~~gv~~~~~~----~~~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv 633 (665)
T PRK07956 558 SIVEFFAVEENRELIDELLEAGVNMEYKG----EEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVV 633 (665)
T ss_pred HHHHHHhhhhHHHHHHHHHHcCCCccccc----cCCCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEE
Confidence 99999999999999999999998875421 23469999999999999899999999999999999999999999999
Q ss_pred EcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11421 650 KGQKPGKKLEKAIKLNIKILDEKNFVKIVKG 680 (687)
Q Consensus 650 ~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~ 680 (687)
+|+++|+|++||+++||+||+|++|++||++
T Consensus 634 ~G~~~gsK~~kA~~lgI~ii~E~~f~~~l~~ 664 (665)
T PRK07956 634 AGEAAGSKLAKAQELGIEVLDEEEFLRLLGE 664 (665)
T ss_pred ECCCCChHHHHHHHcCCeEEcHHHHHHHHhc
Confidence 9999999999999999999999999999964
No 3
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=100.00 E-value=9.2e-186 Score=1578.99 Aligned_cols=651 Identities=31% Similarity=0.496 Sum_probs=613.1
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCC
Q psy11421 14 LSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLD 93 (687)
Q Consensus 14 ~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~ 93 (687)
++++|++|+++|++||++||++++|+|||++||+|+++|++||++||++.+++|||++||+.+...|.||+|++|||||+
T Consensus 5 ~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~~lE~~~p~~~~~~Spt~~Vg~~~~~~f~kv~H~~pMlSL~ 84 (669)
T PRK14350 5 IQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPTLKFGSDLLNDFKEVEHSFPILSLD 84 (669)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCCccCCccccccCCceecCCcccccc
Confidence 46789999999999999999999999999999999999999999999999999999999999888999999999999999
Q ss_pred CCCChHHHHHHHHHHHHhhcc-CCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccC
Q psy11421 94 NGFSDEDVIIFNKRITNELKL-TKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIK 172 (687)
Q Consensus 94 k~~~~~el~~~~~~~~~~l~~-~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~ 172 (687)
|+|+.+||.+|++|+.+.+.. ..+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.
T Consensus 85 k~~~~~el~~~~~r~~~~~~~~~~~~~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~IP~~l~~- 163 (669)
T PRK14350 85 KVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFIDE- 163 (669)
T ss_pred ccCCHHHHHHHHHHHHHhhccCCCCceEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcccchhcCC-
Confidence 999999999999999742211 112579999999999999999999999999999999999999999999999999963
Q ss_pred CCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHH
Q psy11421 173 YPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSEL 252 (687)
Q Consensus 173 ~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~ 252 (687)
|..+|||||+||++++|+++|+++ .++|+||||+|||+|||+||.+++.|+|+||+|+|+..+. . ..+|++.
T Consensus 164 --~~~levRGEv~m~~~~F~~lN~~~----~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~-~-~~t~~e~ 235 (669)
T PRK14350 164 --KVELVLRGEIYITKENFLKINKTL----EKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL-E-LKTNHDA 235 (669)
T ss_pred --CceEEEEEEEEeeHHHHHHHHHhh----hccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC-C-CCCHHHH
Confidence 578999999999999999999876 3689999999999999999999999999999999964332 2 3699999
Q ss_pred HHHHHhcCCCCCCCceEeCC---HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCce
Q psy11421 253 LNWYQKIGLSICGEYSVLSG---VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKE 329 (687)
Q Consensus 253 l~~L~~~Gf~~~~~~~~~~~---~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~ 329 (687)
|++|++|||+++++...+.+ .+++++|+++|.+.|+.+||+|||+|||+|++.+|+.||+|+|+||||||||||+++
T Consensus 236 l~~L~~~GF~v~~~~~~~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~~ 315 (669)
T PRK14350 236 FDKLKKFGFKVNPFCRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESLS 315 (669)
T ss_pred HHHHHHCCCCCCcceEEEcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCce
Confidence 99999999999998888876 999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11421 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (687)
Q Consensus 330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (687)
++|+|++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++.
T Consensus 316 ~~T~l~~I~~qVGRTG~iTPVA~l~PV~l~G~tVsrATLhN~~~I~~~di~iGD~V~V~raGdVIP~I~~v~~~~r~~~- 394 (669)
T PRK14350 316 GFSKVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELVIEKLSVGF- 394 (669)
T ss_pred eEEEEEEEEEecCCceeeeEEEEEEeEEECCEEEEEeccCCHHHHHHcCCCCCCEEEEEecCCCCCceeeecccccCCC-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999888754
Q ss_pred ccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC
Q psy11421 410 KIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN 489 (687)
Q Consensus 410 ~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~ 489 (687)
|.+|++||+||++|++ +++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++|+++|+|++++|||+|+
T Consensus 395 --~~~P~~CP~C~s~l~~--~~~~~~C~n~-~-C~aq~~~~i~hf~sr~aldI~GlG~~~i~~L~~~G~i~~~~Dly~L~ 468 (669)
T PRK14350 395 --FKIPDNCPSCKTALIK--EGAHLFCVNN-H-CPSVIVERIKYFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLYTFN 468 (669)
T ss_pred --CCCCCCCCCCCCEeee--CCEEEEECCC-C-CHHHHHhhhheeccCCcccccCcCHHHHHHHHHcCCcCCHHHHhhCC
Confidence 8899999999999986 4699999996 6 99999999999999999999999999999999999999999999999
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHH-hhcCChHHHHh------cCHHHHhcCCC
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELA-NYFKNLECMFK------ATEEQLLNIPK 562 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La-~~f~sld~l~~------As~eeL~~I~G 562 (687)
.++|++++|||+|+|+||+++|++||+.||+|||+|||||+||+.+|+.|+ ++|++++++.+ ++.++|.+++|
T Consensus 469 ~~~l~~l~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~g 548 (669)
T PRK14350 469 FDRLINLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIKG 548 (669)
T ss_pred HHHHhhccCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCCC
Confidence 999999999999999999999999999999999999999999999999999 89999999986 68899999999
Q ss_pred CCHHHHHHHHHHHcchhHHHHHHHHHhcCcccccCCC-CCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccc
Q psy11421 563 IGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPN-TKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFI 641 (687)
Q Consensus 563 IG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~-~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sV 641 (687)
||+++|++|.+||+++.|.++|++|.+.|+++...+. ....+++|+||+|||||+|+.++|++++++|+++||+|++||
T Consensus 549 iG~~~a~si~~ff~~~~~~~~i~~l~~~gv~~~~~~~~~~~~~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ssV 628 (669)
T PRK14350 549 IGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSINIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCV 628 (669)
T ss_pred ccHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccccccccccCCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEeccc
Confidence 9999999999999999999999999999987653211 112346899999999999999999999999999999999999
Q ss_pred cccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11421 642 SKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKG 680 (687)
Q Consensus 642 sk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~ 680 (687)
|++|||||+|+++|+|++||++|||+||+|++|++||+.
T Consensus 629 Skktd~LV~G~~aGsKl~KA~~LGI~Ii~e~~f~~~l~~ 667 (669)
T PRK14350 629 TKYLDFLLVGEKAGLKLKKANNLGIKIMSLFDIKSYVDL 667 (669)
T ss_pred cCCCcEEEECCCCCchHHHHHHcCCEEecHHHHHHHhcC
Confidence 999999999999999999999999999999999999975
No 4
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=100.00 E-value=1.1e-184 Score=1576.63 Aligned_cols=649 Identities=45% Similarity=0.738 Sum_probs=620.3
Q ss_pred HHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCCChHH
Q psy11421 21 LKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGFSDED 100 (687)
Q Consensus 21 L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~~~~e 100 (687)
|+++|++||++||++|+|+|||++||+|+++|++||++||++.+++|||++||+.+.+.|.||+|++|||||+|+|+.+|
T Consensus 1 L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~~~~~~Spt~~VG~~~~~~f~kv~H~~pMlSL~k~~~~~e 80 (652)
T TIGR00575 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVGAAPLSRFPKVRHSTPMLSLDNAFDEDE 80 (652)
T ss_pred CHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCccccCCCCCccccCcccccccCccccCCcCcCccccCCHHH
Confidence 67899999999999999999999999999999999999999999999999999999889999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEE
Q psy11421 101 VIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEV 180 (687)
Q Consensus 101 l~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~ev 180 (687)
|.+|++|+.+.++ .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|++.+.|..+||
T Consensus 81 l~~~~~r~~~~~~--~~~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDvT~nv~~I~~iP~~i~~~~~p~~lev 158 (652)
T TIGR00575 81 LAAFIKRIRRQLG--LKVEYVVEPKIDGLSVSLTYENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEV 158 (652)
T ss_pred HHHHHHHHHHhcC--CCceEEEEEeccceEEEEEEECCEEEEEEecCCCccchhHhhhhhhhcccchhhcCCCCCceEEE
Confidence 9999999988765 13579999999999999999999999999999999999999999999999999974235889999
Q ss_pred EEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcC
Q psy11421 181 RCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIG 260 (687)
Q Consensus 181 RGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~G 260 (687)
|||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++.. +.+|++.|++|++||
T Consensus 159 RGEv~m~~~~F~~~N~~~~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~~~~~~-~~t~~e~l~~L~~~G 237 (652)
T TIGR00575 159 RGEVFMPKEDFEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGLELP-DATQYEALAWLKKWG 237 (652)
T ss_pred EEEEEEEHHHHHHHHHHHHHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEeccccCCCC-CCCHHHHHHHHHHCC
Confidence 9999999999999999999999999999999999999999999999999999999996433322 379999999999999
Q ss_pred CCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEe
Q psy11421 261 LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQ 340 (687)
Q Consensus 261 f~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~q 340 (687)
|+++++...+.+++++++|+++|.+.|+.+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|++|+||
T Consensus 238 F~v~~~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrwaiA~Kf~~~~~~T~l~~I~~q 317 (652)
T TIGR00575 238 FPVSPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAEEAQTKLLDVVVQ 317 (652)
T ss_pred CCCCCCeEeeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEecCHHHHHHhCccCCCCCceEEEcCCCceeeEEEEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccCCCCCCC
Q psy11421 341 IGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPI 420 (687)
Q Consensus 341 vGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~ 420 (687)
|||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|+++..+|.+|++||+
T Consensus 318 VGRTG~iTPvA~lePV~l~G~~VsrAtLhN~~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~P~~CP~ 397 (652)
T TIGR00575 318 VGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEELDIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPS 397 (652)
T ss_pred cCCCceeeeEEEEeeEEECCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCcCceeeeeccccCCCCCCCCCCCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999989888889999999999
Q ss_pred CCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCcc
Q psy11421 421 CNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS 500 (687)
Q Consensus 421 C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG 500 (687)
||++|++.++++.+||+|+ . ||+|++++|.||+||+||||+|||+++|++||++|+|++++|||+|+.++|.+|+|||
T Consensus 398 C~s~l~~~~~~~~~~C~n~-~-C~aq~~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG 475 (652)
T TIGR00575 398 CGSPLVKIEEEAVIRCPNL-N-CPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFG 475 (652)
T ss_pred CCCEeEecCCcEEEEECCC-C-CHHHHHHHhHHhhcCCccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCcc
Confidence 9999999888899999995 6 9999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhH
Q psy11421 501 NKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLH 580 (687)
Q Consensus 501 ~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n 580 (687)
+|+|+||+++|+.+|+.+|.|||++|||||||+++|+.|+++|+++++|..|+.++|.+++|||+++|++|.+||+++.|
T Consensus 476 ~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~~ 555 (652)
T TIGR00575 476 EKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNN 555 (652)
T ss_pred HHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCcccccCCC-C--CCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCcc
Q psy11421 581 RLLISQLRDVGIYWLNNPN-T--KGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKK 657 (687)
Q Consensus 581 ~~~i~~L~~~Gv~~~~~~~-~--~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~K 657 (687)
+++|++|.+.|+++..... . ...+++|+|++|||||+|..++|++++++|+++||+|++|||++|||||+|+++|+|
T Consensus 556 ~~~i~~L~~~gv~~~~~~~~~~~~~~~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsK 635 (652)
T TIGR00575 556 RQLIKKLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSK 635 (652)
T ss_pred HHHHHHHHHcCCCcccccccccccccCCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCChH
Confidence 9999999999988653211 1 112468999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCeEEeHHHH
Q psy11421 658 LEKAIKLNIKILDEKNF 674 (687)
Q Consensus 658 l~kA~~lgI~Ii~E~~f 674 (687)
++||++|||+||+|++|
T Consensus 636 l~kA~~lgi~ii~E~~~ 652 (652)
T TIGR00575 636 LAKAQELGIPIINEEEL 652 (652)
T ss_pred HHHHHHcCCcEechhhC
Confidence 99999999999999987
No 5
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=100.00 E-value=1.9e-183 Score=1566.28 Aligned_cols=659 Identities=35% Similarity=0.593 Sum_probs=627.3
Q ss_pred cCCChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecc
Q psy11421 7 KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHT 86 (687)
Q Consensus 7 ~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~ 86 (687)
...+.+.++++|++|+++|++||++||++++|+|||++||+|+++|++||++| ++.+++|||++||+.+..+|.||+|+
T Consensus 25 ~~~~~~~~~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~~LE~~~-~~~~~~spt~~Vg~~~~~~f~kv~H~ 103 (689)
T PRK14351 25 EELSEDEAEEQAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDTENSPTRRVGGEPLDELETVEHV 103 (689)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhc-CCCCCCCCCccCCccccccCCceecC
Confidence 34455666789999999999999999999999999999999999999999999 89999999999999999999999999
Q ss_pred ccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCC
Q psy11421 87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP 166 (687)
Q Consensus 87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP 166 (687)
+|||||+|+|+.+|+.+|++|+.+.++ ...|+||||+||+||+|+|+||+|++|+|||||.+|||||+|+++|++||
T Consensus 104 ~pMlSL~k~~~~~el~~f~~r~~~~~~---~~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDVT~nv~~I~~IP 180 (689)
T PRK14351 104 APMLSIDQSGEADDVREFDERVRREVG---AVEYVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVP 180 (689)
T ss_pred CcccccCccCCHHHHHHHHHHHHHhcC---CceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceeHhhhhhhhcccc
Confidence 999999999999999999999988776 36799999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC
Q psy11421 167 LVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP 246 (687)
Q Consensus 167 ~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~ 246 (687)
++|+. .+|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|+..++ . +
T Consensus 181 ~~l~~-~~p~~levRGEv~m~~~~F~~lN~~~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~-~-~ 257 (689)
T PRK14351 181 QKLRG-DYPDFLAVRGEVYMPKDAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASE-L-F 257 (689)
T ss_pred hhhcc-cCCCeEEEEEEEEEEHHHHHHHHHHHHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCC-C-C
Confidence 99974 2588999999999999999999999999999999999999999999999999999999999999965433 2 4
Q ss_pred CCHHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC
Q psy11421 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL 326 (687)
Q Consensus 247 ~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~ 326 (687)
.+|++.|++|++|||+++++.+.+.+++++++|+++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||
T Consensus 258 ~t~~e~l~~L~~~GF~v~~~~~~~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~ 337 (689)
T PRK14351 258 DSHWEELERFPEWGLRVTDRTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARAPRWAFAYKFP 337 (689)
T ss_pred CCHHHHHHHHHHCCCCcCCceEeeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeCCHHHHHHhCccCCCCCceEEEcCC
Confidence 79999999999999999998888999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCC
Q psy11421 327 SKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRP 406 (687)
Q Consensus 327 ~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~ 406 (687)
+++++|+|++|+|||||||+|||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+.+.++
T Consensus 338 ~~~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~G~tVsratLhN~~~i~~~di~iGD~V~V~raGdVIPkI~~vv~~~~~ 417 (689)
T PRK14351 338 ARAEETTIRDIVVQVGRTGRLTPVALLDPVDVGGVTVSRASLHNPAEIEELGVNVGDRVRVKRAGDVIPYVEEVVEKDSE 417 (689)
T ss_pred CceeEEEEEEEEEecCCCceeeeEEEEEeEEECCEEEEEeccCCHHHHHHcCCCCCCEEEEEecCCccceeeeeecccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999987554
Q ss_pred CCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHh
Q psy11421 407 NDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486 (687)
Q Consensus 407 ~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~ 486 (687)
.+ |.+|++||+||++|++ +++.++|+|... ||+|++++|.||+||++|||+|||+++|++|+++|+|++++|||
T Consensus 418 ~~---~~~P~~CP~C~~~l~~--~~~~~~C~n~~~-Cpaq~~~~l~hf~sr~al~I~GLG~k~i~~L~~~g~V~~~~Dl~ 491 (689)
T PRK14351 418 GT---FEFPDTCPVCDSAVER--DGPLAFCTGGLA-CPAQLERSIEHYASRDALDIEGLGEERVQQLVDAGLVESLADLY 491 (689)
T ss_pred CC---CcCCCCCCCCCCEeee--CCceEEcCCCCC-CHHHHHHHHHHHhcccccCCCCcCHHHHHHHHHcCCCCCHHHHH
Confidence 33 7899999999999986 467889999656 99999999999999999999999999999999999999999999
Q ss_pred cCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHH
Q psy11421 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST 566 (687)
Q Consensus 487 ~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~ 566 (687)
+|+.++|..++|||+|+|+||+++|++||+++|+|||+||||||||+++|++|+++|+++++|..|+.++|.+++|||++
T Consensus 492 ~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k 571 (689)
T PRK14351 492 DLTVADLAELEGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPT 571 (689)
T ss_pred HcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccccccccc
Q psy11421 567 TVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTN 646 (687)
Q Consensus 567 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~ 646 (687)
+|++|++||+++.|+++++.|.+.|+++.... ...+++|+|++|||||+|..|+|++++++|+++||+|++|||++||
T Consensus 572 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~--~~~~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~ 649 (689)
T PRK14351 572 VAEEIREFFDSERNRAVIDDLLDHGVDPQPAE--SEGGDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTD 649 (689)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHhccccccccc--ccCCCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCcc
Confidence 99999999999999999999999998765421 2235689999999999999999999999999999999999999999
Q ss_pred EEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11421 647 YLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKG 680 (687)
Q Consensus 647 ~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~ 680 (687)
|||+|+++| +|++||+++||+||+|++|++||++
T Consensus 650 ~Lv~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~~ 684 (689)
T PRK14351 650 YLVVGENPGQSKRDDAEANDVPTLDEEEFEELLAE 684 (689)
T ss_pred EEEEcCCCChhHHHHHHHCCCeEecHHHHHHHHHh
Confidence 999999999 9999999999999999999999986
No 6
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=100.00 E-value=3.9e-153 Score=1280.92 Aligned_cols=532 Identities=21% Similarity=0.318 Sum_probs=501.2
Q ss_pred CChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceecccc
Q psy11421 9 INFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFK 88 (687)
Q Consensus 9 ~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~p 88 (687)
.+...++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+ ||+|++|
T Consensus 25 ~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~~LE~~~p~~~~~~spt~~vg~-------kv~H~~P 97 (562)
T PRK08097 25 WSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPEPRDVPLPPLNG-------KVLHPVA 97 (562)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcCcCCCCCCCCCCCC-------ceECCCC
Confidence 455677889999999999999999999999999999999999999999999999999999999986 9999999
Q ss_pred ccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcc
Q psy11421 89 MMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLV 168 (687)
Q Consensus 89 MlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~ 168 (687)
||||+|+||.+||.+|++++. .|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++
T Consensus 98 MlSL~k~~s~eel~~w~~~~~---------~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~~ 168 (562)
T PRK08097 98 HTGVKKLADKQALARWMAGRS---------DLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQ 168 (562)
T ss_pred cccccccCCHHHHHHHHhhcc---------ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccchh
Confidence 999999999999999998852 59999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCC
Q psy11421 169 LNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSS 248 (687)
Q Consensus 169 l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~ 248 (687)
|+. .|..+|||||+||++++|++.+ .| |+||||+|||+|||+||+++ .|+|+||+|++.. + +.+
T Consensus 169 l~~--~~~~levRGEv~m~~~~F~~~~-----~g---~aNPRN~AAGsLr~~d~~~~-~r~L~~f~y~~~~--~---~~t 232 (562)
T PRK08097 169 LPG--ALANLVLQGELFLRREGHIQQQ-----MG---GINARAKVAGLMMRKDPSPT-LNQIGVFVWAWPD--G---PAS 232 (562)
T ss_pred hcC--CCCeEEEEEEEEEeHHHHHHHh-----cC---cCCchHHHhHHHhhcCcHhh-hccceEEEEECCC--C---CCC
Confidence 974 3778999999999999999632 22 89999999999999999998 8999999999842 2 479
Q ss_pred HHHHHHHHHhcCCCCCC-CceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCC
Q psy11421 249 HSELLNWYQKIGLSICG-EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS 327 (687)
Q Consensus 249 ~~e~l~~L~~~Gf~~~~-~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~ 327 (687)
|++.|++|++|||++++ +.+.+.+.+++++|+++|. |..+||+|||+|||+||+.+|+ |+|+|+||||||||||+
T Consensus 233 ~~e~l~~L~~~GF~v~~~~~~~~~~~~~i~~~~~~~~--r~~l~y~iDGiViKvn~~~~~~--~~ts~~PrWAiAyKf~~ 308 (562)
T PRK08097 233 MPERLAQLATAGFPLTQRYTHPVKNAEEVARWRERWY--RAPLPFVTDGVVVRQAKEPPGR--YWQPGQGEWAVAWKYPP 308 (562)
T ss_pred HHHHHHHHHHCCCCcCccceEeeCCHHHHHHHHHHHh--hccCCCCCCcEEEEecCHHHHh--hccCCCCCceEEEcCCC
Confidence 99999999999999996 7778999999999999886 9999999999999999999998 78999999999999999
Q ss_pred ceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCC
Q psy11421 328 KEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPN 407 (687)
Q Consensus 328 ~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~ 407 (687)
++++|+|++|+|||||||++||||+|+||.|+|+|||||||||+++|+++||++||+|.|+|||||||+|++|+. |++
T Consensus 309 ~~~~T~l~~I~~qVGRTG~iTPVA~lePV~l~GttVsrATLhN~~~i~~~~I~iGD~V~V~raGdVIP~I~~vv~--~~~ 386 (562)
T PRK08097 309 VQQVAEVRAVQFAVGRTGKITVVLELEPVMLDDKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPRLDKVVW--RGA 386 (562)
T ss_pred cEEEEEEEEEEEecCCCceeeEEEEEEEEEeCCEEEEEeecCCHHHHHHcCCCCCCEEEEEecCCCCcceeeeec--ccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999997 455
Q ss_pred CCccccCCCCCCCCCCcceeecCceeEEecC-CCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHh
Q psy11421 408 DSKIFKIPNICPICNSKIIYIESNLIARCSG-SWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLY 486 (687)
Q Consensus 408 ~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n-~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~ 486 (687)
...++.+|+. ++++.+||+| ... ||+|++++|.|||||+||||+|||+++|++|+++|+|++++|||
T Consensus 387 ~~~~~~~P~~-----------~~~~~~~C~n~~~~-Cpaq~~~~i~hf~Sr~amdI~GlGe~~i~~L~~~G~i~~~~Diy 454 (562)
T PRK08097 387 ERTKPTPPDA-----------DRFHSLSCFRASPG-CQEQFLARLVWLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSWL 454 (562)
T ss_pred cCCCCcCCCC-----------CCceEEEeCCCCCC-CHHHHHHHhHhhhcccccCCCCcCHHHHHHHHHcCCcCCHHHHh
Confidence 5556777764 2357899998 555 99999999999999999999999999999999999999999999
Q ss_pred cCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHH
Q psy11421 487 KINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGST 566 (687)
Q Consensus 487 ~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~ 566 (687)
+|+.++|++++|||+|+++||+++|++||+++|+|||+|||||+||+.+|+. +|+++++|..++.++|.+++|||++
T Consensus 455 ~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~~~ak~---~~~~i~~l~~a~~e~l~~i~gIG~~ 531 (562)
T PRK08097 455 ALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQAALNAL---DDRSWQQLLSRSEQQWQQLPGIGEG 531 (562)
T ss_pred cCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHHHHHHH---hcCCHHHHHcCCHHHHhcCCCchHH
Confidence 9999999999999999999999999999999999999999999999988876 8999999999999999999999999
Q ss_pred HHHHHHHHHcchhHHHHHHHHHhcCcc
Q psy11421 567 TVKAFIKFINQPLHRLLISQLRDVGIY 593 (687)
Q Consensus 567 ~A~sI~~ff~~~~n~~~i~~L~~~Gv~ 593 (687)
+|++|++||+++.|++++++|.++|++
T Consensus 532 ~a~si~~~f~~~~~~~~i~~L~~~gv~ 558 (562)
T PRK08097 532 RARQLIAFLQHPEVKALADWLAAQGIT 558 (562)
T ss_pred HHHHHHHHHcCHHHHHHHHHHHHcCCC
Confidence 999999999999999999999998875
No 7
>smart00532 LIGANc Ligase N family.
Probab=100.00 E-value=9e-138 Score=1137.31 Aligned_cols=440 Identities=47% Similarity=0.758 Sum_probs=419.8
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCCC
Q psy11421 15 SFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDN 94 (687)
Q Consensus 15 ~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k 94 (687)
+++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++..++|||++||+.+.++|.||+|++|||||+|
T Consensus 2 ~~~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~~le~~~p~~~~~~spt~~VG~~~~~~f~kv~H~~pMlSL~k 81 (441)
T smart00532 2 QKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVGGKPLEGFNKVRHPVPMLSLDN 81 (441)
T ss_pred hHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHHHHHHhCccccCCCCCccccCcccccCCcceecCCcccCccc
Confidence 46899999999999999999999999999999999999999999999999999999999998889999999999999999
Q ss_pred CCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCC
Q psy11421 95 GFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYP 174 (687)
Q Consensus 95 ~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~ 174 (687)
+|+.+||.+|++++.+.++ .+..|+|||||||+||+|+|++|+|++|+|||||.+|||||+|+++|++||++|+. +.
T Consensus 82 ~~~~~el~~f~~~~~~~~~--~~~~~~~epKiDGlsisL~Ye~G~l~~a~TRGDG~~GeDVT~nv~~i~~iP~~i~~-~~ 158 (441)
T smart00532 82 AFDEDELRAFDERIEKALG--SPFAYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSG-DV 158 (441)
T ss_pred cCCHHHHHHHHHHHHHhcC--CCceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceehhhhhhhhcCcChhhcc-cC
Confidence 9999999999999987765 23679999999999999999999999999999999999999999999999999974 25
Q ss_pred CceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHH
Q psy11421 175 PELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLN 254 (687)
Q Consensus 175 ~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~ 254 (687)
|..+|||||+||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+++..++.....+|++.|+
T Consensus 159 p~~leiRGEv~~~~~~F~~ln~~~~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~~~~~~~t~~e~l~ 238 (441)
T smart00532 159 PERLEVRGEVFMPKEDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFLPKTQSEALK 238 (441)
T ss_pred CCeEEEEceEEEEHHHHHHHHHHHHhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCCCCCCccCHHHHHH
Confidence 88999999999999999999999999999999999999999999999999999999999999975433211268999999
Q ss_pred HHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEE
Q psy11421 255 WYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKI 334 (687)
Q Consensus 255 ~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v 334 (687)
+|++|||+++++...+.+.+++++|+++|.+.|..+||+|||+|||+||+.+|+.||+|+|+||||||||||+++++|+|
T Consensus 239 ~L~~~GF~v~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~l 318 (441)
T smart00532 239 WLKELGFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEEAETKL 318 (441)
T ss_pred HHHHCCCCCCCCeEeeCCHHHHHHHHHHHHHhcccCCCCcCcEEEEecCHHHHHHhCccCCCCCeeEEECCCCceeEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccC
Q psy11421 335 KAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKI 414 (687)
Q Consensus 335 ~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~ 414 (687)
++|+|||||||+|||||+|+||.|+|+||+||||||+++|+++||++||+|.|+|||||||+|++|+.+.|++++.+|.+
T Consensus 319 ~~I~~qVGRTG~iTPvA~lePV~l~G~tVsrATLhN~~~i~~~~i~iGd~V~V~raGdVIP~I~~vv~~~r~~~~~~~~~ 398 (441)
T smart00532 319 LDIIVQVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEEKDIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEM 398 (441)
T ss_pred EEEEEecCCCceeeEEEEEEeEEECCEEEEecccCCHHHHHHcCCCCCCEEEEEECCCcCcceeecccccCCCCCccCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988888889999
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccc
Q psy11421 415 PNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKA 459 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~ 459 (687)
|++||+||++|++.++++.+||+|. . ||+|++++|.||+||+|
T Consensus 399 P~~CP~C~s~l~~~~~~~~~~C~n~-~-C~aq~~~~l~hf~sr~a 441 (441)
T smart00532 399 PTHCPSCGSELVREEGEVDIRCPNP-L-CPAQLIERIIHFASRKA 441 (441)
T ss_pred CCCCCCCCCEeEecCCceEEEeCCC-C-CHHHHHHHHHhhhcCCC
Confidence 9999999999998888899999996 6 99999999999999975
No 8
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=100.00 E-value=9.5e-95 Score=765.07 Aligned_cols=306 Identities=47% Similarity=0.768 Sum_probs=292.6
Q ss_pred HHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcccCCCCcceeccccccCCCCCC
Q psy11421 17 RVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLVGGENSKYVHHTFKMMSLDNGF 96 (687)
Q Consensus 17 ~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~~~~~~~kv~H~~pMlSL~k~~ 96 (687)
+|++|+++|++||++||++++|+|||++||+|+++|++||++||++..++|||++||+.+.+.|.||+|++|||||+|+|
T Consensus 2 ~i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~~le~~~p~~~~~~Spt~~VG~~~~~~f~kv~H~~pMlSL~k~~ 81 (307)
T cd00114 2 RIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVGGTPLSGFKKVRHPVPMLSLDNAF 81 (307)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCcccCCCCCCCcccCccccccCCccCCCCcCccccccC
Confidence 68999999999999999999999999999999999999999999999999999999999888999999999999999999
Q ss_pred ChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCc
Q psy11421 97 SDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPE 176 (687)
Q Consensus 97 ~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~ 176 (687)
+.+||.+|++|+.+.++ .+..|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+. .|.
T Consensus 82 ~~~el~~~~~r~~~~~~--~~~~~~vepKiDGlsisL~Y~~G~L~~a~TRGdG~~GeDVT~nv~~I~~IP~~i~~--~~~ 157 (307)
T cd00114 82 DEEELRAFDERIKRFLG--EEPAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLAG--APE 157 (307)
T ss_pred CHHHHHHHHHHHHHhcC--CCCcEEEEEeccceEEEEEEECCEEEEEEecCCCcchhhHHhhHhhhcccChhhcC--CCC
Confidence 99999999999987775 24689999999999999999999999999999999999999999999999999974 488
Q ss_pred eEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHH
Q psy11421 177 LLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWY 256 (687)
Q Consensus 177 ~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L 256 (687)
.+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||.+++.|+|+||+|+|+..++.+ +.+|++.|++|
T Consensus 158 ~levRGEv~m~~~~F~~~n~~~~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~~~-~~t~~e~l~~L 236 (307)
T cd00114 158 TLEVRGEVFMPKADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLG-PKTQSEALAFL 236 (307)
T ss_pred eEEEEEEEEEEHHHHHHHHHHHHHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccCCC-CCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999997544323 47999999999
Q ss_pred HhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCC
Q psy11421 257 QKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLS 327 (687)
Q Consensus 257 ~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~ 327 (687)
++|||+|+++...+.+++++++|+++|.+.|..+||+|||||||||++.+|+.||.|+|+||||||||||+
T Consensus 237 ~~~GF~v~~~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrWaiA~Kf~~ 307 (307)
T cd00114 237 KEWGFPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPA 307 (307)
T ss_pred HHCCCCCCCCeEEeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCceEEeCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999996
No 9
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=100.00 E-value=3.1e-94 Score=764.33 Aligned_cols=313 Identities=44% Similarity=0.689 Sum_probs=270.7
Q ss_pred hHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHHCCCCCCCCCCccccCcc-cCCCCcceeccccccC
Q psy11421 13 KLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEKYPELLTKDSLTQHVGLV-GGENSKYVHHTFKMMS 91 (687)
Q Consensus 13 ~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~~p~~~~~~spt~~Vg~~-~~~~~~kv~H~~pMlS 91 (687)
+++++|++|+++|++||++||+.++|+|||++||+|+++|++||++||++.+++|||++||+. +...|.+|+|++||||
T Consensus 2 ~~~~~i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L~~le~~~pe~~~~~spt~~Vg~~~~~~~f~kv~H~~pMlS 81 (315)
T PF01653_consen 2 EAKERIEELRKEINRHNYAYYNLGEPIISDAEYDQLFRELKALEAEYPELITPDSPTQRVGGSPPSSKFKKVRHPVPMLS 81 (315)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHHHHHHHHSGGG--TTSGGGGGSSSS-SSSSEEEEESS----
T ss_pred hHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCcccccCCCcccccccccccccCceeeecccccC
Confidence 457899999999999999999999999999999999999999999999999999999999954 5566999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCccccc
Q psy11421 92 LDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNI 171 (687)
Q Consensus 92 L~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~ 171 (687)
|+|+|+.+||.+|++++.+.++.. ...|+|||||||+||+|+|+||+|++|+|||||.+|||||+|+++|++||++|+.
T Consensus 82 L~k~~s~eel~~w~~r~~~~~~~~-~~~~~~e~KiDGlsi~L~Y~~G~L~~a~TRGdG~~GeDvT~n~~~i~~iP~~i~~ 160 (315)
T PF01653_consen 82 LDKAYSEEELRKWLKRVEKALGEE-EEEFVVEPKIDGLSISLIYENGKLVRAATRGDGEVGEDVTHNVRTIKSIPLRIPE 160 (315)
T ss_dssp -EEESSHHHHHHHHHHHHHHCSS--SSEEEEEEEESSEEEEEEEETTEEEEEEEETTSSEEEB-HHHHCTSTTS-SB-SS
T ss_pred ccccCCHHHHHHHHHHHHHHhccc-ccceeEeeccceeEEEEEEeCCEEEEEEEcCCCccchhHHHHHHHHhcCchhhcc
Confidence 999999999999999999988742 1269999999999999999999999999999999999999999999999999985
Q ss_pred CCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHH
Q psy11421 172 KYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSE 251 (687)
Q Consensus 172 ~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e 251 (687)
. |+.+||||||||++++|+++|+++.+.|+++|+||||+|||+|||+||++++.|+|+||+|+|..+++...+.+|++
T Consensus 161 ~--p~~~eVRGEv~m~~~~F~~ln~~~~~~~~~~faNpRN~aAGsLr~~d~~~~~~r~L~f~~y~~~~~~~~~~~~t~~e 238 (315)
T PF01653_consen 161 K--PGRLEVRGEVYMSKSDFEKLNEEREEEGEKPFANPRNAAAGSLRQKDPSITAERKLSFFAYGIGEPEGDLGFNTQSE 238 (315)
T ss_dssp S--SSEEEEEEEEE--HHHHHHHHHHHHHTTS---SSHHHHHHHHHTSSSHHHHHTS--EEEEEEEEEETTSTT-SBHHH
T ss_pred C--CcceEEEEEEEEehhhHHHHHHHHHHhccchhhhhhHHHHHhhhhccchhhhcCeeEEEEEEecccccccChHHHHH
Confidence 3 79999999999999999999999999999999999999999999999999999999999999997655223589999
Q ss_pred HHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCc
Q psy11421 252 LLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSK 328 (687)
Q Consensus 252 ~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~ 328 (687)
.|++|++|||+|+++...+.+.+++++++++|.+.|..+||+|||||||+||+.+|+.||+|+|+|||||||||||+
T Consensus 239 ~l~~L~~~GF~v~~~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~~~~LG~t~~~PrwAiAyKfpae 315 (315)
T PF01653_consen 239 RLQFLKEWGFPVNPYIRFCKSIEEVEEYIEEWEERREELPYPIDGIVIKVNDLALQERLGYTSKHPRWAIAYKFPAE 315 (315)
T ss_dssp HHHHHHHTT--B-TTEEEESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESBHHHHHHH-BESSSBSSEEEEE---G
T ss_pred HHHHHHHcCCCCCcceEecCCHHHHHHHHHHHHhhhhccccccCcEEEEecCHHHHHhcCCcCCCCCeEEEECcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999986
No 10
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=99.97 E-value=1.6e-31 Score=227.67 Aligned_cols=82 Identities=51% Similarity=0.764 Sum_probs=70.5
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCC
Q psy11421 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDS 409 (687)
Q Consensus 330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~ 409 (687)
++|+|++|+|||||||++||||+|+||.|+|++|+||||||+++|+++||++||+|.|+|||||||+|++|+++.|++++
T Consensus 1 ~~T~v~~I~~~vGRtG~itPva~lePV~l~G~~VsratLhN~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r~~~~ 80 (82)
T PF03120_consen 1 QETKVRDIEWQVGRTGKITPVAVLEPVELDGTTVSRATLHNYDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKRTGDE 80 (82)
T ss_dssp EEEEEEEEEEEE-TTSBEEEEEEEEEEECTTCEEEEEE--SHHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG--SS-
T ss_pred CeEEEEEEEEecCCCeEEEEEEEEEEEEECCeEEEEEEecCHHHHHHcCCCCCCEEEEEECCCccceEeEeehhcCCCCC
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999998876
Q ss_pred cc
Q psy11421 410 KI 411 (687)
Q Consensus 410 ~~ 411 (687)
+|
T Consensus 81 ~p 82 (82)
T PF03120_consen 81 QP 82 (82)
T ss_dssp BB
T ss_pred CC
Confidence 53
No 11
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.64 E-value=2.7e-16 Score=168.24 Aligned_cols=77 Identities=44% Similarity=0.691 Sum_probs=72.4
Q ss_pred CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcC---------CCCccHHHHHHc-----CCeEE
Q psy11421 604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQ---------KPGKKLEKAIKL-----NIKIL 669 (687)
Q Consensus 604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~---------~~g~Kl~kA~~l-----gI~Ii 669 (687)
..+|+|++|||||+|..|+|++++++++++||+|++|||++|||||+|+ ++|+|++||++| ||+||
T Consensus 218 ~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~ii 297 (309)
T PRK06195 218 FTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFL 297 (309)
T ss_pred CccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCCcccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcEEe
Confidence 4579999999999999899999999999999999999999999999995 467999999999 99999
Q ss_pred eHHHHHHHHhc
Q psy11421 670 DEKNFVKIVKG 680 (687)
Q Consensus 670 ~E~~f~~~l~~ 680 (687)
+|++|++||..
T Consensus 298 ~E~~f~~l~~~ 308 (309)
T PRK06195 298 NEEEFLQKCKE 308 (309)
T ss_pred cHHHHHHHHhh
Confidence 99999999863
No 12
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.64 E-value=4e-16 Score=167.01 Aligned_cols=74 Identities=16% Similarity=0.239 Sum_probs=71.0
Q ss_pred cCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC--ccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11421 607 LKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVKGF 681 (687)
Q Consensus 607 l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g--~Kl~kA~~lgI~Ii~E~~f~~~l~~~ 681 (687)
++|++|||||+|+ ++|++++++++++||+|++|||++|||||+|+++| +|++||+++||+||+|++|++||+.-
T Consensus 233 ~~g~~~v~TG~l~-~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll~~~ 308 (313)
T PRK06063 233 VQGMRVALSAEVS-RTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELLRAV 308 (313)
T ss_pred cCCCEEEEecCCC-CCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHHHhh
Confidence 5899999999997 89999999999999999999999999999999988 89999999999999999999999754
No 13
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=99.58 E-value=2.6e-15 Score=123.61 Aligned_cols=64 Identities=45% Similarity=0.719 Sum_probs=55.2
Q ss_pred HHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHH
Q psy11421 521 RFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLI 584 (687)
Q Consensus 521 r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i 584 (687)
|||+||||||||+.+|+.|+++|+++++|..|+.++|.+++|||+++|++|++||++++|+++|
T Consensus 1 R~l~aLGI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~~~i 64 (64)
T PF12826_consen 1 RFLFALGIPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENRELI 64 (64)
T ss_dssp HHHHHCTSTT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHHHHH
T ss_pred CeeeeCCCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhhhhC
Confidence 7999999999999999999999999999999999999999999999999999999999998764
No 14
>COG5275 BRCT domain type II [General function prediction only]
Probab=99.50 E-value=4.2e-14 Score=138.43 Aligned_cols=81 Identities=38% Similarity=0.657 Sum_probs=76.8
Q ss_pred CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11421 603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKGF 681 (687)
Q Consensus 603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~~ 681 (687)
..++|.|+.|||||.|..++|++++.++..+||+|..+.|.+|+|||.|+++| +|++|+++|+|+.|+|+.|..++...
T Consensus 153 ~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~LI~~~ 232 (276)
T COG5275 153 ERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDSLIKDT 232 (276)
T ss_pred CcccccccEEEEecccccccchhHHHHHHHhCCeeecccccceeEEEecCCCChHHHHHHHHhCCccccHHHHHHHHhcC
Confidence 45699999999999999999999999999999999999999999999999999 99999999999999999999999765
Q ss_pred cC
Q psy11421 682 ST 683 (687)
Q Consensus 682 s~ 683 (687)
++
T Consensus 233 pa 234 (276)
T COG5275 233 PA 234 (276)
T ss_pred cc
Confidence 43
No 15
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins. RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.
Probab=99.17 E-value=3.9e-10 Score=121.99 Aligned_cols=144 Identities=22% Similarity=0.200 Sum_probs=109.0
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR 198 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~ 198 (687)
.|+||+|+||.++++.|.+|+ +.|.||| |.+++++|++++.+ +|..+.. ..| .+.+.||++++...|..
T Consensus 49 ~~~vEEKlDG~nvri~~~~G~-v~a~TR~-G~i~e~~T~~~~ei--v~~~~~~-~~p-~~iLdGElvg~~~p~v~----- 117 (342)
T cd07894 49 PVAVEEKMNGYNVRIVRIGGK-VLAFTRG-GFICPFTTDRLRDL--IDPEFFD-DHP-DLVLCGEVVGPENPYVP----- 117 (342)
T ss_pred CEEEEEeECCcEEEEEEECCE-EEEEeCC-CccCccchhhHhhh--chHHhhc-cCC-CEEEEEEEEecCCcccc-----
Confidence 799999999999999999998 7999999 99999999999987 5777643 134 48999999998755421
Q ss_pred HHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcCCCCCCCc--eEeCCHHHH
Q psy11421 199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSICGEY--SVLSGVNKL 276 (687)
Q Consensus 199 ~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~Gf~~~~~~--~~~~~~~ei 276 (687)
. . .|. .+++.||+|++...++.. ..++.+..++|.++||+.++.. ..+.+.+++
T Consensus 118 ----~---~-------------~~~---~~~v~F~vFDI~~~~~~~-~lp~~eR~~lLe~lg~~~v~~~~~~~~~d~~~l 173 (342)
T cd07894 118 ----G---S-------------YPE---VEDVGFFVFDIRKKNTGR-PLPVEERRELLEKYGLPTVRLFGEFTADEIEEL 173 (342)
T ss_pred ----c---c-------------Ccc---ccccEEEEEeeEEcCCCC-CCCHHHHHHHHHhcCCCCcceEEEEecCCHHHH
Confidence 0 0 111 268999999998654322 3678999999999999877643 234567788
Q ss_pred HHHHHHHHHhhcCCCCccceEEEEECC
Q psy11421 277 IEFYKKINIKRFNLPYEIDGVVYKINC 303 (687)
Q Consensus 277 ~~~~~~~~~~r~~l~y~iDGiVikv~~ 303 (687)
.++++.+.+.- --|||+|--+
T Consensus 174 ~~~l~~~~~~G------~EGVVlK~~~ 194 (342)
T cd07894 174 KEIIRELDKEG------REGVVLKDPD 194 (342)
T ss_pred HHHHHHHHHCC------CceEEEeccc
Confidence 88877764322 4799998755
No 16
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=99.12 E-value=1.1e-10 Score=137.41 Aligned_cols=78 Identities=21% Similarity=0.249 Sum_probs=71.8
Q ss_pred CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCC---CC-ccHHHHHHcCCeEEeHHHHHHHH
Q psy11421 603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQK---PG-KKLEKAIKLNIKILDEKNFVKIV 678 (687)
Q Consensus 603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~---~g-~Kl~kA~~lgI~Ii~E~~f~~~l 678 (687)
...+|.|++|||||+|+. +|++++++|+.+||+|++|||++|++|++|.+ +| +|+++|+++||+||+|++|++++
T Consensus 186 ~~kpL~G~~fviTGtl~~-sr~elK~~Ie~~GGkvsssVs~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~d~i 264 (815)
T PLN03122 186 PGKPFSGMMISLSGRLSR-THQYWKKDIEKHGGKVANSVEGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLIDSI 264 (815)
T ss_pred cCCCcCCcEEEEeCCCCC-CHHHHHHHHHHcCCEEccccccceEEEEcCccccccCccHHHHHHHcCCcCccHHHHHHHH
Confidence 345899999999999986 99999999999999999999999999999976 55 89999999999999999999999
Q ss_pred hcc
Q psy11421 679 KGF 681 (687)
Q Consensus 679 ~~~ 681 (687)
...
T Consensus 265 ~~~ 267 (815)
T PLN03122 265 EKQ 267 (815)
T ss_pred hcC
Confidence 753
No 17
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=98.76 E-value=3.6e-08 Score=82.91 Aligned_cols=74 Identities=26% Similarity=0.302 Sum_probs=67.0
Q ss_pred CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCC--CCccHHHHHHcCCeEEeHHHHHHHH
Q psy11421 604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQK--PGKKLEKAIKLNIKILDEKNFVKIV 678 (687)
Q Consensus 604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~--~g~Kl~kA~~lgI~Ii~E~~f~~~l 678 (687)
...|.|.+|+| +.+....|++++.+|+.+||++..+++++|++||++.. ...|...|...+|+|++++++.+.|
T Consensus 3 ~~~F~g~~f~i-~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci 78 (78)
T PF00533_consen 3 PKIFEGCTFCI-SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI 78 (78)
T ss_dssp TTTTTTEEEEE-SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred CCCCCCEEEEE-ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence 45799999999 55556899999999999999999999999999999987 5689999999999999999998764
No 18
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=98.74 E-value=8.6e-09 Score=83.75 Aligned_cols=57 Identities=28% Similarity=0.362 Sum_probs=52.6
Q ss_pred cccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 456 sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.++.++|+|+|++++.+|++.| +.|+.||++++.++|..++|||+++|++|++++++
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~G-~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEAG-IKTLEDLANADPEELAEIPGIGEKTAEKIIEAARE 60 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHTT-CSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHHH
T ss_pred HHhhccCCCCCHHHHHHHHhcC-CCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence 4567899999999999999999 69999999999999999999999999999998753
No 19
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=98.73 E-value=1.6e-08 Score=82.74 Aligned_cols=62 Identities=31% Similarity=0.386 Sum_probs=53.3
Q ss_pred EEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHH
Q psy11421 611 IFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKN 673 (687)
Q Consensus 611 ~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~ 673 (687)
+|||||..+ -.|.++..+++.+||++...++++|++||+....|.|+++|.++||+|++.++
T Consensus 2 ~i~~sg~~~-~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 2 VICFSGFSG-KERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp EEEEEEB-T-TTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred EEEECCCCH-HHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence 699999775 47999999999999999999999999999988888999999999999999764
No 20
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins. The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most me
Probab=98.72 E-value=8.2e-08 Score=94.42 Aligned_cols=139 Identities=16% Similarity=0.246 Sum_probs=94.6
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR 198 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~ 198 (687)
.|++|+|+||+.+.+ +|. ++.||+ |+|+|........ +|. +.+.||+++....|+.+
T Consensus 17 ~~~~e~K~DG~R~~~---~~~--~~~SR~----g~~~t~~~~~~~~---------l~~-~ilDGElv~~~~~f~~l---- 73 (174)
T cd07896 17 GYLVSEKLDGVRAYW---DGK--QLLSRS----GKPIAAPAWFTAG---------LPP-FPLDGELWIGRGQFEQT---- 73 (174)
T ss_pred HeeechhhceEEEEE---ecc--EEEecC----CcCCCCCHHHHhh---------CCC-CccCceEEcCCCCHHHH----
Confidence 689999999999854 454 889996 9999976222222 333 78999999987777665
Q ss_pred HHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhc-------CCCCCCCceEeC
Q psy11421 199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKI-------GLSICGEYSVLS 271 (687)
Q Consensus 199 ~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~-------Gf~~~~~~~~~~ 271 (687)
+|.++++++......++.|++|++... ..+..+..+.|.++ .|.+++ ...+.
T Consensus 74 ---------------~~~~~~~~~~~~~~~~~~f~vFDil~~-----~~p~~eR~~~L~~~i~~~~~~~~~~~~-~~~~~ 132 (174)
T cd07896 74 ---------------SSIVRSKKPDDEDWRKVKFMVFDLPSA-----KGPFEERLERLKNLLEKIPNPHIKIVP-QIPVK 132 (174)
T ss_pred ---------------HHHHhcCCCChhhcccceEEEEeCCCC-----CCCHHHHHHHHHHHHHhCCCCcEEEEe-eeeeC
Confidence 344444444333446799999999862 14566666665432 233333 23467
Q ss_pred CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11421 272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (687)
Q Consensus 272 ~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (687)
+.+++.++++.+.+. ..+|+|+|-.|..++
T Consensus 133 ~~~~i~~~~~~~~~~------g~EGlv~K~~ds~Y~ 162 (174)
T cd07896 133 SNEALDQYLDEVVAA------GGEGLMLRRPDAPYE 162 (174)
T ss_pred CHHHHHHHHHHHHhc------CCCeEEEecCCCccc
Confidence 888999988876433 569999998887664
No 21
>PRK09125 DNA ligase; Provisional
Probab=98.62 E-value=3.3e-06 Score=89.56 Aligned_cols=198 Identities=17% Similarity=0.185 Sum_probs=124.4
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYR 198 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~ 198 (687)
.|++|+|+||+-+. .+| +++.|| .|+|+|+--.... .+| .+.+-||+++...+|+.+...
T Consensus 44 ~~~~E~K~DG~R~~---~~~--v~l~SR----~g~~it~p~~~~~---------~~~-~~vLDGElv~~~~~F~~l~~r- 103 (282)
T PRK09125 44 GYLVSEKLDGVRAY---WDG--KQLLTR----QGNPIAAPAWFTA---------GFP-PFPLDGELWAGRGQFEAISSI- 103 (282)
T ss_pred hEEEEeeeeeEeEE---ECC--eEEEcC----CCCcCCCchhHHh---------cCC-CccEeEEEEeCCCCHHHHHHH-
Confidence 69999999999994 366 589999 7888887211111 134 578999999988999877543
Q ss_pred HHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHHHHHHhcCCCC-CCC-----ceEeCC
Q psy11421 199 YHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELLNWYQKIGLSI-CGE-----YSVLSG 272 (687)
Q Consensus 199 ~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l~~L~~~Gf~~-~~~-----~~~~~~ 272 (687)
++++++......++.|++|++...+ .+..+..+.|+++==+. .+. ...+.+
T Consensus 104 ------------------~~~k~~~~~~~~~v~~~vFDll~~~-----gpl~eRr~~L~~li~~~~~~~i~~~~~~~~~~ 160 (282)
T PRK09125 104 ------------------VRDKTPDDAAWRKVRFMVFDLPDAP-----GDFEERLAVLKKLLAKLPSPYIKIIEQIRVRS 160 (282)
T ss_pred ------------------HccCCcchhhhcccEEEEEEcCCCC-----CCHHHHHHHHHHHHhhCCCCcEEEEeEEEcCC
Confidence 2222222122347999999997653 25667777776541111 111 223568
Q ss_pred HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC-cceeeeEE
Q psy11421 273 VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPVA 351 (687)
Q Consensus 273 ~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~iTPvA 351 (687)
.+++.++++.+.+ --..|+|+|--|..+. -| +...| +-+| +...++..|.++.|-.|| +|.+.-..
T Consensus 161 ~~~~~~~~~~~~~------~G~EGiV~K~~ds~Y~--~G---Rs~~w-lKiK-~~~~~d~vIvG~~~g~Gk~~g~~gsll 227 (282)
T PRK09125 161 EAALQQFLDQIVA------AGGEGLMLHRPDAPYE--AG---RSDDL-LKLK-PYYDAEATVIGHLPGKGKFAGMLGALL 227 (282)
T ss_pred HHHHHHHHHHHHH------cCCCEEEEeCCCCCCc--CC---CCCCc-EEEE-ecCCCcEEEEEEEcCCCcccCceeeEE
Confidence 8899998887643 2358999997765554 23 44567 4444 335678999999998874 45443221
Q ss_pred EEEEEEECCEEEEEecCCCHHHHH
Q psy11421 352 LLKPVLIDGITITRATLHNESEIY 375 (687)
Q Consensus 352 ~lePV~l~G~tVsraTLhN~~~i~ 375 (687)
.- .-+|.+++=+|....+.-+
T Consensus 228 v~---~~~g~~~~VgsG~t~~~r~ 248 (282)
T PRK09125 228 VE---TPDGREFKIGSGFSDAERE 248 (282)
T ss_pred EE---eCCCCEEEeCCCCCHHHhc
Confidence 11 1256555445666665543
No 22
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.60 E-value=2.7e-07 Score=74.81 Aligned_cols=70 Identities=41% Similarity=0.550 Sum_probs=63.5
Q ss_pred CeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCcc-HHHHHHcCCeEEeHHHHHHHH
Q psy11421 609 EKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKK-LEKAIKLNIKILDEKNFVKIV 678 (687)
Q Consensus 609 g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~K-l~kA~~lgI~Ii~E~~f~~~l 678 (687)
|..|+|+|.+...+|.+++++++.+||++..+++..+++||+++....+ +..|...+++|++++++.+.+
T Consensus 1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~ 71 (72)
T cd00027 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCL 71 (72)
T ss_pred CCEEEEEecCCCcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHh
Confidence 6789999998557999999999999999999999999999999877644 899999999999999998765
No 23
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f
Probab=98.52 E-value=3.1e-06 Score=85.30 Aligned_cols=165 Identities=16% Similarity=0.162 Sum_probs=104.9
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFIK 193 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~----~F~~ 193 (687)
..|++|+|+||.-+.+.+..|. +++.|| -|.|+|+....+... +. ..|..+.+-||++.... .|..
T Consensus 21 ~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~i~~~---~~--~~~~~~vLDGElv~~~~~~~~~f~~ 90 (201)
T cd07898 21 AAAWVEDKYDGIRAQVHKDGGR-VEIFSR----SLEDITDQFPELAAA---AK--ALPHEFILDGEILAWDDNRGLPFSE 90 (201)
T ss_pred CeEEEEEeeceEEEEEEEeCCE-EEEEcC----CChhchhhhhhHHHH---HH--hCCCCEEEEEEEEEEeCCCCCcHHH
Confidence 4799999999999998776555 699999 467898755433321 11 13557899999986432 3665
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCce----
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYS---- 268 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~---- 268 (687)
+..... . |+.. .. .....++.|++|++...++.++ ..+..|..+.|+++.-+......
T Consensus 91 ~~~~~~---~------~~~~------~~--~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~~ 153 (201)
T cd07898 91 LFKRLG---R------KFRD------KF--LDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAPA 153 (201)
T ss_pred HHHHhc---c------cccc------hh--hhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEeee
Confidence 433211 0 0000 00 1123469999999987555332 24788999999998655433322
Q ss_pred -EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11421 269 -VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (687)
Q Consensus 269 -~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (687)
.+++.+++.++++.+.+ -..+|+|+|--+..++ .| .+...|
T Consensus 154 ~~~~~~~~~~~~~~~~~~------~g~EGim~K~~~s~Y~--~g--~Rs~~w 195 (201)
T cd07898 154 LPVESAEELEAAFARARA------RGNEGLMLKDPDSPYE--PG--RRGLAW 195 (201)
T ss_pred EEcCCHHHHHHHHHHHHH------cCCceEEEeCCCCCcC--CC--CcCCCc
Confidence 34678888888776653 3459999999775543 12 235667
No 24
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.50 E-value=6.5e-07 Score=74.24 Aligned_cols=75 Identities=37% Similarity=0.515 Sum_probs=66.8
Q ss_pred ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccc-cccEEEEcCCCCc--cHHHHHHcCCeEEeHHHHHHHHhc
Q psy11421 606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISK-NTNYLVKGQKPGK--KLEKAIKLNIKILDEKNFVKIVKG 680 (687)
Q Consensus 606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk-~t~~LV~G~~~g~--Kl~kA~~lgI~Ii~E~~f~~~l~~ 680 (687)
+|+|.+|+|+|.+....|+++.+++..+||++...++. +++++|+++.... ++..|...+++|++++++.+.+..
T Consensus 2 ~f~g~~~~~~g~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~~ 79 (80)
T smart00292 2 LFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKA 79 (80)
T ss_pred ccCCeEEEEeCCCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHHC
Confidence 68999999999777789999999999999999999998 9999999886553 368888999999999999988753
No 25
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny
Probab=98.41 E-value=3.9e-06 Score=85.05 Aligned_cols=155 Identities=19% Similarity=0.133 Sum_probs=103.4
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh-----hHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK-----DFI 192 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~-----~F~ 192 (687)
..|++|+|+||.-+.+.+.+| =+++.||+ |.|+|+.+..+...-..+.. ...+.+-||+++... +|+
T Consensus 25 ~~~~~E~K~DG~R~~~~~~~~-~v~~~SR~----~~~~t~~~pel~~~~~~~~~---~~~~iLDGElv~~~~~g~~~~F~ 96 (207)
T cd07901 25 GEAAVEYKYDGIRVQIHKDGD-EVRIFSRR----LEDITNALPEVVEAVRELVK---AEDAILDGEAVAYDPDGRPLPFQ 96 (207)
T ss_pred CcEEEEEeEcceeEEEEEeCC-EEEEEeCC----CccccchhhHHHHHHHhcCC---CCCEEEeCEEEEECCCCCccCHH
Confidence 479999999999999877655 47999996 89999987665432111210 146899999998762 576
Q ss_pred HHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCc--
Q psy11421 193 KLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY-- 267 (687)
Q Consensus 193 ~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~--~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~-- 267 (687)
.+-.+. ++... ......++.|++|++...++.++ .....+..+.|.++.-+. +..
T Consensus 97 ~l~~r~-------------------~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i~~ 156 (207)
T cd07901 97 ETLRRF-------------------RRKYDVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAILL 156 (207)
T ss_pred HHHHHh-------------------ccccchhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcEEE
Confidence 553321 11110 01123579999999987655332 247889999998876543 221
Q ss_pred ---eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11421 268 ---SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (687)
Q Consensus 268 ---~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (687)
..+.+.+++.++++.+.+. -..|||+|--+..+
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y 192 (207)
T cd07901 157 APRIVTDDPEEAEEFFEEALEA------GHEGVMVKSLDSPY 192 (207)
T ss_pred EEEEecCCHHHHHHHHHHHHHc------CCceEEEeCCCCCc
Confidence 2356788999988877543 35899999877544
No 26
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=98.39 E-value=1.5e-07 Score=64.56 Aligned_cols=28 Identities=36% Similarity=0.816 Sum_probs=19.1
Q ss_pred CCCCCCCcceeecCceeEEecCCCCCCHH
Q psy11421 417 ICPICNSKIIYIESNLIARCSGSWIECIA 445 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~ 445 (687)
+||+||++|++.++++++||+|+.. |||
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N~l~-CpA 28 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPNPLS-CPA 28 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--CGC--HH
T ss_pred CcCCCCCEeEcCCCCEeEECCCCCc-CCC
Confidence 5999999999999999999999767 997
No 27
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.37 E-value=1.7e-05 Score=90.66 Aligned_cols=216 Identities=17% Similarity=0.107 Sum_probs=137.3
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh-----hHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK-----DFIK 193 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~-----~F~~ 193 (687)
.|++|+|+||.-+.+...+|. ++..||+ |+|+|+....+......++ ...+.+-||++.-.. .|+.
T Consensus 205 ~~~~E~K~DG~R~qih~~~~~-v~l~SR~----~~d~T~~fPei~~~~~~~~----~~~~ILDGElv~~d~~g~~~~F~~ 275 (508)
T PRK03180 205 PAAVEAKLDGARVQVHRDGDD-VRVYTRT----LDDITARLPEVVEAVRALP----VRSLVLDGEAIALRPDGRPRPFQV 275 (508)
T ss_pred CeEEEEEEceeEEEEEEECCE-EEEEeCC----CCcchhhhHHHHHHHHhCC----CcceeecceEEEECCCCCcCCHHH
Confidence 699999999999999887665 7999996 8899988765543222221 246889999997643 5655
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcc--cccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCC-CCceE
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPK--INKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSIC-GEYSV 269 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~--~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~-~~~~~ 269 (687)
+-.+ ++++.+. .....++.|++|++...+|.++ ..+..+..+.|.++--+.. .....
T Consensus 276 l~~R-------------------~~~k~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~~~~~~~~ 336 (508)
T PRK03180 276 TASR-------------------FGRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAHRVPRLV 336 (508)
T ss_pred HHHH-------------------hccccchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccccccccee
Confidence 4321 1111111 1123579999999987666443 2468888888887632111 11234
Q ss_pred eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeec-Ccceee
Q psy11421 270 LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIG-RTGIIT 348 (687)
Q Consensus 270 ~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvG-RTG~iT 348 (687)
+.+.+++.++++...+. ..-|||+|--+..++ -|. +...| +-+|- .......|.+..|--| |+|.++
T Consensus 337 ~~~~~~~~~~~~~a~~~------g~EGlm~K~~ds~Y~--~Gr--R~~~W-lK~K~-~~t~D~VviG~~~G~Gkr~g~~~ 404 (508)
T PRK03180 337 TADPAAAAAFLAAALAA------GHEGVMVKSLDAPYA--AGR--RGAGW-LKVKP-VHTLDLVVLAAEWGSGRRTGKLS 404 (508)
T ss_pred cCCHHHHHHHHHHHHHc------CCceEEEeCCCCCcC--CCC--CCCCc-EEEcC-CCceEEEEEeeecCCCCCCCCcc
Confidence 56788999988776432 458999998775443 122 23456 56664 5778889999988888 566654
Q ss_pred e--EEEEEEEEECCE--EEEEe-cCCCHHHHHh
Q psy11421 349 P--VALLKPVLIDGI--TITRA-TLHNESEIYR 376 (687)
Q Consensus 349 P--vA~lePV~l~G~--tVsra-TLhN~~~i~~ 376 (687)
. +|..+|= +|. +|-++ |.++-+++++
T Consensus 405 ~~llg~~d~~--~~~l~~vgkv~sG~td~~l~~ 435 (508)
T PRK03180 405 NLHLGARDPA--TGGFVMLGKTFKGMTDAMLAW 435 (508)
T ss_pred ceEEEEEeCC--CCeEEEecCccCCCCHHHHHH
Confidence 3 2333331 244 44444 6666655544
No 28
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.
Probab=98.32 E-value=3e-05 Score=83.00 Aligned_cols=209 Identities=19% Similarity=0.187 Sum_probs=131.7
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK 193 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~ 193 (687)
..|++|+|+||.-+.+...+| -++..|| .|+|+|+....+...-..++ ...+.+-||+++- ..+|+.
T Consensus 12 ~~~~~E~K~DG~R~~~~~~~~-~v~l~SR----~g~~~t~~~p~l~~~~~~~~----~~~~iLDGElv~~d~~g~~~F~~ 82 (298)
T TIGR02779 12 DDWRYEVKYDGYRCLARIEGG-KVRLISR----NGHDWTEKFPILAAALAALP----ILPAVLDGEIVVLDESGRSDFSA 82 (298)
T ss_pred CCEEEEEEEceEEEEEEEeCC-EEEEEeC----CCCchHhHhHHHHHHHHhCC----CCcEEEEeEEEEECCCCCCCHHH
Confidence 469999999999998866555 4799999 78999987644443311121 2368999999983 456766
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC-c-e--
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-Y-S-- 268 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~-~-~-- 268 (687)
+-.. ++... ..++.|++|++...++.++ .....+..+.|+++-=+.... . .
T Consensus 83 l~~r-------------------~~~~~-----~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~~~~~~ 138 (298)
T TIGR02779 83 LQNR-------------------LRAGR-----DRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRY 138 (298)
T ss_pred HHhh-------------------hhcCC-----CCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCCCceeEec
Confidence 5321 11111 1579999999987665432 246778888887762111111 1 1
Q ss_pred EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceee
Q psy11421 269 VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIIT 348 (687)
Q Consensus 269 ~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iT 348 (687)
...+.+++.++++...+. -..|||+|--|..++. | +.+.| +-+| +....+..|.+....-||.|.+.
T Consensus 139 ~~~~~~~~~~~~~~~~~~------g~EGiv~K~~ds~Y~~--G---rs~~W-lK~K-~~~~~d~vV~G~~~g~g~~~~~g 205 (298)
T TIGR02779 139 SVHFEGDGQALLEAACRL------GLEGVVAKRRDSPYRS--G---RSADW-LKLK-CRRRQEFVIGGYTPPNGSRSGFG 205 (298)
T ss_pred ccCchhHHHHHHHHHHHc------CCceEEEeCCCCCCCC--C---CCCCc-EEEc-cCCCCEEEEEEEECCCCCCCccc
Confidence 235677888887766432 3589999998866542 2 36778 4555 33456778888888877665544
Q ss_pred eEE--EEEEEEECCE--EEEEe-cCCCHHHHHh
Q psy11421 349 PVA--LLKPVLIDGI--TITRA-TLHNESEIYR 376 (687)
Q Consensus 349 PvA--~lePV~l~G~--tVsra-TLhN~~~i~~ 376 (687)
... ..++ |. .|-++ |..+.+..++
T Consensus 206 slll~~~~~----~~l~~vg~vgsG~s~~~~~~ 234 (298)
T TIGR02779 206 ALLLGVYEG----GGLRYVGRVGTGFSEAELAT 234 (298)
T ss_pred eEEEEEECC----CeEEEEeEecCCCCHHHHHH
Confidence 332 1222 33 34444 6777766665
No 29
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor
Probab=98.26 E-value=1.3e-05 Score=80.12 Aligned_cols=162 Identities=17% Similarity=0.198 Sum_probs=101.1
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh----hhHHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIKL 194 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~----~~F~~~ 194 (687)
.|++|+|+||.-+.+.+.+| -+++.|| .|+++|+....|...=..+ .+..+.+-||+++-. ..|..+
T Consensus 17 ~~~~e~K~DG~R~~i~~~~~-~v~~~SR----~g~~~t~~~p~l~~~~~~~----~~~~~iLDGElv~~~~~~~~~F~~l 87 (190)
T cd07906 17 DWLYEIKWDGYRALARVDGG-RVRLYSR----NGLDWTARFPELAEALAAL----PVRDAVLDGEIVVLDEGGRPDFQAL 87 (190)
T ss_pred CeEEEEeEceEEEEEEEECC-EEEEEcC----CCCcchhhhHHHHHHHHhc----CCCCEEEEeEEEEECCCCCCCHHHH
Confidence 69999999999999988766 5799999 5788887554433210011 134688999999843 356543
Q ss_pred HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCceEeCCH
Q psy11421 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSGV 273 (687)
Q Consensus 195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~~~~~~ 273 (687)
-. ..++.+ .......+.|++|++...++... ..+..+..+.|..+.-+..+...++...
T Consensus 88 ~~-------------------~~~~~~-~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~~~ 147 (190)
T cd07906 88 QN-------------------RLRLRR-RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF 147 (190)
T ss_pred HH-------------------hhcccc-hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECceE
Confidence 21 111111 12234579999999976554332 2578999999999876653434433322
Q ss_pred -HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11421 274 -NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (687)
Q Consensus 274 -~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (687)
.+..++++++.+ -..+|+|+|--+..+. .|. +.+.|
T Consensus 148 ~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y~--~g~--rs~~w 184 (190)
T cd07906 148 EGGGAALFAAACE------LGLEGIVAKRADSPYR--SGR--RSRDW 184 (190)
T ss_pred cCCHHHHHHHHHH------cCCcEEEEecCCCCcC--CCC--CCCcc
Confidence 222455554432 3469999999885554 233 24667
No 30
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.22 E-value=0.00018 Score=76.12 Aligned_cols=205 Identities=17% Similarity=0.206 Sum_probs=127.5
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh----hhHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK----KDFIK 193 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~----~~F~~ 193 (687)
..|++|+|+||.-+.+.-.+| -+++.|| .|.|+|+....+... ..|..+.+-||++... .+|+.
T Consensus 18 ~~~~~E~K~DG~R~~~~~~~~-~v~l~SR----~g~~~t~~fPe~~~~-------~~~~~~vLDGElv~~d~~g~~~F~~ 85 (275)
T PRK07636 18 ENYITEPKFDGIRLIASKNNG-LIRLYTR----HNNEVTAKFPELLNL-------DIPDGTVLDGELIVLGSTGAPDFEA 85 (275)
T ss_pred CcEEEEEEEceeEEEEEEeCC-EEEEEeC----CCCCchhhhhhHHhh-------hcCCCEEEEeEEEEECCCCCCCHHH
Confidence 369999999999997654455 4799999 688999876554321 1244588999999843 46766
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCceEeCC
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSVLSG 272 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~~~~~ 272 (687)
+-... ++..+ ....++.|++|++...++.++ .....+..+.|+++.-+. +....+..
T Consensus 86 l~~r~-------------------~~~~~--~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~-~~~~~~~~ 143 (275)
T PRK07636 86 VMERF-------------------QSKKS--TKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPH-PNVKIIEG 143 (275)
T ss_pred HHHHh-------------------ccccc--cccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCC-CCEEEccc
Confidence 53211 11111 124679999999987665433 247889999999986543 33333332
Q ss_pred -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceeeeEE
Q psy11421 273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVA 351 (687)
Q Consensus 273 -~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iTPvA 351 (687)
.++..++++...+ -...|||+|--|..++. ..+...| +-.| ..+..+..|.+. ..|..|.+ ++
T Consensus 144 ~~~~~~~~~~~~~~------~g~EGiV~K~~ds~Y~~----g~Rs~~W-lKiK-~~~~~e~vV~G~--~~~~~g~l--lg 207 (275)
T PRK07636 144 IEGHGTAYFELVEE------RELEGIVIKKANSPYEI----NKRSDNW-LKVI-NYQYTDVLITGY--RKEEFGLL--LS 207 (275)
T ss_pred ccccHHHHHHHHHH------cCCcEEEEeCCCCCCCC----CCCCCCe-EEEe-cCCeEEEEEEEE--ecCCCcEE--EE
Confidence 2345566655532 23579999998866531 2345678 6666 346667777666 34445533 43
Q ss_pred EEEEEEECCEEEEEecCCCHHHHHhc
Q psy11421 352 LLKPVLIDGITITRATLHNESEIYRK 377 (687)
Q Consensus 352 ~lePV~l~G~tVsraTLhN~~~i~~~ 377 (687)
. .+|..|-++.-...+..+++
T Consensus 208 ~-----~~g~~~G~vgt~~~~~~~~l 228 (275)
T PRK07636 208 Y-----LDGRSAGIMEFMPYDARKKF 228 (275)
T ss_pred e-----cCCeEEEEECCCCHHHHHHH
Confidence 2 25666666633555554443
No 31
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo
Probab=98.21 E-value=3.7e-05 Score=78.72 Aligned_cols=179 Identities=17% Similarity=0.175 Sum_probs=112.5
Q ss_pred ccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccC-
Q psy11421 87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI- 165 (687)
Q Consensus 87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i- 165 (687)
.|||.- -+.+.+++.+ .+ + ...|++|+|+||.-+.+.|.+|.-++..||. |+|+|+....+...
T Consensus 11 ~PMLA~-~~~~~~~~~~---~~----~---~~~~~~E~K~DG~R~~~h~~~~~~v~l~SR~----g~~~t~~~pel~~~~ 75 (219)
T cd07900 11 KPMLAK-PTKGVSEVLD---RF----E---DKEFTCEYKYDGERAQIHLLEDGKVKIFSRN----LENNTEKYPDIVAVL 75 (219)
T ss_pred ccccCC-ccCCHHHHHH---Hh----C---CCeEEEEEeecceEEEEEEcCCCeEEEECCC----CccccchhhHHHHHH
Confidence 488863 3345555422 22 1 2479999999999999999763347999994 89999887654432
Q ss_pred CcccccCCCCceEEEEEEEEeehh------hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEeccc
Q psy11421 166 PLVLNIKYPPELLEVRCEVLIYKK------DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGE 239 (687)
Q Consensus 166 P~~l~~~~~~~~~evRGEi~~~~~------~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~ 239 (687)
...+.. -+..+.+-||+++-.. .|+.+-.. .+...+......++.|++|++..
T Consensus 76 ~~~~~~--~~~~~iLDGElv~~~~~~g~~~~F~~l~~r-------------------~~~~~~~~~~~~~~~~~vFDiL~ 134 (219)
T cd07900 76 PKSLKP--SVKSFILDSEIVAYDRETGKILPFQVLSTR-------------------KRKDVDANDIKVQVCVFAFDLLY 134 (219)
T ss_pred HHHhcc--cCccEEEeeEEEEEEcCCCCCcChHHHhhh-------------------cccccccccCcccEEEEEEEEEE
Confidence 222211 1456899999987543 45543221 01111111234679999999988
Q ss_pred ccCCCC-CCCHHHHHHHHHhcCCCCCCCc-----eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC--hhhh
Q psy11421 240 LRGMNM-PSSHSELLNWYQKIGLSICGEY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC--LSTQ 307 (687)
Q Consensus 240 ~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~-----~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~--~~~~ 307 (687)
.++..+ ..+..+..+.|.++-=+..... ..+.+.+++.++++.+.+. ..-|||+|--+ ..++
T Consensus 135 l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~~~s~Y~ 204 (219)
T cd07900 135 LNGESLLKKPLRERRELLHSLFKEVPGRFQFATSKDSEDTEEIQEFLEEAVKN------NCEGLMVKTLDSDATYE 204 (219)
T ss_pred ECCchhhcCCHHHHHHHHHHhcCCCCCeEEEEEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCccC
Confidence 766442 2467888888887632222111 2346788999988877543 45899999877 5443
No 32
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=98.20 E-value=3.2e-06 Score=68.67 Aligned_cols=55 Identities=33% Similarity=0.421 Sum_probs=50.2
Q ss_pred HHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 522 FIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 522 ~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
+..-+.|||||+++++.|.+. |.++++|..++.++|.+++|||+++|++|...++
T Consensus 4 ~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 4 FDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred HHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 445568999999999999988 9999999999999999999999999999998764
No 33
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.19 E-value=2.8e-06 Score=92.01 Aligned_cols=74 Identities=18% Similarity=0.173 Sum_probs=69.2
Q ss_pred ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC--ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11421 606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG--KKLEKAIKLNIKILDEKNFVKIVKG 680 (687)
Q Consensus 606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g--~Kl~kA~~lgI~Ii~E~~f~~~l~~ 680 (687)
-.+||.|||||... ++|+++.+.+..+|..++.+||..|.+|||.+... .|...|..+|||+++|++|+++|..
T Consensus 294 lv~Gm~v~~~~e~~-~~~d~li~~~~~agL~y~~~~~r~tslvv~n~~~~~~gk~~~a~~~gipl~~d~~fl~~~~~ 369 (377)
T PRK05601 294 LVAGMEVVVAPEIT-MDPDIIIQAIVRAGLAYSEKLTRQTSVVVCNQTRDLDGKAMHAQRKGIPLLSDVAFLAAVER 369 (377)
T ss_pred cccCcEEEEeCCcc-CCHHHHHHHHHHccchhhhccccceeEEEeCCCCCccchhhhhhhcCCCccCHHHHHHHHHH
Confidence 46899999999986 79999999999999999999999999999998654 9999999999999999999999964
No 34
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....
Probab=98.18 E-value=3.5e-05 Score=77.13 Aligned_cols=157 Identities=17% Similarity=0.189 Sum_probs=101.3
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhc-cCCcccccCCCCceEEEEEEEEe------ehhh
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH-KIPLVLNIKYPPELLEVRCEVLI------YKKD 190 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~-~iP~~l~~~~~~~~~evRGEi~~------~~~~ 190 (687)
..|++|+|+||+-+.+.+.+|. +++.|| .|.++|+....+. .+...+.. -+..+.+-||++. ....
T Consensus 19 ~~~~~e~K~DG~R~~i~~~~~~-v~~~SR----~g~~~~~~~~~l~~~l~~~~~~--~~~~~vLDGElv~~d~~~~~~~~ 91 (202)
T PF01068_consen 19 GPWYVEPKYDGVRCQIHKDGGG-VRLFSR----NGKDITSQFPELAEALRELLFP--DGPDFVLDGELVVLDPNTGSPLP 91 (202)
T ss_dssp SCEEEEEEESSEEEEEEEETTE-EEEEET----TSSB-GGGHHHHHHHHHHHBCT--SCTEEEEEEEEEEBETTTSSBCC
T ss_pred CCeEEEEeEeeEEeeeeecccc-ceeecc----cccchhhHHHHHHHHHHHHhcC--CCCceEEEEEEEEEecCCCcchh
Confidence 4799999999999999887776 689999 6888998544331 12222211 1236999999999 3344
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC--
Q psy11421 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE-- 266 (687)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~-~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~-- 266 (687)
|. ..++.+++.+... ....++.|++|++...++..+ ..+..+..+.|.++--+....
T Consensus 92 f~-------------------~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~~~i~ 152 (202)
T PF01068_consen 92 FQ-------------------ELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPPPRIR 152 (202)
T ss_dssp HH-------------------HHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BTSSEE
T ss_pred HH-------------------HHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCCCcee
Confidence 44 4444443322211 114579999999986554321 247888899988775122222
Q ss_pred ---ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11421 267 ---YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (687)
Q Consensus 267 ---~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (687)
...+.+.+++.++++.+.+.. -.|+|+|--+..+
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~g------~EG~v~K~~~~~Y 189 (202)
T PF01068_consen 153 IVESYVVNSKEELEELFEEAIDQG------FEGLVLKDPDSPY 189 (202)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHTT------SSEEEEEETTSSC
T ss_pred EeeeecCCCHHHHHHHHHHHHHcC------CceEEEECCCCcc
Confidence 234678999999988775433 4899999866444
No 35
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.15 E-value=9.2e-05 Score=85.09 Aligned_cols=220 Identities=19% Similarity=0.178 Sum_probs=134.7
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh-cc-CCcccccCCCCceEEEEEEEEeehh------h
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII-HK-IPLVLNIKYPPELLEVRCEVLIYKK------D 190 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i-~~-iP~~l~~~~~~~~~evRGEi~~~~~------~ 190 (687)
.|++|+|+||.-+.+.+.+|. ++..|| -|+|+|+....+ .. +...++. ...+.+-||++.-.. .
T Consensus 188 ~~~~E~K~DG~R~qih~~~~~-v~l~SR----~g~~~t~~~pei~~~~~~~~~~~---~~~~ILDGElv~~d~~~g~~~~ 259 (514)
T TIGR00574 188 KFYVEYKYDGERVQIHKDGDK-FKIFSR----RLENYTYAYPEIFTEFIKEAFPG---IKSCILDGEMVAIDPETGKILP 259 (514)
T ss_pred ceEEEEeecceEEEEEEcCCE-EEEEcC----CCcccccccchhHHHHHHHhcCc---cceeeecceEEEEEcCCCCCcC
Confidence 799999999999999875555 799999 578999765443 21 1111211 125789999997643 4
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcC-cccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCce
Q psy11421 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLN-PKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYS 268 (687)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~-~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~ 268 (687)
|+.+-... ++.+ .......++.||+|++...++.++ ..+..+..+.|.++-=+.+....
T Consensus 260 F~~l~~r~-------------------~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~ 320 (514)
T TIGR00574 260 FQTLLRRK-------------------RRYDIDSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILESILKPIPNRIE 320 (514)
T ss_pred cHhHHhhh-------------------hhccccccccccceEEEEEEEEEECCcchhcCcHHHHHHHHHHhccCCCCcEE
Confidence 65442211 1101 011123578999999987665432 25788999999886433332222
Q ss_pred -----EeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCC-----CceeeEEEEEEE
Q psy11421 269 -----VLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFL-----SKEALTKIKAIN 338 (687)
Q Consensus 269 -----~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~-----~~~~~T~v~~I~ 338 (687)
.+.+.+++.++++...+. -..|+|+|--+..++ .| .+.+.| +=+|-. .+.....|.+..
T Consensus 321 ~~~~~~~~~~e~~~~~~~~~~~~------g~EGlv~K~~ds~Y~--~G--~Rs~~W-lK~K~~y~~~~~~~~D~vvig~~ 389 (514)
T TIGR00574 321 IAEMKITSNVEELEKFLNEAISE------GCEGLMLKDLKSIYE--PG--KRGWLW-LKFKPEYLEGMGDTLDLVVIGAY 389 (514)
T ss_pred EEEEEecCCHHHHHHHHHHHHHc------CCceEEEecCCCccc--CC--CCCCcc-eeCchhhcccccCceeEEEEeeE
Confidence 245788999988766543 359999998775554 23 345667 344421 356778888988
Q ss_pred EeecC-cceeeeEEE--EEEEEECCE--EEEEe-cCCCHHHHHhcC
Q psy11421 339 IQIGR-TGIITPVAL--LKPVLIDGI--TITRA-TLHNESEIYRKN 378 (687)
Q Consensus 339 ~qvGR-TG~iTPvA~--lePV~l~G~--tVsra-TLhN~~~i~~~~ 378 (687)
+.-|| .|.++.... .++- .|. +|.++ |.+..+.++++.
T Consensus 390 ~g~gk~~g~~~~~l~g~~d~~--~~~~~~v~kvgsG~sd~~l~~l~ 433 (514)
T TIGR00574 390 YGKGKRTGMYGSFLLACYDPE--SEEFKTITKVGTGFTDADLQELG 433 (514)
T ss_pred ecCCccCCceeEEEEEEEcCC--CCeEEEEEEECCCCCHHHHHHHH
Confidence 88774 455444322 2210 022 44444 777777777653
No 36
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=98.15 E-value=8.8e-05 Score=81.10 Aligned_cols=214 Identities=14% Similarity=0.136 Sum_probs=130.8
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh---hhHHHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK---KDFIKLN 195 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~---~~F~~~n 195 (687)
.|.+|+|+||.-+.+.+.+|. ++..|| -|.|+|+....|...-..+ .|..+.+-||++.-. .+|+.+.
T Consensus 25 ~w~~E~K~DG~R~~~~~~~~~-v~l~SR----ng~d~t~~fPel~~~~~~~----~~~~~vLDGEiVv~~~~~~~F~~Lq 95 (350)
T PRK08224 25 GWSYEPKWDGFRCLVFRDGDE-VELGSR----NGKPLTRYFPELVAALRAE----LPERCVLDGEIVVARDGGLDFEALQ 95 (350)
T ss_pred cEEEEEeECeeEEEEEEECCE-EEEEeC----CCCCchhhhHHHHHHHHhh----CCCCEEEeeEEEEeCCCCCCHHHHH
Confidence 699999999999988776665 799999 7899998876654322222 245789999999865 3788775
Q ss_pred HHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCceE---eC
Q psy11421 196 KYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEYSV---LS 271 (687)
Q Consensus 196 ~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~~~---~~ 271 (687)
.... . ++.+ .+++ ....++.|++|++...++.++ .....+..+.|+++ |+..+...+ ..
T Consensus 96 ~r~~---~----~~~~-----~~~~----~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l-~~~~~~i~~~~~~~ 158 (350)
T PRK08224 96 QRIH---P----AASR-----VRKL----AEETPASFVAFDLLALGDRDLTGRPFAERRAALEAA-AAGSGPVHLTPATT 158 (350)
T ss_pred hhhh---c----cccc-----hhhh----hhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHh-cCCCCcEEEecccC
Confidence 3211 0 0101 1111 123469999999988666443 24677888888877 333222233 23
Q ss_pred CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceeeeE-
Q psy11421 272 GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPV- 350 (687)
Q Consensus 272 ~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iTPv- 350 (687)
+.++..++++... .--..|||+|--|..++ -|..+ | +-+|. ....+..|.+..+.-|+ |.+.-.
T Consensus 159 ~~~~~~~~~~~a~------~~G~EGIV~Kr~dS~Y~--~Grr~----W-lKiK~-~~~~d~vI~G~~~g~~~-~~~gsll 223 (350)
T PRK08224 159 DPATARRWFEEFE------GAGLDGVIAKPLDGPYQ--PGKRA----M-FKVKH-ERTADCVVAGYRYHKSG-PVVGSLL 223 (350)
T ss_pred CHHHHHHHHHHHH------hCCCcEEEEeCCCCCcC--CCCcC----E-EEEcc-CCcEEEEEEEEEcCCCC-CccccEE
Confidence 4567777776553 23468999999886554 23322 7 55553 45667788887776655 332221
Q ss_pred -EEEEEEEECCE--EEEEecCCCHHHHHh
Q psy11421 351 -ALLKPVLIDGI--TITRATLHNESEIYR 376 (687)
Q Consensus 351 -A~lePV~l~G~--tVsraTLhN~~~i~~ 376 (687)
+..++ +|. .|-+++..+.+..++
T Consensus 224 lg~~d~---~g~l~~vG~v~Gf~~~~~~~ 249 (350)
T PRK08224 224 LGLYDD---DGQLHHVGVTSAFPMARRRE 249 (350)
T ss_pred EEEECC---CCcEEEEEEECCCCHHHHHH
Confidence 11111 242 455566666665554
No 37
>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases. ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved seq
Probab=98.11 E-value=3e-05 Score=76.76 Aligned_cols=150 Identities=17% Similarity=0.160 Sum_probs=96.4
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY 197 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~ 197 (687)
..|.+|+|+||.-+.+.+.+|. +.++|| .|+++|.-...+.. ..+. ..+..+.+-||++.....+
T Consensus 19 ~~~~~e~K~DG~R~~~~~~~~~-v~~~sR----~g~~~~~~~~~~~~--~~~~--~~~~~~ilDGElv~~~~~~------ 83 (182)
T cd06846 19 DEYYVQEKYDGKRALIVALNGG-VFAISR----TGLEVPLPSILIPG--RELL--TLKPGFILDGELVVENREV------ 83 (182)
T ss_pred CcEEEEEccCceEEEEEEcCCe-EEEEeC----CCCEEecccccccc--hHHh--ccCCCeeEEEEEEeccCCC------
Confidence 4799999999999999887665 789999 57777765433321 0111 1244689999999864433
Q ss_pred HHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCC--CceE-----
Q psy11421 198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG--EYSV----- 269 (687)
Q Consensus 198 ~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~--~~~~----- 269 (687)
....+.|++|++...++.+. .....++++.|+++-=.... ...+
T Consensus 84 ----------------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~~~ 135 (182)
T cd06846 84 ----------------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPLEN 135 (182)
T ss_pred ----------------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEeec
Confidence 12368999999987665332 24678888888776422211 1111
Q ss_pred eC-CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11421 270 LS-GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (687)
Q Consensus 270 ~~-~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (687)
+. ..+++.++++++ .+...||+|+|--+..+. |...+.+.|
T Consensus 136 ~~~~~~~~~~~~~~~------~~~g~EGvi~K~~~s~Y~---~~~gr~~~w 177 (182)
T cd06846 136 APSYDETLDDLLEKL------KKKGKEGLVFKHPDAPYK---GRPGSSGNQ 177 (182)
T ss_pred ccccchHHHHHHHHh------hhcCCceEEEEcCCCCcc---ccCCCCCce
Confidence 11 222356665544 346789999999886663 445566766
No 38
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.
Probab=98.10 E-value=6e-05 Score=76.45 Aligned_cols=157 Identities=17% Similarity=0.114 Sum_probs=100.8
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehh----hHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKK----DFIK 193 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~----~F~~ 193 (687)
..|++|+|+||.-+.+...+| =++..|| .|+|+|+....+...-.. .|..+.+-||+++-.. +|+.
T Consensus 24 ~~~~~E~K~DG~R~~~~~~~~-~v~l~SR----~g~~~t~~~p~l~~~~~~-----l~~~~iLDGElv~~~~~~~~~F~~ 93 (207)
T cd07897 24 SDWQAEWKWDGIRGQLIRRGG-EVFLWSR----GEELITGSFPELLAAAEA-----LPDGTVLDGELLVWRDGRPLPFND 93 (207)
T ss_pred ccEEEEEeEceEEEEEEEcCC-EEEEEeC----CCCcccccchHHHHHHHh-----CCCCeEEEeEEEEecCCCccCHHH
Confidence 379999999999998765444 5799999 467898765544332111 3556899999998654 7877
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCC-CC-----
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC-GE----- 266 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~-~~----- 266 (687)
+..+.. . ++ +... .....++.|++|++...++..+. ....+..+.|.++--+.. ..
T Consensus 94 l~~r~~---~------~~-~~~~-------~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~i~~~~ 156 (207)
T cd07897 94 LQQRLG---R------KT-VGKK-------LLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPPRLDLSP 156 (207)
T ss_pred HHHHhc---c------cc-cchh-------hHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcCCCceeecc
Confidence 643311 0 00 0011 11235789999999876653321 357788888877622221 11
Q ss_pred ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11421 267 YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (687)
Q Consensus 267 ~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (687)
...+.+.+++.++++...+. ...|||+|--+..++
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~------g~EGiv~K~~~s~Y~ 191 (207)
T cd07897 157 LIAFADWEELAALRAQSRER------GAEGLMLKRRDSPYL 191 (207)
T ss_pred eEecCCHHHHHHHHHHHHHc------CCeEEEEeCCCCCcC
Confidence 12356788999988876543 358999999886554
No 39
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more di
Probab=98.04 E-value=0.00023 Score=72.89 Aligned_cols=167 Identities=19% Similarity=0.164 Sum_probs=103.4
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCC---ccccc--CCCCceEEEEEEEEeehh---
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP---LVLNI--KYPPELLEVRCEVLIYKK--- 189 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP---~~l~~--~~~~~~~evRGEi~~~~~--- 189 (687)
..|++|+|+||.-+.+.+.+|. +++.|| .|.|+|+....+...- ..|.. ...+..+.+-||+++...
T Consensus 33 ~~~~~E~K~DG~R~~i~~~~~~-v~l~SR----~g~~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~~~~~~ 107 (225)
T cd07903 33 KPFYIETKLDGERIQLHKDGNE-FKYFSR----NGNDYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVWDKETK 107 (225)
T ss_pred CeEEEEEeeCceEEEEEecCCE-EEEEeC----CCccccccccccccccccchhhhhhccccCcEEEeceEEEEEEcCcC
Confidence 5799999999999999887665 799999 6888887654332210 01100 012457899999997432
Q ss_pred ---hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCC
Q psy11421 190 ---DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICG 265 (687)
Q Consensus 190 ---~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~ 265 (687)
.|..+ ++.++ ++.. ......+.|++|++...++.+. .....+..+.|.++--+...
T Consensus 108 ~~~~f~~l---------------~~~~~--~~~~---~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~~~~ 167 (225)
T cd07903 108 RFLPFGTL---------------KDVAK--LREV---EDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPIPG 167 (225)
T ss_pred eeccchHH---------------HHHHh--hccc---ccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCCCCC
Confidence 34332 11111 1100 1123568999999987655432 24688888889887433222
Q ss_pred Cc-----eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCc
Q psy11421 266 EY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRF 319 (687)
Q Consensus 266 ~~-----~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prw 319 (687)
.. ..+.+.+++.++++.+.+.. ..|+|+|--+..+.. | .+...|
T Consensus 168 ~i~~~~~~~~~~~~~~~~~~~~~~~~g------~EGlv~K~~~s~Y~~--g--~Rs~~w 216 (225)
T cd07903 168 RLEVVKRTEASTKEEIEEALNEAIDNR------EEGIVVKDLDSKYKP--G--KRGGGW 216 (225)
T ss_pred eEEEEEEEeCCCHHHHHHHHHHHHHcC------CceEEEecCCCCCcc--C--CcCCCc
Confidence 22 22456788999888775433 699999998755441 2 245667
No 40
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=98.03 E-value=0.00044 Score=77.91 Aligned_cols=215 Identities=19% Similarity=0.211 Sum_probs=138.9
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhh-hhccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIH-IIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK 193 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~-~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~ 193 (687)
.|.+|+|+||.-+.+...+|. ++.+|| .|+|||+... .+..+=..++ +..+.+-||+++- ..+|+.
T Consensus 134 ~w~~E~K~DG~R~q~h~~~~~-vrl~SR----~g~d~T~~fP~~~~~~~~~l~----~~~~iiDGE~V~~~~~~~~~F~~ 204 (444)
T COG1793 134 DWAYEEKFDGYRVQIHIDGGK-VRLYSR----NGEDWTGRFPDILEAAAEALP----ADDFILDGEIVVLDEEGRLDFQA 204 (444)
T ss_pred CEEEEEeeceEEEEEEEcCCE-EEEEeC----CCccchhhChHHHHHHHhcCC----CCceEEeeeEEEECCCCCCCHHH
Confidence 599999999999999998885 799999 6999998876 3433322232 3468999999995 568887
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhc--C---CCCCC
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKI--G---LSICG 265 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~--~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~--G---f~~~~ 265 (687)
+.+.. +++.+ ......++.||+|++...++.++. ....+..+.|.++ + +...+
T Consensus 205 Lq~r~-------------------~~k~~v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~~~~~~ 265 (444)
T COG1793 205 LQQRL-------------------RRKYDVAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDKIEIAE 265 (444)
T ss_pred HHHHh-------------------hhccchhhhccCCceEEEEEEEEeECCcccccCchHHHHHHHHHHhcccccccccc
Confidence 65432 22211 111334789999999987776542 2556666666553 1 23333
Q ss_pred CceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcc
Q psy11421 266 EYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTG 345 (687)
Q Consensus 266 ~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG 345 (687)
... +.+.+++..+++... ..-+.|||+|--|..++. ..+.-.| +-+| +.++..-.|.+..++-|+-+
T Consensus 266 ~i~-~~~~~~~~~~~~~a~------~~g~EGvv~K~~ds~Y~~----g~R~~~W-~K~K-~~~~~d~vv~G~~~g~Gkr~ 332 (444)
T COG1793 266 RIP-FSDAEEGEAFLEAAI------ELGLEGVVAKRPDSPYRA----GGRSNKW-LKVK-RDETLDLVVVGAEYGKGKRS 332 (444)
T ss_pred cee-ccChhhHHHHHHHHH------hcCceEEEEeCCCCCcCC----CCCCCcc-eEec-cCCcccEEEEEEEecCCccc
Confidence 332 367788888776543 346899999955544441 1122334 3444 33788999999999998865
Q ss_pred eeeeEEEEEEEEECCE-----EEEEecCCCHHHHHh
Q psy11421 346 IITPVALLKPVLIDGI-----TITRATLHNESEIYR 376 (687)
Q Consensus 346 ~iTPvA~lePV~l~G~-----tVsraTLhN~~~i~~ 376 (687)
+-=+-+-.+.-++. .++=.|...-++.++
T Consensus 333 --~~~slll~~~~~~~~~~~~v~kVgtGf~~~~l~~ 366 (444)
T COG1793 333 --LYGSLLLGVYDGDGGGLLYVGKVGTGFSDAELEE 366 (444)
T ss_pred --ccceEEEEEEcCCCceEEEEecccCCCCHHHHHH
Confidence 44455566666664 333345565444433
No 41
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=97.94 E-value=0.00028 Score=82.41 Aligned_cols=216 Identities=17% Similarity=0.151 Sum_probs=134.5
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCC-cccccCCCCceEEEEEEEEeehh------hH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIP-LVLNIKYPPELLEVRCEVLIYKK------DF 191 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP-~~l~~~~~~~~~evRGEi~~~~~------~F 191 (687)
.|++|.|+||.-+.+.+.+|. ++..||+ |+|+|+....|...- ..+. +..+.+-||++.-.. .|
T Consensus 249 ~~~~E~K~DG~R~qih~~~~~-v~l~SR~----~~d~T~~~pel~~~~~~~~~----~~~~ILDGElv~~d~~~g~~~~F 319 (590)
T PRK01109 249 EALVEYKYDGERAQIHKKGDK-VKIFSRR----LENITHQYPDVVEYAKEAIK----AEEAIVEGEIVAVDPETGEMRPF 319 (590)
T ss_pred CeEEEecCCceEEEEEEcCCE-EEEEeCC----chhhccccchHHHHHHHhcC----ccceEEeeeEEEEECCCCcccCh
Confidence 589999999999999886665 7999994 999998876654321 1232 346889999987541 46
Q ss_pred HHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCCc---
Q psy11421 192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGEY--- 267 (687)
Q Consensus 192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~~--- 267 (687)
+.+-.+ . |...... .....++.|++|++...+|..+ ..+..++.+.|.++- ...+..
T Consensus 320 ~~l~~R----~-------r~~~~~~-------~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~-~~~~~~~~~ 380 (590)
T PRK01109 320 QELMHR----K-------RKYDIEE-------AIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIV-KENDKVKLA 380 (590)
T ss_pred HHHhhc----c-------cccchhh-------hcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhc-CCCCceEEe
Confidence 654321 0 1100000 1124579999999988766443 246888888888763 222222
Q ss_pred --eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC--ChhhhhhhCCCCCCCCceEeecCC-------CceeeEEEEE
Q psy11421 268 --SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN--CLSTQKKLGFTSRAPRFALAYKFL-------SKEALTKIKA 336 (687)
Q Consensus 268 --~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~--~~~~~~~lG~ts~~PrwaiA~Kf~-------~~~~~T~v~~ 336 (687)
....+.+++.++++...+. -.-|||+|-- |..++ -| .+...| +|+- .+.....|.+
T Consensus 381 ~~~~~~~~~~~~~~~~~a~~~------g~EGiv~K~~~~ds~Y~--~g--~Rs~~W---lK~K~dy~~~~~~~~DlvviG 447 (590)
T PRK01109 381 ERIITDDVEELEKFFHRAIEE------GCEGLMAKSLGKDSIYQ--AG--ARGWLW---IKYKRDYQSEMADTVDLVVVG 447 (590)
T ss_pred eeEecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCCcC--CC--CCCccH---HHhhHHhhcccCCceeEEEEE
Confidence 2345778999988766543 3589999987 54443 12 345677 5554 3456778888
Q ss_pred EEEeecC-cceeeeE--EEEEEEEECCE--EEEEe-cCCCHHHHHhc
Q psy11421 337 INIQIGR-TGIITPV--ALLKPVLIDGI--TITRA-TLHNESEIYRK 377 (687)
Q Consensus 337 I~~qvGR-TG~iTPv--A~lePV~l~G~--tVsra-TLhN~~~i~~~ 377 (687)
..|--|| +|.+... |..+| =+|. +|-++ |..+.+.++++
T Consensus 448 ~~~g~Gkr~~~~g~~ll~~~d~--~~~~~~~v~kvgtG~sd~~~~~l 492 (590)
T PRK01109 448 AFYGRGRRGGKYGSLLMAAYDP--KTDTFETVCKVGSGFTDEDLDEL 492 (590)
T ss_pred eEeCCCccCCccccEEEEEEcC--CCCeEEEEEEECCCCCHHHHHHH
Confidence 8777665 5555432 22222 1232 34444 77777777654
No 42
>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is
Probab=97.93 E-value=0.00012 Score=73.47 Aligned_cols=158 Identities=15% Similarity=0.115 Sum_probs=98.3
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee---hhhHHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY---KKDFIKL 194 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~---~~~F~~~ 194 (687)
..|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+....+...-..+ .|..+.+-||+++- ..+|+.+
T Consensus 16 ~~~~~E~K~DG~R~~~~~~~~~-v~l~SR----~g~~~t~~~p~~~~~~~~~----~~~~~iLDGElv~~~~~~~~F~~l 86 (194)
T cd07905 16 GGWQYEPKWDGFRCLAFRDGDE-VRLQSR----SGKPLTRYFPELVAAARAL----LPPGCVLDGELVVWRGGRLDFDAL 86 (194)
T ss_pred CceEEEeeeceEEEEEEEeCCE-EEEEeC----CCCchhhhhHHHHHHHHhh----CCCCEEEEeEEEEEcCCCCCHHHH
Confidence 3699999999999998876664 799999 7889997654433211111 24568999999984 3467665
Q ss_pred HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCCCCce---Ee
Q psy11421 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEYS---VL 270 (687)
Q Consensus 195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~~~~~---~~ 270 (687)
-..- . +|.. .. +......++.|++|++...++.++. ....+..+.|.++-=+..+... .+
T Consensus 87 ~~r~---~------~~~~---~~----~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~ 150 (194)
T cd07905 87 QQRI---H------PAAS---RV----RRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPAT 150 (194)
T ss_pred HHHh---c------cccc---ch----hhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEECCcc
Confidence 4321 1 1100 00 1112346799999999876554322 4677888888766211112122 23
Q ss_pred CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11421 271 SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (687)
Q Consensus 271 ~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (687)
.+.+++.++++...+ -..-|||+|--+..+
T Consensus 151 ~~~~~~~~~~~~~~~------~g~EGiv~K~~~s~Y 180 (194)
T cd07905 151 TDRAEAREWLEEFEG------AGLEGVVAKRLDGPY 180 (194)
T ss_pred CCHHHHHHHHHHHHH------CCCceEEEeCCCCCc
Confidence 466777777776543 235899999877554
No 43
>PHA00454 ATP-dependent DNA ligase
Probab=97.91 E-value=0.0027 Score=68.63 Aligned_cols=217 Identities=19% Similarity=0.130 Sum_probs=122.9
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh---ccCCccccc--CCCCceEEEEEEEEeehhhHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII---HKIPLVLNI--KYPPELLEVRCEVLIYKKDFIK 193 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i---~~iP~~l~~--~~~~~~~evRGEi~~~~~~F~~ 193 (687)
.|.+|+|+||.-+.+...+|.=+++.||.- .+++.-+... ..++..+.. ...|..+.+-||++....+|+.
T Consensus 28 ~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g----~~~p~l~~~~~~~~~~~~~~~~~~~~l~~~~vLDGElv~~~~~f~~ 103 (315)
T PHA00454 28 YLIADVKYDGVRGNIVVDNTADHGWLSREG----KTIPALEHLNGFDRRWAKLLNDDRCIFPDGFMLDGELMVKGVDFNT 103 (315)
T ss_pred cEEEEEccceEEEEEEEcCCCeEEEEeCCC----CcccchhhhhhhhhhhhhhhhhhhhcCCCCeEEEEEEEecCCCHHH
Confidence 699999999999998776664479999953 3454322111 112222221 0124578999999997666765
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcC--cccccccccEEEEEecccccCC----CC----CCCHHHHHHHHHhcC---
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLN--PKINKNKILHFFAHGVGELRGM----NM----PSSHSELLNWYQKIG--- 260 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~--~~~~~~r~l~f~~y~~~~~~~~----~~----~~~~~e~l~~L~~~G--- 260 (687)
+. |.|+++. +......++.|++|++...++. .+ .....+.-+.|.++-
T Consensus 104 ~~-------------------~~l~~k~~~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L~~l~~~~ 164 (315)
T PHA00454 104 GS-------------------GLLRRKWKVLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMVPLLMEYF 164 (315)
T ss_pred HH-------------------HHhccCccchhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHHHHHHhhC
Confidence 43 3343332 1222346899999999875522 11 123444445554331
Q ss_pred ----CCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEE
Q psy11421 261 ----LSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKA 336 (687)
Q Consensus 261 ----f~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~ 336 (687)
+..++ ...+.+.+++.++++...+ -...|||+|--|..++. |.. ..|- -+| +...++..|.+
T Consensus 165 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~------~g~EGiv~K~~ds~Y~~--Grr---~~~~-K~K-~~~~~d~vIvG 230 (315)
T PHA00454 165 PEIDWFLSE-SYEVYDMESLQELYEKKRA------EGHEGLVVKDPSLIYRR--GKK---SGWW-KMK-PECEADGTIVG 230 (315)
T ss_pred CCcceEeec-eEEcCCHHHHHHHHHHHHh------CCCceEEEeCCCCCCCC--CCc---cCcE-EEc-ccCceeEEEEE
Confidence 12222 2234578899998876642 34689999987765542 332 2362 444 33467888888
Q ss_pred EEEeecC-c--ceeeeEEEEEEEEECCEEEEEecCCCHHHHHh
Q psy11421 337 INIQIGR-T--GIITPVALLKPVLIDGITITRATLHNESEIYR 376 (687)
Q Consensus 337 I~~qvGR-T--G~iTPvA~lePV~l~G~tVsraTLhN~~~i~~ 376 (687)
..+--|+ . |.+-- -+--. =+|. ...+|..+.+..++
T Consensus 231 ~~~g~g~~~~~g~~~~--~~~~~-~~g~-l~~gtGfs~~~~~~ 269 (315)
T PHA00454 231 VVWGTPGLANEGKVIG--FRVLL-EDGR-VVNATGISRALMEE 269 (315)
T ss_pred EEECCCCccCCceEEE--EEEEe-CCCc-EEEccCCCHHHHHH
Confidence 8887742 3 33322 11000 1343 33477777766654
No 44
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.89 E-value=2.1e-05 Score=95.20 Aligned_cols=76 Identities=26% Similarity=0.298 Sum_probs=68.4
Q ss_pred CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcC---CCCccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11421 604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQ---KPGKKLEKAIKLNIKILDEKNFVKIVKG 680 (687)
Q Consensus 604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~---~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~ 680 (687)
..||.|+.|++.|+|+ .++.+++.+|+.+||+++.+|++.|++||+.. +.++|+++|+++||+|++|+++.+.+..
T Consensus 391 ~~~l~~~~i~i~G~~~-~~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk~~~ipIVsedwL~ds~~~ 469 (981)
T PLN03123 391 SEFLGDLKVSIVGASK-EKVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCFKK 469 (981)
T ss_pred CCCcCCeEEEEecCCC-CcHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHHhc
Confidence 3689999999999996 47899999999999999999999999998886 3569999999999999999999877643
No 45
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc
Probab=97.88 E-value=0.00027 Score=72.00 Aligned_cols=152 Identities=15% Similarity=0.154 Sum_probs=95.9
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhh-hhhhcc-CCcccccCCCCceEEEEEEEEeehh------h
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTN-IHIIHK-IPLVLNIKYPPELLEVRCEVLIYKK------D 190 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n-~~~i~~-iP~~l~~~~~~~~~evRGEi~~~~~------~ 190 (687)
.|++|+|+||.-+.+.+.+|. +++.||+ |.|+|.. +..+.. ++..+.. ...+.+-||+++-.. .
T Consensus 35 ~~~~E~K~DG~R~~i~~~~~~-v~l~SR~----g~~~t~~~~~~~~~~~~~~~~~---~~~~iLDGEiv~~d~~~g~~~~ 106 (213)
T cd07902 35 GMYAEIKYDGERVQVHKQGDN-FKFFSRS----LKPVLPHKVAHFKDYIPKAFPH---GHSMILDSEVLLVDTKTGKPLP 106 (213)
T ss_pred ceEEEeccCCEEEEEEEcCCE-EEEEcCC----CcccccchhHHHHHHHHHhccc---ccceeeeeEEEEEECCCCcccc
Confidence 599999999999988776555 7999995 7888853 222221 2322321 346899999998432 2
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC---
Q psy11421 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE--- 266 (687)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~--- 266 (687)
|..+.. ..+. . ....++.|++|++...++.++ .....+..+.|.++--+....
T Consensus 107 F~~l~~-------------------~~~~--~--~~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~~~~ 163 (213)
T cd07902 107 FGTLGI-------------------HKKS--A--FKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNRIML 163 (213)
T ss_pred cchhhh-------------------hhcc--c--cccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCeEEE
Confidence 332210 0010 0 123469999999887655432 146788888888763222221
Q ss_pred --ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11421 267 --YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (687)
Q Consensus 267 --~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (687)
...+.+.+++.++++.+.+. -..|||+|--+..++
T Consensus 164 ~~~~~~~~~~~l~~~~~~~~~~------g~EGvV~K~~~s~Y~ 200 (213)
T cd07902 164 SEMKFVKKADDLSAMIARVIKE------GLEGLVLKDLKSVYE 200 (213)
T ss_pred EEEEEcCCHHHHHHHHHHHHHC------CCCeEEEeCCCCCcc
Confidence 12346788998888877543 358999999875554
No 46
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.87 E-value=1.6e-05 Score=65.60 Aligned_cols=58 Identities=21% Similarity=0.250 Sum_probs=45.8
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCC
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTT 518 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~ 518 (687)
+|+|+|+|+++.+.|.+.= .|++.|...+.++|..+||+|++.|++|++.++..+++.
T Consensus 5 aLGI~~VG~~~ak~L~~~f--~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~~ 62 (64)
T PF12826_consen 5 ALGIPGVGEKTAKLLAKHF--GSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENRE 62 (64)
T ss_dssp HCTSTT--HHHHHHHHHCC--SCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHHH
T ss_pred eCCCCCccHHHHHHHHHHc--CCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhhh
Confidence 6999999999999998764 599999999999999999999999999999998876543
No 47
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res
Probab=97.87 E-value=0.00031 Score=72.72 Aligned_cols=170 Identities=16% Similarity=0.149 Sum_probs=102.8
Q ss_pred CeeEEEEEccceeEEEEEEe---CCEEEEEEecCCCCccchhhhhhhhhccC-Ccccc----cCCCCceEEEEEEEEeeh
Q psy11421 117 NIEYIAELKFDGIAVNLRYE---YGYLKQASTRGDGNIGENITTNIHIIHKI-PLVLN----IKYPPELLEVRCEVLIYK 188 (687)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~---~G~l~~a~TRGdG~~GeDvT~n~~~i~~i-P~~l~----~~~~~~~~evRGEi~~~~ 188 (687)
...|++|+|.||.-+.+.+. +|.-++..|| -|+|+|+....+..+ ...+. ....+..+.+-||+++-.
T Consensus 21 ~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR----~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILDGEiVv~d 96 (235)
T cd08039 21 SRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSK----SGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILEGEMVVWS 96 (235)
T ss_pred CCcEEEEEeecceEEEEEEecccCCCEEEEEeC----CCCcccccchhHHHHHHHHhhccccccCCCccEEEEeEEEEEE
Confidence 34799999999999999875 2445899999 789999865433211 11110 000135799999996532
Q ss_pred ------hhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCC
Q psy11421 189 ------KDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGL 261 (687)
Q Consensus 189 ------~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf 261 (687)
..|+.+... . ..++.... ...++......++.|++|++...+|..+ ..+..+..+.|.++--
T Consensus 97 ~~~g~~~~F~~L~~~-~--------~~~~~~~~--~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~ 165 (235)
T cd08039 97 DRQGKIDPFHKIRKH-V--------ERSGSFIG--TDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVH 165 (235)
T ss_pred CCCCccCCHHHHHhh-c--------ccccchhc--cccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcc
Confidence 378876321 1 11111000 0111122234679999999987655432 2578889999988743
Q ss_pred CCCCCceE-----e-----CCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11421 262 SICGEYSV-----L-----SGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (687)
Q Consensus 262 ~~~~~~~~-----~-----~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (687)
+++....+ + .+.+++.++++...+. -.-|||+|--+..+.
T Consensus 166 ~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~a~~~------g~EGIv~K~~~S~Y~ 215 (235)
T cd08039 166 VIPGYAGLSERFPIDFSRSSGYERLRQIFARAIAE------RWEGLVLKGDEEPYF 215 (235)
T ss_pred cCCCcEEEEEEEeecccCCCCHHHHHHHHHHHHHc------CCceEEEecCCCCcc
Confidence 33322111 1 2577888887765432 348999999886554
No 48
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.87 E-value=0.00054 Score=79.91 Aligned_cols=187 Identities=16% Similarity=0.160 Sum_probs=116.1
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccC----CcccccCCCCceEEEEEEEEee----hh
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKI----PLVLNIKYPPELLEVRCEVLIY----KK 189 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~i----P~~l~~~~~~~~~evRGEi~~~----~~ 189 (687)
..|++|.|+||.-+.+.+.+|. ++..|| -|+|+|+....|... +..++. ...+.+-||++.- ..
T Consensus 16 ~~w~~E~K~DG~R~~~h~~~~~-V~L~SR----ng~d~T~~fPel~~~~~~~~~~~~~---~~~~ILDGEiVvld~~g~~ 87 (610)
T PRK09633 16 DEWRYEVKYDGFRCLLIIDETG-ITLISR----NGRELTNTFPEIIEFCESNFEHLKE---ELPLTLDGELVCLVNPYRS 87 (610)
T ss_pred CcEEEEEeEcceEEEEEEECCE-EEEEeC----CCCcchhhhhHHHHHHHhhhhcccc---CCceeeeeEEEEecCCCCC
Confidence 3699999999999998887665 799999 689999876654332 222211 1247899999984 46
Q ss_pred hHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCC----
Q psy11421 190 DFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC---- 264 (687)
Q Consensus 190 ~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~---- 264 (687)
+|+.+...... .++.+ +.+ .....++.|++|++...+|.++. .+..+..+.|+++-=+..
T Consensus 88 ~F~~Lq~R~~~------~~~~~-----i~~----~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~ 152 (610)
T PRK09633 88 DFEHVQQRGRL------KNTEV-----IAK----SANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPAS 152 (610)
T ss_pred CHHHHHhhhhc------cccch-----hhh----hhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhcccccc
Confidence 78876543110 11111 111 11346799999999887665432 467777777776511110
Q ss_pred ------CCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEE
Q psy11421 265 ------GEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAIN 338 (687)
Q Consensus 265 ------~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~ 338 (687)
+....+.+.+++.++++...+ ...-|||+|--+..++. ..+...| +-+|. .......|.+..
T Consensus 153 ~~~~~~~~i~~~~~~~~~~~l~~~a~~------~g~EGIV~Kr~dS~Y~~----G~Rs~~W-lKiK~-~~~~d~vI~G~~ 220 (610)
T PRK09633 153 PDPYAKARIQYIPSTTDFDALWEAVKR------YDGEGIVAKKKTSKWLE----NKRSKDW-LKIKN-WRYVHVIVTGYD 220 (610)
T ss_pred cccccccceEEcCCHHHHHHHHHHHHH------cCCceEEEeCCCCCCCC----CCCCCCe-EEEec-cCCceeEEEEEe
Confidence 133455677788887776543 23599999988755421 2244556 45553 355566777764
Q ss_pred E
Q psy11421 339 I 339 (687)
Q Consensus 339 ~ 339 (687)
+
T Consensus 221 ~ 221 (610)
T PRK09633 221 P 221 (610)
T ss_pred c
Confidence 4
No 49
>PHA02587 30 DNA ligase; Provisional
Probab=97.82 E-value=0.0017 Score=74.26 Aligned_cols=222 Identities=13% Similarity=0.123 Sum_probs=130.4
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh----ccCCcccccCCCCceEEEEEEEEeehh-----
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII----HKIPLVLNIKYPPELLEVRCEVLIYKK----- 189 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i----~~iP~~l~~~~~~~~~evRGEi~~~~~----- 189 (687)
.|.+|+|.||.-+.+...+|. ++..|| -|+|+|. ...| ..+...+.. .|..+.+-||++.-..
T Consensus 153 ~~~~E~K~DG~R~q~h~~~~~-v~l~SR----~g~~~~~-~p~i~~~l~~~~~~~~~--~~~~~VLDGElv~~~~~~~~~ 224 (488)
T PHA02587 153 PAYAQLKADGARCFADIDADG-IEIRSR----NGNEYLG-LDLLKEELKKMTAEARQ--RPGGVVIDGELVYVEVETKKP 224 (488)
T ss_pred cEEEEEccCceEEEEEEeCCE-EEEEec----CCccccC-ChhHHHHHHHHhhhhcc--cCCcEEEEeEEEEEecccCCC
Confidence 699999999999999887765 799999 4777753 2221 112222211 2456899999997622
Q ss_pred -------------hH-HHHHHHHHHcCCCCCCChhhhHHhHhh---hcCcccccccccEEEEEecccc----cCCCCCCC
Q psy11421 190 -------------DF-IKLNKYRYHLGLKKFTNPRNAAAGILR---QLNPKINKNKILHFFAHGVGEL----RGMNMPSS 248 (687)
Q Consensus 190 -------------~F-~~~n~~~~~~g~~~f~NpRN~aaG~lr---~~~~~~~~~r~l~f~~y~~~~~----~~~~~~~~ 248 (687)
+| +.+- .|..-.|..+ +.........++.|++|++... .+......
T Consensus 225 ~~~~f~~~~~~~~~f~q~l~-------------~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~p 291 (488)
T PHA02587 225 NGLSFLFDDSKAKEFVGVVA-------------DRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMP 291 (488)
T ss_pred ccchhhcccccccchhhhhh-------------hhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCC
Confidence 11 1111 1221112211 1111123456799999998632 11111246
Q ss_pred HHHHHHHHHhcCCCC--CCCc-----eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceE
Q psy11421 249 HSELLNWYQKIGLSI--CGEY-----SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFAL 321 (687)
Q Consensus 249 ~~e~l~~L~~~Gf~~--~~~~-----~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~Prwai 321 (687)
..+..+.|.++ |.. .+.. ..+.+.+++.+++++..+ --..|||+|--+..++ -| +...| +
T Consensus 292 l~eRr~~L~~l-~~~~~~~~i~l~~~~~~~~~ee~~~~~~~a~~------~G~EGimlK~~ds~Y~--~G---Rs~~W-l 358 (488)
T PHA02587 292 YDDRFSKLAQM-FEDCGYDRVELIENQVVNNLEEAKEIYKRYVD------QGLEGIILKNTDGLWE--DG---RSKDQ-I 358 (488)
T ss_pred HHHHHHHHHHH-HhhcCCCcEEEEeeEEcCCHHHHHHHHHHHHh------CCCCeEEEECCCCCCC--CC---CCCCc-E
Confidence 77888887765 210 1111 235788999998876643 3468999998775553 24 22235 5
Q ss_pred eecCCCceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEE-ecCCCHHHHHhcC
Q psy11421 322 AYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGITITR-ATLHNESEIYRKN 378 (687)
Q Consensus 322 A~Kf~~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsr-aTLhN~~~i~~~~ 378 (687)
=+| +.......|.++.++-+|.|++.-...- .-+|.++-+ .|...-+.+++++
T Consensus 359 KiK-~~~~~dlvVvG~~~~~k~~~~~gs~ll~---~~~g~~~~~vgsGftd~~~~~l~ 412 (488)
T PHA02587 359 KFK-EVIDIDLEIVGVYEHKKDPNKVGGFTLE---SACGKITVNTGSGLTDTTHRKKD 412 (488)
T ss_pred Eec-CCCceEEEEEeEEeCCCCCCceeEEEEE---ecCCcEEEEECCCCChHHhhhhc
Confidence 566 4456888999999987777765433211 114544433 4788888776653
No 50
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=97.80 E-value=0.00064 Score=78.56 Aligned_cols=219 Identities=16% Similarity=0.138 Sum_probs=137.1
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh------hhH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KDF 191 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~------~~F 191 (687)
..|++|+|+||.-+.+.+.+|. ++..|| -|+|+|+....|...-.. .|..+.+-||++.-. ..|
T Consensus 225 ~~~~~E~K~DG~R~qih~~~~~-v~lfSR----~g~d~t~~fPei~~~~~~-----l~~~~ILDGElv~~~~~~~~~~~F 294 (539)
T PRK09247 225 ADWQAEWKWDGIRVQLVRRGGE-VRLWSR----GEELITERFPELAEAAEA-----LPDGTVLDGELLVWRPEDGRPQPF 294 (539)
T ss_pred CcEEEEEeEcceEEEEEEeCCE-EEEEeC----CCccchhhhHHHHHHHHh-----CCCCEEEEeEEEEEECCCCCcCCH
Confidence 3799999999999998776665 799999 577999877665543222 344689999998754 466
Q ss_pred HHHHHHHHHcCCCCCCChhhhHHhHhhhcCc--ccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCC-C-C
Q psy11421 192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNP--KINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSIC-G-E 266 (687)
Q Consensus 192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~--~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~-~-~ 266 (687)
+.+..+ ++++.. ......++.|++|++...+|.++ .....++.+.|.++ |... . .
T Consensus 295 ~~l~~R-------------------~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~-~~~~~~~~ 354 (539)
T PRK09247 295 ADLQQR-------------------IGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEAL-IARLPDPR 354 (539)
T ss_pred HHHHHH-------------------hcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHH-hcccCCCe
Confidence 665432 111111 11123579999999988766443 24677888888765 2211 1 1
Q ss_pred -----ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEee
Q psy11421 267 -----YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQI 341 (687)
Q Consensus 267 -----~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qv 341 (687)
...+.+.+++.+++++..+ -...|+|+|--+..++ -|.. ...| +=+|-........|.+..|--
T Consensus 355 i~~~~~~~~~~~~e~~~~~~~a~~------~g~EGlm~K~~~s~Y~--~Grr--~~~W-lK~K~~~~t~DlVvig~~~G~ 423 (539)
T PRK09247 355 LDLSPLVPFSDWDELAALRAAARE------RGVEGLMLKRRDSPYL--VGRK--KGPW-WKWKRDPLTIDAVLMYAQRGH 423 (539)
T ss_pred EEecCceecCCHHHHHHHHHHHHH------CCCceEEEecCCCCcC--CCCC--cchh-hcccCCCCcEEEEEEEeecCC
Confidence 2234678899988876643 3469999997774443 2221 2234 234433346777888777766
Q ss_pred cC-cceeee--EEEEEEEEECC--EEEEEe-cCCCHHHHHhc
Q psy11421 342 GR-TGIITP--VALLKPVLIDG--ITITRA-TLHNESEIYRK 377 (687)
Q Consensus 342 GR-TG~iTP--vA~lePV~l~G--~tVsra-TLhN~~~i~~~ 377 (687)
|| +|.++. +|..+|=.=.+ ++|-++ |.++-++++++
T Consensus 424 Gkr~g~~~~~lla~~~~~~~~~~~~~v~kvgsGftd~~l~~l 465 (539)
T PRK09247 424 GRRASLYTDYTFGVWDGPEGGRQLVPFAKAYSGLTDEEIKQL 465 (539)
T ss_pred CCcCCccccEEEEEEcCCCCceeEEEEEEECCCCCHHHHHHH
Confidence 65 465654 46554421001 255565 88888888766
No 51
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=97.76 E-value=0.0014 Score=78.05 Aligned_cols=209 Identities=17% Similarity=0.142 Sum_probs=127.1
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee----hhhHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIK 193 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~ 193 (687)
..|++|.|+||.-+.+.+.+|. ++..|| -|.|+|+....|..+...+. ...+.+-||+++- ..+|+.
T Consensus 477 ~~w~~E~K~DG~R~~~~~~~g~-vrL~SR----nG~d~T~~fPel~~~~~~l~----~~~~ILDGEiVvld~~G~~~F~~ 547 (764)
T PRK09632 477 SQWAFEGKWDGYRLLAEADHGA-LRLRSR----SGRDVTAEYPELAALAEDLA----DHHVVLDGEIVALDDSGVPSFGL 547 (764)
T ss_pred CCEEEEEEECceeEEEEEeCCE-EEEEeC----CCCCccccchhHHHHHhhCC----CcceeeeeEEEEeCCCCCCCHHH
Confidence 3699999999999988887776 799999 78999998766554444442 2368899999984 346765
Q ss_pred HHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCCCCceEeCC
Q psy11421 194 LNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSICGEYSVLSG 272 (687)
Q Consensus 194 ~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~~~~~~~~~ 272 (687)
+... ....++.|++|++...+|.++. ....+..+.|+++- ...+...+...
T Consensus 548 Lq~r---------------------------~~~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~-~~~~~i~~s~~ 599 (764)
T PRK09632 548 LQNR---------------------------GRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALA-PSGGSLTVPPL 599 (764)
T ss_pred Hhhh---------------------------hhcCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhh-CCCCcEEecce
Confidence 4321 0124699999999887765432 46778888887763 21221222111
Q ss_pred -HHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC-cceeeeE
Q psy11421 273 -VNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR-TGIITPV 350 (687)
Q Consensus 273 -~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR-TG~iTPv 350 (687)
..++.++++...+ --.-|||+|--|..++ -| .+...| +-+|. ....+..|.+..+.-|| .|.+.-.
T Consensus 600 ~~~~~~~~l~~a~~------~GlEGIVaKr~dS~Y~--pG--rRs~~W-lKiK~-~~~~e~VI~G~~~g~G~r~g~~gsL 667 (764)
T PRK09632 600 LPGDGAEALAYSRE------LGWEGVVAKRRDSTYQ--PG--RRSSSW-IKDKH-WRTQEVVIGGWRPGEGGRSSGIGSL 667 (764)
T ss_pred ecccHHHHHHHHHH------cCCcEEEEeCCCCCCC--CC--CcCCCe-EEEec-CCceEEEEEEEEcCCCCcCCceeeE
Confidence 1134445544432 3468999999885553 12 124456 45553 34456777777776663 4444333
Q ss_pred EEEEEEEECC--EEEEEe-cCCCHHHHHhc
Q psy11421 351 ALLKPVLIDG--ITITRA-TLHNESEIYRK 377 (687)
Q Consensus 351 A~lePV~l~G--~tVsra-TLhN~~~i~~~ 377 (687)
..= |.=+| ..|-++ |..+.+..+++
T Consensus 668 LlG--v~d~~~L~yvGkVGTGftd~~l~~L 695 (764)
T PRK09632 668 LLG--IPDPGGLRYVGRVGTGFTERELASL 695 (764)
T ss_pred EEE--EEcCCeeEEEEEEeCCCCHHHHHHH
Confidence 211 11122 344455 77887777663
No 52
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=97.70 E-value=0.00012 Score=73.43 Aligned_cols=53 Identities=15% Similarity=0.295 Sum_probs=47.5
Q ss_pred cCCCCCCHHHHHHHHhhcCC---hHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11421 526 LGIRHVGETTAKELANYFKN---LECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~s---ld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
+.|||||+++|..|+++|+. .+.+.+++.++|.+++|||+++|+.|...++..
T Consensus 76 ~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~ 131 (192)
T PRK00116 76 ISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDK 131 (192)
T ss_pred hcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 57999999999999999987 667788899999999999999999999888654
No 53
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=97.67 E-value=2.5e-05 Score=82.49 Aligned_cols=59 Identities=20% Similarity=0.205 Sum_probs=54.1
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccHHHHHHHHHHHHHccc
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL 516 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~ 516 (687)
..|.++|+|||++..||+++.|.++++|-. +....+..++|||+|++++|+.++.....
T Consensus 94 ~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~ 153 (326)
T COG1796 94 PLLKVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEE 153 (326)
T ss_pred HHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhh
Confidence 478999999999999999999999999998 67889999999999999999999987544
No 54
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=97.64 E-value=6.8e-05 Score=86.51 Aligned_cols=53 Identities=21% Similarity=0.313 Sum_probs=50.4
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
.+|||||+++.+.|+++|||++++..||.+||.+++||+.++|+.|.++|+..
T Consensus 517 ~~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 569 (574)
T PRK14670 517 TKIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEKQ 569 (574)
T ss_pred ccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence 38999999999999999999999999999999999999999999999999653
No 55
>KOG2841|consensus
Probab=97.60 E-value=4.9e-05 Score=76.73 Aligned_cols=60 Identities=32% Similarity=0.450 Sum_probs=54.2
Q ss_pred HHHHHHc-CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchh
Q psy11421 520 SRFIYAL-GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPL 579 (687)
Q Consensus 520 ~r~L~aL-GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~ 579 (687)
.+++..| .||+|++.-|..|+.+||++..+.+|+.++|.+++|+|+..|+.|++||+.|.
T Consensus 191 s~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~pf 251 (254)
T KOG2841|consen 191 SSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQPF 251 (254)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhccc
Confidence 3455544 79999999999999999999999999999999999999999999999998763
No 56
>PRK08609 hypothetical protein; Provisional
Probab=97.58 E-value=2.4e-05 Score=90.78 Aligned_cols=58 Identities=26% Similarity=0.253 Sum_probs=52.3
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccHHHHHHHHHHHHHccc
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSKL 516 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~ 516 (687)
.+.|+|+||+++.+||+...|+|++||.. +...+|..++|||+|++++|+.+|+..+.
T Consensus 90 l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~~~ 148 (570)
T PRK08609 90 LLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGK 148 (570)
T ss_pred HhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHHhc
Confidence 56899999999999999888999999998 56778999999999999999999987543
No 57
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=97.58 E-value=0.00011 Score=74.88 Aligned_cols=52 Identities=21% Similarity=0.279 Sum_probs=49.3
Q ss_pred cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
..|||||+++++.|+++ |+|++.|..|+.++|.+++|||.++|+.|.++|+.
T Consensus 6 ~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~ 58 (232)
T PRK12766 6 EDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGG 58 (232)
T ss_pred ccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcc
Confidence 37899999999999999 99999999999999999999999999999999953
No 58
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.53 E-value=0.0031 Score=75.84 Aligned_cols=179 Identities=18% Similarity=0.147 Sum_probs=113.0
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEee----hhhHHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIY----KKDFIKL 194 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~----~~~F~~~ 194 (687)
.|++|.|+||.-+.+.+.+|. ++..|| -|+|+|+....|...-..+. .....+-|||++- ..+|+.+
T Consensus 250 ~W~~E~K~DG~R~~a~~~gg~-vrL~SR----nG~d~T~~fPel~~~~~~l~----~~~~ILDGEIVvld~~G~~~F~~L 320 (860)
T PRK05972 250 GWIYEIKFDGYRILARIEGGE-VRLFTR----NGLDWTAKLPALAKAAAALG----LPDAWLDGEIVVLDEDGVPDFQAL 320 (860)
T ss_pred ceEEEeeeCcEEEEEEEECCE-EEEEeC----CCCccccccHHHHHHHHhcC----CCceeEeEEEEEECCCCCCCHHHH
Confidence 699999999999999887776 699999 68899988665543322221 2357899999984 4577766
Q ss_pred HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCC-CCCceEeCC
Q psy11421 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSI-CGEYSVLSG 272 (687)
Q Consensus 195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~-~~~~~~~~~ 272 (687)
.... +.. ...++.|++|++...+|.++. ....+..+.|+++-=+. .+...++..
T Consensus 321 q~r~-------------------~~~-----~~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~s~~ 376 (860)
T PRK05972 321 QNAF-------------------DEG-----RTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFSEH 376 (860)
T ss_pred HHHh-------------------hcc-----CCCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEece
Confidence 4321 000 023689999999887765432 46788888888763111 122333332
Q ss_pred H-HHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecC
Q psy11421 273 V-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGR 343 (687)
Q Consensus 273 ~-~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGR 343 (687)
+ .+..++++... .--..|||+|--|..++. | +...| +=+|.- ...+..|-+....-|+
T Consensus 377 ~~~~g~~ll~~a~------~~GlEGIVaKr~dS~Y~~--G---Rs~~W-lKiK~~-~~~E~VIgGy~~~~Gk 435 (860)
T PRK05972 377 FDAGGDAVLASAC------RLGLEGVIGKRADSPYVS--G---RSEDW-IKLKCR-ARQEFVIGGYTDPKGS 435 (860)
T ss_pred ecchHHHHHHHHH------HcCCceEEEeCCCCCCCC--C---CCCCc-EEEecC-CCceEEEEEEeCCCCc
Confidence 2 23444554442 234689999998866641 3 45567 445532 3346677676665554
No 59
>PLN03113 DNA ligase 1; Provisional
Probab=97.51 E-value=0.0028 Score=75.44 Aligned_cols=221 Identities=17% Similarity=0.142 Sum_probs=130.9
Q ss_pred eeEEEEEccceeEEEEEEe-CCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeeh------hh
Q psy11421 118 IEYIAELKFDGIAVNLRYE-YGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYK------KD 190 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~-~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~------~~ 190 (687)
..|++|.|.||.-+.+.|. +|. ++..|| -|+|+|+....+...-..+... ....+.+-||++.-. -.
T Consensus 391 ~~~~~E~KyDGeR~QiH~~~~g~-v~lfSR----n~ed~T~~fPel~~~~~~~~~~-~~~~~ILDGEiVa~d~~~~~~lp 464 (744)
T PLN03113 391 MEFTCEYKYDGERAQIHFLEDGS-VEIYSR----NAERNTGKYPDVVVAISRLKKP-SVKSFILDCELVAYDREKKKILP 464 (744)
T ss_pred CCEEEEEeeccceEEEEEecCCE-EEEEeC----CCCcccccchhHHHHHHHhccc-cCCCEEEEeEEEEEECCCCCcCC
Confidence 4799999999999999984 665 799999 6899998876543321122100 124689999999753 35
Q ss_pred HHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCC-CCHHHHHHHHHhcCCCCC-CCce
Q psy11421 191 FIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMP-SSHSELLNWYQKIGLSIC-GEYS 268 (687)
Q Consensus 191 F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~-~~~~e~l~~L~~~Gf~~~-~~~~ 268 (687)
|+.+-.+ . |.-+. + .....++.||+|++...+|..+. .+..++.+.|.++ |... ....
T Consensus 465 Fq~Lq~R-~----------rk~~~--~------~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~-~~~~~~~i~ 524 (744)
T PLN03113 465 FQILSTR-A----------RKNVV--M------SDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYES-FEEDPGFFQ 524 (744)
T ss_pred HHHHHhh-h----------ccccc--h------hccccceEEEEEeccccCccChhcCCHHHHHHHHHHH-hccCCCcEE
Confidence 7665432 1 11000 0 01125799999999887765432 4677888888775 4322 2222
Q ss_pred E-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC-ChhhhhhhCCCCCCCCceEeecCCC-----ceeeEEEEEE
Q psy11421 269 V-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN-CLSTQKKLGFTSRAPRFALAYKFLS-----KEALTKIKAI 337 (687)
Q Consensus 269 ~-----~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~-~~~~~~~lG~ts~~PrwaiA~Kf~~-----~~~~T~v~~I 337 (687)
+ ..+.+++.+|++...+ .-.-|||+|-- ..+.++ ...+...| +=+|-.. +.....|.+-
T Consensus 525 ~~~~~~~~~~ee~~~~~~~ai~------~g~EGlmvK~l~~dS~Y~---pGkRs~~W-lKlK~dy~~~~~dtlDlVvIGa 594 (744)
T PLN03113 525 FATAITSNDLEEIQKFLDAAVD------ASCEGLIIKTLNKDATYE---PSKRSNNW-LKLKKDYMESIGDSLDLVPIAA 594 (744)
T ss_pred EeeeeccCCHHHHHHHHHHHHH------cCCceEEEeccCCCCCcc---CCCCCCCe-EEEechhhccccccccEEEEEE
Confidence 2 3468889998876643 35689999972 111221 12245567 3444221 2445566666
Q ss_pred EEeec-CcceeeeE--EEEEEEEECCE--EEEEe-cCCCHHHHHh
Q psy11421 338 NIQIG-RTGIITPV--ALLKPVLIDGI--TITRA-TLHNESEIYR 376 (687)
Q Consensus 338 ~~qvG-RTG~iTPv--A~lePV~l~G~--tVsra-TLhN~~~i~~ 376 (687)
.|--| |+|.++.. |..+|- +|. +|-++ |.+.-+++++
T Consensus 595 ~~G~GkR~g~~g~fLla~yd~~--~~~~~~v~KvgTGfsd~~l~~ 637 (744)
T PLN03113 595 FHGRGKRTGVYGAFLLACYDSN--KEEFQSICKIGTGFSEAVLEE 637 (744)
T ss_pred EeCCCCcCCccceEEEEEEcCC--CCEEEEeeEECCCCCHHHHHH
Confidence 66555 56665543 344432 122 34454 7777776665
No 60
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=97.43 E-value=0.00018 Score=83.02 Aligned_cols=50 Identities=24% Similarity=0.373 Sum_probs=48.1
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
.+|||||+++.+.|+++|||++++..||.++|.++ |||+++|+.|+++|+
T Consensus 517 d~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 517 DKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred ccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 38999999999999999999999999999999999 999999999999884
No 61
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=97.41 E-value=0.00048 Score=82.26 Aligned_cols=122 Identities=16% Similarity=0.191 Sum_probs=90.0
Q ss_pred hhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc-cCCHHHHHHHcC
Q psy11421 449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK-LTTFSRFIYALG 527 (687)
Q Consensus 449 ~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk-~~~l~r~L~aLG 527 (687)
..|..|.|- . .|+|+|+++++++++.-....+.-|.+ ..+.|..++|+|+|.++.|.+++++.+ ...+..||..+|
T Consensus 78 ~~i~~yL~s-~-~~~GIG~~~A~~iv~~fg~~~~~~i~~-~~~~L~~v~gi~~~~~~~i~~~~~~~~~~~~~~~~L~~~g 154 (720)
T TIGR01448 78 EGIVAYLSS-R-SIKGVGKKLAQRIVKTFGEAAFDVLDD-DPEKLLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLG 154 (720)
T ss_pred HHHHHHHhc-C-CCCCcCHHHHHHHHHHhCHhHHHHHHh-CHHHHhcCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHcC
Confidence 344455542 2 599999999999999877555554443 467899999999999999999998755 345556777777
Q ss_pred CCCCCHHHHHHHHhhcCCh-HHHHhcCHHHHh-cCCCCCHHHHHHHHHHHc
Q psy11421 528 IRHVGETTAKELANYFKNL-ECMFKATEEQLL-NIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 528 Ip~vG~~~Ak~La~~f~sl-d~l~~As~eeL~-~I~GIG~~~A~sI~~ff~ 576 (687)
|+ ...|.+|.++|+.- -+....++=.|. .++|||-++|..|...+.
T Consensus 155 i~---~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g 202 (720)
T TIGR01448 155 IG---IKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALG 202 (720)
T ss_pred CC---HHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcC
Confidence 76 67899999999742 223333444555 599999999999877663
No 62
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=97.41 E-value=0.0016 Score=66.33 Aligned_cols=156 Identities=20% Similarity=0.176 Sum_probs=96.8
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKY 197 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~ 197 (687)
..|++|+|.||+-+.+...+..-+.++||+ |++++.....+..+. ... ..+....+-||++.....
T Consensus 41 ~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~----~~~~~~~~~~~~~~~-~~~--~~~~~~ilDGElv~~~~~------- 106 (215)
T cd07895 41 NDYFVCEKSDGVRYLLLITGRGEVYLIDRK----NDVFKVPGLFFPRRK-NLE--PHHQGTLLDGELVIDKVP------- 106 (215)
T ss_pred CCeEEEEeEcCeEEEEEEecCCcEEEEeCC----CCeEEeccccCCCcc-ccc--ccccCeeeEEEEEEEcCC-------
Confidence 479999999999998866541457999996 456666544432110 011 123467899999965311
Q ss_pred HHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC----------
Q psy11421 198 RYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE---------- 266 (687)
Q Consensus 198 ~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~---------- 266 (687)
+ ...+.|++|++....|... .....++++.|.++-......
T Consensus 107 ----~------------------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~ 158 (215)
T cd07895 107 ----G------------------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKA 158 (215)
T ss_pred ----C------------------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcC
Confidence 0 2368999999987665432 246788888888764332110
Q ss_pred ----ceEeC---CHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeec
Q psy11421 267 ----YSVLS---GVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYK 324 (687)
Q Consensus 267 ----~~~~~---~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~K 324 (687)
..... ..+++....+.+ +..++...||+|+|-.+..++- | +.+.| +=||
T Consensus 159 ~~~~~i~~k~~~~~~~~~~~~~~~---~~~~~~~~EGlIfk~~~~~Y~~--G---r~~~~-lKwK 214 (215)
T cd07895 159 KEPFSVRLKDFFPLYKIEKLFEKI---IPKLPHENDGLIFTPNDEPYVP--G---TDKNL-LKWK 214 (215)
T ss_pred CCCeEEEecceEeHHhHHHHHHhc---cccCCCCCCCEEEccCCCCccC--c---cCCcc-eeeC
Confidence 01111 233444444433 3467899999999999876542 2 56677 5555
No 63
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.31 E-value=0.0003 Score=82.01 Aligned_cols=52 Identities=23% Similarity=0.360 Sum_probs=50.1
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
.+|||||+++++.|+++|+|++++..|+.++|.+++|||+++|++|.+||++
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence 4999999999999999999999999999999999999999999999999964
No 64
>PRK14973 DNA topoisomerase I; Provisional
Probab=97.30 E-value=0.0012 Score=80.49 Aligned_cols=127 Identities=15% Similarity=0.133 Sum_probs=101.1
Q ss_pred hhhhhcc----cccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCH-HHHH
Q psy11421 449 AGLQHFS----SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTF-SRFI 523 (687)
Q Consensus 449 ~~i~~F~----sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l-~r~L 523 (687)
+++.-|+ -...|.++|+-+.++++||++|+ +++.|+-.+..+.|+.++|+.+-.+.++..........+- .++.
T Consensus 790 ~~~~~~a~~~~~~~~~~~~gv~~~~~~~~~~~G~-~~~~d~~~a~p~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~ 868 (936)
T PRK14973 790 ASLLAEAKSLCNISRLKEIGVPAVSLKKYQEAGF-DTPEDFCSVHPAYLALKTGISPETICRHAKLVCEKLGRPVPEKIS 868 (936)
T ss_pred HHHHHHHHHHHHHHhhcccCCCHHHHHHHHHhcC-CCHHHHHhcCHHHHhcCCCCChhhHHHHHHHHHHHhcCCCchhhh
Confidence 3555555 33489999999999999999996 9999999999999999999999999888666552211110 0111
Q ss_pred ---------HHcCCCCCCHHHHHHHHh-hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 524 ---------YALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 524 ---------~aLGIp~vG~~~Ak~La~-~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
..+.|+|+|+.+...|.. .+.+.+.|.+++.++|....||+.+.+..++.+..
T Consensus 869 ~~~~~~~~~el~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~ 931 (936)
T PRK14973 869 KAAFERGRAELLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK 931 (936)
T ss_pred hhhhcccchhhhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence 136789999999987764 47789999999999999999999999999888764
No 65
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=97.21 E-value=0.00051 Score=69.96 Aligned_cols=54 Identities=24% Similarity=0.316 Sum_probs=50.6
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
...+|+|+|++++.+|+++|+ .|+.+|-..+.++|.+++|||++.|++|++.+.
T Consensus 4 ~L~~IpGIG~krakkLl~~GF-~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGF-ESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCC-CCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 356899999999999999995 999999999999999999999999999999875
No 66
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=97.14 E-value=0.0011 Score=66.47 Aligned_cols=57 Identities=16% Similarity=0.261 Sum_probs=45.3
Q ss_pred cccccCCCCHHHHHHHHHCCCCCCh-HHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTA-VDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i-~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
..++|+|+|||++.++++.-....+ ..+..-+.+.|.++||+|+|+|++|+..+...
T Consensus 74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~ 131 (192)
T PRK00116 74 LLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDK 131 (192)
T ss_pred HHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 3678999999999999986533332 23445677899999999999999999998754
No 67
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=97.08 E-value=0.0011 Score=68.81 Aligned_cols=53 Identities=25% Similarity=0.464 Sum_probs=51.0
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
..|||||...|..|+.+|+|+.++..|+.++|..+.|||++.|..|+.||..+
T Consensus 185 ~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~ 237 (254)
T COG1948 185 ESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTE 237 (254)
T ss_pred HcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhch
Confidence 58999999999999999999999999999999999999999999999999765
No 68
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=96.96 E-value=0.0015 Score=70.81 Aligned_cols=52 Identities=19% Similarity=0.285 Sum_probs=48.3
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
-.||++++..|+.|.++||++..+.+|+.++|.+++|||++.|..|++.+..
T Consensus 290 s~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~R 341 (352)
T PRK13482 290 SKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSR 341 (352)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999999999998877654
No 69
>TIGR01209 RNA ligase, Pab1020 family. Members of this family are found, so far, in a single copy per genome and largely in thermophiles, of which only Aquifex aeolicus is bacterial rather than archaeal. PSI-BLAST converges after a single iteration to the whole of this family and reveals no convincing similarity to any other protein. The member protein Pab1020 has been characterized as an RNA ligase with circularization activity.
Probab=96.96 E-value=0.015 Score=63.76 Aligned_cols=165 Identities=23% Similarity=0.213 Sum_probs=97.8
Q ss_pred eccccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhc
Q psy11421 84 HHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH 163 (687)
Q Consensus 84 ~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~ 163 (687)
+|-.+++.|+.+ +.+.+. ...+++|.|+||--+.+...+|++ .|.||| |.+=-==|+.++..-
T Consensus 60 P~I~R~~~L~~g------------i~~~f~---~~~v~vEEKlDG~Nvri~~~~g~l-~a~tRG-gyicp~tt~r~~~~~ 122 (374)
T TIGR01209 60 PHIKRILLLRPG------------IKRHFK---DPEVVVEEKMNGYNVRIVKYGGNV-YALTRG-GFICPFTTERLPDLI 122 (374)
T ss_pred CCcceeeccchh------------hHHhcC---CCcEEEEEeecCceEEEEeECCEE-EEEccC-cccCCCcHHHHHHHh
Confidence 566688888875 222221 235999999999999998889985 899999 332110112333332
Q ss_pred cCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCC
Q psy11421 164 KIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM 243 (687)
Q Consensus 164 ~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~ 243 (687)
+ ..+..+ . .++.+-||++=+..- |+ +.+... ...+..||+|++-..+..
T Consensus 123 ~--~~~~~d-~-p~l~LcGE~iGpenp---------------Y~-----------~hs~~y-~~l~~~FfvFDI~d~~t~ 171 (374)
T TIGR01209 123 D--LEFFDD-N-PDLVLCGEMAGPENP---------------YT-----------PEYYPE-VKEDLGFFLFDIREGKTN 171 (374)
T ss_pred h--HHhhcc-C-CCeEEEEEEcCCCCC---------------Cc-----------ccCccc-cCCCceEEEEEEEECCCC
Confidence 2 233321 2 358889998733111 10 000101 122689999998543222
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCceEeCCHHHHH-H---HHHHHHHhhcCCCCccceEEEEECCh
Q psy11421 244 NMPSSHSELLNWYQKIGLSICGEYSVLSGVNKLI-E---FYKKINIKRFNLPYEIDGVVYKINCL 304 (687)
Q Consensus 244 ~~~~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~-~---~~~~~~~~r~~l~y~iDGiVikv~~~ 304 (687)
. +-+..+..++++.+|++.++..... +.+++. + .++.+.+.. =-|||+|-.+.
T Consensus 172 ~-~L~~~er~~l~e~yglp~Vpvlg~~-~~~~~~~~~~eii~~L~~~g------REGVVlK~~~~ 228 (374)
T TIGR01209 172 R-SLPVEERLELAEKYGLPHVEILGVY-TADEAVEEIYEIIERLNKEG------REGVVMKDPEM 228 (374)
T ss_pred c-cCCHHHHHHHHHHCCCCccceeeEE-cHHHHHHHHHHHHHHhhhcC------cceEEEcCccc
Confidence 2 3688899999999999988754443 344444 3 333333221 37999997653
No 70
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=96.92 E-value=0.0014 Score=76.52 Aligned_cols=50 Identities=32% Similarity=0.426 Sum_probs=47.8
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
+|||||++++++|+++|+|++++..||.++|.++ ||.++|+.|+++|+.+
T Consensus 556 ~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~~ 605 (624)
T PRK14669 556 EIPGVGAKTVQRLLKHFGSLERVRAATETQLAAV--VGRAAAEAIIAHFTTE 605 (624)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcCc
Confidence 9999999999999999999999999999999998 9999999999999654
No 71
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=96.91 E-value=0.0014 Score=45.85 Aligned_cols=30 Identities=33% Similarity=0.667 Sum_probs=25.9
Q ss_pred ChHHHHhcCHHHHhcCCCCCHHHHHHHHHH
Q psy11421 545 NLECMFKATEEQLLNIPKIGSTTVKAFIKF 574 (687)
Q Consensus 545 sld~l~~As~eeL~~I~GIG~~~A~sI~~f 574 (687)
+++.+..++.++|.++||||+++|..|.+|
T Consensus 1 ~~~g~~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 1 SLDGLIPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 357788899999999999999999999876
No 72
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=96.90 E-value=0.0015 Score=76.60 Aligned_cols=49 Identities=29% Similarity=0.451 Sum_probs=47.3
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
.+|||||+++++.|+.+|+|+++|..|+.++|.++ ||+++|++|.+||+
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~As~eeL~~v--ig~k~A~~I~~~~~ 620 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAKASLEELAAV--AGPKTAETIYRYYH 620 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhC
Confidence 59999999999999999999999999999999999 99999999999985
No 73
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=96.87 E-value=0.0013 Score=76.55 Aligned_cols=51 Identities=20% Similarity=0.295 Sum_probs=47.9
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
.|||||+++.+.|+++|||++++..||.++|.+++||+.++|+.|...-..
T Consensus 612 ~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 612 RLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred cCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 899999999999999999999999999999999999999999999875543
No 74
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=96.84 E-value=0.0015 Score=76.39 Aligned_cols=51 Identities=29% Similarity=0.431 Sum_probs=48.7
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
..|||||+++++.|.++|||++++..|+.++|.+++|||++.|+.|.++|+
T Consensus 640 ~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~ 690 (694)
T PRK14666 640 QRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLK 690 (694)
T ss_pred hhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHH
Confidence 389999999999999999999999999999999999999999999999874
No 75
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=96.68 E-value=0.002 Score=74.50 Aligned_cols=49 Identities=20% Similarity=0.269 Sum_probs=46.7
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.+|||||+++.+.|++||+|+..+..|+.+||.++ ||+.++|+.|++++
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEKIYEAL 581 (581)
T ss_pred ccCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHHHc-CCCHHHHHHHHhhC
Confidence 48999999999999999999999999999999999 99999999998764
No 76
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=96.56 E-value=0.0032 Score=74.23 Aligned_cols=80 Identities=24% Similarity=0.383 Sum_probs=52.1
Q ss_pred cccccCCCCHHHHHHHHHCC---CCCChHHHhcCChhhhhcccCccHHHHHHHHHHH---HHcccCCHHHHHHHcCCCCC
Q psy11421 458 KAMNIIGLGKKMIEKLVNAN---IVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV 531 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g---~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I---e~sk~~~l~r~L~aLGIp~v 531 (687)
+.+.++|+|+|++++|++.- .-..+..++ ..+.+||+|++.|..|++.+ ++-++.+...+ ..|+|+
T Consensus 467 ~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L-----~aLgIpgVG~~~ak~L~~~f~sl~~l~~As~eeL---~~i~GI 538 (652)
T TIGR00575 467 DLLELEGFGEKSAQNLLNAIEKSKEKPLARLL-----FALGIRHVGEVTAKNLAKHFGTLDKLKAASLEEL---LSVEGV 538 (652)
T ss_pred HHhhccCccHHHHHHHHHHHHHhccCcHHHHH-----hhccCCCcCHHHHHHHHHHhCCHHHHHhCCHHHH---hcCCCc
Confidence 46678999999998887631 111222222 24567899999998888765 23333333322 368889
Q ss_pred CHHHHHHHHhhcCC
Q psy11421 532 GETTAKELANYFKN 545 (687)
Q Consensus 532 G~~~Ak~La~~f~s 545 (687)
|+.+|..|.+.|.+
T Consensus 539 G~~~A~~I~~ff~~ 552 (652)
T TIGR00575 539 GPKVAESIVNFFHD 552 (652)
T ss_pred CHHHHHHHHHHHhh
Confidence 99999888887754
No 77
>PRK14973 DNA topoisomerase I; Provisional
Probab=96.51 E-value=0.023 Score=69.58 Aligned_cols=149 Identities=13% Similarity=0.246 Sum_probs=106.2
Q ss_pred CCCCCCCCCcceee--cC--ceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCCh
Q psy11421 415 PNICPICNSKIIYI--ES--NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINF 490 (687)
Q Consensus 415 P~~CP~C~~~l~~~--~~--~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~ 490 (687)
...||.||.+++.. .| +-++-| + . |..... ..+++-+++|+|+++.++|-.++ +.++.++-..+.
T Consensus 635 ~~~Cp~CG~p~~~~~r~Gr~g~fl~C--P-~-C~~~~~------~~~~~~~~~~~~~~~~~k~~~~~-~~~~~~~~~~~~ 703 (936)
T PRK14973 635 DEVCPIHHLNHVRLIRKGARPWDIGC--P-L-CSHIES------NTESLLLMPSMTEELLQKLNAVH-IYTVSELASREP 703 (936)
T ss_pred CCCCCCCCCCceEEeecCCCcccccC--c-c-ccchhh------cccchhhccccchhhhhhhhhcc-CCchhhhccCCH
Confidence 46899999864432 22 235557 3 3 743221 33467789999999999999888 588899988888
Q ss_pred hhhhcccCccHHHHHHHHHHHHH-----cccCCHHHHHHHcCCCCCCHHHHHHHHh----hcCChHHHHhcCHHHHhcCC
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQK-----SKLTTFSRFIYALGIRHVGETTAKELAN----YFKNLECMFKATEEQLLNIP 561 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~-----sk~~~l~r~L~aLGIp~vG~~~Ak~La~----~f~sld~l~~As~eeL~~I~ 561 (687)
+.+...-+.+.+.+.++...-+. .+...+.+|+...=.|.=|...|+.+.. ...++..|..|++.+|.. .
T Consensus 704 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~ 782 (936)
T PRK14973 704 EALAKSLGLSKKEAEKLIREAGDVLELLRRRSELRKFVRKHVPPRRGRSHAKIMKALISSGINDIAALARADPADLKK-A 782 (936)
T ss_pred hHhhhhcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCccHHHHHHHHHhcCcchHHHHhhCCHHHHHH-c
Confidence 88887667777777777665322 1234677888888888778777765543 346788899999887765 4
Q ss_pred CCCHHHHHHHHHHH
Q psy11421 562 KIGSTTVKAFIKFI 575 (687)
Q Consensus 562 GIG~~~A~sI~~ff 575 (687)
|+++.-+.++.++-
T Consensus 783 ~~sE~~~~~~~~~a 796 (936)
T PRK14973 783 GLSEAEAASLLAEA 796 (936)
T ss_pred CCCHHHHHHHHHHH
Confidence 89988888877765
No 78
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=96.47 E-value=0.0052 Score=51.04 Aligned_cols=52 Identities=23% Similarity=0.299 Sum_probs=43.9
Q ss_pred ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+-=||+..+...|-.+| |.++.||..++.++|..++|||+|+.+.|.+.+++
T Consensus 15 ~~L~LS~Ra~n~L~~~~-I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~e 66 (66)
T PF03118_consen 15 EDLGLSVRAYNCLKRAG-IHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLKE 66 (66)
T ss_dssp GGSTSBHHHHHHHHCTT---BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHHH
T ss_pred HHhCCCHHHHHHHHHhC-CcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHcC
Confidence 44579999999998887 69999999999999999999999999999887753
No 79
>PRK08609 hypothetical protein; Provisional
Probab=96.44 E-value=0.0059 Score=71.16 Aligned_cols=85 Identities=13% Similarity=0.195 Sum_probs=66.4
Q ss_pred hhhhcccCccHHHHHHHHHHHHHcccCCHH--------HHHHHcCCCCCCHHHHHHHHhh--cCChHHHHhcCH-HHHhc
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQKSKLTTFS--------RFIYALGIRHVGETTAKELANY--FKNLECMFKATE-EQLLN 559 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~--------r~L~aLGIp~vG~~~Ak~La~~--f~sld~l~~As~-eeL~~ 559 (687)
.+|.++||+|++.|++|.+-++.-+-..|. .++.-+.|||||+++|+++-+. +.|+++|..|.. ..+..
T Consensus 48 ~~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~ 127 (570)
T PRK08609 48 DDFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQA 127 (570)
T ss_pred hhhccCCCcCHHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhh
Confidence 378999999999999998877643222222 3555569999999999999864 569999998754 35889
Q ss_pred CCCCCHHHHHHHHHHH
Q psy11421 560 IPKIGSTTVKAFIKFI 575 (687)
Q Consensus 560 I~GIG~~~A~sI~~ff 575 (687)
++|||+++.+.|...+
T Consensus 128 ~~gfg~k~~~~il~~i 143 (570)
T PRK08609 128 LAGFGKKTEEKILEAV 143 (570)
T ss_pred ccCcchhHHHHHHHHH
Confidence 9999999999986655
No 80
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=96.40 E-value=0.0044 Score=71.98 Aligned_cols=49 Identities=27% Similarity=0.415 Sum_probs=46.9
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.|||||+++++.|+++|+|++++..|+.++|.+++|+|+++|+.|.+++
T Consensus 529 ~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~~~~ 577 (577)
T PRK14668 529 DVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETIRERL 577 (577)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHhC
Confidence 8999999999999999999999999999999999999999999998763
No 81
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA 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=96.33 E-value=0.0038 Score=62.66 Aligned_cols=52 Identities=21% Similarity=0.443 Sum_probs=43.0
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhc-CC---hhhhhcccCccHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-IN---FKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~---~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
..++|+|+|||++..+.. +-++.+|.. +. ...|.++||||+|+|++|+-.+.
T Consensus 73 ~L~~V~GIGpK~Al~iL~---~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk 128 (191)
T TIGR00084 73 ELIKVNGVGPKLALAILS---NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELK 128 (191)
T ss_pred HHhCCCCCCHHHHHHHHh---cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 478999999999999965 347888887 33 37799999999999999995554
No 82
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=96.33 E-value=0.078 Score=56.97 Aligned_cols=168 Identities=20% Similarity=0.171 Sum_probs=111.5
Q ss_pred eeccccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh
Q psy11421 83 VHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII 162 (687)
Q Consensus 83 v~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i 162 (687)
.+|..+|+-|+.+ +.+|.. ...++||.|+||-.+.+.--+|+ +-|+||| |-+====|+.++.+
T Consensus 68 fPkI~R~llL~p~-----ik~~F~----------~~~v~VEEKmnGYNVRV~k~~g~-vyAiTRg-G~ICPfTT~r~~~l 130 (382)
T COG1423 68 FPKIRRALLLEPT-----IKKHFG----------RGKVVVEEKMNGYNVRVVKLGGE-VYAITRG-GLICPFTTERLRDL 130 (382)
T ss_pred Cchhheeeccchh-----hHhhcC----------CCcEEEEEeccCceEEEEEECCE-EEEEecC-ceecCchhHHHHhh
Confidence 4677788888865 444432 13799999999999999877887 5899999 76555556666654
Q ss_pred ccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccC
Q psy11421 163 HKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG 242 (687)
Q Consensus 163 ~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~ 242 (687)
||+.+..+ +| .+.+-||.+=+. .||- . .++ . ...++.||.|++..-..
T Consensus 131 --~~~eff~d-~p-~lvlcgEmvG~e---------------nPYv------~-----~~~-y-~~e~v~fFvFDire~~t 178 (382)
T COG1423 131 --IDLEFFDD-YP-DLVLCGEMVGPE---------------NPYV------P-----GPY-Y-EKEDVGFFVFDIREKNT 178 (382)
T ss_pred --cchhhHhh-CC-CcEEEEEeccCC---------------CCCC------C-----CCC-C-ccCCceEEEEEEEecCC
Confidence 56666543 45 578899987331 2221 1 111 1 23579999999976322
Q ss_pred CCCCCCHHHHHHHHHhcCCCCCCCceEeC--CH-HHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11421 243 MNMPSSHSELLNWYQKIGLSICGEYSVLS--GV-NKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (687)
Q Consensus 243 ~~~~~~~~e~l~~L~~~Gf~~~~~~~~~~--~~-~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (687)
. -+-++.+.++.+.+.||+.+....... .. ++|...++++.+... -|||+|-.|..+
T Consensus 179 g-r~Lp~eer~~l~ekYgl~~V~~fg~~~~~e~~eei~eIve~L~keGR------EGVV~Kdpdm~~ 238 (382)
T COG1423 179 G-RPLPVEERLELAEKYGLPHVEIFGEFPADEAGEEIYEIVERLNKEGR------EGVVMKDPDMRV 238 (382)
T ss_pred C-CCCCHHHHHHHHHHcCCCceEEeeeechhHhHHHHHHHHHHHhhcCC------cceEecCccccc
Confidence 1 246899999999999999775333221 12 445555666654332 699999888544
No 83
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.28 E-value=0.0053 Score=72.57 Aligned_cols=80 Identities=18% Similarity=0.339 Sum_probs=48.6
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhh---hcccCccHHHHHHHHHHH---HHcccCCHHHHHHHcCCCCC
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNL---LRLDRVSNKLANNILLAI---QKSKLTTFSRFIYALGIRHV 531 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L---~~l~gfG~Ksa~~Ll~~I---e~sk~~~l~r~L~aLGIp~v 531 (687)
+.+.++|+|+|+.++|+++ +..--...-+++ +.++|+|++.|..|++.+ +.-++.+...+ ..|+||
T Consensus 480 ~L~~l~gfG~Ksa~~ll~~-----Ie~sk~~~l~R~l~algi~~IG~~~ak~L~~~f~sl~~l~~As~eeL---~~i~GI 551 (665)
T PRK07956 480 DLLGLEGFGEKSAQNLLDA-----IEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEEL---AAVEGV 551 (665)
T ss_pred HHhcCcCcchHHHHHHHHH-----HHHhhcCCHHHhhHhhhccCcCHHHHHHHHHHcCCHHHHHhCCHHHH---hccCCc
Confidence 4567888888888888763 111111121222 356888888888777644 33333343332 367888
Q ss_pred CHHHHHHHHhhcCC
Q psy11421 532 GETTAKELANYFKN 545 (687)
Q Consensus 532 G~~~Ak~La~~f~s 545 (687)
|+.+|..|.+.|.+
T Consensus 552 G~~~A~sI~~ff~~ 565 (665)
T PRK07956 552 GEVVAQSIVEFFAV 565 (665)
T ss_pred CHHHHHHHHHHHhh
Confidence 88888888777754
No 84
>KOG1968|consensus
Probab=96.27 E-value=0.0032 Score=75.88 Aligned_cols=70 Identities=27% Similarity=0.227 Sum_probs=67.3
Q ss_pred CCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHH
Q psy11421 603 NKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEK 672 (687)
Q Consensus 603 ~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~ 672 (687)
...++.|.+|++||.++.+.+..++..++.+|+.+..+++.+|+++++|++++ .|+++++++.+++++|+
T Consensus 170 ~~~~~s~~~~~~tg~ld~~~~~s~~~~~k~~~~~~~~~ls~kt~~s~~~~e~~~~kle~~~~~~~~~~~e~ 240 (871)
T KOG1968|consen 170 WSKPLSGIKFTPTGVLDDIGTGSAEPSLKEFGASKTESLSDKTVESCLGDEAIAKKLEKIKELEIPVLLEE 240 (871)
T ss_pred ccCCCcCceeeecCcccccccccchhhhhhccccccccCCCCcceeecCccccchhhcccccccccccchh
Confidence 35689999999999999999999999999999999999999999999999998 99999999999999999
No 85
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.25 E-value=0.0056 Score=72.48 Aligned_cols=17 Identities=18% Similarity=0.063 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHh
Q psy11421 16 FRVTELKKELHRHNIAY 32 (687)
Q Consensus 16 ~~i~~L~~~l~~~~~~Y 32 (687)
.+|+.|.++|+.+...|
T Consensus 61 ~eYD~L~~eL~~LE~~~ 77 (689)
T PRK14351 61 RAYDALFARLQALEDAF 77 (689)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 58899999999888876
No 86
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.00 E-value=0.025 Score=57.03 Aligned_cols=72 Identities=15% Similarity=0.223 Sum_probs=50.7
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHH----HHhcCHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLEC----MFKATEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~----l~~As~eeL~~I~GIG~ 565 (687)
.||-..|=||..+....+. ..-++++|||+++|..++..|+ .+. +..-+.+.|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF--------------~~Li~V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~~~L~~vpGIGk 118 (194)
T PRK14605 54 REDALSLFGFATTEELSLF--------------ETLIDVSGIGPKLGLAMLSAMN-AEALASAIISGNAELLSTIPGIGK 118 (194)
T ss_pred ecCCceeeCCCCHHHHHHH--------------HHHhCCCCCCHHHHHHHHHhCC-HHHHHHHHHhCCHHHHHhCCCCCH
Confidence 4566666677766544333 2225889999999998888875 444 34557888999999999
Q ss_pred HHHHHHHHHHc
Q psy11421 566 TTVKAFIKFIN 576 (687)
Q Consensus 566 ~~A~sI~~ff~ 576 (687)
++|+.|.--++
T Consensus 119 KtAerIilELk 129 (194)
T PRK14605 119 KTASRIVLELK 129 (194)
T ss_pred HHHHHHHHHHH
Confidence 99999665443
No 87
>PRK13766 Hef nuclease; Provisional
Probab=95.93 E-value=0.011 Score=71.42 Aligned_cols=53 Identities=26% Similarity=0.459 Sum_probs=50.5
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
.+|||||+..|+.|.++|++++++..++.++|.+++|+|++.|+.|.+||+.+
T Consensus 718 ~~ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~~ 770 (773)
T PRK13766 718 ESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSE 770 (773)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhh
Confidence 48999999999999999999999999999999999999999999999999765
No 88
>PRK07758 hypothetical protein; Provisional
Probab=95.87 E-value=0.019 Score=50.72 Aligned_cols=51 Identities=18% Similarity=0.177 Sum_probs=46.5
Q ss_pred cCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.++|+-.....|..+| |.++.||..+++++|+++.|||+|+.+.|.+.+.+
T Consensus 39 ~~~LSvRA~N~Lk~AG-I~TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 39 LSLLSAPARRALEHHG-IHTVEELSKYSEKEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred CccccHHHHHHHHHcC-CCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence 4578888999999998 59999999999999999999999999999988765
No 89
>PRK00254 ski2-like helicase; Provisional
Probab=95.78 E-value=0.028 Score=67.52 Aligned_cols=52 Identities=25% Similarity=0.484 Sum_probs=49.4
Q ss_pred cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
..|||+|+.++++|.++ |++++++..|+.++|.+++|||+++|++|.++++.
T Consensus 648 ~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~ 700 (720)
T PRK00254 648 MRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGV 700 (720)
T ss_pred hcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhcc
Confidence 48999999999999999 99999999999999999999999999999999863
No 90
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=95.77 E-value=0.081 Score=54.00 Aligned_cols=115 Identities=18% Similarity=0.188 Sum_probs=74.0
Q ss_pred CCHHHHHHHcCCCCCCH-HHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccc
Q psy11421 517 TTFSRFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL 595 (687)
Q Consensus 517 ~~l~r~L~aLGIp~vG~-~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~ 595 (687)
..|-.++..-|+|+-.. ..|+.|+++|+++..+..|+.++|+.++|+|...|-++..-+.-. +.....-...+..+.
T Consensus 27 ~ELLailLrtG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~--~R~~~~~~~~~~~i~ 104 (224)
T COG2003 27 AELLAILLRTGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAKAIQIKAAIELG--KRILAERLREGVVIT 104 (224)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHHHHHHHHHHHHH--HHHHHHHhccCCccC
Confidence 34555666678886433 567899999999999999999999999999998888776644211 011111111111111
Q ss_pred cCC--------------C------CCCCCCccCCeEEEEEcCCCc---CCHHHHHHHHHhc
Q psy11421 596 NNP--------------N------TKGNKNYLKEKIFVFTGSLYA---FKRNEAIILIENL 633 (687)
Q Consensus 596 ~~~--------------~------~~~~~~~l~g~~vv~TG~l~~---~~R~e~~~~i~~~ 633 (687)
+++ . --+..+.+=....+|+|+++. ++|+-++..+..+
T Consensus 105 sp~~~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~lf~GTi~~s~V~PREI~k~Al~~n 165 (224)
T COG2003 105 SPEAVAEYLRAELGGEEREHFVVLYLDSQNRLIATETLFIGTLNVSEVHPREIFKEALKYN 165 (224)
T ss_pred CHHHHHHHHHHHhhhhHHHHHHHHHhcCcCceecceeEEeeecccceecHHHHHHHHHHhc
Confidence 110 0 012334556778999999875 5888888777654
No 91
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.75 E-value=0.037 Score=55.72 Aligned_cols=71 Identities=13% Similarity=0.170 Sum_probs=44.9
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~ 565 (687)
.||-..|=||..+....+. + .-+++.|||+++|-.++..+ +.+++. +-+...|.++||||+
T Consensus 53 rED~~~LYGF~t~~Er~lF------------~--~LisVsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpGIGk 117 (196)
T PRK13901 53 REDELKLFGFLNSSEREVF------------E--ELIGVDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKGIGN 117 (196)
T ss_pred ecCCceeeCCCCHHHHHHH------------H--HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence 3555566677655443332 1 22577888888887777665 344444 346778888888888
Q ss_pred HHHHHHHHHH
Q psy11421 566 TTVKAFIKFI 575 (687)
Q Consensus 566 ~~A~sI~~ff 575 (687)
++|+.|.--+
T Consensus 118 KtAeRIIlEL 127 (196)
T PRK13901 118 KMAGKIFLKL 127 (196)
T ss_pred HHHHHHHHHH
Confidence 8888876444
No 92
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.67 E-value=0.039 Score=55.32 Aligned_cols=73 Identities=16% Similarity=0.229 Sum_probs=48.7
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~ 565 (687)
.||-..|=||..+....+. +.| +++.|||+++|-.++..+ +.+++. +-+...|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF------------~~L--i~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpGIGk 118 (188)
T PRK14606 54 SQDGITLYGFSNERKKELF------------LSL--TKVSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPGISK 118 (188)
T ss_pred ecCCceeeCCCCHHHHHHH------------HHH--hccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence 4556666677655443322 222 578888888888888665 355444 447788999999999
Q ss_pred HHHHHHHHHHcc
Q psy11421 566 TTVKAFIKFINQ 577 (687)
Q Consensus 566 ~~A~sI~~ff~~ 577 (687)
++|+.|.--+++
T Consensus 119 KtAerIilELkd 130 (188)
T PRK14606 119 KTAERIVMELKD 130 (188)
T ss_pred HHHHHHHHHHHH
Confidence 999988754433
No 93
>PRK00254 ski2-like helicase; Provisional
Probab=95.66 E-value=0.014 Score=69.99 Aligned_cols=54 Identities=20% Similarity=0.326 Sum_probs=50.1
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.+.|+|+|++++.+|+++|+ .|+.||..++.++|.+++|+|+|.|++|.+.+..
T Consensus 647 L~~ipgig~~~~~~l~~~g~-~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~ 700 (720)
T PRK00254 647 LMRLPMIGRKRARALYNAGF-RSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGV 700 (720)
T ss_pred hhcCCCCCHHHHHHHHHccC-CCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhcc
Confidence 34799999999999999995 9999999999999999999999999999998763
No 94
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.64 E-value=0.033 Score=56.10 Aligned_cols=53 Identities=23% Similarity=0.312 Sum_probs=42.1
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhc----CChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK----INFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~----L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..+.|+|+|||++..+.+.. ++.+|.. =+.+.|.++||+|+|+|++|+-.+..
T Consensus 74 ~Li~V~GIGpK~Al~ILs~~---~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~ 130 (194)
T PRK14605 74 TLIDVSGIGPKLGLAMLSAM---NAEALASAIISGNAELLSTIPGIGKKTASRIVLELKD 130 (194)
T ss_pred HHhCCCCCCHHHHHHHHHhC---CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 36789999999999999965 4555544 24577999999999999998766643
No 95
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=95.55 E-value=0.012 Score=67.95 Aligned_cols=19 Identities=32% Similarity=0.422 Sum_probs=15.6
Q ss_pred cccccCCCCHHHHHHHHHC
Q psy11421 458 KAMNIIGLGKKMIEKLVNA 476 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~ 476 (687)
+.+.++|+|+|.+++|+++
T Consensus 460 ~l~~l~gfgeks~~nll~a 478 (562)
T PRK08097 460 QLANTPGIGKARAEQLWHQ 478 (562)
T ss_pred HHhcCcCccHHHHHHHHHH
Confidence 5777899999999998763
No 96
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA 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=95.55 E-value=0.024 Score=57.01 Aligned_cols=69 Identities=17% Similarity=0.206 Sum_probs=48.3
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhc----CHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKA----TEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~A----s~eeL~~I~GIG~ 565 (687)
.+|-..|=||..+....+ |..-++++|||+++|..|+..+ +.+++..| +...|.++||||+
T Consensus 53 red~~~LyGF~~~~Er~l--------------F~~L~~V~GIGpK~Al~iL~~~-~~~el~~aI~~~d~~~L~~ipGiGk 117 (191)
T TIGR00084 53 REDAELLFGFNTLEEREL--------------FKELIKVNGVGPKLALAILSNM-SPEEFVYAIETEEVKALVKIPGVGK 117 (191)
T ss_pred ecCCceeeCCCCHHHHHH--------------HHHHhCCCCCCHHHHHHHHhcC-CHHHHHHHHHhCCHHHHHhCCCCCH
Confidence 455556667775544333 2333688999999998888765 35555443 5678999999999
Q ss_pred HHHHHHHH
Q psy11421 566 TTVKAFIK 573 (687)
Q Consensus 566 ~~A~sI~~ 573 (687)
++|+.|.-
T Consensus 118 KtAerIil 125 (191)
T TIGR00084 118 KTAERLLL 125 (191)
T ss_pred HHHHHHHH
Confidence 99999873
No 97
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=95.45 E-value=0.014 Score=54.29 Aligned_cols=61 Identities=16% Similarity=0.303 Sum_probs=45.2
Q ss_pred ChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcC
Q psy11421 481 TAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNI 560 (687)
Q Consensus 481 ~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I 560 (687)
.+-||-+++.++|..+||+|++.|++|++..+. +.+ | ++.++|.++
T Consensus 58 ~~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~--~g~------------------------f--------~s~eeL~~V 103 (120)
T TIGR01259 58 AAVNINAASLEELQALPGIGPAKAKAIIEYREE--NGA------------------------F--------KSVDDLTKV 103 (120)
T ss_pred CCEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh--cCC------------------------c--------CCHHHHHcC
Confidence 345777788888888888888888888887654 111 2 356778888
Q ss_pred CCCCHHHHHHHHHHH
Q psy11421 561 PKIGSTTVKAFIKFI 575 (687)
Q Consensus 561 ~GIG~~~A~sI~~ff 575 (687)
+|||+++++.|..|+
T Consensus 104 ~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 104 SGIGEKSLEKLKDYA 118 (120)
T ss_pred CCCCHHHHHHHHhce
Confidence 888888888887765
No 98
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=95.41 E-value=0.037 Score=46.06 Aligned_cols=23 Identities=35% Similarity=0.531 Sum_probs=17.5
Q ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 553 TEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 553 s~eeL~~I~GIG~~~A~sI~~ff 575 (687)
+.++|.+++|||+++++.|..|+
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhhc
Confidence 56777778888888888877764
No 99
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=95.41 E-value=0.022 Score=68.64 Aligned_cols=51 Identities=20% Similarity=0.353 Sum_probs=48.1
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCC-HHHHHHHHHHHcch
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIG-STTVKAFIKFINQP 578 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG-~~~A~sI~~ff~~~ 578 (687)
+.|||||+..|+.|+.+|+|+.+|.+|+.++|..+ +| ++.|+.|++||+.+
T Consensus 760 ~~lPgI~~~~a~~ll~~f~si~~l~~as~eeL~~~--iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 760 LKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNEL--IGDEEAAKRLYDFLRTE 811 (814)
T ss_pred HHCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCCHHHHHHHHHHhccc
Confidence 49999999999999999999999999999999996 88 99999999999865
No 100
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.40 E-value=0.058 Score=53.82 Aligned_cols=72 Identities=19% Similarity=0.329 Sum_probs=48.0
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHh----cCHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFK----ATEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~----As~eeL~~I~GIG~ 565 (687)
.||-..|=||..+.-..+. ..-+++.|||+++|-.++..+ +.+++.. -+...|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF--------------~~Li~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpGIGk 118 (183)
T PRK14601 54 KEDSNKLYGFLDKDEQKMF--------------EMLLKVNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPGIGP 118 (183)
T ss_pred ecCCceeeCCCCHHHHHHH--------------HHHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence 4556666677755433222 222578888888888777665 3555544 36788999999999
Q ss_pred HHHHHHHHHHc
Q psy11421 566 TTVKAFIKFIN 576 (687)
Q Consensus 566 ~~A~sI~~ff~ 576 (687)
++|+.|.--++
T Consensus 119 KtAeRIilELk 129 (183)
T PRK14601 119 KSAKRIIAELS 129 (183)
T ss_pred HHHHHHHHHHH
Confidence 99998765443
No 101
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.36 E-value=0.058 Score=54.41 Aligned_cols=73 Identities=18% Similarity=0.240 Sum_probs=48.2
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~ 565 (687)
.||-..|=||..+....+. + .-+++.|||+++|-.++..+ +.++|. +-+...|.++||||+
T Consensus 54 rEd~~~LyGF~~~~Er~lF------------~--~Li~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpGIGk 118 (195)
T PRK14604 54 REDALTLYGFSTPAQRQLF------------E--LLIGVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPGIGK 118 (195)
T ss_pred ecCCceeeCCCCHHHHHHH------------H--HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence 4555566677755443332 2 22578888888888877665 355444 346788889999999
Q ss_pred HHHHHHHHHHcc
Q psy11421 566 TTVKAFIKFINQ 577 (687)
Q Consensus 566 ~~A~sI~~ff~~ 577 (687)
++|+.|.--+++
T Consensus 119 KtAerIilELk~ 130 (195)
T PRK14604 119 KTAERIVLELKG 130 (195)
T ss_pred HHHHHHHHHHHH
Confidence 999888755543
No 102
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=95.27 E-value=0.042 Score=59.97 Aligned_cols=64 Identities=23% Similarity=0.244 Sum_probs=46.4
Q ss_pred hhhhcccCccHHHHHHHHHHHHHcccC--------CHH-HHHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCH
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQKSKLT--------TFS-RFIYALGIRHVGETTAKELANY-FKNLECMFKATE 554 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~--------~l~-r~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~ 554 (687)
++|.++||+|++.|++|.+-++.-+-. +.. -++.=+.|||||+++|+.+.+. +.|+++|..+-.
T Consensus 48 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~~ 121 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKE 121 (334)
T ss_pred HHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhccc
Confidence 478899999999999999887642211 111 2444469999999999988872 458888876643
No 103
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=95.27 E-value=0.047 Score=65.51 Aligned_cols=75 Identities=15% Similarity=0.138 Sum_probs=40.5
Q ss_pred ccCccHHHHHHHHHHHHH-----cccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHH
Q psy11421 496 LDRVSNKLANNILLAIQK-----SKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKA 570 (687)
Q Consensus 496 l~gfG~Ksa~~Ll~~Ie~-----sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~s 570 (687)
++|+|+|+|++|++.+-. -.+.+ .+ -..|||+|++.++.|.+.+....... ..-.+..-.|++...|..
T Consensus 89 ~~GIG~~~A~~iv~~fg~~~~~~i~~~~-~~---L~~v~gi~~~~~~~i~~~~~~~~~~~--~~~~~L~~~gi~~~~a~k 162 (720)
T TIGR01448 89 IKGVGKKLAQRIVKTFGEAAFDVLDDDP-EK---LLEVPGISKANLEKFVSQWSQQGDER--RLLAGLQGLGIGIKLAQR 162 (720)
T ss_pred CCCcCHHHHHHHHHHhCHhHHHHHHhCH-HH---HhcCCCCCHHHHHHHHHHHHHhHHHH--HHHHHHHHcCCCHHHHHH
Confidence 567777777777665421 11111 11 12567777777776666553222211 122344555777777777
Q ss_pred HHHHHc
Q psy11421 571 FIKFIN 576 (687)
Q Consensus 571 I~~ff~ 576 (687)
|+++|.
T Consensus 163 i~~~yg 168 (720)
T TIGR01448 163 IYKFYQ 168 (720)
T ss_pred HHHHHh
Confidence 777663
No 104
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=95.16 E-value=0.029 Score=52.17 Aligned_cols=47 Identities=9% Similarity=0.183 Sum_probs=37.5
Q ss_pred ccccccCCCCHHHHHHHHHC----CCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11421 457 RKAMNIIGLGKKMIEKLVNA----NIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 457 r~~l~I~GLG~k~i~~L~~~----g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
...+.++|+|+++++++++. |... +.++|..++|+|+|.+++|.+.|
T Consensus 68 ~eL~~lpGIG~~~A~~Ii~~R~~~g~f~--------s~eeL~~V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 68 EELQALPGIGPAKAKAIIEYREENGAFK--------SVDDLTKVSGIGEKSLEKLKDYA 118 (120)
T ss_pred HHHhcCCCCCHHHHHHHHHHHHhcCCcC--------CHHHHHcCCCCCHHHHHHHHhce
Confidence 35678999999999999984 4443 34677889999999999987654
No 105
>PRK02362 ski2-like helicase; Provisional
Probab=95.14 E-value=0.021 Score=68.71 Aligned_cols=63 Identities=21% Similarity=0.281 Sum_probs=52.9
Q ss_pred HHhhhhhcccc---cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11421 447 RKAGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 447 ~~~~i~~F~sr---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
+.++|.|=+.. ..+.|||+|++++.+|+++| |+|+.||..++.++|.++ ||+|.|++|++++.
T Consensus 639 l~~~l~~gv~~~~~~L~~ip~i~~~~a~~l~~~g-i~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~ 704 (737)
T PRK02362 639 LEKRVEYGVREELLDLVGLRGVGRVRARRLYNAG-IESRADLRAADKSVVLAI--LGEKIAENILEQAG 704 (737)
T ss_pred HHHHHHhCCCHHHHHHhCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhC
Confidence 34444443332 46789999999999999977 699999999999999999 99999999999976
No 106
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.07 E-value=0.049 Score=55.29 Aligned_cols=73 Identities=18% Similarity=0.209 Sum_probs=52.8
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHH----HhcCHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM----FKATEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l----~~As~eeL~~I~GIG~ 565 (687)
.||-..|=||..+....+. ..-+++.|||+++|-.++..+. .++| .+-+...|.++||||+
T Consensus 55 rEd~~~LyGF~~~~Er~lF--------------~~Li~V~GIGpK~Al~iLs~~~-~~~l~~aI~~~D~~~L~~ipGIGk 119 (203)
T PRK14602 55 REDALELFGFATWDERQTF--------------IVLISISKVGAKTALAILSQFR-PDDLRRLVAEEDVAALTRVSGIGK 119 (203)
T ss_pred ecCcceeeCCCCHHHHHHH--------------HHHhCCCCcCHHHHHHHHhhCC-HHHHHHHHHhCCHHHHhcCCCcCH
Confidence 4666677788766443332 2226889999999998888764 5544 4558899999999999
Q ss_pred HHHHHHHHHHcc
Q psy11421 566 TTVKAFIKFINQ 577 (687)
Q Consensus 566 ~~A~sI~~ff~~ 577 (687)
++|+.|.--+++
T Consensus 120 KtAerIilELkd 131 (203)
T PRK14602 120 KTAQHIFLELKY 131 (203)
T ss_pred HHHHHHHHHHHH
Confidence 999998755443
No 107
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.02 E-value=0.069 Score=53.43 Aligned_cols=48 Identities=19% Similarity=0.302 Sum_probs=31.3
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
+++.|||+++|-.++..+ +.+++. +-|...| ++||||+++|+.|.--+
T Consensus 76 isV~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 76 VKVSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred hCcCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHH
Confidence 467777777777776655 344443 3356667 78888888887776444
No 108
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=94.99 E-value=0.027 Score=66.64 Aligned_cols=81 Identities=17% Similarity=0.252 Sum_probs=52.4
Q ss_pred cccccCCCCHHHHHHHHHCC---CCCChHHHhcCChhhhhcccCccHHHHHHHH-HHH---HHccc------CCHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNAN---IVVTAVDLYKINFKNLLRLDRVSNKLANNIL-LAI---QKSKL------TTFSRFIY 524 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g---~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll-~~I---e~sk~------~~l~r~L~ 524 (687)
+.+.++|+|+|.+++|+++- .=..+.-++. =+.+|++|++.|+.|. ..+ ++-.+ .++.++
T Consensus 471 ~l~~l~g~geksa~nl~~~Ie~sk~~~l~r~l~-----ALGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l-- 543 (669)
T PRK14350 471 RLINLKGFKDKRINNLKRSIEASKKRPFSKLLL-----SMGIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKL-- 543 (669)
T ss_pred HHhhccCccHHHHHHHHHHHHHHhCCCHHHHHH-----HcCCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHH--
Confidence 56678999999999998741 1123344333 2457889998888877 332 22111 222232
Q ss_pred HcCCCCCCHHHHHHHHhhcCCh
Q psy11421 525 ALGIRHVGETTAKELANYFKNL 546 (687)
Q Consensus 525 aLGIp~vG~~~Ak~La~~f~sl 546 (687)
+.|+|||+.+|..|.+.|.+-
T Consensus 544 -~~i~giG~~~a~si~~ff~~~ 564 (669)
T PRK14350 544 -LKIKGIGEKIALNIIEAFNDK 564 (669)
T ss_pred -hhCCCccHHHHHHHHHHHcCH
Confidence 368999999999998888653
No 109
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=94.85 E-value=0.039 Score=64.09 Aligned_cols=57 Identities=21% Similarity=0.253 Sum_probs=51.1
Q ss_pred cccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 454 FSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 454 F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+-| ...+|+|+||++..+|++.- .|+.+|..++.++|.++||++++.|++|++.+.+
T Consensus 512 ~~s-~L~~I~GiG~kr~~~LL~~F--gs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 512 IKL-NYTKIKGIGEKKAKKILKSL--GTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred ccc-ccccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 345 36699999999999999975 5999999999999999999999999999999865
No 110
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=94.80 E-value=0.2 Score=46.70 Aligned_cols=83 Identities=22% Similarity=0.215 Sum_probs=60.9
Q ss_pred CCCCHHHHHHHHHCCCCCChHHHhcCCh-----hhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHH
Q psy11421 463 IGLGKKMIEKLVNANIVVTAVDLYKINF-----KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAK 537 (687)
Q Consensus 463 ~GLG~k~i~~L~~~g~I~~i~DL~~L~~-----~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak 537 (687)
||+|++...+|-+.| |.|..||+.... ..|..--|+..+...++... .++ .-|||||+.-|.
T Consensus 1 pgi~~~~~~~L~~~G-I~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~---------AdL---~ri~gi~~~~a~ 67 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAG-IKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQ---------ADL---MRIPGIGPQYAE 67 (122)
T ss_pred CCCCHHHHHHHHHcC-CCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhH---------HHh---hhcCCCCHHHHH
Confidence 799999999997777 699999999653 23655556666555444321 122 268999999998
Q ss_pred HHHh-hcCChHHHHhcCHHHHh
Q psy11421 538 ELAN-YFKNLECMFKATEEQLL 558 (687)
Q Consensus 538 ~La~-~f~sld~l~~As~eeL~ 558 (687)
.|.. .+.|+++|..+++++|.
T Consensus 68 LL~~AGv~Tv~~LA~~~p~~L~ 89 (122)
T PF14229_consen 68 LLEHAGVDTVEELAQRNPQNLH 89 (122)
T ss_pred HHHHhCcCcHHHHHhCCHHHHH
Confidence 8774 48899999998887764
No 111
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.61 E-value=0.066 Score=54.06 Aligned_cols=73 Identities=14% Similarity=0.189 Sum_probs=50.5
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHH----HhcCHHHHhcCCCCCH
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM----FKATEEQLLNIPKIGS 565 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l----~~As~eeL~~I~GIG~ 565 (687)
.||-..|=||..+....+. +. -+++.|||+++|-.++..+ +.+++ .+-|...|.++||||+
T Consensus 53 rEd~~~LyGF~~~~Er~lF------------~~--L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpGIGk 117 (197)
T PRK14603 53 REDALSLYGFPDEDSLELF------------EL--LLGVSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASGVGK 117 (197)
T ss_pred ccCCceeeCcCCHHHHHHH------------HH--HhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCH
Confidence 4555666677755443322 22 2578899999988888765 35444 4457889999999999
Q ss_pred HHHHHHHHHHcc
Q psy11421 566 TTVKAFIKFINQ 577 (687)
Q Consensus 566 ~~A~sI~~ff~~ 577 (687)
++|+.|.--+++
T Consensus 118 KtAerIilELkd 129 (197)
T PRK14603 118 KLAERIALELKG 129 (197)
T ss_pred HHHHHHHHHHHH
Confidence 999998755543
No 112
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.60 E-value=0.039 Score=51.55 Aligned_cols=26 Identities=19% Similarity=0.344 Sum_probs=16.9
Q ss_pred HHHhcCChhhhhcccCccHHHHHHHH
Q psy11421 483 VDLYKINFKNLLRLDRVSNKLANNIL 508 (687)
Q Consensus 483 ~DL~~L~~~~L~~l~gfG~Ksa~~Ll 508 (687)
-||-+.+..+|.++||+|++.|++|+
T Consensus 53 IdiN~A~~~el~~lpGigP~~A~~IV 78 (132)
T PRK02515 53 IDLNNSSVRAFRQFPGMYPTLAGKIV 78 (132)
T ss_pred ccCCccCHHHHHHCCCCCHHHHHHHH
Confidence 35556666666666777766666666
No 113
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=94.55 E-value=0.06 Score=58.14 Aligned_cols=55 Identities=22% Similarity=0.215 Sum_probs=50.2
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
....++|+|++++++|.+.|+ .|+.||+.++.++|..+.|++++.+.+|++....
T Consensus 7 ~l~~l~gIg~~~a~~L~~~Gi-~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREAGY-DTVEAIAVASPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred cHhhcCCCCHHHHHHHHHcCC-CCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 456799999999999999995 8999999999999999999999999999988754
No 114
>PRK01172 ski2-like helicase; Provisional
Probab=94.46 E-value=0.067 Score=63.70 Aligned_cols=63 Identities=17% Similarity=0.173 Sum_probs=54.0
Q ss_pred hhhhhcccc---cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11421 449 AGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 449 ~~i~~F~sr---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
.||.|=+.. ..|.|||+|..++.+|+++| ++|+.||-.++.+++..+.|+|++.+++|+++..
T Consensus 601 ~rl~~gv~~~~~~L~~ip~~~~~~a~~l~~~g-~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~ 666 (674)
T PRK01172 601 IRIKEGIREDLIDLVLIPKVGRVRARRLYDAG-FKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM 666 (674)
T ss_pred HHHHcCCCHHHHhhcCCCCCCHHHHHHHHHcC-CCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence 345555443 35679999999999999999 5999999999999999999999999999999843
No 115
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.43 E-value=0.12 Score=51.70 Aligned_cols=53 Identities=15% Similarity=0.269 Sum_probs=43.9
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..+.+.|+|||++-.+.... ++.+|..+ +...|.++||+|+|+|++|+-.+..
T Consensus 74 ~Li~VsGIGpK~Al~ILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkd 130 (183)
T PRK14601 74 MLLKVNGIGANTAMAVCSSL---DVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSD 130 (183)
T ss_pred HHhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 36789999999999998754 77788773 3467889999999999999988764
No 116
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=94.21 E-value=0.058 Score=37.75 Aligned_cols=28 Identities=29% Similarity=0.358 Sum_probs=22.3
Q ss_pred hHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11421 482 AVDLYKINFKNLLRLDRVSNKLANNILL 509 (687)
Q Consensus 482 i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~ 509 (687)
...+...+.++|.++||+|+++|+.|+.
T Consensus 2 ~~g~~pas~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 2 LDGLIPASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHHTSSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCCcCCCCHHHHHhCCCcCHHHHHHHHh
Confidence 3456667889999999999999998875
No 117
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=94.19 E-value=0.044 Score=63.79 Aligned_cols=81 Identities=19% Similarity=0.284 Sum_probs=39.4
Q ss_pred cccccccCCCCHHHHHHHHHCC---CCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH---cccCCHHHHHHHcCCC
Q psy11421 456 SRKAMNIIGLGKKMIEKLVNAN---IVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK---SKLTTFSRFIYALGIR 529 (687)
Q Consensus 456 sr~~l~I~GLG~k~i~~L~~~g---~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~---sk~~~l~r~L~aLGIp 529 (687)
..+.+.++|+|++.+++|+++- .=.+..-|+. =+.++.+|++.|..|...+.. -...++..+ ..||
T Consensus 478 ~~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~-----aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l---~~i~ 549 (667)
T COG0272 478 EEDLLSLEGFGEKSAENLLNAIEKSKKQPLARFLY-----ALGIRHVGETTAKSLARHFGTLEALLAASEEEL---ASIP 549 (667)
T ss_pred HHHHhhccchhhhHHHHHHHHHHHhccCCHHHHHH-----HcCCchhhHHHHHHHHHHhhhHHHHHhcCHHHH---hhcc
Confidence 3556667777777777666521 0011111111 134556666666666554432 111222111 2466
Q ss_pred CCCHHHHHHHHhhcC
Q psy11421 530 HVGETTAKELANYFK 544 (687)
Q Consensus 530 ~vG~~~Ak~La~~f~ 544 (687)
+||..+|..|.+.|.
T Consensus 550 giG~~vA~si~~ff~ 564 (667)
T COG0272 550 GIGEVVARSIIEFFA 564 (667)
T ss_pred chhHHHHHHHHHHHc
Confidence 666666666665554
No 118
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.09 E-value=0.12 Score=52.00 Aligned_cols=53 Identities=13% Similarity=0.347 Sum_probs=44.0
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..+.|.|+|||++-.+.... ++.+|..+ +...|.++||+|+|+|++|+-.+..
T Consensus 73 ~LisVsGIGPK~ALaILs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkd 129 (196)
T PRK13901 73 ELIGVDGIGPRAALRVLSGI---KYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRG 129 (196)
T ss_pred HHhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 36789999999999998754 67777762 3567899999999999999988764
No 119
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=94.07 E-value=0.078 Score=62.47 Aligned_cols=54 Identities=9% Similarity=0.056 Sum_probs=49.2
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..++|+|+|++++.+|++.- .|+.+|...+.++|.+++|+|++.|++|++.++.
T Consensus 638 ~L~~IPGIGpkr~k~LL~~F--GSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~~ 691 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERF--GSLQAMAAAGEEGLAAVPGIGPARAAALHEHLKT 691 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHh--CCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHHH
Confidence 46789999999999999974 4999999999999999999999999999998864
No 120
>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins.
Probab=94.07 E-value=0.25 Score=53.43 Aligned_cols=128 Identities=16% Similarity=0.134 Sum_probs=79.2
Q ss_pred CeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhh--------h-hhhhhccCCcccccCC--CCceEEEEEEEE
Q psy11421 117 NIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENIT--------T-NIHIIHKIPLVLNIKY--PPELLEVRCEVL 185 (687)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT--------~-n~~~i~~iP~~l~~~~--~~~~~evRGEi~ 185 (687)
...|+++.|+||.-.+++|.+|.-++...| +|..++|-. + +...|..+...|.... -...+.|-||++
T Consensus 24 ~~ewvatEKlhGaNfsi~~~~~~~i~~akR-~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl~ 102 (325)
T TIGR02307 24 LTEWVAREKIHGTNFSIIIERDFKVTCAKR-TGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGELA 102 (325)
T ss_pred CceEEEEEEecCcceEEEEeCCceEEEeec-ccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEee
Confidence 348999999999999999988833577777 566665422 1 1112333333332110 135799999998
Q ss_pred eehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccC--CCCCCCHHHHHHHHHhcC-CC
Q psy11421 186 IYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRG--MNMPSSHSELLNWYQKIG-LS 262 (687)
Q Consensus 186 ~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~--~~~~~~~~e~l~~L~~~G-f~ 262 (687)
=. .+.+|.+ -. .++|++|++..+.. ..+ -+.-+.++.+...| |+
T Consensus 103 G~-----------------~~q~~~~--------------Y~-~~~fyaFdI~~~~~~~~~~-L~~d~~~e~~~~~~~l~ 149 (325)
T TIGR02307 103 GP-----------------GYQKPVV--------------YS-DKDFYAFDIKYTETSDDVT-LVDDYMMESFCNVPKLK 149 (325)
T ss_pred cC-----------------cccCccc--------------cc-cccEEEEEEEEeccCcceE-ecHHHHHHHHHHcCCcc
Confidence 32 2444544 11 47999999854421 112 35556777888886 88
Q ss_pred CCCCceEeCCHHHHHHH
Q psy11421 263 ICGEYSVLSGVNKLIEF 279 (687)
Q Consensus 263 ~~~~~~~~~~~~ei~~~ 279 (687)
.++. ....++++++++
T Consensus 150 ~ap~-L~rGt~~e~l~~ 165 (325)
T TIGR02307 150 YAPL-LGRGTLDELLAF 165 (325)
T ss_pred cchh-hcccCHHHHHhc
Confidence 7653 334678887775
No 121
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.97 E-value=0.053 Score=54.67 Aligned_cols=53 Identities=23% Similarity=0.365 Sum_probs=43.3
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..+.|.|+|||+.-.+.... ++.+|..+ +...|.++||+|+|+|++|+-.++.
T Consensus 74 ~Li~V~GIGpK~Al~iLs~~---~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~ 130 (195)
T PRK14604 74 LLIGVSGVGPKAALNLLSSG---TPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKG 130 (195)
T ss_pred HHhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 36789999999999998754 66777762 3567889999999999999988764
No 122
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.92 E-value=0.062 Score=54.54 Aligned_cols=52 Identities=21% Similarity=0.352 Sum_probs=43.0
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.+.+.|+|||++-.+.... ++.+|..+ +...|.++||+|+|+|++|+-.+..
T Consensus 76 Li~V~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkd 131 (203)
T PRK14602 76 LISISKVGAKTALAILSQF---RPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKY 131 (203)
T ss_pred HhCCCCcCHHHHHHHHhhC---CHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHH
Confidence 6789999999999999854 66777762 3567899999999999999988764
No 123
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.91 E-value=0.058 Score=54.06 Aligned_cols=53 Identities=23% Similarity=0.384 Sum_probs=42.8
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..+.|.|+|||++-.+.... ++.+|..+ +...|.++||+|+|+|++|+-.+..
T Consensus 74 ~Li~V~GIGpK~AL~iLs~~---~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkd 130 (188)
T PRK14606 74 SLTKVSRLGPKTALKIISNE---DAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKD 130 (188)
T ss_pred HHhccCCccHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 36789999999999998753 66777762 3466889999999999999988764
No 124
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=93.88 E-value=0.25 Score=50.71 Aligned_cols=83 Identities=24% Similarity=0.341 Sum_probs=50.9
Q ss_pred HHHHHHHHCCCC-----CChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHH
Q psy11421 468 KMIEKLVNANIV-----VTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKEL 539 (687)
Q Consensus 468 k~i~~L~~~g~I-----~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~L 539 (687)
+.+..|.+.+.. .++.+|..++.++|.++ -||-..+|..|.+-.+ .+
T Consensus 50 ~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~-------------------------~i 104 (218)
T PRK13913 50 KSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSE-------------------------NI 104 (218)
T ss_pred HHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHH-------------------------HH
Confidence 444556665432 38999999988887765 4787777776665322 22
Q ss_pred HhhcCChHHHH-hcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 540 ANYFKNLECMF-KATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 540 a~~f~sld~l~-~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.+.|++++.+. ..+.++|.+++|||+++|..|.-|-
T Consensus 105 ~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya 141 (218)
T PRK13913 105 LKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYV 141 (218)
T ss_pred HHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHH
Confidence 22333333222 1234678888888888888776654
No 125
>PHA02142 putative RNA ligase
Probab=93.87 E-value=0.57 Score=51.49 Aligned_cols=147 Identities=18% Similarity=0.217 Sum_probs=80.0
Q ss_pred CeeEEEEEccceeEEEEEEe--CCEEEE--------EEecCCCCccc---hh-----hhh-----hhhhccCCcccccCC
Q psy11421 117 NIEYIAELKFDGIAVNLRYE--YGYLKQ--------ASTRGDGNIGE---NI-----TTN-----IHIIHKIPLVLNIKY 173 (687)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~--~G~l~~--------a~TRGdG~~Ge---Dv-----T~n-----~~~i~~iP~~l~~~~ 173 (687)
...|.++.|+||.|+++.|. .+.+.. |.+..+|..|- +. ..| +.. .+||..|..
T Consensus 168 ~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~-~~i~~~l~~-- 244 (366)
T PHA02142 168 DVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVEN-YQIVDRLKE-- 244 (366)
T ss_pred CceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHH-cCcHHHHHh--
Confidence 46799999999999999754 111111 11222332221 11 111 112 236666653
Q ss_pred CCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCCCCCHHHHH
Q psy11421 174 PPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNMPSSHSELL 253 (687)
Q Consensus 174 ~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~~~~~~e~l 253 (687)
.+..+.|.||+|=+ |. |.+.--. ..-+|++|++-..+...+ -++.+..
T Consensus 245 ~~~~iaIqGEl~Gp---------------------------~I--Q~N~~~~--~~~~F~vF~v~~i~~~~y-l~~~e~~ 292 (366)
T PHA02142 245 LGMSVAIQGELMGP---------------------------GI--QKNRENF--DKYRIFAFRAWFIDEQRF-ATDEEFQ 292 (366)
T ss_pred hCCcEEEEEEEecc---------------------------cc--cCccccC--CCCceEEEEEEEecccee-CCHHHHH
Confidence 35679999999931 11 2221111 123799998732222223 5777888
Q ss_pred HHHHhcCCCCCCCc------eEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEEC
Q psy11421 254 NWYQKIGLSICGEY------SVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKIN 302 (687)
Q Consensus 254 ~~L~~~Gf~~~~~~------~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~ 302 (687)
++++++|++.++.. ....+++|++++-. . ..-.+-.--|+|+|--
T Consensus 293 ~~~~~~gl~~VPvL~~~~~~~~~~s~eE~L~~A~-~---p~~~~~~~EGiViKp~ 343 (366)
T PHA02142 293 DLCRTLGMEIVPQLGYSYPFQEFTNVKEMLAAAD-I---PSINHKIAEGVVYKSV 343 (366)
T ss_pred HHHHHcCCceeeeecccccccccCCHHHHHhhcC-C---CcccccccceEEEeec
Confidence 89999999876532 11237888887642 0 1111112479999763
No 126
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=93.82 E-value=0.2 Score=38.60 Aligned_cols=47 Identities=17% Similarity=0.325 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11421 465 LGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 465 LG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
+.+.++.+|+++| +.++.||-.+..++|..++|+++..+.+|+....
T Consensus 1 i~~~~~~~L~~~G-~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~ 47 (50)
T TIGR01954 1 IDEEIAQLLVEEG-FTTVEDLAYVPIDELLSIEGFDEETAKELINRAR 47 (50)
T ss_pred CCHHHHHHHHHcC-CCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHH
Confidence 4578999999999 5899999999999999999999999999987654
No 127
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.76 E-value=0.061 Score=54.30 Aligned_cols=53 Identities=25% Similarity=0.314 Sum_probs=43.1
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..+.+.|+|||++-.+.... ++.+|..+ +...|.++||+|+|+|++|+-.+..
T Consensus 73 ~L~~V~GIGpK~AL~iLs~~---~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 73 LLLGVSGVGPKLALALLSAL---PPALLARALLEGDARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred HHhCcCCcCHHHHHHHHcCC---CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 36789999999999998754 66777762 3567889999999999999987754
No 128
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=93.73 E-value=0.31 Score=48.30 Aligned_cols=84 Identities=15% Similarity=0.277 Sum_probs=54.9
Q ss_pred HHHHHHHCCCCCChHHHhcCChhhhhcc---c----CccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHh
Q psy11421 469 MIEKLVNANIVVTAVDLYKINFKNLLRL---D----RVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELAN 541 (687)
Q Consensus 469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~----gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~ 541 (687)
.+..|++.-...++.+|..+..++|..+ . ||-..+|.+|.+. |+.|.+
T Consensus 39 A~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~-------------------------a~~iie 93 (177)
T TIGR03252 39 GPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQAL-------------------------AQYVVD 93 (177)
T ss_pred HHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHH-------------------------HHHHHH
Confidence 3447765333368999998887666544 1 6777777766653 333443
Q ss_pred hc-CChHHHHhc----C---HHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 542 YF-KNLECMFKA----T---EEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 542 ~f-~sld~l~~A----s---~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
.| ++++.|..+ + .++|.+++|||+++|.-+..+|..
T Consensus 94 ~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 94 TYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred HhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 33 355556541 1 368999999999999998877643
No 129
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.64 E-value=0.064 Score=53.68 Aligned_cols=52 Identities=19% Similarity=0.333 Sum_probs=40.9
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcC----ChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKI----NFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L----~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
..+.+.|+|||++-.+.... ++.+|..+ +...| ++||+|+|+|++|+-.+..
T Consensus 74 ~LisV~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~ 129 (186)
T PRK14600 74 MLVKVSGVNYKTAMSILSKL---TPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQY 129 (186)
T ss_pred HHhCcCCcCHHHHHHHHccC---CHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence 36789999999999998754 67777762 24557 9999999999999977754
No 130
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=93.64 E-value=0.12 Score=55.43 Aligned_cols=51 Identities=25% Similarity=0.263 Sum_probs=47.7
Q ss_pred ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11421 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
.|+|+|++++++|.+.|+ .|+.||..++.++|..+.|++++.|+.|++...
T Consensus 3 ~i~gig~~~~~~L~~~Gi-~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGY-DTFEAIAVASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred ccCCCCHHHHHHHHHcCC-CCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 689999999999999995 899999999999999999999999999988775
No 131
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=93.53 E-value=0.14 Score=51.87 Aligned_cols=50 Identities=18% Similarity=0.311 Sum_probs=33.2
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHH----hcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMF----KATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~----~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
+.+.|||+++|-.++..+ +++.|. ..+..-|.++||||+++|+.|.--+.
T Consensus 76 isVnGIGpK~ALaiLs~~-~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 76 ISVNGIGPKLALAILSNL-DPEELAQAIANEDVKALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred HccCCccHHHHHHHHcCC-CHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHh
Confidence 345666666666555443 344443 34678899999999999999876543
No 132
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=93.27 E-value=0.24 Score=53.01 Aligned_cols=114 Identities=16% Similarity=0.160 Sum_probs=73.0
Q ss_pred ccccCCCCHHHHHHHHHC-C----CCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc---------cCCHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNA-N----IVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK---------LTTFSRFIY 524 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~-g----~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk---------~~~l~r~L~ 524 (687)
.|++.|=-+=.+....++ + .=+++++++.. ..+..|+|+|+..|++|..-++.-. ..|. -++.
T Consensus 18 ~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~--~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P~-gl~~ 94 (326)
T COG1796 18 YMELEGENPFKIRAYRKAAQSLENLTEDLEEIEER--GRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVPE-GLEP 94 (326)
T ss_pred HHHhcCCCccchHHHHHHHHhhhhcccchHHHHhh--cccCCCCCccHHHHHHHHHHHHcCccHHHHHHHHhCCc-chHH
Confidence 466666664233322221 1 11345555543 2578899999999988887765321 2232 2555
Q ss_pred HcCCCCCCHHHHHHHHhhc--CChHHHHhcCH-HHHhcCCCCCHHHHHHHHHHH
Q psy11421 525 ALGIRHVGETTAKELANYF--KNLECMFKATE-EQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 525 aLGIp~vG~~~Ak~La~~f--~sld~l~~As~-eeL~~I~GIG~~~A~sI~~ff 575 (687)
-|.+||+|++.-..|...+ .+++.|..|-. -.+..+.|+|++.+..|.++.
T Consensus 95 Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i 148 (326)
T COG1796 95 LLKVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENI 148 (326)
T ss_pred HhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHH
Confidence 6789999997777777654 57777776543 357789999999988887754
No 133
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=93.06 E-value=0.19 Score=59.17 Aligned_cols=60 Identities=15% Similarity=0.088 Sum_probs=54.1
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFS 520 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~ 520 (687)
.-+|+|+|+++..+|++.- .|+.+|..++.++|.+++|++++.|++|+.+-.+|-..|.+
T Consensus 610 L~~IpGiG~kr~~~LL~~F--gS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~ 669 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHF--GSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVR 669 (691)
T ss_pred cccCCCCCHHHHHHHHHHh--cCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchh
Confidence 5589999999999999975 59999999999999999999999999999998887777654
No 134
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=92.93 E-value=0.22 Score=53.77 Aligned_cols=62 Identities=26% Similarity=0.364 Sum_probs=42.8
Q ss_pred hhhhcccCccHHHHHHHHHHHHHcccCCHH--------HHHHHcCCCCCCHHHHHHHHh-hcCChHHHHhc
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQKSKLTTFS--------RFIYALGIRHVGETTAKELAN-YFKNLECMFKA 552 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~--------r~L~aLGIp~vG~~~Ak~La~-~f~sld~l~~A 552 (687)
+++.++||+|++.|++|.+-++.-+-..+. -++.=++|||||+++|+.+.+ .+.|+++|..+
T Consensus 45 ~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~~lGi~sl~dL~~a 115 (307)
T cd00141 45 EEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKA 115 (307)
T ss_pred HHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHHHcCCCCHHHHHHH
Confidence 356888999999998888877652222222 233445899999999988883 25677777765
No 135
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=92.86 E-value=0.19 Score=41.77 Aligned_cols=58 Identities=16% Similarity=0.159 Sum_probs=39.3
Q ss_pred HHHhcCChhhhhc-ccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhh
Q psy11421 483 VDLYKINFKNLLR-LDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANY 542 (687)
Q Consensus 483 ~DL~~L~~~~L~~-l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~ 542 (687)
-||-++..+.|.. +||+|++.|++|++...... ++..+-.-..++|+|.+++++|...
T Consensus 8 invNta~~~~L~~~ipgig~~~a~~Il~~R~~~g--~~~s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 8 VNINTATAEELQRAMNGVGLKKAEAIVSYREEYG--PFKTVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred eECcCCCHHHHHhHCCCCCHHHHHHHHHHHHHcC--CcCCHHHHHcCCCCCHHHHHHHHhh
Confidence 4566677778888 88888888888888776432 2222222246788888888877644
No 136
>KOG2534|consensus
Probab=92.69 E-value=0.78 Score=49.01 Aligned_cols=136 Identities=16% Similarity=0.199 Sum_probs=78.6
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHH--------HHH-HcCCCCCCHHHHHHHH-hhcCChHHHHhcCHHHHhc
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSR--------FIY-ALGIRHVGETTAKELA-NYFKNLECMFKATEEQLLN 559 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r--------~L~-aLGIp~vG~~~Ak~La-~~f~sld~l~~As~eeL~~ 559 (687)
.+++.+|||+|+|.|.+|.+-++.-.-..+.+ .|. =-+|-|||.++|++-- ..|.|++.+. -+.+.|..
T Consensus 55 ~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~R-k~~~kft~ 133 (353)
T KOG2534|consen 55 GEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVR-KKPDKFTR 133 (353)
T ss_pred HHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHH-hCHHHHHH
Confidence 57788899999999999988776533333322 222 2388999999987544 4688888888 45566654
Q ss_pred CCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcc
Q psy11421 560 IPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVN 639 (687)
Q Consensus 560 I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~ 639 (687)
-.-+| -+-++=|-..-.++....+... |. ......+.+..+.+||.+.. | .
T Consensus 134 qqk~G----l~yy~Df~~~v~ReE~~~i~~~-V~-------~av~~~~p~~~vt~~GsfRR--------------G---k 184 (353)
T KOG2534|consen 134 QQKAG----LKYYEDFLKRVTREEATAIQQT-VQ-------EAVWAFDPEAFVTVTGSFRR--------------G---K 184 (353)
T ss_pred HHHHh----HHHHHHHhhhccHHHHHHHHHH-HH-------HHHhhcCCCcEEEEeccccC--------------C---c
Confidence 43232 2222222111112211221110 00 00112456889999999742 2 3
Q ss_pred cccccccEEEEcCCCC
Q psy11421 640 FISKNTNYLVKGQKPG 655 (687)
Q Consensus 640 sVsk~t~~LV~G~~~g 655 (687)
++..++|+|+.-...+
T Consensus 185 ~~ggDvD~LithP~~~ 200 (353)
T KOG2534|consen 185 KMGGDVDFLITHPGST 200 (353)
T ss_pred ccCCCeeEEEeCCCCC
Confidence 4556899999865443
No 137
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=92.63 E-value=0.14 Score=53.70 Aligned_cols=50 Identities=20% Similarity=0.300 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
.||.+-......+...|++++.+..||.++|.+++|||+..|..|.+.++
T Consensus 297 kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~Gl~ 346 (349)
T COG1623 297 KIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIKEGLS 346 (349)
T ss_pred cCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence 67777777888999999999999999999999999999999999988764
No 138
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=92.61 E-value=0.18 Score=58.65 Aligned_cols=50 Identities=18% Similarity=0.207 Sum_probs=46.3
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
..+|+|+|+++..+|+++- .|+.+|..++.++|.++ |++++.|++|++.+
T Consensus 516 Ld~I~GiG~kr~~~Ll~~F--gs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l 565 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNF--KTLYDFLKADDEELKKL-GIPPSVKQEVKKYL 565 (567)
T ss_pred cccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHh
Confidence 5689999999999999975 59999999999999999 99999999998876
No 139
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=92.39 E-value=0.18 Score=48.67 Aligned_cols=58 Identities=21% Similarity=0.342 Sum_probs=35.6
Q ss_pred HHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCC
Q psy11421 484 DLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKI 563 (687)
Q Consensus 484 DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GI 563 (687)
+|-+.+.++|..|||+|+++|+.|++.-++. -+ |. +.+||.+++||
T Consensus 90 NiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~--G~------------------------f~--------sv~dL~~v~Gi 135 (149)
T COG1555 90 NINTASAEELQALPGIGPKKAQAIIDYREEN--GP------------------------FK--------SVDDLAKVKGI 135 (149)
T ss_pred cccccCHHHHHHCCCCCHHHHHHHHHHHHHc--CC------------------------CC--------cHHHHHhccCC
Confidence 3444556777777777777777777654431 11 33 34666667777
Q ss_pred CHHHHHHHHHHH
Q psy11421 564 GSTTVKAFIKFI 575 (687)
Q Consensus 564 G~~~A~sI~~ff 575 (687)
|+++-+.+..++
T Consensus 136 G~~~~ekl~~~i 147 (149)
T COG1555 136 GPKTLEKLKDYI 147 (149)
T ss_pred CHHHHHHHHhhc
Confidence 777776666543
No 140
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=92.25 E-value=0.073 Score=43.89 Aligned_cols=30 Identities=23% Similarity=0.231 Sum_probs=22.0
Q ss_pred HHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 484 DLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 484 DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
||-+++.++|..+||+|++.|++|++..++
T Consensus 7 diN~as~~eL~~lpgi~~~~A~~Iv~~R~~ 36 (65)
T PF12836_consen 7 DINTASAEELQALPGIGPKQAKAIVEYREK 36 (65)
T ss_dssp ETTTS-HHHHHTSTT--HHHHHHHHHHHHH
T ss_pred cCccCCHHHHHHcCCCCHHHHHHHHHHHHh
Confidence 566678889999999999999999886543
No 141
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=92.05 E-value=0.27 Score=46.08 Aligned_cols=41 Identities=15% Similarity=0.242 Sum_probs=32.5
Q ss_pred CCCCCCHHHHHHHHhh--cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 527 GIRHVGETTAKELANY--FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~--f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.+||||++.|++|.++ |. +.|||.+++|||++..+.+..+.
T Consensus 65 ~lpGigP~~A~~IV~nGpf~--------sveDL~~V~GIgekqk~~l~k~~ 107 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYD--------SVEDVLNLPGLSERQKELLEANL 107 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCC--------CHHHHHcCCCCCHHHHHHHHHhh
Confidence 4899999999999863 44 56889999999998777766654
No 142
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=92.02 E-value=0.14 Score=51.85 Aligned_cols=20 Identities=25% Similarity=0.464 Sum_probs=9.4
Q ss_pred hhhcccCccHHHHHHHHHHH
Q psy11421 492 NLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 492 ~L~~l~gfG~Ksa~~Ll~~I 511 (687)
-|.++||+|+|.|++|+-.+
T Consensus 109 ~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 109 ALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred hhhcCCCCCHHHHHHHHHHH
Confidence 34444455555554444443
No 143
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=91.97 E-value=0.12 Score=55.83 Aligned_cols=47 Identities=30% Similarity=0.355 Sum_probs=35.2
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK 515 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk 515 (687)
..++|+|+||+++.+|| +..|+|++||...- |.|+.++++.+|+..+
T Consensus 86 ~l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a~----------g~k~~~~i~~gl~~~~ 132 (307)
T cd00141 86 LLLRVPGVGPKTARKLY-ELGIRTLEDLRKAA----------GAKLEQNILIGLEYYE 132 (307)
T ss_pred HHHcCCCCCHHHHHHHH-HcCCCCHHHHHHHh----------ccccHHHHHHHHHHHH
Confidence 34678888888888888 44468888888732 7788888888887543
No 144
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=91.65 E-value=0.22 Score=58.44 Aligned_cols=52 Identities=23% Similarity=0.297 Sum_probs=47.3
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
...|+|+|+++..+|++.- .|+.+|+..+.++|.+++|+|++.|++|.+.+.
T Consensus 545 L~~IpGIG~k~~k~Ll~~F--gS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~ 596 (598)
T PRK00558 545 LDDIPGIGPKRRKALLKHF--GSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596 (598)
T ss_pred HhhCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhc
Confidence 4589999999999999965 589999999999999999999999999998764
No 145
>PRK00024 hypothetical protein; Reviewed
Probab=91.34 E-value=0.56 Score=48.37 Aligned_cols=57 Identities=21% Similarity=0.306 Sum_probs=45.8
Q ss_pred HHHHHHHcCCCCCCH-HHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 519 FSRFIYALGIRHVGE-TTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 519 l~r~L~aLGIp~vG~-~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
|-.+|...|+|+-.. ..|+.|.++|+++.++..++.++|.+++|||+..|..|..-+
T Consensus 29 LLa~lL~~g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~ 86 (224)
T PRK00024 29 LLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAAL 86 (224)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHH
Confidence 334455668886443 478888899999999999999999999999999998776544
No 146
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.30 E-value=0.4 Score=49.25 Aligned_cols=57 Identities=21% Similarity=0.325 Sum_probs=46.0
Q ss_pred HHHHHHHcCCCCC-C-HHHHHHHHhhc---CChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 519 FSRFIYALGIRHV-G-ETTAKELANYF---KNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 519 l~r~L~aLGIp~v-G-~~~Ak~La~~f---~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
|-.+|...|.|+- . ...|+.|.++| +++..+..++.++|.+++|||+..|..|..-+
T Consensus 19 LLailL~~g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~ 80 (218)
T TIGR00608 19 LLAIILRTGTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAV 80 (218)
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHH
Confidence 3445556788865 2 25788888899 99999999999999999999999888876654
No 147
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=91.16 E-value=0.19 Score=39.82 Aligned_cols=27 Identities=37% Similarity=0.386 Sum_probs=20.6
Q ss_pred cccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11421 460 MNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (687)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (687)
++|-|+|++|++++++.|+ +|++||-.
T Consensus 5 ~~I~GVG~~tA~~w~~~G~-rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGI-RTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHHHTT---SHHHHHH
T ss_pred hhcccccHHHHHHHHHhCC-CCHHHHhh
Confidence 4799999999999999885 99999953
No 148
>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain. RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes []. Members of this RNA ligase family include: RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [, , ]. RNA editing ligase 2 (REL2), which may be active in U-insertion editing []. RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [, ]. ; PDB: 2HVS_B 2HVR_A 1S68_A 2HVQ_A 1XDN_A.
Probab=90.71 E-value=0.3 Score=48.35 Aligned_cols=155 Identities=15% Similarity=0.118 Sum_probs=74.7
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCC------ccchhhhh-----hhhhccCCcccc---cCCCCceEEEEEEE
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGN------IGENITTN-----IHIIHKIPLVLN---IKYPPELLEVRCEV 184 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~------~GeDvT~n-----~~~i~~iP~~l~---~~~~~~~~evRGEi 184 (687)
+|+++.|+||-++++.+.++.-++..+|..-. .|-+...+ +..+. ....+. ....+..+.|.||+
T Consensus 2 e~vvtEKldGtn~~i~~~~~~~~~~~~R~~~l~~~~~f~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~i~GE~ 80 (186)
T PF09414_consen 2 EVVVTEKLDGTNFSIYFDNDGRVRFQSRSHILDPNEDFFGYQSGDNRYWAQARWLF-ELLKLAELASELLPENIIIYGEL 80 (186)
T ss_dssp EEEEEEE-SSEEEEEEEEECTCEEEEETTEE--TT---TTCHHHHHHCHHHHHHHH-HHHHHHCCEC----SEEEEEEEE
T ss_pred eEEEEEEeCCccEEEEEeCCCceeEeccccccCccccccccccchHHHHHHHHHHH-hhhhhhhhcccccceEEEEEEEe
Confidence 58999999999999988655434555654311 11111111 11111 111111 00136789999999
Q ss_pred EeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCC---CCCCCHHHHHHHHHhcCC
Q psy11421 185 LIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGM---NMPSSHSELLNWYQKIGL 261 (687)
Q Consensus 185 ~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~---~~~~~~~e~l~~L~~~Gf 261 (687)
+=-+. ..-.|.= + ...+..|++|++...... .+ -+..+...++..+||
T Consensus 81 ~G~~~--------------~Iq~~~~--------~------~~~~~~F~~Fdi~~~~~~~~~~~-l~~~~~~~~~~~~gl 131 (186)
T PF09414_consen 81 VGAKP--------------SIQKNRY--------Q------LDPPKDFYVFDIYDIDEQGEIRY-LSWDEVREFAEELGL 131 (186)
T ss_dssp ECEEC--------------TTCSS------------------ECCCEEEEEEEEEEETCCGEEE--HHHHHHHHHCCCT-
T ss_pred eeecc--------------ccccccc--------c------cCCCceEEEEEEEEcCCCCeeEE-CCHHHHHHHHHHCCC
Confidence 95220 0001100 0 012689999998765321 12 356677788889999
Q ss_pred CCCCCceEeCCHHHHHHHHHHHHHh-hcCCCCccceEEEEECCh
Q psy11421 262 SICGEYSVLSGVNKLIEFYKKINIK-RFNLPYEIDGVVYKINCL 304 (687)
Q Consensus 262 ~~~~~~~~~~~~~ei~~~~~~~~~~-r~~l~y~iDGiVikv~~~ 304 (687)
+++|.... ..+.+...+-.....- ...-+=.-=|+|+|..+.
T Consensus 132 ~~VPvl~~-g~~~~~~~~~~~~~~~~~~~~~~~~EGiVik~~~~ 174 (186)
T PF09414_consen 132 KTVPVLYR-GTFTELDDLDDLFESGKPSGEGNIREGIVIKPEDE 174 (186)
T ss_dssp EES-ECEE-ECHHHHCTS-CCGBBTTS-STT-B--EEEEEETTT
T ss_pred CEeCEEEE-EccchhhhhhHHHhhcccCCCCCccCEEEEEEeEe
Confidence 98874322 2444433321110000 111123346999999874
No 149
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=90.38 E-value=0.33 Score=56.73 Aligned_cols=50 Identities=16% Similarity=0.196 Sum_probs=45.4
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
...|+|+|++++.+|++.- .|+.+++.++.++|.++||+|++.|+.|.+.
T Consensus 527 L~~IpGIG~kr~~~LL~~F--GS~~~I~~As~eeL~~vpGi~~~~A~~I~~~ 576 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRF--GSVEGVREASVEDLRDVPGVGEKTAETIRER 576 (577)
T ss_pred HhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHh
Confidence 4479999999999999975 5999999999999999999999999998764
No 150
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=90.38 E-value=1.1 Score=45.73 Aligned_cols=42 Identities=21% Similarity=0.093 Sum_probs=29.0
Q ss_pred HHHHHHHHHCCCCCChHHHhcCChhhhhc---ccCccHHHHHHHHHH
Q psy11421 467 KKMIEKLVNANIVVTAVDLYKINFKNLLR---LDRVSNKLANNILLA 510 (687)
Q Consensus 467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~---l~gfG~Ksa~~Ll~~ 510 (687)
.+....|++.- .+++|+..+..++|.+ -=||-..+|.+|++-
T Consensus 48 n~at~~Lf~~~--~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~ 92 (211)
T COG0177 48 NKATPALFKRY--PTPEDLLNADEEELEELIKSIGLYRNKAKNIKEL 92 (211)
T ss_pred HHHHHHHHHHc--CCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHH
Confidence 45556666644 5999999988765543 248888888887753
No 151
>PRK10702 endonuclease III; Provisional
Probab=90.25 E-value=1.1 Score=45.70 Aligned_cols=78 Identities=15% Similarity=0.223 Sum_probs=50.9
Q ss_pred HHHHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhc
Q psy11421 467 KKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF 543 (687)
Q Consensus 467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f 543 (687)
.+.+..|+... .++++|..+..++|..+ -||-..+|.+|++..+. +.+.|
T Consensus 48 ~~~~~~L~~~~--pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~-------------------------i~~~~ 100 (211)
T PRK10702 48 NKATAKLYPVA--NTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRI-------------------------LLEQH 100 (211)
T ss_pred HHHHHHHHHHc--CCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHH-------------------------HHHHc
Confidence 34455666542 58999999998888753 36767888888765432 11222
Q ss_pred CC-hHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 544 KN-LECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 544 ~s-ld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
+. + ..+.++|.+++|||+++|..|.-|.
T Consensus 101 ~~~~----p~~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 101 NGEV----PEDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred CCCC----CchHHHHhcCCcccHHHHHHHHHHH
Confidence 21 1 1246788888888888888887544
No 152
>KOG1929|consensus
Probab=89.56 E-value=0.53 Score=56.56 Aligned_cols=75 Identities=21% Similarity=0.221 Sum_probs=68.0
Q ss_pred CccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC-ccHHHHHHcCCeEEeHHHHHHHHhc
Q psy11421 605 NYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG-KKLEKAIKLNIKILDEKNFVKIVKG 680 (687)
Q Consensus 605 ~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g-~Kl~kA~~lgI~Ii~E~~f~~~l~~ 680 (687)
..+.|..||.||... ..|.+++.++..+||+.-.+.+..+.++++..... .|++.|..++++|++++++..-.+.
T Consensus 102 p~~~~~~Vc~tgl~~-~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~ 177 (811)
T KOG1929|consen 102 PGFFGLKVCLTGLSG-DEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEK 177 (811)
T ss_pred CcccceEEEecccch-HHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhcc
Confidence 357899999999864 48999999999999999999999999999988766 9999999999999999999987754
No 153
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=89.09 E-value=0.68 Score=50.58 Aligned_cols=55 Identities=18% Similarity=0.165 Sum_probs=48.5
Q ss_pred ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccC
Q psy11421 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT 517 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~ 517 (687)
.||++++..++.|+++-. |+..++.++.++|..++|+|++.|..|.+.+.+.+..
T Consensus 291 ~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl~e~ 345 (352)
T PRK13482 291 KIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARAIREGLSRLAEQ 345 (352)
T ss_pred cCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHHHHH
Confidence 489999999999999864 9999999999999999999999999988887765443
No 154
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=88.74 E-value=0.26 Score=46.30 Aligned_cols=23 Identities=17% Similarity=0.541 Sum_probs=18.7
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+-+|||.||+||.+..| ..||++
T Consensus 27 L~~hCp~Cg~PLF~KdG--~v~CPv 49 (131)
T COG1645 27 LAKHCPKCGTPLFRKDG--EVFCPV 49 (131)
T ss_pred HHhhCcccCCcceeeCC--eEECCC
Confidence 34799999999998655 569987
No 155
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=88.67 E-value=0.76 Score=49.33 Aligned_cols=50 Identities=24% Similarity=0.349 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
.|||||+.++++|.+. |.++++|..++.++|.++.|+++..|+.+.+...
T Consensus 3 ~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred ccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 5799999999999987 9999999999999999999999988888877664
No 156
>KOG0967|consensus
Probab=87.89 E-value=6.1 Score=46.07 Aligned_cols=179 Identities=17% Similarity=0.234 Sum_probs=108.5
Q ss_pred ccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEE-eCCEEEEEEecCCCCccchhhhhhhhhcc-
Q psy11421 87 FKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY-EYGYLKQASTRGDGNIGENITTNIHIIHK- 164 (687)
Q Consensus 87 ~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y-~~G~l~~a~TRGdG~~GeDvT~n~~~i~~- 164 (687)
.|||. | -...+.+.++|.+ +..|+||+|.||=-..+.+ ++|. +...+| .+|+.|....-|-.
T Consensus 345 KPMLA--k--pTK~i~evl~rf~-------~~~FTCEyKYDGeRAQIH~~edG~-v~IfSR----N~E~~T~kYPDi~~~ 408 (714)
T KOG0967|consen 345 KPMLA--K--PTKGIQEVLERFQ-------DKAFTCEYKYDGERAQIHKLEDGT-VEIFSR----NSENNTGKYPDIIEV 408 (714)
T ss_pred cchhc--C--cchhHHHHHHHhh-------CceeEEEeecCceeeeeEEccCCc-EEEEec----ccccccccCccHHHH
Confidence 48975 2 2235666777764 3589999999999999986 6776 688999 78888887654332
Q ss_pred CCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccc-ccccccEEEEEecccccCC
Q psy11421 165 IPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKI-NKNKILHFFAHGVGELRGM 243 (687)
Q Consensus 165 iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~-~~~r~l~f~~y~~~~~~~~ 243 (687)
+++.... --..+.+-||++--..+ |. ---+|. +.-+=++++-.. ...-..+.|+|++....|.
T Consensus 409 ~~~~~kp--~v~sFIlD~EvVA~Dr~----~~-----~IlpFQ-----vLSTRkRk~v~v~dikV~Vcvf~FDily~ng~ 472 (714)
T KOG0967|consen 409 ISKLKKP--SVKSFILDCEVVAWDRE----KG-----KILPFQ-----VLSTRKRKNVDVNDIKVKVCVFVFDILYLNGE 472 (714)
T ss_pred HHHhhCC--ccceeEEeeeEEEEecc----CC-----ccCchh-----hhhhhhccccchhhceEEEEEEEEeeeeeCCh
Confidence 3322221 01478999999854322 10 012232 111112222211 1122578899998876654
Q ss_pred CCC-CCHHHHHHHHHhcCCCCCCCceE-----eCCHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11421 244 NMP-SSHSELLNWYQKIGLSICGEYSV-----LSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303 (687)
Q Consensus 244 ~~~-~~~~e~l~~L~~~Gf~~~~~~~~-----~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~ 303 (687)
.+. ..-.+.-+.|.+-+=.+..+..+ +.++++|..|.++.. +--.-|+-||+=|
T Consensus 473 ~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~eiq~Fl~~sv------~~~cEGlMvKtLd 532 (714)
T KOG0967|consen 473 SLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDIDEIQEFLEESV------QNSCEGLMVKTLD 532 (714)
T ss_pred hhhhhhHHHHHHHHHhhcccCCCceeEeeeeccCCHHHHHHHHHHhh------ccCcceeEEEeec
Confidence 321 45667777777764444444444 356889999887543 3445789988865
No 157
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=87.67 E-value=0.7 Score=54.49 Aligned_cols=59 Identities=17% Similarity=0.229 Sum_probs=50.2
Q ss_pred cccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccC
Q psy11421 454 FSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLT 517 (687)
Q Consensus 454 F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~ 517 (687)
+-| ...+|+|+|+++..+|++.- .|+.+|..++.++|.++ +|++.|++|++.+..+-..
T Consensus 550 ~~S-~L~~IpGIG~kr~~~LL~~F--gSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~~~~~ 608 (624)
T PRK14669 550 RTS-ELLEIPGVGAKTVQRLLKHF--GSLERVRAATETQLAAV--VGRAAAEAIIAHFTTEEAA 608 (624)
T ss_pred HHH-HHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcCcCCC
Confidence 334 36689999999999999975 59999999999999997 9999999999998755443
No 158
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=87.54 E-value=1 Score=48.82 Aligned_cols=54 Identities=22% Similarity=0.246 Sum_probs=48.5
Q ss_pred cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
|.-.|||+.++++|-++|+ .|+.|+...+..+|..+.|+.+..+++|++...+.
T Consensus 4 ~~~~g~~~~~~~~L~~~g~-~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~ 57 (313)
T TIGR02238 4 LQAHGINAADIKKLKSAGI-CTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI 57 (313)
T ss_pred hhcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence 3346899999999999995 89999999999999999999999999999987654
No 159
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=87.38 E-value=0.82 Score=47.77 Aligned_cols=52 Identities=21% Similarity=0.356 Sum_probs=46.5
Q ss_pred cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+.|||+|++.+..|++.- .|+.++++++.+.|..++|+|+|.|..|..-+..
T Consensus 185 ~s~pgig~~~a~~ll~~f--gS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t 236 (254)
T COG1948 185 ESIPGIGPKLAERLLKKF--GSVEDVLTASEEELMKVKGIGEKKAREIYRFLRT 236 (254)
T ss_pred HcCCCccHHHHHHHHHHh--cCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhc
Confidence 579999999999999864 5899999999999999999999999999887753
No 160
>PTZ00035 Rad51 protein; Provisional
Probab=86.83 E-value=1.1 Score=48.95 Aligned_cols=55 Identities=24% Similarity=0.232 Sum_probs=48.9
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
.+.-+||++.++++|-++|+ .|+.||...+..+|..+.|+++..|++|++...+.
T Consensus 25 ~l~~~g~~~~~~~kL~~~g~-~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 25 KLQSAGINAADIKKLKEAGI-CTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred HHhcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 34458999999999999995 89999999999999999999999999999877653
No 161
>PRK01172 ski2-like helicase; Provisional
Probab=86.76 E-value=2.6 Score=50.35 Aligned_cols=55 Identities=22% Similarity=0.311 Sum_probs=48.1
Q ss_pred HHHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 521 r~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
..+.-+.|||+|..+|++|.+. +.|+.++..++.+++.++.|+|++.|++|.+..
T Consensus 610 ~~~~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~ 665 (674)
T PRK01172 610 DLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA 665 (674)
T ss_pred HHHhhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence 4444458999999999988864 899999999999999999999999999998863
No 162
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=86.66 E-value=0.65 Score=34.48 Aligned_cols=28 Identities=21% Similarity=0.510 Sum_probs=21.7
Q ss_pred CCCCCCCCcceeecC--ceeEEecCCCCCCH
Q psy11421 416 NICPICNSKIIYIES--NLIARCSGSWIECI 444 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~--~~~~~C~n~~~~C~ 444 (687)
..||.||++|+...+ +.++-|+|.+. |.
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~-C~ 31 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCSNYPE-CK 31 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECCCCCC-cC
Confidence 369999999986533 57888999766 85
No 163
>PRK00420 hypothetical protein; Validated
Probab=86.05 E-value=0.5 Score=43.39 Aligned_cols=24 Identities=17% Similarity=0.534 Sum_probs=18.6
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+..+||.||+||.+..+ ...+|++
T Consensus 22 l~~~CP~Cg~pLf~lk~-g~~~Cp~ 45 (112)
T PRK00420 22 LSKHCPVCGLPLFELKD-GEVVCPV 45 (112)
T ss_pred ccCCCCCCCCcceecCC-CceECCC
Confidence 46899999999987433 3679987
No 164
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=86.02 E-value=1.3 Score=48.03 Aligned_cols=52 Identities=19% Similarity=0.183 Sum_probs=46.3
Q ss_pred ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+--+|.-.+..-|-.+| |.++.||..++.++|+++++||+||.+.|.+.+++
T Consensus 252 ~~L~LS~R~~n~Lk~~~-I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~~ 303 (310)
T PRK05182 252 EELELSVRSYNCLKRAG-INTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAE 303 (310)
T ss_pred HHhccchHHHHHHHHcC-CcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHHHH
Confidence 33478888888888887 69999999999999999999999999999998876
No 165
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=85.53 E-value=0.77 Score=39.03 Aligned_cols=26 Identities=27% Similarity=0.488 Sum_probs=23.9
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKA 552 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~A 552 (687)
||||||+++|..|...|++++.+..+
T Consensus 26 gv~giG~k~A~~ll~~~~~~~~~~~~ 51 (75)
T cd00080 26 GVPGIGPKTALKLLKEYGSLENLLEN 51 (75)
T ss_pred CCCcccHHHHHHHHHHhCCHHHHHHH
Confidence 79999999999999999999988864
No 166
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=85.30 E-value=1.1 Score=52.22 Aligned_cols=119 Identities=17% Similarity=0.199 Sum_probs=73.6
Q ss_pred HHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhh
Q psy11421 372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGL 451 (687)
Q Consensus 372 ~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i 451 (687)
+.++++||.+- .|-|.|.-+ ..+.. +...++.+|..-|.=. -|.+.-++++.|-... + +..+.=
T Consensus 462 ~vl~~l~~~~~-viglaK~~~------~~~~~---~~~~~~~l~~~~p~l~-~lq~irDEaHrfAi~~-h----R~~R~k 525 (581)
T COG0322 462 EVLKELGLDIP-VIGLAKGEE------ELLLP---GPGEEFDLPPNSPALY-LLQRIRDEAHRFAITY-H----RKKRSK 525 (581)
T ss_pred HHHHHcCCCcc-EEEEEecCc------eeEec---CCCceecCCCCCHHHH-HHHHHHHHHHHHHHHH-H----HHHhhh
Confidence 44566666544 555555444 11111 1223455555333210 0112234455554442 2 333333
Q ss_pred hhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 452 QHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 452 ~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
.++-| ...+|+|+|+++.++|.+.- .|+.++..++.++|..+ |++++.|++|.+.
T Consensus 526 ~~~~s-~Ld~I~GiG~~r~~~LL~~F--gs~~~i~~As~eel~~v-gi~~~~a~~i~~~ 580 (581)
T COG0322 526 AMLQS-SLDDIPGIGPKRRKALLKHF--GSLKGIKSASVEELAKV-GISKKLAEKIYEA 580 (581)
T ss_pred hhhcC-ccccCCCcCHHHHHHHHHHh--hCHHHHHhcCHHHHHHc-CCCHHHHHHHHhh
Confidence 44444 46789999999999999865 48999999999999999 9999999999865
No 167
>PRK10736 hypothetical protein; Provisional
Probab=85.30 E-value=5.8 Score=44.06 Aligned_cols=113 Identities=9% Similarity=0.102 Sum_probs=70.7
Q ss_pred HHHHcCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccccCCC--
Q psy11421 522 FIYALGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWLNNPN-- 599 (687)
Q Consensus 522 ~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~-- 599 (687)
+|.-..+||+|..+.++|.++|++.. .++.++|... |++++.+..+.++ ......+.++.+.+.|+.+-....
T Consensus 7 ~l~L~~~~giG~~~~~~L~~~~~~~~---~~~~~~l~~~-g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~~i~~~d~~ 81 (374)
T PRK10736 7 WLRLMSVSSLYGDKMVRIAHRLLAQS---QIDAVVLQAT-GLTLRQAQQFLQL-PRKSLESTLRWLEQPNHHLLTADSEF 81 (374)
T ss_pred HHHHHhCCCCCHHHHHHHHHHhcChh---hCCHHHHHHc-CCCHHHHHHHhcc-CHHHHHHHHHHHHhcCCEEEccCchh
Confidence 34444789999999999999999887 4677888776 8999888888654 333334456667677776432100
Q ss_pred ----------CC------CCCCccCCeEEEEEcCCCc--CCHHHHHHH---HHhcCCEEcc
Q psy11421 600 ----------TK------GNKNYLKEKIFVFTGSLYA--FKRNEAIIL---IENLGGKVVN 639 (687)
Q Consensus 600 ----------~~------~~~~~l~g~~vv~TG~l~~--~~R~e~~~~---i~~~Gg~v~~ 639 (687)
.. ..-..+....|.+.|+-.. +.+.-++.+ +.+.|..|+|
T Consensus 82 YP~~L~~i~dpP~vLf~~G~~~~l~~~~iaiVGsR~~s~yg~~~~~~l~~~la~~g~~IVS 142 (374)
T PRK10736 82 YPPQLLAIADYPGALFVSGELAALHSPQLAVVGSRAHSWYGERWGRLFCEELAKNGLTITS 142 (374)
T ss_pred chHHHhhCCCCCeEEEEeCCHHHccCCeEEEECCCCCCHHHHHHHHHHHHHHHHCCCEEEC
Confidence 00 1111345578999999652 223333333 3344766666
No 168
>KOG3226|consensus
Probab=85.07 E-value=2.4 Score=46.18 Aligned_cols=71 Identities=15% Similarity=0.085 Sum_probs=65.2
Q ss_pred ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHH
Q psy11421 606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKI 677 (687)
Q Consensus 606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~ 677 (687)
.|+|-.||++|.-. -.|.++...+-.+|++..-.-+...+.|||.-...-|+.+-+-+|=.||+-++..+.
T Consensus 317 lL~GVV~VlSGfqN-P~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~C 387 (508)
T KOG3226|consen 317 LLEGVVFVLSGFQN-PERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITEC 387 (508)
T ss_pred hhhceEEEEecccC-chHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhcccCCceEeeHHHHHHH
Confidence 57999999999875 589999999999999999999999999999988789999999999999999988754
No 169
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=84.77 E-value=1.5 Score=47.14 Aligned_cols=53 Identities=17% Similarity=0.201 Sum_probs=46.2
Q ss_pred cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
++--+|.-.+..-|-.+| |.++.||..++.++|+++++||+||.+.|.+.+++
T Consensus 237 I~~L~LSvR~~n~Lk~~~-I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l~~ 289 (297)
T TIGR02027 237 IEELDLSVRSYNCLKRAG-IHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAE 289 (297)
T ss_pred HHHhCccHHHHhHHHHcC-CcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHHHH
Confidence 444567788888888887 69999999999999999999999999999988765
No 170
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=84.71 E-value=1.5 Score=47.30 Aligned_cols=50 Identities=24% Similarity=0.372 Sum_probs=44.3
Q ss_pred CCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 527 GIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
.+||||++++++|.+. |.++++|..++.++|.++.|+++..|+.+.+..+
T Consensus 10 ~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~ 60 (317)
T PRK04301 10 DLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAR 60 (317)
T ss_pred hcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 5799999999988876 8999999999999999999999999998887554
No 171
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=84.42 E-value=5.2 Score=40.54 Aligned_cols=107 Identities=19% Similarity=0.276 Sum_probs=54.8
Q ss_pred HHHHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHH----------HHHHHcccCCHHHHHHHcCCCCCCH
Q psy11421 467 KKMIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNIL----------LAIQKSKLTTFSRFIYALGIRHVGE 533 (687)
Q Consensus 467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll----------~~Ie~sk~~~l~r~L~aLGIp~vG~ 533 (687)
++-++.|-.++. -++..|..++.++|..+ -||=..+|..|. .+++..++..++..| |+|.|||+
T Consensus 49 ekAlenLk~~~~-~~l~~I~~~~~~~L~elIrpsGFYnqKa~rLk~l~k~l~~~~~~~~~~~~~~~R~~L--L~iKGIG~ 125 (215)
T COG2231 49 EKALENLKNEGI-LNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLESFKSEVLREEL--LSIKGIGK 125 (215)
T ss_pred HHHHHHHHHccc-CCHHHHhcCCHHHHHHHHhccchHHHHHHHHHHHHHHHHHHhhhhhccchHHHHHHH--HccCCcch
Confidence 455666666664 45777777777666554 567666666652 222222222233444 56777777
Q ss_pred HHHHHHHhhc-CChHHHHhc-CHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 534 TTAKELANYF-KNLECMFKA-TEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 534 ~~Ak~La~~f-~sld~l~~A-s~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
.+|..|+-+. ....-+.++ +..=+..+-++-++.-+.|+.+|.
T Consensus 126 ETaDsILlYa~~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe 170 (215)
T COG2231 126 ETADSILLYALDRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFE 170 (215)
T ss_pred hhHHHHHHHHhcCcccchhHHHHHHHHHhcccccccHHHHHHHHH
Confidence 7776665442 211112211 122233444444444555666664
No 172
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=84.34 E-value=0.66 Score=54.27 Aligned_cols=30 Identities=37% Similarity=0.534 Sum_probs=28.4
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhcCHHH
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKATEEQ 556 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~As~ee 556 (687)
+|||||+++.+.|+++|||++++..||.++
T Consensus 545 ~I~GIG~kr~~~LL~~Fgs~~~i~~As~ee 574 (574)
T TIGR00194 545 KIPGVGEKRVQKLLKYFGSLKGIKKASVEE 574 (574)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhCCccC
Confidence 899999999999999999999999999764
No 173
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=84.13 E-value=1.6 Score=47.88 Aligned_cols=56 Identities=25% Similarity=0.231 Sum_probs=49.0
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
+.|.=.||++.++++|-++|+ .|+.||...+..+|..+.|+.+..|.+|++...+.
T Consensus 32 ~~l~~~g~~~~~~~kL~~~g~-~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~ 87 (344)
T PLN03187 32 DKLISQGINAGDVKKLQDAGI-YTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKL 87 (344)
T ss_pred HHHhhCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 344458899999999999995 89999999999999999999999999999876553
No 174
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=84.06 E-value=3.4 Score=39.67 Aligned_cols=23 Identities=30% Similarity=0.629 Sum_probs=18.2
Q ss_pred CHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 553 TEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 553 s~eeL~~I~GIG~~~A~sI~~ff 575 (687)
..++|.+++|||+++|+.+.-|-
T Consensus 81 ~~~~L~~l~GIG~~tA~~~l~~~ 103 (158)
T cd00056 81 AREELLALPGVGRKTANVVLLFA 103 (158)
T ss_pred cHHHHHcCCCCCHHHHHHHHHHH
Confidence 35778889999999888877654
No 175
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=83.93 E-value=0.8 Score=30.72 Aligned_cols=18 Identities=33% Similarity=0.473 Sum_probs=13.4
Q ss_pred hhhcccCccHHHHHHHHH
Q psy11421 492 NLLRLDRVSNKLANNILL 509 (687)
Q Consensus 492 ~L~~l~gfG~Ksa~~Ll~ 509 (687)
+|.+++|+|+|+|++|++
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 466777888887777775
No 176
>PRK13766 Hef nuclease; Provisional
Probab=83.31 E-value=1.7 Score=52.65 Aligned_cols=51 Identities=12% Similarity=0.212 Sum_probs=44.2
Q ss_pred ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.|+|+|++++.+|++.- .++.+++.++.++|..++|+|++.|+.|.+.++.
T Consensus 719 ~ipgig~~~a~~Ll~~f--gs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~ 769 (773)
T PRK13766 719 SLPDVGPVLARNLLEHF--GSVEAVMTASEEELMEVEGIGEKTAKRIREVVTS 769 (773)
T ss_pred cCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhh
Confidence 68999999999999863 5899999999999999999999999998887764
No 177
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=83.24 E-value=5.2 Score=38.00 Aligned_cols=66 Identities=23% Similarity=0.329 Sum_probs=40.3
Q ss_pred ChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhc-CChHHHHhcCHHH
Q psy11421 481 TAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYF-KNLECMFKATEEQ 556 (687)
Q Consensus 481 ~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f-~sld~l~~As~ee 556 (687)
++.+|..++.++|..+ -||....|+.|.+..+. +.+.+ +.++ ...++
T Consensus 23 ~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~-------------------------~~~~~~~~~~----~~~~~ 73 (149)
T smart00478 23 TPEDLAAADEEELEELIRPLGFYRRKAKYLIELARI-------------------------LVEEYGGEVP----DDREE 73 (149)
T ss_pred CHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHH-------------------------HHHHHCCCcc----HHHHH
Confidence 7888888888776332 27877888877754322 11111 1111 13466
Q ss_pred HhcCCCCCHHHHHHHHHHH
Q psy11421 557 LLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 557 L~~I~GIG~~~A~sI~~ff 575 (687)
|.+++|||+++|+.+.-|-
T Consensus 74 L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 74 LLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHcCCCCcHHHHHHHHHHH
Confidence 7788888888888766543
No 178
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=83.17 E-value=1.3 Score=52.27 Aligned_cols=49 Identities=24% Similarity=0.303 Sum_probs=44.2
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
..+|+|+|+++...|.+.- .|+.+|..++.++|.++ +|++.|++|.+.+
T Consensus 571 L~~I~GIG~k~a~~Ll~~F--gs~~~i~~As~eeL~~v--ig~k~A~~I~~~~ 619 (621)
T PRK14671 571 LTDIAGIGEKTAEKLLEHF--GSVEKVAKASLEELAAV--AGPKTAETIYRYY 619 (621)
T ss_pred hhcCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHHHH--hCHHHHHHHHHHh
Confidence 5689999999999999875 48899999999999998 9999999998875
No 179
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=83.11 E-value=3.4 Score=31.59 Aligned_cols=41 Identities=27% Similarity=0.328 Sum_probs=33.7
Q ss_pred HHHHHHHH-hhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11421 533 ETTAKELA-NYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK 573 (687)
Q Consensus 533 ~~~Ak~La-~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ 573 (687)
+..+..|. +.|.+++.+..++.++|..++|+++..+..+..
T Consensus 3 ~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~ 44 (50)
T TIGR01954 3 EEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELIN 44 (50)
T ss_pred HHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHH
Confidence 44555555 458999999999999999999999988887764
No 180
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=82.56 E-value=1 Score=33.96 Aligned_cols=24 Identities=17% Similarity=0.513 Sum_probs=18.5
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+-++||.||.||.+..++ ..+|++
T Consensus 16 L~~~Cp~C~~PL~~~k~g-~~~Cv~ 39 (41)
T PF06677_consen 16 LDEHCPDCGTPLMRDKDG-KIYCVS 39 (41)
T ss_pred hcCccCCCCCeeEEecCC-CEECCC
Confidence 457999999999985443 568976
No 181
>KOG2841|consensus
Probab=82.42 E-value=1.8 Score=44.60 Aligned_cols=59 Identities=14% Similarity=0.113 Sum_probs=51.1
Q ss_pred hhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 449 ~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.++.+|.. .|+|++.--+..|...- -|+..|.....++|...+|+|+.+|++|++.+..
T Consensus 191 s~~~~~Lt----~i~~VnKtda~~LL~~F--gsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~ 249 (254)
T KOG2841|consen 191 SSLLGFLT----TIPGVNKTDAQLLLQKF--GSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQ 249 (254)
T ss_pred HHHHHHHH----hCCCCCcccHHHHHHhc--ccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhc
Confidence 36777764 79999999999888754 3889999999999999999999999999998864
No 182
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=82.05 E-value=0.62 Score=50.92 Aligned_cols=29 Identities=28% Similarity=0.285 Sum_probs=26.1
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcC
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKI 488 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L 488 (687)
.++|+|+||+++.+||+ ..|+|++||...
T Consensus 91 l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 91 FTNVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred HHccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 46899999999999999 668999999874
No 183
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=81.93 E-value=5.2 Score=42.58 Aligned_cols=69 Identities=20% Similarity=0.189 Sum_probs=38.3
Q ss_pred HHHHHHHCCCCCChHHHhcCChhhhhcc-c--CccHHHHHHHHHHHHHccc---CCHHHHHHH-cCCCCCCHHHHHHHH
Q psy11421 469 MIEKLVNANIVVTAVDLYKINFKNLLRL-D--RVSNKLANNILLAIQKSKL---TTFSRFIYA-LGIRHVGETTAKELA 540 (687)
Q Consensus 469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~--gfG~Ksa~~Ll~~Ie~sk~---~~l~r~L~a-LGIp~vG~~~Ak~La 540 (687)
...+|++. .-|+.+|..++.++|.++ . |+- ..|.+|.+..+.-.+ ..+..-... +.+||||+.+|..++
T Consensus 47 ~~~rl~~~--fpt~~~La~a~~eeL~~~~~~lG~y-~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il 122 (275)
T TIGR01084 47 YFERFLER--FPTVQALANAPQDEVLKLWEGLGYY-ARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAIL 122 (275)
T ss_pred HHHHHHHh--CCCHHHHHCcCHHHHHHHHHHCCcH-HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHH
Confidence 44445543 368999999998888443 2 554 357677665443211 111122222 366777777766554
No 184
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=81.92 E-value=1 Score=37.01 Aligned_cols=30 Identities=27% Similarity=0.491 Sum_probs=22.3
Q ss_pred HHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 548 CMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 548 ~l~~As~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
++..|+.++|.++||||+..|++|.+|-..
T Consensus 7 diN~as~~eL~~lpgi~~~~A~~Iv~~R~~ 36 (65)
T PF12836_consen 7 DINTASAEELQALPGIGPKQAKAIVEYREK 36 (65)
T ss_dssp ETTTS-HHHHHTSTT--HHHHHHHHHHHHH
T ss_pred cCccCCHHHHHHcCCCCHHHHHHHHHHHHh
Confidence 356788999999999999999999987543
No 185
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=81.72 E-value=0.9 Score=43.91 Aligned_cols=43 Identities=21% Similarity=0.288 Sum_probs=33.4
Q ss_pred HHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHh
Q psy11421 547 ECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRD 589 (687)
Q Consensus 547 d~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~ 589 (687)
=++..||.++|..++|||++.|+.|.+|-.......-++.|..
T Consensus 89 vNiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 89 VNINTASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred ccccccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 3678899999999999999999999998754433344666644
No 186
>PRK09482 flap endonuclease-like protein; Provisional
Probab=81.65 E-value=1.7 Score=45.82 Aligned_cols=26 Identities=35% Similarity=0.709 Sum_probs=23.4
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKA 552 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~A 552 (687)
|+||||+++|..|++.|++++.+...
T Consensus 186 GVpGIG~KtA~~LL~~~gsle~i~~~ 211 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFRSLENIYES 211 (256)
T ss_pred CCCCcChHHHHHHHHHhCCHHHHHHh
Confidence 78999999999999999999999753
No 187
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=80.96 E-value=4.5 Score=40.31 Aligned_cols=139 Identities=17% Similarity=0.145 Sum_probs=76.4
Q ss_pred eEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhhc--cCCccccc--CCCCceEEEEEEEEeehhhHHHH
Q psy11421 119 EYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHIIH--KIPLVLNI--KYPPELLEVRCEVLIYKKDFIKL 194 (687)
Q Consensus 119 ~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i~--~iP~~l~~--~~~~~~~evRGEi~~~~~~F~~~ 194 (687)
.|+|.+|-||+-.-|...++ =+-++.|- .++..+. ..|..... ........+-||+++....
T Consensus 17 ~Y~V~eKaDG~Ryll~i~~~-~~ylidr~---------~~~~~v~~~~~p~~~~~~~~~~~~~TLLDGElV~d~~~---- 82 (192)
T PF01331_consen 17 DYFVCEKADGTRYLLLITDN-GVYLIDRK---------NNVFKVDNLHFPSKKDSSDGRHHQDTLLDGELVLDKDP---- 82 (192)
T ss_dssp -EEEEEEESSEEEEEEEEEE-EEEEEETT---------S-EEEESSST-ECTTC--TTCEGCSEEEEEEEEEEECT----
T ss_pred CcEEEECCCCcEEEEEEecc-eEEEEeCC---------CcEEEecCcccccccccccccccCCEEEEEEEEcccCC----
Confidence 69999999999997755443 23455553 3444444 24444320 0123468899999987432
Q ss_pred HHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhc------------CC
Q psy11421 195 NKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKI------------GL 261 (687)
Q Consensus 195 n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~------------Gf 261 (687)
. .+.+.|.+|++...+|... -....++|.+|++. |-
T Consensus 83 ----------------------------~---~~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~ 131 (192)
T PF01331_consen 83 ----------------------------G---EKKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGI 131 (192)
T ss_dssp ----------------------------T---CEEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTS
T ss_pred ----------------------------C---CCceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhcccccc
Confidence 0 2358999999887666432 13455666666421 10
Q ss_pred -CC--CCCceEeCCH---HHHHHHHHHHHHhhcCCCCccceEEEEECCh
Q psy11421 262 -SI--CGEYSVLSGV---NKLIEFYKKINIKRFNLPYEIDGVVYKINCL 304 (687)
Q Consensus 262 -~~--~~~~~~~~~~---~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~ 304 (687)
.. .+.......+ ..+.... .......+++++||+|+.=++.
T Consensus 132 ~~~~~~pf~i~~K~~~~~~~~~~~~--~~~~~~~l~h~~DGLIFtp~~~ 178 (192)
T PF01331_consen 132 IKKKKEPFSIRIKDFFPIYQIEKLL--FEEFIPKLPHETDGLIFTPVNT 178 (192)
T ss_dssp CTCTTSSSEEEE---EEGGGHHHHC--HHCCCCCTTSTEEEEEEEESSS
T ss_pred ccccccceeeeccccHHHHhhHHHH--HHHhhccCCCCCCEEEEecCCC
Confidence 00 1111111111 2222211 3456788999999999987764
No 188
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=80.78 E-value=2.4 Score=45.79 Aligned_cols=34 Identities=26% Similarity=0.481 Sum_probs=25.2
Q ss_pred CCCCCCCCC-cceeecCceeEEecCCCCCCHHHHHhhhh
Q psy11421 415 PNICPICNS-KIIYIESNLIARCSGSWIECIAQRKAGLQ 452 (687)
Q Consensus 415 P~~CP~C~~-~l~~~~~~~~~~C~n~~~~C~~q~~~~i~ 452 (687)
+..||.||+ .++.+.....+.|.+ |-.-+-.++.
T Consensus 11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~----CG~Vl~e~~i 45 (310)
T PRK00423 11 KLVCPECGSDKLIYDYERGEIVCAD----CGLVIEENII 45 (310)
T ss_pred CCcCcCCCCCCeeEECCCCeEeecc----cCCccccccc
Confidence 457999998 565555667899987 8766666665
No 189
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=80.46 E-value=7.8 Score=38.77 Aligned_cols=76 Identities=17% Similarity=0.244 Sum_probs=45.1
Q ss_pred HHHHHHHCCCCCChHHHhcCChhhhhcc---cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcC-
Q psy11421 469 MIEKLVNANIVVTAVDLYKINFKNLLRL---DRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFK- 544 (687)
Q Consensus 469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l---~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~- 544 (687)
...+|++. + .++.+|..++.++|.++ -||-..+|+.|.+-.+... +.|+
T Consensus 47 ~~~~l~~~-~-pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~i~-------------------------~~~~~ 99 (191)
T TIGR01083 47 ATKKLFEV-Y-PTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILV-------------------------ERYGG 99 (191)
T ss_pred HHHHHHHH-C-CCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHHHH-------------------------HHcCC
Confidence 34445543 2 48889998888887432 3776677777765433211 1111
Q ss_pred ChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 545 NLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 545 sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.++. +.++|.+++|||+++|..+.-|-
T Consensus 100 ~~~~----~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 100 EVPE----DREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred CCch----HHHHHHhCCCCcHHHHHHHHHHH
Confidence 1111 24678888888888888776654
No 190
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=80.42 E-value=3.4 Score=47.09 Aligned_cols=65 Identities=17% Similarity=0.179 Sum_probs=52.4
Q ss_pred CHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 443 C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
|-+...+. ++...++|++.+....|.++| |.|+.||-......|..+++++..++.+|..+.+..
T Consensus 199 C~~~~~~~------~~lslv~gi~~~~~~~L~~~G-I~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~a~ 263 (457)
T TIGR03491 199 CEAVAKEE------GHLSLVPGIGPSRYRLLQELG-IHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQARAQ 263 (457)
T ss_pred HHHHHHhc------CCeeecCCCCHHHHHHHHHcC-CCcHHHHhcCCccccccccccCHHHHHHHHHHHHHH
Confidence 76655432 345579999999999999999 699999999876678888899999999988766543
No 191
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=80.41 E-value=3 Score=44.23 Aligned_cols=99 Identities=16% Similarity=0.211 Sum_probs=61.8
Q ss_pred EecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCC--hhhhhcccCccHHHHHHHHHHHH
Q psy11421 435 RCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN--FKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 435 ~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~--~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
||.+... -+.-.++.|.+|.+++.|| +..|.+++--.-..++.|-+-.. .--|.++|++-..-++|++..+.
T Consensus 241 Y~~~~e~-d~~~~l~~l~~ls~~~lL~-----~~~i~kvlGY~~~~~~~d~~vspRGYR~l~kIpRlp~~iv~nlV~~F~ 314 (349)
T COG1623 241 YHKEDEV-DIEAVLEELQSLSDEELLD-----PENIAKVLGYPKTTEADDSLVSPRGYRLLNKIPRLPFAIVENLVRAFG 314 (349)
T ss_pred HhcCccc-CHHHHHHHHHhccchhhCC-----HHHHHHHhCCCCcchhcccccCchhhHHHhcCcCccHHHHHHHHHHHh
Confidence 5666433 6777888899988776654 66666666433333333311111 23477788888888888888775
Q ss_pred HcccCCHHHHHHHc-----CCCCCCHHHHHHHHhhcC
Q psy11421 513 KSKLTTFSRFIYAL-----GIRHVGETTAKELANYFK 544 (687)
Q Consensus 513 ~sk~~~l~r~L~aL-----GIp~vG~~~Ak~La~~f~ 544 (687)
. |.+++.|. .+.|||+..|+.|.+..+
T Consensus 315 ~-----l~~il~As~edL~~VeGIGe~rAr~i~~Gl~ 346 (349)
T COG1623 315 T-----LDGILEASAEDLDAVEGIGEARARAIKEGLS 346 (349)
T ss_pred h-----HHHHHHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence 4 34555543 567888888887775543
No 192
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=79.96 E-value=0.16 Score=45.78 Aligned_cols=25 Identities=28% Similarity=0.507 Sum_probs=21.5
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHh
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFK 551 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~ 551 (687)
|+||||+++|..|++.|+|++++..
T Consensus 22 GV~GIG~KtA~~LL~~ygsle~i~~ 46 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEYGSLENILA 46 (101)
T ss_dssp --TTSTCHCCCCCHHHHTSCHCCCC
T ss_pred CCCCCCHHHHHHHHHHcCCHHHHHH
Confidence 7899999999999999999998876
No 193
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=79.94 E-value=2.2 Score=44.33 Aligned_cols=26 Identities=31% Similarity=0.556 Sum_probs=23.0
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKA 552 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~A 552 (687)
||||||+++|..|++.|++++++..+
T Consensus 187 Gv~GiG~ktA~~Ll~~~gsle~i~~~ 212 (240)
T cd00008 187 GVPGIGEKTAAKLLKEYGSLEGILEN 212 (240)
T ss_pred CCCccCHHHHHHHHHHhCCHHHHHHh
Confidence 78999999999999999999988764
No 194
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=79.85 E-value=4.4 Score=43.39 Aligned_cols=63 Identities=13% Similarity=0.180 Sum_probs=50.6
Q ss_pred hhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 449 AGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 449 ~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+++-.+.+ ..+.+|++|++.+.+|.+.| +.++.||..++.+++..+-|++++.++.+++.++.
T Consensus 144 q~~w~~~~-~L~Qlp~i~~~~~~~l~~~~-i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~ 206 (312)
T smart00611 144 QALWPTDS-PLLQLPHLPEEILKRLEKKK-VLSLEDLLELEDEERGELLGLLDAEGERVYKVLSR 206 (312)
T ss_pred HhhCCCCC-ccccCCCCCHHHHHHHHhCC-CCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 34444433 58899999999999998776 68999999999888888888888888888776543
No 195
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=79.55 E-value=2.3 Score=39.66 Aligned_cols=49 Identities=24% Similarity=0.224 Sum_probs=40.5
Q ss_pred CHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhh
Q psy11421 443 CIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLL 494 (687)
Q Consensus 443 C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~ 494 (687)
|+++.+.++.--+ +.|.|+|+|+..+..|+.+|+ .|+.+|=..+.++|.
T Consensus 41 i~~~~l~~w~~~A--dL~ri~gi~~~~a~LL~~AGv-~Tv~~LA~~~p~~L~ 89 (122)
T PF14229_consen 41 ISERNLLKWVNQA--DLMRIPGIGPQYAELLEHAGV-DTVEELAQRNPQNLH 89 (122)
T ss_pred CCHHHHHHHHhHH--HhhhcCCCCHHHHHHHHHhCc-CcHHHHHhCCHHHHH
Confidence 7788888877766 588999999999999999995 899888777665554
No 196
>PRK02362 ski2-like helicase; Provisional
Probab=79.07 E-value=4.7 Score=48.73 Aligned_cols=54 Identities=20% Similarity=0.345 Sum_probs=46.6
Q ss_pred HHHHHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHc
Q psy11421 521 RFIYALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 521 r~L~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~ 576 (687)
.++.-+.|||+|+.+|++|.+. +.++++|..++.++|.++ +|+++|++|.+.+.
T Consensus 650 ~~~~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~ 704 (737)
T PRK02362 650 ELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILEQAG 704 (737)
T ss_pred HHHHHhCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhC
Confidence 4455568999999999988753 789999999999999999 99999999988765
No 197
>PRK13910 DNA glycosylase MutY; Provisional
Probab=79.00 E-value=4.9 Score=43.10 Aligned_cols=65 Identities=18% Similarity=0.172 Sum_probs=39.8
Q ss_pred CChHHHhcCChhhhhcc-cCcc-HHHHHHHHHHHHHccc-----CCHHHHHHHcCCCCCCHHHHHHHHh-hcCC
Q psy11421 480 VTAVDLYKINFKNLLRL-DRVS-NKLANNILLAIQKSKL-----TTFSRFIYALGIRHVGETTAKELAN-YFKN 545 (687)
Q Consensus 480 ~~i~DL~~L~~~~L~~l-~gfG-~Ksa~~Ll~~Ie~sk~-----~~l~r~L~aLGIp~vG~~~Ak~La~-~f~s 545 (687)
.++++|-.++.++|+++ .|.| -..|.+|.+..+.-.+ .|. .+=.-+.+||||+.+|..++. .|+-
T Consensus 23 Pt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~~i~~~~~g~~P~-~~~~L~~LpGIG~kTA~aIl~~af~~ 95 (289)
T PRK13910 23 PTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAEICVKEHHSQLPN-DYQSLLKLPGIGAYTANAILCFGFRE 95 (289)
T ss_pred CCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCCCCCh-hHHHHHhCCCCCHHHHHHHHHHHCCC
Confidence 58899999998888663 3444 1358888776653221 221 122224788888888876664 3553
No 198
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=78.22 E-value=33 Score=40.16 Aligned_cols=180 Identities=15% Similarity=0.086 Sum_probs=98.2
Q ss_pred ccchhhhhhhhhccCCcccccCCCCceEEEEEEEEe----ehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCccccc
Q psy11421 151 IGENITTNIHIIHKIPLVLNIKYPPELLEVRCEVLI----YKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINK 226 (687)
Q Consensus 151 ~GeDvT~n~~~i~~iP~~l~~~~~~~~~evRGEi~~----~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~ 226 (687)
-|+|+|+....|...-..+. ...+.+-||+++ ...+|+.+... ++. ..
T Consensus 3 ng~d~T~~fPel~~~~~~l~----~~~~ILDGElVvld~~G~~~F~~Lq~~-------------------~~~-----~~ 54 (552)
T TIGR02776 3 NGHDWTKRFPEIVKALALLK----LLPAWIDGEIVVLDERGRADFAALQNA-------------------LSA-----GA 54 (552)
T ss_pred CcCcchhhhHHHHHHHhhCC----CCCEEEEEEEEEECCCCCCCHHHHHHH-------------------HHh-----cc
Confidence 68999988876654433332 236899999998 34567765331 010 12
Q ss_pred ccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCC-CCCceEeC-CHHHHHHHHHHHHHhhcCCCCccceEEEEECC
Q psy11421 227 NKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSI-CGEYSVLS-GVNKLIEFYKKINIKRFNLPYEIDGVVYKINC 303 (687)
Q Consensus 227 ~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~-~~~~~~~~-~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~ 303 (687)
..++.|++|++...+|.++ .....+..+.|+++-=+. .....++. ..++..++++...+ --..|||+|--+
T Consensus 55 ~~pv~~~vFDlL~l~G~dL~~~Pl~eRr~~L~~ll~~~~~~~i~~~~~~~~~~~~~~~~a~~------~G~EGIV~K~~d 128 (552)
T TIGR02776 55 SRPLTYYAFDLLFLSGEDLRDLPLEERKKRLKQLLKAQDEPAIRYSDHFESDGDALLESACR------LGLEGVVSKRLD 128 (552)
T ss_pred cCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEeeeecccHHHHHHHHHH------CCCceEEEeCCC
Confidence 3579999999988766443 146778888887652111 11111111 11222345554432 336899999988
Q ss_pred hhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEE--EEEe-cCCCHHHHHh
Q psy11421 304 LSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGIT--ITRA-TLHNESEIYR 376 (687)
Q Consensus 304 ~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~t--Vsra-TLhN~~~i~~ 376 (687)
..++ -| ++..| +-+|. ....+..|.+....- |++..... =+.=+|.- |-++ |..+.+..++
T Consensus 129 S~Y~--~G---Rs~~W-lKlK~-~~~~e~vI~Gy~~~~---r~~gslLl--g~~d~g~l~~vgkVgsGfsd~~~~~ 192 (552)
T TIGR02776 129 SPYR--SG---RSKDW-LKLKC-RRRQEFVITGYTPPN---RRFGALLV--GVYEGGQLVYAGKVGTGFGADTLKT 192 (552)
T ss_pred CCCC--CC---CCcch-hcccc-cccceEEEEEEecCC---CceeeEEE--EEecCCeEEEEEEEcCCCCHHHHHH
Confidence 5553 23 55667 44453 344566776655443 22222211 01115553 3354 6677666653
No 199
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=78.16 E-value=2.2 Score=37.89 Aligned_cols=31 Identities=23% Similarity=0.215 Sum_probs=26.2
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCCh
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINF 490 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~ 490 (687)
..+|||+|+++.+.|..-| |.+++||-.-+.
T Consensus 14 L~~iP~IG~a~a~DL~~LG-i~s~~~L~g~dP 44 (93)
T PF11731_consen 14 LTDIPNIGKATAEDLRLLG-IRSPADLKGRDP 44 (93)
T ss_pred HhcCCCccHHHHHHHHHcC-CCCHHHHhCCCH
Confidence 4589999999999999888 589988877554
No 200
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=78.02 E-value=2.5 Score=29.65 Aligned_cols=26 Identities=27% Similarity=0.729 Sum_probs=13.3
Q ss_pred CCCCCCCcce-e--e-cCc-eeEEecCCCCCCH
Q psy11421 417 ICPICNSKII-Y--I-ESN-LIARCSGSWIECI 444 (687)
Q Consensus 417 ~CP~C~~~l~-~--~-~~~-~~~~C~n~~~~C~ 444 (687)
-||.||-.+. - . .|+ ..+||+|+ . |.
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrcsnp-a-cd 33 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRCSNP-A-CD 33 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEES-T-T---
T ss_pred cCCccCceEEEEeecCCCcEEEEEcCCC-c-cc
Confidence 5999997532 1 1 222 56899996 5 85
No 201
>smart00475 53EXOc 5'-3' exonuclease.
Probab=77.85 E-value=2.4 Score=44.74 Aligned_cols=26 Identities=35% Similarity=0.583 Sum_probs=23.1
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFKA 552 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~A 552 (687)
|+||||+++|..|++.|++++++...
T Consensus 190 GV~GIG~KtA~~Ll~~ygsle~i~~~ 215 (259)
T smart00475 190 GVPGIGEKTAAKLLKEFGSLENILEN 215 (259)
T ss_pred CCCCCCHHHHHHHHHHhCCHHHHHHH
Confidence 78999999999999999999988753
No 202
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=77.45 E-value=4.3 Score=44.05 Aligned_cols=53 Identities=26% Similarity=0.239 Sum_probs=47.2
Q ss_pred ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
.=.||++.++.+|-++|+ .|+.||+..+..+|.++-|+.+..+.+++..+.+.
T Consensus 5 ~~~~~~~~~~~~l~~~g~-~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~~~ 57 (316)
T TIGR02239 5 EGNGITAADIKKLQEAGL-HTVESVAYAPKKQLLEIKGISEAKADKILAEAAKL 57 (316)
T ss_pred hcCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence 335799999999999995 89999999999999999999999999999887653
No 203
>PRK07758 hypothetical protein; Provisional
Probab=77.07 E-value=5.7 Score=35.38 Aligned_cols=39 Identities=18% Similarity=0.350 Sum_probs=31.1
Q ss_pred HHHHHH-hhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11421 535 TAKELA-NYFKNLECMFKATEEQLLNIPKIGSTTVKAFIK 573 (687)
Q Consensus 535 ~Ak~La-~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ 573 (687)
....|. +.+.++.+|...+.+||.++.|+|++..+.|.+
T Consensus 46 A~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIke 85 (95)
T PRK07758 46 ARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRK 85 (95)
T ss_pred HHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHH
Confidence 444443 357899999999999999999999988776654
No 204
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=77.06 E-value=8.4 Score=44.10 Aligned_cols=102 Identities=16% Similarity=0.252 Sum_probs=67.8
Q ss_pred cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCC-H---HHH-HHHcCCCCCCHH
Q psy11421 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTT-F---SRF-IYALGIRHVGET 534 (687)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~-l---~r~-L~aLGIp~vG~~ 534 (687)
++..++.+..++.|++.|+ .++.++.....++|..++||.+..++.|........... . ... -.-+.++++...
T Consensus 359 ~~~~~ide~~~~~l~~~g~-~~~e~~~~~~~~el~~i~~~~ee~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 437 (470)
T PRK09202 359 MEALDIDEEIAQLLVEEGF-SSLEELAYVPVEELLEIEGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRE 437 (470)
T ss_pred hhhccccHHHHHHHHHcCc-ccHHHHhcCCHHHHhhccCCCHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhccccCHH
Confidence 4678889999999999997 799999999999999999999999998888775322110 0 000 001224555555
Q ss_pred HHHHHHh-hcCChHHHHhcCHHHHhcCCC
Q psy11421 535 TAKELAN-YFKNLECMFKATEEQLLNIPK 562 (687)
Q Consensus 535 ~Ak~La~-~f~sld~l~~As~eeL~~I~G 562 (687)
.+..+.. .+.+.+.+...+.+++..+.+
T Consensus 438 ~~~~~~~~~~~~~edl~~~~~d~~~~~~~ 466 (470)
T PRK09202 438 LAFKLAEKGIKTLEDLAEQAVDELIDIEG 466 (470)
T ss_pred HHHhhhhcCCcchhhhhhccchhhhhccc
Confidence 5544443 244556666555555555433
No 205
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=76.49 E-value=2 Score=30.31 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=15.3
Q ss_pred CCCCCCCCcceeecCceeEEecC
Q psy11421 416 NICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
..||.||++++..+++-..+|++
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~ 26 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPS 26 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESS
T ss_pred cccCcCCccccCCCCcCEeECCC
Confidence 47999999999888888899954
No 206
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=76.37 E-value=2.3 Score=28.50 Aligned_cols=20 Identities=30% Similarity=0.602 Sum_probs=16.7
Q ss_pred HHhcCCCCCHHHHHHHHHHH
Q psy11421 556 QLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 556 eL~~I~GIG~~~A~sI~~ff 575 (687)
+|.+++|||+++|+.|.++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57889999999999988743
No 207
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=75.87 E-value=2.7 Score=40.39 Aligned_cols=55 Identities=16% Similarity=0.330 Sum_probs=37.8
Q ss_pred HHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccCCCCCCCCCCcceee
Q psy11421 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYI 428 (687)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~ 428 (687)
-+..++....-+ .+.| +++++..++.+|+..-.-.- ..-.+.+.||.||++|+..
T Consensus 50 ~~l~~~~~~~~~-~~li-~~~~~~~QL~ev~~~~~l~~-~~~~~~sRC~~CN~~L~~v 104 (147)
T PF01927_consen 50 RDLLKRRRVSGG-VILI-RSDDPEEQLREVLERFGLKL-RLDPIFSRCPKCNGPLRPV 104 (147)
T ss_pred HHHHHHhhccCC-EEEE-cCCCHHHHHHHHHHHcCCcc-ccCCCCCccCCCCcEeeec
Confidence 356777777666 5566 99999999999986432111 1122358999999998754
No 208
>KOG0966|consensus
Probab=75.58 E-value=86 Score=37.96 Aligned_cols=163 Identities=16% Similarity=0.177 Sum_probs=99.2
Q ss_pred eeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhh---hccCCcccccCCCC---ceEEEEEEEEeehhhH
Q psy11421 118 IEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHI---IHKIPLVLNIKYPP---ELLEVRCEVLIYKKDF 191 (687)
Q Consensus 118 ~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~---i~~iP~~l~~~~~~---~~~evRGEi~~~~~~F 191 (687)
-.|++|.|+||=-|.|.|..|.+ +-.|| -|-|-|.+... ...+-..|.+. .+ ....+-||...=...-
T Consensus 250 ~~f~lEtK~DGERiQlHk~g~~~-~yfSR----Ng~dyT~~yg~s~~~g~lt~~i~~~-f~~~v~~cILDGEMm~wD~~~ 323 (881)
T KOG0966|consen 250 QDFYLETKFDGERIQLHKDGGEY-KYFSR----NGNDYTYEYGASYAHGTLTQRIHGA-FNKEVESCILDGEMMTWDTKT 323 (881)
T ss_pred CceEEEeeccCceEEEEecCCEE-EEEec----CCcchhhhcCcccccccccHHHHhh-hhhcchheEecceEEEeecch
Confidence 57999999999999999987775 67787 45666754321 11222222211 11 2477899987644433
Q ss_pred HHHHHHHHHcCCCCCCChhhhHHhHhhhcCcccccccccEEEEEecccccCCCC-CCCHHHHHHHHHhcCCCCCCC----
Q psy11421 192 IKLNKYRYHLGLKKFTNPRNAAAGILRQLNPKINKNKILHFFAHGVGELRGMNM-PSSHSELLNWYQKIGLSICGE---- 266 (687)
Q Consensus 192 ~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~~~~~r~l~f~~y~~~~~~~~~~-~~~~~e~l~~L~~~Gf~~~~~---- 266 (687)
+++ . +|-..+ .+..+.+.. ..-...++.|++..-.|..+ ..+..+.++.|...=-+....
T Consensus 324 ~~f----~-----~~G~~~-----dik~~~~~~-~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~ 388 (881)
T KOG0966|consen 324 KRF----C-----PFGSNS-----DIKELSSRD-GSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIV 388 (881)
T ss_pred hhh----c-----cCCchh-----hHHHhhccc-cCCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEEe
Confidence 221 1 122122 222222211 22357889999887655432 357778888887764433321
Q ss_pred -ceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhhh
Q psy11421 267 -YSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLSTQ 307 (687)
Q Consensus 267 -~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~~ 307 (687)
...+.+.+++.++.++-.+.++ -|||+|--+..++
T Consensus 389 ~~~~~~~~edi~~~f~~ai~~~~------EGIVlK~~~S~Y~ 424 (881)
T KOG0966|consen 389 RSEVGSTKEDIEQFFEEAIDNGE------EGIVLKKPDSSYV 424 (881)
T ss_pred ehhhcccHHHHHHHHHHHHhcCC------CceEEeccCcccC
Confidence 2246789999998887776666 7999998776554
No 209
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=75.45 E-value=6.4 Score=43.25 Aligned_cols=55 Identities=29% Similarity=0.302 Sum_probs=49.1
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
.+.-.||++..+.+|-++|+ .|+.|+...+..+|..+-|+.+..+++++..+.+.
T Consensus 30 ~l~~~gi~~~~i~kL~~~g~-~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~~~~ 84 (342)
T PLN03186 30 QLQASGIAALDIKKLKDAGI-HTVESLAYAPKKDLLQIKGISEAKVEKILEAASKL 84 (342)
T ss_pred HHHhCCCCHHHHHHHHHcCC-CcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 34458899999999999995 89999999999999999999999999999888654
No 210
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=74.40 E-value=2.9 Score=30.23 Aligned_cols=23 Identities=17% Similarity=0.495 Sum_probs=11.4
Q ss_pred CCCCCCCCcceee----cCceeEEecC
Q psy11421 416 NICPICNSKIIYI----ESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~----~~~~~~~C~n 438 (687)
++||.||++|+.. ++...+.|++
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~ 27 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPA 27 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETT
T ss_pred CccccccChhhhhcCCCCCccceECCC
Confidence 3799999999853 3346677864
No 211
>KOG1929|consensus
Probab=73.87 E-value=5 Score=48.54 Aligned_cols=74 Identities=24% Similarity=0.234 Sum_probs=65.3
Q ss_pred CCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHH
Q psy11421 604 KNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIV 678 (687)
Q Consensus 604 ~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l 678 (687)
..+++|.+||-||.=. ..|+++-..+..+||.+....+..++.||+|.-.++|...|.-.++++++-++..-+.
T Consensus 7 ~~~~~~v~~~~t~i~p-~~~~~l~~~~~~~Gg~~~~~~t~~~thli~~~~~s~~~~~a~~~~~~~~~~~wi~~~~ 80 (811)
T KOG1929|consen 7 SKPMSGVTFSPTGINP-IKREELSKKFIKLGGIDFKDFTPSVTHLIVGSVTSSKYAAAHRFDIKVLDSSWIDYIY 80 (811)
T ss_pred CcccCCceeccCcCCH-HHHHHHHHHHHhcCceeeeccCCcCceeecccccccchhhhhcCCCceecchHHHHHH
Confidence 4588999999999854 5899999999999999999999999999999988888888888899999987765443
No 212
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=73.49 E-value=4.8 Score=44.83 Aligned_cols=50 Identities=18% Similarity=0.276 Sum_probs=39.0
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCC---------------hhhhhcccCccHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKIN---------------FKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~---------------~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
..-+++|+|+++.++|.+.| |.++.||..+. ...|.. .||++....|++.
T Consensus 173 pv~~l~GiG~~~~~kL~~~G-I~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~--~fG~~~g~~l~~~ 237 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAHG-ISSVRDLQEFSNRNRQTVGAAPSLLELLLMVK--EFGEGIGQRIWKL 237 (379)
T ss_pred CccccCCcCHHHHHHHHHcC-CCcHHHHHhCCcccccccccccccccHHHHHH--HHCHHHHHHHHHH
Confidence 35579999999999999987 79999999887 555555 3777666666554
No 213
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=73.34 E-value=1.7 Score=29.25 Aligned_cols=20 Identities=25% Similarity=0.497 Sum_probs=13.8
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+..||.||.++.. ...||++
T Consensus 2 ~~~Cp~Cg~~~~~----~~~fC~~ 21 (26)
T PF13248_consen 2 EMFCPNCGAEIDP----DAKFCPN 21 (26)
T ss_pred cCCCcccCCcCCc----ccccChh
Confidence 5689999996542 3457866
No 214
>KOG0966|consensus
Probab=73.30 E-value=9 Score=45.77 Aligned_cols=77 Identities=18% Similarity=0.276 Sum_probs=61.2
Q ss_pred CCCccCCeEEE-EEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEE--cCCCCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11421 603 NKNYLKEKIFV-FTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVK--GQKPGKKLEKAIKLNIKILDEKNFVKIVK 679 (687)
Q Consensus 603 ~~~~l~g~~vv-~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~--G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~ 679 (687)
.++.|.|..|| +.|+-...++.+++++|..+||+++..|..++.++|+ |.....+-..|.+.+-.||..+++++.+.
T Consensus 630 ~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~~~~~~cdVl~p~Wlldcc~ 709 (881)
T KOG0966|consen 630 ISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQAIKRSCDVLKPAWLLDCCK 709 (881)
T ss_pred hhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHHHHhccCceeeHHHHHHHHh
Confidence 45678888876 5777766789999999999999999999987777774 66655555666666999999999987654
No 215
>PRK07220 DNA topoisomerase I; Validated
Probab=73.00 E-value=5.1 Score=48.50 Aligned_cols=47 Identities=30% Similarity=0.355 Sum_probs=36.9
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANN 506 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ 506 (687)
+-+++|+|+++.++|-.++ +.++.++-..+.+++.+--+++.+...+
T Consensus 688 ~~~~~~~~~kt~~Kl~~~~-i~t~~~l~~a~~~~~a~~~~is~~~~~~ 734 (740)
T PRK07220 688 IKDIKGIGKKTAEKLEEAG-ITTVEALAEADPVELSKTTKISVKKIKS 734 (740)
T ss_pred hhcccccchhhhhhhhhcC-ccchhhhccCCHHHhhhhcCCchhhhhh
Confidence 4679999999999999988 5888999888888888755555554443
No 216
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=72.88 E-value=4.8 Score=43.89 Aligned_cols=49 Identities=31% Similarity=0.415 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.|.-....-|-.+| |.++.||...+.++|++++.||+||.+.|.+.+++
T Consensus 269 ~LSvRs~NcLk~a~-I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L~~ 317 (327)
T CHL00013 269 ELSVRAYNCLKRAN-IHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEALQK 317 (327)
T ss_pred cCchhhhhhhhhcC-ccCHHHHHhcCHHHHhhhhccCHhHHHHHHHHHHH
Confidence 45556666666666 79999999999999999999999999999999865
No 217
>PRK03352 DNA polymerase IV; Validated
Probab=72.63 E-value=4.4 Score=44.22 Aligned_cols=50 Identities=20% Similarity=0.240 Sum_probs=40.9
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
..=+++|+|+++.++|...| |.++.||..+....|... ||.+.+..|...
T Consensus 178 pl~~l~gig~~~~~~L~~~G-i~ti~dl~~l~~~~L~~~--fG~~~~~~l~~~ 227 (346)
T PRK03352 178 PTDALWGVGPKTAKRLAALG-ITTVADLAAADPAELAAT--FGPTTGPWLLLL 227 (346)
T ss_pred CHHHcCCCCHHHHHHHHHcC-CccHHHHhcCCHHHHHHH--hChHHHHHHHHH
Confidence 45578999999999998877 699999999998888875 887766655544
No 218
>PRK14976 5'-3' exonuclease; Provisional
Probab=72.44 E-value=3.1 Score=44.42 Aligned_cols=25 Identities=32% Similarity=0.667 Sum_probs=23.1
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHh
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFK 551 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~ 551 (687)
|+||||+++|..|++.|++++.+..
T Consensus 195 GVpGIG~KtA~~LL~~~gsle~i~~ 219 (281)
T PRK14976 195 GVKGIGPKTAIKLLNKYGNIENIYE 219 (281)
T ss_pred CCCcccHHHHHHHHHHcCCHHHHHH
Confidence 7899999999999999999999875
No 219
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=70.58 E-value=5.3 Score=44.74 Aligned_cols=50 Identities=20% Similarity=0.167 Sum_probs=41.7
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCC--hhhhhcccCccHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKIN--FKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~--~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
.=+|+|+|+++.++|...| |.++.||..+. ...|... ||.+.+..|++..
T Consensus 224 v~~l~GIG~~~~~~L~~~G-i~t~~dl~~~~~~~~~L~~~--fG~~~g~~L~~~a 275 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKLF-GDTCGGLELRSKTKEKLQKV--LGPKTGEKLYDYC 275 (404)
T ss_pred HhHhCCCCHHHHHHHHHcC-CcchHHHHhCcccHHHHHHH--HCHHHHHHHHHHh
Confidence 4578999999999999988 68999999987 7888874 9987777776643
No 220
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=70.29 E-value=20 Score=38.38 Aligned_cols=70 Identities=24% Similarity=0.218 Sum_probs=38.0
Q ss_pred CCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHHHhcC----H
Q psy11421 479 VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECMFKAT----E 554 (687)
Q Consensus 479 I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l~~As----~ 554 (687)
--+++.|..+..++|... |+-..+++-|.+ +|+.+++..-+++.+...+ .
T Consensus 144 fptpe~l~~~~~~~l~~~-g~s~~Ka~yi~~-------------------------~A~~~~~g~~~~~~l~~~~~e~a~ 197 (285)
T COG0122 144 FPTPEQLAAADEEALRRC-GLSGRKAEYIIS-------------------------LARAAAEGELDLSELKPLSDEEAI 197 (285)
T ss_pred CCCHHHHHhcCHHHHHHh-CCcHHHHHHHHH-------------------------HHHHHHcCCccHHHhccCCHHHHH
Confidence 357777777777777654 444444444433 2222232222334444333 3
Q ss_pred HHHhcCCCCCHHHHHHHHHH
Q psy11421 555 EQLLNIPKIGSTTVKAFIKF 574 (687)
Q Consensus 555 eeL~~I~GIG~~~A~sI~~f 574 (687)
+.|++++|||+.+|+.+.-|
T Consensus 198 e~L~~i~GIG~WTAe~~llf 217 (285)
T COG0122 198 EELTALKGIGPWTAEMFLLF 217 (285)
T ss_pred HHHHcCCCcCHHHHHHHHHH
Confidence 56777778887777776554
No 221
>cd08689 C2_fungal_Pkc1p C2 domain found in protein kinase C (Pkc1p) in Saccharomyces cerevisiae. This family is named after the protein kinase C in Saccharomyces cerevisiae, Pkc1p. Protein kinase C is a member of a family of Ser/Thr phosphotransferases that are involved in many cellular signaling pathways. PKC has two antiparallel coiled-coiled regions (ACC finger domain) (AKA PKC homology region 1 (HR1)/ Rho binding domain) upstream of the C2 domain and two C1 domains downstream. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains, like those of PKC, are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that
Probab=70.26 E-value=5.6 Score=36.33 Aligned_cols=53 Identities=21% Similarity=0.255 Sum_probs=41.9
Q ss_pred EEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceeeeEEEE
Q psy11421 297 VVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALL 353 (687)
Q Consensus 297 iVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iTPvA~l 353 (687)
++|||+|....+. .++++|||.=.|.|+=+ ....|.=+.|..+ .+..+|||.|
T Consensus 27 V~IKved~~kaRT--r~srnd~WnE~F~i~Vd-k~nEiel~VyDk~-~~~~~Pi~ll 79 (109)
T cd08689 27 VSIKVEDVERART--KPSRNDRWNEDFEIPVE-KNNEEEVIVYDKG-GDQPVPVGLL 79 (109)
T ss_pred EEEEECCEEEEec--cCCCCCcccceEEEEec-CCcEEEEEEEeCC-CCeecceeee
Confidence 7899999743332 46899999999999985 6777888888875 5688899976
No 222
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=69.94 E-value=2.7 Score=41.55 Aligned_cols=53 Identities=17% Similarity=0.255 Sum_probs=48.2
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
.-|++|...-+..++..++++..+..|+.+++..+.|+|...|+.+.++++.|
T Consensus 170 ~~i~~Vnksds~~~L~d~g~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln~p 222 (224)
T COG5241 170 ILIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLP 222 (224)
T ss_pred EEEEeeccccHHHHHHHHHHHHHHhccchhHHHHHHccCHHHHHHHHHHhccc
Confidence 45788888889999999999999999999999999999999999999988654
No 223
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=68.59 E-value=3.9 Score=41.39 Aligned_cols=39 Identities=36% Similarity=0.589 Sum_probs=31.5
Q ss_pred HHHHhhcCChHHHHhcC-HHHHhcCCCCCHHHHHHHHHHH
Q psy11421 537 KELANYFKNLECMFKAT-EEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 537 k~La~~f~sld~l~~As-~eeL~~I~GIG~~~A~sI~~ff 575 (687)
+.|+.+|.+++.+.... .++|.+|.|||+.+|.+|.-|.
T Consensus 96 k~l~~~~~~~~~~~~~~~R~~LL~iKGIG~ETaDsILlYa 135 (215)
T COG2231 96 KNLAKFFINLESFKSEVLREELLSIKGIGKETADSILLYA 135 (215)
T ss_pred HHHHHHhhhhhccchHHHHHHHHccCCcchhhHHHHHHHH
Confidence 44577888887776543 6899999999999999998765
No 224
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=68.55 E-value=5.7 Score=48.48 Aligned_cols=48 Identities=21% Similarity=0.282 Sum_probs=27.6
Q ss_pred ccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCcc-HHHHHHHHHHHH
Q psy11421 461 NIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS-NKLANNILLAIQ 512 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG-~Ksa~~Ll~~Ie 512 (687)
.|||+|++.+..|.+. +.|+.+|.+++.++|..+ +| ++.|++|.+.+.
T Consensus 761 ~lPgI~~~~a~~ll~~--f~si~~l~~as~eeL~~~--iG~~~~A~~i~~fl~ 809 (814)
T TIGR00596 761 KLPGVTKKNYRNLRKK--VKSIRELAKLSQNELNEL--IGDEEAAKRLYDFLR 809 (814)
T ss_pred HCCCCCHHHHHHHHHH--cCCHHHHHhCCHHHHHHH--hCCHHHHHHHHHHhc
Confidence 3566666666666654 356666666666566553 55 666666655553
No 225
>PRK01216 DNA polymerase IV; Validated
Probab=68.42 E-value=6.9 Score=43.10 Aligned_cols=48 Identities=27% Similarity=0.398 Sum_probs=40.1
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~ 509 (687)
.=.++|+|+++.++|...| |.++.||+.+....|... ||......|.+
T Consensus 180 i~~l~giG~~~~~~L~~~G-i~TigdL~~~~~~~L~~r--fG~~~~~~L~~ 227 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLG-VNKLVDTLRIEFDELKGI--IGEAKAKYLFS 227 (351)
T ss_pred cccccCCCHHHHHHHHHcC-CCcHHHHhcCCHHHHHHH--HCHHHHHHHHH
Confidence 4468999999999998887 699999999998888874 99766666554
No 226
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=68.01 E-value=4.3 Score=40.49 Aligned_cols=61 Identities=25% Similarity=0.392 Sum_probs=37.3
Q ss_pred cCCCCCCEEE--EEecCCccceeeccccCCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhh
Q psy11421 377 KNIQIGDTVV--VHRSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGL 451 (687)
Q Consensus 377 ~~i~iGd~V~--v~raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i 451 (687)
-.++|||.|. |..-| =|.-.+... + +-. .+-..|+.|+.+|++ .+..++|+| |-..-.++|
T Consensus 117 d~f~~GDivrA~Vis~~--~~~~Lst~~---~-dlG--VI~A~CsrC~~~L~~--~~~~l~Cp~----Cg~tEkRKi 179 (188)
T COG1096 117 DAFRIGDIVRARVISTG--DPIQLSTKG---N-DLG--VIYARCSRCRAPLVK--KGNMLKCPN----CGNTEKRKI 179 (188)
T ss_pred cccccccEEEEEEEecC--CCeEEEecC---C-cce--EEEEEccCCCcceEE--cCcEEECCC----CCCEEeeee
Confidence 4789999886 44444 222222111 1 111 123589999999998 457899988 765555554
No 227
>KOG1921|consensus
Probab=67.55 E-value=18 Score=37.75 Aligned_cols=34 Identities=32% Similarity=0.504 Sum_probs=22.7
Q ss_pred HHHHHHHhhcC-ChHHHHhcCHHHHhcCCCCCHHHHHHH
Q psy11421 534 TTAKELANYFK-NLECMFKATEEQLLNIPKIGSTTVKAF 571 (687)
Q Consensus 534 ~~Ak~La~~f~-sld~l~~As~eeL~~I~GIG~~~A~sI 571 (687)
++|+.|..+|+ ++. ++.++|.++||||+++|.-.
T Consensus 141 kta~IL~d~f~gDIP----~~v~dLlsLPGVGPKMa~L~ 175 (286)
T KOG1921|consen 141 KTAKILQDKFDGDIP----DTVEDLLSLPGVGPKMAHLT 175 (286)
T ss_pred HHHHHHHHHhCCCCc----hhHHHHhcCCCCchHHHHHH
Confidence 35667777764 232 35678888888888888654
No 228
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=66.75 E-value=12 Score=31.12 Aligned_cols=34 Identities=21% Similarity=0.338 Sum_probs=27.9
Q ss_pred hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 542 YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 542 ~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.+.++..|...+.++|.+++|||.+..+.|.+.+
T Consensus 31 ~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L 64 (66)
T PF03118_consen 31 GIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKL 64 (66)
T ss_dssp T--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHH
T ss_pred CCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHH
Confidence 3668999999999999999999999999887755
No 229
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=65.52 E-value=4.5 Score=37.26 Aligned_cols=25 Identities=20% Similarity=0.788 Sum_probs=19.0
Q ss_pred CCCCCCcceeecCceeEEecCCCCCCHHHHHhh
Q psy11421 418 CPICNSKIIYIESNLIARCSGSWIECIAQRKAG 450 (687)
Q Consensus 418 CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~ 450 (687)
||+||++|+.. .+.|++ |...+.++
T Consensus 1 CPvCg~~l~vt----~l~C~~----C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGGELVVT----RLKCPS----CGTEIEGE 25 (113)
T ss_pred CCCCCCceEEE----EEEcCC----CCCEEEee
Confidence 99999999853 589977 87666553
No 230
>PRK10880 adenine DNA glycosylase; Provisional
Probab=65.51 E-value=16 Score=40.39 Aligned_cols=74 Identities=20% Similarity=0.228 Sum_probs=47.4
Q ss_pred HHHHHHHCCCCCChHHHhcCChhhhhcc-c--CccHHHHHHHHHHHHHc---ccCCHHHHHHH-cCCCCCCHHHHHHHHh
Q psy11421 469 MIEKLVNANIVVTAVDLYKINFKNLLRL-D--RVSNKLANNILLAIQKS---KLTTFSRFIYA-LGIRHVGETTAKELAN 541 (687)
Q Consensus 469 ~i~~L~~~g~I~~i~DL~~L~~~~L~~l-~--gfG~Ksa~~Ll~~Ie~s---k~~~l~r~L~a-LGIp~vG~~~Ak~La~ 541 (687)
...+|++. .-|+.+|-.++.++|.++ . |+- ..|.+|.+..+.- .+..+...... +.+||||+.+|..++.
T Consensus 51 ~~~rl~~~--fPt~~~La~a~~eel~~~~~glGyy-~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~ 127 (350)
T PRK10880 51 YFERFMAR--FPTVTDLANAPLDEVLHLWTGLGYY-ARARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILS 127 (350)
T ss_pred HHHHHHHH--CcCHHHHHCcCHHHHHHHHHcCChH-HHHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHH
Confidence 34455553 368999999988888753 3 554 3688887765543 22233333333 4899999999987775
Q ss_pred -hcCC
Q psy11421 542 -YFKN 545 (687)
Q Consensus 542 -~f~s 545 (687)
.|+-
T Consensus 128 ~af~~ 132 (350)
T PRK10880 128 LSLGK 132 (350)
T ss_pred HHCCC
Confidence 4553
No 231
>PRK03858 DNA polymerase IV; Validated
Probab=65.40 E-value=7.3 Score=43.31 Aligned_cols=48 Identities=17% Similarity=0.225 Sum_probs=40.4
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~ 509 (687)
.=+++|+|+++.++|.+.| |.++.||..+....|... ||...++.|.+
T Consensus 175 l~~l~Gig~~~~~~L~~~G-i~t~~dl~~l~~~~L~~~--fG~~~~~~l~~ 222 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAHG-ITTVGDVAELPESALVSL--LGPAAGRHLHA 222 (396)
T ss_pred hhhcCCCCHHHHHHHHHhC-CCcHHHHhcCCHHHHHHH--hCcHHHHHHHH
Confidence 4568999999999998887 699999999998888875 88777766654
No 232
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=65.10 E-value=15 Score=39.84 Aligned_cols=21 Identities=19% Similarity=0.433 Sum_probs=18.2
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q psy11421 554 EEQLLNIPKIGSTTVKAFIKF 574 (687)
Q Consensus 554 ~eeL~~I~GIG~~~A~sI~~f 574 (687)
.++|.+++|||+++|..|.-|
T Consensus 219 ~~~L~~l~GIG~~tAd~vll~ 239 (310)
T TIGR00588 219 REALCELPGVGPKVADCICLM 239 (310)
T ss_pred HHHHHhCCCccHHHHHHHHHH
Confidence 478999999999999988765
No 233
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=64.35 E-value=5.6 Score=29.02 Aligned_cols=16 Identities=19% Similarity=0.154 Sum_probs=7.8
Q ss_pred hcccCccHHHHHHHHH
Q psy11421 494 LRLDRVSNKLANNILL 509 (687)
Q Consensus 494 ~~l~gfG~Ksa~~Ll~ 509 (687)
-.++|+|+|+|.+|++
T Consensus 19 ~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 19 PGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCcccHHHHHHHHH
Confidence 3445555555555443
No 234
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=64.32 E-value=2.8 Score=34.13 Aligned_cols=29 Identities=24% Similarity=0.473 Sum_probs=20.8
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhh
Q psy11421 415 PNICPICNSKIIYIESNLIARCSGSWIECIAQRKAG 450 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~ 450 (687)
-+|||.||.++..+ ..+|+. . |.....++
T Consensus 3 HkHC~~CG~~Ip~~----~~fCS~--~-C~~~~~k~ 31 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD----ESFCSP--K-CREEYRKR 31 (59)
T ss_pred CCcCCcCCCcCCcc----hhhhCH--H-HHHHHHHH
Confidence 46999999998743 458976 3 98765543
No 235
>KOG3084|consensus
Probab=64.19 E-value=3.4 Score=44.31 Aligned_cols=29 Identities=28% Similarity=0.503 Sum_probs=25.3
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCCCCHH
Q psy11421 415 PNICPICNSKIIYIESNLIARCSGSWIECIA 445 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~ 445 (687)
-+.||.||+++..++++..+.|.+. . ||.
T Consensus 150 ykFCp~CG~~tkp~e~g~k~~Cs~~-~-C~~ 178 (345)
T KOG3084|consen 150 YKFCPGCGSPTKPEEAGTKLQCSDE-T-CPS 178 (345)
T ss_pred hccCcccCCCcccccCCccceeecc-c-CCc
Confidence 4689999999998888899999984 6 986
No 236
>PRK03348 DNA polymerase IV; Provisional
Probab=63.63 E-value=8.8 Score=43.77 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=40.9
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
.=.++|+|+++.++|...| |+++.||..+....|... ||.+....|++.
T Consensus 182 v~~L~GIG~~t~~~L~~lG-I~TigDLa~l~~~~L~~~--fG~~~g~~L~~~ 230 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRLG-IETIGDLAALSEAEVANL--LGATVGPALHRL 230 (454)
T ss_pred ccccCCCCHHHHHHHHHcC-CccHHHHhcCCHHHHHHH--HCHHHHHHHHHH
Confidence 4468999999999998877 699999999999889875 887777766543
No 237
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=63.33 E-value=8.7 Score=42.42 Aligned_cols=50 Identities=22% Similarity=0.212 Sum_probs=40.7
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcC--ChhhhhcccCccHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKI--NFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L--~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
.=+++|+|+++.++|.+.-.|.++.||..+ ....|... ||.+.++.|++.
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~--fG~~~g~~l~~~ 235 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEH--FGEKLGEWLYNL 235 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHH--HHHHHHHHHHHH
Confidence 457899999999888766568999999999 88888774 888777777654
No 238
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.09 E-value=6.6 Score=34.35 Aligned_cols=24 Identities=21% Similarity=0.575 Sum_probs=19.9
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+-.||+|+++.+.......|.|..
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~k 58 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRK 58 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCC
Confidence 557999999988777778899964
No 239
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=61.75 E-value=8.6 Score=31.85 Aligned_cols=20 Identities=25% Similarity=0.494 Sum_probs=17.8
Q ss_pred HHhcCCCCCHHHHHHHHHHH
Q psy11421 556 QLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 556 eL~~I~GIG~~~A~sI~~ff 575 (687)
++..++|||+.+|..|.+|+
T Consensus 48 ~~~~l~gIG~~ia~kI~E~l 67 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEIL 67 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHHH
Confidence 49999999999999998876
No 240
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.26 E-value=12 Score=38.47 Aligned_cols=67 Identities=12% Similarity=0.173 Sum_probs=46.5
Q ss_pred HHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 445 AQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 445 ~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
+.+++-|..-+.+..+++..|....++.+...| ++.+++.++.++|.+++|+|+.+|..|...++-.
T Consensus 17 ~ELLailL~~g~~~~~~~~~lA~~ll~~f~~~g---~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~El~ 83 (218)
T TIGR00608 17 YELLAIILRTGTPKGLDVLSLSKRLLDVFGRQD---SLGHLLSAPPEELSSVPGIGEAKAIQLKAAVELA 83 (218)
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHHHHhcccC---CHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHHHH
Confidence 445666665555433355555555554432213 7889999999999999999999999998887754
No 241
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=60.37 E-value=6.3 Score=26.28 Aligned_cols=21 Identities=24% Similarity=0.483 Sum_probs=13.4
Q ss_pred CCCCCCcceeecCceeEEecC
Q psy11421 418 CPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 418 CP~C~~~l~~~~~~~~~~C~n 438 (687)
|-+||..|.-.+-.+.+.|+|
T Consensus 1 C~sC~~~i~~r~~~v~f~CPn 21 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPN 21 (24)
T ss_pred CccCCCcccCcccCceEeCCC
Confidence 667777766444456666766
No 242
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=59.66 E-value=5.6 Score=30.28 Aligned_cols=26 Identities=19% Similarity=0.443 Sum_probs=19.9
Q ss_pred CCCCCCCCcceeecCceeEEecCCCCCCHHHH
Q psy11421 416 NICPICNSKIIYIESNLIARCSGSWIECIAQR 447 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~ 447 (687)
..||.||.- .|..-+.|-|. + ||..+
T Consensus 12 rkCp~CGt~----NG~R~~~CKN~-~-C~~~~ 37 (44)
T PF14952_consen 12 RKCPKCGTY----NGTRGLSCKNK-S-CPQVF 37 (44)
T ss_pred ccCCcCcCc----cCcccccccCC-c-cchhh
Confidence 479999973 35677899995 6 98754
No 243
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=59.61 E-value=6.3 Score=30.53 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=16.0
Q ss_pred CCCCCCCcceeecCc--eeEEecC
Q psy11421 417 ICPICNSKIIYIESN--LIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~--~~~~C~n 438 (687)
.||.||+.|...++. ..+.|+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~ 25 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRK 25 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCc
Confidence 799999988765442 3678865
No 244
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=59.55 E-value=48 Score=35.43 Aligned_cols=70 Identities=14% Similarity=0.084 Sum_probs=42.3
Q ss_pred CCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHccc--CC------HHHHHHH-cCCCCCCHHHHHHHH-hhcCChHH
Q psy11421 479 VVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKL--TT------FSRFIYA-LGIRHVGETTAKELA-NYFKNLEC 548 (687)
Q Consensus 479 I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~--~~------l~r~L~a-LGIp~vG~~~Ak~La-~~f~sld~ 548 (687)
.-++++|..++.++|..+ |++..+|+.|.+--+...+ .+ ....... +.|||||+.+|.-++ ..++..|.
T Consensus 155 FPtpe~La~~~~~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~ 233 (283)
T PRK10308 155 FPTPERLAAADPQALKAL-GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDV 233 (283)
T ss_pred CCCHHHHHcCCHHHHHHC-CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCC
Confidence 368899999998899887 8998888887765544322 11 1112222 356677766665444 23444443
Q ss_pred H
Q psy11421 549 M 549 (687)
Q Consensus 549 l 549 (687)
+
T Consensus 234 f 234 (283)
T PRK10308 234 F 234 (283)
T ss_pred C
Confidence 3
No 245
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=59.35 E-value=6.1 Score=30.19 Aligned_cols=22 Identities=23% Similarity=0.392 Sum_probs=11.4
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.||..++..+....++|++
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~ 26 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPY 26 (46)
T ss_pred ECCCCCCEEEECCCCCceECCC
Confidence 4666666555443333455544
No 246
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=59.29 E-value=13 Score=41.95 Aligned_cols=76 Identities=16% Similarity=0.214 Sum_probs=57.3
Q ss_pred CCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhc
Q psy11421 416 NICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLR 495 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~ 495 (687)
.+|-.|. ||+ . |.++..+ +++.+=++|+++.+-..|.+.| |.|++||-+.+...+..
T Consensus 206 ~rC~~C~------------f~p---~-C~~~a~e------~~~L~Lv~Gi~~~r~~~l~~~G-I~Ti~~LA~~~~~~~~~ 262 (474)
T COG2251 206 ARCTTCQ------------FEP---Q-CESEALE------EDDLSLVPGITPSRYDVLEEVG-ITTIEDLADASLPILEL 262 (474)
T ss_pred hhhhHhh------------cch---h-hhHHHhh------ccceeccCCCCHHHHHHHHHcC-cchHHHHHhccccchhh
Confidence 4787773 563 3 9887654 5566668899999999999999 69999999988877877
Q ss_pred ccCccHHHHHHHHHHHHHc
Q psy11421 496 LDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 496 l~gfG~Ksa~~Ll~~Ie~s 514 (687)
+-|+=.+.+..+.-+...+
T Consensus 263 ~~ga~~~~~~~l~~qa~~~ 281 (474)
T COG2251 263 VAGALTALAAQLVLQARAR 281 (474)
T ss_pred hhhhHHHHHHHHHHHHHhh
Confidence 7665466666666665543
No 247
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=59.28 E-value=13 Score=40.65 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=38.8
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
..=.++|+|+++.++|-..| |+++.||..+..+.|.. .||. ....+++.
T Consensus 177 pl~~l~gig~~~~~~L~~~G-i~ti~dL~~~~~~~L~~--rfG~-~~~~l~~~ 225 (344)
T cd01700 177 PVGDVWGIGRRTAKKLNAMG-IHTAGDLAQADPDLLRK--KFGV-VGERLVRE 225 (344)
T ss_pred ChhhcCccCHHHHHHHHHcC-CCcHHHHhcCCHHHHHH--HHHH-HHHHHHHH
Confidence 34468999999999998887 69999999999888886 4885 45555543
No 248
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=59.01 E-value=8.9 Score=28.85 Aligned_cols=22 Identities=27% Similarity=0.534 Sum_probs=16.0
Q ss_pred CCCCCCCcc-eeecCceeEEecC
Q psy11421 417 ICPICNSKI-IYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l-~~~~~~~~~~C~n 438 (687)
.||.||+.. +.+.....+.|++
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~ 24 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPN 24 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETT
T ss_pred CCcCCcCCceEEcCCCCeEECCC
Confidence 599999864 4454556789976
No 249
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.89 E-value=7.5 Score=35.15 Aligned_cols=29 Identities=34% Similarity=0.813 Sum_probs=20.8
Q ss_pred cCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHh
Q psy11421 413 KIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKA 449 (687)
Q Consensus 413 ~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~ 449 (687)
.+|..||.||.++... .++|+| |...+.+
T Consensus 4 ~~~~~cPvcg~~~iVT----eL~c~~----~etTVrg 32 (122)
T COG3877 4 KVINRCPVCGRKLIVT----ELKCSN----CETTVRG 32 (122)
T ss_pred CCCCCCCcccccceeE----EEecCC----CCceEec
Confidence 4677899999987643 589988 6554444
No 250
>PRK13844 recombination protein RecR; Provisional
Probab=58.84 E-value=7.3 Score=39.47 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=17.9
Q ss_pred hhhhcccCccHHHHHHHHHHHHHc
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
+.|..|||+|+|+|++|.-.+=+.
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~ 38 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDK 38 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcC
Confidence 457788888888888887766443
No 251
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=58.14 E-value=7.3 Score=33.70 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=21.1
Q ss_pred ccccccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11421 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (687)
Q Consensus 457 r~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (687)
+..-++|+||++..+.|.+.| |.|++||..
T Consensus 3 ~~l~~LpNig~~~e~~L~~vG-I~t~~~L~~ 32 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVG-IHTVEDLRE 32 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT---SHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHcC-CCCHHHHHH
Confidence 345689999999999999999 688888776
No 252
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.26 E-value=8.1 Score=39.01 Aligned_cols=23 Identities=22% Similarity=0.339 Sum_probs=17.3
Q ss_pred hhhhcccCccHHHHHHHHHHHHH
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+.|..|||+|+|+|++|.-.+=+
T Consensus 11 ~~l~~LPGIG~KsA~RlA~~ll~ 33 (195)
T TIGR00615 11 ESLKKLPGIGPKSAQRLAFHLLK 33 (195)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHc
Confidence 46778888888888888766643
No 253
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=56.91 E-value=5.9 Score=28.49 Aligned_cols=11 Identities=45% Similarity=1.244 Sum_probs=9.6
Q ss_pred CCCCCCCCCCc
Q psy11421 414 IPNICPICNSK 424 (687)
Q Consensus 414 ~P~~CP~C~~~ 424 (687)
.|+.||.||.+
T Consensus 17 ~p~~CP~Cg~~ 27 (34)
T cd00729 17 APEKCPICGAP 27 (34)
T ss_pred CCCcCcCCCCc
Confidence 68899999975
No 254
>PRK00076 recR recombination protein RecR; Reviewed
Probab=56.90 E-value=8.3 Score=38.99 Aligned_cols=23 Identities=17% Similarity=0.296 Sum_probs=17.3
Q ss_pred hhhhcccCccHHHHHHHHHHHHH
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+.|..|||+|+|+|++|.-.+=+
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll~ 33 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLLQ 33 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHc
Confidence 45778888888888888766643
No 255
>PRK14133 DNA polymerase IV; Provisional
Probab=56.08 E-value=15 Score=40.01 Aligned_cols=49 Identities=31% Similarity=0.424 Sum_probs=39.1
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
.=.++|+|+++.++|...| |+++.||..+..+.|... ||. ....+++..
T Consensus 175 v~~l~gig~~~~~~L~~~G-i~ti~dl~~l~~~~L~~r--fG~-~g~~l~~~a 223 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNIG-IYTIEDLLKLSREFLIEY--FGK-FGVEIYERI 223 (347)
T ss_pred ccccCCCCHHHHHHHHHcC-CccHHHHhhCCHHHHHHH--HhH-HHHHHHHHh
Confidence 4468999999999998877 699999999998888875 884 555555544
No 256
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=54.69 E-value=16 Score=32.58 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=25.5
Q ss_pred cCCCCCCHHHHHHHHh-hcCChHHHHhcCHHHH
Q psy11421 526 LGIRHVGETTAKELAN-YFKNLECMFKATEEQL 557 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~-~f~sld~l~~As~eeL 557 (687)
..||+||+++|+-|.. -+.++++|...++++|
T Consensus 15 ~~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~L 47 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLLGIRSPADLKGRDPEEL 47 (93)
T ss_pred hcCCCccHHHHHHHHHcCCCCHHHHhCCCHHHH
Confidence 3799999999987764 3678999999887654
No 257
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=54.28 E-value=4.9 Score=32.62 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=23.0
Q ss_pred CCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHh
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSGSWIECIAQRKA 449 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~ 449 (687)
.|..|-|||-.|...+..+.+.|+| |-...+.
T Consensus 8 ~~~~CtSCg~~i~p~e~~v~F~CPn----CGe~~I~ 39 (61)
T COG2888 8 DPPVCTSCGREIAPGETAVKFPCPN----CGEVEIY 39 (61)
T ss_pred CCceeccCCCEeccCCceeEeeCCC----CCceeee
Confidence 3678999998886666778888887 6544433
No 258
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=54.00 E-value=5.4 Score=26.18 Aligned_cols=18 Identities=28% Similarity=0.597 Sum_probs=12.0
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.||.++.. ...||++
T Consensus 1 ~Cp~CG~~~~~----~~~fC~~ 18 (23)
T PF13240_consen 1 YCPNCGAEIED----DAKFCPN 18 (23)
T ss_pred CCcccCCCCCC----cCcchhh
Confidence 48999988752 2346765
No 259
>PRK02406 DNA polymerase IV; Validated
Probab=53.90 E-value=17 Score=39.60 Aligned_cols=48 Identities=27% Similarity=0.389 Sum_probs=38.1
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~ 509 (687)
..-+++|+|+++.++|-..| |.++.||..+..+.|... ||. ....+++
T Consensus 169 pi~~l~giG~~~~~~L~~~G-i~ti~dl~~l~~~~L~~~--fG~-~~~~l~~ 216 (343)
T PRK02406 169 PVEKIPGVGKVTAEKLHALG-IYTCADLQKYDLAELIRH--FGK-FGRRLYE 216 (343)
T ss_pred CcchhcCCCHHHHHHHHHcC-CCcHHHHHhCCHHHHHHH--HhH-HHHHHHH
Confidence 35578999999999998777 699999999998888875 774 4444444
No 260
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=52.98 E-value=6.4 Score=40.83 Aligned_cols=28 Identities=29% Similarity=0.533 Sum_probs=11.1
Q ss_pred CCCCCCCCc-ceeecC---ceeEEecCCCCCCHHHH
Q psy11421 416 NICPICNSK-IIYIES---NLIARCSGSWIECIAQR 447 (687)
Q Consensus 416 ~~CP~C~~~-l~~~~~---~~~~~C~n~~~~C~~q~ 447 (687)
-.||.||+. |..-++ -.+++|++ |.++.
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~----C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPN----CNEEY 63 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TT----T--EE
T ss_pred CcCCCCCChhHhhccCCCccceeECCC----CchHH
Confidence 479999997 665433 37899987 87654
No 261
>PRK03980 flap endonuclease-1; Provisional
Probab=52.98 E-value=12 Score=40.25 Aligned_cols=25 Identities=32% Similarity=0.503 Sum_probs=22.2
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHh
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFK 551 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~ 551 (687)
||||||+++|-.|.+.|++++++..
T Consensus 193 GI~GIG~ktA~kLi~~~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHHCCCHHHHHH
Confidence 8899999999999999999988876
No 262
>PRK10445 endonuclease VIII; Provisional
Probab=52.77 E-value=9.2 Score=40.41 Aligned_cols=22 Identities=27% Similarity=0.548 Sum_probs=17.6
Q ss_pred CCCCCCCccee--ecCceeEEecC
Q psy11421 417 ICPICNSKIIY--IESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~--~~~~~~~~C~n 438 (687)
.||.||+++.+ ..+...+||++
T Consensus 237 ~Cp~Cg~~I~~~~~~gR~t~~CP~ 260 (263)
T PRK10445 237 ACERCGGIIEKTTLSSRPFYWCPG 260 (263)
T ss_pred CCCCCCCEeEEEEECCCCcEECCC
Confidence 59999999874 35668899976
No 263
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=52.64 E-value=11 Score=38.05 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=15.4
Q ss_pred hhhhcccCccHHHHHHHHHHHHH
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+.|.+|||+|+|+|++|.-.+=+
T Consensus 12 ~~l~kLPGvG~KsA~R~AfhLL~ 34 (198)
T COG0353 12 DALKKLPGVGPKSAQRLAFHLLQ 34 (198)
T ss_pred HHHhhCCCCChhHHHHHHHHHHc
Confidence 34667788888888777655433
No 264
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=52.48 E-value=15 Score=28.29 Aligned_cols=30 Identities=27% Similarity=0.487 Sum_probs=19.3
Q ss_pred CCCCCCCcceeec--------CceeEEecCCCCCCHHHHH
Q psy11421 417 ICPICNSKIIYIE--------SNLIARCSGSWIECIAQRK 448 (687)
Q Consensus 417 ~CP~C~~~l~~~~--------~~~~~~C~n~~~~C~~q~~ 448 (687)
.||.||++..... -+....|.|. . |-..++
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~-~-Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNP-E-CGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCC-c-CCCEEE
Confidence 5999999765321 1355669995 5 865443
No 265
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.19 E-value=11 Score=46.50 Aligned_cols=21 Identities=19% Similarity=0.327 Sum_probs=14.5
Q ss_pred hhhhcccCccHHHHHHHHHHH
Q psy11421 491 KNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
+-+-.+||+|+|+|.+|++..
T Consensus 185 DnIpGVpGIG~KtA~kLL~~y 205 (887)
T TIGR00593 185 DNIPGVKGIGEKTAAKLLQEF 205 (887)
T ss_pred cCCCCCCCcCHHHHHHHHHHc
Confidence 446677777777777777653
No 266
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=50.74 E-value=10 Score=39.90 Aligned_cols=24 Identities=13% Similarity=0.357 Sum_probs=20.1
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
-.+||.||+++....++...+|++
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~ 122 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPH 122 (256)
T ss_pred CccccccCCCCeecCCceeEECCC
Confidence 459999999998777788888965
No 267
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=50.65 E-value=8.6 Score=40.80 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=19.1
Q ss_pred CCCCCCCcceee--cCceeEEecCCCCCCHH
Q psy11421 417 ICPICNSKIIYI--ESNLIARCSGSWIECIA 445 (687)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n~~~~C~~ 445 (687)
.||.||+++.+. .+...+||++ |..
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~----CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEKIKQGGRSTFFCPR----CQK 273 (274)
T ss_pred CCCCCCCeeEEEEECCCCcEECcC----CCC
Confidence 599999998743 4568899976 853
No 268
>PRK01810 DNA polymerase IV; Validated
Probab=50.20 E-value=20 Score=40.01 Aligned_cols=49 Identities=22% Similarity=0.168 Sum_probs=39.2
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
.=+++|+|+++.++|...| |.++.||..+....|... ||. ....+++..
T Consensus 181 v~~l~giG~~~~~~L~~~G-i~tigdL~~~~~~~L~~r--fG~-~g~~l~~~a 229 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIG-IQTIGDLAKADEHILRAK--LGI-NGVRLQRRA 229 (407)
T ss_pred HhhcCCcCHHHHHHHHHcC-CCcHHHHHhCCHHHHHHH--HhH-HHHHHHHHh
Confidence 3357899999999998887 699999999998888764 885 466666544
No 269
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=50.16 E-value=22 Score=38.33 Aligned_cols=52 Identities=19% Similarity=0.092 Sum_probs=40.4
Q ss_pred cccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11421 454 FSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (687)
Q Consensus 454 F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~ 509 (687)
|...--+++.|+|+++.++|.+.| |.++.||..+....|.. .||.+ ...++.
T Consensus 167 ~l~~lp~~~~gig~~~~~~L~~~G-i~t~~dl~~~~~~~l~~--rfG~~-~~~l~~ 218 (335)
T cd03468 167 LLAPLPVAALRLPPETVELLARLG-LRTLGDLAALPRAELAR--RFGLA-LLLRLD 218 (335)
T ss_pred ccCCCChhHhCCCHHHHHHHHHhC-cccHHHHHhCChHHHHh--hcCHH-HHHHHH
Confidence 334344689999999999998887 69999999999888887 48865 444444
No 270
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=49.81 E-value=23 Score=38.56 Aligned_cols=49 Identities=14% Similarity=0.125 Sum_probs=36.2
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCC-hhhhhcccCccHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKIN-FKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~-~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
.=+++|+|+++.++|.+.| |.++.||..+. ...+.. .|| +.+..+++..
T Consensus 175 i~~l~giG~~~~~~L~~~G-i~ti~dl~~~~~~~~l~~--~fg-~~~~~l~~~a 224 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAVG-INPIGDLLAASPDALLAL--WGG-VSGERLWYAL 224 (343)
T ss_pred hhhcCCCCHHHHHHHHHcC-CCcHHHHhcCCHHHHHHH--Hhh-HHHHHHHHHh
Confidence 3458999999999998888 69999999998 444444 355 4566665543
No 271
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=49.62 E-value=11 Score=37.98 Aligned_cols=30 Identities=13% Similarity=0.179 Sum_probs=20.8
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (687)
..+-||-||-+.---=+.+|+|+|+.-++.
T Consensus 87 ~~I~IPELg~~iePG~~s~G~ITtIEGvL~ 116 (201)
T COG1779 87 ATIYIPELGLEIEPGPASEGFITTIEGVLE 116 (201)
T ss_pred ccEEcccCceEeccccccCceEehHHHHHH
Confidence 456788887766666666788888766654
No 272
>PRK03103 DNA polymerase IV; Reviewed
Probab=49.57 E-value=22 Score=39.78 Aligned_cols=50 Identities=14% Similarity=0.170 Sum_probs=39.9
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
.=.++|+|+++.++|-+.| |.++.||..+..+.|... ||. ....+++...
T Consensus 183 i~~l~gig~~~~~~L~~~G-i~tigdl~~~~~~~L~~~--fG~-~~~~l~~~a~ 232 (409)
T PRK03103 183 VRKLFGVGSRMEKHLRRMG-IRTIGQLANTPLERLKKR--WGI-NGEVLWRTAN 232 (409)
T ss_pred HhhcCCccHHHHHHHHHcC-CCCHHHHhcCCHHHHHHH--HCH-HHHHHHHHhc
Confidence 3457999999999998887 799999999998888875 884 4666665543
No 273
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=49.12 E-value=8.6 Score=37.84 Aligned_cols=12 Identities=42% Similarity=1.317 Sum_probs=9.9
Q ss_pred cCCCCCCCCCCc
Q psy11421 413 KIPNICPICNSK 424 (687)
Q Consensus 413 ~~P~~CP~C~~~ 424 (687)
..|..||+||.+
T Consensus 147 e~P~~CPiCga~ 158 (166)
T COG1592 147 EAPEVCPICGAP 158 (166)
T ss_pred CCCCcCCCCCCh
Confidence 369999999974
No 274
>PRK03760 hypothetical protein; Provisional
Probab=49.04 E-value=20 Score=33.16 Aligned_cols=53 Identities=13% Similarity=0.092 Sum_probs=37.7
Q ss_pred EEEEeecCcceeeeEEEEEEEEEC--CEEEEEecCCCHHHHHhcCCCCCCEEEEEe
Q psy11421 336 AINIQIGRTGIITPVALLKPVLID--GITITRATLHNESEIYRKNIQIGDTVVVHR 389 (687)
Q Consensus 336 ~I~~qvGRTG~iTPvA~lePV~l~--G~tVsraTLhN~~~i~~~~i~iGd~V~v~r 389 (687)
||.| +.+.|+|.=++.+.|-.+- +..+..|==-|++.+.++||++||+|.+.+
T Consensus 62 DiiF-ld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 62 DVIF-LDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred EEEE-ECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHHHcCCCCCCEEEEee
Confidence 4444 4667787777777776532 233445555689999999999999998876
No 275
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=48.63 E-value=6.7 Score=41.29 Aligned_cols=35 Identities=20% Similarity=0.372 Sum_probs=25.6
Q ss_pred CCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcc
Q psy11421 417 ICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFS 455 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~ 455 (687)
.||.|+++|...+ ..++|.|. + |-....+...+|.
T Consensus 4 ~CP~C~~~l~~~~--~~~~C~~~-h-~fd~a~~Gy~~ll 38 (272)
T PRK11088 4 QCPLCHQPLTLEE--NSWICPQN-H-QFDCAKEGYVNLL 38 (272)
T ss_pred cCCCCCcchhcCC--CEEEcCCC-C-CCccccCceEEec
Confidence 5999999997533 46999996 6 7666666565554
No 276
>PRK02794 DNA polymerase IV; Provisional
Probab=48.53 E-value=20 Score=40.30 Aligned_cols=48 Identities=19% Similarity=0.240 Sum_probs=38.2
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
.=.++|+|+++.++|...| |.++.||..+....|... ||. .+..+++.
T Consensus 211 l~~L~GiG~~~~~~L~~~G-I~tigdL~~l~~~~L~~r--fG~-~g~~l~~~ 258 (419)
T PRK02794 211 VGIIWGVGPATAARLARDG-IRTIGDLQRADEADLMRR--FGS-MGLRLWRL 258 (419)
T ss_pred hhhhCCCCHHHHHHHHHhc-cchHHHHhhCCHHHHHHH--HhH-HHHHHHHH
Confidence 4468999999999998877 699999999998888764 885 45555543
No 277
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=48.21 E-value=21 Score=38.33 Aligned_cols=65 Identities=22% Similarity=0.291 Sum_probs=45.7
Q ss_pred CCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcccc
Q psy11421 529 RHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIYWL 595 (687)
Q Consensus 529 p~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~ 595 (687)
|.+.++++..|...-.-.=.+..|+.++|..+||||.+.|..|..--+-. +-..+.|+..|+.+.
T Consensus 304 ~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~Rr~~--rl~~e~Lkk~Gvvlk 368 (404)
T COG4277 304 PDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMTRRRT--RLTLEDLKKLGVVLK 368 (404)
T ss_pred CCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHHhhhc--ccCHHHHhhhceeee
Confidence 56778888877632111246788999999999999999999987643221 123677888887653
No 278
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=48.06 E-value=15 Score=39.59 Aligned_cols=25 Identities=28% Similarity=0.597 Sum_probs=21.8
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHh
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFK 551 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~ 551 (687)
||||||+++|..|++.|++++.+..
T Consensus 202 GV~GIG~ktA~~Ll~~~gs~e~i~~ 226 (310)
T COG0258 202 GVKGIGPKTALKLLQEYGSLEGLYE 226 (310)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHH
Confidence 5899999999999999998887775
No 279
>KOG0442|consensus
Probab=47.81 E-value=20 Score=43.27 Aligned_cols=52 Identities=21% Similarity=0.354 Sum_probs=47.5
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcch
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
|++|||-...+..+..+|+++..+.+.+.++|..+-|. ...|..|++||+..
T Consensus 824 l~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~el~~~-~~~a~~LYdFi~~~ 875 (892)
T KOG0442|consen 824 LSLPGVSYINYRNLRHKFKSLKELANSSQEELSELLGV-HENAKLLYDFIHTE 875 (892)
T ss_pred hcCCCccHHHHHHHHHHhhHHHHHHhCcHHHHHHHhcc-hHHHHHHHHHHHHh
Confidence 79999999999999999999999999999999999776 89999999999754
No 280
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=47.67 E-value=16 Score=40.12 Aligned_cols=27 Identities=33% Similarity=0.468 Sum_probs=23.7
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhc
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKA 552 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~A 552 (687)
-||||||+++|-.|.+.|++++++...
T Consensus 239 ~Gv~GIG~ktA~kli~~~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKEHGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHh
Confidence 389999999999999999999988653
No 281
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=47.12 E-value=9.9 Score=37.24 Aligned_cols=52 Identities=19% Similarity=0.342 Sum_probs=36.8
Q ss_pred HHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCCCccccCC--CCCCCCCCcceee
Q psy11421 372 SEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFKIP--NICPICNSKIIYI 428 (687)
Q Consensus 372 ~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~~P--~~CP~C~~~l~~~ 428 (687)
..+++. ..|-.....++-++.=|+..++.... .. +...| +.||.||.+|+..
T Consensus 57 ~L~~r~--k~g~~~i~i~~~s~~~Ql~e~~~~~~--l~-~~~~~e~~RCp~CN~~L~~v 110 (165)
T COG1656 57 ELYKRA--KLGIKAILIRSDSIEEQLAEFLARLG--LK-PRLFPEFSRCPECNGELEKV 110 (165)
T ss_pred HHHHHh--hccCceEEEeCCCHHHHHHHHHHHhc--cc-hhcccccccCcccCCEeccC
Confidence 566776 77778888899999999988865221 11 12234 6999999998754
No 282
>PRK05755 DNA polymerase I; Provisional
Probab=46.92 E-value=15 Score=45.52 Aligned_cols=28 Identities=14% Similarity=0.246 Sum_probs=19.0
Q ss_pred hhhhcccCccHHHHHHHHHHHHHcccCCHHHHH
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQKSKLTTFSRFI 523 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L 523 (687)
+-+-.+||+|+|+|.+|++.. .++..++
T Consensus 187 DnipGv~GiG~ktA~~Ll~~~-----gsle~i~ 214 (880)
T PRK05755 187 DNIPGVPGIGEKTAAKLLQEY-----GSLEGLY 214 (880)
T ss_pred CCCCCCCCccHHHHHHHHHHc-----CCHHHHH
Confidence 457777888888888887653 3455665
No 283
>PTZ00035 Rad51 protein; Provisional
Probab=46.70 E-value=37 Score=37.23 Aligned_cols=52 Identities=21% Similarity=0.199 Sum_probs=42.8
Q ss_pred HHcCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 524 YALGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 524 ~aLGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
..|.-+|+++...++|.+. |.++..+..++..+|.++.|+++..|+.|.+..
T Consensus 24 ~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~ 76 (337)
T PTZ00035 24 EKLQSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAA 76 (337)
T ss_pred HHHhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHH
Confidence 3344477888888887754 889999999999999999999999999888644
No 284
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=46.58 E-value=15 Score=26.03 Aligned_cols=19 Identities=32% Similarity=0.434 Sum_probs=15.3
Q ss_pred ccccCCCCHHHHHHHHHCC
Q psy11421 459 AMNIIGLGKKMIEKLVNAN 477 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g 477 (687)
.=++.|+|++|.++|.+.|
T Consensus 13 i~~~~GIG~kt~~kL~~~G 31 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKLNKLG 31 (32)
T ss_dssp GGGSTTS-HHHHHHHHCTT
T ss_pred HHhhCCccHHHHHHHHHcc
Confidence 4479999999999998766
No 285
>PRK14173 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=46.28 E-value=38 Score=36.40 Aligned_cols=58 Identities=12% Similarity=0.221 Sum_probs=44.3
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-++++++.++.++ +..+.-.+.+|+++. .|.+.|+++||.. ++|++|++.+.+...+.
T Consensus 15 i~~~l~~~v~~l~------~~P~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 86 (287)
T PRK14173 15 VYAELRARLAKLP------FVPHLRVVRLGEDPASVSYVRLKDRQAKALGLRSQVEVLPESTSQEELLELIARLNADP 86 (287)
T ss_pred HHHHHHHHHHHhC------CCCcEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 4677888888875 445778888998753 7999999999874 46999999987654443
No 286
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=46.13 E-value=18 Score=38.97 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=18.6
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHH
Q psy11421 527 GIRHVGETTAKELANYFKNLECMF 550 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~ 550 (687)
||||||+++|-.|.+.|++++.+.
T Consensus 227 gv~giG~k~A~~li~~~~~~~~~~ 250 (316)
T cd00128 227 GIPGIGPVTALKLIKKYGDIEKDI 250 (316)
T ss_pred CCCCccHHHHHHHHHHcCChHHHH
Confidence 788888888888888888765443
No 287
>KOG2906|consensus
Probab=46.13 E-value=15 Score=32.88 Aligned_cols=26 Identities=23% Similarity=0.549 Sum_probs=18.7
Q ss_pred CCCCCCCCcceeecCce--eEEecCCCCCCHH
Q psy11421 416 NICPICNSKIIYIESNL--IARCSGSWIECIA 445 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~~--~~~C~n~~~~C~~ 445 (687)
..||.||.-|+.+.|+. .+.|. . ||-
T Consensus 2 ~FCP~Cgn~Live~g~~~~rf~C~---t-CpY 29 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGESCNRFSCR---T-CPY 29 (105)
T ss_pred cccCCCCCEEEEecCCeEeeEEcC---C-CCc
Confidence 47999999998876654 45563 3 875
No 288
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=46.12 E-value=29 Score=29.36 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=18.3
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (687)
..-.|+|+|++++.+|+.+- .++..++.
T Consensus 23 ~i~gv~giG~k~A~~ll~~~--~~~~~~~~ 50 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKEY--GSLENLLE 50 (75)
T ss_pred cCCCCCcccHHHHHHHHHHh--CCHHHHHH
Confidence 34467788888888877652 35555555
No 289
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=46.07 E-value=31 Score=30.97 Aligned_cols=47 Identities=17% Similarity=0.103 Sum_probs=35.9
Q ss_pred CHHHHHHHHHCCCCCChHHHhcC-Ch---hhhhcccCccHHHHHHHHHHHHH
Q psy11421 466 GKKMIEKLVNANIVVTAVDLYKI-NF---KNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 466 G~k~i~~L~~~g~I~~i~DL~~L-~~---~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.+..+..|..+| |.|+.||... .. .=-..+||+|.++|..|..-+..
T Consensus 22 ~p~va~~L~aaG-i~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awLa~ 72 (96)
T PF12482_consen 22 PPRVARRLAAAG-IRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWLAA 72 (96)
T ss_pred CHHHHHHHHHcC-CchHHHHHHHHHHccchHHHhCcccchHHHHHHHHHHHH
Confidence 377889999888 5899999873 22 12567889999999888887754
No 290
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=45.81 E-value=21 Score=28.28 Aligned_cols=26 Identities=35% Similarity=0.372 Sum_probs=16.8
Q ss_pred cCCCCCCHHHHHHHHh-hcCChHHHHh
Q psy11421 526 LGIRHVGETTAKELAN-YFKNLECMFK 551 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~-~f~sld~l~~ 551 (687)
.+|.|||+.+|+.+.+ .+.|++.|..
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhcccccHHHHHHHHHhCCCCHHHHhh
Confidence 4789999999987764 4788888754
No 291
>PF13549 ATP-grasp_5: ATP-grasp domain; PDB: 1WR2_A.
Probab=45.72 E-value=44 Score=34.47 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChh
Q psy11421 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLS 305 (687)
Q Consensus 247 ~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~ 305 (687)
-+..|..+.|..+|+++++ ..++++.+++.+..+.+ .|+ +|+|+.+..
T Consensus 10 L~e~e~~~lL~~yGI~~~~-~~~~~~~~ea~~~a~~i-------g~P---vvlKi~sp~ 57 (222)
T PF13549_consen 10 LTEAEAKELLAAYGIPVPP-TRLVTSAEEAVAAAEEI-------GFP---VVLKIVSPD 57 (222)
T ss_dssp E-HHHHHHHHHTTT-------EEESSHHHHHHHHHHH--------SS---EEEEEE-TT
T ss_pred cCHHHHHHHHHHcCcCCCC-eeEeCCHHHHHHHHHHh-------CCC---EEEEEecCC
Confidence 3678999999999999987 45788999999887765 576 899998743
No 292
>PRK09482 flap endonuclease-like protein; Provisional
Probab=45.68 E-value=38 Score=35.76 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=32.1
Q ss_pred ccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 457 r~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
-+.-.|+|+||||+.+|+++=. |++.||.- +.++ +.+..++|.+..+.
T Consensus 182 DnIpGVpGIG~KtA~~LL~~~g--sle~i~~~----~~~~---~~~~~~~L~~~~~~ 229 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLNQFR--SLENIYES----LDAL---PEKWRKKLEEHKEM 229 (256)
T ss_pred cCCCCCCCcChHHHHHHHHHhC--CHHHHHHh----HHHh---hHHHHHHHHHhHHH
Confidence 3445689999999999998743 77788752 2222 34666667666554
No 293
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=45.59 E-value=19 Score=34.04 Aligned_cols=40 Identities=18% Similarity=0.255 Sum_probs=32.7
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccC
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDR 498 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~g 498 (687)
+.-.|.|+||+.-..|.+.| |-++++|-.++..++..+++
T Consensus 68 DLt~I~GIGPk~e~~Ln~~G-I~tfaQIAAwt~~di~~id~ 107 (133)
T COG3743 68 DLTRISGIGPKLEKVLNELG-IFTFAQIAAWTRADIAWIDD 107 (133)
T ss_pred cchhhcccCHHHHHHHHHcC-CccHHHHHhcCHHHHHHHHh
Confidence 56679999999999998888 57999999988777665543
No 294
>PRK11827 hypothetical protein; Provisional
Probab=45.44 E-value=16 Score=29.88 Aligned_cols=22 Identities=32% Similarity=0.732 Sum_probs=17.9
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.|..+|....+...+.|..
T Consensus 10 aCP~ckg~L~~~~~~~~Lic~~ 31 (60)
T PRK11827 10 ACPVCNGKLWYNQEKQELICKL 31 (60)
T ss_pred ECCCCCCcCeEcCCCCeEECCc
Confidence 6999999999776666788865
No 295
>PRK07945 hypothetical protein; Provisional
Probab=45.25 E-value=26 Score=38.35 Aligned_cols=49 Identities=16% Similarity=0.074 Sum_probs=37.5
Q ss_pred hhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHh
Q psy11421 492 NLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELAN 541 (687)
Q Consensus 492 ~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~ 541 (687)
+|.++||+|+..|++|.+-++.-+-..|.++....+=-+ |+..+.+|.-
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~~~~~~~-g~~l~~~~~~ 98 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAGRVPDYLAELRADAEPLG-GGALRAALRG 98 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhcCCHHHHHHHHHhhcCCc-cHHHHHHHhh
Confidence 688999999999999998887654445666666665446 8888887765
No 296
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=44.99 E-value=34 Score=29.62 Aligned_cols=23 Identities=30% Similarity=0.420 Sum_probs=16.2
Q ss_pred HHhcCCCCCHHHHHHHHHHHcch
Q psy11421 556 QLLNIPKIGSTTVKAFIKFINQP 578 (687)
Q Consensus 556 eL~~I~GIG~~~A~sI~~ff~~~ 578 (687)
-|.+|||||+.+|..|...+.+.
T Consensus 3 ~l~sipGig~~~a~~llaeigd~ 25 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDI 25 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCc
Confidence 46677788877777777766554
No 297
>PTZ00205 DNA polymerase kappa; Provisional
Probab=44.80 E-value=24 Score=41.25 Aligned_cols=47 Identities=23% Similarity=0.294 Sum_probs=37.6
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~ 509 (687)
.=+|+|+|+++.++|-..| |.++.||+....+ |..+ |+++....++.
T Consensus 311 V~ki~GIG~~t~~~L~~~G-I~TigDLa~~~~~-l~~~--f~~k~l~~llG 357 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLG-ITTLSDIYNRRVE-LCYI--LHNNLFRFLLG 357 (571)
T ss_pred cceeCCcCHHHHHHHHHcC-CCcHHHHhcCCHH-HHHH--hHHHHHHHHhC
Confidence 4579999999999998887 7999999998753 4443 78887776664
No 298
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=44.36 E-value=37 Score=36.58 Aligned_cols=50 Identities=22% Similarity=0.298 Sum_probs=34.2
Q ss_pred cccccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccHHHHHHHHHHHHHcc
Q psy11421 456 SRKAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSNKLANNILLAIQKSK 515 (687)
Q Consensus 456 sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk 515 (687)
|-+.-+|+|+||||+.+|++.-. +++.||. +. ...++..+++.+.++...
T Consensus 197 sDnipGV~GIG~ktA~~Ll~~~g--s~e~i~~~~~--------~~~~~~~~~l~~~~~~af 247 (310)
T COG0258 197 SDNIPGVKGIGPKTALKLLQEYG--SLEGLYENLD--------IIKKKTREKLLEDKEKAF 247 (310)
T ss_pred ccCCCCCCCcCHHHHHHHHHHhC--CHHHHHHhhh--------hhcchhhHHHHHHHHHHh
Confidence 34445589999999999988754 6666665 22 455677777777776543
No 299
>PTZ00217 flap endonuclease-1; Provisional
Probab=43.80 E-value=20 Score=40.24 Aligned_cols=25 Identities=28% Similarity=0.503 Sum_probs=17.7
Q ss_pred CCCCCCHHHHHHHHhhcCChHHHHh
Q psy11421 527 GIRHVGETTAKELANYFKNLECMFK 551 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f~sld~l~~ 551 (687)
||||||+++|-.|.+.|++++++..
T Consensus 239 gi~GIG~ktA~~Li~~~gsle~il~ 263 (393)
T PTZ00217 239 TIKGIGPKTAYKLIKKYKSIEEILE 263 (393)
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHH
Confidence 6777777777777777777776653
No 300
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=43.77 E-value=8.1 Score=31.40 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=15.6
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
|..|-|||.+|.-.+..+.+.|+|
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPn 30 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPN 30 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCC
Confidence 446777777776444456677766
No 301
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=43.67 E-value=35 Score=36.43 Aligned_cols=52 Identities=17% Similarity=0.216 Sum_probs=43.9
Q ss_pred cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcc
Q psy11421 526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQ 577 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~ 577 (687)
+.+|++|...++.|.+. ..+++++..++.+++..+-|+++..+..|.++++.
T Consensus 154 ~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~ 206 (312)
T smart00611 154 LQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSR 206 (312)
T ss_pred ccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 47899999999998864 67899999999999999889988888888877543
No 302
>PTZ00446 vacuolar sorting protein SNF7-like; Provisional
Probab=43.29 E-value=49 Score=33.43 Aligned_cols=52 Identities=13% Similarity=0.160 Sum_probs=42.1
Q ss_pred cCCChhhHHHHHHHHHHHHHHHHHHhccCCCCCCChHHHHHHHHHHHHHHHH
Q psy11421 7 KKINFSKLSFRVTELKKELHRHNIAYYLYDNPIISDNKYDQLLFELKKIEEK 58 (687)
Q Consensus 7 ~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~~le~~ 58 (687)
+++|++++..=++++.+++...+.--=..+.|..+|.+-|.|..||.+|+.+
T Consensus 125 k~~~idkVd~lmDei~E~~e~~~EIseaLs~~~~~~~DEdELe~ELe~Le~e 176 (191)
T PTZ00446 125 NEINTQKVEKIIDTIQENKDIQEEINQALSFNLLNNVDDDEIDKELDLLKEQ 176 (191)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHH
Confidence 5688888877777888888888877666677766888999999999999864
No 303
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=42.94 E-value=33 Score=38.60 Aligned_cols=41 Identities=22% Similarity=0.371 Sum_probs=34.8
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN 501 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~ 501 (687)
..=+++|+|+++.++|-..| |.|+.||..+....|... ||.
T Consensus 180 Pv~~l~GiG~~~~~~L~~lG-i~TigdL~~~~~~~L~~~--fG~ 220 (422)
T PRK03609 180 PVEEVWGVGRRISKKLNAMG-IKTALDLADTNIRFIRKH--FNV 220 (422)
T ss_pred ChhhcCCccHHHHHHHHHcC-CCcHHHHhcCCHHHHHHH--HCH
Confidence 35579999999999998877 699999999998888775 773
No 304
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=42.55 E-value=43 Score=33.40 Aligned_cols=53 Identities=15% Similarity=0.207 Sum_probs=32.4
Q ss_pred CChhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHc-CCCCCCHHHHHHHH
Q psy11421 488 INFKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYAL-GIRHVGETTAKELA 540 (687)
Q Consensus 488 L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aL-GIp~vG~~~Ak~La 540 (687)
+..+.|.-|||+|+|...+|++.-++..=.+|..+-.-. |+++.-...++++.
T Consensus 113 ~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv~gl~~p~~~i~~RIl 166 (181)
T PF04919_consen 113 LRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERVKGLHDPVKLIVERIL 166 (181)
T ss_dssp SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHHHHHHH
T ss_pred HHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHhccCCCHHHHHHHHHH
Confidence 446889999999999999999987765545677776666 57665444444444
No 305
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=42.41 E-value=61 Score=25.27 Aligned_cols=44 Identities=23% Similarity=0.224 Sum_probs=34.3
Q ss_pred HHHHHHHHHCCCCCChHHHhcCChhhhhcccCccH-HHHHHHHHHHHH
Q psy11421 467 KKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN-KLANNILLAIQK 513 (687)
Q Consensus 467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~-Ksa~~Ll~~Ie~ 513 (687)
+.-+..|.++++ +..+|..++.++|..+ |+.. -...+|+.+|+.
T Consensus 17 ~~y~~~f~~~~i--~g~~L~~l~~~dL~~l-gi~~~g~r~~i~~~i~~ 61 (63)
T cd00166 17 GQYADNFRENGI--DGDLLLLLTEEDLKEL-GITLPGHRKKILKAIQK 61 (63)
T ss_pred HHHHHHHHHcCC--CHHHHhHCCHHHHHHc-CCCCHHHHHHHHHHHHH
Confidence 777888888886 8889999999999876 5654 666777777765
No 306
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=42.24 E-value=22 Score=25.47 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=18.3
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+..|+.||++++.......++|.+
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~ 26 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIF 26 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEccc
Confidence 457999999988744456788976
No 307
>KOG2534|consensus
Probab=42.11 E-value=29 Score=37.48 Aligned_cols=52 Identities=15% Similarity=0.141 Sum_probs=35.9
Q ss_pred HHHHHHcCCCCCCHHHHHHHHhhc--CChHH---HHhc----CHHHHhcCCCCCHHHHHHH
Q psy11421 520 SRFIYALGIRHVGETTAKELANYF--KNLEC---MFKA----TEEQLLNIPKIGSTTVKAF 571 (687)
Q Consensus 520 ~r~L~aLGIp~vG~~~Ak~La~~f--~sld~---l~~A----s~eeL~~I~GIG~~~A~sI 571 (687)
...-.+-+|||+|++.|+++-+-. |.+.+ +.+. +..=+.+|-|||.++|+.-
T Consensus 53 ~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~W 113 (353)
T KOG2534|consen 53 TSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKW 113 (353)
T ss_pred ccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHH
Confidence 345567799999999998776432 44444 4431 2345788999999999763
No 308
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=41.58 E-value=17 Score=38.59 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=17.4
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11421 417 ICPICNSKIIYI--ESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (687)
.||.||+++.+. .+-..+||++
T Consensus 246 pCprCG~~I~~~~~~gR~t~~CP~ 269 (272)
T PRK14810 246 PCLNCKTPIRRVVVAGRSSHYCPH 269 (272)
T ss_pred cCCCCCCeeEEEEECCCccEECcC
Confidence 599999998743 4567889976
No 309
>KOG3524|consensus
Probab=41.22 E-value=20 Score=42.31 Aligned_cols=69 Identities=19% Similarity=0.313 Sum_probs=58.6
Q ss_pred ccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHH
Q psy11421 606 YLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKI 677 (687)
Q Consensus 606 ~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~ 677 (687)
++.|...||||.... ..++-.++..+||-|..--..+|+.+|+....|.|+.-|... ++++-.++.-.-
T Consensus 118 ~m~~vvlcfTg~rkk--~e~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t~-~~~~rp~wv~~a 186 (850)
T KOG3524|consen 118 LMKDVVMCFTGERKK--KEELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALVG-VPTMRPDWVTEA 186 (850)
T ss_pred hhcCceeeeeccchh--hHHHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEeec-cceechHhhhhh
Confidence 678999999999863 348999999999999999888999999998888888888777 888887776543
No 310
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=40.92 E-value=50 Score=36.36 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=39.7
Q ss_pred cCCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcCCCCCHHHHHHHHH
Q psy11421 526 LGIRHVGETTAKELANY-FKNLECMFKATEEQLLNIPKIGSTTVKAFIK 573 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ 573 (687)
|.-+|+++..+++|.+. |.++..+..++..+|.++.|+++..|+.|.+
T Consensus 34 l~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~ 82 (344)
T PLN03187 34 LISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICE 82 (344)
T ss_pred HhhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHH
Confidence 33366778888877754 8899999999999999999999999888765
No 311
>KOG2875|consensus
Probab=40.56 E-value=32 Score=36.53 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=27.4
Q ss_pred HHHHHHhhcCC---hHHHHhcCH----HHHhcCCCCCHHHHHHHHH
Q psy11421 535 TAKELANYFKN---LECMFKATE----EQLLNIPKIGSTTVKAFIK 573 (687)
Q Consensus 535 ~Ak~La~~f~s---ld~l~~As~----eeL~~I~GIG~~~A~sI~~ 573 (687)
+|+.|.+..+. +..+..++. +.|..+||||+++|..|.-
T Consensus 191 ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~L 236 (323)
T KOG2875|consen 191 TARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICL 236 (323)
T ss_pred HHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhh
Confidence 55666666666 344444443 5689999999999998764
No 312
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.32 E-value=19 Score=38.26 Aligned_cols=22 Identities=27% Similarity=0.484 Sum_probs=17.5
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11421 417 ICPICNSKIIYI--ESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (687)
.||.||+++.+. .+...+||++
T Consensus 237 pC~~Cg~~I~~~~~~gR~ty~Cp~ 260 (269)
T PRK14811 237 PCPRCGTPIEKIVVGGRGTHFCPQ 260 (269)
T ss_pred CCCcCCCeeEEEEECCCCcEECCC
Confidence 599999998743 4667899976
No 313
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=40.32 E-value=49 Score=35.86 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHh-hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 529 RHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 529 p~vG~~~Ak~La~-~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.|+++..+++|.+ .|.|+..+..++..+|.++.|+++..|+.|.+-.
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~ 54 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAA 54 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 4577888887775 4899999999999999999999999999888744
No 314
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.26 E-value=18 Score=38.53 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=17.9
Q ss_pred CCCCCCCCcceee--cCceeEEecC
Q psy11421 416 NICPICNSKIIYI--ESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~--~~~~~~~C~n 438 (687)
+.||.||+++.+. .+...+||++
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~ 279 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPN 279 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCC
Confidence 3599999998743 5668899976
No 315
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=39.82 E-value=17 Score=26.34 Aligned_cols=26 Identities=23% Similarity=0.517 Sum_probs=16.5
Q ss_pred CCCCCCCCcceeecC-ceeEEecCCCCCCHH
Q psy11421 416 NICPICNSKIIYIES-NLIARCSGSWIECIA 445 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~-~~~~~C~n~~~~C~~ 445 (687)
..||.||+-|...++ .....|.+ |+.
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~----C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRT----CGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESS----SS-
T ss_pred eeCCCCCccceEcCCCccCcCCCC----CCC
Confidence 479999998875443 22237866 765
No 316
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.81 E-value=17 Score=28.52 Aligned_cols=22 Identities=27% Similarity=0.505 Sum_probs=14.8
Q ss_pred CCCCCCCCcceeecCceeEEecC
Q psy11421 416 NICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
..||.||+. ........+.|..
T Consensus 21 ~fCP~Cg~~-~m~~~~~r~~C~~ 42 (50)
T PRK00432 21 KFCPRCGSG-FMAEHLDRWHCGK 42 (50)
T ss_pred CcCcCCCcc-hheccCCcEECCC
Confidence 489999995 3223445778855
No 317
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.67 E-value=18 Score=38.33 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=17.5
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11421 417 ICPICNSKIIYI--ESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (687)
.||.||+++.+. .+...+||++
T Consensus 247 pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (272)
T TIGR00577 247 PCRRCGTPIEKIKVGGRGTHFCPQ 270 (272)
T ss_pred CCCCCCCeeEEEEECCCCCEECCC
Confidence 599999998753 4567889976
No 318
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=39.62 E-value=59 Score=28.33 Aligned_cols=27 Identities=30% Similarity=0.470 Sum_probs=12.1
Q ss_pred ccCCCCHHHHHHHHHC---CCCCChHHHhc
Q psy11421 461 NIIGLGKKMIEKLVNA---NIVVTAVDLYK 487 (687)
Q Consensus 461 ~I~GLG~k~i~~L~~~---g~I~~i~DL~~ 487 (687)
.|+|||++.+++++++ |--.|+.|++.
T Consensus 31 ~Ikglg~~~a~~I~~~R~~g~f~s~~df~~ 60 (90)
T PF14579_consen 31 AIKGLGEEVAEKIVEERENGPFKSLEDFIQ 60 (90)
T ss_dssp GSTTS-HHHHHHHHHHHHCSS-SSHHHHHH
T ss_pred hcCCCCHHHHHHHHHhHhcCCCCCHHHHHH
Confidence 4555555555555542 23344444443
No 319
>PRK12495 hypothetical protein; Provisional
Probab=39.51 E-value=15 Score=37.55 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=18.1
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
...+||.||.||-...| ..||+.
T Consensus 41 sa~hC~~CG~PIpa~pG--~~~Cp~ 63 (226)
T PRK12495 41 TNAHCDECGDPIFRHDG--QEFCPT 63 (226)
T ss_pred chhhcccccCcccCCCC--eeECCC
Confidence 45799999999986644 568977
No 320
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=39.50 E-value=36 Score=43.72 Aligned_cols=53 Identities=19% Similarity=0.322 Sum_probs=45.3
Q ss_pred cccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 460 MNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 460 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
++--+|.-.....|-.+| |.++.||...++++|+++.+||+||.+.|.+.+++
T Consensus 1316 ieeL~LSvRs~NcLk~ag-I~tvgdLv~~se~eLlkikN~GkKSl~EIkekL~e 1368 (1460)
T PRK14906 1316 YDDLGVSQRWANKFSEAG-IETVGDLIGKTEEDLLRIEGIGAKAIEELKDGLEA 1368 (1460)
T ss_pred hcccchhhhHHHHHHHcC-CCcHHHHhhCCHHHHhhccCCCcchHHHHHHHHHH
Confidence 344456677788888887 69999999999999999999999999999988876
No 321
>TIGR00612 ispG_gcpE 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase. Chlamydial members of the family have a long insert. The family is largely restricted to Bacteria, where it is widely but not universally distributed. No homology can be detected between the GcpE family and other proteins.
Probab=39.02 E-value=20 Score=39.14 Aligned_cols=14 Identities=36% Similarity=0.499 Sum_probs=12.8
Q ss_pred CCCCEEEEEecCCc
Q psy11421 380 QIGDTVVVHRSGNV 393 (687)
Q Consensus 380 ~iGd~V~v~raGdV 393 (687)
+||||+.|+.++|-
T Consensus 223 GIGDTIRVSLT~dP 236 (346)
T TIGR00612 223 GIGDTIRVSLTDDP 236 (346)
T ss_pred CCCCeEEEECCCCc
Confidence 58999999999995
No 322
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=38.56 E-value=29 Score=28.71 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=16.9
Q ss_pred hhhcccCccHHHHHHHHHHHH
Q psy11421 492 NLLRLDRVSNKLANNILLAIQ 512 (687)
Q Consensus 492 ~L~~l~gfG~Ksa~~Ll~~Ie 512 (687)
++..|||+|++.+++|.+-++
T Consensus 48 ~~~~l~gIG~~ia~kI~E~le 68 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEILE 68 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHHHC
Confidence 488899999999988876553
No 323
>PRK14976 5'-3' exonuclease; Provisional
Probab=38.31 E-value=58 Score=34.77 Aligned_cols=46 Identities=26% Similarity=0.406 Sum_probs=30.4
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
.-.|+|+||||+.+|+++- .|++++|. .+.+++ .+..++|.++.+.
T Consensus 193 ipGVpGIG~KtA~~LL~~~--gsle~i~~----~~~~~~---~~~~~~L~~~~~~ 238 (281)
T PRK14976 193 IKGVKGIGPKTAIKLLNKY--GNIENIYE----NIDKIK---KKIKNKLSEAKEK 238 (281)
T ss_pred CCCCCcccHHHHHHHHHHc--CCHHHHHH----hHHHHh---HHHHHHHHHhHHH
Confidence 3458999999999999864 37777775 222222 3556666666554
No 324
>PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=38.10 E-value=49 Score=35.43 Aligned_cols=61 Identities=10% Similarity=0.236 Sum_probs=44.4
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-++++++.++.+..+ .+..+.-.+.+|+++. .|.+.|+++||.. ++|+++++.+++.+.+.
T Consensus 13 i~~~ik~~v~~l~~~---g~~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~d~ 87 (282)
T PRK14182 13 VKGEVATEVRALAAR---GVQTGLTVVRVGDDPASAIYVRGKRKDCEEVGITSVEHHLPATTTQAELLALIARLNADP 87 (282)
T ss_pred HHHHHHHHHHHHHhC---CCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 356677777665322 3456788889998753 7999999999885 48999999997665554
No 325
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=38.00 E-value=24 Score=43.47 Aligned_cols=38 Identities=29% Similarity=0.425 Sum_probs=26.9
Q ss_pred EEEecCCccceeeccccCCC------------CCC-------CccccCCCCCCCCCC
Q psy11421 386 VVHRSGNVIPKITSSILSLR------------PND-------SKIFKIPNICPICNS 423 (687)
Q Consensus 386 ~v~raGdVIP~I~~vv~~~r------------~~~-------~~~~~~P~~CP~C~~ 423 (687)
.|.|+++|+|++........ .+. ...+..|..||.|++
T Consensus 235 iV~r~S~v~P~l~~a~f~C~~~~~~~~~~~~~C~~~~~~~~~~g~~~~P~~C~~C~~ 291 (915)
T PTZ00111 235 TVVRQTWIVPEITMACFRCRGQKKIGLNDYQPCTCEHYEYVIQGEVNEPLLCNECNS 291 (915)
T ss_pred EEEEccCcchhhEEEEEECCCCCcccCCccccCCccccccccCCcccCCCCCCCCCC
Confidence 36799999999988776543 111 124557999999996
No 326
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=37.87 E-value=30 Score=35.36 Aligned_cols=20 Identities=35% Similarity=0.566 Sum_probs=17.5
Q ss_pred HHHHh-cCCCCCHHHHHHHHH
Q psy11421 554 EEQLL-NIPKIGSTTVKAFIK 573 (687)
Q Consensus 554 ~eeL~-~I~GIG~~~A~sI~~ 573 (687)
.++|. +++|||+++|..+.-
T Consensus 117 R~~Ll~~lpGIG~KTAd~vL~ 137 (208)
T PRK01229 117 REFLVKNIKGIGYKEASHFLR 137 (208)
T ss_pred HHHHHHcCCCCcHHHHHHHHH
Confidence 47899 999999999999873
No 327
>PF01071 GARS_A: Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; InterPro: IPR020561 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the A-domain of the enzyme, and is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase.; PDB: 1GSO_A 3LP8_A 2IP4_A 1VKZ_A 2QK4_A 2XD4_A 2XCL_A 3MJF_A 2YRW_A 2YS6_A ....
Probab=37.68 E-value=63 Score=32.70 Aligned_cols=44 Identities=23% Similarity=0.540 Sum_probs=31.3
Q ss_pred HHHHHhcCCCCCCCceEeCCHHHHHHHHHHHHHhhcCCCCccceEEEEECChhh
Q psy11421 253 LNWYQKIGLSICGEYSVLSGVNKLIEFYKKINIKRFNLPYEIDGVVYKINCLST 306 (687)
Q Consensus 253 l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiVikv~~~~~ 306 (687)
=++|++.|.|+.. ...+++.+++.+|++.+ ..|+ +|||.|-++.
T Consensus 7 K~fm~~~~IPTa~-~~~f~~~~~A~~~l~~~-----~~p~----~ViKadGla~ 50 (194)
T PF01071_consen 7 KEFMKRYGIPTAK-YKVFTDYEEALEYLEEQ-----GYPY----VVIKADGLAA 50 (194)
T ss_dssp HHHHHHTT-SB---EEEESSHHHHHHHHHHH-----SSSE----EEEEESSSCT
T ss_pred HHHHHHcCCCCCC-eeEECCHHHHHHHHHhc-----CCCc----eEEccCCCCC
Confidence 3578899999985 56778999999999865 3333 8999987543
No 328
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=37.55 E-value=46 Score=35.86 Aligned_cols=48 Identities=29% Similarity=0.333 Sum_probs=37.0
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
.=+++|+|.++.++|...| |.++.||..+....|... || +.+..+++.
T Consensus 173 l~~l~gig~~~~~~L~~~G-i~ti~dl~~~~~~~L~~~--~g-~~~~~l~~~ 220 (334)
T cd03586 173 VRKIPGVGKVTAEKLKELG-IKTIGDLAKLDVELLKKL--FG-KSGRRLYEL 220 (334)
T ss_pred chhhCCcCHHHHHHHHHcC-CcCHHHHHcCCHHHHHHH--Hh-HHHHHHHHH
Confidence 4578999999999998877 689999999988888773 55 345444443
No 329
>PRK00024 hypothetical protein; Reviewed
Probab=37.46 E-value=52 Score=33.95 Aligned_cols=35 Identities=11% Similarity=0.160 Sum_probs=29.7
Q ss_pred CChHHHhcCChhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 480 VTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 480 ~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
.++.+++.++.++|.+++|+|+.+|..|...++..
T Consensus 55 gsL~~l~~as~~eL~~i~GIG~akA~~L~a~~El~ 89 (224)
T PRK00024 55 GSLRGLLDASLEELQSIKGIGPAKAAQLKAALELA 89 (224)
T ss_pred CCHHHHHhCCHHHHhhccCccHHHHHHHHHHHHHH
Confidence 37888999999999999999999998888777754
No 330
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=37.05 E-value=18 Score=27.45 Aligned_cols=14 Identities=36% Similarity=0.902 Sum_probs=11.8
Q ss_pred CCCCCCCCCcceee
Q psy11421 415 PNICPICNSKIIYI 428 (687)
Q Consensus 415 P~~CP~C~~~l~~~ 428 (687)
|..||.||+.|...
T Consensus 2 ~~~C~~Cg~~l~~i 15 (47)
T PF13005_consen 2 PRACPDCGGELKEI 15 (47)
T ss_pred CCcCCCCCceeeEC
Confidence 67899999998754
No 331
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=36.90 E-value=22 Score=30.79 Aligned_cols=40 Identities=18% Similarity=0.207 Sum_probs=25.0
Q ss_pred cCCCCCCHHHHHHHHhhcCChHHHHhcCHHHHhcCCCCCHHH
Q psy11421 526 LGIRHVGETTAKELANYFKNLECMFKATEEQLLNIPKIGSTT 567 (687)
Q Consensus 526 LGIp~vG~~~Ak~La~~f~sld~l~~As~eeL~~I~GIG~~~ 567 (687)
+.|||||..+|-.|+..+++++.+.+ ..+|.+.-|+.+..
T Consensus 5 ~sipGig~~~a~~llaeigd~~rF~~--~~~l~~~~Gl~P~~ 44 (87)
T PF02371_consen 5 TSIPGIGPITAATLLAEIGDISRFKS--AKQLASYAGLAPRP 44 (87)
T ss_pred cCCCCccHHHHHHHHHHHcCchhccc--chhhhhcccccccc
Confidence 35788888777777777776655543 34566655554443
No 332
>PRK14185 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=36.66 E-value=44 Score=35.95 Aligned_cols=60 Identities=13% Similarity=0.212 Sum_probs=43.4
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCC
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTE 684 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~ 684 (687)
|+++++.++.+..+. .+..+.-.+.+|+++. .|.+.|+++||.. +++++|++.+.+.+.+
T Consensus 14 ~~~l~~~v~~l~~~~--g~~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D 87 (293)
T PRK14185 14 KQEIAAEVAEIVAKG--GKRPHLAAILVGHDGGSETYVANKVKACEECGFKSSLIRYESDVTEEELLAKVRELNQD 87 (293)
T ss_pred HHHHHHHHHHHHhcc--CCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 566777777653332 2345777888898743 7999999999987 6789999988765544
No 333
>PF10772 DUF2597: Protein of unknown function (DUF2597); InterPro: IPR019708 This entry is represented by Bacteriophage HP1, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents proteins with unknown function and is restricted to Proteobacteria. One of the proteins is annotated to a predictive tail tube protein.
Probab=36.66 E-value=1.1e+02 Score=28.84 Aligned_cols=54 Identities=22% Similarity=0.203 Sum_probs=37.2
Q ss_pred chhhhhhh--hhccCCcccccCCCCceEEEEEEEEeehhhHHHHHHHHHHcCCCCCCChhhhHHhHhhhcCcc
Q psy11421 153 ENITTNIH--IIHKIPLVLNIKYPPELLEVRCEVLIYKKDFIKLNKYRYHLGLKKFTNPRNAAAGILRQLNPK 223 (687)
Q Consensus 153 eDvT~n~~--~i~~iP~~l~~~~~~~~~evRGEi~~~~~~F~~~n~~~~~~g~~~f~NpRN~aaG~lr~~~~~ 223 (687)
-|||.|-. +-++||.-. ..+.++--||+=+.-.+|..+.+.. ..|||-|.+.|-
T Consensus 19 l~ItDns~vaqtrGvPdG~----v~GdV~aegEiEldt~nf~~l~~aA-------------~~AGSwR~i~~~ 74 (134)
T PF10772_consen 19 LDITDNSAVAQTRGVPDGY----VDGDVSAEGEIELDTKNFNLLSEAA-------------KSAGSWRGIPPF 74 (134)
T ss_pred EEeecCceeeecCCCCCCc----cccceeeeEEEEEcHHHHHHHHHHH-------------HhcCCccCCCcc
Confidence 34555422 224567533 4578999999999999999887652 268888887764
No 334
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=36.63 E-value=32 Score=25.58 Aligned_cols=22 Identities=23% Similarity=0.576 Sum_probs=13.5
Q ss_pred CCCCCCCcceee--cCceeEEecC
Q psy11421 417 ICPICNSKIIYI--ESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~--~~~~~~~C~n 438 (687)
+||.|+..|+.. .+-...+|++
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~ 24 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPS 24 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCC
Confidence 599999877632 2334445754
No 335
>KOG2043|consensus
Probab=36.55 E-value=45 Score=41.28 Aligned_cols=67 Identities=18% Similarity=0.184 Sum_probs=55.6
Q ss_pred eEEEEEcCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHh
Q psy11421 610 KIFVFTGSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVK 679 (687)
Q Consensus 610 ~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~ 679 (687)
-.+.|+|... ..-++..++.+|+.+.+|.+.-|++++.--.-..|+-.|..+|++|+++.++...+.
T Consensus 660 ~~~lfs~~~~---~~~~k~~~k~lg~s~~ss~~e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k 726 (896)
T KOG2043|consen 660 IEVLFSDKND---GKNYKLAKKFLGGSVASSDSEATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLK 726 (896)
T ss_pred eeeeeeeccC---chhhhhHHhhccceeecccccceeeeehhhhccHHHHhhhccCCcccchHHHHHHhh
Confidence 3588999874 566888999999999999998888777633445899999999999999999988764
No 336
>PHA00626 hypothetical protein
Probab=36.52 E-value=27 Score=28.13 Aligned_cols=36 Identities=28% Similarity=0.425 Sum_probs=21.1
Q ss_pred CCCCCCCc-ceeec---C-ceeEEecCCCCCCHHHHHhhhhhcccccccccCC
Q psy11421 417 ICPICNSK-IIYIE---S-NLIARCSGSWIECIAQRKAGLQHFSSRKAMNIIG 464 (687)
Q Consensus 417 ~CP~C~~~-l~~~~---~-~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~I~G 464 (687)
.||.|||. +++.. + ...+.|.. | -|+++++++.-.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkd----C--------GY~ft~~~~~~~~ 42 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCD----C--------GYNDSKDAFGERG 42 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCC----C--------CCeechhhhhhcc
Confidence 69999994 44321 1 23344533 4 5788887765444
No 337
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=36.51 E-value=67 Score=34.18 Aligned_cols=53 Identities=19% Similarity=0.249 Sum_probs=35.0
Q ss_pred cccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHH
Q psy11421 458 KAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 458 ~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
..+.+||+|++.+.+|-..| |.++.||..++.+++..+=+..+..++.+++.+
T Consensus 149 ~L~Qlp~i~~~~~~~l~~~~-i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~ 201 (314)
T PF02889_consen 149 PLLQLPHIGEESLKKLEKRG-IKTLQDLRDLSPEELEELLNRNPPFGKEILEVA 201 (314)
T ss_dssp GGGGSTT--HHHHHHHHHTT---SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHH
T ss_pred hhhcCCCCCHHHHHHHhccC-CCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHH
Confidence 57889999999999999977 679999999988777766444444455444443
No 338
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=36.24 E-value=60 Score=29.44 Aligned_cols=72 Identities=14% Similarity=0.131 Sum_probs=38.5
Q ss_pred CCCceEeecCCCceeeEE-------EEEEEEeecCcceeeeEEEEE-EEEECC----EEEEEecCCCHHHHHhcCCCCCC
Q psy11421 316 APRFALAYKFLSKEALTK-------IKAINIQIGRTGIITPVALLK-PVLIDG----ITITRATLHNESEIYRKNIQIGD 383 (687)
Q Consensus 316 ~PrwaiA~Kf~~~~~~T~-------v~~I~~qvGRTG~iTPvA~le-PV~l~G----~tVsraTLhN~~~i~~~~i~iGd 383 (687)
.|.-++=|.||.....|- =+||.| +.+.|+|+=+.... |=...- ..+..|==-|++.++++||++||
T Consensus 24 ~~~~gMLF~~~~~~~~~~~M~~~~~pLDi~f-ld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~~~~~~i~~Gd 102 (108)
T PF02643_consen 24 PPDEGMLFIFPCPSVHTFWMKNTRFPLDIAF-LDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGWFEKLGIKVGD 102 (108)
T ss_dssp -TTEEEEEEECCEEEEEE--TT--S-EEEEE-E-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTHHHHHT--TT-
T ss_pred CCCcEEEEecCCCCeEEEEEEccceeEEEEE-ECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCchhhcCCCCCC
Confidence 333456666655444331 134444 46788888888887 444322 22333434578999999999999
Q ss_pred EEEEE
Q psy11421 384 TVVVH 388 (687)
Q Consensus 384 ~V~v~ 388 (687)
+|.+.
T Consensus 103 ~v~~~ 107 (108)
T PF02643_consen 103 RVRIE 107 (108)
T ss_dssp EEE--
T ss_pred EEEec
Confidence 99874
No 339
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=36.15 E-value=21 Score=26.14 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=16.3
Q ss_pred CCCCCCCCcceee-----cCceeEEecC
Q psy11421 416 NICPICNSKIIYI-----ESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~-----~~~~~~~C~n 438 (687)
..||.|++..... .++..++|++
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~ 30 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPK 30 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCC
Confidence 3699999976533 2467889976
No 340
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=36.11 E-value=26 Score=31.83 Aligned_cols=14 Identities=36% Similarity=0.916 Sum_probs=11.4
Q ss_pred CCCCCCCCCcceee
Q psy11421 415 PNICPICNSKIIYI 428 (687)
Q Consensus 415 P~~CP~C~~~l~~~ 428 (687)
|..||.||.+.+..
T Consensus 2 p~~CpYCg~~~~l~ 15 (102)
T PF11672_consen 2 PIICPYCGGPAELV 15 (102)
T ss_pred CcccCCCCCeeEEc
Confidence 78999999987644
No 341
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=35.97 E-value=62 Score=32.74 Aligned_cols=53 Identities=21% Similarity=0.308 Sum_probs=39.7
Q ss_pred cCCCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCCccHHHHHHcCCeEEeHHHHHHHHhcc
Q psy11421 616 GSLYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPGKKLEKAIKLNIKILDEKNFVKIVKGF 681 (687)
Q Consensus 616 G~l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g~Kl~kA~~lgI~Ii~E~~f~~~l~~~ 681 (687)
|.|++.+-=++--++..+||.|++| .. .=..-|++||++.++...|..||.+.
T Consensus 157 GiLDSapDlDvLLLAkELdaavVss------------D~-Gir~WAe~LGlrfv~a~~Fp~ml~ey 209 (221)
T COG1458 157 GILDSAPDLDVLLLAKELDAAVVSS------------DE-GIRTWAEKLGLRFVDAFKFPEMLEEY 209 (221)
T ss_pred ccccccchhHHHHHHHHhCceEEec------------ch-hHHHHHHHhCCeeeCHhhhHHHHHHH
Confidence 4465555556677888899888766 22 33457899999999999999999753
No 342
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=35.65 E-value=1.2e+02 Score=30.48 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=23.8
Q ss_pred hhhhhcccCccHHHHHHHHHHHHHcccCCHHHHHHHc
Q psy11421 490 FKNLLRLDRVSNKLANNILLAIQKSKLTTFSRFIYAL 526 (687)
Q Consensus 490 ~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aL 526 (687)
-+.|.-|||+|+|...+|++.-++..=.+|..+-.-.
T Consensus 129 LH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~Rv 165 (202)
T COG1491 129 LHQLELLPGIGKKTMWAILEERKKKPFESFEDIKERV 165 (202)
T ss_pred HHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHHHh
Confidence 4678888888888888888765543223444444444
No 343
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=35.42 E-value=30 Score=28.33 Aligned_cols=22 Identities=27% Similarity=0.773 Sum_probs=19.5
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.|..+|...+....++|..
T Consensus 10 aCP~~kg~L~~~~~~~~L~c~~ 31 (60)
T COG2835 10 ACPVCKGPLVYDEEKQELICPR 31 (60)
T ss_pred eccCcCCcceEeccCCEEEecc
Confidence 6999999999888888899976
No 344
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=35.42 E-value=13 Score=30.03 Aligned_cols=25 Identities=24% Similarity=0.400 Sum_probs=17.8
Q ss_pred CCCCCCCCCCcceeecCceeEEecCCCCCCHH
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSGSWIECIA 445 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~ 445 (687)
+-.|||.||.++.. | ..+|+. . |.+
T Consensus 7 PH~HC~VCg~aIp~--d--e~~CSe--~-C~e 31 (64)
T COG4068 7 PHRHCVVCGKAIPP--D--EQVCSE--E-CGE 31 (64)
T ss_pred CCccccccCCcCCC--c--cchHHH--H-HHH
Confidence 34799999999873 3 347876 3 873
No 345
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=35.12 E-value=23 Score=29.11 Aligned_cols=15 Identities=33% Similarity=0.678 Sum_probs=11.5
Q ss_pred CCCCCCCc-ceeecCc
Q psy11421 417 ICPICNSK-IIYIESN 431 (687)
Q Consensus 417 ~CP~C~~~-l~~~~~~ 431 (687)
.||.|||+ +..++.+
T Consensus 20 ~CP~Cgs~~~te~W~G 35 (64)
T COG2093 20 ICPVCGSTDLTEEWFG 35 (64)
T ss_pred cCCCCCCcccchhhcc
Confidence 49999997 7666654
No 346
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=34.46 E-value=36 Score=28.94 Aligned_cols=41 Identities=17% Similarity=0.402 Sum_probs=26.7
Q ss_pred CCCCCCCcceeec------C--ceeEEecCCCCCCHHHH--Hhhhhhcccccc
Q psy11421 417 ICPICNSKIIYIE------S--NLIARCSGSWIECIAQR--KAGLQHFSSRKA 459 (687)
Q Consensus 417 ~CP~C~~~l~~~~------~--~~~~~C~n~~~~C~~q~--~~~i~~F~sr~~ 459 (687)
.||.||++..... + +....|.|. . |-..+ ...+.|+.|+.+
T Consensus 3 ~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~-e-Cg~tF~t~es~s~tis~p~ 53 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITDTTKERYHQCQNV-N-CSATFITYESVQRYIVKPG 53 (72)
T ss_pred cCCCCCCccEEEEChhcChhhheeeeecCCC-C-CCCEEEEEEEEEEEEcCCC
Confidence 6999999764321 1 345669995 6 98766 346667776644
No 347
>PRK14188 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=34.21 E-value=71 Score=34.46 Aligned_cols=61 Identities=8% Similarity=0.194 Sum_probs=43.7
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCe--E------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK--I------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~--I------i~E~~f~~~l~~~s~~~ 685 (687)
++++++.++.+..+. .+..+.-.+.+|+++. .|.+.|+++||. + +++++|++.+...+.+.
T Consensus 15 ~~~i~~~v~~l~~~~--g~~p~La~i~vg~~~~s~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~i~~lN~d~ 89 (296)
T PRK14188 15 RATVAAEVARLKAAH--GVTPGLAVVLVGEDPASQVYVRSKGKQTKEAGMASFEHKLPADTSQAELLALIARLNADP 89 (296)
T ss_pred HHHHHHHHHHHHHcc--CCCCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 566777777653211 2456788888998753 699999999996 4 48999999987665543
No 348
>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.
Probab=34.14 E-value=64 Score=27.96 Aligned_cols=57 Identities=18% Similarity=0.243 Sum_probs=33.2
Q ss_pred ChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhhhhhhh
Q psy11421 97 SDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITTNIHII 162 (687)
Q Consensus 97 ~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~n~~~i 162 (687)
+.+++......+...+-...+......-|.+|+.|++ |.-|+++ = .|.+-..-+...
T Consensus 8 ~~~~i~~l~~~y~~~~~~~~~p~~~f~aK~~~~tIt~-Y~SGKV~---F-----QG~~Ae~~A~~~ 64 (81)
T PF11858_consen 8 TSEQIEKLKKYYKPYLTSSKPPYAVFQAKYNGVTITA-YKSGKVV---F-----QGKNAEQEAAKW 64 (81)
T ss_dssp -HHHHHHHHHHSTT-B-SS--TTEEEEEEETTEEEEE-ETTSEEE---E-----ESTTHHHHHHTT
T ss_pred CHHHHHHHHHHHHHhcccCCCCCEEEEEeCCCeEEEE-EeCCeEE---E-----ECCCHHHHHHHh
Confidence 4456666655553322111234577889999999987 9999864 1 355555554443
No 349
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=34.07 E-value=36 Score=27.26 Aligned_cols=25 Identities=32% Similarity=0.770 Sum_probs=16.1
Q ss_pred CCCCCCCcceeecC--c------eeEEecCCCCCCHH
Q psy11421 417 ICPICNSKIIYIES--N------LIARCSGSWIECIA 445 (687)
Q Consensus 417 ~CP~C~~~l~~~~~--~------~~~~C~n~~~~C~~ 445 (687)
-||.||++-+.... . ..++|.+ |-+
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~----Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTD----CGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCC----CCC
Confidence 39999987553321 1 5677876 755
No 350
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=33.91 E-value=28 Score=37.90 Aligned_cols=73 Identities=19% Similarity=0.355 Sum_probs=39.9
Q ss_pred CCCCEEEEEecCCccceeecccc--------CCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhh
Q psy11421 380 QIGDTVVVHRSGNVIPKITSSIL--------SLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGL 451 (687)
Q Consensus 380 ~iGd~V~v~raGdVIP~I~~vv~--------~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i 451 (687)
+|||||.|+.++|- +.+|.. ..|... ..--.||.||-.... ++ . --.|..+++
T Consensus 225 GIGDTIRVSLt~~P---~~EV~V~~eILqslglR~~~----v~~iaCP~CGR~~~d------v~-----~-~~~~~~~~~ 285 (361)
T COG0821 225 GIGDTIRVSLTADP---VEEVKVAQEILQSLGLRSRG----VEVIACPTCGRTEFD------VI-----Q-TLNEVEQRL 285 (361)
T ss_pred cCCceEEEecCCCc---hhhhHHHHHHHHHhCccccC----ceEEECCCCCceeeh------HH-----H-HHHHHHHHh
Confidence 57999999999997 333321 111111 112369999964321 10 1 224566666
Q ss_pred hhcccccccc-------cCCCCHHHHHHH
Q psy11421 452 QHFSSRKAMN-------IIGLGKKMIEKL 473 (687)
Q Consensus 452 ~~F~sr~~l~-------I~GLG~k~i~~L 473 (687)
.|--. -|+ +.|.||..-..+
T Consensus 286 ~~~~~--pl~VAVMGCVVNGPGEak~Adi 312 (361)
T COG0821 286 EHLKT--PLKVAVMGCVVNGPGEAKHADI 312 (361)
T ss_pred hccCC--CceEEEEEeEecCCcchhccce
Confidence 66432 144 467888665443
No 351
>PRK14166 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=33.89 E-value=63 Score=34.64 Aligned_cols=60 Identities=15% Similarity=0.207 Sum_probs=43.4
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCe---E-----EeHHHHHHHHhcccCC
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK---I-----LDEKNFVKIVKGFSTE 684 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~---I-----i~E~~f~~~l~~~s~~ 684 (687)
-++++++.++.+-.+ .++.+.-.+.+|+++. .|.+.|+++||. + ++|++|++.+...+.+
T Consensus 13 i~~~l~~~v~~l~~~---g~~P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~D 86 (282)
T PRK14166 13 IKEELKEKNQFLKSK---GIESCLAVILVGDNPASQTYVKSKAKACEECGIKSLVYHLNENTTQNELLALINTLNHD 86 (282)
T ss_pred HHHHHHHHHHHHHhC---CCCceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 356677777765322 3456788888998743 799999999988 2 5788999998765544
No 352
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=33.88 E-value=28 Score=28.60 Aligned_cols=24 Identities=21% Similarity=0.499 Sum_probs=18.1
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
...||.||...........+.|++
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~ 51 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPN 51 (69)
T ss_pred ccCccCcccccccccccceEEcCC
Confidence 457999999877634557788976
No 353
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=33.80 E-value=27 Score=37.19 Aligned_cols=23 Identities=22% Similarity=0.352 Sum_probs=18.2
Q ss_pred CCCCCCCCcceee--cCceeEEecC
Q psy11421 416 NICPICNSKIIYI--ESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~--~~~~~~~C~n 438 (687)
+-|+.||+++++. .+-..+||++
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~ 270 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPV 270 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCC
Confidence 3599999998754 5667899977
No 354
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=33.78 E-value=34 Score=28.88 Aligned_cols=27 Identities=19% Similarity=0.442 Sum_probs=16.2
Q ss_pred ccCCCCCCCCCCcceee--cCceeEEecC
Q psy11421 412 FKIPNICPICNSKIIYI--ESNLIARCSG 438 (687)
Q Consensus 412 ~~~P~~CP~C~~~l~~~--~~~~~~~C~n 438 (687)
|..-..||-|+.+|.+. =|-+++||.+
T Consensus 27 ~~~~a~CPdC~~~Le~LkACGAvdYFC~~ 55 (70)
T PF07191_consen 27 YKKEAFCPDCGQPLEVLKACGAVDYFCNH 55 (70)
T ss_dssp EEEEEE-TTT-SB-EEEEETTEEEEE-TT
T ss_pred ceecccCCCcccHHHHHHHhcccceeecc
Confidence 44445799999998754 3568899976
No 355
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=33.75 E-value=70 Score=34.24 Aligned_cols=58 Identities=10% Similarity=0.172 Sum_probs=44.0
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-++++++.++.+| ++.+.-.+.+|+++. .|.+.|+++||.. ++|++|++.+.....+.
T Consensus 12 i~~~~~~~v~~lg------~~P~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 83 (279)
T PRK14178 12 RLELLKEEIIESG------LYPRLATVIVGDDPASQMYVRMKHRACERVGIGSVGIELPGDATTRTVLERIRRLNEDP 83 (279)
T ss_pred HHHHHHHHHHHhC------CCCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 3677888888873 445777888998754 7999999999873 47889999987655443
No 356
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family. The member of this family from Deinococcus radiodurans, a species that withstands and recovers from extensive radiation or dessication damage, is an apparent RNA ligase. It repairs RNA stand breaks in nicked DNA:RNA and RNA:RNA but not DNA:DNA duplexes. It has adenylyltransferase activity associated with the C-terminal domain. Related proteins also in this family are found in Streptomyces avermitilis MA-4680 and in bacteriophage 44RR2.8t. The phage example is unsurprising since one mechanism of host cell defense against phage is cleavage and inactivation of certain tRNA molecules. A fungal sequence from Neurospora crassa scores between trusted and noise cutofffs and may be similar in function.
Probab=33.69 E-value=70 Score=35.24 Aligned_cols=68 Identities=10% Similarity=0.023 Sum_probs=38.0
Q ss_pred CeeEEEEEccceeEEEEEEe--CCEEEEEEecCCCCccchhhh---h-----hhhhccCCcccccCCCCceEEEEEEEEe
Q psy11421 117 NIEYIAELKFDGIAVNLRYE--YGYLKQASTRGDGNIGENITT---N-----IHIIHKIPLVLNIKYPPELLEVRCEVLI 186 (687)
Q Consensus 117 ~~~~~~e~KiDGlsi~l~Y~--~G~l~~a~TRGdG~~GeDvT~---n-----~~~i~~iP~~l~~~~~~~~~evRGEi~~ 186 (687)
...|.++.|+||.|+++.|. +|.+- ....|=....-++-. | ++. .+||..|........+.|.||+|=
T Consensus 158 ~~~~~~TeKldGss~tv~~~~~~~~~~-~~~~Gvcsr~~~l~~~~~~~~W~~a~~-~~i~~~l~~~~~~~~vaiqGEl~G 235 (341)
T TIGR02306 158 GEKVAKTEKLHGTSITVAWVTDEERFL-VLSKGVASRNLVLRENADNKYWKAVEN-YQIVDRAKAAELRMSVAIFGEVMG 235 (341)
T ss_pred CceEEEEEEecceeEEEEEecCCcccc-cccceeecCCcccccCCCchhHHHHHh-cChHHHHhhcccCceEEEEEEEeC
Confidence 35799999999999999874 33221 111221111222111 1 111 346766652113457999999993
No 357
>smart00475 53EXOc 5'-3' exonuclease.
Probab=33.54 E-value=58 Score=34.34 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=20.8
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (687)
.-.|+|+||||+.+|+++-. |++.+|.
T Consensus 188 ipGV~GIG~KtA~~Ll~~yg--sle~i~~ 214 (259)
T smart00475 188 IPGVPGIGEKTAAKLLKEFG--SLENILE 214 (259)
T ss_pred CCCCCCCCHHHHHHHHHHhC--CHHHHHH
Confidence 44579999999999998642 7777775
No 358
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=33.34 E-value=21 Score=35.46 Aligned_cols=12 Identities=42% Similarity=1.074 Sum_probs=10.1
Q ss_pred CCCCCCCCccee
Q psy11421 416 NICPICNSKIIY 427 (687)
Q Consensus 416 ~~CP~C~~~l~~ 427 (687)
+.||+||+++.+
T Consensus 154 ~~Cp~CG~~~~~ 165 (177)
T COG1439 154 DFCPICGSPLKR 165 (177)
T ss_pred CcCCCCCCceEE
Confidence 589999998764
No 359
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=33.25 E-value=74 Score=34.15 Aligned_cols=61 Identities=15% Similarity=0.207 Sum_probs=43.9
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-|+++++.++.+-.+ .++.+.-.+.+|+++. .|.+.|+++||.. +++++|++.+++...+.
T Consensus 15 i~~~lk~~i~~l~~~---g~~p~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~d~ 89 (285)
T PRK14189 15 LRAEAAQRAAALTAR---GHQPGLAVILVGDNPASQVYVRNKVKACEDNGFHSLKDRYPADLSEAELLARIDELNRDP 89 (285)
T ss_pred HHHHHHHHHHHHHhC---CCCCeEEEEEeCCCchHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence 366777777765322 2456788888998753 7999999999875 45899999987654443
No 360
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=33.14 E-value=23 Score=25.19 Aligned_cols=11 Identities=36% Similarity=1.238 Sum_probs=9.1
Q ss_pred CCCCCCCCCCc
Q psy11421 414 IPNICPICNSK 424 (687)
Q Consensus 414 ~P~~CP~C~~~ 424 (687)
.|..||.||.+
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 57799999974
No 361
>PRK14193 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=33.14 E-value=65 Score=34.56 Aligned_cols=60 Identities=13% Similarity=0.271 Sum_probs=42.6
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
++++++.++.+-.+ .+..+.-.+.+|+++. .|.+.|+++||.. ++|++|++.+.....+.
T Consensus 16 ~~~l~~~v~~l~~~---g~~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~D~ 89 (284)
T PRK14193 16 KADLAERVAALKEK---GITPGLGTVLVGDDPGSQAYVRGKHRDCAEVGITSIRRDLPADATQEELNAVIDELNADP 89 (284)
T ss_pred HHHHHHHHHHHHhC---CCCceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 56666666665322 2456777888998743 7999999999883 45899999987655443
No 362
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=33.01 E-value=38 Score=24.80 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=16.1
Q ss_pred CCCCCCCCCcc-eeec-----CceeEEecC
Q psy11421 415 PNICPICNSKI-IYIE-----SNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l-~~~~-----~~~~~~C~n 438 (687)
.-+||.|++.- +... |...++|..
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~ 34 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKD 34 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCc
Confidence 45899999976 5432 346777854
No 363
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=32.85 E-value=27 Score=32.21 Aligned_cols=58 Identities=24% Similarity=0.393 Sum_probs=39.2
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccC
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFST 683 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~ 683 (687)
++++++.++.+..+ .++.+.-.+.+|++++ .|.+.|+++||.. +++++|++.+...+.
T Consensus 13 ~~~l~~~i~~l~~~---~~~P~Laii~vg~d~~S~~Y~~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~i~~lN~ 84 (117)
T PF00763_consen 13 KEELKEEIEKLKEK---GITPKLAIILVGDDPASISYVRSKQKAAEKLGIEFELIELPEDISEEELLELIEKLNE 84 (117)
T ss_dssp HHHHHHHHHHHHHC---T---EEEEEEES--HHHHHHHHHHHHHHHHHT-EEEEEEE-TTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhc---CCCcEEEEEecCCChhHHHHHHHHHHHHHHcCCceEEEECCCCcCHHHHHHHHHHHhC
Confidence 56677777776554 5666888889998753 7889999999873 489999998875443
No 364
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=32.59 E-value=27 Score=25.45 Aligned_cols=14 Identities=21% Similarity=0.532 Sum_probs=10.3
Q ss_pred CCCCCCCCCCccee
Q psy11421 414 IPNICPICNSKIIY 427 (687)
Q Consensus 414 ~P~~CP~C~~~l~~ 427 (687)
.+..||.||+++.+
T Consensus 25 ~~~~CP~Cg~~~~r 38 (41)
T smart00834 25 PLATCPECGGDVRR 38 (41)
T ss_pred CCCCCCCCCCccee
Confidence 35679999996543
No 365
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=32.55 E-value=29 Score=41.26 Aligned_cols=27 Identities=26% Similarity=0.613 Sum_probs=19.5
Q ss_pred CCCCCCCCccee--ecCceeEEecCCCCCC
Q psy11421 416 NICPICNSKIIY--IESNLIARCSGSWIEC 443 (687)
Q Consensus 416 ~~CP~C~~~l~~--~~~~~~~~C~n~~~~C 443 (687)
..||.||..++. ...+.++.|.|.+. |
T Consensus 590 ~~CPkCg~~l~~~~~k~g~f~gCs~yp~-C 618 (618)
T TIGR01057 590 GKCPKCGGKLVSKYAKKGRFVGCSNYPE-C 618 (618)
T ss_pred CCCCcCCCeeeeeecCCccEEECCCCCC-C
Confidence 469999998763 23356799999645 7
No 366
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=32.54 E-value=33 Score=25.35 Aligned_cols=31 Identities=29% Similarity=0.597 Sum_probs=21.1
Q ss_pred CCCCCCcce------eecCceeEEecCCCCCCHHHHHhhh
Q psy11421 418 CPICNSKII------YIESNLIARCSGSWIECIAQRKAGL 451 (687)
Q Consensus 418 CP~C~~~l~------~~~~~~~~~C~n~~~~C~~q~~~~i 451 (687)
|-.||.++. +..+...++|-+ . |..|+.+++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~--t-C~~~fk~k~ 37 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCP--T-CLSQFKKKL 37 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECH--H-HHHHHHhhC
Confidence 455666443 335567888988 4 999998764
No 367
>PRK14181 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=32.11 E-value=84 Score=33.76 Aligned_cols=58 Identities=14% Similarity=0.195 Sum_probs=44.6
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-++++++.++.+| .+.+.-.+.+|+++. .|.+.|+++||.. ++++++++.+.+.+.+.
T Consensus 12 i~~~~k~~v~~l~------~~P~LaiI~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~d~ 83 (287)
T PRK14181 12 ILATIKENISASS------TAPGLAVVLIGNDPASEVYVGMKVKKATDLGMVSKAHRLPSDATLSDILKLIHRLNNDP 83 (287)
T ss_pred HHHHHHHHHHHhC------CCCcEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 4678888888884 346778888898743 7999999999874 47889999987665543
No 368
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=32.11 E-value=87 Score=29.68 Aligned_cols=65 Identities=26% Similarity=0.209 Sum_probs=45.4
Q ss_pred HHHhhcCCCCccceEEEEECChhhhhhhCCCCCCCCceEeecCCCceeeEEEEEEEEeecCcceeeeEEEEEEEEECCEE
Q psy11421 283 INIKRFNLPYEIDGVVYKINCLSTQKKLGFTSRAPRFALAYKFLSKEALTKIKAINIQIGRTGIITPVALLKPVLIDGIT 362 (687)
Q Consensus 283 ~~~~r~~l~y~iDGiVikv~~~~~~~~lG~ts~~PrwaiA~Kf~~~~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~t 362 (687)
+..++..+.-...|.|+++-.-+. ..|+|-|+-+-. + +|.|
T Consensus 30 f~~~qs~~qv~g~G~V~~vLpdd~-----~GsrHQ~Fiv~l------------------~----------------~g~t 70 (131)
T PF11948_consen 30 FENQQSDVQVSGCGTVVKVLPDDN-----KGSRHQRFIVRL------------------S----------------SGQT 70 (131)
T ss_pred HHhhccCeeEeccEEEEEECcccC-----CCCcceEEEEEe------------------C----------------CCCE
Confidence 445677777777999999965322 245566664322 1 2666
Q ss_pred EEEecCCCHHHHHhcC-CCCCCEEEEE
Q psy11421 363 ITRATLHNESEIYRKN-IQIGDTVVVH 388 (687)
Q Consensus 363 VsraTLhN~~~i~~~~-i~iGd~V~v~ 388 (687)
|-=| ||.+..-+.. |+.||+|.+.
T Consensus 71 llIa--hNIDlaprip~l~~GD~V~f~ 95 (131)
T PF11948_consen 71 LLIA--HNIDLAPRIPWLQKGDQVEFY 95 (131)
T ss_pred EEEE--eccCccccCcCcCCCCEEEEE
Confidence 6666 9999998886 9999999875
No 369
>PRK07945 hypothetical protein; Provisional
Probab=32.06 E-value=70 Score=35.01 Aligned_cols=46 Identities=15% Similarity=0.173 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHHHHhhc--CChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 527 GIRHVGETTAKELANYF--KNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 527 GIp~vG~~~Ak~La~~f--~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.|||||+.+|.+|.+.. |+++.+...- .+.... | |+.++..|+-=+
T Consensus 53 ~~~giG~~~a~~i~e~~~tg~~~~l~~l~-~~~~~~-~-g~~l~~~~~~D~ 100 (335)
T PRK07945 53 SLPGIGPKTAKVIAQALAGRVPDYLAELR-ADAEPL-G-GGALRAALRGDL 100 (335)
T ss_pred cCCCcCHHHHHHHHHHHhcCCHHHHHHHH-HhhcCC-c-cHHHHHHHhhhc
Confidence 68999999888877643 4444333211 111112 6 888888777644
No 370
>PF09511 RNA_lig_T4_1: RNA ligase; InterPro: IPR019039 Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity []. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. Please see the following relevant references: [, ]. ; PDB: 2C5U_B.
Probab=32.04 E-value=31 Score=35.32 Aligned_cols=61 Identities=16% Similarity=0.082 Sum_probs=31.1
Q ss_pred ceeccccccCCCCCCChHHHHHHHHHHHHhhccCCCeeEEEEEccceeEEEEEE-eCCEEEEEEecC
Q psy11421 82 YVHHTFKMMSLDNGFSDEDVIIFNKRITNELKLTKNIEYIAELKFDGIAVNLRY-EYGYLKQASTRG 147 (687)
Q Consensus 82 kv~H~~pMlSL~k~~~~~el~~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y-~~G~l~~a~TRG 147 (687)
...+.+..-+++|.|+..|...+...- +. .....+.+..|+||.=|++.| .+|.+ ...|+|
T Consensus 13 ~~~~~Iv~R~~~KFFN~~E~~~t~~~~---l~-~~~~p~~v~~K~dGsli~~~~~~~g~~-~~~SK~ 74 (221)
T PF09511_consen 13 DKTGRIVARPFDKFFNIGENPETKWDA---LE-KLQTPVEVYEKEDGSLIFIPYLDDGEL-IVASKG 74 (221)
T ss_dssp TEEEEEEE-------BTTSSGGGSS-----GG--G--EEEEEEE--SEEE-EEEEETTEE-EEEETT
T ss_pred CCCCeEEECCCCCcccCCCcccccccc---cc-cccccEEEEEecCcEEEEEeeecCCeE-EEEecC
Confidence 346777778899999999987654321 11 012389999999995552444 67876 566766
No 371
>smart00746 TRASH metallochaperone-like domain.
Probab=31.90 E-value=42 Score=22.36 Aligned_cols=27 Identities=22% Similarity=0.640 Sum_probs=15.9
Q ss_pred CCCCCCcce--------eecCceeEEecCCCCCCHHHH
Q psy11421 418 CPICNSKII--------YIESNLIARCSGSWIECIAQR 447 (687)
Q Consensus 418 CP~C~~~l~--------~~~~~~~~~C~n~~~~C~~q~ 447 (687)
||.||..+. ..++....||.. . |-+..
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~--~-c~~~~ 35 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSS--K-CLSKF 35 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCH--H-HHHHH
Confidence 788887654 223445667765 3 66544
No 372
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=31.60 E-value=66 Score=25.84 Aligned_cols=48 Identities=23% Similarity=0.307 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCcc-HHHHHHHHHHHHHc
Q psy11421 464 GLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVS-NKLANNILLAIQKS 514 (687)
Q Consensus 464 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG-~Ksa~~Ll~~Ie~s 514 (687)
|+ ++-+..|.+.|+ .....|..|+.++|.++ |+. .....+|+++|++-
T Consensus 17 gl-~~y~~~f~~~~i-~g~~~L~~l~~~~L~~l-GI~~~~~r~kll~~i~~L 65 (66)
T PF07647_consen 17 GL-EQYADNFRENGI-DGLEDLLQLTEEDLKEL-GITNLGHRRKLLSAIQEL 65 (66)
T ss_dssp TC-GGGHHHHHHTTC-SHHHHHTTSCHHHHHHT-TTTHHHHHHHHHHHHHHH
T ss_pred Cc-HHHHHHHHHcCC-cHHHHHhhCCHHHHHHc-CCCCHHHHHHHHHHHHHc
Confidence 66 667777777774 66688888999999877 664 44557888888753
No 373
>PRK14171 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=31.52 E-value=82 Score=33.86 Aligned_cols=61 Identities=15% Similarity=0.325 Sum_probs=42.5
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
++++++.++++-.+- .+..+.-.+.+|+++. .|.+.|+++||.. ++|++|++.+...+.+.
T Consensus 15 ~~~lk~~v~~l~~~~--g~~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~~l~~~I~~LN~D~ 89 (288)
T PRK14171 15 LADLKLEIQELKSQT--NASPKLAIVLVGDNPASIIYVKNKIKNAHKIGIDTLLVNLSTTIHTNDLISKINELNLDN 89 (288)
T ss_pred HHHHHHHHHHHHhcc--CCCCeEEEEEeCCCccHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence 556666666652211 2345777888998753 7999999999874 46899999988765554
No 374
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=31.34 E-value=29 Score=25.13 Aligned_cols=22 Identities=23% Similarity=0.637 Sum_probs=13.9
Q ss_pred CCCCCCCcceeec-----CceeEEecC
Q psy11421 417 ICPICNSKIIYIE-----SNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~-----~~~~~~C~n 438 (687)
.||.|++.....+ ++...+|++
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~ 30 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGK 30 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCC
Confidence 5888988654332 234678876
No 375
>PRK14190 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=30.68 E-value=75 Score=34.08 Aligned_cols=61 Identities=18% Similarity=0.279 Sum_probs=43.3
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-|+++++.++.+..+ .+..+.-.+.+|+++. .|.+.|+++||.. +++++|++.+.+...+.
T Consensus 15 i~~~l~~~v~~l~~~---g~~P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 89 (284)
T PRK14190 15 KREQLKEEVVKLKEQ---GIVPGLAVILVGDDPASHSYVRGKKKAAEKVGIYSELYEFPADITEEELLALIDRLNADP 89 (284)
T ss_pred HHHHHHHHHHHHHhC---CCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 367777777765432 3445677777898743 7999999999875 46789999987655443
No 376
>PRK08402 replication factor A; Reviewed
Probab=30.52 E-value=27 Score=38.67 Aligned_cols=24 Identities=25% Similarity=0.472 Sum_probs=19.4
Q ss_pred CCCCCCCCCCcceeecCceeEEecC
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+| .||.|+.++..+++...++|.+
T Consensus 212 y~-aCp~CnKkv~~~~~~~~~~Ce~ 235 (355)
T PRK08402 212 YD-ACPECRRKVDYDPATDTWICPE 235 (355)
T ss_pred Ee-cCCCCCeEEEEecCCCCEeCCC
Confidence 44 7999999988666667899986
No 377
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=30.48 E-value=1.8e+02 Score=32.89 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=34.3
Q ss_pred HHhcCCEEcc-----cccccccEEEEcCC--CC-ccHHHHHHcCCeEEeHHHHHHHH
Q psy11421 630 IENLGGKVVN-----FISKNTNYLVKGQK--PG-KKLEKAIKLNIKILDEKNFVKIV 678 (687)
Q Consensus 630 i~~~Gg~v~~-----sVsk~t~~LV~G~~--~g-~Kl~kA~~lgI~Ii~E~~f~~~l 678 (687)
+++.|..+.. .+ .+.|++|++.. +. .=++.|++.||+|++|-||+..+
T Consensus 48 l~~~gi~~~~~~~~~~~-~~~d~vv~spgi~~~~~~~~~a~~~~i~i~~~~e~~~~~ 103 (461)
T PRK00421 48 LLELGAIIFIGHDAENI-KDADVVVYSSAIPDDNPELVAARELGIPVVRRAEMLAEL 103 (461)
T ss_pred HHHCCCEEeCCCCHHHC-CCCCEEEECCCCCCCCHHHHHHHHCCCcEEeHHHHHHHH
Confidence 4556666532 12 25789999873 33 45889999999999999997554
No 378
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=30.28 E-value=96 Score=32.21 Aligned_cols=27 Identities=19% Similarity=0.302 Sum_probs=21.6
Q ss_pred ccccCCCCHHHHHHHHHCCCCCChHHHhc
Q psy11421 459 AMNIIGLGKKMIEKLVNANIVVTAVDLYK 487 (687)
Q Consensus 459 ~l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 487 (687)
.-.|+|+|||++.+|+++- .|++++|.
T Consensus 185 ipGv~GiG~ktA~~Ll~~~--gsle~i~~ 211 (240)
T cd00008 185 IPGVPGIGEKTAAKLLKEY--GSLEGILE 211 (240)
T ss_pred CCCCCccCHHHHHHHHHHh--CCHHHHHH
Confidence 3457999999999999874 47888876
No 379
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.15 E-value=25 Score=39.55 Aligned_cols=73 Identities=21% Similarity=0.360 Sum_probs=40.4
Q ss_pred cCCCCCCEEEEEecCCccceeeccccCCCCCCCcccc-CCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcc
Q psy11421 377 KNIQIGDTVVVHRSGNVIPKITSSILSLRPNDSKIFK-IPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFS 455 (687)
Q Consensus 377 ~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~~~~~~-~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~ 455 (687)
..|.+||.|.+. |.|=|+.+.+-+- +.-.-.++. .-..||.||..+.-...+ .++|.. |--+.-....+-+
T Consensus 314 ~~L~pGD~i~~~--G~~~~~~~n~ek~-~v~~l~~~~~~~p~Cp~Cg~~m~S~G~~-g~rC~k----Cg~~~~~~~~~~v 385 (421)
T COG1571 314 RKLIPGDEITVY--GSVKPGTLNLEKF-QVLKLARYERVNPVCPRCGGRMKSAGRN-GFRCKK----CGTRARETLIKEV 385 (421)
T ss_pred HhcCCCCEEEEe--cCccccceeEEEE-EEEEeeeeEEcCCCCCccCCchhhcCCC-Cccccc----ccccCCccccccc
Confidence 378999998874 6666665443210 000000111 123799999987654333 889964 7655544444433
Q ss_pred cc
Q psy11421 456 SR 457 (687)
Q Consensus 456 sr 457 (687)
-|
T Consensus 386 ~r 387 (421)
T COG1571 386 PR 387 (421)
T ss_pred cc
Confidence 33
No 380
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=30.13 E-value=1.9e+02 Score=32.84 Aligned_cols=55 Identities=20% Similarity=0.253 Sum_probs=37.9
Q ss_pred HHHHHHHHhcCCEEcccc----cccccEEEEcC--CCC-ccHHHHHHcCCeEEeHHHHHHHH
Q psy11421 624 NEAIILIENLGGKVVNFI----SKNTNYLVKGQ--KPG-KKLEKAIKLNIKILDEKNFVKIV 678 (687)
Q Consensus 624 ~e~~~~i~~~Gg~v~~sV----sk~t~~LV~G~--~~g-~Kl~kA~~lgI~Ii~E~~f~~~l 678 (687)
..+.+.+++.|..+...- ....|++|++. .+. .=+..|++.||+|+++-+|+..+
T Consensus 54 ~~~~~~l~~~gv~~~~~~~~~~~~~~D~Vv~s~Gi~~~~~~~~~a~~~gi~v~~~~e~~~~~ 115 (480)
T PRK01438 54 RALAAILEALGATVRLGPGPTLPEDTDLVVTSPGWRPDAPLLAAAADAGIPVWGEVELAWRL 115 (480)
T ss_pred HHHHHHHHHcCCEEEECCCccccCCCCEEEECCCcCCCCHHHHHHHHCCCeecchHHHHHHh
Confidence 345566777887775321 23578898876 333 44678899999999999986443
No 381
>PLN02616 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=30.09 E-value=69 Score=35.52 Aligned_cols=70 Identities=17% Similarity=0.302 Sum_probs=47.0
Q ss_pred EEEcC-CCcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCe--------EEeHHHHHHH
Q psy11421 613 VFTGS-LYAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK--------ILDEKNFVKI 677 (687)
Q Consensus 613 v~TG~-l~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~--------Ii~E~~f~~~ 677 (687)
.+.|+ +..--|+++++.++.+..+. .++.+.-.+.+|+++. .|.+.|+++||. -++|+++++.
T Consensus 75 ildGk~iA~~i~~~lk~~v~~lk~~~--g~~P~LaiIlvG~dpaS~~Yv~~k~K~~e~~GI~~~~~~lpe~~te~ell~~ 152 (364)
T PLN02616 75 VIDGKAVAKKIRDEITIEVSRMKESI--GVVPGLAVILVGDRKDSATYVRNKKKACDSVGINSFEVRLPEDSTEQEVLKF 152 (364)
T ss_pred EeEhHHHHHHHHHHHHHHHHHHHHcC--CCCCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHH
Confidence 46665 22224566776666653221 2456788888998753 799999999997 3578899999
Q ss_pred HhcccCC
Q psy11421 678 VKGFSTE 684 (687)
Q Consensus 678 l~~~s~~ 684 (687)
+++...+
T Consensus 153 I~~LN~D 159 (364)
T PLN02616 153 ISGFNND 159 (364)
T ss_pred HHHHcCC
Confidence 8765444
No 382
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=29.99 E-value=58 Score=24.81 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=19.0
Q ss_pred HHHHHhcCCCCCCEEEEEecCC
Q psy11421 371 ESEIYRKNIQIGDTVVVHRSGN 392 (687)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGd 392 (687)
.+..+.++|.+||.|.+.-.|+
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~ 34 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGD 34 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETT
T ss_pred HHHHHHcCCCCCCEEEEEEeCC
Confidence 3556789999999999999987
No 383
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=29.88 E-value=74 Score=25.38 Aligned_cols=45 Identities=27% Similarity=0.364 Sum_probs=33.1
Q ss_pred HHHHHHHHHCCCCCChHHHhcCChhhhhcccCccH-HHHHHHHHHHHHc
Q psy11421 467 KKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSN-KLANNILLAIQKS 514 (687)
Q Consensus 467 ~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~-Ksa~~Ll~~Ie~s 514 (687)
++-+..| .++.| +...|..|+.++|.++ |+.. --..+|+.+|+.-
T Consensus 18 ~~y~~~F-~~~~i-~g~~L~~lt~~dL~~l-gi~~~ghr~ki~~~i~~L 63 (64)
T PF00536_consen 18 EQYAENF-EKNYI-DGEDLLSLTEEDLEEL-GITKLGHRKKILRAIQKL 63 (64)
T ss_dssp GGGHHHH-HHTTS-SHHHHTTSCHHHHHHT-T-SSHHHHHHHHHHHHHH
T ss_pred HHHHHHH-HcCCc-hHHHHHhcCHHHHHHc-CCCCHHHHHHHHHHHHHh
Confidence 4455555 67764 7889999999999997 5544 7788899988764
No 384
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=29.84 E-value=55 Score=36.03 Aligned_cols=49 Identities=20% Similarity=0.237 Sum_probs=39.5
Q ss_pred ccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHH
Q psy11421 457 RKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILL 509 (687)
Q Consensus 457 r~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~ 509 (687)
....++.|+|+.+.++|...| |.++.||-..+.+.|... ||... ..|..
T Consensus 176 Lpv~~~~GvG~~~~~~l~~~G-i~ti~dl~~~~~~~L~~~--~g~~~-~~l~~ 224 (354)
T COG0389 176 LPVLEFWGVGKVTAEKLRRLG-ISTIGDLAETDLDALKKR--FGKLG-ERLYR 224 (354)
T ss_pred CChhhhCCCCHHHHHHHHHcC-ChhHHHHHhcCHHHHHHH--HhHhH-HHHHH
Confidence 357899999999999999999 899999999777777664 77655 55553
No 385
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=29.80 E-value=1.7e+02 Score=29.21 Aligned_cols=64 Identities=19% Similarity=0.334 Sum_probs=36.4
Q ss_pred hcCCCCCCEEEEE--ecCCccceeeccccCCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhh
Q psy11421 376 RKNIQIGDTVVVH--RSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQ 452 (687)
Q Consensus 376 ~~~i~iGd~V~v~--raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~ 452 (687)
+..+++||.|.+. ..+ +++.=...+ ..-.. +-..||.||.+++... -..+.|++ |-....+++.
T Consensus 116 ~~~~~~GD~V~akV~~i~---~~i~LS~k~---~~lGv--v~a~~~~~g~~~~~~~-~~~~~c~~----~~~~e~rkva 181 (189)
T PRK09521 116 TDAFKIGDIVRAKVISYT---DPLQLSTKG---KDLGV--IYAMCSRCRTPLVKKG-ENELKCPN----CGNIETRKLS 181 (189)
T ss_pred HhccCCCCEEEEEEEecC---CcEEEEEec---CCceE--EEEEccccCCceEECC-CCEEECCC----CCCEEeeccc
Confidence 3458999998755 233 333322221 11111 2348999999998543 24689987 6544444444
No 386
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=29.76 E-value=49 Score=36.85 Aligned_cols=71 Identities=30% Similarity=0.331 Sum_probs=0.0
Q ss_pred CCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhcccccccc---------------cCCCCHHH----------HH
Q psy11421 417 ICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSSRKAMN---------------IIGLGKKM----------IE 471 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~sr~~l~---------------I~GLG~k~----------i~ 471 (687)
.|| ||++++ .. ...|+.-.+.|..-. |.|+|.++ ++
T Consensus 261 ~Cp-CG~~i~-------------~G-----V~~Rv~eLad~~~~~p~~rppy~~~iPL~ei~~~~~~~~~~~k~v~~~~~ 321 (374)
T TIGR00375 261 NCP-CGGRIK-------------KG-----VSDRLRELSDQKLEHPVPRPPYVHLIPLAEVIGVGPKKGIFTKAVQSLWE 321 (374)
T ss_pred CCC-CCCcce-------------ec-----hHHHHHHHhcCCCCCCCCCCCeeeeCCHHHHHhhhcCCCCccHHHHHHHH
Q ss_pred HHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHH
Q psy11421 472 KLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLA 510 (687)
Q Consensus 472 ~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~ 510 (687)
+|+++-. .-+.=|.+...++|.+.- ++.|+.|...
T Consensus 322 ~l~~~fG-~E~~iL~~~~~eel~~~~---~~~a~~I~~~ 356 (374)
T TIGR00375 322 KLKKAFG-TEIAVLHEAAEEDLARVV---PKVAALIVKF 356 (374)
T ss_pred HHHHHhc-cHHHHHhcCCHHHHHHHH---HHHHHHHHHH
No 387
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=29.59 E-value=2e+02 Score=26.85 Aligned_cols=73 Identities=21% Similarity=0.278 Sum_probs=54.0
Q ss_pred HHHHHHHcCCCCCCHHHHH-HHHhhcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHHcchhHHHHHHHHHhcCcc
Q psy11421 519 FSRFIYALGIRHVGETTAK-ELANYFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFINQPLHRLLISQLRDVGIY 593 (687)
Q Consensus 519 l~r~L~aLGIp~vG~~~Ak-~La~~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~ 593 (687)
..+.+..+.++.-+...|. .|-++||+-..+..+-.++|.+++.+...-+.+++.+...- ...+..|...|..
T Consensus 42 A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~~~~~l~~l~~~~~~d~~~L~~~~~~v--~~~i~~L~~lg~~ 115 (145)
T PF03564_consen 42 AKELIRGLPLSEENYEEAWELLEERYGNPRRIIQALLEELRNLPPISNDDPEALRSLVDKV--NNCIRALKALGVN 115 (145)
T ss_pred HHHHHHcccccchhhHHHHHHHHHHhCCchHHHHHHHHHHhccccccchhHHHHHHHHHHH--HHHHHHHHHcCCC
Confidence 3456666666666655664 55678999888888888999999998888888888877543 2357788877754
No 388
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=29.52 E-value=94 Score=21.79 Aligned_cols=28 Identities=25% Similarity=0.293 Sum_probs=20.2
Q ss_pred HHHHHHHHHhccCCCCCCChHHHHHHHHHHH
Q psy11421 23 KELHRHNIAYYLYDNPIISDNKYDQLLFELK 53 (687)
Q Consensus 23 ~~l~~~~~~YY~~~~p~isD~~YD~L~~~L~ 53 (687)
++|+....+|= +-.||++||.+...+|.
T Consensus 3 ~~L~~L~~l~~---~G~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 3 DRLEKLKELYD---KGEISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHHHH---cCCCCHHHHHHHHHHHh
Confidence 34555565553 45999999999988774
No 389
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=29.51 E-value=94 Score=30.51 Aligned_cols=67 Identities=22% Similarity=0.354 Sum_probs=40.2
Q ss_pred CCCCCCEEEEE--------ecCCccceeeccccCCCCCCCccccCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHh
Q psy11421 378 NIQIGDTVVVH--------RSGNVIPKITSSILSLRPNDSKIFKIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKA 449 (687)
Q Consensus 378 ~i~iGd~V~v~--------raGdVIP~I~~vv~~~r~~~~~~~~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~ 449 (687)
-|+.||..+|- |.++.|==+ |...|+..... -+-=.|+.|+..|. ++.+.|.+- . .|+..
T Consensus 73 ~L~eGd~flvP~gvpHsP~r~~~t~~Lv---IE~~r~~~~~d-~~~wyc~~c~~~~~----e~~f~~~d~-~---~~~~~ 140 (159)
T TIGR03037 73 PIREGDIFLLPPHVPHSPQRPAGSIGLV---IERKRPQGELD-GFQWFCPQCGHKLH----RAEVQLENI-V---TDLPP 140 (159)
T ss_pred EECCCCEEEeCCCCCcccccCCCcEEEE---EEeCCCCCCCc-ceEEECCCCCCeEE----EEEEEecCh-h---hhhHH
Confidence 46777777763 445544333 33334433210 12337999988776 357889883 4 57888
Q ss_pred hhhhccc
Q psy11421 450 GLQHFSS 456 (687)
Q Consensus 450 ~i~~F~s 456 (687)
-+..|.+
T Consensus 141 ~~~~f~~ 147 (159)
T TIGR03037 141 VFEHFYS 147 (159)
T ss_pred HHHHHhC
Confidence 8888875
No 390
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=29.42 E-value=87 Score=33.91 Aligned_cols=60 Identities=12% Similarity=0.205 Sum_probs=44.2
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCC
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTE 684 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~ 684 (687)
-++++++.++.+..+ .+..+.-.+.+|+++. .|.+.|+++||.. ++|++|++.+.....+
T Consensus 16 i~~~lk~~i~~l~~~---g~~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~t~~~l~~~I~~lN~D 89 (301)
T PRK14194 16 VLAQVREDVRTLKAA---GIEPALAVILVGNDPASQVYVRNKILRAEEAGIRSLEHRLPADTSQARLLALIAELNAD 89 (301)
T ss_pred HHHHHHHHHHHHHhC---CCCCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHcCC
Confidence 466777777776432 3456888888998753 7999999999874 3789999998765444
No 391
>PRK14184 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=29.16 E-value=83 Score=33.81 Aligned_cols=60 Identities=12% Similarity=0.173 Sum_probs=42.0
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCC
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTE 684 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~ 684 (687)
|+++++.++.+-.+- .+..+.-.+.+|+++. .|.+.|+++||.. ++|++|++.++....+
T Consensus 14 ~~~l~~~v~~l~~~~--g~~P~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~d 87 (286)
T PRK14184 14 REELKTEVAALTARH--GRAPGLAVILVGEDPASQVYVRNKERACEDAGIVSEAFRLPADTTQEELEDLIAELNAR 87 (286)
T ss_pred HHHHHHHHHHHHhcc--CCCCEEEEEEeCCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 566666666542211 2345777888898753 7999999999874 4689999998765444
No 392
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=29.12 E-value=38 Score=25.38 Aligned_cols=14 Identities=36% Similarity=0.705 Sum_probs=10.2
Q ss_pred CCCCCCCCCC-ccee
Q psy11421 414 IPNICPICNS-KIIY 427 (687)
Q Consensus 414 ~P~~CP~C~~-~l~~ 427 (687)
.+..||.||+ .+.+
T Consensus 25 ~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 25 DPVPCPECGSTEVRR 39 (42)
T ss_pred CCCcCCCCCCCceEE
Confidence 4678999998 5443
No 393
>PRK12496 hypothetical protein; Provisional
Probab=28.81 E-value=23 Score=34.75 Aligned_cols=16 Identities=6% Similarity=-0.099 Sum_probs=12.7
Q ss_pred EEEEEeehhhHHHHHH
Q psy11421 181 RCEVLIYKKDFIKLNK 196 (687)
Q Consensus 181 RGEi~~~~~~F~~~n~ 196 (687)
-||+|++.+.++++..
T Consensus 19 ~~~i~tp~~V~~Ev~d 34 (164)
T PRK12496 19 DGEHYTTPSVVEEVKD 34 (164)
T ss_pred CCCEEecHHHHHHHhC
Confidence 4889999999887643
No 394
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=28.73 E-value=2e+02 Score=29.39 Aligned_cols=55 Identities=20% Similarity=0.175 Sum_probs=33.3
Q ss_pred cCChhhhhcc----c-CccHHHHHHHHHHHHH------cc--cCC---HHHHHHHc-CCCCCCHHHHHHHHhhc
Q psy11421 487 KINFKNLLRL----D-RVSNKLANNILLAIQK------SK--LTT---FSRFIYAL-GIRHVGETTAKELANYF 543 (687)
Q Consensus 487 ~L~~~~L~~l----~-gfG~Ksa~~Ll~~Ie~------sk--~~~---l~r~L~aL-GIp~vG~~~Ak~La~~f 543 (687)
.++.++|..+ . ||-..+|.+|.+..+. .. +.+ ++..| + .+||||+++|.-++...
T Consensus 68 ~~~~eeL~~~Ir~~Gygf~~~KAk~I~~~~~~~~~l~~~~~~~~~~~~~R~~L--l~~lpGIG~KTAd~vL~~~ 139 (208)
T PRK01229 68 YLSEEELEEKLKEVGHRFYNKRAEYIVEARKLYGKLKEIIKADKDQFEAREFL--VKNIKGIGYKEASHFLRNV 139 (208)
T ss_pred CCCHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHhccCCchHHHHHH--HHcCCCCcHHHHHHHHHHc
Confidence 4555555444 2 4888888888665542 11 112 22233 5 89999999998777433
No 395
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.73 E-value=48 Score=24.93 Aligned_cols=14 Identities=36% Similarity=0.747 Sum_probs=10.9
Q ss_pred CCCCCCCCCcceee
Q psy11421 415 PNICPICNSKIIYI 428 (687)
Q Consensus 415 P~~CP~C~~~l~~~ 428 (687)
|..||.||+.-+..
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 67899999876543
No 396
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=28.70 E-value=73 Score=27.98 Aligned_cols=12 Identities=33% Similarity=0.385 Sum_probs=9.8
Q ss_pred cCCCCCCEEEEE
Q psy11421 377 KNIQIGDTVVVH 388 (687)
Q Consensus 377 ~~i~iGd~V~v~ 388 (687)
..++.||.|.|.
T Consensus 46 ~~l~~Gd~V~v~ 57 (91)
T cd04482 46 RLLIPGDEVTVY 57 (91)
T ss_pred CCCCCCCEEEEE
Confidence 478999998876
No 397
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=28.64 E-value=63 Score=34.57 Aligned_cols=21 Identities=29% Similarity=0.297 Sum_probs=17.7
Q ss_pred HHHHhcCCCCCHHHHHHHHHH
Q psy11421 554 EEQLLNIPKIGSTTVKAFIKF 574 (687)
Q Consensus 554 ~eeL~~I~GIG~~~A~sI~~f 574 (687)
.++|.+++|||+.+|+.+.-|
T Consensus 206 ~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 206 MKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred HHHHhcCCCcCHHHHHHHHHH
Confidence 578999999999999887644
No 398
>PRK14168 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=28.62 E-value=81 Score=34.07 Aligned_cols=61 Identities=15% Similarity=0.238 Sum_probs=43.1
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
++++++.++.+..+. .++.+.-.+.+|+++. .|.+.|+++||.. +++++|++.+...+.+.
T Consensus 16 ~~~lk~~v~~l~~~~--g~~P~LaiI~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~D~ 90 (297)
T PRK14168 16 LEEIRGEVAELKEKY--GKVPGLVTILVGESPASLSYVTLKIKTAHRLGFHEIQDNQSVDITEEELLALIDKYNNDD 90 (297)
T ss_pred HHHHHHHHHHHHHcC--CCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 556666666653211 2346778888998753 7899999999874 68999999988765543
No 399
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=28.46 E-value=21 Score=28.10 Aligned_cols=10 Identities=30% Similarity=1.029 Sum_probs=5.5
Q ss_pred CCCCCCCcce
Q psy11421 417 ICPICNSKII 426 (687)
Q Consensus 417 ~CP~C~~~l~ 426 (687)
.||.|+++|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 8999999885
No 400
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=28.33 E-value=32 Score=34.81 Aligned_cols=28 Identities=18% Similarity=0.433 Sum_probs=20.9
Q ss_pred HHhcCCCCCCEEEEEecCCccceeecccc
Q psy11421 374 IYRKNIQIGDTVVVHRSGNVIPKITSSIL 402 (687)
Q Consensus 374 i~~~~i~iGd~V~v~raGdVIP~I~~vv~ 402 (687)
|...+|.+||.|.+ ++||+||.=..++.
T Consensus 47 i~~~~L~~GDiI~l-~~g~~vPaD~~ll~ 74 (230)
T PF00122_consen 47 IPSSELVPGDIIIL-KAGDIVPADGILLE 74 (230)
T ss_dssp EEGGGT-TTSEEEE-ETTEBESSEEEEEE
T ss_pred chHhhccceeeeec-ccccccccCcccee
Confidence 55679999999999 77999996444443
No 401
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=28.30 E-value=26 Score=29.18 Aligned_cols=23 Identities=26% Similarity=0.681 Sum_probs=14.3
Q ss_pred CCCCCCCCcce--------eecCceeEEecC
Q psy11421 416 NICPICNSKII--------YIESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~--------~~~~~~~~~C~n 438 (687)
..|-.||+++. +.+|.+.+||.+
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~Fcss 34 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFCSS 34 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEech
Confidence 36899999875 233445555555
No 402
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=28.30 E-value=49 Score=31.28 Aligned_cols=30 Identities=23% Similarity=0.483 Sum_probs=23.1
Q ss_pred CCCCCCCCCcceeecC--ceeEEecCCCCCCHH
Q psy11421 415 PNICPICNSKIIYIES--NLIARCSGSWIECIA 445 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~--~~~~~C~n~~~~C~~ 445 (687)
-..||.||.+++...+ +.++-|.|.+. |..
T Consensus 17 ~~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~-C~~ 48 (140)
T COG0551 17 GQICPKCGKNMVKKFGKYGIFLGCSNYPK-CDY 48 (140)
T ss_pred CccCCcCCCeeEEEEccCCeEEEeCCCCC-CCC
Confidence 3579999999885433 37888999876 976
No 403
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=27.93 E-value=1.1e+02 Score=25.66 Aligned_cols=25 Identities=16% Similarity=0.396 Sum_probs=21.9
Q ss_pred HHHHHhcCCCCCCEEEEEecCCccce
Q psy11421 371 ESEIYRKNIQIGDTVVVHRSGNVIPK 396 (687)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdVIP~ 396 (687)
++.+.++++.. ..|.|...|+++|+
T Consensus 21 ~dLL~~l~~~~-~~vav~vNg~iVpr 45 (68)
T COG2104 21 ADLLAQLGLNP-EGVAVAVNGEIVPR 45 (68)
T ss_pred HHHHHHhCCCC-ceEEEEECCEEccc
Confidence 57788888876 89999999999995
No 404
>PLN02897 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=27.82 E-value=87 Score=34.50 Aligned_cols=73 Identities=16% Similarity=0.208 Sum_probs=48.7
Q ss_pred EEEEEcCC-CcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHH
Q psy11421 611 IFVFTGSL-YAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFV 675 (687)
Q Consensus 611 ~vv~TG~l-~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~ 675 (687)
...+.|+- ..--++++++.++.+..+. .+..+.-.+.+|+++. .|.+.|+++||.. ++|++|+
T Consensus 56 ~~ildGk~vA~~i~~~lk~~v~~l~~~~--g~~P~LaiIlvGddpaS~~Yv~~k~K~a~~~GI~~~~~~l~~~~te~ell 133 (345)
T PLN02897 56 TVVIDGNVIAEEIRTKIASEVRKMKKAV--GKVPGLAVVLVGQQRDSQTYVRNKIKACEETGIKSLLAELPEDCTEGQIL 133 (345)
T ss_pred ceEeehHHHHHHHHHHHHHHHHHHHhcc--CCCCeEEEEEeCCChHHHHHHHHHHHHHHhcCCEEEEEECCCCCCHHHHH
Confidence 34567752 2224667777777752221 2345777888998743 7999999999875 4688999
Q ss_pred HHHhcccCCc
Q psy11421 676 KIVKGFSTET 685 (687)
Q Consensus 676 ~~l~~~s~~~ 685 (687)
+.+.+...+.
T Consensus 134 ~~I~~lN~D~ 143 (345)
T PLN02897 134 SALRKFNEDT 143 (345)
T ss_pred HHHHHHhCCC
Confidence 9987655443
No 405
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=27.37 E-value=22 Score=33.75 Aligned_cols=27 Identities=33% Similarity=0.585 Sum_probs=19.9
Q ss_pred HHHHHhcCCCCCCEEEEEecCCccceeecccc
Q psy11421 371 ESEIYRKNIQIGDTVVVHRSGNVIPKITSSIL 402 (687)
Q Consensus 371 ~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~ 402 (687)
...++.+||||||+|.|.= |++.-+|.
T Consensus 52 ~~dv~~LDlRIGD~Vkv~~-----~k~~yiV~ 78 (131)
T PF08605_consen 52 NEDVKYLDLRIGDTVKVDG-----PKVTYIVV 78 (131)
T ss_pred cccEeeeeeecCCEEEECC-----CCccEEEE
Confidence 3457889999999999975 65544443
No 406
>PRK14169 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.35 E-value=98 Score=33.19 Aligned_cols=60 Identities=10% Similarity=0.231 Sum_probs=42.6
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
++++++.++.+-.+ .++.+.-.+.+|+++. .|.+.|+++||.. ++|++|++.+.+.+.+.
T Consensus 14 ~~~l~~~v~~l~~~---g~~P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 87 (282)
T PRK14169 14 LADLKQTVAKLAQQ---DVTPTLAVVLVGSDPASEVYVRNKQRRAEDIGVRSLMFRLPEATTQADLLAKVAELNHDP 87 (282)
T ss_pred HHHHHHHHHHHHhC---CCCCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 56677777765322 3445777888898743 7999999999874 46789999987655443
No 407
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=27.30 E-value=45 Score=26.71 Aligned_cols=11 Identities=36% Similarity=0.851 Sum_probs=6.2
Q ss_pred CCCCCCCccee
Q psy11421 417 ICPICNSKIIY 427 (687)
Q Consensus 417 ~CP~C~~~l~~ 427 (687)
.||.||..+..
T Consensus 4 ~CP~CG~~iev 14 (54)
T TIGR01206 4 ECPDCGAEIEL 14 (54)
T ss_pred CCCCCCCEEec
Confidence 46666665543
No 408
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.19 E-value=91 Score=31.60 Aligned_cols=19 Identities=11% Similarity=0.329 Sum_probs=15.4
Q ss_pred CCCccCCeEEEEEcCCCcC
Q psy11421 603 NKNYLKEKIFVFTGSLYAF 621 (687)
Q Consensus 603 ~~~~l~g~~vv~TG~l~~~ 621 (687)
.++.+.|..+|+-|.++.+
T Consensus 95 ~~~~y~G~YhVL~G~iSPl 113 (195)
T TIGR00615 95 KTKEFRGRYHVLGGHISPL 113 (195)
T ss_pred hhCccceEEEEccCccCcc
Confidence 4567899999999988753
No 409
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.04 E-value=38 Score=36.09 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=20.6
Q ss_pred CCCCCCCCcceeecCceeEEecC
Q psy11421 416 NICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
..||.||+++...+++....|++
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~ 134 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPK 134 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCC
Confidence 48999999999888888899977
No 410
>PRK00076 recR recombination protein RecR; Reviewed
Probab=26.96 E-value=87 Score=31.79 Aligned_cols=18 Identities=17% Similarity=0.156 Sum_probs=14.9
Q ss_pred CCCccCCeEEEEEcCCCc
Q psy11421 603 NKNYLKEKIFVFTGSLYA 620 (687)
Q Consensus 603 ~~~~l~g~~vv~TG~l~~ 620 (687)
.++.+.|+.+|+-|.++.
T Consensus 95 ~s~~y~G~YhVL~G~isp 112 (196)
T PRK00076 95 RTGEYRGLYHVLGGLLSP 112 (196)
T ss_pred hhCcCceEEEEecCCcCC
Confidence 456789999999998875
No 411
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=26.83 E-value=93 Score=33.43 Aligned_cols=61 Identities=15% Similarity=0.167 Sum_probs=43.4
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-++++++.++.+-.+ .++.+.-.+.+|+++. .|.+.|+++||.. ++|++|++.++..+.+.
T Consensus 15 i~~~~~~~v~~l~~~---g~~p~Laii~vg~~~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~d~ 89 (286)
T PRK14175 15 YRQGLQDQVEALKEK---GFTPKLSVILVGNDGASQSYVRSKKKAAEKIGMISEIVHLEETATEEEVLNELNRLNNDD 89 (286)
T ss_pred HHHHHHHHHHHHHhc---CCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 356777777765322 2456777888998743 7999999999874 45789999987655443
No 412
>PRK14191 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=26.36 E-value=1e+02 Score=33.16 Aligned_cols=61 Identities=13% Similarity=0.255 Sum_probs=43.2
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
++++++.++.+..+. .++.+.-.+.+|+++. .|.+.|+++||.. +++++|++.+++.+.+.
T Consensus 14 ~~~l~~~v~~l~~~~--g~~P~LaiI~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 88 (285)
T PRK14191 14 EKDLKNKIQILTAQT--GKRPKLAVILVGKDPASQTYVNMKIKACERVGMDSDLHTLQENTTEAELLSLIKDLNTDQ 88 (285)
T ss_pred HHHHHHHHHHHHhcC--CCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 566666666653221 2456788888998743 7999999999874 46889999988765543
No 413
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=25.98 E-value=38 Score=37.26 Aligned_cols=14 Identities=36% Similarity=0.508 Sum_probs=12.6
Q ss_pred CCCCEEEEEecCCc
Q psy11421 380 QIGDTVVVHRSGNV 393 (687)
Q Consensus 380 ~iGd~V~v~raGdV 393 (687)
+|||||.|+.++|-
T Consensus 232 GIGDTiRVSLt~~P 245 (360)
T PRK00366 232 GIGDTIRVSLTADP 245 (360)
T ss_pred cCCCeEEEeCCCCC
Confidence 57999999999994
No 414
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.97 E-value=32 Score=31.10 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=9.4
Q ss_pred CCCCCCCCcce
Q psy11421 416 NICPICNSKII 426 (687)
Q Consensus 416 ~~CP~C~~~l~ 426 (687)
+.||.||+++.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred ccCCCCCCccc
Confidence 58999999875
No 415
>PRK14177 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.93 E-value=1.1e+02 Score=32.76 Aligned_cols=62 Identities=18% Similarity=0.235 Sum_probs=43.0
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-++++++.++.+..+ +....+.-.+.+|+++. .|.+.|+++||.. ++|++|++.+...+.+.
T Consensus 15 i~~~lk~~i~~l~~~--~~~~P~Laii~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~s~~el~~~I~~lN~D~ 90 (284)
T PRK14177 15 IRNEIRETIEERKTK--NKRIPKLATILVGNNPASETYVSMKVKACHKVGMGSEMIRLKEQTTTEELLGVIDKLNLDP 90 (284)
T ss_pred HHHHHHHHHHHHHhc--CCCCCeEEEEEeCCChhHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 366677777765322 11234677888898743 7899999999872 47899999987665544
No 416
>PRK13844 recombination protein RecR; Provisional
Probab=25.71 E-value=1e+02 Score=31.46 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=14.7
Q ss_pred CCCccCCeEEEEEcCCCc
Q psy11421 603 NKNYLKEKIFVFTGSLYA 620 (687)
Q Consensus 603 ~~~~l~g~~vv~TG~l~~ 620 (687)
.++.+.|..+|+-|.++.
T Consensus 99 ~t~~y~G~YhVL~G~isp 116 (200)
T PRK13844 99 EAGIYRGKYFVLNGRISP 116 (200)
T ss_pred hhCccceEEEEccCccCc
Confidence 456789999999998864
No 417
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=25.67 E-value=60 Score=27.47 Aligned_cols=20 Identities=20% Similarity=0.592 Sum_probs=12.8
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.|+.+|.+.. ..++|..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~ 22 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEA 22 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETT
T ss_pred cCCCCCCccEEeC--CEEECcc
Confidence 6999999998765 3456654
No 418
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=25.63 E-value=77 Score=27.61 Aligned_cols=54 Identities=13% Similarity=0.262 Sum_probs=36.1
Q ss_pred hhcccCccHHHHHHHHHHHHHcccCCHHHHHHHcCCCCCCHHHHHHHHhhcCChHHH
Q psy11421 493 LLRLDRVSNKLANNILLAIQKSKLTTFSRFIYALGIRHVGETTAKELANYFKNLECM 549 (687)
Q Consensus 493 L~~l~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp~vG~~~Ak~La~~f~sld~l 549 (687)
|..+.|+|++.|+.|++.-+...=.++..|+..+. ++.....+.|. ..|.+|.+
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~~--~i~~~~le~Li-~aGafd~~ 82 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRLP--KINKRQLEALI-KAGAFDSF 82 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS---TS-HHHHHHHH-HTTTTTTC
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHHh--cCCHHHHHHHH-HCCCcccc
Confidence 67789999999999999877333357889999884 45566666665 33545444
No 419
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=25.56 E-value=42 Score=24.52 Aligned_cols=17 Identities=18% Similarity=0.663 Sum_probs=13.2
Q ss_pred cCCCCCCCCCCcceeec
Q psy11421 413 KIPNICPICNSKIIYIE 429 (687)
Q Consensus 413 ~~P~~CP~C~~~l~~~~ 429 (687)
..+..|..||++|++..
T Consensus 19 ~~~~~Cd~cg~~L~qR~ 35 (36)
T PF05191_consen 19 KVEGVCDNCGGELVQRK 35 (36)
T ss_dssp SSTTBCTTTTEBEBEEG
T ss_pred CCCCccCCCCCeeEeCC
Confidence 35679999999988653
No 420
>PF08734 GYD: GYD domain; InterPro: IPR014845 These proteins of unknown function are usually less than 100 amino acids in length. They may belong to the dimeric alpha/beta barrel superfamily.
Probab=25.53 E-value=1.3e+02 Score=26.50 Aligned_cols=56 Identities=25% Similarity=0.355 Sum_probs=38.3
Q ss_pred HHHHHHHHHhcCCEEccc--ccccccEEEEcCCCCc----cHHHH-HHcC------CeEEeHHHHHHHH
Q psy11421 623 RNEAIILIENLGGKVVNF--ISKNTNYLVKGQKPGK----KLEKA-IKLN------IKILDEKNFVKIV 678 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~s--Vsk~t~~LV~G~~~g~----Kl~kA-~~lg------I~Ii~E~~f~~~l 678 (687)
++.+.++++++||++.+. +-..-|++++-+-|.. ++.-+ ...| .+.++.++|.+++
T Consensus 22 ~~a~~~~~e~~Gg~l~~~y~t~G~yD~v~i~eaPD~~~a~~~~l~i~~~G~v~~et~~a~~~~e~~~~~ 90 (91)
T PF08734_consen 22 AEAVRALIEALGGKLKSFYWTLGEYDFVVIVEAPDDETAAAASLAIRSSGNVRTETLRAFPWDEFDEIV 90 (91)
T ss_pred HHHHHHHHHHcCCEEEEEEEecCCCCEEEEEEcCCHHHHHHHHHHHHcCCceEEEEEecCCHHHHHHHh
Confidence 466889999999999865 5567888888876542 22211 1123 5678888888765
No 421
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=25.51 E-value=92 Score=31.55 Aligned_cols=20 Identities=15% Similarity=0.223 Sum_probs=16.0
Q ss_pred CCCccCCeEEEEEcCCCcCC
Q psy11421 603 NKNYLKEKIFVFTGSLYAFK 622 (687)
Q Consensus 603 ~~~~l~g~~vv~TG~l~~~~ 622 (687)
..+.+.|..+|+-|.++.++
T Consensus 96 ~~~~f~G~YhVL~G~lspl~ 115 (198)
T COG0353 96 KTGEFRGLYHVLGGLLSPLD 115 (198)
T ss_pred HhcccCeeEEEecCccCccc
Confidence 34579999999999988653
No 422
>PRK14186 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.45 E-value=1e+02 Score=33.36 Aligned_cols=61 Identities=13% Similarity=0.126 Sum_probs=41.7
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
|+++++.++.+-.+. .+..+.-.+.+|+++. .|.+.|+++||.. +++++|.+.++....+.
T Consensus 15 ~~~lk~~v~~l~~~~--g~~p~LaiI~vgdd~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 89 (297)
T PRK14186 15 EQRLQAQIESNLPKA--GRPPGLAVLRVGDDPASAVYVRNKEKACARVGIASFGKHLPADTSQAEVEALIAQLNQDE 89 (297)
T ss_pred HHHHHHHHHHHHHhc--CCCceEEEEEeCCChHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 566666666542111 2345777888898743 7999999999886 35889999987655443
No 423
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=25.31 E-value=47 Score=29.28 Aligned_cols=52 Identities=19% Similarity=0.304 Sum_probs=31.9
Q ss_pred HHHHHcCCCCCCHHHHHHHHhhcCC--hHHHHhcCHHHHhc-CCCCCHHHHHHHHHHHc
Q psy11421 521 RFIYALGIRHVGETTAKELANYFKN--LECMFKATEEQLLN-IPKIGSTTVKAFIKFIN 576 (687)
Q Consensus 521 r~L~aLGIp~vG~~~Ak~La~~f~s--ld~l~~As~eeL~~-I~GIG~~~A~sI~~ff~ 576 (687)
.+|..+||+ ...|.+|.+.|++ ++.|.. ++=.|.. +.|||=++|.+|..-+.
T Consensus 13 ~~L~~~gl~---~~~a~kl~~~yg~~ai~~l~~-nPY~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 13 AFLQEYGLS---PKLAMKLYKKYGDDAIEILKE-NPYRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp HHHHHTT-----HHHHHHHHHHH-TTHHHHHHH--STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHHcCCC---HHHHHHHHHHHhHHHHHHHHH-ChHHHHHHccCCCHHHHHHHHHHcC
Confidence 455556665 5788888888875 223332 3334555 88999999988887653
No 424
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=25.28 E-value=81 Score=37.94 Aligned_cols=40 Identities=25% Similarity=0.395 Sum_probs=26.9
Q ss_pred EEEecCCCHHHHHhcC-CCCCCEEE----EEecCCccceeecccc
Q psy11421 363 ITRATLHNESEIYRKN-IQIGDTVV----VHRSGNVIPKITSSIL 402 (687)
Q Consensus 363 VsraTLhN~~~i~~~~-i~iGd~V~----v~raGdVIP~I~~vv~ 402 (687)
++--++++-..|+++. =.+|-.|. |.|+.+|.|.+..+.-
T Consensus 86 ~~~~~~~~~~~iR~l~s~~igkLV~v~GiV~r~s~v~p~~~~~~~ 130 (682)
T COG1241 86 VRFKNLPNRLSIRELRSEHIGKLVSVEGIVTRASEVRPRLKKAVF 130 (682)
T ss_pred EEecCCcCCcChhhCchhhCCcEEEEEEEEEecccccceeEEEEE
Confidence 3334444444566655 45787776 6799999999987764
No 425
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=25.17 E-value=51 Score=29.03 Aligned_cols=49 Identities=27% Similarity=0.271 Sum_probs=24.8
Q ss_pred cCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhc-ccCccHHHHHHHHHHH
Q psy11421 462 IIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLR-LDRVSNKLANNILLAI 511 (687)
Q Consensus 462 I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~-l~gfG~Ksa~~Ll~~I 511 (687)
=-||+++.+.+|++.=.-.++ +...-+.=.|.. ++|+|=|.|++|...+
T Consensus 17 ~~gl~~~~a~kl~~~yg~~ai-~~l~~nPY~L~~~i~gi~F~~aD~iA~~~ 66 (94)
T PF14490_consen 17 EYGLSPKLAMKLYKKYGDDAI-EILKENPYRLIEDIDGIGFKTADKIALKL 66 (94)
T ss_dssp HTT--HHHHHHHHHHH-TTHH-HHHHH-STCCCB-SSSSBHHHHHHHHHTT
T ss_pred HcCCCHHHHHHHHHHHhHHHH-HHHHHChHHHHHHccCCCHHHHHHHHHHc
Confidence 346777777777775332222 222222222444 6777777777666554
No 426
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=25.15 E-value=35 Score=37.09 Aligned_cols=16 Identities=31% Similarity=0.785 Sum_probs=12.8
Q ss_pred CCCCCCCCCcceeecC
Q psy11421 415 PNICPICNSKIIYIES 430 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~ 430 (687)
+-.||+||++|...-|
T Consensus 25 ~ffCPaC~~~l~lK~G 40 (342)
T COG4469 25 RFFCPACGSQLILKQG 40 (342)
T ss_pred ccccCCCCCeeeeecC
Confidence 4589999999986544
No 427
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=24.92 E-value=41 Score=29.81 Aligned_cols=24 Identities=21% Similarity=0.491 Sum_probs=17.7
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.-.||.||..-+....-..|.|..
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~ 58 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKK 58 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETT
T ss_pred CCcCCCCCCceeEEeeeEEeecCC
Confidence 457999999877655556799965
No 428
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=24.84 E-value=36 Score=23.09 Aligned_cols=9 Identities=33% Similarity=1.224 Sum_probs=5.8
Q ss_pred CCCCCCCcc
Q psy11421 417 ICPICNSKI 425 (687)
Q Consensus 417 ~CP~C~~~l 425 (687)
.||.|++.+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 577777654
No 429
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.76 E-value=43 Score=24.34 Aligned_cols=22 Identities=32% Similarity=0.567 Sum_probs=15.6
Q ss_pred CCCCCCCcceee-----cCceeEEecC
Q psy11421 417 ICPICNSKIIYI-----ESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~-----~~~~~~~C~n 438 (687)
.||.|+...... +.+..++|++
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~ 30 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSK 30 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCC
Confidence 599999865433 3467888976
No 430
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=24.69 E-value=55 Score=29.96 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=16.2
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.|+|+.+..++ ..+.|+-
T Consensus 4 ~CP~C~seytY~dg-~~~iCpe 24 (109)
T TIGR00686 4 PCPKCNSEYTYHDG-TQLICPS 24 (109)
T ss_pred cCCcCCCcceEecC-CeeECcc
Confidence 59999999887654 5677854
No 431
>PRK07726 DNA topoisomerase III; Provisional
Probab=24.63 E-value=44 Score=40.05 Aligned_cols=27 Identities=19% Similarity=0.563 Sum_probs=19.2
Q ss_pred CCCCCCCCcceee--cCceeEEecCCCCCCH
Q psy11421 416 NICPICNSKIIYI--ESNLIARCSGSWIECI 444 (687)
Q Consensus 416 ~~CP~C~~~l~~~--~~~~~~~C~n~~~~C~ 444 (687)
..||.||.+++.. ..+.++.|+|. . |.
T Consensus 611 ~~CP~C~~~~~~~~~~~~~f~~Cs~~-~-~~ 639 (658)
T PRK07726 611 PKCPDCGKPMLKVKGKNGKMLVCQDR-E-CG 639 (658)
T ss_pred ccccccCccceeecccCCeeEecCCC-c-cc
Confidence 4699999988632 33567899995 4 54
No 432
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=24.45 E-value=1.3e+02 Score=33.12 Aligned_cols=51 Identities=20% Similarity=0.278 Sum_probs=40.7
Q ss_pred HcCCCCCCHHHHHHHHh-hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 525 ALGIRHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 525 aLGIp~vG~~~Ak~La~-~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
.|.-.|+++..+++|.+ .|.|++.+..++..+|.++.||++..++.+....
T Consensus 30 ~l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~ 81 (342)
T PLN03186 30 QLQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAA 81 (342)
T ss_pred HHHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 33336677878887765 4999999999999999999999999887766544
No 433
>KOG2875|consensus
Probab=24.40 E-value=1.2e+02 Score=32.55 Aligned_cols=88 Identities=16% Similarity=0.163 Sum_probs=48.2
Q ss_pred CHHHHHhhhhhcccc---cccccCCCCHHHHHHHHHCCCCCChHHHhc-CChhhhhcccCccH------HHHHHHHHH--
Q psy11421 443 CIAQRKAGLQHFSSR---KAMNIIGLGKKMIEKLVNANIVVTAVDLYK-INFKNLLRLDRVSN------KLANNILLA-- 510 (687)
Q Consensus 443 C~~q~~~~i~~F~sr---~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~-L~~~~L~~l~gfG~------Ksa~~Ll~~-- 510 (687)
--+++-+.+.+||+- ..++|+|+-= .++ .|+..|-. -.+++|.++ |||= .+|+.|++.
T Consensus 131 NIaRIT~Mve~fc~~fG~~i~~~dg~~~--------h~F-Psl~~L~g~~~Ea~LR~~-gfGYRAkYI~~ta~~l~~~~g 200 (323)
T KOG2875|consen 131 NIARITGMVERFCQAFGPRIIQLDGVDY--------HGF-PSLQALAGPEVEAELRKL-GFGYRAKYISATARALQEKQG 200 (323)
T ss_pred cHHHHHHHHHHHHHhhCcceEeecCccc--------ccC-ccHHHhcCcHhHHHHHHc-CcchhHHHHHHHHHHHHHhcc
Confidence 446676777777762 2344555421 111 22222221 124567776 7883 244444432
Q ss_pred ----HHHcccCCHHHHHHHc-CCCCCCHHHHHHHH
Q psy11421 511 ----IQKSKLTTFSRFIYAL-GIRHVGETTAKELA 540 (687)
Q Consensus 511 ----Ie~sk~~~l~r~L~aL-GIp~vG~~~Ak~La 540 (687)
++..+..++...-.+| -+||||.++|.=|+
T Consensus 201 ~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 201 GLAWLQSLRKSSYEEAREALCSLPGVGPKVADCIC 235 (323)
T ss_pred cchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhh
Confidence 3334446777777777 68999999997444
No 434
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.09 E-value=38 Score=34.12 Aligned_cols=22 Identities=32% Similarity=0.732 Sum_probs=14.4
Q ss_pred CCCCCCCc-----ceee-cCceeEEecC
Q psy11421 417 ICPICNSK-----IIYI-ESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~-----l~~~-~~~~~~~C~n 438 (687)
.||+||+. +.+. ..+..++|.|
T Consensus 8 ~Cp~Cg~eev~hEVik~~g~~~lvrC~e 35 (201)
T COG1326 8 ECPSCGSEEVSHEVIKERGREPLVRCEE 35 (201)
T ss_pred ECCCCCcchhhHHHHHhcCCceEEEccC
Confidence 59999942 2222 3356889977
No 435
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.98 E-value=52 Score=30.44 Aligned_cols=45 Identities=11% Similarity=0.146 Sum_probs=28.2
Q ss_pred eeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcC-CCCCCEEEEEe
Q psy11421 330 ALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKN-IQIGDTVVVHR 389 (687)
Q Consensus 330 ~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~-i~iGd~V~v~r 389 (687)
..++|+.|.+.||+- +|+.-..-. +=++.+.+-- +-.|+++.|.+
T Consensus 22 ~~~~V~~V~l~IG~l--------------s~V~pe~L~-faf~~~~~~T~~~ega~L~Ie~ 67 (117)
T PRK00564 22 QAHKIEKVVVGIGER--------------SGMDKSLFV-SAFETFREESLVCKDAILDIVD 67 (117)
T ss_pred CCCeEEEEEEEEccc--------------cCcCHHHHH-HHHHHHhcCCcccCCCEEEEEe
Confidence 456899999999963 222211111 1245566666 78899998876
No 436
>PLN02516 methylenetetrahydrofolate dehydrogenase (NADP+)
Probab=23.97 E-value=2.7e+02 Score=30.18 Aligned_cols=127 Identities=15% Similarity=0.151 Sum_probs=0.0
Q ss_pred cCccHHHHHHHHHHHHHcccCCHHHHHHHcCCC-CCCHHHHHHHHhhcCChHHHHhcCHHHHhc---CCCCCHHHHHHHH
Q psy11421 497 DRVSNKLANNILLAIQKSKLTTFSRFIYALGIR-HVGETTAKELANYFKNLECMFKATEEQLLN---IPKIGSTTVKAFI 572 (687)
Q Consensus 497 ~gfG~Ksa~~Ll~~Ie~sk~~~l~r~L~aLGIp-~vG~~~Ak~La~~f~sld~l~~As~eeL~~---I~GIG~~~A~sI~ 572 (687)
+...+.....+++.+++..+.. =+|..+-+| ++............+++|.|...+.-.|.. -+++-+-|+..+
T Consensus 78 ~~~s~~el~~~I~~lN~D~~V~--GIlvq~PlP~~id~~~i~~~I~p~KDVDGl~~~n~g~l~~~~~~~~~~PcTp~av- 154 (299)
T PLN02516 78 ENISEAELISKVHELNANPDVH--GILVQLPLPKHINEEKILNEISLEKDVDGFHPLNIGKLAMKGREPLFLPCTPKGC- 154 (299)
T ss_pred CCCCHHHHHHHHHHHhCCCCCC--eEEEecCCCCCcCHHHHHhccCcccccCccCHhhHhhHhcCCCCCCCCCCCHHHH-
Q ss_pred HHHcchhHHHHHHHHHhcCcccccCCCCCCCCCccCCeEEEEEcCCCcCCHHHHHHHHHhcCCEEccc---------ccc
Q psy11421 573 KFINQPLHRLLISQLRDVGIYWLNNPNTKGNKNYLKEKIFVFTGSLYAFKRNEAIILIENLGGKVVNF---------ISK 643 (687)
Q Consensus 573 ~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~~~l~g~~vv~TG~l~~~~R~e~~~~i~~~Gg~v~~s---------Vsk 643 (687)
++-|..+|+ ++.||++|+-|.-. .==.-+..++.+.|++|+.- .++
T Consensus 155 -----------i~lL~~~~i-------------~l~Gk~vvVIGRS~-iVGkPla~lL~~~~ATVtvchs~T~nl~~~~~ 209 (299)
T PLN02516 155 -----------LELLSRSGI-------------PIKGKKAVVVGRSN-IVGLPVSLLLLKADATVTVVHSRTPDPESIVR 209 (299)
T ss_pred -----------HHHHHHhCC-------------CCCCCEEEEECCCc-cchHHHHHHHHHCCCEEEEeCCCCCCHHHHHh
Q ss_pred cccEEEEc
Q psy11421 644 NTNYLVKG 651 (687)
Q Consensus 644 ~t~~LV~G 651 (687)
+-|++|++
T Consensus 210 ~ADIvv~A 217 (299)
T PLN02516 210 EADIVIAA 217 (299)
T ss_pred hCCEEEEc
No 437
>PRK14172 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=23.96 E-value=1.2e+02 Score=32.51 Aligned_cols=61 Identities=13% Similarity=0.269 Sum_probs=41.7
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCC
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTE 684 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~ 684 (687)
-|+++++.++.+-.+ +-...+.-.+.+|+++. .|.+.|+++||.. +++++|++.+.....+
T Consensus 14 i~~~lk~~i~~l~~~--g~~~P~Laii~vg~d~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~d 88 (278)
T PRK14172 14 IKEEIKNFVEERKEN--GLSIPKIASILVGNDGGSIYYMNNQEKVANSLGIDFKKIKLDESISEEDLINEIEELNKD 88 (278)
T ss_pred HHHHHHHHHHHHHhc--CCCCceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCC
Confidence 366777777765322 11124677888898753 6899999999886 4688999988765443
No 438
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=23.49 E-value=49 Score=26.56 Aligned_cols=9 Identities=56% Similarity=1.527 Sum_probs=6.8
Q ss_pred CCCCCCCcc
Q psy11421 417 ICPICNSKI 425 (687)
Q Consensus 417 ~CP~C~~~l 425 (687)
.||.||.+.
T Consensus 6 ~CP~CgnKT 14 (55)
T PF14205_consen 6 LCPICGNKT 14 (55)
T ss_pred ECCCCCCcc
Confidence 588888765
No 439
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=23.43 E-value=68 Score=33.52 Aligned_cols=94 Identities=20% Similarity=0.259 Sum_probs=58.4
Q ss_pred eeeEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEecCCccceeeccccCCCCCC
Q psy11421 329 EALTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHRSGNVIPKITSSILSLRPND 408 (687)
Q Consensus 329 ~~~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~raGdVIP~I~~vv~~~r~~~ 408 (687)
....+|.+|+..-+||. |+|.+. .-+|.. + =.|.-.|+.+||.|.. |.-.| ..+++
T Consensus 38 ~~~g~V~~IeyDPnRsa---~IAlv~--~~~g~~-~-------YIiAp~gl~~Gd~I~s---g~~~~--------i~~Gn 93 (238)
T PRK09612 38 TLRGKVVDILHDPGRNA---PVAKVK--FENGEE-F-------LILAPEGLYVGQEIEI---GPSAE--------IKPGN 93 (238)
T ss_pred ceeEEEEEEEECCCCCC---eEEEEE--eCCCCE-E-------EEEccCCCCCCCEEEe---CCCCC--------CCCcc
Confidence 35689999999999994 556554 234432 1 1245569999999995 32211 12344
Q ss_pred Cccc-cCCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhh
Q psy11421 409 SKIF-KIPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAG 450 (687)
Q Consensus 409 ~~~~-~~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~ 450 (687)
..++ .+|.-|..|+-++..-+++. +|... . |-+|++.+
T Consensus 94 ~lpL~~IP~Gt~I~NIE~~pG~Ggk--l~RSA-G-t~A~Ii~k 132 (238)
T PRK09612 94 TLPLGEIPEGTPVCNIESRPGDGGK--FARSS-G-TYALVVGH 132 (238)
T ss_pred ccCHhhCCCCCEEEEEEecCCCCcc--eEEcC-C-CeEEEEEe
Confidence 4444 57888888887766444433 45442 4 77777664
No 440
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=23.28 E-value=43 Score=27.45 Aligned_cols=13 Identities=38% Similarity=0.613 Sum_probs=9.4
Q ss_pred CCCCCCCCCCcce
Q psy11421 414 IPNICPICNSKII 426 (687)
Q Consensus 414 ~P~~CP~C~~~l~ 426 (687)
+|-.|++||..+-
T Consensus 3 iPVRCFTCGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFTCGKVIG 15 (60)
T ss_dssp -SSS-STTTSBTC
T ss_pred CceecCCCCCChh
Confidence 6889999998774
No 441
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.14 E-value=83 Score=36.49 Aligned_cols=57 Identities=19% Similarity=0.348 Sum_probs=35.8
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhc---ccccccccCCCCHHHHHHHHHCC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHF---SSRKAMNIIGLGKKMIEKLVNAN 477 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F---~sr~~l~I~GLG~k~i~~L~~~g 477 (687)
+-.||.|+.+|+.......++|.. |-.+ ..+-+. |+-..|.-.|.|-+.++..+...
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l~Ch~----Cg~~--~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~ 281 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKLRCHY----CGYQ--EPIPKTCPQCGSEDLVYKGYGTEQVEEELAKL 281 (505)
T ss_pred ccCCCCCCCceEEecCCCeEEcCC----CcCc--CCCCCCCCCCCCCeeEeecccHHHHHHHHHhh
Confidence 457999999998655556788864 3211 111111 22234677889988888777654
No 442
>PRK14167 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=23.01 E-value=1.3e+02 Score=32.62 Aligned_cols=61 Identities=11% Similarity=0.199 Sum_probs=43.2
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
-|+++++.++.+... .+..+.-.+.+|+++. .|.+.|+++||.. +++++|++.+.+.+.+.
T Consensus 14 i~~~l~~~v~~l~~~---g~~P~LaiI~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 88 (297)
T PRK14167 14 IRDDLTDAIETLEDA---GVTPGLATVLMSDDPASETYVSMKQRDCEEVGIEAIDVEIDPDAPAEELYDTIDELNADE 88 (297)
T ss_pred HHHHHHHHHHHHHhC---CCCceEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 366777776665321 2456788888898753 7999999999874 45789999987665543
No 443
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=22.68 E-value=2.6e+02 Score=24.91 Aligned_cols=49 Identities=18% Similarity=0.132 Sum_probs=36.9
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHh----------ccCCCCCCChHHHHHHHHHHHHHHHH
Q psy11421 10 NFSKLSFRVTELKKELHRHNIAY----------YLYDNPIISDNKYDQLLFELKKIEEK 58 (687)
Q Consensus 10 ~~~~~~~~i~~L~~~l~~~~~~Y----------Y~~~~p~isD~~YD~L~~~L~~le~~ 58 (687)
..+++.++|..|+++|+.+...= =-+++=.|+|++++.-++++...-++
T Consensus 3 ~~s~I~~eIekLqe~lk~~e~keaERigr~AlKaGL~eieI~d~eL~~~FeeIa~RFrk 61 (92)
T PF07820_consen 3 SSSKIREEIEKLQEQLKQAETKEAERIGRIALKAGLGEIEISDAELQAAFEEIAARFRK 61 (92)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCHHHHHHHHHHHHHHHhc
Confidence 45778889999999888876421 12467799999999999999775544
No 444
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.66 E-value=39 Score=32.89 Aligned_cols=13 Identities=31% Similarity=1.025 Sum_probs=9.9
Q ss_pred CCCCCCCcceeec
Q psy11421 417 ICPICNSKIIYIE 429 (687)
Q Consensus 417 ~CP~C~~~l~~~~ 429 (687)
.||.||++|+..+
T Consensus 130 ~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 130 TCPRCGAMLDYLD 142 (158)
T ss_pred cCCCCCCEeeecc
Confidence 6999998887543
No 445
>PRK03352 DNA polymerase IV; Validated
Probab=22.65 E-value=1.3e+02 Score=32.78 Aligned_cols=63 Identities=21% Similarity=0.227 Sum_probs=39.4
Q ss_pred CccH-HHHHHHHHHHHHccc------CCHHHHHHHc---CCCCCCHHHHHHHHhh-cCChHHHHhcCHHHHhcC
Q psy11421 498 RVSN-KLANNILLAIQKSKL------TTFSRFIYAL---GIRHVGETTAKELANY-FKNLECMFKATEEQLLNI 560 (687)
Q Consensus 498 gfG~-Ksa~~Ll~~Ie~sk~------~~l~r~L~aL---GIp~vG~~~Ak~La~~-f~sld~l~~As~eeL~~I 560 (687)
|+|. |.+.+|.....+... ..+.++|..+ .+||||++++++|.+. +.++.+|...+..+|.+.
T Consensus 142 Gia~nk~lAklaa~~~Kp~g~~~~~~~~~~~~L~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~ 215 (346)
T PRK03352 142 GIGDNKLRAKIATGFAKPAGVFRLTDANWMAVMGDRPTDALWGVGPKTAKRLAALGITTVADLAAADPAELAAT 215 (346)
T ss_pred eecCCHHHHHHHHhhcCCCcEEEECHHHHHHHHhcCCHHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHH
Confidence 4443 555666655433211 1344677766 3589999999888643 457777777777777665
No 446
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=22.41 E-value=1.2e+02 Score=32.95 Aligned_cols=47 Identities=19% Similarity=0.247 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHh-hcCChHHHHhcCHHHHhcCCCCCHHHHHHHHHHH
Q psy11421 529 RHVGETTAKELAN-YFKNLECMFKATEEQLLNIPKIGSTTVKAFIKFI 575 (687)
Q Consensus 529 p~vG~~~Ak~La~-~f~sld~l~~As~eeL~~I~GIG~~~A~sI~~ff 575 (687)
+|+++....+|.+ .|.++..+..++..+|.++.|++...+..+....
T Consensus 7 ~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~ 54 (316)
T TIGR02239 7 NGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEA 54 (316)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4577877777764 5899999999999999999999998888776643
No 447
>PRK14724 DNA topoisomerase III; Provisional
Probab=22.35 E-value=84 Score=39.54 Aligned_cols=52 Identities=17% Similarity=0.322 Sum_probs=34.3
Q ss_pred CCCCCCCcceeecCceeEEecCC-C-------CCCHHHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCC
Q psy11421 417 ICPICNSKIIYIESNLIARCSGS-W-------IECIAQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVV 480 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~-~-------~~C~~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~ 480 (687)
.||.||..+. +.+..+.|.|. . . |.-.+-+ .+++| + +..+.+.+|+..|...
T Consensus 757 ~CPkCg~~v~--e~gk~y~Cs~~~~~~~~~~~~-C~f~i~k---~i~gK-----~-is~~~~~kLl~~GkT~ 816 (987)
T PRK14724 757 PCPKCGAPVF--EHGSNYVCEKSVPTLAQPTPS-CTFKSGQ---VILQQ-----P-IEREQMQKLLATGKTD 816 (987)
T ss_pred CCCCCCCceE--eecceEEcCCCcccccCCCCC-CCceecc---cccCc-----C-CCHHHHHHHHhcCCcc
Confidence 6999999865 35677999983 1 4 8643211 12333 2 5889999999887643
No 448
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=22.32 E-value=83 Score=31.42 Aligned_cols=23 Identities=22% Similarity=0.224 Sum_probs=16.4
Q ss_pred hhhhcccCccHHHHHHHHHHHHH
Q psy11421 491 KNLLRLDRVSNKLANNILLAIQK 513 (687)
Q Consensus 491 ~~L~~l~gfG~Ksa~~Ll~~Ie~ 513 (687)
+.|+++||+|+|+|+-++..+.+
T Consensus 115 e~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 115 RRLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred HHHHcCCCCCHHHHHHHHHHHHH
Confidence 46777888888888777665544
No 449
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=22.09 E-value=53 Score=29.34 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=18.8
Q ss_pred CCCCCCCcceeecCceeEEecCCCCCCHHHH
Q psy11421 417 ICPICNSKIIYIESNLIARCSGSWIECIAQR 447 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~ 447 (687)
+||.||+.|...+ ..++|.+ |....
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~----C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPS----CGYEK 26 (104)
T ss_pred CCcccCcccccCC--CeEECcC----CCCcc
Confidence 7999999997543 4689976 87654
No 450
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=22.08 E-value=3.2e+02 Score=31.24 Aligned_cols=34 Identities=12% Similarity=0.061 Sum_probs=26.9
Q ss_pred cccEEEEcCC--CC-ccHHHHHHcCCeEEeHHHH-HHH
Q psy11421 644 NTNYLVKGQK--PG-KKLEKAIKLNIKILDEKNF-VKI 677 (687)
Q Consensus 644 ~t~~LV~G~~--~g-~Kl~kA~~lgI~Ii~E~~f-~~~ 677 (687)
..|++|.... +. .=+++|++.||||++|-+| +..
T Consensus 69 ~~d~vV~SpgI~~~~p~~~~a~~~~i~i~~~~el~~~~ 106 (468)
T PRK04690 69 AFDVVVKSPGISPYRPEALAAAARGTPFIGGTALWFAE 106 (468)
T ss_pred CCCEEEECCCCCCCCHHHHHHHHcCCcEEEHHHHHHHH
Confidence 5788998763 33 5588999999999999998 543
No 451
>PRK10220 hypothetical protein; Provisional
Probab=22.04 E-value=66 Score=29.48 Aligned_cols=21 Identities=38% Similarity=0.768 Sum_probs=16.1
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.|+++.+..+ +..+.|+-
T Consensus 5 ~CP~C~seytY~d-~~~~vCpe 25 (111)
T PRK10220 5 HCPKCNSEYTYED-NGMYICPE 25 (111)
T ss_pred cCCCCCCcceEcC-CCeEECCc
Confidence 5999999988765 45677864
No 452
>PRK14176 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.01 E-value=1.4e+02 Score=32.06 Aligned_cols=70 Identities=13% Similarity=0.215 Sum_probs=47.2
Q ss_pred EEcCC-CcCCHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHH
Q psy11421 614 FTGSL-YAFKRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIV 678 (687)
Q Consensus 614 ~TG~l-~~~~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l 678 (687)
+.|+- ..-=++++++.++.+-.+. .++.+.-.+.+|+++. .|.+.|+++||.. +++++|++.+
T Consensus 11 ldGk~iA~~i~~~l~~~i~~l~~~~--g~~P~Laii~vg~d~aS~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I 88 (287)
T PRK14176 11 IDGKALAKKIEAEVRSGVERLKSNR--GITPGLATILVGDDPASKMYVRLKHKACERVGIRAEDQFLPADTTQEELLELI 88 (287)
T ss_pred EEhHHHHHHHHHHHHHHHHHHHhcc--CCCCeEEEEEECCCcchHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHH
Confidence 55542 2223667777777753221 3456788888998753 7999999999863 4688999998
Q ss_pred hcccCCc
Q psy11421 679 KGFSTET 685 (687)
Q Consensus 679 ~~~s~~~ 685 (687)
++.+.+.
T Consensus 89 ~~LN~D~ 95 (287)
T PRK14176 89 DSLNKRK 95 (287)
T ss_pred HHHhCCC
Confidence 7665544
No 453
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.85 E-value=66 Score=29.36 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=16.7
Q ss_pred CCCCCCCcceeecCceeEEecC
Q psy11421 417 ICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~~~~~~~~~~C~n 438 (687)
.||.|+++-+.+++. .+.|+.
T Consensus 5 ~cp~c~sEytYed~~-~~~cpe 25 (112)
T COG2824 5 PCPKCNSEYTYEDGG-QLICPE 25 (112)
T ss_pred CCCccCCceEEecCc-eEeCch
Confidence 499999998887665 778865
No 454
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.80 E-value=62 Score=24.64 Aligned_cols=22 Identities=27% Similarity=0.632 Sum_probs=13.6
Q ss_pred CCCCCCCcce-eecCceeEEecC
Q psy11421 417 ICPICNSKII-YIESNLIARCSG 438 (687)
Q Consensus 417 ~CP~C~~~l~-~~~~~~~~~C~n 438 (687)
.||.||+.-. ...+...+.|.+
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~ 42 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKA 42 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCC
Confidence 5999998522 333345677744
No 455
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=21.71 E-value=78 Score=26.46 Aligned_cols=17 Identities=24% Similarity=0.354 Sum_probs=13.2
Q ss_pred HHHHhcCCCCCCEEEEE
Q psy11421 372 SEIYRKNIQIGDTVVVH 388 (687)
Q Consensus 372 ~~i~~~~i~iGd~V~v~ 388 (687)
+.+++.|+..||+|.|-
T Consensus 47 ~~L~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 47 DALRKAGAKDGDTVRIG 63 (69)
T ss_pred HHHHHcCCCCCCEEEEc
Confidence 34577899999999874
No 456
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.68 E-value=3.4e+02 Score=35.00 Aligned_cols=38 Identities=13% Similarity=0.253 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHhcCCCCCCCceE---eCCHHHHHHHHHHHH
Q psy11421 247 SSHSELLNWYQKIGLSICGEYSV---LSGVNKLIEFYKKIN 284 (687)
Q Consensus 247 ~~~~e~l~~L~~~Gf~~~~~~~~---~~~~~ei~~~~~~~~ 284 (687)
.+..+.+.+-.+.|.|..|.+.. --+.+++....+.+.
T Consensus 474 p~~~eA~~~s~~~~~pLHP~yty~W~dis~e~~~~L~~~~~ 514 (1337)
T PRK14714 474 PTVEEAAHWATEYGAPLHPYYTYLWHDISVEQVRALADAVA 514 (1337)
T ss_pred CCHHHHHHHHHHhCCCCCCCeeeeeccCCHHHHHHHHHHHH
Confidence 47889999999999998864332 235667666555444
No 457
>PRK03858 DNA polymerase IV; Validated
Probab=21.64 E-value=1.3e+02 Score=33.50 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=14.4
Q ss_pred EEEEECCEEEEEecCCCHHHHHhcCCCCCCEE
Q psy11421 354 KPVLIDGITITRATLHNESEIYRKNIQIGDTV 385 (687)
Q Consensus 354 ePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V 385 (687)
.||-+++..|.-|+ .+-+..||+.|-.+
T Consensus 29 ~Pv~V~~~~V~a~s----y~Ar~~GV~~gm~~ 56 (396)
T PRK03858 29 RPVIVGGGVVLAAS----YEAKAYGVRTAMGG 56 (396)
T ss_pred CcEEEeCCEEEEeC----HHHHHhCCCCCChH
Confidence 44444444444443 34556677777443
No 458
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=21.56 E-value=58 Score=29.99 Aligned_cols=44 Identities=9% Similarity=0.232 Sum_probs=26.8
Q ss_pred eEEEEEEEEeecCcceeeeEEEEEEEEECCEEEEEecCCCHHHHHhcCCCCCCEEEEEe
Q psy11421 331 LTKIKAINIQIGRTGIITPVALLKPVLIDGITITRATLHNESEIYRKNIQIGDTVVVHR 389 (687)
Q Consensus 331 ~T~v~~I~~qvGRTG~iTPvA~lePV~l~G~tVsraTLhN~~~i~~~~i~iGd~V~v~r 389 (687)
.++|+.|.++||+- +|+.-..... =++.+.+-.+-.|+...|..
T Consensus 23 ~~~V~~V~l~iG~l--------------s~V~p~~L~f-af~~~~~~t~~ega~L~I~~ 66 (115)
T TIGR00100 23 AKKVTRVTLEIGEL--------------SCVNPSQLQF-AFEVVREGTVAEGAKLNIED 66 (115)
T ss_pred CCeEEEEEEEEccc--------------cccCHHHHHH-HHHHHhCCCccCCCEEEEEe
Confidence 45899999999963 3322221111 14445666777788888765
No 459
>PF04551 GcpE: GcpE protein; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 0016114 terpenoid biosynthetic process, 0055114 oxidation-reduction process; PDB: 2Y0F_C 3NOY_A.
Probab=21.52 E-value=42 Score=36.96 Aligned_cols=38 Identities=21% Similarity=0.164 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHhcCCCCCCCceEeCCHHHHHHHHHHHH
Q psy11421 247 SSHSELLNWYQKIGLSICGEYSVLSGVNKLIEFYKKIN 284 (687)
Q Consensus 247 ~~~~e~l~~L~~~Gf~~~~~~~~~~~~~ei~~~~~~~~ 284 (687)
.+-.+.++.|.++||.-.--+...++.....+.|+.+.
T Consensus 160 esA~~~~~~le~~~f~~iviSlKsSdv~~~i~ayr~la 197 (359)
T PF04551_consen 160 ESALEHVRILEELGFDDIVISLKSSDVPETIEAYRLLA 197 (359)
T ss_dssp HHHHHHHHHHHHCT-GGEEEEEEBSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCcEEEEEEeCChHHHHHHHHHHH
Confidence 34456778888999953322333456666666666554
No 460
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=21.52 E-value=54 Score=34.99 Aligned_cols=23 Identities=26% Similarity=0.566 Sum_probs=10.4
Q ss_pred CCCCCCCCCcc----eeec---CceeEEec
Q psy11421 415 PNICPICNSKI----IYIE---SNLIARCS 437 (687)
Q Consensus 415 P~~CP~C~~~l----~~~~---~~~~~~C~ 437 (687)
..+||+||++= +..+ |...++|.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs 201 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCS 201 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEET
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcC
Confidence 35899999952 1222 45788885
No 461
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=21.40 E-value=81 Score=25.79 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=19.9
Q ss_pred CChhhhhcccCccHHHHHHHHHHH
Q psy11421 488 INFKNLLRLDRVSNKLANNILLAI 511 (687)
Q Consensus 488 L~~~~L~~l~gfG~Ksa~~Ll~~I 511 (687)
.+.+||.++ ||++-.|.+|+.+-
T Consensus 4 v~k~dLi~l-Gf~~~tA~~IIrqA 26 (59)
T PF11372_consen 4 VTKKDLIEL-GFSESTARDIIRQA 26 (59)
T ss_pred cCHHHHHHc-CCCHHHHHHHHHHH
Confidence 467899999 99999999998763
No 462
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.24 E-value=46 Score=33.15 Aligned_cols=12 Identities=25% Similarity=0.617 Sum_probs=9.7
Q ss_pred CCCCCCCcceee
Q psy11421 417 ICPICNSKIIYI 428 (687)
Q Consensus 417 ~CP~C~~~l~~~ 428 (687)
.||.||++|+..
T Consensus 138 ~Cp~Cg~~L~~~ 149 (178)
T PRK06266 138 RCPQCGEMLEEY 149 (178)
T ss_pred cCCCCCCCCeec
Confidence 799999988743
No 463
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=21.16 E-value=1.5e+02 Score=31.84 Aligned_cols=61 Identities=10% Similarity=0.275 Sum_probs=42.8
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
|+++++.++.+..+- .+..+.-.+.+|+++. +|.+.|+++||.. +++++|++.+++.+.+.
T Consensus 14 ~~~lk~~v~~~~~~~--g~~P~La~I~vg~d~as~~Yv~~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~ 88 (282)
T PRK14180 14 KERLATQVQEYKHHT--AITPKLVAIIVGNDPASKTYVASKEKACAQVGIDSQVITLPEHTTESELLELIDQLNNDS 88 (282)
T ss_pred HHHHHHHHHHHHhcc--CCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 666777777653211 2456788888898753 6999999999874 35789999987655443
No 464
>KOG2041|consensus
Probab=21.14 E-value=1.5e+02 Score=35.51 Aligned_cols=53 Identities=19% Similarity=0.317 Sum_probs=42.3
Q ss_pred HHHHHHHHhhccCCCeeEEEEEccceeEEEEEEeCCEEEEEEecCCCCccchhhh
Q psy11421 103 IFNKRITNELKLTKNIEYIAELKFDGIAVNLRYEYGYLKQASTRGDGNIGENITT 157 (687)
Q Consensus 103 ~~~~~~~~~l~~~~~~~~~~e~KiDGlsi~l~Y~~G~l~~a~TRGdG~~GeDvT~ 157 (687)
.|++-+-..- ..++...+.+-.||--|-++|++|-.+-..--||-..|.|+--
T Consensus 104 sW~EEMiNnR--nKSvV~SmsWn~dG~kIcIvYeDGavIVGsvdGNRIwgKeLkg 156 (1189)
T KOG2041|consen 104 SWCEEMINNR--NKSVVVSMSWNLDGTKICIVYEDGAVIVGSVDGNRIWGKELKG 156 (1189)
T ss_pred cHHHHHhhCc--CccEEEEEEEcCCCcEEEEEEccCCEEEEeeccceecchhcch
Confidence 4666554321 2357789999999999999999999999999999999988753
No 465
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=21.02 E-value=2.1e+02 Score=32.79 Aligned_cols=57 Identities=11% Similarity=0.164 Sum_probs=43.1
Q ss_pred CHHHHHHHHHhcCCEEcccccc----cccEEEEcCC--CC-ccHHHHHHcCCeEEeHHHHHHHH
Q psy11421 622 KRNEAIILIENLGGKVVNFISK----NTNYLVKGQK--PG-KKLEKAIKLNIKILDEKNFVKIV 678 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk----~t~~LV~G~~--~g-~Kl~kA~~lgI~Ii~E~~f~~~l 678 (687)
......+.+++.|+.+--.-+. ..+.+|+|.- .+ .-+..|+++||||++-.+|+.-|
T Consensus 40 ~~~~~t~~L~~~G~~i~~gh~~~ni~~~~~VV~s~Ai~~~NpEi~~A~e~~ipi~~r~e~Lael 103 (459)
T COG0773 40 AESPMTQRLEALGIEIFIGHDAENILDADVVVVSNAIKEDNPEIVAALERGIPVISRAEMLAEL 103 (459)
T ss_pred cccHHHHHHHHCCCeEeCCCCHHHcCCCceEEEecccCCCCHHHHHHHHcCCCeEcHHHHHHHH
Confidence 3344778888899888554332 4677888873 33 78999999999999999999754
No 466
>PF14164 YqzH: YqzH-like protein
Probab=20.97 E-value=2.7e+02 Score=23.17 Aligned_cols=38 Identities=18% Similarity=0.289 Sum_probs=28.1
Q ss_pred HHHHHHHHHh-ccCCCCCCChHHHHHHHHHHHHHHHHCC
Q psy11421 23 KELHRHNIAY-YLYDNPIISDNKYDQLLFELKKIEEKYP 60 (687)
Q Consensus 23 ~~l~~~~~~Y-Y~~~~p~isD~~YD~L~~~L~~le~~~p 60 (687)
+.|.+.=++| |+.....+|+.|+-.|.+.+...-.+.|
T Consensus 8 Kmi~~~l~QYg~d~~~~pls~~E~~~L~~~i~~~~~~~~ 46 (64)
T PF14164_consen 8 KMIINCLRQYGYDVECMPLSDEEWEELCKHIQERKNEEP 46 (64)
T ss_pred HHHHHHHHHhCCcccCCCCCHHHHHHHHHHHHHHHhcCC
Confidence 4444444455 6778899999999999999987655554
No 467
>PRK14183 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.89 E-value=1.4e+02 Score=31.93 Aligned_cols=61 Identities=11% Similarity=0.202 Sum_probs=43.3
Q ss_pred HHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCeE--------EeHHHHHHHHhcccCCc
Q psy11421 623 RNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIKI--------LDEKNFVKIVKGFSTET 685 (687)
Q Consensus 623 R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~I--------i~E~~f~~~l~~~s~~~ 685 (687)
|+++++.++.+..+ ..++.+.-.+.+|+++. .|.+.|+++||.. +++++|++.++..+.+.
T Consensus 14 ~~~l~~~v~~l~~~--~g~~P~Laii~vgdd~as~~Yv~~k~k~a~~~Gi~~~~~~l~~~~~~~~l~~~I~~lN~D~ 88 (281)
T PRK14183 14 KENVKKEVDELKLV--KNIVPGLAVILVGDDPASHTYVKMKAKACDRVGIYSITHEMPSTISQKEILETIAMMNNNP 88 (281)
T ss_pred HHHHHHHHHHHHhc--CCCCCeEEEEEeCCCHHHHHHHHHHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence 56777777765321 12456788888898743 7999999999873 37889999987655443
No 468
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=20.87 E-value=45 Score=30.00 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=9.2
Q ss_pred CCCCCCCCcce
Q psy11421 416 NICPICNSKII 426 (687)
Q Consensus 416 ~~CP~C~~~l~ 426 (687)
..||+||.++.
T Consensus 48 ~~cP~Cge~~~ 58 (102)
T PF04475_consen 48 TICPKCGEELD 58 (102)
T ss_pred ccCCCCCCccC
Confidence 58999999874
No 469
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=20.83 E-value=1e+02 Score=31.88 Aligned_cols=62 Identities=21% Similarity=0.245 Sum_probs=44.0
Q ss_pred HHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcc
Q psy11421 447 RKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSK 515 (687)
Q Consensus 447 ~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk 515 (687)
+++-+..-.. +.+++-.|+...++.| .++.+|+..+.++|..++|+|..+|-.|...++.++
T Consensus 29 LLailLrtG~-~~~~~~~la~~lL~~f------g~L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~~ 90 (224)
T COG2003 29 LLAILLRTGT-KGESVLDLAKELLQEF------GSLAELLKASVEELSSVKGIGLAKAIQIKAAIELGK 90 (224)
T ss_pred HHHHHHhcCC-CCCCHHHHHHHHHHHc------ccHHHHHhCCHHHHhhCCCccHHHHHHHHHHHHHHH
Confidence 3444443333 3455555555544443 368889999999999999999999999999888765
No 470
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.71 E-value=62 Score=30.96 Aligned_cols=92 Identities=16% Similarity=0.313 Sum_probs=53.0
Q ss_pred CCCCCCCCcceeecCceeEEecCCCCCCH---HHHHhhhhhccccc----c-----cccCCCCHHHHHHHHHCCCCCCh-
Q psy11421 416 NICPICNSKIIYIESNLIARCSGSWIECI---AQRKAGLQHFSSRK----A-----MNIIGLGKKMIEKLVNANIVVTA- 482 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~~~~~C~n~~~~C~---~q~~~~i~~F~sr~----~-----l~I~GLG~k~i~~L~~~g~I~~i- 482 (687)
.+||.||...+.. +. -.|+. |- .+...++..|.-.. | -+.-|+.++.|.+++++|-+.-.
T Consensus 4 ~nC~~CgklF~~~--~~-~iCp~----C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 4 ANCPKCGRLFVKT--GR-DVCPS----CYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred ccccccchhhhhc--CC-ccCHH----HhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 5899999987752 22 24754 65 45566777776521 1 12457778888888888765422
Q ss_pred -HHHhc-CC-hhhhhcccCccHHHHHHHHHHHHHc
Q psy11421 483 -VDLYK-IN-FKNLLRLDRVSNKLANNILLAIQKS 514 (687)
Q Consensus 483 -~DL~~-L~-~~~L~~l~gfG~Ksa~~Ll~~Ie~s 514 (687)
+.|+. .. -.....-..|=++=..+|...++..
T Consensus 77 ~~nl~~~CE~CG~~I~~Gr~C~~C~~~l~~~l~~~ 111 (137)
T TIGR03826 77 FPNLGYPCERCGTSIREGRLCDSCAGELKRQLSAG 111 (137)
T ss_pred CCCCcCcccccCCcCCCCCccHHHHHHHHHHHHHH
Confidence 22221 11 1334444455566666666666554
No 471
>COG0190 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]
Probab=20.58 E-value=1.7e+02 Score=31.36 Aligned_cols=62 Identities=16% Similarity=0.266 Sum_probs=45.2
Q ss_pred CHHHHHHHHHhcCCEEcccccccccEEEEcCCCC------ccHHHHHHcCCe--------EEeHHHHHHHHhcccCCc
Q psy11421 622 KRNEAIILIENLGGKVVNFISKNTNYLVKGQKPG------KKLEKAIKLNIK--------ILDEKNFVKIVKGFSTET 685 (687)
Q Consensus 622 ~R~e~~~~i~~~Gg~v~~sVsk~t~~LV~G~~~g------~Kl~kA~~lgI~--------Ii~E~~f~~~l~~~s~~~ 685 (687)
-++++++.++++.. ....+.+.-.+.+|+++. +|.+.|++.||. -++++++++.+++...+.
T Consensus 12 i~~~lk~~v~~~~~--~~~~~P~LavilvgddpaS~~YV~~K~k~~~~iGi~~~~~~l~~~~t~~eLl~~I~~lN~D~ 87 (283)
T COG0190 12 IREELKEKVEALKA--KGGFKPGLAVILVGDDPASQVYVRSKKKAAEEIGIASELYDLPEDITEEELLALIDELNADP 87 (283)
T ss_pred HHHHHHHHHHHHHh--ccCCCceEEEEEeCCCHHHHHHHHHHHHHHHHcCCeeEEEeCCCcCCHHHHHHHHHHhcCCC
Confidence 36677777777655 444556777788888743 799999999965 368999999987655443
No 472
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=20.56 E-value=38 Score=26.93 Aligned_cols=29 Identities=31% Similarity=0.647 Sum_probs=14.7
Q ss_pred CCCCCCCCCCcceeecCceeEEecCCCCCCHHHHHhhhhhccc
Q psy11421 414 IPNICPICNSKIIYIESNLIARCSGSWIECIAQRKAGLQHFSS 456 (687)
Q Consensus 414 ~P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~~~~i~~F~s 456 (687)
-|..||.|+..+ .. + |--+.--.|.||..
T Consensus 23 ~PatCP~C~a~~-----------~~--s-rnLrRHle~~H~~k 51 (54)
T PF09237_consen 23 QPATCPICGAVI-----------RQ--S-RNLRRHLEIRHFKK 51 (54)
T ss_dssp --EE-TTT--EE-----------SS--H-HHHHHHHHHHTTTS
T ss_pred CCCCCCcchhhc-----------cc--h-hhHHHHHHHHhccc
Confidence 477899998633 22 2 44455556888864
No 473
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=20.54 E-value=79 Score=28.05 Aligned_cols=24 Identities=29% Similarity=0.681 Sum_probs=18.0
Q ss_pred CCCCCCCCCcceeecCceeEEecC
Q psy11421 415 PNICPICNSKIIYIESNLIARCSG 438 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n 438 (687)
+-.||.||..-+....-..|.|..
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~ 59 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKG 59 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCC
Confidence 568999998766655666788854
No 474
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.49 E-value=48 Score=27.47 Aligned_cols=23 Identities=26% Similarity=0.651 Sum_probs=15.0
Q ss_pred CCCCCCCCcceeecCc-eeEEecC
Q psy11421 416 NICPICNSKIIYIESN-LIARCSG 438 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~~-~~~~C~n 438 (687)
-.||.||.++++.+.. -.=||..
T Consensus 8 v~CP~Cgkpv~w~~~s~frPFCSk 31 (65)
T COG3024 8 VPCPTCGKPVVWGEESPFRPFCSK 31 (65)
T ss_pred ccCCCCCCcccccccCCcCcchhH
Confidence 3699999999975432 2234544
No 475
>KOG2093|consensus
Probab=20.29 E-value=88 Score=38.27 Aligned_cols=63 Identities=25% Similarity=0.279 Sum_probs=50.7
Q ss_pred hcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChhhhhcccCccHHHHHHHHHHHHHcccCC
Q psy11421 453 HFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFKNLLRLDRVSNKLANNILLAIQKSKLTT 518 (687)
Q Consensus 453 ~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~Ll~~Ie~sk~~~ 518 (687)
++.+-..=|.||+|-.+-.+|...+ |.+.-||-..+...|.+. ||+|.+++|+.+..---+.|
T Consensus 545 Fis~~~v~~LPGVG~sm~~kL~s~~-i~tCgdLq~~T~~kl~k~--~G~Klgq~i~~~CrG~Dd~P 607 (1016)
T KOG2093|consen 545 FISQLKVDDLPGVGSSMKSKLVSQF-IQTCGDLQLITLIKLRKV--FGPKLGQKIYRGCRGIDDDP 607 (1016)
T ss_pred HhhhcccccCCCccHHHHHHHHHhc-cchhHHHHHHHHHHHHhh--hcccHHHHHHHhcCCCcCCh
Confidence 3333345689999999999999999 899999988888888875 99999999998875444444
No 476
>PRK05776 DNA topoisomerase I; Provisional
Probab=20.29 E-value=67 Score=38.62 Aligned_cols=29 Identities=14% Similarity=0.343 Sum_probs=20.7
Q ss_pred CCCCCCCCCcc----eeecC----ceeEEecCCCCCCH
Q psy11421 415 PNICPICNSKI----IYIES----NLIARCSGSWIECI 444 (687)
Q Consensus 415 P~~CP~C~~~l----~~~~~----~~~~~C~n~~~~C~ 444 (687)
...||.||.++ +...+ +.++-|.|.+. |.
T Consensus 596 ~~~Cp~Cg~~l~~~~~~~~~~~~~~~f~~c~~~p~-c~ 632 (670)
T PRK05776 596 VGKCKICGREAYKDGLCKYHYEAKKRLVKAYEEWK-ER 632 (670)
T ss_pred CCcCCCCCCccccCceEEecccCCccceecCCCcc-cc
Confidence 35799999988 43322 35888999656 86
No 477
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=20.24 E-value=65 Score=24.89 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=7.6
Q ss_pred CCCCCCCCC
Q psy11421 415 PNICPICNS 423 (687)
Q Consensus 415 P~~CP~C~~ 423 (687)
+..||.||+
T Consensus 26 ~~~CP~Cg~ 34 (52)
T TIGR02605 26 LATCPECGG 34 (52)
T ss_pred CCCCCCCCC
Confidence 557999998
No 478
>PHA02325 hypothetical protein
Probab=20.23 E-value=91 Score=25.84 Aligned_cols=30 Identities=17% Similarity=0.309 Sum_probs=16.1
Q ss_pred CCCCCCCCCcceeecCceeEEecCCCCCCHHHH
Q psy11421 415 PNICPICNSKIIYIESNLIARCSGSWIECIAQR 447 (687)
Q Consensus 415 P~~CP~C~~~l~~~~~~~~~~C~n~~~~C~~q~ 447 (687)
|+.||.|+... .+|.-.+.=++... ||--+
T Consensus 3 ~k~CPkC~A~W--ldgqhYWsgTgk~g-~~~DL 32 (72)
T PHA02325 3 TKICPKCGARW--LDGQHYWSGTGKKG-NPHDL 32 (72)
T ss_pred ccccCccCCEe--EcceeeeccCCCcC-Cchhh
Confidence 67899999743 34433333344333 55433
No 479
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.19 E-value=49 Score=30.32 Aligned_cols=12 Identities=33% Similarity=1.052 Sum_probs=9.0
Q ss_pred CCCCCCCCCcce
Q psy11421 415 PNICPICNSKII 426 (687)
Q Consensus 415 P~~CP~C~~~l~ 426 (687)
|-+||.||+...
T Consensus 26 PivCP~CG~~~~ 37 (108)
T PF09538_consen 26 PIVCPKCGTEFP 37 (108)
T ss_pred CccCCCCCCccC
Confidence 668999988554
No 480
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.08 E-value=49 Score=29.34 Aligned_cols=16 Identities=44% Similarity=0.854 Sum_probs=11.1
Q ss_pred cccCCCCCCCCCCcce
Q psy11421 411 IFKIPNICPICNSKII 426 (687)
Q Consensus 411 ~~~~P~~CP~C~~~l~ 426 (687)
++..|..||.|.|+..
T Consensus 72 ~ik~pSRCP~CKSE~I 87 (97)
T COG3357 72 KIKKPSRCPKCKSEWI 87 (97)
T ss_pred ccCCcccCCcchhhcc
Confidence 4566888888877543
No 481
>PRK07219 DNA topoisomerase I; Validated
Probab=20.04 E-value=62 Score=39.88 Aligned_cols=76 Identities=24% Similarity=0.364 Sum_probs=0.0
Q ss_pred CCCCCCCCcceeecC--ceeEEecCCCCCCH--HHHHhhhhhcccccccccCCCCHHHHHHHHHCCCCCChHHHhcCChh
Q psy11421 416 NICPICNSKIIYIES--NLIARCSGSWIECI--AQRKAGLQHFSSRKAMNIIGLGKKMIEKLVNANIVVTAVDLYKINFK 491 (687)
Q Consensus 416 ~~CP~C~~~l~~~~~--~~~~~C~n~~~~C~--~q~~~~i~~F~sr~~l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~ 491 (687)
..||.||.+++...+ +..+.|.+.+. |. .+...... ..-..-+..|.|.++.++|-.+| +.+..++-..+.+
T Consensus 734 ~~CpkCg~~l~~~k~~~g~~~~Cs~~p~-C~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 809 (822)
T PRK07219 734 EKCPECGLPLLRVKGGFGDELGCCNNPK-CNYTEKQKKEKE--SKSELEALKGVGAKTAEKLKDAG-VETVTDLTAADPD 809 (822)
T ss_pred CCCCCCCCeEEEEecCCCceeeeCCCCC-CCcccccccccc--ccccchhccccCccccccccccc-cccccccccCCHH
Q ss_pred hhhc
Q psy11421 492 NLLR 495 (687)
Q Consensus 492 ~L~~ 495 (687)
....
T Consensus 810 ~~~~ 813 (822)
T PRK07219 810 AVAA 813 (822)
T ss_pred Hhhc
Done!